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      Volume 45, All articles

      Continuous Article Publishing mode

    • Advancements in molecular marker technologies and their applications in diversity studies

      PALAKURTHI RAMESH GUNTI MALLIKARJUNA SHAIK SAMEENA ANAND KUMAR KOLA GURULAKSHMI B VIGNESWARA REDDY P CHANDRA OBUL REDDY AKILA CHANDRA SEKHAR

      More Details Abstract Fulltext PDF

      Crop improvement is a continuous effort, since some 10,000 years ago when primitive man made the transitionfrom hunting and foraging to domestication and crop cultivation. Since then, man-made interventions havechanged the entire scenario of crop evolution, by means of genetic alterations of plants and animals made tosatisfy man’s needs. The process of domestication has led to dramatic changes in their appearance, quality andproductivity that have contributed substantially to global food security. The tremendous decline in cultivableland, freshwater, and increasing risk of biotic and abiotic stress demand immediate attention on cropimprovement to cope with the higher demand of ~40% of the food by 2020. Therefore, plant genetic variationplays a key role in plant breeding for its improvement. Most of the genetic variations useful for cropimprovement have been deposited and maintained in seed gene banks across the world; they need to be broughtinto the mainstream of breeding lines. Recent advances and progress made in molecular markers have beensubstantial tools for deeper insights of genetics, and greatly complemented breeding strategies. Integration of thenext-generation sequencing (NGS) technologies with precise phenotyping, association mapping, proteome andmetabolome studies has increased the chances of finding candidate genes and their allelic variants controlling atrait of interest. Further, these functional markers (FMMs), genotype-by-sequencing and association mappingmethodologies have opened new avenues for identification of novel genetic resources (lines) that can facilitateaccelerated crop breeding programs for increased yield, high nutritional quality, and tolerance to a variety ofabiotic and biotic stresses. The details of popular molecular markers, advancement in the technologies andstrategies for crop diversity studies and their application in crop breeding programs are presented here.

    • Quorum sensing-induced phenotypic switching as a regulatory nutritional stress response in a competitive two-species biofilm: An individual-based cellular automata model

      TEJESH REDDY CHIRATHANAMETTU PARAG D PAWAR

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      Competition for nutrients in a polymicrobial biofilm may lead to susceptible species being subjected to nutritionalstress. The influence of bacterial growth rates and interspecies interactions on their susceptibility and response tonutritional stress is not well understood. Pseudomonas aeruginosa and Staphylococcus aureus are two prevalentcausative pathogens that coexist in biofilm-associated infections. Despite being the slower-growing species, P.aeruginosa dominates in a two-species biofilm by inducing phenotypic switching of S. aureus to a metabolicallychallengedsmall colony variant (SCV) via the release of 2-heptyl-4-hydroxyquinoline N-oxide (HQNO). Wehypothesize that P. aeruginosa experiences nutritional stress in competition with S. aureus, and that the release ofHQNO is an adaptive response to nutritional stress.We present an individual-based two-species biofilm model inwhich interactions between entities induce emergent properties. As the biofilm matured, the difference in growthrates of the two species caused a non-uniform distribution of nutrients leading to nutritional stress for P. aeruginosaand a concurrent increase in the proportion of S. aureus subpopulation. The latter resulted in increasedrelease of autoinducer, and subsequently the upregulation of P. aeruginosa cells via quorum sensing. UpregulatedP. aeruginosa cells released HQNO at enhanced rates, thereby inducing phenotypic switching of S. aureus toSCVs which consume nutrient at a reduced rate. This shifted the nutrient distribution back in favor of P.aeruginosa, thereby relieving nutritional stress. Increase in nutritional stress potentiated the transformation of S.aureus into SCVs. HQNO production decreased once nutritional stress was relieved, indicating that phenotypicswitching acts as a regulatory stress-adaptive response.

    • MMR-proficient and MMR-deficient colorectal cancer cells: 5-Fluorouracil treatment response and correlation to CD133 and MGMT expression

      JAIME A OLIVER RAU´L ORTIZ CRISTINA JIME´NEZ-LUNA LAURA CABEZA GLORIA PERAZZOLI OCTAVIO CABA CRISTINA MESAS CONSOLACIO´N MELGUIZO JOSE PRADOS

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      Cancer stem cells (CSCs) from colorectal cancer (CRC), characterized by CD133 expression, have beenassociated with 5-fluorouracile (5-FU) chemoresistance. DNA repair mechanisms, such as O6-alkylguanineDNA alkyltransferase (MGMT) and mismatch repair (MMR) systems, have also been correlated to 5-FUresistance in CRC. The aim of this study was to evaluate the modulation of CD133 and MGMT in MMRproficientand MMR-deficient CRC cells under 5-FU treatment and the effect of this drug in CSCs. CD133 andMGMT methylation status were determined in MMR-proficient (SW480 and HT29) and MMR-deficient (RKOand HCT116) cell lines by methylation-specific PCRs. SW480 and RKO were selected to determine modulationof CD133, MGMT and MMR expression after 5-FU treatment by qPCR. In addition, CD133, MGMTand MMR were analyze in SW480 and RKO CSCs. No association between promoter methylation and MGMTand CD133 expression was found. 5-FU treatment increased CD133 expression independently to MMR statusin SW480 and RKO and was able to increase hMLH1 expression in RKO, a MMR-deficient cell line. RKO/CSCs overexpressed CD133 and MMR (hMSH2 and hMSH6) while SW480/CSCs showed a significantincrease in CD133, MMR (hMLH1, hMSH2 and hMSH6) and MGMT, moreover 5-FU resistance thanparental cell lines. Thus, although CSCs 5-FU chemoresistance appears to be independently to MMR status,hMLH1 might play a key role in CSC response to 5-FU. New drugs exploding these differences could benefitthe prognostic of patients with CRC.

    • Plant abiotic stress tolerance: Insights into resilience build-up

      PENNA SUPRASANNA

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      Climate change and the consequential unpredictable environmental stress conditions negatively impact cropproductivity. It has thus become a challenge to develop solutions for food security and sustainable agriculturein the backdrop of increasing population pressure and dwindling land and water resources. This furthernecessitates that focus of international research should be on curtailing yield losses through improved cropbreeding practices and genetic manipulation for the development of resistant crop varieties. Plants beingsessile, have developed a complex regulatory network of genetic machinery which includes transcriptionfactors, small RNAs, signalling pathways, stress sensors and defense pathways. Needless to say, researchefforts have exploited this genetic reservoir for manipulating crop plants for tolerance or resistance againstdifferent stresses. In the past few decades, significant achievement has been made for developing transgenicplants for a wide variety of single or multiple stress tolerance associated traits. Several regulatory mechanismshave been identified to fine tune and tailor the tolerance response in target sensitive crops. The advent ofmetabolic engineering has added new dimensions to manipulate stress tolerance pathways. Novel strategies areneeded to develop stable, superior performing lines under challenging field environment without yield penaltyand significant success has to be achieved to translate the research outcome from lab-to-land to reach farmer’sfields.

    • An update and perspectives on the use of promoters in plant genetic engineering

      DIVYA KUMMARI SUDHAKAR REDDY PALAKOLANU P B KAVI KISHOR POOJA BHATNAGAR-MATHUR PRASANTH SINGAM VINCENT VADEZ KIRAN K SHARMA

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      Genetically engineered plants have varied applications in agriculture for enhancing the values of food and feed.Genetic engineering aims to introduce selected genetic regions with desirable traits into target plants for bothspatial and temporal expressions. Promoters are the key elements responsible for regulating gene expressionsby modulating the transcription factors (TFs) through recognition of RNA polymerases. Based on theirrecognition and expression, RNA polymerases were categorized into RNA pol II and pol III promoters.Promoter activity and specificity are the two prime parameters in regulating the transgene expression. Since theuse of constitutive promoters like Cauliflower mosaic virus (CaMV) 35S may lead to adverse effects on nontargetorganisms or ecosystem, inducible/tissue specific promoters and/or the RNA pol III promoters providemyriad opportunities for gene expressions with controlled regulation and with minimum adverse effects.Besides their role in transgene expression, their influence in synthetic biology and genome editing are alsodiscussed. This review provides an update on the importance, current prospects, and insight into the advantagesand disadvantages of promoters reported thus far would help to utilize them in the endeavour to developnutritionally and agronomically improved transgenic crops for commercialization.

    • RNA silencing technology: A boon for crop improvement

      MANCHIKATLAV RAJAM

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      RNA interference (RNAi) is a powerful tool for gene silencing in different organisms, including plants. It isbeing used in functional genomics to decipher the function of genes. This technology has also witnessed avariety of potential applications in agriculture for crop improvement, including the development of crops forresistance against biotic (weeds, pathogens, insect pests and nematode parasites) and abiotic stresses (drought,high and low temperature, etc.), nutritional quality improvement, healthier oils, delayed ripening, male sterility,modification of flowering time and flower colour, alteration of plant architecture, enhancement of secondaryproducts, and removal of allergens and toxins. RNAi has several advantages over traditional transgenicapproaches as genetically modified RNAi plants do not contain transgene protein, however the risk assessmentof these plants should be examined to rule out any off-target effects.

    • Freeing the brake: Proliferation needs primary cilium to disassemble

      PRIYADARSHINI HALDER SHILPA KHATUN SHUBHRA MAJUMDER

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      Primary cilia are non-motile, microtubule-based, antennae-like organelle that protrude out from the cell surface and perform sensory function or transduce physiological signals in majority of the vertebrate cells. Cilia are assembled on basal bodies that are transformed centrioles. The assembly-disassembly of primary cilia maypose an additional measure on regulating cell cycle in vertebrate cells. While primary cilia are commonly found in differentiated or quiescent cells that are not cycling, disassembly of primary cilia may promote re-entry of these cells into the mitotic cycle, and support proliferation. Many cancer tissues or cancer-derived cells exhibitloss of primary cilia. However, primary cilia may also promote tumorigenesis in some contexts through growth-promoting signalling. This review will shed light on recent advancements of temporal coordination of ciliary disassembly and cell cycle progression, with a focus on how cilia loss may support tumorigenesis in various epithelial cancers.

    • MicroRNAs as potential targets for improving rice yield via plant architecture modulation: Recent studies and future perspectives

      RANJEET KAUR RUPAM KUMAR BHUNIA MANCHIKATLA VENKAT RAJAM

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      Ensuring agricultural food security is a major concern for the future world, and being the second mostconsumed crop, rice yield needs an urgent upliftment. Grain yield is a pleiotropic trait that employs a plethoraof genes functioning in complex signalling cascades. The yield related genes are controlled by variousregulatory factors including the microRNAs (miRNAs), the small 20–22 nucleotide (nt) non-coding RNAs,which have emerged as the master ribo-regulators of eukaryotic genes. Plant miRNAs can bind to highlycomplementary sequences in the target messenger RNAs (mRNAs) and negatively regulate gene expression tocoordinate the various biological processes involved in plant development. In rice, an ideal plant architecture(IPA) has been regarded as the key to attain high yield and several miRNAs have been deciphered to playimportant roles in orchestrating vital regulatory procedures for achieving optimum plant morphological yieldrelated traits like less unproductive tillers, more panicle branches and heavier grains. In this review, we presentand discuss the various genetic engineering strategies undertaken to manipulate the miRNA-mRNA expressionlevels in order to achieve improved grain output by modulation of rice plant architecture and recent advancesmade in this regard.

    • Elucidation and genetic intervention of CO2 concentration mechanism in Chlamydomonas reinhardtii for increased plant primary productivity

      KOKKANTI MALLIKARJUNA KELAM NARENDRA RAGIREDDYPALEM RAGALATHA BASUTHKAR J RAO

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      The rising global population is forcing the need for adapting alternative sustainable technologies for enhancedcrop productivity. The CO2 Concentration Mechanisms (CCMs) evolved in algae to counter the inefficient CO2fixing enzyme, RuBisCo and slower diffusion of CO2 in water offers good scope for the above purpose. TheCCMs are single-celled CO2 supply mechanisms that depend on multiple CO2/HCO3

      - transporters andacclimation states and accumulate 100-fold more CO2 than low CO2 environments. Although some insightshave been obtained regarding the CCMs of blue-green algae and green algae like Chlamydomonas reinhardtii,further progress needs to take place to understand the molecular and biochemical basis for intracellulartransport of CO2. In this review, complete information pertaining to the core CCM is presented and discussedin light of the available literature. In addition to this, information on CO2/HCO3

      - sensing, photo-acclimation inlow CO2, liquid-like nature of pyrenoid, untapped potential of high CO2 responses and high CO2 requiringmutants, and prospects of engineering CCM components into higher plants are presented and discussed.

    • Genetic engineering of crops for insect resistance: An overview

      ASHWINI TALAKAYALA SUMALATHA KATTA MALLIKARJUNA GARLADINNE

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      Phytophagous insect incidence is a serious threat for reduction of crop productivity globally. There is anestimation of one fourth of crop is being destroyed by insects annually. Indeed, the development of insect resistantcrops is a great milestone in agriculture to increase crop yield and reduce pesticide dependency.Genetic engineering facilitates development of insect resistant crops by expressing bacterial delta-endotoxins andvegetative insecticidal proteins and other plant genes like lectins, protease inhibitors, etc. In addition, RNAinterference and genome editing through CRISPR Cas9 also provides new solutions for the development ofinsect-resistant crops. The resultant genetically modified crops showed resistance against lepidopteran, dipteran,homopteran and coleopteran insects. The insect-resistant crops have made a significant economic impactworldwide in terms of higher yield and low pesticide usage. In this review, we focus on different strategies fordeveloping transgenics against insect pest control by expressing different insecticidal proteins in crops.

    • Curvularia eragrostidis, a new threat to large cardamom (Amomum subulatum Roxb.) causing leaf blight in Sikkim

      KABITA GURUNG KHASHTI DASILA ANITA PANDEY NILADRI BAG

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      Large cardamom (Amomum subulatum Roxb.) is now affected by several diseases caused by both viruses andfungi. At present, leaf blight is considered a major threat to cardamom cultivation in Sikkim. During the pasttwo decades, cultivation of the crop in this region has dropped by almost 60%. Hence, to quantify the severityof leaf blight damage and identification of the causal organism for the disease, a survey was conducted fromMay to August 2017 in different large cardamom growing regions of Sikkim. During this survey, a typicalsymptom of leaf blight was observed on cardamom leaves in many locations. The leaves with blights werecollected, surface sterilized, and inoculated on potato dextrose agar (PDA). The pathogen was isolated as pureculture, and on the basis of morphological and microscopic characteristics, the fungus was identified species ofCurvularia. Molecular characterization of the fungal isolate with ITS-rDNA partial gene amplification usinguniversal primers (ITS4 and ITS5), showed 100% similarity with Curvularia eragrostidis (family: Pleosporaceae).The fungal isolate and nucleotide sequence was deposited in National Fungal Culture Collection ofIndia (NFCCI), Pune and NCBI with accession numbers NFCCI 4541 and MN710527, respectively. This is thefirst report on the occurrence of C. eragrostidis pathogen causing leaf blight of large cardamom grown inSikkim.

    • Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management

      JOHNSON BESLIN JOSHI LOGANATHAN ARUL JEGADEESAN RAMALINGAM SIVAKUMAR UTHANDI

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      Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of riceworldwide. The pathogen reported to cause 70% crop loss in some of the susceptible genotypes under diseasefavoring environments, viz., temperature ranging between 25 to 34 deg C and relative humidity more than 70%. InXoo, about 245 genes govern the pathogenicity and host specificity. The hypersensitive response andpathogenicity (hrp) genes responsible for disease occurrence were clustered in the pathogenicity island of 31.3Kb. The protein secreted through type three secretory system and type one secretory system mediates infectionand establishment of the pathogen inside the host. However, elicitor molecules from Xoo triggered the resistantresponse in rice against the pathogen. An array of resistant genes (R genes) was known to be invoked by thehost to combat the bacterial infection. To date, of the 45 Xa genes in rice, nine were cloned and characterized.The evolution of new races has made the task of developing resistant rice genotypes more challenging as itdemands a comprehensive breeding strategy involving the best use of R genes from the existing gene pool.Thus, to combat the infection from the existing races and to slow down the emergence of new Xoo races,pyramiding two or more R genes was found to be effective against bacterial blight disease. In India, thesuccessfully commercialized example includes the development of rice genotypes, viz., Improved Pusa Basmati-1, Improved Samba Mahsuri, PR106, Type 3 Basmati, and Mahsuri with selected R genes, viz., xa5, Xa4,xa13 and Xa21 against bacterial blight resistance. This review primarily portray Xoo-rice interactions andprovides opportunities for its effective management through sustainable technologies.

    • Plant phenomics: High-throughput technology for accelerating genomics

      RATNAKUMAR PASALA BRIJ BIHARI PANDEY

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      Plant phenomics is a high-throughput path-breaking area that meets all the requirements for the collection ofaccurate, rapid and multi-faceted phenotypic data. Plant phenomics is an approach to envisage complex traitsthat are appropriate for selection, and provides relevant information as to why particular genotype can stand outin particular environmental conditions. The technique of plant phenotyping can be operated in variousdimensions, from the gene to the whole-plant level under a specific environment, and management practices.Through this review, we discuss the recent advances in plant phenomics, highlighting different field andconfined high-throughput technologies for utilization in forward and reverse genetics. These plant phenomicstechnique are very relevant in stress identification, study physiological processes, rapid and efficient screening,dissection and confirmation for understanding the genetic basis of different traits, genes and aspects. High-throughputphenomics technologies are essential to avoid human error and to reduce time consumption whilephenotyping large germplasm populations, or for confirmation of gene or trait functional analysis.

    • Helicobacter pylori: Perturbation and restoration of gut microbiome

      ANKITA SAXENA ASISH KUMAR MUKHOPADHYAY SHOMA PAUL NANDI

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      Alternate remedies with natural products provides unlimited opportunities for new drug development. Thesecan be either as pure compounds or as standardized set of compounds. The phytochemicals and secondarymetabolites are in great demand for screening bioactive compounds and plays an important role towards drugdevelopment. Natural products have many advantages over to synthetic chemical drugs. Helicobacter pylori(H. pylori) a Gram-negative bacteria has been classified as Class I carcinogen by World Health Organization in1994. Current treatment regimens for H. pylori is ‘triple therapy’ administrated for two weeks which includes acombination of two antibiotics like Amoxicillin and Clarithromycin and a proton pump inhibitor (PPI) likeLansoprazole, and for ‘quadruple therapy’ in addition to antibiotics and a PPI, Bismuth is used. Antibioticresistance can be named as the main factor for failure of treatment of H. pylori infection. The need of the houris to develop a herbal remedy that could combat the growth of H. pylori. Probiotics can also be used as

      ‘feasible’ tool for H. pylori infection management. Present review is an attempt to briefly discuss about thepathogenicity, genetic predisposition, perturbation of gut microbiota due to antibiotic treatment and restorationof healthy gut microbiota with phytochemicals and probiotics.

    • RNA silencing of hormonal biosynthetic genes impairs larval growth and development in cotton bollworm, Helicoverpa armigera

      ANJALI JAIWAL KALLEDA NATARAJASWAMY MANCHIKATLA VENKAT RAJAM

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      The cotton bollworm, Helicoverpa armigera, is a highly polyphagous pest, causing enormous losses to variouseconomically important crops. The identification and in vitro functional validation of target genes of a pest is aprerequisite to combat pest via host-mediated RNA interference (RNAi). In the present study, six hormonalbiosynthesis genes of H. armigera were chosen and evaluated by feeding insect larvae with dsRNAs correspondingto each target gene, viz., juvenile hormone acid methyltransferase ( HaJHAMT), prothoracicotropichormone ( HaPTTH), pheromone biosynthesis-activating peptide ( HaPBAP), molt regulating transcription factor(HaHR3), activated protein 4 (HaAP-4) and eclosion hormone precursor ( HaEHP). The loss of function phenotypesfor these hormonal genes were observed by releasing second instar larvae on to artificial diet containingtarget gene-specific dsRNAs. Ingestion of dsRNAs resulted in mortality ranging from 60% to 90%, reduced larvalweight, phenotypic deformities and delayed pupation. The quantitative real-time PCR (qRT-PCR) analysisshowed that the target gene transcript levels were decreased drastically (31% to 77%) as compared to control orunrelated control ( GFP-dsRNA), and correlated well with the mortality and developmental defects of larvae.Also, a comparison of the silencing efficacy of un-diced long HaPTTH-dsRNA with RNase III diced HaPTTH-dsRNA(siRNAs) revealed that long dsRNAs were more efficient in silencing the target gene. These resultsindicated that the hormonal biosynthesis genes have varied sensitivity towards RNAi and could be the vital targetsfor insect resistance in crop plants like cotton which are infested by H. armigera.

    • Expansion and characterization of cells from surgically removed intervertebral disc fragments in xenogen-free medium

      SIMRAN MUJAWAR KRUTTIKA IYENGAR SUNIL NADKARNI RITA MULHERKAR

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      Low back pain due to degeneration of intervertebral disc (IVD) is a major health problem resulting insignificant disability as well as adding to the economic burden. Discectomy is a very common procedure doneworldwide to relieve this pain. At present all the surgically removed disc tissue is mostly discarded. However,there are reports that state that progenitor cells in the IVD can be grown ex vivo and have the potential to beused for IVD repair and regeneration. We report here that viable cells can be harvested from surgicallyremoved, herniated disc tissue and can be potentially used in cell based therapy. Further, we have successfullyreplaced xenogenic supplements such as foetal bovine serum with either autologous serum or human plateletlysate for culturing IVD cells from patient’s surgically removed disc tissue, without loss of any cell characteristics,including cell surface markers, growth factor secretion in the conditioned medium and osteogenic andchondrogenic differentiation potential in vitro. The present work will not only contribute to overcoming someof the major barriers in carrying out human clinical trials, but also provide a cheap, alternate source of proteinsand growth factors for growing IVD cells ex vivo for therapy.

    • Long non-coding RNA CASC2 targeting miR-18a suppresses glioblastoma cell growth, metastasis and EMT in vitro and in vivo

      JUN WANG CHAO QIN CHEN ZHONG YONG WEN SHA KE BO LIAO

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      Long non-coding RNAs (lncRNAs) cancer susceptibility candidate 2 (CASC2) has been characterized as atumor suppressor in glioma. Although CASC2 may predict the prognosis of glioma patients, the role andmechanism of CASC2 in human glioblastoma remain to be fully illuminated. Expression of CASC2 and miR-18a was detected using RT-qPCR. Cell growth was evaluated by MTT assay, colony formation assay, and flowcytometry; metastasis and epithelial-mesenchymal transition (EMT) were determined with transwell assay andWestern blot, respectively. The target binding between CASC2 and miR-18a was predicted on Starbasesoftware, and confirmed by luciferase reporter assay and RNA immunoprecipitation. Xenograft experimentmeasured tumor growth. As a result, CASC2 was downregulated and miR-18a was upregulated in glioblastomatumor tissues and cells (T98 and A172). Overexpression of CASC2 promoted apoptosis rate and E-cadherinexpression, but suppressed cell viability, colony-forming ability, migration, invasion, and expression ofN-cadherin and Vimentin in T98 and A172 cells, accompanied with tumor growth inhibition in vivo; whereas,silencing of CASC2 exerted the opposite effect on cell growth, metastasis and EMT of T98 and A172 cellsin vitro. However, reintroduction of miR-18a could reverse CASC2 upregulation-mediated suppression onabove cell behaviors in vitro. More importantly, miR-18a was a downstream target for CASC2, and wasnegatively regulated by CASC2. Collectively, this study demonstrated that CASC2 served as tumor suppressorin glioblastoma by inhibiting cell growth, metastasis and EMT both in vitro and in vivo partially via CASC2-miR-18a axis.

    • VacPred: Sequence-based prediction of plant vacuole proteins using machine-learning techniques

      ARVIND KUMAR YADAV DEEPAK SINGLA

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      Subcellular localization prediction of the proteome is one of major goals of large-scale genome or proteomesequencing projects to define the gene functions that could be possible with the help of computationalmodeling techniques. Previously, different methods have been developed for this purpose using multi-labelclassification system and achieved a high level of accuracy. However, during the validation of our blind datasetof plant vacuole proteins, we observed that they have poor performance with accuracy value range from

      ~1.3% to 48.5%. The results showed that the previously developed methods are not very accurate for the plantvacuole protein prediction and thus emphasize the need to develop a more accurate and reliable algorithm. Inthis study, we have developed various compositions as well as PSSM-based models and achieved a highaccuracy than previously developed methods. We have shown that our best model achieved ~63% accuracyon blind dataset, which is far better than currently available tools. Furthermore, we have implemented our bestmodels in the form of GUI-based free software called ‘VacPred’ which is compatible with both Linux andWindow platform. This software is freely available for download at www.deepaklab.com/vacpred.

    • Mouse model for endometriosis is characterized by proliferation and inflammation but not epithelial-to-mesenchymal transition and fibrosis

      ANURADHA MISHRA MOSAMI GALVANKAR SHANTASHRI VAIDYA UDDHAV CHAUDHARI DEEPAK MODI

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      Endometriosis is a common disorder of unknown etiology, and non-surgical therapies are still a challenge. Tounderstand the pathogenesis and preclinical testing of drugs for endometriosis, animal models are highlydesirous. Herein, we carried out longitudinal characterization of a mouse model for endometriosis whereuterine tissue was transplanted onto the intestinal mesentery. During the course of lesion development from day15 to 60 post-induction, the ectopic endometrium became pale, fluid-filled and the animals developed peritonealadhesions. Most lesions resembled a well-differentiated type of endometriosis and ~13% of animalshad mixed type of lesions. There was extensive stromal compaction in the ectopic tissue. During the progressionof endometriosis, there was increased proliferation of epithelial and stromal cells as evident by PCNAstaining. Cyp19a1 (aromatase) mRNA was detected in the ectopic lesions on day 15 and 30 post-induction ofendometriosis, by day 60 the expression was reduced. As compared to the control endometrium, the mRNAlevels of Esr1 progressively reduced while the levels of inflammation associated genes (Esr2, Ifng, Tnf andIl1b) increased in the ectopic lesions. Infiltration of macrophages and polymorphonuclear leucocytes was alsoobserved in the ectopic lesions indicative of inflammation. As compared to control, there was no change inlevels of Cytokeratin and E-cadherin in the epithelial cells of ectopic endometrium. We did not observeexcessive collagen deposition or alpha-SMA positive myofibroblasts in the stroma of the ectopic endometrium.Thus, epithelial-to-mesenchymal transition and fibrosis are not detected in the mouse model of endometriosis.Our results show that the mouse model of endometriosis mimics some but not all the features of humanendometriosis.

    • Differential transcriptome analysis in HPV-positive and HPV-negative cervical cancer cells through CRISPR knockout of miR-214

      PRAKRITI SEN POOJA GANGULY KIRTI K KULKARNI ROLI BUDHWAR NILADRI GANGULY

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      In this study we have investigated the effects of a tumour suppressor microRNA, miR-214, on gene expressionin HPV-positive (CaSki) and HPV-negative cervical cancer cells (C33A) by RNA sequencing using nextgeneration sequencing. The HPV-positive and HPV-negative cervical cancer cells were either miR-214-knocked-out or miR-214-overexpressed. Gene expression analysis showed that a total of 904 genes wereupregulated and 365 genes were downregulated between HPV-positive and HPV-negative cervical cancer cellswith a fold change of ±2. Furthermore, 11 differentially expressed and relevant genes (TNFAIP3, RAB25,MET, CYP1B1, NDRG1, CD24, LOXL2, CD44, PMS2, LATS1 and MDM1) which showed a fold change of ±5were selected to confirm by real-time PCR. This study represents the first report of miR-214 on global geneexpression in the context of HPV.

    • High-throughput sequencing reveals the molecular mechanisms determining the stay-green characteristic in soybeans

      CHENG WANG LE GAO RUN ZHI LI YE WANG YANG YING LIU XIN ZHANG HAO XIE

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      Senescence is an internally systematized degeneration process leading to death in plants. Leaf yellowing, oneof the most prominent features of plant aging may lead to reduced crop yields. The molecular mechanism ofresponses to senescence in soybean leaves is not completely clear. In our research, two soybean varieties wereselected with different stay-green traits: stay-green variety (BN106) and non-stay-green variety (KF14). RNAsamples extracted from the leaves of two varieties were sequenced and compared using high-throughputsequencing. Six key enzyme genes in chlorophyll degradation pathways were studied to analyze the changes intheir expression at seedling, flowering and maturation stage. Meanwhile, the construction of the genetictransformation process had been constructed to identify the function of putative gene by RNA-interference. Atotal of 4329 DEGs were involved in 52 functional groups and 254 KEGG pathways. Twelve genes encodingsenescence-associated and inducible chloroplast stay-green protein showed significant differential expression.MDCase and PAO have a significant expression in BN106 that may be the key factors affecting the maintenanceof green characteristics. In addition, the function of GmSGRs has been identified by genetic transformation.The loss of GmSGRs may cause soybean seeds to change from yellow to green. In summary, ourresults revealed fundamental information about the molecular mechanism of aging in soybeans with differentstay-green characteristics. The work of genetic transformation lays a foundation for putative gene functionstudies that could contribute to postpone aging in soybeans.

    • Low-light and its effects on crop yield: Genetic and genomic implications

      MADHUSMITA PANIGRAHY NEELOFAR MAJEED KISHORE C S PANIGRAHI

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      Shade indicates decreased sunlight. The agricultural importance of shade imparts to its deteriorative effect of cropyield. Rice is not only the most widely used food crop by a third of the population of the world, but it has also beenestablished as the modelmonocot plant for study. This article describes several important aspects of shade on rice yieldwith appropriate examples in other plants such as Arabidopsis. To start with, how different environmental or growthconditions create shade is explained. Themorphological, physiological and biochemical characteristics due to differentkinds of shade are selectively explained. The molecular characteristics of rice under shade from genetic, genomic andepigenetic studied are discussed. Signalling components for the manifestation of shade tolerance responses and theirinterconnection with other signalling networks and hormone pathway components are from recent reports. A list ofgenes, micro-RNAs and metabolites that are involved in shade responses is presented. Lastly, implications forsustainable yield under shade is discussed. This review will be useful not only for cutting-edge information on shadetolerance but will also build framework for upcoming new rice varieties with sustainable yield under shade.

    • Downregulation of hsa_circ_0000936 sensitizes resistant glioma cells to temozolomide by sponging miR-1294

      LIN HUA LIFA HUANG XIN ZHANG HAOKE FENG

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      Glioma is one of the most aggressive forms of brain tumor and is hallmarked by high rate of mortality,metastasis and drug resistance. Herein, we explore the role of circular RNA (circRNA) hsa_circ_0000936 inthe resistance of glioma cells to temozolomide (TMZ). In this study, Relative changes in gene expression levelswere compared using qRT-PCR. The role of hsa_circ_0000936 was characterized by cell count kit -8 assay andflow cytometry. Luciferase reporter assay was carried out for target validation.We found that hsa_circ_0000936was upregulated in glioma tissues as compared to their adjacent normal tissues. Increased expression ofhsa_circ_0000936 was found in the glioma tissues of patients showing resistance to TMZ compared with thatof patients showing sensitivity to TMZ. The upregulation of hsa_circ_0000936 was also confirmed in TMZresistantglioma cells. miR-1294 was downregulated in TMZ-resistant glioma cells and identified as a directtarget of hsa_circ_0000936. Downregulation of hsa_circ_0000936 increased the sensitivity of TMZ-resistantglioma cells towards TMZ. Moreover, restoration of miR-1294 could abrogate the promoting effect ofhsa_circ_0000936 on TMZ resistance in TMZ-resistant glioma cells. In conclusion, downregulation ofhsa_circ_0000936 sensitizes TMZ-resistant glioma cells to TMZ by sponging miR-1294, suggesting thathsa_circ_0000936 may be a potential target for overcoming the resistance of glioma cells to TMZ.

    • Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products

      ABHISHEK SHARMA VIKAS TIWARI RAMANATHAN SOWDHAMINI

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      The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough.In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causativepathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is oneof the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome(SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model atarget non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virusand hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approveddrugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtualscreening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously knownanti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practicedin Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like torecommend uptake of these small molecules for suspect COVID patients until it is approved by competentnational or international authorities.

    • RNAi suppressor: The hidden weapon of SARS-CoV

      SUMONA KARJEE SUNIL KUMAR MUKHERJEE

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      The two biological evidences to endorse the antiviral activity of RNA interference (RNAi) are biogenesis ofviral-siRNA (v-siRNA) by the host and encoding of RNAi-suppressor protein by viral genome. It has beenrecently established that mammals and mammalian cell lines mount antiviral RNAi to defend themselvesagainst the invading viruses. The large part of viral pathogenicity is also due to the RNAi suppressor proteins.In this context it is only natural to ask what kinds of RNAi suppressors are encoded by the Severe AcuteRespiratory Syndrome Coronavirus 2 (SARS-CoV-2), the central character of the present pandemic. Thefollowing mini review addresses this question.

    • Immunomodulatory properties of bone marrow mesenchymal stem cells

      APARNA MOHANTY NARESH POLISETTI GEETA K VEMUGANTI

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      Bone marrow mesenchymal stem cells (BM-MSCs) are multipotent progenitor cells of mesodermal originpossessing multilineage differentiation potential and ease of expansion in vitro. Over the years, these cells havegained attention owing to their potential in cell-based therapies in treating various diseases. In particular, thewide spectrum of immunoregulatory/immunomodulatory role of MSCs in various clinical conditions hasgained immense attention. The immunomodulatory properties of BM-MSCs are mediated by either cell–cellcontact (interactions with various immune cells in a context-dependent manner), paracrine mode of action orextracellular vesicles, making them a potential option as immunosuppressants/immunomodulators in treatingvarious clinical conditions. A plethora of studies have demonstrated that MSCs do so by exhibiting a profoundeffect on various immune cells for example they can inhibit the proliferation of T cells, B cells, and naturalkiller cells; modulate the activities of dendritic cells and induce regulatory T cells both in vitro and in vivo. Inthis review we aim at briefly elucidating the characteristics of BM-MSCs, specifically addressing the currentunderstanding on the hypoimmunogeneticity and immunomodulatory properties of the same with specificreference to their interactions with B cells, T cells, Dendritic cells and natural killer cells. We also aim atreviewing the secretory profile and their role in some clinical conditions that have shown promising outcomes.

    • Sensitization of hepatocellular carcinoma cells towards doxorubicin and sorafenib is facilitated by glucosedependent alterations in reactive oxygen species, P-glycoprotein and DKK4

      SURBHI CHOUHAN SNAHLATA SINGH DIPTI ATHAVALE PRANAY RAMTEKE MURALIDHARAN VANUOPADATH BIPIN G NAIR SUDARSLAL SADASIVAN NAIR MANOJ KUMAR BHAT

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      Altered glucose uptake and metabolism is the key characteristic of cancer cells including hepatocellularcarcinoma (HCC). However, role of glucose availability in chemotherapeutic outcome of HCC is unclear. Thepresent study investigates the effect of glucose facilitated sensitization of HCC cells towards doxorubicin(DOX) and sorafenib (SORA). In HCC cells, we observed that hyperglycemic culture condition (HG) isassociated with increased sensitivity towards DOX and SORA. P-glycoprotein (P-gp), a transporter involved indrug efflux, was elevated in HCC cells in NG, rendering them less susceptible to DOX and SORA. Further, thisstudy demonstrated that knockdown of dickkopf protein 4 (DKK4), a Wnt antagonist protein, causes enhancedglucose uptake and reduction in P-gp level rendering HCC cells in NG sensitive to DOX and SORA.Moreover, HG elevates the level of intracellular reactive oxygen species (ROS), which regulates P-gp.Alteration in intracellular ROS did not directly affect regulation of DKK4 in HCC cells. Functional assayssuggest that alterations in DKK4 and P-gp level in HCC cells are dependent on glucose availability andchanges in ROS level because of enhanced glucose utilization, respectively. Collectively, the present studyhighlights direct involvement of glucose-induced ROS, DKK4 and P-gp in altering the sensitivity of HCC cellstowards DOX and SORA.

    • Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers

      O O OYEBANJI E C CHUKWUMA KA BOLARINWA O I ADEJOBI SB ADEYEMI A O AYOOLA

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      The families Lamiaceae and Verbenaceae comprise several closely related species that possess high morphologicalsynapomorphic traits. Hence, there is a tendency of species misidentification using only the morphologicalcharacters. Herein, we evaluated the discriminatory power of the universal DNA barcodes (matKand rbcL) for 53 species spanning the two families. Using these markers, we inferred phylogenetic relationshipsand conducted species delimitation analysis using four delimitation methods: Automated Barcode GapDiscovery (ABGD), TaxonDNA, Bayesian Poisson Tree Processes (bPTP) and General Mixed Yule Coalescent(GMYC). The phylogenetic reconstruction based on the matK gene resolved the relationships between thefamilies and further suggested the expansion of the Lamiaceae to include some core Verbanaceae genus, e.g.,Gmelina. The rbcL marker using the TaxonDNA method displayed high species delimitation resolutions, whilethe ABGD, GMYC, and bPTP generated different number of Operational Taxonomic Units/genetic clusters.Our results underscored the efficiency of the matK and rbcL genes as reliable markers for resolving phylogeneticrelationships and species delimitation of both families, respectively. The current study provides insightsinto the DNA barcode applications in these families, at the same time contributing to the current understandingof genetic divergence patterns in angiosperms.

    • PRIGSA2: Improved version of protein repeat identification by graph spectral analysis

      BROTO CHAKRABARTY NITA PAREKH

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      Tandemly repeated structural motifs in proteins form highly stable structural folds and provide multiplebinding sites associated with diverse functional roles. The tertiary structure and function of these proteins aredetermined by the type and copy number of the repeating units. Each repeat type exhibits a unique pattern ofintra- and inter-repeat unit interactions that is well-captured by the topological features in the network representationof protein structures. Here we present an improved version of our graph based algorithm, PRIGSA,with structure-based validation and filtering steps incorporated for accurate detection of tandem structuralrepeats. The algorithm integrates available knowledge on repeat families with de novo prediction to detectrepeats in single monomer chains as well as in multimeric protein complexes. Three levels of performanceevaluation are presented: comparison with state-of-the-art algorithms on benchmark dataset of repeat and nonrepeatproteins, accuracy in the detection of members of 13 known repeat families reported in UniProt andexecution on the complete Protein Data Bank to show its ability to identify previously uncharacterizedproteins. A ~3-fold increase in the coverage of the members of 13 known families and 3408 noveluncharacterized structural repeat proteins are identified on executing it on PDB. PRIGSA2 is available at http://bioinf.iiit.ac.in/PRIGSA2/.

    • Receptors involved in dexketoprofen analgesia in murine visceral pain

      V NORIEGA F SIERRALTA P POBLETE N ARANDA R SOTOMAYOR-ZA´RATE J C PRIETO H F MIRANDA

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      Various animal models, especially rodents, are used to study pain, due to the difficulty of studying it inhumans. Many drugs that produce analgesia have been studied and there is evidence among whichNSAIDs deserve to be highlighted. Dexketoprofen (DEX) provides a broad antinociceptive profile indifferent types of pain; therefore, this study was designed to evaluate the profile of antinociceptivepotency in mice. Analgesic activity was evaluated using the acetic acid abdominal constriction test(writhing test), a chemical model of visceral pain. Dose-response curves for i.p. DEX administration (1,3, 10, 30 and 100 mg/kg), using at least six mice in each of at least five doses, was obtained before and30 min after pre-treatment with different pharmacological agents. Pretreatment of the mice with opioidreceptor antagonists was not effective; however, the serotonin receptor antagonist and nitric oxidesynthase inhibitor produce a significant increase in DEX-induced antinociception. The data from thepresent study shows that DEX produces antinociception in the chemical twisting test of mice, which isexplained with difficulty by the simple inhibition of COX. This effect appears to be mediated by othermechanisms in which the contribution of the NO and 5-HT pathways has an important effect on DEXinducedantinociception.

    • Human placental laminin: Role in neuronal differentiation, cell adhesion and proliferation

      CHAITALI MUKHERJEE SURAIYA SALEEM SROMONA DAS SUBHAS CHANDRA BISWAS DEBASISH BHATTACHARYYA

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      Human placental extract has wound healing potential. Immuno-blots revealed presence of laminin in placentalextract (70 ± 0.257 ug/ml; n=3). It was purified using immuno-affinity chromatography. SDS-PAGE and SEHPLCindicated a188 kDa protein with some small peptides. Since placental laminin existed in its truncatedform, its roles in cellular migration, differentiation and wound healing were verified. Induction of cellularmigration and motility in rat fibroblasts were enhanced by placental laminin as observed from scratch woundassay. Promotion of neuronal differentiation of PC12 cells by placental laminin was observed by phase contrastmicroscopy. Confocal images showed presence of laminin on the cell surface and along the axonal processes.Significant interaction between integrin receptors and laminin responsible for cellular differentiation wasdemonstrated from co-localization experiments. Union between integrin receptor and its synthetic antagonistrevealed retarded pattern of neurite outgrowth in laminin treated cells. Animal model studies revealed fasterwound healing in the presence of placental laminin. Induction of re-epithelialization and angiogenesis inwound area by cellular proliferation and adhesion were observed. The cytokine levels showed an initial riseand gradual fall over the duration of wound healing on application of the fragmented laminin. Thus, roles ofplacental laminin in neuronal differentiation and wound healing were indicated.

    • Cardiac differentiation of bone-marrow-resident c-kit+ stem cells by L-carnitine increases through secretion of VEGF, IL6, IGF-1, and TGF-β as clinical agents in cardiac regeneration

      EZZATOLLAH FATHI RAHELEH FARAHZADI ILJA VIETOR SARA JAVANMARDI

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      The idea of regenerating lost myocardium via cell-based therapies remains as highly considerable. C-kit+ stem/progenitor cells are represented to be suitable candidates for cardiac regeneration compared to other stem cells.A multitude of cytokines from these cells are known to give such multifunctional properties; however, theassociated mechanisms of these factors are yet to be totally understood. The aim of the present study was toinvestigate the in vitro effect of L-carnitine (LC) on cardiac differentiation of c-kit+ cells using a cytokinessecretion assay. For this purpose, bone-marrow-resident-c-kit+ cells were enriched by MACS method, andwere differentiated to cardiac cells using cardiomyocyte differentiation medium in the absence (control group)and presence of LC (experimental group). Also, characterization of enriched c-kit+ cells was performed usingflow cytometry and immunocytochemistry. In the following, the cells were subjected to real-time PCR andWestern blotting assay for gene and protein assessment, respectively. Afterward, culture medium was collectedfrom both control (-LC) and experimental groups (+ LC) for cytokine measurement. It was found that 0.2mM LC significantly increased the mRNA and protein expression of cardiac markers of Ang-1, Ang-2, C-TnI,VEGF, vWF, and SMA in c-kit+-cardiomyogenic-differentiated cells. Also, the significant presence of IL-6,IGF-1, TGF-beta, and VEGF were obvious in the cultured media from the experimental group compared with thecontrol group. It can be concluded that the mentioned in vitro effects of LC on cardiac differentiation of c-kit+cells could have resulted from the secreted cytokines IL-6, IGF-1, TGF-beta, and VEGF.

    • miRNA-mediated regulation of auxin signaling pathway during plant development and stress responses

      JAYANTI JODDER

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      Auxin is one of the most important plant growth hormones, playing a crucial role in development as well as instress responses. Auxin biosynthesis and signaling pathway comprises a series of events including auxinperception by the receptor, activation, and function of auxin response factors and control by auxin repressors.All these factors are regulated by several different microRNAs during leaf, flower and fruit development,anther development, nodulation, lateral and adventitious root development, potato tuber development as wellas during heat stress, submergence, boron toxicity, aluminium stress responses, etc., as depicted in the availableliterature. In this review a thorough study on miRNA-mediated regulation of auxin biosynthesis and signalinghas been done in various plant species. The data gathered can be utilized to point out the particular miRNAmediatedregulation module which can be utilized to modulate the expression of the miRNA and therebymodulation of the auxin pathway. Information in this review would be beneficial to utilize the miRNAexpression to generate the protocol for engineering plants with altered auxin signaling pathway to obtain betteryield and improved stress tolerance.

    • G604S-HERG mutation in LQT2 leads to autophagy via the UPR-related pathway

      YUN ZHAO SHUTING MA MIAOMIAO CAO CHAOFENG SUN

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      Congenital long QT syndrome (LQTS) is a heart channel disease associated with fatal ventricular arrhythmiasor cardiac arrest. Human ether-a-go-go-related gene (HERG) mutation is one of the main causes in type 2LQTS since it may lead to abundant immature HERG channel protein accumulate in the endoplasmic reticulum(ER). In our study, we have successfully constructed the G604S-HERG mutation in HEK293 cells anddemonstrated that the immature HERG protein on ER via Western blot and immunofluorescence. Herein wefound that unfolded protein reaction (UPR) process has been activated in order to counter this endoplasmicreticulum stress (ERS) since the main sensors got upregulated. Meanwhile, autophagy was also observed inthis process and verified by Western blot and transmission electron microscopy. To explore the relationshipunderlying autophagy and UPR in the condition of ERS, we found that PERK-EIF2-alpha-CHOP axis was activated.Our findings provides insight for G604S-HERG mutation in type 2 LQTS.

    • RECK and TIMP-2 mediate inhibition of MMP-2 and MMP-9 by Annona muricata

      G DRISHYA JYOTSNA NAMBIAR SANU K SHAJI MURALIDHARAN VANUOPADATH A ACHUTHAN ABISHEK KUMAR ASHNA ALIAS AYESHA SHERIF CATHERINE JOSEPH P DIVYA DAMU SUNIL KUMAR CHINCHU BOSE SOBHA VIJAYAN NAIR S SUDARSLAL GEETHA B KUMAR S LAKSHMI BIPIN G NAIR

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      Up-regulation of MMP-2 and MMP-9 plays a significant role in promoting cancer progression by degradingthe components of the extracellular matrix, thereby enhancing the migration of tumor cells. Although the antiproliferativeand apoptotic effect of Annona muricata is well established, its effect on MMP-2 and MMP-9, amajor target in several types of cancers, has not been studied. Powdered samples of various parts of A.muricata like fruit, stem, seed, and twig extracted using aqueous methanol showed significant dose-dependentinhibition of MMP-2 and MMP-9 in a highly metastatic fibrosarcoma cell line, HT1080. Additionally, theseextracts also up-regulated the expression of several endogenous inhibitors of MMP-2 and MMP-9 likeREversion-inducing Cysteine-rich protein with Kazal motifs (RECK) and Tissue Inhibitor of Metalloproteinase-2 (TIMP-2). Furthermore, primary cells developed from tumor tissues obtained from patients notexposed to chemotherapy, also exhibited similar results. Remarkably, the inhibition of MMP-2 and MMP-9observed was tumor specific, with the A. muricata fruit extract showing only 2% inhibition in cells obtainedfrom normal tissues, when compared to 60% inhibition observed in cells obtained from tumor samples. Thepresent study elucidates a novel mechanism by which A. muricata extracts selectively exhibit their anti-canceractivity in tumor cells by down-regulating MMP-2 and MMP-9 that are important biomarkers in cancer.

    • Advances in gene therapy for hemophilia

      OLIVIA A ROBLES-RODRI´GUEZ JOSE´ J PE´REZ-TRUJILLO ARNULFO VILLANUEVA-OLIVO LAURA VILLARREAL-MARTI´NEZ LUIS J MARFIL-RIVERA HUMBERTO RODRI´GUEZ-ROCHA ARACELY GARCI´A-GARCI´A ODILA SAUCEDO-CA´ RDENAS MARI´A J LOERA-ARIAS ROBERTO MONTES DE OCA-LUNA

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      Hemophilia is a hereditary disorder that can be life-threatening in individuals who have severe spontaneousbleeding resulting from minor trauma or surgery. Although replacement therapy of the missing exogenousfactor has improved patients’ quality of life, it has not been possible to establish a long-term treatment. Due tothe severity of the disease and the need for repetitive doses throughout the patient’s life, replacement therapyhas become a high-cost treatment option; therefore, the development of self-sustainable long-term therapies iscritical. Hemophilia is a good candidate for gene therapy because it is a monogenic disease that can becounteracted by expression of the missing factor. In this article, we review some of the most relevant advancesin gene therapy for this illness.

    • Drug targets for COVID-19 therapeutics: Ongoing global efforts

      AMBRISH SAXENA

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      The current global pandemic COVID-19 caused by the SARS-CoV-2 virus has already inflicted insurmountabledamage both to the human lives and global economy. There is an immediate need for identificationof effective drugs to contain the disastrous virus outbreak. Global efforts are already underway at a war footingto identify the best drug combination to address the disease. In this review, an attempt has been made tounderstand the SARS-CoV-2 life cycle, and based on this information potential druggable targets againstSARS-CoV-2 are summarized. Also, the strategies for ongoing and future drug discovery against the SARSCoV-2 virus are outlined. Given the urgency to find a definitive cure, ongoing drug repurposing efforts beingcarried out by various organizations are also described. The unprecedented crisis requires extraordinary effortsfrom the scientific community to effectively address the issue and prevent further loss of human lives andhealth.

    • Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity

      SOMNATH ROY AMRITA BANERJEE NABANEETA BASAK TORIT BARAN BAGCHI NIMAI PRASAD MANDAL BHASKAR CHANDRA PATRA ANUP KUMAR MISRA SANJEEV KUMAR SINGH RANBIR SINGH RATHI ARUNAVA PATTANAYAK

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      The sticky rice of Assam is traditionally classified as bora (glutinous) and chokuwa (semi-glutinous) basedon their stickiness after cooking. The Waxy (Wx) gene encodes for granule-bound starch synthase (GBSS)that controls the synthesis of amylose, which is a key determinant of rice end-use quality attributes. In thisreport, we analysed the level of variation in grain quality traits in a collection of bora and chokuwacultivars, and examined the nucleotide diversity at the Wx locus of selected rice accessions to identify thepossible cause of low-amylose in these rice cultivar groups. The Wx gene sequencing from 24 bora andchokuwa cultivars revealed several nucleotide variations that can explain the variation in the amylosephenotypes. The nucleotide polymorphisms in the downstream intron regions were similar to those reportedin Bangladeshi Beruin cultivars. Among the Wx polymorphisms, the CTn microsatellite in exon 1 and G/TSNP in intron 1 (G/T-Int1) should be considered for marker assisted breeding involving bora cultivars. TheWx gene tree, classified the bora accessions possessing the G/T-Int1 SNP as japonicas. However, clusteranalysis using microsatellite markers classified the bora and chokuwa cultivars as indica, and intermediateof indica-aus. The findings of this study supplemented our understanding on the evolution of the Wx geneunder human selection. The results will assist plant breeders to effectively improve the bora and chokuwalandraces.

    • Choline-betaine pathway contributes to hyperosmotic stress and subsequent lethal stress resistance in Pseudomonas protegens SN15-2

      DANYAN TANG XIAOBING WANG JIAN WANG MENGFEI WANG YAPING WANG WEI WANG

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      Pseudomonas protegens SN15-2, a typical non-spore-forming rhizosphere bacterium, has excellent biocontrolcapabilities; thus, it is necessary to explore the stress resistance of SN15-2. The choline–glycine betainepathway is considered as an important mechanism by which bacteria adapt to stressful environments. In thiswork, we demonstrated that the expression of the betA and betB genes, which are involved in the choline–glycine betaine pathway in SN15-2, was highly increased by 12-fold and 26-fold, respectively, by hyperosmoticstress and choline treatment. The accumulation of betaine in SN15-2 (5.54 g/L) was significantly higherthan that in the mutants $\Delta$ betA (3.44 g/L) and $\Delta$ betB (2.68 g/L) under hyperosmotic stress and cholinetreatment. Moreover, choline enhanced the growth of SN15-2 greatly, but it did not enhance the growth of $\Delta$betB under hyperosmotic stress. Choline combined with hyperosmotic adaptation significantly increased thelethal stress resistance of SN15-2 while the resistance of $\Delta$ betA and $\Delta$ betB was significantly decreased. Thisresearch illuminated a strategy underlying the adaptation to osmotic stress in P. protegens and provided aneffective method to improve the stress resistance of this species, thus provided a theoretical basis for thepractical application of P. protegens SN15-2.

    • Mitochondrial reactive oxygen species cause major oxidative mitochondrial DNA damages and repair pathways

      ZHENQIU HUANG YINNAN CHEN YANMIN ZHANG

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      Mitochondria-derived reactive oxygen species (mROS) are produced at a variety of sites and affect the functionof bio-molecules. The anti-oxidant system from both mitochondria and cytosol tightly coordinate to maintainthe redox balance of cells and reduce damage from mROS. Mitochondrial DNA (mtDNA) are highly susceptibleto mROS, and are easily oxidized to accumulate DNA modifications. Frequent oxidative damages inmtDNA have been associated with neurological degeneration, inflammasomes, tumorigenesis, and malignantprogression. Among mitochondrial DNA repair pathways, the base excision repair pathway has been extensivelycharacterized to remove some of oxidative damages in mtDNA as efficiently as the nuclear base excisionrepair. The implications of other pathways remain unclear. This review focuses on: (i) Sources of mROS andthe antioxidant system to balance redox status; (ii) major mtDNA lesions or damages from mROS-mediatedoxidation and the reported repair pathways or repairing factors; (iii) cellular response of oxidized mtDNA andmethods to identify oxidatively generated DNA modifications in pathological conditions. DNA damagescaused by mROS have been increasingly implicated in diseases and aging, and thus we critically discussmethods of the oxidative modifications evaluation and the complexity of non-canonical DNA repair pathwaysin mitochondria.

    • Comparative study of the SBP-box gene family in rice siblings

      PRIYA RANI AGARWAL ANSUMAN LAHIRI

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      SBP-box genes are a class of plant-specific transcription factors which have a common DNA-binding domain(SBP-domain) with an unusual zinc-finger architecture. Many of the genes in this class are thought to play adevelopmental role and a few are involved in the determination of plant architecture. We have made acomparative study of these genes in the genomes of rice (Oryza sativa japonica and Oryza sativa indica) andits nine siblings using a recently proposed hybrid method for orthology and paralogy detection (HyPPO).According to HyPPO, the SBP-box proteins of rice siblings could be divided into twenty primary orthologousgroups on the basis of their overall sequence features. This contrasts with a much less number of groups foundin earlier work with other plant genomes using phylogenetic analysis of the SBP-domains only. The orthologousgroups reported by HyPPO showed close correspondence in exon–intron structure and motif conservation.Comparison between different Oryza species revealed disparity in the maintenance of orthologousgenes which may result in their different developmental characteristics. Inclusion of the SBP-box proteins fromA. thaliana did not result in any change in the orthologous groups except for the A. thaliana proteins beingadded to some of the existing groups. The closer correspondence between the proteins in the primaryorthologous clusters is expected to help in a more reliable prediction of their functions. It is also expected toprovide better insight into the evolutionary history of this class of plant-specific proteins.

    • Current global vaccine and drug efforts against COVID-19: Pros and cons of bypassing animal trials

      BIJAYEETA DEB HEMAL SHAH SUCHI GOEL

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      COVID-19 has become one of the biggest health concern, along with huge economic burden. With no clearremedies to treat the disease, doctors are repurposing drugs like chloroquine and remdesivir to treat COVID-19patients. In parallel, research institutes in collaboration with biotech companies have identified strategies to useviral proteins as vaccine candidates for COVID-19. Although this looks promising, they still need to pass thetest of challenge studies in animal models. As various models for SARS-CoV-2 are under testing phase,biotech companies have bypassed animal studies and moved to Phase I clinical trials. In view of the presentoutbreak, this looks a justified approach, but the problem is that in the absence of animal studies, we can neverpredict the outcomes in humans. Since animal models are critical for vaccine development and SARS-CoV-2has different transmission dynamics, in this review we compare different animal models of SARS-CoV-2 withhumans for their pathogenic, immune response and transmission dynamics that make them ideal models forvaccine testing for COVID-19. Another issue of using animal model is the ethics of using animals for research;thus, we also discuss the pros and cons of using animals for vaccine development studies.

    • Elevated expression of stemness genes in adipose-derived mesenchymal stem cells cultured on fibrin scaffold

      AREZOO MOUSAVIFARD ELAHE POURAZIZI NAJAFABADI MAHSHID AKHAVAN RAHNAMA AZADEH ANBARLOU AMIR ATASHI

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      In regenerative medicine, MSCs need to be pluripotent for better results. In this study, the effect of fibrinscaffold on expression of stemness genes was examined. Adipose-derived MSCs were cultured in tissue cultureplates (2D) and 3-dimensional (3D) fibrin scaffolds. The effect of fibrin scaffold on proliferation of adiposederivedMSCs was evaluated by MTT assay. The expression of stemness genes (OCT4 and SOX2) wereevaluated by qRT-PCR, and flow cytometry was done for Nanog protein level. Cultured MSCs on fibrinscaffold were able to proliferate according to data obtained by MTT assay. Expression of OCT4 and SOX2 hada significant increase in cells were cultured in 3D condition compared to 2D condition (P less than 0.05). Also,increased expression of Nanog protein in 3D culture was observed (P less than 0.05). OCT4 and SOX2 in 3Dcondition increased two-fold and three-fold respectively in 2D and 3D conditions. Moreover, expression ofNanog increased 30% more than in 2D condition. Evaluation of important pluripotency regulators such asOCT4, SOX2, and Nanog showed that fibrin scaffolds are useful instruments to maintain stemness of MSCs,which is essential in field of stem cell therapy and regenerative medicine.

    • CRISPR-mediated knockdown of miR-214 modulates cell fate in response to anti-cancer drugs in HPV-negative and HPVpositive cervical cancer cells

      PRAKRITI SEN SAYAM GHOSAL RUDRANIL HAZRA RIMJHIM MOHANTY SOLOMON AREGA BIKASH SAHU NILADRI GANGULY

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      Cervical cancer is the fourth most common cause of mortality in women worldwide. In this study weinvestigated the effect of a tumour suppressor microRNA miR-214 in modulating the cell death againstchemotherapeutic drugs like Doxorubicin, Cisplatin and Paclitaxel. CRISPR-facilitated knockdown andplasmid-based overexpression of miR-214 was performed in cervical cancer cell lines HeLa, C33A and CaSki.It was observed that knocking out miR-214 resulted in reduced apoptosis and cell migration upon drugtreatments; while overexpression of miR-214 resulted in marginal increase in apoptosis and cell migrationwhen treated with drugs. However, miR-214 had very little effect on production of reactive oxygen species.Our results also indicate that Doxorubicin was least effective and Paclitaxel most effective in inducing celldeath. A combination of miR-214 overexpression and Paclitaxel treatment was found to be most effective ininducing cell death in cervical cancer cells. Analysis of cell cycle phases followed by apoptotic markers alsoshowed that miR-214 overexpression along with Paclitaxel treatment caused an increase in PARP and declineof PI-3 kinase/Akt levels. Therefore, miR-214 levels determine the fate of the cancer cell duringchemotherapeutic treatment.

    • Dynamics of sequestering the limiting p300/CBP, viral cis-regulatory elements, and disease

      HANAN POLANSKY HAVA SCHWAB

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      Many studies showed that the p300/CBP coactivator is limiting. Here we review three studies that showed howtranscription complexes formed on viral cis-regulator elements compete with cellular transcription complexesby sequestrating the p300/CBP coactivator. According to the microcompetition model, this sequestering cancause disease. We use the microcompetition model to explain how a specific type of sequestering, caused by alatent virus that has an active cis-regulatory element in its promoter/enhancer that binds the transcriptioncomplex p300/CBP.GABP can cause diseases such as cancer, atherosclerosis, diabetes, and certain autoimmunediseases.

    • miR-17-5p mitigates endometriosis by directly regulating VEGFA

      QIN-XIA PANG ZHOU LIU

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      Endometriosis is a common disease in women, which impairs the quality of life in patients. Recently, accumulatingevidences reported that miRNAs play an essential role in diagnosis and treatment of endometriosis.However, the regulatory mechanism of miRNAs has not been fully explored. The expression of miR-17-5p andVEGFA was detected using qRT-PCR. The protein level of VEGFA was measured via Western blot. Cellproliferation was determined by CCK-8 assay. Cell migration and invasion were measured via transwell assay.The relationship of miR-17-5p and VEGFA were verified via luciferase reporter assay. Then miR-17-5p wasremarkably down-regulated in endometriosis tissues, serums and cells, and overexpression of miR-17-5pinhibited cell proliferation, migration and invasion in endometriosis. Results showed that VEGFA was significantlyup-regulated in endometriosis tissues and cells and acted as a target of miR-17-5p. Moreover, miR-17-5p negatively regulated VEGFA expression in endometriosis. Otherwise, up-regulation of VEGFAimproved cell proliferative, migrated and invasive ability in ECSCs with transfection of miR-17-5p mimicsgroup. Our data showed miR-17-5p inhibits cell proliferation, migration and invasion in endometriosis bydirectly repressing VEGFA expression.

    • Atorvastatin ameliorates viral burden and neural stem/ progenitor cell (NSPC) death in an experimental model of Japanese encephalitis

      MASOOD AHMAD WANI SRIPARNA MUKHERJEE SUVADIP MALLICK IRSHAD AKBAR ANIRBAN BASU

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      Japanese encephalitis virus, a neurotropic flavivirus, causes sporadic encephalitis with nearly 25% fatal casereports. JEV infects neural stem/progenitor cells (NSPCs) and decreases their proliferation. Statin, a commonlyused class of cholesterol lowering drug, has been shown to possess potent anti-inflammatory and neuroprotectiveeffects in acute brain injury and chronic neurodegenerative conditions. Here, we aimed to check theefficacy of atorvastatin in alleviating the symptoms of Japanese encephalitis (JE). Using BALB/c mouse modelof JEV infection, we observed that atorvastatin effectively reduces viral load in the subventricular zone (SVZ)of infected pups and decreases the resultant cell death. Furthermore, atorvastatin abrogates microglial activationand production of proinflammatory cyto/chemokine production post JEV infection in vivo. It alsoreduced interferon-beta response in the neurogenic environs. The neuroprotective role of atorvastatin is againevident from the rescued neurosphere size and decreased cell death in vitro. It has also been observed that uponatorvastatin administration, cell cycle regulatory proteins and cell survival proteins are also restored to theirrespective expression level as observed in uninfected animals. Thus the antiviral, immunomodulatory andneuroprotective roles of atorvastatin reflect in our experimental observations. Therefore, this drug broadens apath for future therapeutic measures against JEV infection.

    • Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

      ARINDAM MAITRA MAMTA CHAWLA SARKAR HARSHA RAHEJA NIDHAN K BISWAS SOHINI CHAKRABORTI ANIMESH KUMAR SINGH SHEKHAR GHOSH SUMANTA SARKAR SUBRATA PATRA RAJIV KUMAR MONDAL TRINATH GHOSH ANANYA CHATTERJEE HASINA BANU AGNIVA MAJUMDAR SREEDHAR CHINNASWAMY NARAYANASWAMY SRINIVASAN SHANTA DUTTA SAUMITRA DAS

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      Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal andoropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2aclade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were alsodetected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein.Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz.G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutationsreside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S2 domain,which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observedbetween these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations ofmiRNA binding and structure were also predicted for these mutations. More importantly, the possibleimplications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of Sprotein have also been discussed. Results report for the first time a bird’s eye view on the accumulation ofmutations in SARS-CoV-2 genome in Eastern India.

    • Apigenin attenuates myocardial infarction-induced cardiomyocyte injury by modulating Parkin-mediated mitochondrial autophagy

      ZILIANG WANG HAO ZHANG ZUHENG LIU ZHUANG MA DONGQI AN DINGLI XU

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      We aimed to detect whether the effect of apigenin (Apig) on the myocardial infarction-induced cardiomyocyte injury ofmouse myocardial cells and acute myocardial infarction (AMI) mice was through regulating Parkin expression viamiR-103-1-5p. The myocardial infarction cardiomyocyte model (Hypoxia/reoxygenation) was first constructed, thenthe mouse myocardial cells were treated with Apig, and the expression of miR-103-1-5p was decreased and theexpression of Parkin was increased by qRT-PCR and Western blot. It was confirmed by miRNA pulldown andluciferase reporter system that miR-103-1-5p in mouse myocardial cells can bind to Parkin mRNA and inhibit Parkinexpression.Next, a lentiviral vector silenced Parkin and overexpressingmiR-103-1-5pwas constructed and transfectedinto Apig-treated cells. Autophagy was detected by mitochondrial autophagy marker proteins [atypical protein kinaseC (aPKC)-interacting protein (p62) and bcl-2/Adenovirus E1B 19-kd interacting protein 3 (BNIP3)] via Western blot,mitochondrial function was detected by JC-1 probe, and apoptosis was detected by flow cytometry. It was confirmedthat Apig regulated mitochondria autophagy through miR-103-1-5p and Parkin, which ultimately affected cardiomyocytedeath. Finally, an AMI mouse model was constructed, and then the mice were treated with Apig. Theinfarct size was detected by triphenyl tetrazolium chloride (TTC) staining, and the Apig relieved the myocardialinfarction. The expression of miR-103-1-5p was decreased and the expression of Parkin was increased by qRT-PCRand Western blot. The above results simplified that the cardio protection of Apig and miR-103-1-5p against injury ofmyocardial infarction cardiomyocyte by targeting Parkin. These results provided a novel treatment against myocardialinfarction cardiomyocyte.

    • Evaluation of memory in persons with mesial temporal lobe sclerosis: A combined fMRI and VBM study

      KAPIL CHAUDHARY MANJARI TRIPATHI P SARAT CHANDRA ASHIMA NEHRA S SENTHIL KUMARAN

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      Persons with drug refractory TLE have the option of being managed by surgery. They may develop memoryimpairment with specific etiology of mesial temporal sclerosis and anterior temporal lobe resection (ATLR).The study evaluated the semantic verbal memory outcomes in pre- and post-surgery temporal lobe epilepsy(TLE) patients using functional MRI and voxel morphometric methods. Twenty consecutive persons withdrug-resistant epilepsy (DRE) and 20 healthy controls were recruited after obtaining the institute ethicsapproval. The fMRI scans were performed on a 1.5 T MR Scanner using standardized semantic verbal memorytasks using a native Hindi paradigm, before and after an anterior temporal lobectomy (in cases). A task-basedfunctional connectivity (FC) was estimated using a conn toolbox. Data analysis was carried out using thestatistical parametric imaging (SPM12) and CAT12 toolbox. Post-surgery TLE group showed increased robustFC in the right middle and posterior temporal regions as compared to pre-surgery session. A significantreduction in grey matter volume was observed in the left temporal lobe post-operatively as compared to presurgeryand healthy control groups. In the post-surgery TLE group, neuropsychological scores were reduced inspecific PGI domains such as visuospatial, working memory, and executive functioning. Our results may helpin understanding of memory reorganization in TLE post-operatively.

    • Contrasting the expression pattern change of polyamine oxidase genes and photosynthetic efficiency of maize (Zea mays L.) genotypes under drought stress

      HADIS PAKDEL SEYEDEH BATOOL HASSANI ALI AKBAR GHOTBI-RAVANDI FRANC¸OISE BERNARD

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      The aim of this study was to contrast the effects of drought stress on polyamine oxidases gene expression andactivity as well as photosynthetic efficiency in relatively tolerant (Karoon) and sensitive (260) maize genotype.d Reduction in leaf relative water content as a result of drought led to increase in root growth, butdiminished shoot growth indices. Under drought stress, activity of antioxidant enzyme, catalase, significantlyincreased in both genotypes, whereas significant higher activity of superoxide dismutase and peroxidase wasonly observed in Karoon genotype. Expression of polyamine oxidase (PAO) genes (zmPAO1, zmPAO2,zmPAO3, zmPAO4, zmPAO5, zmPAO6) and activity of enzymatic polyamine oxidation was increased in bothgenotypes under drought stress. The enhancement in PAO gene expression and enzyme activity was moreprominent in Karoon cultivar compared to 260. Chlorophyll a fluorescence and fast induction kinetics werenegatively influenced by drought stress. These parameters were more affected in 260 cultivar compared withKaroon. Our results suggest that under drought stress, higher activity of polyamine oxidase pathway in backconversionof Spermine and spermidine to putrescine (protectant of photosynthetic apparatus) as well as higherantioxidant enzymes activity in Karoon cultivar, may play a role in higher efficiency of photosynthetic processin this cultivar.

    • Assessment of telomerase as drug target in breast cancer

      RISHI KUMAR JAISWAL PRAMOD KUMAR YADAVA

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      Telomerase is a specialized enzyme which maintains telomere length at the extreme end of the chromosome.Over 90% of all cases of cancer show high expression of telomerase while in normal cells, its expression isextremely low or undetectable. Detection of telomerase activity in a wide range of breast cancer makestelomerase an interesting target for diagnosis and therapy. In this review, we have aimed to describe telomeraseas a therapeutic and accurate diagnostic target in breast cancer. Telomerase performs many extracurricularactivities apart from maintaining telomere length; here, we have also tried to address its role in epithelialmesenchymaltransition (EMT) of breast cancer progression.

    • Involvement of eIF2α in halofuginone-driven inhibition of TGF-β1-induced EMT

      MINGYUAN DUAN XIAOBING WEI ZHE CHENG DUNJIANG LIU HANNA FOTINA XIAOJING XIA JIANHE HU

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      Halofuginone (HF) is an extract from the widely used traditional Chinese medicine (TCM) Dichroa febrifugathat facilitates the recovery of wounds and attenuates hepatic fibrosis. However, the role of HF in theepithelial-mesenchymal transition (EMT) of IPEC-J2 cells remains unclear. The current study explored theanti-EMT effect of HF in IPEC-J2 cells and illustrates its molecular mechanism. Transforming growth factorb1 (TGF-beta-1), as a recognized profibrogenic cytokine, decreased the level of the epithelial marker E-cadherinand increased the level of the mesenchymal markers, such as N-cadherin, fibronectin (FN), vimentin (Vim),and a-smooth muscle actin (a-SMA), in IPEC-J2 cells depending on the exposure time and dose. HF markedlyprevented the EMT induced by TGF-beta-1. Dissection of the mechanism revealed that HF inhibited IPEC-J2 cellEMT via modulating the phosphorylation of SMAD2/3 and the SMAD2/3-SMAD4 complexnuclear translocation. Furthermore, HF could promote the phosphorylation of eukaryotic translation initiationfactor-2-alpha (eIF2-alpha), which modulates the SMAD signaling pathway. These results suggested that HF inhibitsTGF-beta-1-induced EMT in IPEC-J2 cells through the eIF2a/SMAD signaling pathway. Our findings suggest thatHF can serve as a potential anti-EMT agent in intestinal fibrosis therapy.

    • Prognostic significance of low expression of B-cell translocation gene 1 (BTG1) in skin squamous cell carcinoma

      GONGQI LI YINHONG YUE WENXIU LI YUMEI CHEN HOUZHEN FAN JUN YUAN ZHONGMING CHEN JUN LIU

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      Although the B-cell translocation gene 1 (BTG1) plays an important role in apoptosis and negatively regulatescell proliferation, BTG1 expression in skin squamous cell carcinoma (SCC) has not been reported. In this study,we wanted to investigate the significance of BTG1 expression in SCC and adjacent tissues. The expression ofBTG1 protein and mRNA in SCC tissues and adjacent tissues were detected by immunohistochemistrytechnique (IHC), Western blot and reverse transcriptase-polymerase chain reaction (RT-PCR). IHC stainingshowed that the positive expression rate of BTG1 protein in SCC tissues was 54.00%; and the positive rate was90.50% in the adjacent tissues. Western blot showed that the expression of BTG1 protein in SCC tissues wassignificantly lower than that in the adjacent tissues (P\0.05). RT-PCR showed that the positive rate of BTG1mRNA in SCC was 50.50%, which was significantly lower than that in adjacent tissues 89.00% (P\0.05).Both BTG1 mRNA and protein expression are related to tumor diameter, stage, tumor metastasis and thedegree of tumor differentiation in SCC. Patients exhibiting lower BTG1 protein expression in the SCC tissueshad a significantly shorter disease-specific survival rate. BTG1 protein expression, tumor diameter, tumors siteand stage were independent factors affecting the overall survival of postoperative patients. Further, BTG1overexpression inhibited A431 cell proliferation ability, while BTG silencing enhanced A431 cell proliferationability. The lower expression of BTG1 in SCC may be associated with the occurrence, development andprognosis of SCC.

    • Vitamin D regulates cell viability, migration and proliferation by suppressing galectin-3 (Gal-3) gene in ovarian cancer cells

      JIE JI XUE CHENG WEI WANG JINGMIN ZHANG

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      Vitamin D deficiency is identified as a risk factor for the occurrence and recurrence of ovarian cancer.Galectin-3 (Gal-3) participates in many physiological and pathological processes. In present study, serumvitamin D level was detected using chemiluminescence enzyme immunoassay. Gal-3 expression wasexamined using real-time polymerase chain reaction (PCR), Western blot and immunocytochemistry analysis.SKOV3 cells viability was assessed by the water-soluble tetrazolium salt (WST-1) assay, the migrationof SKOV3 cells was detected using transwell assay, and the proliferation of SKOV3 cells was measured by3H-thymidine incorporation (3H-TdR). Our study demonstrated that vitamin D levels were lower in 40ovarian cancer patients: vitamin D deficiency is closely related to the pathogenesis of ovarian cancer.Treatment with vitamin D reduced the migration and proliferation of ovarian cancer cells. Gal-3 wasoverexpressed in ovarian cancer, which could induce the viability, migration and proliferation ability ofovarian cancer cells, and these effects were abrogated by vitamin D downregulating the expression of Gal-3gene. Therefore, our results support that vitamin D may suppress Gal-3-induced viability, migration andproliferation ability of ovarian cancer cells, which suggests that the use of vitamin D may have beneficialeffects in preventing and treating ovarian cancer.

    • Global efforts on vaccines for COVID-19: Since, sooner or later, we all will catch the coronavirus

      RAJU MUKHERJEE

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      COVID-19 is an emerging infectious disease that has turned into a pandemic. It spreads through droplet transmissionof the new coronavirus SARS-CoV-2. It is an RNA virus displaying a spike protein as the major surfaceprotein with significant sequence similarity to SARS-CoV which causes severe acute respiratory syndrome. Thereceptor binding domain of the spike protein interacts with the human angiotensin converting enzyme 2 and isconsidered as the antigenic determinant for stimulating an immune response. While multiple candidate vaccines arecurrently under different stages of development, there are no known therapeutic interventions at the moment. Thisreview describes the key genetic features that are being considered for generating vaccine candidates by employinginnovative technologies. It also highlights the global efforts being undertaken to deliver vaccines for COVID-19through unprecedented international cooperation and future challenges post development.

    • A human cell polarity protein Lgl2 regulates influenza A virus nucleoprotein exportation from nucleus in MDCK cells

      JING LIU HAIYING WANG MENGDAN FANG XUEXIN CHEN XIAOBO ZENG

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      In this study, the regulatory effect of the overexpression of polarity protein Lgl2 on the nuclear export ofinfluenza A virus nucleoprotein in infected cells was investigated. A stable Tet-Off inducible MDCK cell lineexpressing a fusion protein comprising Lgl2 and an enhanced yellow fluorescent protein were used. TCID50analysis and neuraminidase activity analysis revealed that replication of influenza Avirus was inhibited in Lgl2overexpressing cells. By immunofluorescence microscopical observation at different time point post virusinfection, a retention of NP in cellular nucleus was found in Lgl2 overexpressing cells. Compared with normalMDCK cells, change in claudin-1 distribution between cell contacts caused by Lgl2 overexpression impairedthe barrier function of tight junction. These results suggest that changes in cell polarity induced by Lgl2overexpressing will affect virus NP transportation.

    • MiR-140-3p inhibits natural killer cytotoxicity to human ovarian cancer via targeting MAPK1

      JIAYING WANG MIAOHUA ZHU XIAOMING ZHOU TINGTING WANG YANNI XI ZHANG JING WENJIN XI

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      Natural killer (NK) cells have pivotal role in immunotherapy of human ovarian cancer (OC). AlthoughmicroRNAs (miRNAs) participate in dysfunction of NK cells, how and whether miR-140-3p regulates cytotoxicityof NK cells in OC are uncertain. miR-140-3p and mitogen activated protein kinase 1 (MAPK1)abundances were examined via quantitative real-time polymerase chain reaction or western blot. Tumornecrosis factor-a (TNF-alpha) and interferon-c (IFN-gamma) abundances were examined via enzyme linkedimmunosorbent assay. NK cytotoxicity to OC was evaluated via lactate dehydrogenase release. The relevanceof miR-140-3p and MAPK1 was proved via luciferase activity analysis. Murine xenograft experiment wasapplied to assess the function of miR-140-3p on NK cytotoxicity. miR-140-3p was elevated and MAPK1 wasdeclined in NK cells from OC patients, while the levels were reversed after treatment of interleukin-2 (IL-2).MiR-140-3p addition mitigated IFN-gamma and TNF-alpha production induced via IL-2 as well as NK-92 cytotoxicityto OC cells. Additionally, MAPK1 was negatively regulated via miR-140-3p and ablated the influence of miR-140-3p on cytotoxicity, cytokines levels. Besides, miR-140-3p enrichment facilitated tumor growth via suppressingfunction of NK cells in a xenograft model. miR-140-3p suppressed NK cytotoxicity to OC cells viamediating MAPK1, indicating a new avenue of ameliorating NK cells function for OC treatment.

    • MiR-222 inhibition alleviates Staphylococcal Enterotoxin B-induced inflammatory acute lung injury by targeting Foxo3

      LIANG CHEN JUN CHEN GUOGANG XIE LIMEI ZHU

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      Acute lung injury (ALI) is a common acute and severe disease in clinical practice. Staphylococcal EnterotoxinB (SEB) is a superantigen that can cause inflammatory ALI. MiR-222 has been demonstrated to be upregulatedin SEB-induced inflammatory ALI, but its exact roles and functions remain ill-defined. In this study, SEBexposure led to inflammatory ALI and high expression of miR-222 in model mice and lung infiltratingmononuclear cells, but the inflammatory response and high expression of miR-222 were restored in miR-222-/-mice. Moreover, we investigated the roles of miR-222 in vitro and observed that the concentrations ofinflammatory cytokines and the expression of miR-222 were all elevated in SEB-activated splenocytes andmiR-222 inhibition reversed the effects. Foxo3 was confirmed as a direct target of miR-222. Interestingly, SEBexposure led to a decrease of Foxo3 expression, and Foxo3 knockdown partially reversed the promotion ofFoxo3 and the inhibition of inflammatory cytokines induced by miR-222 inhibitor in SEB-activated splenocytes.Our data indicated that miR-222 inhibition could alleviate SEB-induced inflammatory ALI by directlytargeting Foxo3, shedding light on the potential therapeutic of miR-222 for SEB-induced inflammation in thelung.

    • Axonal cytomechanics in neuronal development

      SAMPADA P MUTALIK AURNAB GHOSE

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      For more than a century, mechanical forces have been predicted to govern many biological processes duringdevelopment, both at the cellular level and in tissue homeostasis. The cytomechanics of the thin and highlyextended neuronal axons have intrigued generations of biologists and biophysicists. However, our knowledgeof the biophysics of neurite growth and development is far from complete. Due to its motile behavior and itsimportance in axonal pathfinding, the growth cone has received significant attention. A considerable amount ofinformation is now available on the spatiotemporal regulation of biochemical signaling and remodeling of thegrowth cone cytoskeleton. However, the cytoskeletal organization and dynamics in the axonal shaft werepoorly explored until recently. Driven by advances in microscopy, there has been a surge of interest in theaxonal cytoskeleton in the last few years. A major emerging area of investigation is the relationship betweenthe axonal cytoskeleton and the diverse mechanobiological responses of neurons. This review attempts tosummarize our current understanding of the axonal cytoskeleton and its critical role in governing axonalmechanics in the context of neuronal development.

    • Deciphering the interaction of benzoxaborole inhibitor AN2690 with connective polypeptide 1 (CP1) editing domain of Leishmania donovani leucyl-tRNA synthetase

      SMRITI TANDON REETIKA MANHAS NEHA TIWARI MANOJ MUNDE RAMACHANDRAN VIJAYAN SAMUDRALA GOURINATH ROHINI MUTHUSWAMI RENTALA MADHUBALA

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      Leucyl-tRNA synthetases (LRS) catalyze the linkage of leucine with tRNALeu. A large insertion CP1 domain(Connective Polypeptide 1) in LRS is responsible for post-transfer editing of mis-charged aminoacyl-tRNAs.Here, we characterized the CP1 domain of Leishmania donovani, a protozoan parasite, and its role in editingactivity and interaction with broad spectrum anti-fungal, AN2690. The deletion mutant of LRS, devoid of CP1domain (LRS-CP1D) was constructed, followed by determination of its role in editing and aminoacylation.Binding of AN2690 and different amino acids with CP1 deletion mutant and full length LRS was evaluatedusing isothermal titration calorimetry (ITC) and molecular dynamics simulations. The recombinant LRS-CP1 Deltaprotein did not catalyze the aminoacylation and the editing reaction when compared to full-length LRS. Thus,indicating that CP1 domain was imperative for both aminoacylation and editing activities of LRS. Bindingstudies with different amino acids indicated selectivity of isoleucine by CP1 domain over other amino acids.These studies also indicated high affinity of AN2690 with the editing domain. Molecular docking studiesindicated that AN2690-CP1 domain complex was stabilized by hydrogen bonding and hydrophobic interactionsresulting in high binding affinity between the two. Our data suggests CP1 is crucial for the function of L.donovani LRS.

    • Identification of miRNAs linked to peanut nodule functional processes

      MARI´A SOLEDAD FIGUEREDO DAMIEN FORMEY JOHAN RODRI´GUEZ FERNANDO IBA´N˜ EZ GEORGINA HERNA´ NDEZ ADRIANA FABRA

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      microRNAs (miRNAs) are non-coding small RNAs that regulate gene expression at post-transcriptional level.Thousands of miRNAs have been identified in legumes, but studies about miRNAs linked to peanut nodulefunctionality are scarce. In this work we analyzed transcriptional changes in peanut nodules to identifymiRNAs involved in functional processes of these organs. We found 32 miRNAs precursors differentiallyexpressed in nodules compared with roots, and predicted the potential targets of their corresponding maturemiRNAs. Among them, 20 belong to 14 conserved miRNAs families and 12 are Arachis hypogaea-specificmiRNAs. Expression levels of 3 miRNAs (ahy-miR399, ahy-miR159 and ahy-miR3508) were confirmedexperimentally by qPCR. We also demonstrated that the expression of these miRNAs was not affected byinoculation of a biocontrol bacterium or a fungal pathogen. The catalogue of differentially expressed miRNAprecursors and the expression of the corresponding mature miRNA potential targets in the nodules of A.hypogaea obtained in this work is a database of strong candidates, including A. hypogaea-specific miRNAs, forthe regulation of the nodule functionality. The analysis of their role in this process will certainly lead to thecharacterization of essential regulators in these particular aeschynomenoid nodules.

    • Bioluminescence emissions from the Indian winter species of firefly Diaphanes sp.

      MANA MOHAN RABHA UPAMANYU SHARMA ANURUP GOHAIN BARUA

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      Numerous studies have been carried out on different aspects of the light from summer-active fireflies. Characteristicsof this light have led to very interesting conclusions on the chemiluminescence reaction as well as onthe nature of the light from live fireflies. Here we present a first report on bioluminescence emissions from anewly found winter-active Indian species of firefly Diaphanes sp. The steady-state emission spectrum from thisspecies comes out to be apparently similar to those from the other two Indian summer species, Luciolapraeusta and Asymmetricata circumdata: asymmetric in nature with a little bit of change in the position of thepeak wavelength and in the width of the full width at half maximum. An increase in temperature toapproximately 28 deg C causes a red-shift in the peak wavelength, which probably indicates denaturation of theenzyme luciferase in the live, flashing condition. Emissions in the time domain reveal that the light is nevercompletely off – it decreases in intensity to a low value, sometimes very close to zero, and then increases – acharacteristic unheard-of till date. Flash durations are considerably longer than those from the two Indiansummer species; those become shorter at about 28 deg C and increase to noticeably larger values at highertemperatures.

    • Modulatory effect of Tim-3/Galectin-9 axis on T-cell-mediated immunity in pulmonary tuberculosis

      JING KANG ZHI-FENG WEI MING-XIAN LI JING-HUA WANG

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      Patients affected by pulmonary tuberculosis (PTB) manifest deficiencies in innate cellular immunity. The Tim-3/Galectin-9 axis is an important regulator of Th1 cell immunity, leading to Th1 cell apoptosis. Herein, thisstudy aims to clarify the underlying roles of the Tim-3/Galectin-9 axis in T-cell immunity in PTB. Peripheralblood mononuclear cells (PBMCs) were extracted from subjects with and without PTB to examine theexpression of CD4, CD8, CD25, and Tim-3 under the stimulation of Mycobacterium tuberculosis (MTB) andpurified protein derivative (PPD). In addition, the expression of Tim-3 and Galectin-9 in PBMCs was determined.The Tim-3/Galectin-9 axis in the PBMCs was activated or blocked to detect the secreted levels of IFN-gamma,TNF-alpha, IL-2, and IL-22. MTB stimulation increased the expression of CD4, CD8, CD25, Tim-3, andGalectin-9 in PBMCs. The blockade of Tim-3/Galectin-9 axis resulted in reduced secretion of IFN-gamma, TNF-alpha,IL-2, and IL-22 from T-cells. Moreover, Tim-3+CD4+T, Tim-3+CD8+, and Tim-3+CD25+T cells exhibited agreater ability to inhibit the replication of MTB in macrophages. Taken conjointly, the blockade of Tim-3/Galectin-9 axis inhibits the secretion of inflammatory cytokines in T-cells to regulate the T-cell immunity inPTB.

    • Let-7a-5p represses proliferation, migration, invasion and epithelial-mesenchymal transition by targeting Smad2 in TGF-β2-induced human lens epithelial cells

      HUIFENG LIU BING JIANG

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      Transforming growth factor β2 (TGF-β2)/Smad signaling is widely accepted as a key inducer of proliferationand epithelial-mesenchymal transition (EMT) of human lens epithelial cells (LECs), contributing to thedevelopment of posterior capsule opacification (PCO). Increasing evidence shows that microRNAs (miRNAs)play important roles in PCO pathogenesis. Herein, we aimed to explore the role and molecular mechanism oflet-7a-5p on TGF-β2-induced proliferation and EMT in LECs. qRT-PCR was performed to detect theexpression of let-7a-5p and Smad2 mRNA. Western blot was used to determine the Smad2 level and theinduction of EMT. The targeted correlation between let-7a-5p and Smad2 was confirmed using dual-luciferasereporter and RNA immunoprecipitation assays. CCK-8 assay was employed to determine cell proliferation, andtranswell assays were performed to assess cell migration and invasion. We found that TGF-β2 induced EMT ofLECs, and TGF-β2 upregulated Smad2 expression and reduced let-7a-5p expression in LECs. Smad2 was adirect target of let-7a-5p. Moreover, let-7a-5p upregulation repressed proliferation, migration, invasion andEMT in TGF-β2-induced LECs. But, Smad2 expression restoration abrogated the inhibitory effect of let-7a-5pupregulation. In conclusion, our data indicated that let-7a-5p upregulation repressed TGF-β2-induced proliferation,migration, invasion and EMT at least partly by targeting Smad2 in LECs, highlighting that let-7a-5pmight act as a promising therapeutic target to intervene to the progression of PCO.

    • A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements

      RODERICH BRANDSCH MARIUS MIHASAN

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      The 165,137 bp plasmid pAO1 of Paenarthrobacter nicotinovorans carries the genes of a nicotine catabolicpathway. The genes are organized into several gene modules responsible for the catabolism of L- and D-nicotineto nicotine blue, a-ketoglutarate and succinate. Various modules of these genes have been shown to be presentin gram-positive (Gram+) soil bacteria. The presence of the identical pAO1 nic-genes on the 288,370 bpplasmid pZXY21 of Arthrobacter sp. ZXY2 (96% to 100% at the nucleotide level) permitted the identificationof the limits of this DNA fragment. At the 5' end of the nic-genes are located the ORFs of two predictedintegrases of the tyrosine recombinase family with conserved R, H, R and Y catalytic residues and that of asmall transposase with a predicted leucine zipper motive. They are related to Tn554A, Tn554B and Tn554C ofStaphylococcus aureus and suggest that the entire nic-genes DNA fragment represents a large catabolictransposon. Surprisingly the nic-genes on pZXY21 were found to be interspersed by mobile elements encodingtransposases of various IS families. Insertion of these IS elements disrupts nicotine degradation and divide thenic-genes DNA into potentially new transposons. This finding may illustrate how nicotine catabolic genes canbe mobilized and spread by horizontal gene transfer to other soil bacteria.

    • Geriatric infections: Decreased immunity or evolved opportunists?

      ULFAT BAIG VIDHYA LAXMI AKANKSHA OJHA MILIND WATVE

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      In host–parasite co-evolution, parasites are assumed to have an advantage owing to their shorter generationtime. Evolution of pathogens within the lifetime of a host individual is implicated as a strong selective force inthe evolution of sex and aging in the host. However, this assumption or its testable predictions have not beenexamined empirically. We classified infectious bacteria and viruses into those that can have continued longtermexistence on the host body (group 1) versus those that have only a short-term interaction during an activeinfection (group 2). We surveyed the literature for age-specific incidence data about infections from both thegroups. The age trends of the two groups show contrasting patterns. The incidence of infections by all group 1pathogens showed a 2.28- to 28-fold increase in older ages. In group 2, 6 out of the 9 pathogens showed asignificant declining trend in incidence with age. In both groups, there was greater mortality or morbidityamong the infected in the old-age classes. These patterns are better explained by pathogen evolution than byage-related decline in immunity.

    • Long non-coding RNA H19 promotes osteogenic differentiation of human bone marrow-derived mesenchymal stem cells by regulating microRNA-140-5p/SATB2 axis

      HU BI DONG WANG XIAOYU LIU GANG WANG XUEJIAN WU

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      The osteogenic differentiation of mesenchymal stem cells (MSCs) has potential clinical values in the treatmentof bone-related diseases. Long non-coding RNA H19 and microRNA-140-5p (miR-140-5p) have attractedmuch attention of researchers by virtue of their biological importance in cell differentiation and bone formation.Moreover, bioinformatics analyses suggest that miR-140-5p have the potential to bind with H19 andSATB homeobox 2 (SATB2). In this study, we further explored whether H19 could regulate osteogenicdifferentiation of human bone marrow-derived MSCs (BM-MSCs) by miR-140-5p/SATB2 axis. RT-qPCRassay was conducted to examine the expression of H19, miR-140-5p and SATB2. The osteogenic differentiationcapacity of BM-MSCs was assessed through alkaline phosphatase (ALP) activity and osteogenic markerexpression. The relationships among H19, miR-140-5p and SATB2 were examined through bioinformaticsanalyses, luciferase reporter assay, RIP assay and RNA pull-down assay. H19 expression was remarkablyincreased and miR-140-5p expression was dramatically reduced during osteogenic differentiation of BMMSCs.Functional analyses revealed that H19 overexpression or miR-140-5p depletion accelerated osteogenicdifferentiation of BM-MSCs. Conversely, H19 loss or miR-140-5p increase suppressed osteogenic differentiationof BM-MSCs. MiR-140-5p was confirmed as a target of H19, and miR-140-5p could bind to SATB2 aswell. Moreover, H19 knockdown reduced SATB2 expression by upregulating miR-140-5p. Additionally, miR-140-5p depletion antagonized the inhibitory effect of H19 knockdown on osteogenic differentiation of BMMSCs.And, miR-140-5p inhibited osteogenic differentiation of BM-MSCs by targeting SATB2. In conclusion,H19 promoted osteogenic differentiation of BM-MSCs through regulating miR-140-5p/SATB2 axis, deepeningour understanding on the molecular mechanisms of H19 in coordinating osteogenesis.

    • α-Helical protein absorption at post-traumatic epileptic foci monitored by Fourier transform infrared mapping

      SIYANG XIANG DONG ZHAO HONGXIA HAO XU WANG LING LI TIANTONG YANG

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      Tissue analysis by Fourier transform infrared (FTIR) imaging can determine the biodistribution of molecules,without pre-analytical modification. We aimed to study the infrared spectroscopic changes of α-helical proteinsat post-traumatic epileptic (PTE) foci by FTIR. FITR mapping was applied to detect α-helical proteins in ratbrain tissue samples with post-traumatic epilepsy. Histological examination of brain sections showed that therat model of PTE was successfully established. At the PTE foci, high α-helical absorption regions wereevident, where the color difference and absorption were significantly different from those in the low-absorptionregions. This provided a distinctive and characteristic pattern at the site of lesions. The use of FTIR imagingmeans that it is possible to measure the molecular structural changes resulting from PTE pathologies in tissues,providing a novel adjunct to conventional pathological diagnostic techniques.

    • Catalytic and structural effects of flexible loop deletion in organophosphorus hydrolase enzyme: A thermostability improvement mechanism

      GHOLAMREZA FARNOOSH KHOSRO KHAJEH MOZAFAR MOHAMMADI KAZEM HASSANPOUR ALI MOHAMMAD LATIFI HOSSEIN AGHAMOLLAEI

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      Thermostability improvement of enzymes used industrially or commercially would develop their capacity andcommercial potential due to increased enzymatic competence and cost-effectiveness. Several stabilizing factorshave been suggested to be the base of thermal stability, like proline replacements, disulfide bonds, surface looptruncation and ionic pair networks creation. This research evaluated the mechanism of increasing the rigidity oforganophosphorus hydrolase enzyme by flexible loop truncation. Bioinformatics analysis revealed that themutated protein retains its stability after loop truncation (five amino acids deleted). The thermostability of thewild-type (OPH-wt) and mutated (OPH-D5) enzymes were investigated by half-life, DGi, and fluorescence andfar-UV CD analysis. Results demonstrated an increase half-life and DGi in OPH-D5 compared to OPH-wt.These results were confirmed by extrinsic fluorescence and circular dichroism (CD) spectrometry experiments,therefore, as rigidity increased in OPHD5 after loop truncation, half-life and DGi also increased. Based onthese findings, a strong case is presented for thermostability improvement of OPH enzyme by flexible looptruncation after bioinformatics analysis.

    • PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines

      KRISHNENDU BANERJEE TANMOY JANA ZHUMUR GHOSH SUDIPTO SAHA

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      Pluripotency in stem cells is regulated by a complex network between the transcription factors, signalingmolecules, mRNAs, and epigenetic regulators like non-coding RNAs. Different pluripotent stem cell (PSC)lines were isolated and characterized to study the regulatory network topology to understand the mechanismthat control developmental potential of pluripotent cells. PSCRIdb is a manually curated database of regulatoryinteractions including protein–protein, protein–DNA, gene–gene, and miRNA–mRNA interactions in mouseand human pluripotent stem cells including embryonic stem cells and embryonic carcinoma cells. At present,22 different mouse and human pluripotent stem-cell-line-specific regulatory interactions are compiled in thedatabase. Detailed information of the four types of interaction data are presented in tabular format andgraphical network view in Cytoscape layout. The database is available at http://bicresources.jcbose.ac.in/ssaha4/pscridb. The database contains 3037 entries of experimentally validated molecular interactions that canbe useful for systematic study of pluripotency integrating multi-omics data. In summary, the database can be auseful resource for identification of regulatory networks present in different pluripotent stem cell lines.

    • LncRNA XIST knockdown ameliorates oxidative low-density lipoprotein-induced endothelial cells injury by targeting miR-204-5p/TLR4

      GUOYONG LU PENG TIAN YONGXIN ZHU XIAOHUA ZUO XIAOQIANG LI

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      Oxidative low-density lipoprotein (ox-LDL)-induced endothelial cell injury is a key contributor toatherosclerosis development. However, the role and mechanism of long noncoding RNA X-inactive specifictranscript (XIST) in atherosclerosis remain largely unknown. The ox-LDL-induced human umbilical veinendothelial cells (HUVECs) injury was analyzed by cell viability, apoptosis, inflammatory cytokines secretionand oxidative stress. The expression levels of XIST, microRNA-204-5p (miR-204-5p) and toll-like receptor 4(TLR4) were detected by quantitative real-time polymerase chain reaction and western blot, respectively. Thetarget interaction between miR-204-5p and XIST or TLR4 was explored by bioinformatics analysis, luciferaseassay and RNA immunoprecipitation. The expression of XIST was enhanced in ox-LDL-treatedHUVECs. Knockdown of XIST attenuated ox-LDL-induced viability inhibition, apoptosis production,inflammatory response and oxidative stress in HUVECs. XIST was validated as a sponge of miR-204-5pand TLR4 acted as a target of miR-204-5p. Knockdown of miR-204-5p reversed silence of XISTmediatedsuppressive role in ox-LDL-induced injury. TLR4 alleviated miR-204-5p-mediated inhibitiveeffect on ox-LDL-induced injury. Moreover, XIST could regulate TLR4 expression by spongingmiR-204-5p. In conclusion, silence of XIST displayed a protective role in ox-LDL-induced injury inHUVECs by regulating miR-204-5p/TLR4 axis, providing a novel mechanism for understanding thepathogenesis of atherosclerosis.

    • The long non-coding RNA MIAT/miR-139-5p/MMP2 axis regulates cell migration and invasion in non-small-cell lung cancer

      FANYE ZENG NING YU YANYAN HAN JULAITI AINIWAER

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      Non-small-cell lung cancer (NSCLC) is a complex disease which is influenced by multiple factors. Recentstudies demonstrated that long non-coding RNA (lncRNA) MIAT was involved in tumor metastasis. However,the underlying mechanism of MIAT in NSCLC remains largely unknown. In this study, MIAT, miR-139-5pand MMP2 expression were measured by quantitative reverse transcriptase PCR (QRT-PCR) or Westernblotting, respectively, and we found the expression of MIAT and MMP2 were elevated, while miR-139-5p wasdecreased in NSCLC tissues and cell lines. Transwell assay showed MIAT and MMP2 functioned as anoncogene to induce cell migration and invasion in NSCLC, but miR-139-5p served as a tumor suppressor inNSCLC to inhibit cell migration and invasion. Besides that, in vivo experiments also indicated MIAT deletioninhibited tumor growth. The relationship between miR-139-5p and MIAT or MMP2 was then confirmed byLuciferase reporter assay, and the results showed that MIAT directly interacted with miR-139-5p and miR-139-5p targetedly suppressed MMP2 in NSCLC cells. Furthermore, expression analysis showed that MIAT indirectlyregulated MMP2 by sponging miR-139-5p. Finally, rescue assay suggested that miR-139-5p restorationreversed MIAT-overexpression-induced promotion on the migration and invasion of NSCLC cells. In conclusion,our results demonstrated that lncRNA MIAT modulated the migration and invasion of NSCLC byregulating miR-139-5p and MMP2.

    • T cell costimulation, checkpoint inhibitors and anti-tumor therapy

      DIPANKAR NANDI SANMOY PATHAK TARU VERMA MADHULIKA SINGH AVIK CHATTOPADHYAY SAMRIDDHI THAKUR ABINAYA RAGHAVAN ABHIJEET GOKHROO VIJAYAMAHANTESH

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      The hallmarks of the adaptive immune response are specificity and memory. The cellular response is mediatedby T cells which express cell surface T cell receptors (TCRs) that recognize peptide antigens in complex withmajor histocompatibility complex (MHC) molecules on antigen presenting cells (APCs). However, binding ofcognate TCRs with MHC-peptide complexes alone (signal 1) does not trigger optimal T cell activation. Inaddition to signal 1, the binding of positive and negative costimulatory receptors to their ligands modulates Tcell activation. This complex signaling network prevents aberrant activation of T cells. CD28 is the mainpositive costimulatory receptor on naı¨ve T cells; upon activation, CTLA4 is induced but reduces T cellactivation. Further studies led to the identification of additional negative costimulatory receptors known ascheckpoints, e.g. PD1. This review chronicles the basic studies in T cell costimulation that led to the discoveryof checkpoint inhibitors, i.e. antibodies to negative costimulatory receptors (e.g. CTLA4 and PD1) whichreduce tumor growth. This discovery has been recognized with the award of the 2018 Nobel prize in Physiology/Medicine. This review highlights the structural and functional roles of costimulatory receptors, themechanisms by which checkpoint inhibitors work, the challenges encountered and future prospects.

    • Effects of nicorandil on neurobehavioral function, BBB integrity, edema and stereological parameters of the brain in the sub-acute phase of stroke in a rat model

      MARYAM OWJFARD MOHAMMAD REZA BIGDELI ANAHID SAFARI MOHAMMAD REZA NAMAVAR

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      Blood–brain barrier (BBB) disruption, inflammation, and cell death are the pathogenic mechanisms of cerebralischemia/reperfusion (I/R) injury. Nicorandil protects ischemic injury via some of these mechanisms. The aimof this study was to investigate the therapeutic effects of this drug on the brain ischemia after transient middlecerebral artery occlusion (MCAO) and clarify the NF-kappa B and Nrf2-dependent mechanisms modulated by thisdrug. Sixty-six rats were randomized into sham, MCAO and MCAO + nicorandil groups with oral gavage for3 days. Cerebral I/R injury were induced by a transient MCAO for 1 h and neurobehavioral scores wereperformed for 3 days. In addition to measurement of BBB disruption and brain water content, the total andinfarct volume, density, and total number of neurons, non-neurons and dead neurons in the right cortex wereestimated by unbiased stereological methods. RT-PCR was performed to analyze the expression levels of NF-kappa Band Nrf2. Although nicorandil treatment in the sub-acute brain ischemia did not have a prominent effect onneurobehavioral function and number of neurons, non-neurons and dead neurons probably through up-regulationof NF-kappa B, it, however, improved ischemia-induced BBB disruption and brain edema and showed asignificant reduction in the infarction volume probably through up-regulation of Nrf2.

    • miR-140-3p inhibits progression of non-small cell lung cancer by targeting Janus kinase 1

      CHUAN HU YONG ZOU LUAN-LIAN JING

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      microRNAs (miRNAs) have gained more attention due to the biological functions in many cancers, includingnon-small cell lung cancer (NSCLC). However, the roles and the mechanism of miR-140-3p in NSCLCprogression remain poorly understood. In this study, the expression levels of miR-140-3p and Janus kinase 1(JAK1) were measured in NSCLC tissues and cells by quantitative real-time PCR. Cell viability, apoptosis,migration and invasion were detected by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl-trtrazolium bromide, flowcytometry, Western blot or trans-well assay, respectively. Murine xenograft model was conducted to analyzethe anti-tumor effect of miR-140-3p in vivo. Interaction between miR-140-3p and JAK1 was probed byluciferase reporter activity and Western blot. We found that miR-140-3p expression was down-regulated andJAK1 expression was increased in NSCLC tissues and cells compared with those in corresponding controls.Moreover, overexpression of miR-140-3p inhibited cell viability, migration and invasion while promoted cellapoptosis in NSCLC cells and suppressed NSCLC xenograft tumor growth in vivo. Besides, JAK1 was provedas a target of miR-140-3p and its restoration reversed miR-140-3p-mediated regulatory effect on progression ofNSCLC. We concluded that miR-140-3p inhibited NSCLC progression by targeting JAK1, providing a novelavenue for treatment of NSCLC.

    • miR-4417 suppresses keloid fibrosis growth by inhibiting CyclinD1

      PEI LIU YAOTIAN HU LIN XIA MIN DU ZHENSHENG HU

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      Mounting evidence has reported that microRNAs (miRNAs) play irreplaceable roles in the development ofkeloid fibrosis. miR-4417 has been reported to contribute to nickel chloride-promoted lung epithelial cellfibrogenesis and tumorigenesis. However, whether miR-4417 is involved in keloid fibrogenesis as well as itsunderlying mechanisms remain largely elusive. In this study, the expression levels of miR-4417 and CyclinD1in keloid tissues and fibroblasts were examined by qRT-PCR. Cell proliferation was determined by CCK assay.Western blot and flow cytometry were performed to evaluate cell apoptosis. Cell migration and invasion weremeasured by Transwell assay. Luciferase reporter assay was used to confirm the relationship between miR-4417 and CyclinD1. As a result, we found that miR-4417 was significantly down-regulated in keloid tissuesand fibroblasts. miR-4417 up-regulation led to the suppression of proliferation, migration, and invasion, whileinduced cell apoptosis in keloid fibroblasts. However, miR-4417 depletion exerted an opposite effect.CyclinD1 harbored the binding sites with miR-4417. Besides, the expression of CyclinD1 was evidentlydecreased in keloid tissues and fibroblasts. Meanwhile, miR-4417 was negatively correlated with CyclinD1 inkeloid tissue. The effect of CyclinD1 knockdown on keloid fibroblasts was similar to that of miR-4417overexpression. Furthermore, the elevated of CyclinD1 expression rescued the effect of miR-4417 up-regulationon keloid fibroblasts. miR-4417/CyclinD1 axis was required for cell proliferation, apoptosis, migration,and invasion in keloid fibroblasts. In conclusion, miR-4417 and CyclinD1 may be potential therapeutic targetsfor the treatment of keloid.

    • Ephedrannin B exerts anti-viral and anti-inflammatory properties in BEAS-2B cells infected with respiratory syncytial virus

      SHU HOU XIAOYAN XU YATING WANG YAN YANG

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      Ephedrannin B (EPB) has been shown to exert anti-inflammatory effects. However, the effect of EPB onrespiratory syncytial virus infection (RSV) is not known. In this study, the cytotoxic effect of EPB wasevaluated in BEAS-2B cells using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Reversetranscription quantitative polymerase chain reaction and Western blot assays were performed to determinethe expression of target genes. The anti-viral effect of EPB was assessed by determining viral titers usingplaque assay. We found that RSV infection caused a marked increase in interleukin (IL)-6, IL-8, IL-1beta andtumor necrosis factor (TNF)-alpha production and release, which was concentration-dependently attenuated byEPB treatment. Furthermore, EPB decreased the expression of RSV fusion gene in RSV-infected BEAS-2Bcells. Concomitantly, EPB treatment led to an obvious inhibition of viral replication in BEAS-2B cells.Besides, EPB suppressed RSV-induced mitogen-activated protein kinase/nuclear factor kappa-light-chainenhancerof activated B cells signaling. In conclusion, EPB exerts anti-viral and anti-inflammatory propertiesin BEAS-2B cells infected with RSV.

    • LncRNA XIST interacts with miR-454 to inhibit cells proliferation, epithelial mesenchymal transition and induces apoptosis in triple-negative breast cancer

      XIAOHUA LI LILI HOU LEI YIN SHUAI ZHAO

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      Triple-negative breast cancer (TNBC) is a one of the subtypes of breast cancer which accounts for approximately10–20% of all breast cancers. LncRNA XIST (XIST) is reported to be dysfunctional in numerous tumortypes and is involved in the key pathways of cancer initiation, progression and metastasis. Thus, in the presentstudy, we explored the detailed molecular mechanism of XIST in TNBC. XIST was down-regulated in TNBCtissues and cell lines. Overexpressed XIST inhibited cell proliferation, epithelial mesenchymal transition(EMT) and induced apoptosis in vitro as well as suppressed TNBC tumor growth in vivo. MicroRNA (miR)-454 was up-regulated in TNBC tissues and cell lines. Knockdown of miR-454 inhibited TNBC progression bysuppressing cell proliferation, EMT and inducing cell apoptosis. Moreover, miR-454 was predicted andconfirmed to be a target of XIST, and rescue assay indicated that overexpressed miR-454 could reverse XISTrestoration mediated-anti-tumor effects on TNBC cells. In conclusion, XIST interacts with miR-454 to inhibitcells proliferation, EMT and induce apoptosis in TNBC, indicating a promising treatment strategy for TNBCpatients.

    • Quantitative detection of neurotransmitter using aptamer: From diagnosis to therapeutics

      KOEL SINHA CHITRANGADA DAS MUKHOPADHYAY

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      Neurotransmitters, the small molecule chemical messenger responsible for nervous system regulation and cancontrol joy, fear, depression, insomnia, craving for carbohydrates, drugs, and alcohols. Variation in neurotransmitterlevels is a characteristic manifestation of several neurological diseases. Accurate diagnosis of thesediseases caused due to an imbalance in neurotransmitter level followed by impaired transmission of signalsbetween neurons and other body parts remains a great challenge for the clinicians. Recent evidences reveal,artificial single-stranded nucleotides called ‘aptamer’ are widely used as biosensors, antibody substitutes,diagnostic agents, and for targeted therapy. These aptamers are superior candidate both for early detection anddiagnosis of many neurological disorders caused due to suboptimal level of neurotransmitters. Presently, noninvasiveneurotransmitter detection by aptamer has been found to be an easy, fast, and cost-effective choice. Inaddition, increased specificity, stability, affinity, and reproducibility of aptamers, high throughput screening ofaptamer-based sensing platforms have been observed. Moreover, clinical applicability of aptamer has alsoproved to be efficacious, though still at a preliminary stage. Herein, we review salient features of aptamerbasedsensing technology used for neurotransmitter detection particularly their chemical modifications,selection, assay development, immobilization, therapeutic efficiency, and stability for early diagnosis of diseasescaused due to neurotransmitter imbalance.

    • Quinacrine causes apoptosis in human cancer cell lines through caspase-mediated pathway and regulation of small-GTPase

      ANGELA SAMANTA GEETHANJALI RAVINDRAN ANGSHUMAN SARKAR

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      Quinacrine (QC), an FDA-approved anti-malarial drug, has shown to have anticancer activities. Due to its

      ‘shotgun’ nature, QC has become an inevitable candidate for combination chemotherapy. There is lack of studyof the molecular interplay between colorectal cancer (CRC) microenvironment and its metastasis. In this study,we focused on the differential anti-cancerous effect of QC on two different human cancer cell lines, HCT 116and INT 407. Results suggest that cytotoxicity increased in both the cell lines with an increase in QCconcentration. The expression patterns of small-GTPases and caspases were altered significantly in QC-treatedcells compared to non-treated cells. HSP70 and p53 showed comparable differences in the expression pattern.The wound-healing assay showed an increase in the denuded zone, with an increase in the concentration ofQC. The formation of apoptotic nuclei increased with a rise in the concentration of QC in both the cell lines.The decrease and increase in caspase 9 and caspase 3 expression respectively were studied, confirmingapoptosis by the extrinsic pathway.

    • Resveratrol protects H9c2 cells against hypoxia-induced apoptosis through miR-30d-5p/SIRT1/NF-κB axis

      XIA HAN LU ZHANG YINGCAI LIU MENGHAI WU XINGCHAO LI ZENG TANG ZHANG TAO LI

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      Previous studies have demonstrated the cardioprotective role of resveratrol (Res). However, the underlyingmolecular mechanisms involved in the protective role of Res are still largely unknown. H9c2 cells weredistributed into five groups: normal condition (Control), DMSO, 20 mMRes (dissolved with DMSO), hypoxia(Hyp), and Res+Hyp. Cell apoptosis was evaluated using flow cytometry and protein analysis of cleavedcaspase 3 (cle-caspase 3). qRT-PCR assay was performed to measure the expression of microRNA-30d-5p(miR-30d-5p). MTT assay was performed to evaluate the cell proliferation. The relationship between miR-30d-5p and silent information regulator 1 (SIRT1) was confirmed by luciferase reporter, RNA immunoprecipitation(RIP), and western blot assays. Western blot was performed to analyze NF-κB/p65 and I-κBa expressions. Ourdata showed that hypoxia enhanced apoptosis and NF-κB signaling pathway, which was alleviated by Restreatment. Hypoxia increased the expression of miR-30d-5p while decreased the SIRT1 expression, which wasalso attenuated by Res treatment. Furthermore, miR-30d-5p depletion inhibited the proliferation, reducedapoptosis and decreased the expression of cle-caspase 3 in H9c2 cells with hypoxia treatment. Luciferasereporter, RIP, and western blot assays further confirmed that miR-30d-5p negatively regulated the expression ofSIRT1. Interestingly, the rescue-of-function experiments further indicated that knockdown of SIRT1 attenuatedthe effect of miR-30d-5p depletion on proliferation, apoptosis NF-κB signaling pathway inH9c2 cells withhypoxia treatment. In addition, the suppression of NF-κB signaling pathway increased cell viability whiledecreased cell apoptosis in hypoxia-mediatedH9c2 cells. Our data suggested Res mayprotectH9c2 cells againsthypoxia-induced apoptosis through miR-30d-5p/SIRT1/NF-κB axis.

    • Transcriptome-wide identification and profiling of miRNAs in a stress-tolerant conifer Sabina chinensis

      XIAN-GE HU SHAN-SHAN ZHOU YING YANG HUI LIU SHRESTHA ANIL QING WANG WEI ZHAO QIONG GAO YOUSRY A EL-KASSABY TONGLI WANG YUE LI JIAN-FENG MAO

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      miRNAs are important regulatory components involving in many biological processes, including plantdevelopment, vegetative and reproductive growth, and stress response. However, identification and characterizationof miRNAs still remain limited for conifer species. In this study, with deep sequencing, we obtained1,314,450 unique reads with 18–30 nt length from a stress-tolerant conifer, Sabina chinensis. We identified 37conserved and 103 novel miRNAs, their unique characteristics were further analyzed, and 10 randomlyselected were validated by qRT-PCR. Through miRNA target predictions and annotations, we found miRNAmay have several targets as well a target could be regulated by several miRNAs, and a total of 2,397 mRNAswere predicted to be targets of the 140 miRNAs. These targets included not only important transcription factorssuch as auxin response factors, but also indispensable non-transcriptional factor proteins. Pathway-basedanalysis showed that S. chinensis miRNAs are involved in 172 metabolic pathways, of which 3 were discoveredin adaptation-related pathways, indicating their possible relevance to the species’ stress-tolerancecharacteristics. This study is expected to lay the foundation for exploring the regulative roles of miRNAs indevelopment, growth, and response to environmental stresses of S. chinensis.

    • Silencing of HOXB9 suppresses cellular proliferation, angiogenesis, migration and invasion of prostate cancer cells

      HAO XU SHANGJUN WU XIN SHEN DING WU ZHENGUO QIN HAO WANG XIAOGANG CHEN XIAOQING SUN

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      The Homeobox B9 (HOXB9) is a homeodomain-containing transcription factor that participates in the progressionof various malignancies. Nevertheless, the functional role of HOXB9 in prostate cancer cells is largelyunknown. Hence, we aimed to address the effect of HOXB9 on the progression of prostate cancer cells. Smallinterfering RNA (siRNA) against HOXB9 was used to downregulate HOXB9 expression in PC3 and DU145cells. Western blotting was performed to detect the expression levels of HOXB9 and other related proteins. Cellproliferation was tested by the Cell Counting Kit-8 (CCK-8) and cell cycle and apoptosis were investigated byflow cytometry. Angiogenesis was examined using tube formation assays The Transwell assays were carriedout to assess the migratory and invasive capacities of cells. Here, we found that HOXB9 knockdown significantlyreduced cell proliferation via inducing cell cycle arrest at G1 phase. This treatment also reducedangiogenesis, migration and invasion abilities of PC3 and DU145 cells in vitro. We also found that HOXB9knockdown inhibits the activation of the PI3K/AKT signaling pathway in prostate cancer cells. In conclusion,our findings revealed that HOXB9 promotes prostate cancer progression and might be a novel and effectivetherapeutic target for human prostate cancer.

    • Yeast glutaredoxin, GRX4, functions as a glutathione S-transferase required for red ade pigment formation in Saccharomyces cerevisiae

      ASHWIN KUMAR JAINARAYANAN SHAMBHU YADAV ANAND KUMAR BACHHAWAT

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      The adenine biosynthetic mutants ade1 and ade2 of Saccharomyces cerevisiae accumulate a characteristic redpigment in their vacuoles under adenine limiting conditions. This red pigmentation phenotype, widely used in avariety of genetic screens and assays, is the end product of a glutathione-mediated detoxification pathway,where the glutathione conjugates are transported into the vacuole. The glutathione conjugation step, however,has still remained unsolved. We show here, following a detailed analysis of all the members of the thioredoxinfoldsuperfamily, the involvement of the monothiol glutaredoxin GRX4 as essential for pigmentation. GRX4plays multiple roles in the cell, and we show that the role in ade pigmentation does not derive from itsregulatory role of the iron transcription factor, Aft1p, but a newly identified GST activity of the protein that wecould demonstrate using purified Grx4p. Further, we demonstrate that the GRX domain of GRX4 and its activesite cysteine C171 is critical for this activity. The findings thus solve a decades old enigma on a critical step inthe formation of this red pigmentation.

    • Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair

      AVINASH SRIVASTAVA RAKESH K MISHRA

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      GAGA associated factor (GAF) is a sequence-specific DNA binding transcription factor that is evolutionarilyconserved from flies to humans. Emerging evidence shows a context-dependent function of vertebrate GAF(vGAF, a.k.a. ThPOK) in multiple processes like gene activation, repression, and enhancer-blocking. Wehypothesize that context-dependent interaction of vGAF with a diverse set of proteins forms the basis for themultifunctional nature of vGAF. To this end, we deciphered the protein–protein interactome of vGAF andshow that vGAF interacts with chromatin remodelers, RNA metabolic machinery, transcriptional activators/repressors, and components of DNA repair machinery. We further validated the biological significance of ourprotein–protein interaction data with functional studies and established a novel role of vGAF in DNA repairand cell-survival after UV-induced DNA damage. One of the major risk factors for skin cutaneous melanoma isprolonged exposure of UV and subsequent DNA damage. vGAF is highly expressed in normal skin tissue.Interestingly, our analysis of high-throughput RNA-sequencing data shows that vGAF is heavily downregulatedacross all major stages of skin cutaneous melanoma suggesting its potential as a diagnostic biomarker.Taken together, our study provides a plausible explanation for the diverse gene regulatory functions of vGAFand unravels its novel role in DNA repair.

    • MicroRNA-143–5p modulates pulmonary artery smooth muscle cells functions in hypoxic pulmonary hypertension through targeting HIF-1α

      BI TANG MING-MING TANG QING-MEI XU JIAN-LU GUO LING XUAN JING ZHOU XIAO-JING WANG HENG ZHANG PIN-FANG KANG

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      This paper explores the potential mechanism of microRNA-143–5p regulation effects on pulmonary arterysmooth muscle cells (PASMCs) functions in hypoxic pulmonary hypertension (HPH) via targeting HIF-1α,which may offer a new idea for HPH therapy. PASMCs were transfected with mimics control/miR-143–5pmimics or inhibitor control/miR-143–5p inhibitor. We used Western blotting and RT-qPCR to detect the proteinand mRNA expressions, CCK-8 assay to detect cellular viability, Annexin V-FITC/PI staining and caspase-3/cleaved caspase-3 protein to evaluate cellular apoptosis, transwell migration experiment for cellularmigration measurement and Dual luciferase reporter gene assay to prove the target of miR-143–5p. Cells underhypoxic condition presented the decreased protein and mRNA expressions of a-smooth muscle actin (SM-α-actin),Myocardin, smooth muscle myosin heavy chain (SMMHC), and smooth muscle-22α (SM22α),Calponin1 and Hypoxia-inducible factor-1α (HIF-1α), the increased cell viability and miR-143–5p level; Overexpressionof miR-143–5p obviously reduced vascular smooth muscle-specific contraction marker proteinlevels and cellular apoptosis, increased cellular migration of PASMCs with hypoxia stimulation; Low-expressionof miR-143–5p caused the opposite changes, while co-transfected with Si HIF-1a blocked thebeneficial effects of miR-143–5p inhibition on PASMCs under hypoxia. MicroRNA-143–5p can promote thephenotype conversion, proliferation and migration of pulmonary artery smooth muscle cells under hypoxiccondition through direct targeting of HIF-1α.

    • Aleurothrixus trachoides (Back) can transmit begomovirus from Duranta to potato, tomato and bell pepper

      K CHANDRASHEKAR ASHUTOSH RAO ASAWARI GORANE RAJ VERMA SAVARNI TRIPATHI

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      Solanum whitefly, Aleurothrixus trachoides (Back). (Hemiptera: Aleyrodidae) was considered as a non-virusvector by European and Mediterranean Plant Protection Organization (EPPO) reports. However, in the presentstudy it was found to transmit Duranta leaf curl virus (DLCV) to tomato, bell pepper and potato. A. trachoidesinfested field samples of Duranta sp (100%) and tomato (20%) tested positive for begomovirus by PCR usingbegomovirus degenerate primers and primers specific to Tomato leaf curl New Delhi virus showing ampliconof 520 bp and 2.7 Kb respectively. The DNA samples of A. trachoides collected from virus positive durantaand tomato plants also tested positive for the virus. Virulent whiteflies from duranta could successfully transmitDLCV to bell pepper (26%) and tomato (13%) plants as confirmed by Rolling Circle Amplification. The rate ofvirus transmission by A. trachoides from DLCV inoculated tomato to bell pepper and tomato to potato was100% and tomato to tomato was 80%. The results suggest whitefly A. trachoides as the vector for DLCVand tothe best of our knowledge, this is the first report for A. trachoides as vector of begomovirus. These findingssuggest need for reconsideration of A. trachoides as a virus-vector. This will have great impact on solanaceousvegetable cultivation in India and other parts of the world.

    • MicroRNA-20b-5p regulates propofol-preconditioning-induced inhibition of autophagy in hypoxia-and-reoxygenation-stimulated endothelial cells

      WANG ZHEN DING HUI SONG WENYING SONG YULONG

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      Ischemia-reperfusion (IR) injury is a major cause of clinical emergencies during and after surgical procedures.Propofol protects the heart from cardiovascular IR injury by inhibiting autophagy. MicroRNAs (miRNAs)participate in anesthetic-regulated cardiovascular injury. MiR-20b-5p targets unc-51-like autophagy activatingkinase 1 (ULK1). Its role in propofol-modulated cardiovascular IR injury remains unclear, however. In thisstudy, we used an in vitro model of hypoxia-reoxygenation (HR)-induced injury to human umbilical veinendothelial cells (HUVECs) to determine the protective effect of miR-20b-5p in cells preconditioned withpropofol. We found that miR-20b-5p was significantly higher and ULK1 was lower in propofol-preconditionedHUVECs with HR injury than in HUVECs with HR injury only. Additionally, miR-20b-5p overexpressionincreased cell viability and repressed autophagy and apoptosis more in propofol-preconditioned HUVECs withHR injury than in HUVECs with HR injury only. A luciferase reporter assay confirmed the target reactionbetween miR-20b-5p and ULK1. Overexpression of ULK1 restrained the protective effect of miR-20b-5p inpropofol-preconditioned HUVECs with HR injury. In conclusion, our results indicate that propofol inhibitsautophagic cell death via the miR-20b-5p-ULKI axis and that ULK1 may be a therapeutic target for cardiovascularIR injury.

    • β-Actin facilitates etoposide-induced p53 nuclear import

      WENJING QI JINJIAO LI XIAOHUA PEI YUESHUANG KE QINGPAN BU XIUZHEN NI

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      As a tumor suppressor, p53 preserves genomic integrity in eukaryotes. However, limited evidence is availablefor the p53 shuttling between the cytoplasm and nucleus. Previous studies have shown that β-actin polymerizationnegatively regulates p53 nuclear import through its interaction with p53. In this study, we found thatDNA damage induces both b-actin and p53 accumulation in the nucleus. b-actin knockdown impaired thenuclear transport of p53. Additionally, b-actin could interact with p53 which was enhanced in response togenotoxic stress. Furthermore, N terminal deletion mutants of p53 shows reduced levels of association with β-actin.We further identified Ser15, Thr18 and Ser20 of p53 are critical to the β-actin: p53 interaction, whichupon mutation into alanine abrogates the binding. Taken together, this study reveals that β-actin regulates thenuclear import of p53 through protein–protein interaction.

    • X-Module: A novel fusion measure to associate co-expressed gene modules from condition-specific expression profiles

      TULIKA KAKATI DHRUBA K BHATTACHARYYA JUGAL K KALITA

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      A gene co-expression network (CEN) is of biological interest, since co-expressed genes share commonfunctions and biological processes or pathways. Finding relationships among modules can reveal inter-modularpreservation, and similarity in transcriptome, functional, and biological behaviors among modules of the sameor two different datasets. There is no method which explores the one-to-one relationships and one-to-manyrelationships among modules extracted from control and disease samples based on both topological andsemantic similarity using both microarray and RNA seq data. In this work, we propose a novel fusion measureto detect mapping between modules from two sets of co-expressed modules extracted from control and diseasestages of Alzheimer’s disease (AD) and Parkinson’s disease (PD) datasets. Our measure considers bothtopological and biological information of a module and is an estimation of four parameters, namely, semanticsimilarity, eigengene correlation, degree difference, and the number of common genes. We analyze the consensusmodules shared between both control and disease stages in terms of their association with diseases. Wealso validate the close associations between human and chimpanzee modules and compare with the state-ofthe-art method. Additionally, we propose two novel observations on the relationships between modules forfurther analysis.

    • Glyoxal modification mediates conformational alterations in silk fibroin: Induction of fibrillation with amyloidal features

      SAURADIPTA BANERJEE

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      Silkwormsilk protein fibroin is widely exploited to develop novel silk-based biomaterials due to its stable b-sheetstructure, providing high crystallinity and tensile strength. The polymorphic behaviour of silk fibroin provides awindow to modulate its structural transitions during self-assembly for different functional outcomes. Most studiesare therefore mainly focused on formation of well-developed beta-sheet structure and self-assembly of silk fibroinwhich are regulated by many parameters. Glyoxal, a highly reactive alpha-oxoaldehyde, reacts with different proteinsto form advanced glycation end products (AGEs) following Maillard-like reaction. Considering the significanceof protein modification by glyoxal-derived AGEs, in the present study the effect of glyoxal (250, 500 and1000 micro-M) on the structure of silk fibroin has been investigated. CD and fluorescence studies reveal that higherconcentrations of the a-oxoaldehyde induce considerable alterations of secondary and tertiary structure of theprotein leading to aggregation following incubation with for 3 weeks. The aggregates exhibit fibrillar morphologywith amyloidal nature as evident from SEM, FTIR and XRD experiments. The findings highlight that glycationinducedmodification can be a possible approach for modulating the conformation of the silk protein which may berelevant in connection to clinical, biomedical or synthetic biology based applications.

    • Development of transgenic cotton (Narasimha) using triple gene Cry2Ab-Cry1F-Cry1Ac construct conferring resistance to lepidopteran pest

      SUMALATHA KATTA ASHWINI TALAKAYALA MALIREDDY K REDDY UMA ADDEPALLY MALLIKARJUNA GARLADINNE

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      High-yielding Indian cotton varieties are not amenable for regeneration and transformation because they arerecalcitrant in nature. In this work, we have developed Narasimha (NA1325) cotton variety by introducing three Crygenes driven by three different promoters conferring insect resistance. The meristematic region of embryo axisexplants were infected and co-cultivated with Agrobacterium tumefacience (LBA4404) harbouring pMDC100vector with three Cry gene cassettes (a-globulin : Cry2Ab, DECaMV35s : Cry1F and nodulin : Cry1Ac) with Npt IIas a selectable marker gene. Out of 1010 embryo axes explants infected, 121 (T0) regenerated under two rounds ofkanamycin selectionmedium.About 2551T1 seedswere collected from111T0 plants and these seeds screened againwith kanamycin at seedling stage. The transgenic plants were characterized by PCR, real time quantitative PCR,lateral flow strip protein assay and insect bioassay. Out of 145 kanamycin resistant plants (T1), twelve showedamplification of all four transgenes: Npt II, Cry2Ab, Cry1F and Cry1Ac through PCR with expected amplicons as395, 870, 840 and 618 bp, respectively. Further, lateral flow strip test revealed Cry1F and Cry1Ac proteinsaccumulated in 12 plants, whereas Cry2Ab protein was detected in eight only. The transcripts of all three Cry geneswere accumulated significantly higher in transgenic plants at T2 generation. The transgenic lines showed effectiveresistance againstHelicoverpa armigera and Spodoptera litura larvae. The T2 line L-3 exhibited highest percentageof insect mortality, in which transcripts of all cry genes were accumulated higher than other plants. The transgeniccotton plants carrying triple Cry genes could be an excellent germplasmresource for the breeders for introgressions.

    • Target-specific gene delivery in plant systems and their expression: Insights into recent developments

      DEBDYUTI NANDY AMRITA MAITY ARUP KUMAR MITRA

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      In order to improve crop plants in terms of their yield, drought resistance, pest resistance, nutritional value, etc.,modern agriculture has relied upon plant genetic engineering. Since the advent of recombinant DNA technology,several tools have been used for genetic transformations in plants such as Agrobacterium tumefaciens,virus-mediated gene transfer, direct gene transfer systems such as electroporation, particle gun, microinjectionand chemical methods. All these traditional methods lack specificity and the transgenes are integrated atrandom sites in the plant DNA. Recently novel techniques for gene targeting have evolved such as engineerednucleases such as Zinc Finger Nucleases, Transcription Activator like effector nucleases, Clustered regularinterspaced short palindromic repeats. Other advances include improvement in tools for delivery of geneediting components which include carrier proteins, and carbon nanotubes. The present review focuses on thelatest techniques for target specific gene delivery in plants, their expression and future directions in plantbiotechnology.

    • Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins

      ANIL BHATTARAI ISAAC ARNOLD EMERSON

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      Intrinsically disordered proteins (IDPs) are highly flexible and undergo disorder to order transition uponbinding. They are highly abundant in human proteomes and play critical roles in cell signaling and regulatoryprocesses. This review mainly focuses on the dynamics of disordered proteins including their conformationalheterogeneity, protein–protein interactions, and the phase transition of biomolecular condensates that arecentral to various biological functions. Besides, the role of RNA-mediated chaperones in protein folding andstability of IDPs were also discussed. Finally, we explored the dynamic binding interface of IDPs as noveltherapeutic targets and the effect of small molecules on their interactions.

    • Activation of RelA by pppGpp as the basis for its differential toxicity over ppGpp in Escherichia coli

      RAJESHREE SANYAL RAJENDRAN HARINARAYANAN

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      The nucleotide derivatives (p)ppGpp, comprising ppGpp and pppGpp, are important signalling molecules thatcontrol various facets of gene regulation and protein synthesis in Escherichia coli. Their synthesis is catalysedby RelA (in response to amino acid limitation) and by SpoT (in response to the limitation of carbon source orfatty acids). SpoT is also a hydrolase for degradation of both ppGpp and pppGpp, while GppA catalyses theconversion of pppGpp to ppGpp. Here we provide evidence to show that pppGpp exerts heightened toxicitycompared to that by ppGpp. Thus, gppA spoT double mutants exhibited lethality under conditions in which thesingle mutants were viable. The extent of RelA-catalysed (p)ppGpp accumulation in the gppA spoT strain wassubstantially greater than that in its isogenic gppA? derivative. The data is interpreted in terms of a model inwhich toxicity of pppGpp in the gppA spoT mutants is mediated by its activation of RelA so as to result in avicious cycle of (p)ppGpp synthesis.

    • Comprehensive molecular insights into the stress response dynamics of rice (Oryza sativa L.) during rice tungro disease by RNA-seq-based comparative whole transcriptome analysis

      GAURAV KUMAR INDRANIL DASGUPTA

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      Rice tungro is a serious viral disease of rice resulting from infection by two viruses, Rice tungro bacilliformvirus and Rice tungro spherical virus. To gain molecular insights into the global gene expression changes inrice during tungro, a comparative whole genome transcriptome study was performed on healthy and tungroaffectedrice plants using Illumina Hiseq 2500. About 10 GB of sequenced data comprising about 50 millionpaired end reads per sample were then aligned on to the rice genome. Gene expression analysis revealedaround 959 transcripts, related to various cellular pathways concerning stress response and hormonal homeostasisto be differentially expressed. The data was validated through qRT-PCR. Gene ontology and pathwayanalyses revealed enrichment of transcripts and processes similar to the differentially expressed genes categories.In short, the present study is a comprehensive coverage of the differential gene expression landscapeand provides molecular insights into the infection dynamics of the rice-tungro virus system.

    • Computational prediction of active sites and ligands in different AHL quorum quenching lactonases and acylases

      ZULKAR NAIN UTPAL KUMAR ADHIKARI FARUQ ABDULLA NAHID HOSSAIN NIRMAL CHANDRA BARMAN FARIHA JASIN MANSUR HIROYUKI AZAKAMI MOHAMMAD MINNATUL KARIM

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      With the emergence of multidrug-resistant ‘superbug’, conventional treatments become obsolete. Quorumquenching (QQ), enzyme-dependent alteration of quorum sensing (QS), is now considered as a promisingantimicrobial therapy because of its potentiality to impede virulence gene expression without resulting ingrowth inhibition and antibiotic resistance. In our study, we intended to compare between two major QQenzyme groups (i.e., AHL lactonases and AHL acylases) in terms of their structural and functional aspects.The amino acid composition-based principal component analysis (PCA) suggested that probably there is nostructural and functional overlapping between the two groups of enzymes as well as within the lactonaseenzymes but the acylases may functionally be affected by one another. In subcellular localization analysis,we also found that most lactonases are cytoplasmic while acylases are periplasmic. Investigation on thesecondary structural features showed random coil dominates over a-helix and b-sheet in all evaluatedenzymes. For structural comparison, the tertiary structures of the selected proteins were modelled andsubmitted to the PMDB database (Accession ID: PM0081007 to PM0081018). Interestingly, sequencealignment revealed the presence of several conserved domains important for functions in both proteingroups. In addition, three amino acid residues, namely aspartic acid, histidine, and isoleucine, were commonin the active sites of all protein models while most frequent ligands were found to be 3C7, FEO, and PAC.Importantly, binding interactions of predicted ligands were similar to that of native QS signal molecules.Furthermore, hydrogen bonds analysis suggested six proteins are more stable than others. We believe thatthe knowledge of this comparative study could be useful for further research in the development of QSbaseduniversal antibacterial strategies.

    • Effects of biotic and abiotic factors on biofilm growth dynamics and their heterogeneous response to antibiotic challenge

      LAKSHMI MACHINENI

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      Over the last couple of decades, with the crisis of new antimicrobial arsenal, multidrug-resistant clinicalpathogens have been observed extensively. In clinical and medical settings, these persistent pathogens predominantlygrow as complex heterogeneous structures enmeshed in a self-produced exopolysaccharide matrix,termed as biofilms. Since biofilms can rapidly form by adapting new environmental surroundings and havepotential effect on human health, it is critical to study them promptly and consistently. Biofilm infections arechallenging in the contamination of medical devices and implantations, food processing and pharmaceuticalindustrial settings, and in dental area caries, periodontitis and so on. The persistence of infections associatedwith biofilms has been mainly attributed to the increased antibiotic resistance offered by the cells growing inbiofilms. In fact, it is well known that this recalcitrance of bacterial biofilms is multifactorial, and there areseveral resistance mechanisms that may act in parallel in order to provide an enhanced level of resistance to thebiofilm. In combination, distinct resistance mechanisms significantly decrease our ability to control anderadicate biofilm-associated infections with current antimicrobial arsenal. In addition, various factors areknown to influence the process of biofilm formation, growth dynamics, and their heterogeneous responsetowards antibiotic therapy. The current review discusses the contribution of cellular and physiochemical factorson the growth dynamics of biofilm, especially their role in antibiotic resistance mechanisms of bacterialpopulation living in surface attached growth mode. A systematic investigation on the effects and treatment ofbiofilms may pave the way for novel therapeutic strategies to prevent and treat biofilms in healthcare andindustrial settings.

    • A transmission ratio distortion and the ‘max-4’ ascus phenotype: Do both reflect the same Bateson-Dobzhansky-Muller Incompatibility emerging during trans-species introgression of translocations in Neurospora?

      SELVAM REKHA DURGADAS P KASBEKAR

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      The ${T(EB4)}^{Nt}a$, ${T(IBj5)}^{Nt}a$, and ${T(B362i)}^{Nt}A$ strains were constructed by introgressing the insertional translocations EB4, IBj5, and B362i from Neurospora crassa into the related species N. tetrasperma. Theprogeny from crosses of ${T(IBj5)}^{Nt}a$ and ${T(B362i)}^{Nt}A$ with opposite mating-type derivatives of the standard N. tetrasperma strain 85 exhibited a unique and unprecedented transmission ratio distortion (TRD) that disfavored homokaryons produced following alternate segregation relative to those produced following adjacent-1 segregation. The TRD was not evident among the [mat A + mat a] dikaryons produced following either segregation. Further, crosses of the ${T(IBj5)}^{Nt}a$ and ${T(B362i)}^{Nt}A$ strains with the Eight spore (E) mutant showed an unusual ascus phenotype called ‘max-4’. We propose that the TRD and the max-4 phenotype are manifestations of the same Bateson-Dobzhansky-Muller incompatibility (BDMI). Since the TRD selects against 2/3 ofthe homokaryotic progeny from each introgression cross, the BDMI would have enriched for the dikaryotic progeny in the viable ascospores, and thus, paradoxically, facilitated the introgressions.

    • Acid-functionalized single-walled carbon nanotubes alter epithelial tight junctions and enhance paracellular permeability

      ANAND P SINGH MD BABU MIA RAJIV K SAXENA

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      Due to their unique properties, carbon nanotubes (CNTs) are being widely explored for industrial and medicalapplications. This has necessitated a thorough assessment of the effect of CNTs on human and animalphysiology and health. Impact of CNTs on epithelial tight junctions has not been evaluated in the context oftheir toxic effects in many biological systems. In the present study, we examined the effect of acid functionalizedsingle-walled carbon nanotubes (AF-SWCNTs) on the function and expression of two tight junctionproteins (ZO-1 and occludin) in the Madin-Darby canine kidney (MDCK) cell line. Treatment of MDCK cellswith AF-SWCNT resulted in a downregulation of tight junction proteins, decreased trans-epithelial electricalresistance (TER), increased paracellular permeability, and disruption of tight junctions. Taken together, ourdata demonstrate that AF-SWCNT disrupts tight junction barrier by downregulating tight junction proteins inMDCK epithelial cells.

    • Do males bond? A study of male-male relationships in Nicobar long-tailed macaques Macaca fascicularis umbrosus

      PARTHA SARATHI MISHRA ARIJIT PAL AVADHOOT D VELANKAR HONNAVALLI N KUMARA MEWA SINGH

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      In primates, males compete for a mate, which is a non-sharable resource. This makes the conditions lessconducive for males to have stable relationships. One such special kind of relationship is a bond where theinteractions are reciprocated, equitable and differentiated. Bonds in macaque societies are based on the degreeof within-group contest competition for mates which is dependent on the synchronization of female fertilephase and reliability of fertility signals. Species of the Fascicularis group, including Nicobar subspecies, showintermediate reliability in the signals with mild peaks, and studies have shown reciprocity but no differentiation.We conducted a study on a group of wild Nicobar long-tailed macaques Macaca fascicularis umbrosusto understand the existing patterns of male-male relationships. We examined whether there is reciprocity inaffiliation among the individuals and whether the rate of affiliation is balanced. We also measured the dominancelinearity and steepness in the group to understand the monopolizability of females. We used socialnetwork analysis to understand whether the relations are differentiated based on hierarchical position andwhether the high-ranking individuals are the most central individuals in the distribution of grooming in thegroup. We found that there is reciprocity among the males although that is not equitable. There was no rank relateddifferentiation of affiliation among the males of the group. Instead, the identities of individualsinfluenced affiliation patterns. Our results correspond to the existent strong relationships but lack of social bondotherwise found in the Fascicularis group of macaques.

    • TET methylcytosine oxidases: new insights from a decade of research

      CHAN-WANG J LIO XIAOJING YUE ISAAC F LO´ PEZ-MOYADO MAMTA TAHILIANI L ARAVIND ANJANA RAO

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      In mammals, DNA methyltransferases transfer a methyl group from S-adenosylmethionine to the 5 position ofcytosine in DNA. The product of this reaction, 5-methylcytosine (5mC), has many roles, particularly insuppressing transposable and repeat elements in DNA. Moreover, in many cellular systems, cell lineagespecification is accompanied by DNA demethylation at the promoters of genes expressed at high levels in thedifferentiated cells. However, since direct cleavage of the C-C bond connecting the methyl group to the 5position of cytosine is thermodynamically disfavoured, the question of whether DNA methylation wasreversible remained unclear for many decades. This puzzle was solved by our discovery of the TET (Ten-Eleven Translocation) family of 5-methylcytosine oxidases, which use reduced iron, molecular oxygen and thetricarboxylic acid cycle metabolite 2-oxoglutarate (also known as alpha-ketoglutarate) to oxidise the methyl groupof 5mC to 5-hydroxymethylcytosine (5hmC) and beyond. TET-generated oxidised methylcytosines areintermediates in at least two pathways of DNA demethylation, which differ in their dependence on DNAreplication. In the decade since their discovery, TET enzymes have been shown to have important roles inembryonic development, cell lineage specification, neuronal function and cancer. We review these findings anddiscuss their implications here.

    • Role of genomic imprinting in mammalian development

      THUSHARA THAMBAN VIPLOVE AGARWAAL SANJEEV KHOSLA

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      Non-mendelian inheritance refers to the group of phenomena and observations related to the inheritance ofgenetic information that cannot be merely explained by Mendel’s laws of inheritance. Phenomenon includingGenomic imprinting, X-chromosome Inactivation, Paramutations are some of the best studied examples ofnon-mendelian inheritance. Genomic imprinting is a process that reversibly marks one of the two homologousloci, chromosome or chromosomal sets during development, resulting in functional non-equivalence of geneexpression. Genomic imprinting is known to occur in a few insect species, plants, and placental mammals.Over the years, studies on imprinted genes have contributed immensely to highlighting the role of epigeneticmodifications and the epigenetic circuitry during gene expression and development. In this review, we discussthe phenomenon of genomic imprinting in mammals and the role it plays especially during fetoplacentalgrowth and early development.

    • Cellular environment controls the dynamics of histone H3 lysine 56 acetylation in response to DNA damage in mammalian cells

      RAGHAVENDRA VADLA NIRUPAMA CHATTERJEE DEVYANI HALDAR

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      Epigenetic changes play a crucial role in sensing signals and responding to fluctuations in the extracellularenvironment. How the cellular micro-environment affects DNA damage response signalling in chromatincontext is not extensively studied. Histone acetylation is dynamic and very sensitive to changes in theextracellular environment. Existing literature on H3 lysine 56 acetylation (H3K56ac) levels upon DNA damagein mammals presents a conflicting picture. The occurrence of both increased and decreased H3K56ac uponDNA damage in our experiments led us to investigate the role of the micro-environment on H3K56ac. Here,we show that the global levels of H3K56ac increase as cells grow from low density to high density whileSIRT1 and SIRT6 expression decrease. Additionally, rising lactic acid levels increase H3K56ac. Our resultsshow that cell density and accumulation of metabolites affect dynamics of H3K56ac in response to DNAdamage. Upon DNA damage, H3K56ac increases in low density cells with low initial acetylation, whileacetylation decreases in high cell density cells. These results highlight that H3K56ac levels upon DNA damageare dependent on the metabolites in the extracellular milieu which impact chromatin structure by regulatingchromatin modifying enzymes. Accumulation of lactic acid at high cell density reflects conditions similar to thetumour micro-environment. As H3K56ac increases in tumours, lactic acid and low pH might alter H3K56ac intumours, leading to deregulated gene expression, contributing to tumour progression.

    • Recent advances in the spatial organization of the mammalian genome

      YATENDRA KUMAR DIPTA SENGUPTA WENDYA BICKMORE

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      The mammalian genome is complex and presents a dynamic structural organization that reflects function.Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but notlimited to transcription, replication and repair, and in many biological contexts such as early development,differentiation and physiological adaptations. However, there is limited understating of how 3D organization ofthe mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad ofgenomics methods—propelled by next-generation sequencing—have advanced our knowledge of genomeorganization to a great extent. In this review, we discuss nuclear compartments in general and recent advancesin the understanding of how mammalian genome is organized in these compartments with an emphasis ondynamics at the nuclear periphery.

    • When histones are under glucose starvation

      JAEHYOUN LEE SEUNGHEE OH SUSAN M ABMAYR JERRY L WORKMAN

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      Under nutritional stress, cells undergo metabolic rewiring that results in changes of various cellular processesthat include gene transcription. This transcriptional regulation requires dynamic chromatin remodeling thatinvolves histone post-translational modifications. There are several histone marks that may act as switchesupon starvation for stress-response pathways.

    • The CBX family of proteins in transcriptional repression and memory

      JONGMIN KIM ROBERT E KINGSTON

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      For mammals to develop properly, master regulatory genes must be repressed appropriately in a heritablemanner. This review concerns the Polycomb Repressive Complex 1 (PRC1) family and the relationshipbetween the establishment of repression and memory of the repressed state. The primary focus is on the CBXfamily of proteins in PRC1 complexes and their role in both chromatin compaction and phase separation.These two activities are linked and might contribute to both repression and memory.

    • Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease

      SWETA SIKDER STEPHANIE KAYPEE TAPAS K KUNDU

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      Besides the fundamental components of the chromatin, DNA and octameric histone, the non-histone chromatinproteins and non-coding RNA play a critical role in the organization of functional chromatin domains. Thenon-histone chromatin proteins therefore regulate the transcriptional outcome in both physiological andpathophysiological state as well. They also help to maintain the epigenetic state of the genome indirectly.Several transcription factors and histone interacting factors also contribute in the maintenance of the epigeneticstates, especially acetylation by the induction of autoacetylation ability of p300/CBP. Alterations of KATactivity have been found to be causally related to disease manifestation, and thus could be potential therapeutictarget.

    • Role of nucleosome positioning in 3D chromatin organization and loop formation

      HUNGYO KHARERIN PAIKE J BHAT RANJITH PADINHATEERI

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      We present a physics-based polymer model that can investigate 3D organization of chromatin accounting for DNA elasticity,DNA-bending due to nucleosomes, and 1D organization of nucleosomes along DNA. We find that the packing density ofchromatin oscillates between densities corresponding to highly folded and extended configurations as we change thenucleosome organization (length of linker DNA). We compute the looping probability of chromatin and show that thepresence of nucleosomes increases the looping probability of the chain compared to that of a bare DNA. We also show thatlooping probability has a large variability depending on the nature of nucleosome organization and density of linker histones.

    • Picking a nucleosome lock: Sequence- and structure-specific recognition of the nucleosome

      MATTHEW M MAKOWSKI GUILLAUME GAULLIER KAROLIN LUGER

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      The nucleosome presents a formidable barrier to DNA-templated transcription by the RNA polymerase IImachinery. Overcoming this transcriptional barrier in a locus-specific manner requires sequence-specificrecognition of nucleosomal DNA by ‘pioneer’ transcription factors (TFs). Cell fate decisions, in turn, dependon the coordinated action of pioneer TFs at cell lineage-specific gene regulatory elements. Although it isalready appreciated that pioneer factors play a critical role in cell differentiation, our understanding of thestructural and biochemical mechanisms by which they act is still rapidly expanding. Recent research hasrevealed novel insight into modes of nucleosome-TF binding and uncovered kinetic principles by whichnucleosomal DNA compaction affects both TF binding and residence time. Here, we review progress and arguethat these structural and kinetic studies suggest new models of gene regulation by pioneer TFs.

    • Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects

      ARUMUGAM SRINIVASAN RAKESH K MISHRA

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      The epigenetic memory is an essential aspect of multicellular organisms to maintain several cell types and their geneexpression pattern. This complex process uses a number of protein factors and specific DNA elements within thedevelopmental cues to achieve this. The protein factors involved in the process are the Polycomb group (PcG)members, and, accordingly, the DNA sequences that interact with these proteins are called Polycomb ResponseElements (PREs). Since the PcG proteins are highly conserved among higher eukaryotes, including insects, andfunction at thousands of sites in the genomes, it is expected that PREs may also be present across the genome.However,the studies on PREs in insect species, other thanDrosophila, is currently lacking.We took a bioinformatics approach todevelop an inclusive PRE prediction tool, ‘PRE Mapper’, to address this need. By applying this tool on the Drosophilamelanogaster genome, we predicted more than 20,000 PREs.When compared with the available PRE prediction methods, thistool shows far better performance by correctly identifying the in vivo binding sites of PcG proteins, identified bygenome-scale ChIP experiments. Further analysis of the predicted PREs shows their cohabitation with chromatindomain boundary elements at several places in the Drosophila genome, possibly defining a composite epigeneticmodule.We analysed 10 insect genomes in this context and find several conserved features in PREs across the insectspecies with some variations in their occurrence frequency. These analyses leading to the identification of PREin insectgenomes contribute to our understanding of epigenetic mechanisms in these organisms.

    • Role of PfGCN5 in nutrient sensing and transcriptional regulation in Plasmodium falciparum

      MUKUL RAWAT RASHIM MALHOTRA SHARVANI SHINTRE SAMARENDRA PANI KRISHANPAL KARMODIYA

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      Malaria is a deadly, infectious disease caused by the parasite Plasmodium, leading to millions of deathsworldwide. Plasmodium requires a coordinated pattern of sequential gene expression for surviving in bothinvertebrate and vertebrate host environments. As parasites largely depend on host resources, they also developefficient mechanisms to sense and adapt to variable nutrient conditions in the environment and modulate theirvirulence. Earlier we have shown that PfGCN5, a histone acetyltransferase, binds to the stress-responsive andvirulence-related genes in a poised state and regulates their expression under temperature and artemisinintreatment conditions in P. falciparum. In this study, we show upregulation of PfGCN5 upon nutrient stresscondition. With the help of chromatin immunoprecipitation coupled high-throughput sequencing (ChIP-seq)and transcriptomic (RNA-sequencing) analyses, we show that PfGCN5 is associated with the genes that areimportant for the maintenance of parasite cellular homeostasis upon nutrient stress condition. Furthermore, weidentified various metabolic enzymes as interacting partners of PfGCN5 by immunoprecipitation coupled withmass spectroscopy, possibly acting as a sensor of nutrient conditions in the environment. We also demonstratedthat PfGCN5 interacts and acetylates PfGAPDH in vitro. Collectively, our data provides important insights intotranscriptional deregulation upon nutrient stress condition and elucidate the role of PfGCN5 during nutrientstress condition.

    • The conserved aspartate in motif III of b family AdoMet-dependent DNA methyltransferase is important for methylation

      AATHIRA GOPINATH MANASI KULKARNI ISHTIYAQ AHMED OM PRAKASH CHOUHAN KAYARAT SAIKRISHNAN

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      S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) are involved in diverse cellularfunctions. These enzymes show little sequence conservation but have a conserved structural fold. The DNAMTases have characteristic motifs that are involved in AdoMet binding, DNA target recognition and catalysis.Motif III of these MTases have a highly conserved acidic residue, often an aspartate, whose functionalsignificance is not clear. Here, we report a mutational study of the residue in the beta family MTase of the Type IIIrestriction-modification enzyme EcoP15I. Replacement of this residue by alanine affects its methylationactivity. We propose that this residue contributes to the affinity of the enzyme for AdoMet. Analysis of thestructures of DNA, RNA and protein MTases reveal that the acidic residue is conserved in all of them, andinteracts with N6 of the adenine moiety of AdoMet. Interestingly, in the SET-domain protein lysine MTases,which have a fold different from other AdoMet-dependent MTases, N6 of the adenine moiety is hydrogenbonded to the main chain carbonyl group of the histidine residue of the highly conserved motif III. Our studyreveals the evolutionary conservation of a carbonyl group in DNA, RNA and protein AdoMet-dependentMTases for specific interaction by hydrogen bond with AdoMet, despite the lack of overall sequenceconservation.

    • Mining histone methyltransferases and demethylases from whole genome sequence

      PARUL GULATI SURBHI KOHLI ANKITA NARANG VANI BRAHMACHARI

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      Epigenetic regulation through post-translational modification of histones, especially methylation, is wellconserved in evolution. Although there are several insect genomes sequenced, an analysis with a focus on theirepigenetic repertoire is limited. We have utilized a novel work-flow to identify one or more domains as highprioritydomain (HPD), if present in at least 50% of the genes of a given functional class in the referencegenome, namely, that of Drosophila melanogaster. Based on this approach, we have mined histone methyltransferasesand demethylases from the whole genome sequence of Aedes aegypti (Diptera), the pea aphidAcyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera),the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum(Coleoptera). We identified 38 clusters consisting of arginine methyltransferases, lysine methyltransferases anddemethylases using OrthoFinder, and the presence of HPD was queried in these sequences using InterProScan.This approach led us to identify putative novel members and currently inaccurate ones. Other than the highprioritydomains, these proteins contain shared and unique domains that can mediate protein–protein interaction.Phylogenetic analysis indicates that there is different extent of protein sequence similarity; averagesimilarity between histone lysine methyltransferases varies from 41% (for active mark) to 48% (for repressivemark), arginine methyltransferases is 51%, and demethylases is 52%. The method utilized here facilitatesreliable identification of desired functional class in newly sequenced genomes.

    • Origin of RNA Polymerase II pause in eumetazoans: Insights from Hydra

      PULI CHANDRAMOULI REDDY SAURABH J PRADHAN KRISHANPAL KARMODIYA SANJEEV GALANDE

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      Multicellular organisms have evolved sophisticated mechanisms for responding to various developmental,environmental and physical stimuli by regulating transcription. The correlation of distribution of RNAPolymerase II (RNA Pol II) with transcription is well established in higher metazoans, however genome-wideinformation about its distribution in early metazoans, such as Hydra, is virtually absent. To gain insights intoRNA Pol II-mediated transcription and chromatin organization in Hydra, we performed chromatin immunoprecipitation(ChIP)-coupled high-throughput sequencing (ChIP-seq) for RNA Pol II and Histone H3. Strikingly,we found that Hydra RNA Pol II is uniformly distributed across the entire gene body, as opposed to itscounterparts in bilaterians such as human and mouse. Furthermore, correlation with transcriptome datarevealed that the levels of RNA Pol II correlate with the magnitude of gene expression. Strikingly, thecharacteristic peak of RNA Pol II pause typically observed in bilaterians at the transcription start sites (TSSs)was not observed in Hydra. The RNA Pol II traversing ratio in Hydra was found to be intermediate to yeastand bilaterians. The search for factors involved in RNA Pol II pause revealed that RNA Pol II pausingmachinery was most likely acquired first in Cnidaria. However, only a small subset of genes exhibited thepromoter proximal RNP Pol II pause. Interestingly, the nucleosome occupancy is highest over the subset ofpaused genes as compared to total Hydra genes, which is another indication of paused RNA Pol II at thesegenes. Thus, this study provides evidence for the molecular basis of RNA Pol II pause early during theevolution of multicellular organisms.

    • Metabolic choreography of gene expression: nutrient transactions with the epigenome

      BABUKRISHNA MANIYADATH U S SANDRA ULLAS KOLTHUR-SEETHARAM

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      Eukaryotic complexity and thus their ability to respond to diverse cues are largely driven by varyingexpression of gene products, qualitatively and quantitatively. Protein adducts in the form of post-translationalmodifications, most of which are derived from metabolic intermediates, allow fine tuning of gene expressionat multiple levels. With the advent of high-throughput and high-resolution mapping technologies there hasbeen an explosion in terms of the kind of modifications on chromatin and other factors that govern geneexpression. Moreover, even the classical notion of acetylation and methylation dependent regulation oftranscription is now known to be intrinsically coupled to biochemical pathways, which were otherwiseregarded as ‘mundane’. Here we have not only reviewed some of the recent literature but also havehighlighted the dependence of gene regulatory mechanisms on metabolic inputs, both direct and indirect. Wehave also tried to bring forth some of the open questions, and how our understanding of gene expression haschanged dramatically over the last few years, which has largely become metabolism centric. Finally,metabolic regulation of epigenome and gene expression has gained much traction due to the increasedincidence of lifestyle and age-related diseases.

    • The role of histone modifications in leukemogenesis

      NOAH W BIRCH ALI SHILATIFARD

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      Histone modifications play a critical role in coordinating accurate gene expression. Aside from geneticmutations which cause altered DNA sequence, it has become increasingly clear that aberrant post-translationalmodifications of histone tails are also associated with leukemogenesis. The functional roles of specific histonemarks has informed the basis of our understanding for underlying mechanisms of leukemia, while globalanalyses of interacting histone modifications has begun to distinguish subtypes of leukemia with prognosticand therapeutic implications. In this current era of personalized and precision medicine, it will be necessary tonot only identify the specific genetic mutations present in a patient’s leukemia but to also appreciate thedynamic chromatin states which are driven by histone modifications that can aid our diagnostic and therapeuticstrategies for improved management of leukemia.

    • Phase-separation in chromatin organization

      GEETA J NARLIKAR

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      The organization of chromatin into different types of compact versus open states provides a means to fine tune generegulation. Recent studies have suggested a role for phase-separation in chromatin compaction, raising new possibilitiesfor regulating chromatin compartments. This perspective discusses some specific molecular mechanismsthat could leverage such phase-separation processes to control the functions and organization of chromatin.

    • Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes

      SANKET SHAH TRIPTI VERMA MUDASIR RASHID NIKHIL GADEWAL SANJAY GUPTA

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      Epigenetic mechanisms including the post-translational modifications of histones, incorporation of histonevariants and DNA methylation have been suggested to play an important role in genome plasticity by allowingthe cellular environment to define gene expression and the phenotype of an organism. Studies over the pastdecade have elucidated how these epigenetic mechanisms are significant in orchestrating various biologicalprocesses and contribute to different pathophysiological states. However, the role of histone isoforms and theirimpact on different phenotypes and physiological processes associated with diseases are not fully clear. Thisreview is focussed on the recent advances in our understanding of the complexity of eukaryotic H2A isoformsand their roles in defining nucleosome organization. We elaborate on their potential roles in genomic complexityand regulation of gene expression, and thereby on their overall contribution towards cellular phenotypeand development of diseases.

    • Hypoxia-induced changes in intragenic DNA methylation correlate with alternative splicing in breast cancer

      DEEPAK PANT SATHIYA PANDI NARAYANAN NAGARJUN VIJAY SANJEEV SHUKLA

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      The tumor microenvironment is marked by gradients in the level of oxygen and nutrients, with oxygen levelsreaching a minimum at the core of the tumor, a condition known as tumor hypoxia. Mediated by members of theHIF family of transcription factors, hypoxia leads to a more aggressive tumor phenotype by transactivation ofseveral genes as well as reprogramming of pre-mRNA splicing. Intragenic DNA methylation, which is known toaffect alternative splicing in cancer, could be one of several reasons behind the changes in splicing patterns underhypoxia. Here, we have tried to establish a correlation between intragenicDNA methylation and alternative usageof exons in tumor hypoxia. First, we have generated a customhypoxia signature consisting of 34 genes that are upregulatedunder hypoxia and are direct targets of HIF-1alpha. Using this gene expression signature, we have successfullystratified publicly available breast cancer patient samples into hypoxia positive and hypoxia negativegroups followed by mining of differentially spliced isoforms between these groups. The Hypoxia Hallmarksignature from MSigDB was also used independently to stratify the same tumor samples into hypoxic andnormoxic.We found that 821 genes were showing differential splicing between samples stratified using a customsignature, whereas, 911 genes were showing differential splicing between samples stratified using the MSigDBsignature. Finally, we performed multiple correlation tests between the methylation levels (beta) of microarrayprobes located within 1 kilo base pairs of isoform-specific exons using those exons’ expression levels in the samepatient samples in which the methylation level was recorded. We found that the expression level of one of theexons ofDHX32 and BICD2 significantly correlated with the methylation levels, and we were also able to predictpatient survival (p-value: 0.02 for DHX32 and 0.0024 for BICD2). Our findings provide new insights into thepotential functional role of intragenic DNA methylation in modulating alternative splicing during hypoxia.

    • A novel role of tumor suppressor ZMYND8 in inducing differentiation of breast cancer cells through its dual-histone binding function

      SHRAVANTI MUKHERJEE SABYASACHI SEN SANTANU ADHIKARY AMRITA SENGUPTA PRATITI MANDAL DIPAK DASGUPTA PARTHA CHAKRABARTI SIDDHARTHA ROY CHANDRIMA DAS

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      Accumulating evidences indicate the involvement of epigenetic deregulations in cancer. While some epigeneticregulators with aberrant functions in cancer are targeted for improving therapeutic outcome in patients,reinstating the functions of tumor-suppressor-like epigenetic regulators might further potentiate anti-cancertherapies. Epigenetic reader zinc-finger MYND-type-containing 8 (ZMYND8) has been found to be endowedwith multiple anti-cancer functions like inhibition of tumor cell migration and proliferation. Here, we reportanother novel tumor suppressor role of ZMYND8 as an inducer of differentiation in breast cancer cells, byupregulating differentiation genes. Interestingly, we also demonstrated that ZMYND8 mediates all its antitumorroles through a common dual-histone mark binding to H4K16Ac and H3K36Me2. We validated thesefindings by both biochemical and biophysical analyses. Furthermore, we also confirmed the differentiationinducingpotential of ZMYND8 in vivo, using 4T1 murine breast cancer model in Balb/c mice. Differentiationtherapy holds great promise in cancer therapy, since it is non-toxic and makes the cancer cells therapysensitive.In this scenario, we propose epigenetic reader ZMYND8 as a potential therapeutic candidate fordifferentiation therapy in breast cancer.

    • Editorial Topical collection on Chromatin Biology and Epigenetics

      GEETA NARLIKAR SANJEEV GALANDE

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