• Volume 44, Issue 4

      September 2019

    • Long non-coding RNAs: Fine-tuning the developmental responses in plants

      RIDDHI DATTA SOUMITRA PAUL

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      Plant developmental biology is associated with various gene regulatory pathways involved in different phases of their lifecycle. In course of development, growth and differentiation of different organs in plants are regulated by specific sets ofgene expression. With the advances in genomic and bioinformatic techniques, particularly high-throughput sequencingtechnology, many transcriptional units with no protein-coding potential have been discovered. Previously thought to be thedark matters of genome, long non-coding RNAs (lncRNAs) are gradually gaining importance as crucial players in generegulation during different developmental phases. Some lncRNAs, showing complementarity to microRNAs (miRNAs), areused as endogenous target mimics of specific miRNA family. A number of lncRNAs can also act as natural antisensetranscripts to attenuate the expression of coding genes. Although lncRNA-mediated regulations have extensively beenstudied in animals, plant lncRNA research is still in its initial phase. The present review highlights the regulatory mechanismand different physiological aspects of lncRNAs in plant development. In plants, lncRNAs are found to be associatedwith a number of plant developmental functions such as lateral root development, vernalization, photomorphogenesis,pollen development, fiber development and nodulation. Understanding these potent roles of lncRNAs in plant developmentcan further provide novel tools for crop improvement programs in future.

    • Analysis of nine cases of oral foreign body granuloma related to biomaterials

      LARISSA SANTOS AMARAL ROLIM CAIO CE´SAR DA SILVA BARROS JULIANA CAMPOS PINHEIRO PATRI´CIA TEIXEIRA DE OLIVEIRA LE´LIA BATISTA DE SOUZA PEDRO PAULO DE ANDRADE SANTOS

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      Foreign bodies can penetrate the interior of soft and, sometimes, hard, tissues in various ways, including through openwounds, lacerations and traumatic accidents. However over the years, evidence of links between the use of dental materialsand lately, significant involvement of aesthetic filler materials as foreign bodies in the oral and perioral region have beenreported. Foreign body granulomas (FBGs) may develop from this exogenous material, histopathologically characterizedby the presence of chronic inflammation and a high amount of macrophages. This study presents nine FBG cases affectingthe oral and perioral regions, and carries out a literature review on the main clinical, histopathological and materialcharacteristics used in dental and dermatological procedures related to the appearance of this type of granuloma.

    • In silico structure analysis of alphaviral RNA genomes shows diversity in the evasion of IFIT1-mediated innate immunity

      SAILEN BARIK

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      The IFIT (interferon-induced proteins with tetratricopeptide repeats) family constitutes a major arm of the antiviral functionof type I interferon (IFN). Human IFIT1, the earliest discovered member of this family, inhibits several viruses of positivestrandRNA genome. IFIT1 specifically recognizes single-stranded RNAwith canonical 7-methylguanylate cap at the 50 end(Cap0), and inhibits their translation by competing with eIF4E (eukaryotic initiation factor 4E), an essential factor for 50Caprecognition. Recently, a novel viral mechanism of IFIT1 suppression was reported, in which an RNA hairpin in the 50untranslated region (50UTR) of the viral genome prevented recognition by IFIT1 and enhanced virus growth. Here, I haveanalyzed the in silico predicted structures in the 50UTR of the genomes of the Alphaviruses, a large group of envelopedRNA virus with positive-sense single-stranded genome. The results uncovered a large ensemble of RNA secondarystructures of diverse size and shape in the different viruses, which showed little correspondence to the phylogeny of theviruses. Unexpectedly, the 50UTR of several viral genomes in this family did not fold into any structure, suggesting eithertheir extreme sensitivity to IFIT1 or the existence of alternative viral mechanisms of subverting IFIT1 function.

    • MiR-212-3p inhibits cell proliferation and promotes apoptosis by targeting nuclear factor IA in bladder cancer

      XIAOMING WU HAO CHEN GAOYUE ZHANG JIANHUI WU WEI ZHU YANQIN GU YI HE

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      Accumulating evidence suggest that microRNAs play crucial roles in the development and progression of bladder cancer(BC). Here, we found that miR-212-3p was significantly down-regulated and negatively correlated with nuclear factor IA(NFIA) in human BC tissues. Bioinformatics analysis predicted that NFIA was a target gene of miR-212-3p. Then BC celllines, T24 and J82 cells were transfected with miR-212-3p mimics or siNFIA to obtain miR-212-3p overexpression or NFIAknockdown cell lines, respectively. Quantitative real-time PCR was used to determine the expression of miR-212-3p andNFIA. Western blot analysis was utilized to detect NFIA expression. MTT assay showed either miR-212-3 overexpression orNFIA knockdown significantly inhibited the BC cell proliferation. Double staining with Annexin V-APC and 7-AAD showedthe total number of apoptotic BC cells were remarkably increased after miR-212-3p overexpression or NFIA knockdown.Collectively, our results indicated that miR-212-3p targeting NFIA might serve as a promising target for BC.

    • Comprehensive transcriptomics and proteomics analyses of rice stripe virus-resistant transgenic rice

      YANG XU LVJIE BI ZIPENG YU CHAO LIN LIMING GAN LIFEI ZHU HAIYANG LI YUNZHI SONG CHANGXIANG ZHU

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      Stable transgenic rice line (named KRSV-1) with strong resistance against rice stripe virus was generated using the genesequence of disease-specific protein by RNA interference. Comprehensive safety assessment of transgenic plants has turnedinto a significant field of genetic modification food safety. In this study, a safety assessment of KRSV-1 was carried out in astepwise approach. The molecular analysis exhibited that KRSV-1 harbored one copy number of transgene, which wasintegrated into the intergenic non-coding region of chromosome 2 associated with inter-chromosomal translocations of 1.6-kb segments of chromosome 8. Then, transcriptomics and proteomics analyses were carried out to detect the unintendedeffects as a result of the integration of the transgene. Although 650 dramatically differentially expressed genes (DDEGs)and 357 differentially expressed proteins were detected between KRSV-1 and wild-type (WT) by transcriptomics andproteomics analyses, no harmful members in the form of toxic proteins and allergens were observed. Encouragingly, thenutritional compositions of seeds from KRSV-1 were comparable with WT seeds. The results of this entire study ofmolecular analysis, transcriptome and proteome profile of KRSV-1 revealed that no detrimental changes in the form of toxicproteins and allergens were detected in the transgenic rice line due to the integration of the transgene.

    • Real-time monitoring of translocation of selected type-III effectors from Xanthomonas oryzae pv. oryzae into rice cells

      BIAN HUIJIE LIYUAN ZHANG LEI CHEN WENZHAN WANG HONGTAO JI HANSONG DONG

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      Type-III (T3) effectors PthXo1 and AvrXa10 of Xanthomonas oryzae pv. oryzae are translocated into rice cells to inducevirulence and avirulence on susceptible- and resistant-rice varieties Nipponbare and IRBB10, respectively. The translocationneeds the bacterial T3 translocator Hpa1 and rice Oryza sativa plasma membrane protein OsPIP1;3. Here, weemployed the b-lactamase (BlaM) reporter system to observe PthXo1 and AvrXa10 translocation. The system wasestablished to monitor effectors of animal-pathogenic bacteria by quantifying the BlaM hydrolysis product [P] and fluorescenceresonance energy transfer (FRET) of the substrate. The feasibility of the BlaM reporter in rice protoplasts wasevaluated by three criteria. The first criterion indicated differences between both [P] and FRET levels among wild types andOsPIP1;3-overexpressing and OsPIP1;3-silenced lines of both Nipponbare and IRBB10. The second criterion indicateddifferences between [P] and FRET levels in the presence and absence of Hpa1. The last criterion elucidated the coincidenceof PthXo1 translocation with induced expression of the PthXo1 target gene in protoplasts of Nipponbare and the coincidenceof AvrXa10 translocation with induced expression of the AvrXa10 target gene in protoplasts of IRBB10. Theseresults provide an experimental avenue for real-time monitoring of bacterial T3 effector translocation into plant cells with apathological consequence.

    • A cross-eyed geneticist’s view IV. Neurospora genes and inversions collude to cheat Mendel

      DURGADAS P KASBEKAR

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    • Biopolymers augment viral vectors based gene delivery

      BALAJI BALAKRISHNAN ERNEST DAVID

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      The success of viral vectors mediated gene therapy is still hampered by immunogenicity and insufficient transgeneexpression. Alternatively, non-viral vectors mediated gene delivery has the advantage of low immunogenicity despiteshowing low transgene expression. By carefully considering the advantages of each approach, hybrid vectors are currentlybeing developed by modifying the viral vectors using non-viral biopolymers. This review provides an overview of thehybrid vectors currently being developed.

    • Stability analysis of a prey refuge predator–prey model with Allee effects

      UNAL UFUKTEPE BURCIN KULAHCIOGLU OLCAY AKMAN

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      We constructed a discrete-time predator–prey model by adding prey refuge and Allee effects (predator saturation on preyand mate limitation on predator) to an earlier prey–predator model and examined its dynamics. We show the existence ofpositive fixed points and study the stability properties. The numerical simulations and bifurcation diagrams verify theimpact of refuge and the Allee mechanism on the system.

    • Adiponectin inhibits vascular smooth muscle cell calcification induced by beta-glycerophosphate through JAK2/STAT3 signaling pathway

      YAN LU YICHAO MA RUIHUA WANG JING SUN BEIBEI GUO RUIPENG WEI YONGPING JIA

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      Vascular calcification is a common problem in the elderly with diabetes, heart failure and end-stage renal disease. Thedifferentiation of vascular smooth muscle cells (VSMCs) into osteoblasts is the main feature, but the exact mechanismremains unclear. It is not clear whether adiponectin (APN) affects osteogenic differentiation of VSMCs. This study aims toexplore the effect of APN on vascular calcification by using a cell model induced by beta-glycerophosphate (b-GP).VSMCs were isolated and treated with b-GP and APN in this study. The alkaline phosphatase (ALP) activity andexpression levels of Runx2, BMP-2, collagen type I and osteocalcin were determined. The expression levels of STAT3 andp-STAT3 in nucleus and cytoplasm of VSMCs were analyzed. The results showed that APN significantly inhibited theexpression of ALP, Runx2, BMP-2, collagen I, osteocalcin and the formation of the mineralized matrix in VSMCs inducedby b-GP. APN reduces the osteogenic differentiation of VSMCs induced by b-GP and down-regulates the expression of theosteogenic transcription factor osterix by inhibiting STATS3 phosphorylation and nuclear transport. APN may be one of thepotential candidates for clinical treatment of vascular calcification.

    • 5-Azacytidine and trichostatin A enhance the osteogenic differentiation of bone marrow mesenchymal stem cells isolated from steroid-induced avascular necrosis of the femoral head in rabbit

      PENG ZHANG FULIN TAO QINGHU LI SHUAI WU BAISHENG FU PING LIU

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      Bone marrow mesenchymal stem cells (BMSCs) play an important role in the process of bone repair. The present studyinvestigated the effect of 5-azacytidine (AZA) and trichostatin A (TSA) on BMSC behaviors in vitro. The role of WNTfamily member 5A (WNT5A)/WNT family member 5A (WNT7A)/b-catenin signaling was also investigated. BMSCs wereisolated from a steroid-induced avascular necrosis of the femoral head (SANFH) rabbit model. The third-generation ofBMSCs was used after identification. The results revealed obvious degeneration and necrosis in the SANFH rabbit model.AZA, TSA and TSA + AZA increased BMSC proliferation in a time-dependent fashion. AZA, TSA and TSA + AZAinduced the cell cycle release from the G0/G1 phase and inhibited apoptosis in BMSCs. AZA, TSA and TSA + AZAtreatment significantly decreased caspase-3 and caspase-9 activities. The treatment obviously increased the activity andrelative mRNA expression of alkaline phosphatase. The treatment also significantly up-regulated the proteins associatedwith osteogenic differentiation, including osteocalcin and runt-related transcription factor 2 (RUNX2), and Wnt/b-cateninsignal transduction pathway-related proteins b-catenin, WNT5A and WNT7A. The relative levels of Dickkopf-relatedprotein 1 (an inhibitor of the canonical Wnt pathway) decreased remarkably. Notably, TSA + AZA treatment exhibited astronger adjustment ability than either single treatment. Collectively, the present studies suggest that AZA, TSA and TSA +AZA promote cell proliferation and osteogenic differentiation in BMSCs, and these effects are potentially achieved via upregulationof WNT5A/WNT7A/b-catenin signaling.

    • Protein profiling of SH-SY5Y neuroblastoma cells: The effect of rhein

      ZUZANA COCKOVA HANA UJCIKOVA PETR TELENSKY JIRI NOVOTNY

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      4,5-Dihydroxyanthraquinone-2-carboxylic acid (Rhein) has been shown to have various physiological and pharmacologicalproperties including anticancer activity and modulatory effects on bioenergetics. In this study, we explored the impact ofrhein on protein profiling of undifferentiated (UC) and differentiated (DC) SH-SY5Y cells. Besides that, the cellularmorphology and expression of differentiation markers were investigated to determine the effect of rhein on retinoic acidinducedneuronal cell differentiation. Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry we evaluated the changes in the proteome of both UC and DC SH-SY5Y cellsafter 24 h treatment with rhein. Validation of selected differentially expressed proteins and the assessment of neuronaldifferentiation markers were performed by western blotting. Proteomic analysis revealed significant changes in theabundance of 15 proteins linked to specific cellular processes such as cytoskeleton structure and regulation, mitochondrialfunction, energy metabolism, protein synthesis and neuronal plasticity. We also observed that the addition of rhein to thecultured cells during differentiation resulted in a significantly reduced neurite outgrowth and decreased expression ofneuronal markers. These results indicate that rhein may strongly interfere with the differentiation process of SH-SY5Yneuroblastoma cells and is capable of inducing marked proteomic changes in these cells.

    • Life cycle assessment of Chlorella species producing biodiesel and remediating wastewater

      PRACHI NAWKARKAR AMIT KUMAR SINGH MALIK ZAINUL ABDIN SHASHI KUMAR

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      Constantly rising energy demands, finite fossil fuel reserves and deteriorating environmental conditions have invokedworldwide interest to explore the sustainable sources of renewable biofuels. Locally adapted photosynthetic oleaginousmicroalgae with rapid growth on variable temperatures could be an ideal way for bioremediating the wastewater (WW) whileproducing the feedstock for biodiesel. To test this notion, an unknown strain was isolated from a sewage fed lake (Neela-Hauz).It was discerned as Chlorella sorokiniana-I using the 16S rDNA and 18S rDNA barcodes. The culture conditions such as pH,illumination, different temperature ranges and growth medium were cohesively optimized prior to the assessment of C.sorokiniana-I’s efficacy to remediate the WW and biodiesel production. The strain has thrived well up to 40 deg C when continuouslygrown for 15 days. The highest lipid accumulation and biomass productivity were recorded in 100%WW. Fatty acidmethyl ester (FAME) content was observed to be more than twice in WW (47%), compared to control synthetic media, TAP(20%) and BG11 (10%), which indicate the importance of this new isolate for producing economically viable biodiesel.Moreover, it is highly efficient in removing the total nitrogen (77%), total phosphorous (81%), iron (67%) and calcium (42%)from the WW. The quality of WW was considerably improved by reducing the overall chemical oxygen demand (48%),biological oxygen demand (47%) and alkalinity (15%). Thus, C. sorokiniana-I could be an ideal alga for the tropical countriesin the remediation of WW while producing feedstock for biodiesel in a cost-effective manner.

    • Effect of ions and inhibitors on the catalytic activity and structural stability of S. aureus enolase

      VIJAY HEMMADI AVIJIT DAS OM PRAKASH CHOUHAN SUMIT BISWAS MALABIKA BISWAS

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      The glycolytic enzyme enolase of Staphylococcus aureus is a highly conserved enzyme which binds to human plasminogenthereby aiding the infection process. The cloning, overexpression and purification of S. aureus enolase as well as the effectof various metals upon the catalytic activity and structural stability of the enzyme have been reported. The recombinantenzyme (rSaeno) has been purified to homogeneity in abundant amounts (60 mg/L of culture) and the kinetic parameters(Km = 0.23 ± 0.013 9 10-3 M; Vmax = 90.98 ± 0.00052 U/mg) and the optimum pH were calculated. This communicationfurther reports that increasing concentrations of Na? ions inhibit the enzyme while increasing concentrations of K?ions were stimulatory. In case of divalent cations, it was found that Mg2? stimulates the activity of rSaeno while the rest ofthe divalent cations (Zn2+, Mn2+, Fe2+, Cu2+, Ni2+ and Ca2+) lead to a dose-dependent loss in the activity with a total lossof activity in the presence of Hg2+ and Cr2+. The circular dichroism data indicate that other than Hg2+, Ni2+ and to acertain extent Cu2+, none of the other ions destabilized rSaeno. The inhibitory roles of fluorides, as well as neurotoxiccompounds upon the catalytic activity of rSaeno, have also been studied. Conformational changes in rSaeno (induced byions) were studied using partial trypsin digestion.

    • The inner workings of intracellular heterotypic and homotypic membrane fusion mechanisms

      MARIEL DELGADO CRUZ KYOUNGTAE KIM

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      Intracellular trafficking is a field that has been intensively studied for years and yet there remains much to be learned. Part ofthe reason that there is so much obscurity remaining in this field is due to all the pathways and the stages that define cellulartrafficking. One of the major steps in cellular trafficking is fusion. Fusion is defined as the terminal step that occurs when acargo-laden vesicle arrives at the proper destination. There are two types of fusion within a cell: homotypic and heterotypicfusion. Homotypic fusion occurs when the two membranes merging together are of the same type such as vacuole tovacuole fusion. Heterotypic fusion occurs when the two membranes at play are of different types such as when anendosomal membrane fuses with a Golgi membrane. In this review, we will focus on all the protein components – Rabs,Golgins, Multisubunit tethers, GTPases, protein phosphatases and SNAREs – that have been known to function in both ofthese types of fusion. We hope to develop a model of how all of these constituents function together to achieve membranefusion. Membrane fusion is a biological process absolutely necessary for proper intracellular trafficking. Due to the degreeof importance multiple proteins are required for it to be properly carried through. Whether we are talking about heterotypicor homotypic fusion, any defects in the fusion machinery can result in disease states such as Parkinson’s and Alzheimer’sdisease. Although much research has significantly expanded our knowledge of fusion, there is still much more to belearned.

    • miR-183-5p enhances the radioresistance of colorectal cancer by directly targeting ATG5

      SHENG ZHENG YONG-FU ZHONG DE-MING TAN YUE XU HUAI-XIANG CHEN DAN WANG

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      Radioresistance is a material obstacle for effective treatment of colorectal cancer (CRC). Thus, the discovery of a novelbiomarker for determining the CRC radiosensitivity is necessary. Recent studies have confirmed that miR-183-3p regulatescell phenotypes and tumor growth in various cancers. However, the role and mechanism of this micro-ribonucleic acid inCRC radiosensitivity remains unclear. Here, the abundances of miR-183-5p and ATG5 mRNAwere detected by a real-timequantitative reverse transcription polymerase chain reaction. Kaplan–Meier survival analysis was carried out to explore thecorrelation between miR-183-5p and patient prognosis. Cell viability was evaluated by the MTT assay. Survival fractionanalysis through colony formation was performed to assess the cell radiation response. Bioinformatic, luciferase andwestern blot assays were employed to verify the targeted interaction between miR-183-5p and ATG5. The results showedthat an elevated abundance of miR-183-5p and a reduced ATG5 level in CRC were associated with the poor prognosis. Theknockdown of miR-183-5p enhanced the sensitivity of CRC cells to radiation, inflected by the decreased cell viability andsurvival fraction. Mechanically, ATG5 was targeted by miR-183-5p. The addition of ATG5 conferred the radiosensitivity ofthe CRC cells, which was revered by miR-183-5p restoration. Furthermore, miR-183-5p knockdown hindered the tumorgrowth by repressing ATG5 in vivo after radiation treatment. In summary, the output data indicated that miR-183-5pheightened the radiation response of the CRC cells by targeting ATG5, promising a novel therapeutic target for CRCpatients with radioresistance.

    • PET imaging study of brown adipose tissue (BAT) activity in mice devoid of receptor for advanced glycation end products (RAGE)

      YU-SHIN DING NOEEN MALIK SEBASTIAN MENDOZA DANIEL TUCHMAN CARMEN HURTADO DEL POZO RAQUEL LOPEZ DIEZ ANN-MARIE SCHMIDT

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      Brown adipose tissue (BAT) is responsible for adaptive thermogenesis. We previously showed that genetic deficiency ofreceptor for advanced glycation end products (RAGE) prevented the effects of high-fat diet (HFD). This study was tocompare BAT activity in RAGE knock out (Ager-/-, RKO) and wild-type (WT) mice after treated with HFD or LFD.

      [18F]FDG PET-CT imaging under identical cold-stimulated conditions and mean standard uptake values (SUVmean), ratio ofSUViBAT/SUVmuscle (SUVR, muscle as the reference region) and %ID/g were used for BAT quantification. The resultsshowed that [18F]FDG uptake (e.g., SUVR) in WT-HFD mice was significantly reduced (three-fold) as compared to that inWT-LFD (1.40 ± 0.07 and 4.03 ± 0.38; P = 0.004). In contrast, BAT activity in RKO mice was not significantly affectedby HFD, with SUVRRKO-LFD: 2.14 ± 0.10 and SUVRRKO-LFD: 1.52 ± 0.13 (P = 0.3). The uptake in WT-LFD was almostdouble of that in RKO-LFD (P = 0.004); however, there was no significant difference between RKO-HFD and WT-HFDmice (P = 0.3). These results, corroborating our previous findings on the measurement of mRNA transcripts for UCP1 inthe BAT, suggest that RAGE may contribute to altered energy expenditure and provide a protective effect against HFD byAger deletion (Ager -/-).

    • PEGylated Lipova E120 liposomes loaded with celecoxib: in-vitro characterization and enhanced in-vivo anti-inflammatory effects in rat models

      VIVEK DAVE ASHISH GUPTA PRIYANKA SINGH KAJAL TAK SWAPNIL SHARMA

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      The goal of the current investigation was to prepare PEGylated Lipova E120 liposomes loaded with celecoxib for theeffective treatment of rheumatoid arthritis (RA). PEGylated liposomes were prepared and were characterized using techniquessuch as particle size distribution, polydispersity index (PDI), zeta potential, encapsulation efficiency and in-vitrorelease, in-vivo and stability studies. The morphological study was characterized by scanning electron microscopy andtransmission electron microscopy. To determine the interaction between drug and polymer Fourier transform infrared,Raman, thermogravimetric analysis and differential scanning calorimetry studies were performed. Results show that formulationF6 was optimized with a particle size of 92.12 ± 1.7 nm, a PDI of 0.278 ± 0.22, a zeta potential of

      - 40.8 ± 1.7 mV with a maximum encapsulation of 96.6 ± 0.05% of drug in the PEGylated liposomes. The optimizedformulation shows a maximum release of drug i.e. 94.45 ± 1.13% in 72 h. Tail immersion assay shows that the optimizedformulation F6 significantly increases the reaction time and carrageenan-induced assay shows that the optimized formulationinhibits the increase in paw edema thus providing a pain relief treatment in RA. These results suggest that thePEGylated liposomes provide a sustained release of celecoxib and helps in effective treatment of RA.

    • Association of BDNF rs6265 and MC4R rs17782313 with metabolic syndrome in Pakistanis

      SOBIA RANA AYESHA SULTANA ADIL ANWAR BHATTI

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      The current case–control study sought the association of BDNF rs6265 and MC4R rs17782313 with metabolic syndrome(MetS), MetS components and other related metabolic parameters in a sample of Pakistani subjects. Fasting high-densitylipoprotein cholesterol (HDL-C) and homeostatic model assessment of insulin sensitivity showed a significantly lowermean whereas body mass index (BMI), waist circumference, systolic blood pressure (SBP), diastolic blood pressure (DBP),fasting blood glucose, insulin, total cholesterol (TC), low-density lipoprotein cholesterol, very-low-density lipoproteincholesterol, triglycerides (TG), cholesterol to HDL-C ratio, TG to HDL-C ratio, homeostatic model assessment of insulinresistance, visceral adiposity index, lipid accumulation product and the product of TG and glucose showed a significantlyhigher mean in the presence of MetS. Reduced HDL-C appeared as the most frequent and hypertriglyceridemia as the leastfrequent component of MetS whereas clustering of reduced HDL-C + abdominal obesity (AO) + hyperglycemia appearedas the most prevalent combination of MetS components. Moreover, BDNF rs6265 showed BMI and gender independentassociation with increased risk of MetS in Pakistani individuals whereas MC4R rs17782313 showed BMI and genderdependent association with increased risk of MetS in Pakistani females. In addition, BDNF rs6265 and MC4R rs17782313showed gender-dependent associations with decreased risk of having low HDL-C in males and increased risk of havingabdominal obesity in females, respectively. However, no association was observed for metabolic variables other thancomponents of MetS across genotypes of both BDNF rs6265 and MC4R rs17782313.

    • Calycosin down-regulates c-Met to suppress development of glioblastomas

      XIAOHU NIE YUE ZHOU XIAOBING LI JIE XU XUYAN PAN RUI YIN BIN LU

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      The antitumor effect of calycosin has been widely studied, but the targets of calycosin against glioblastomas are stillunclear. In this study we focused on revealing c-Met as a potential target of calycosin suppressing glioblastomas. In thisstudy, suppressed-cell proliferation and cell invasion together with induced-cell apoptosis appeared in calycosin-treatedU251 and U87 cells. Under treatment of calycosin, the mRNA expression levels of Dtk, c-Met, Lyn and PYK2 wereobserved in U87 cells. Meanwhile a western blot assay showed that c-Met together with matrix metalloproteinases-9(MMP9) and phosphorylation of the serine/threonine kinase AKT (p-AKT) was significantly down-regulated by calycosin.Furthermore, overexpressed c-Met in U87 enhanced the expression level of MMP9 and p-AKT and also improved cellinvasion. Additionally, the expression levels of c-Met, MMP9 and p-AKT were inhibited by calycosin in c-Met overexpressedcells. However, an AKT inhibitor (LY294002) only effected on MMP9 and p-AKT, not on c-Met. These datacollectively indicated that calycosin possibility targeting on c-Met and exert an anti-tumor role via MMP9 and AKT.

    • Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus

      SAWAR KHAN XIAOCHAO ZHAO YINI HOU CHUNXIU YUAN YUMEI LI XIAOPING LUO JIANZHI LIU XINGANG FENG

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      The parasitic nematode Haemonchus contortus is one of the world’s most important parasites of small ruminants that causessignificant economic losses to the livestock sector. The population structure and selection in its various strains are poorlyunderstood. No study so far compared its different populations using genome-wide data. Here, we focused on differentgeographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK andAustralia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure andselection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, andidentified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB,82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (p =0.0092–0.0133) within each strain, and a significant differentiation level (average Fst = 0.34264) among them. Chinesepopulations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HBshowed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) privateselective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selectivesweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing canbe used to assess the signature of selection in H. contortus.

    • Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

      REKHA KANDASWAMY MOHAN KUMAR RAMASAMY RAMESHTHANGAM PALANIVEL USHA BALASUNDARAM

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      Pseudomonas putida is widely used as a biocontrol agent, however, mechanisms by which it initiates the plants’ defenseresponse remains obscure. To gain an insight into the molecular changes that occur in plants upon plant growth-promotingrhizobacteria colonization, root transcriptome analysis by using a microarray was performed in rice using P. putida RRF3 (arice rhizosphere isolate). Data analysis revealed a differential regulation of 61 transcripts (48 h post-treatment), of which,majority corresponded to defense response, cell wall modification and secondary metabolism. Seven genes encodingsalicylic acid (SA) responsive pathogenesis-related proteins were up-regulated significantly (fold change ranges from 1 to4), which suggests that RRF3 has a profound impact on a SA-mediated defense signaling mechanism in rice. Investigationsperformed at later stages of RRF3 colonization by real-time polymerase chain reaction and high-performance liquidchromatography (HPLC) analysis confirmed the above results, demonstrating RRF3 as a potent biocontrol agent. Further,the impact of RRF3 colonization on root exudation, in particular, exudation of SA was investigated by HPLC. However,analysis revealed RRF3 to have a negative impact on root exudation of SA. Overall, this study shows that P. putida RRF3immunizes the rice plants by re-organizing the root transcriptome to stimulate plant defense responses (‘priming’), andsimultaneously protects itself from the primed plants by altering the rhizosphere chemical constituents.

    • Analysis of chickpea gene co-expression networks and pathways during heavy metal stress

      BIRENDRA SINGH YADAV SWATI SINGH SAMEER SRIVASTAVA ASHUTOSH MANI

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      Crop productivity and yield are adversely affected by abiotic and biotic stresses. Therefore, finding out the genesresponsible for stress tolerance is a significant stride towards crop improvement. A gene co-expression network is apowerful tool to detect the most connected genes during heavy metal (HM) stress in plants. The most connected genes maybe responsible for HM tolerance by altering the different metabolic pathways during the biotic and abiotic stress. In thesame line we have performed the GSE86807 microarray analysis of chickpea during exposure to chromium, cadmium andarsenic and analyzed the data. Common differentially expressed genes (DEGs) during exposure to chromium, cadmium andarsenic were identified and a co-expression network study was carried out. Hub and bottleneck genes were explored on thebasis of degree and betweenness centrality, respectively. A gene set enrichment analysis study revealed that genes likehaloacid dehydrogenase, cinnamoyl CoA reductase, F-box protein, GDSL esterase lipase, cellulose synthase, b-glucosidase13 and isoflavone hydroxylase are significantly enriched and regulate the different pathways like riboflavin metabolism,phenyl propanoid biosynthesis, amino acid biosynthesis, isoflavonoid biosynthesis and indole alkaloid biosynthesis.

    • Does cartilageER-alpha overexpression correlate with osteoarthritic chondrosenescence? Indications from Labisia pumila OA mitigation

      IFFAH NADHIRA MADZUKI SENG FONG LAU NOR AIJRATUL ASIKIN MOHAMAD SHALAN NUR ILIYANI MOHD ISHAK SUHAILA MOHAMED

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      Chondrosenescence (chondrocyte senescence) and subchondral bone deterioration in osteoarthritic rats were analyzed aftertreatment with the estrogenic herb Labisia pumila (LP) or diclofenac. Osteoarthritis (OA) was induced in bilaterallyovariectomized (OVX) rats by injecting mono-iodoacetate into the right knee joints. Rats were grouped (n = 8) into nontreatedOVX?OA control, OVX?OA ? diclofenac (5 mg/kg) (positive control), OVX?OA ? LP leaf extract (150 and300 mg/kg) and healthy sham control. After 8 weeks’ treatment, their conditions were evaluated via serum biomarkers,knee joint histology, bone histomorphometry, protein and mRNA expressions. The LP significantly reduced cartilageerosion, femur bone surface alteration, bone loss and porosity and increased trabecular bone thickness better than diclofenacand the non-treated OA. The cartilage catabolic markers’ (matrix metalloproteinase (MMP)-13, RUNX2, COL10a, ERa,CASP3 and HIF-2a) mRNA expressions were down-regulated and serum bone formation marker, PINP, was increased byLP in a dose-dependent manner. The LP (containing myricetin and gallic acid) showed protection against chondrosenescence,chondrocyte death, hypoxia-induced cartilage catabolism and subchondral bone deterioration. The bone and cartilageprotective effects were by suppressing proteases (collagen break-down), bone resorption and upregulating subchondralbone restoration. The cartilage ERa over-expression showed a strong positive correlation with MMP-13, COL10a1, histological,micro-computed tomography evidence for cartilage degradation and chondrosenescence.

    • Down-regulation effects of IFN-alpha on p11, 5-htr1b and 5-HTR4 protein levels were affected by NH4CL or MG132 treatment in SH-sy5y cells

      JIQIANG GUO HUAXIA DING ZHUANGWEI LV JUNNA JIAO HUI WANG YANHONG JI

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      In previous studies, we found interferon-a (IFN-a) could reduce protein levels of p11, 5-hydroxytryptamine receptor 1b(5-HT1b) and 5-hydroxytryptamine receptor 4 (5-HT4), but does not influence their messenger RNA levels in SH-sy5ycells. Thus, we investigated the post-transcriptional modulation of these molecules by IFN-a. SH-sy5y cells were treatedwith IFN-a, NH4Cl or MG132 alone or in combination, and then the protein levels of p11, 5-HT1b and 5-HT4 wereanalyzed by western blots. The regulatory effects of p11 on 5-HT1b and 5-HT4 were also determined in p11 knock-downcells. NH4Cl but not MG132 could reverse the protein level of p11 in IFN-a-treated SH-sy5y cells. MG132 could recoverthe protein levels of 5-HT1b and 5-HT4 in p11 knock-down cells. The down-regulation effects of IFN-a on p11, 5-HT1band 5-HT4 were associated with the lysosome and ubiquitin–proteasome-mediated pathways. p11 was identified as a potentregulator to modulate the ubiquitination of 5-HT1b and 5-HT4. Therefore, it could be potential target therapies in IFN-a induceddepression.

    • miR-425-5p suppresses tumorigenesis and DDP resistance in human-prostate cancer by targeting GSK3 β and inactivating the Wnt/β-catenin signaling pathway

      SHENG LIU QIN WANG YIN LIU ZONG-YU XIA

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      Prostate cancer (PCa) represents the most frequently diagnosed cancer in men. Cisplatin, also known as cis-diamminedichloroplatinum(DDP), is a standard chemotherapeutic agent used to treat PCa, and DDP resistance remains one important obstacle inDDP-based chemotherapy. In our research, we found miR-425-5p was down-regulated in PCa and even lower in DDP-resistantPCa determined by quantitative polymerase chain reaction; in contrast, GSK3b mRNA expression was upregulated in PCa andeven higher in DDP-resistant PCa. Moreover, there was a modest but significant inverse correlation between the expression ofGSK3bmRNA and miR-425-5p. Functional experiments showed that miR-425-5p mimic inhibited DDP resistance as evidencedby a promoted apoptosis rate (flow cytometry) and suppressed cell viability (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide assay) and expressions of MDR1 andMRP1 (western blotting) in DU145/DDP and PC3/DDP cells. Luciferase reporterassay and RNA immunoprecipitation identifiedGSK3b was a potential target of miR-425-5p. The effect ofmiR-425-5pmimic onDDP resistance was partially reversed by pcDNA-GSK3b. Mechanically, miR-425-5p mimic reduced expression of b-catenin,cyclin D1 and C-myc, which was further blocked when GSK3b overexpressed. In vivo experiments, recovery of GSK3bprevented xenograft tumor growth and DDP resistance in the presence of miR-425-5p mimic. To sum up, miR-425-5p upregulationmight sensitize human PCa to DDP by targeting GSK3b and inactivating the Wnt/b-catenin signaling pathway.

    • Correction to: Development of typological classification and its relationship to microdifferentiation in ethnic India

      K C MALHOTRA T S VASULU

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      In the July 2019 issue of the Journal of Biosciences, in the article titled ‘‘Development of typological classification and itsrelationship to microdifferentiation in ethnic India’’ by K C Malhotra and T S Vasulu (DOI: 10.1007/s12038-019-9880-8;volume 44, article 64), the affiliations of T S Vasulu have been wrongly mentioned as:3Formerly Associate Professor of Anthropology & Human Genetics, Indian Statistical Institute, Kolkata, India4Present Address: 25, RM Banerjee Road, Bon Hoogly, Baranagar, Kolkata 700108, IndiaThe correct affiliations should read as:3Retired Professor of Anthropology & Human Genetics, Indian Statistical Institute, Kolkata, India4Present Address: 5, RM Banerjee Road, Bon Hoogly, Baranagar, Kolkata 700108, India

    • Machine-learning techniques for the prediction of protein–protein interactions

      DEBASREE SARKAR SUDIPTO SAHA

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      Protein–protein interactions (PPIs) are important for the study of protein functions and pathways involved in differentbiological processes, as well as for understanding the cause and progression of diseases. Several high-throughput experimentaltechniques have been employed for the identification of PPIs in a few model organisms, but still, there is a huge gapin identifying all possible binary PPIs in an organism. Therefore, PPI prediction using machine-learning algorithms hasbeen used in conjunction with experimental methods for discovery of novel protein interactions. The two most popularsupervised machine-learning techniques used in the prediction of PPIs are support vector machines and random forestclassifiers. Bayesian-probabilistic inference has also been used but mainly for the scoring of high-throughput PPI datasetconfidence measures. Recently, deep-learning algorithms have been used for sequence-based prediction of PPIs. Severalclustering methods such as hierarchical and k-means are useful as unsupervised machine-learning algorithms for theprediction of interacting protein pairs without explicit data labelling. In summary, machine-learning techniques have beenwidely used for the prediction of PPIs thus allowing experimental researchers to study cellular PPI networks.

    • Biosensor design using an electroactive label-based aptamer to detect bisphenol A in serum samples

      MARYAM NAZARI SOHEILA KASHANIAN RONAK RAFIPOUR KOBRA OMIDFAR

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      A new and simple procedure was applied to detect bisphenol A (BPA) based on a BPA aptamer and its complementarystrand (Comp. Str.). An electrode was modified with a mixture of carboxylated multiwalled carbon nanotubes and chitosan.The Comp. Str. was immobilized on a modified-glassy carbon electrode (GCE) surface via covalent binding. After theincubation of the aptamer with the electrode surface, it could interact with the Comp. Str. In the presence of BPA, itsaptamer will interact with the analyte, resulting in some changes in the configuration and leading to separation from theelectrode surface. Due to the attached ferrocene (Fc) group on the 5' head of the aptamer, the redox current of Fc hasreduced. This aptasensor can sense the level of BPA in the linear range of 0.2–2 nM, with a limit of detection of 0.38 nMand a sensitivity of 24.51 lA/nM. The proposed aptasensor showed great reliability and selectivity. The acceptable selectivityis due to the specificity of BPA binding to its aptamer. The serum sample was used as a real sample; the aptasensorwas able to effectively recover the spiked BPA amounts. It can on-site monitor the BPA in serum samples withacceptable recoveries.

    • Deconstructing age reprogramming

      PRIM B SINGH PETR P LAKTIONOV ANDREW G NEWMAN

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      It has been proposed that age reprogramming enables old cells to be rejuvenated without passage through an embryonicstage (Singh and Zacouto in J. Biosci. 35 315–319, 2010). As such, age reprogramming stands apart from the inducedpluripotent stem (iPS) and nuclear transfer-embryonic stem (NT-ES) cell therapies where histo-compatible cells are producedonly after passage through an embryonic stage. It avoids many of the disadvantages associated with iPS and NT-EScell therapies. Experimental evidence in support of age reprogramming is burgeoning. Here, we discuss possible newapproaches to enhance age reprogramming, which will have considerable benefits for regenerative therapies.

    • Genetic relatedness and its causal role in the evolution of insect societies

      TUOMAS K PERNU HEIKKI HELANTERA¨

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      The role of genetic relatedness in social evolution has recently come under critical attention. These arguments are herecritically analyzed, both theoretically and empirically. It is argued that when the conceptual structure of the theory of naturalselection is carefully taken into account, genetic relatedness can be seen to play an indispensable role in the evolution of bothfacultative and advanced eusociality. Although reviewing the empirical evidence concerning the evolution of eusocialityreveals that relatedness does not play a role in the initial appearance of helper phenotypes, this follows simply from the factthat natural selection – of which relatedness is a necessary component – does not play a causal role in the origin of any traits.Further, separating two logically distinct elements of causal explanation – necessity and sufficiency – explains why the debatelingers on: although relatedness plays a necessary role in the evolution of helping and advanced eusociality, relatedness aloneis not sufficient for their appearance. Therefore, if the relatedness variable in a given data set is held at a uniformly high value,then it indeed may turn out that other factors occupy a more prominent role. However, this does not change the fact that highrelatedness functions as a necessary background condition for the evolution of advanced eusociality.

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