• Volume 41, Issue 3

September 2016,   pages  325-561

• What history tells us XLI. Ubiquitin and proteolysis

• Desiccation stress induces developmental heterochrony in Drosophila melanogaster

Stressful environments are known to perturb developmental patterns in insects. In the purview of desiccation as astressor, relatively little is known about the developmental consequences linked with desiccation tolerance. In thisstudy, we have particularly focused on the exploration of the temporal profile of postembryonic development inresponse to desiccation exposure in Drosophila melanogaster and the associated trade-offs. We document a correlationbetween variations in 20-hydroxyecdysone levels and the altered timing of metamorphic events during the lifecycle. Following desiccation, we observed an extension in the larval longevity whereas the duration of the pupal andadult stages was significantly shortened. Alternately, feeding of 20-hydroxyecdysone apparently led to the restorationof the normal temporal pattern of development in the desiccated group. In spite of the desiccation-responsiveheterochronic shifts in development, the overall lifespan post recovery remained almost unaltered among thedesiccated and undesiccated groups suggesting plasticity in developmental control. This observation reminisces

‘canalization-like’ phenomenon that buffers alterations in the overall lifespan. We thus identified a desiccation responsiveperiod in the lifespan of D. melanogaster during which variations in ecdysone levels are capable to alter thetemporal course of development.

• Mossambicus tilapia (Oreochromis mossambicus) collected from water bodies impacted by urban waste carries extended-spectrum beta-lactamases and integron-bearing gut bacteria

Oreochromis mossambicus (Peters 1852) (Tilapia) is one of the most consumed fish globally. Tilapia thrives well inenvironments polluted by urban waste, which invariably contain antibiotic-resistant bacteria and antibiotic resistance genes(ARGs). Thus, Tilapia surviving in such polluted environments may serve as a potential source for dissemination of ARGs.To investigate this, we isolated bacterial strains from gut of Tilapia found in polluted rivers and lakes near Pune, India, andstudied the prevalence of resistance genes bymolecularmethods. A total of 91 bacterial strains were obtained, which includefish pathogens and human pathogens such as Aeromonas hydrophila, Klebsiella pneumoniae, E. coli, Serratia marcescens,Enterobacter spp. and Shigella spp. Overall the prevalence of class 1 integrons, class 2 integrons, extended-spectrum betalactamases(ESBLs) bla_{CTX-M}, bla_{SHV} and aac(6')-Ib-cr gene was 38%, 24%, 38%, 31% and 31% respectively. Forty-twopercent of the Enterobacteriaceae strains carried bla_{CTX-M} gene, which is a common ESBL gene in clinics. The studydemonstrates that tilapia found in the polluted waters can serve as reservoirs and an alternative route for human exposure toclinically important ARG-carrying bacteria. The consumption and handling of these fish may pose a potential health risk.

• Bacillus subtilis Hfq: A role in chemotaxis and motility

Hfq is a global post-transcriptional regulator that modulates the translation and stability of target mRNAs and therebyregulates pleiotropic functions, such as growth, stress, virulence and motility, in many Gram-negative bacteria.However, comparatively little is known about the regulation and function(s) of Hfq in Gram-positive bacteria.Recently, in Bacillus subtilis, a role for Hfq in stationary phase survival has been suggested, although the possibilityof Hfq having an additional role(s) cannot be ruled out. In this study we show that an ortholog of Hfq in B. subtilis isregulated by the stress sigma factor, σB, in addition to the stationary phase sigma factor, σH. We further demonstratethat Hfq positively regulates the expression of flagellum and chemotaxis genes (fla/che) that control chemotaxis andmotility, thus assigning a new function for Hfq in B. subtilis.

• Diazinon degradation by a novel strain Ralstonia sp. DI-3 and X-ray crystal structure determination of the metabolite of diazinon

Diazinon is a widely used organophosphorus insecticide often detected in the environment. A highly effectivediazinon-degrading Ralstonia sp. strain DI-3 was isolated from agricultural soil. Strain DI-3 can utilize dimethoateas its sole carbon source for growth and degrade an initial concentration of 100 mg·L^{−1} diazinon to non-detectablelevels within 60 h in liquid culture. A small amount of second carbon source as co-substrate could slightly enhance thebiodegradation of diazinon. In addition, a less toxic metabolic intermediate formed during the degradation of diazinonmediated by strain DI-3 was purified using thin-layer chromatography (TLC) and identified based on single-crystal Xraydiffraction analysis, allowing a degradation pathway for diazinon by pure culture to be proposed. Finally, this isthe first providing authentic evidence to describe the metabolite.

• Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO_{2} for environmental remediation

Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridiumljungdahlii utilize electric currents as an electron source from the cathode to reduce CO_{2} to extracellular, multicarbon,exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly fromCO_{2} is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion ofCO_{2} implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acidand hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In ourstudy, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at −400 mV by aDC power supply at 37°C, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment ofbio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in lesstime. The main aim of the research was to investigate the impact of low-cost substrate CO_{2}, and the longercathode recovery range was due to bacterial reduction of CO_{2} to multicarbon chemical commodities withelectrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energyefficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acidand hexanol being in excess of 80% proved that BES was a remarkable technology.

• Indomethacin treatment reduces microglia activation and increases numbers of neuroblasts in the subventricular zone and ischaemic striatum after focal ischaemia

Neuroblasts from the subventricular zone (SVZ) migrate to striatum following stroke, but most of them die inthe ischaemic milieu and this can be related to exacerbated microglial activation. Here, we explored theeffects of the non-steroidal anti-inflammatory indomethacin on microglial activation, neuronal preservation andneuroblast migration following experimental striatal stroke in adult rats. Animals were submitted toendothelin-1 (ET-1)-induced focal striatal ischaemia and were treated with indomethacin or sterile saline(i.p.) for 7 days, being perfused after 8 or 14 days. Immunohistochemistry was performed to assess neuronalloss (anti-NeuN), microglial activation (anti-Iba1, ED1) and migrating neuroblasts (anti-DCX) by countingNeuN, ED1 and DCX-positive cells in the ischaemic striatum or SVZ. Indomethacin treatment reducedmicroglia activation and the number of ED1^{+} cells in both 8 and 14 days post injury as compared withcontrols. There was an increase in the number of DCX^{+} cells in both SVZ and striatum at the same survivaltimes. Moreover, there was a decrease in the number of NeuN^{+} cells in indomethacin-treated animals ascompared with the control group at 8 days but not after 14 days post injury. Our results suggest thatindomethacin treatment modulates microglia activation, contributing to increased neuroblast proliferation inthe SVZ and migration to the ischaemic striatum following stroke.

• Tumour suppressive function of HUWE1 in thyroid cancer

HUWE1 (the HECT, UBA, and WWE domain-containing protein 1) is an ubiquitin E3 ligase which plays animportant role in coordinating diverse cellular processes. It has been found to be dysregulated in various cancer typeand its functions in tumorigenesis remain controversial. The potential tumour suppressive role of HUWE1 in thyroidcancer development was investigated by knocking down HUWE1 in three authentic thyroid cancer cell lines, WRO,FTC133 and BCPAP, followed by various functional assays, including cell proliferation, scratch wound healing andinvasion assays. Xenograft experiment was performed to examine in vivo tumour suppressive properties of HUWE1.Small-interfering RNA mediated knockdown of HUWE1 promoted cell proliferation, cell migration and invasion inthyroid cancer cells. Overexpression of HUWE1 conferred partial sensitivity to chemo drugs interfering with DNAreplication in these cells. Moreover, HUWE1 was found to be down-regulated in human thyroid cancer tissuescompared with matched normal thyroid tissues. In addition, overexpression of HUWE1 significantly inhibited tumourgrowth in vivo using xenograft mouse models. Mechanistic investigation revealed that HUWE1 can regulate p53protein level through its stabilization. HUWE1 functions as a tumour suppressor in thyroid cancer progression, whichmay represent a novel therapeutic target for prevention or intervention of thyroid cancer.

• Sirtuin 1 and 7 mediate resveratrol-induced recovery from hyper-anxiety in high-fructose-fed prediabetic rats

Hyperglycaemia in diabetes is either caused by reduced availability of insulin (type 1 diabetes, T1D) or insulinresistance to the cells (type 2 diabetes, T2D). In recent years, the prevalence of T2D has increased to an alarmingproportion, encompassing 95% of the total diabetic burden, probably due to economy-driven changes in lifestyle.Recent epidemiological studies show comorbid depression, anxiety and related mental illness. To explore themolecular mechanisms underlying this comorbid conditions, we used Sprague–Dawley rats on high-fructose dietfor 8 weeks to induce prediabetic condition. Rats with this metabolic syndrome also showed hyper-anxiety when theywere subjected to anxiety-related behavioural assays. Rats were administered with resveratrol, an activator of sirtuins,and metformin, a standard antidiabetic drug, simultaneously with fructose. We observed that resveratrol was moreeffective in protecting from both the metabolic (prediabetic) and affective (anxiety) disorders than metformin.Molecular studies showed that recovery was associated with the upregulation of few nuclear sirtuins that actepigenetically – Sirt 1 and 7, which were significantly attenuated in the striatum of prediabetic rats. In conclusion,our study showed that hyper-anxiety associated with prediabetic condition is ameliorated by resveratrol throughmodulation of sirtuins, which is more or less similar to metformin.

• Microstructural abnormalities of uncinate fasciculus as a function of impaired cognition in schizophrenia: A DTI study

Neuropsychological studies have reported that attention, memory, language, motor and emotion processing areimpaired in schizophrenia. It is known that schizophrenia involves structural alterations in the white matter of brainthat contribute to the pathophysiology of the disorder. Uncinate fasciculus (UNC), a bundle of white matter fibres,plays an important role in the pathology of this disorder and involved in cognitive functions such as memory, languageand emotion processing. Therefore, the present study aimed to investigate microstructural changes in UNC fibre inschizophrenia patients relative to controls and its correlation with neuropsychological scores.Diffusion tensor imaging (DTI) and Hindi version of Penn Computerised Neuropsychological Battery test wasperformed in 14 schizophrenia patients and 14 controls. DTI measures [fractional anisotropy (FA) and meandiffusivity (MD)] from UNC fibre were calculated and a comparison was made between patients and controls.Pearson’s correlation was performed between neuropsychological scores and DTI measures.Schizophrenia patientsshowed significantly reduced FA values in UNC fibre compared to controls. In schizophrenia patients, a positivecorrelation of attention, spatial memory, sensorimotor dexterity and emotion with FA was observed. These findingssuggest that microstructural changes in UNC fibre may contribute to underlying dysfunction in the cognitive functionsassociated with schizophrenia.

• Impact of the PPAR gamma-2 gene polymorphisms on the metabolic state of postmenopausal women

The relationship Pro12Ala (rs1801282) and C1431T (rs3856806) polymorphisms of PPAR gamma-2 with glucose and lipid metabolism is not clear after menopause. We investigated the impact of the Pro12Ala and C1431T silentsubstitution in the 6th exon in PPAR gamma-2 gene on nutritional and metabolic status in 271 postmenopausal women(122 lean and 149 obese). The general linear model (GLM) approach to the two-way analysis of variance (ANOVA) was used to infer the interactions between the analysed genotypes. The frequency of the Pro-T haplotype was higher in obese than in lean women ($p\lt 0.0349$). In the analysed GLM models according to obesity status, the C1431C genotypewas related to a lower glucose concentration ($\beta=-0.2103$) in lean women, and to higher folliculotropic hormone FSH levels ($\beta=0.1985$) and lower waist circumferences ($\beta=-0.1511$) in obese women. The influence of C1431C waspresent regardless of the occurrence of the Pro12Ala polymorphism. The co-existence of the C1431C and Pro12Progenotypes was related to lower values for triceps skinfold thickness compared those for the T1241/X and Ala12/X polymorphisms ($\beta=-0.1425$). The presence of C1431C decreased the differences between triceps values that weredetermined by Pro or Ala allele. In conclusion, C1431T polymorphism seems to have a more essential influence onanthropometric and biochemical parameters than is the case with Pro12Ala polymorphism.

• An angiotensin I-converting enzyme insertion/deletion polymorphism is associated with Pakistani asthmatic cases and controls

Asthma is a chronic disease due to inflammation of the airways of lungs that is clinically characterized by variablesymptoms including wheezing, coughing and shortness of breath. Angiotensin I-converting enzyme (ACE) plays a majorrole in fibrous tissue formation and is highly expressed in lungs. The main aim of this research work was to study the roleof ACE insertion/deletion (I/D) polymorphism, rs4646994, in asthma in Pakistani patients. A total of 854 subjects,including 333 asthma patients and 521 ethnically matched controls, were studied. The ACE (I/D) polymorphism wasgenotyped using polymerase chain reaction (PCR). Chi-square, Fisher’s exact and Hardy–Weinberg equilibrium testswere used to compare groups. Homozygous insertion genotype II ($p \ lt 0.0001$, $OR=3.38$) and insertion allele (I) wassignificantly more frequent in Pakistani asthmatics than in healthy controls ($p=0.0007, OR=1.40$). The ID genotype ($p \lt 0.0001$, $OR=0.43$) and the deletion allele (D) were associated with protection of disease in Pakistani patients($p=0.0007, OR=0.71$). These data suggest the involvement of ACE I/D polymorphism in asthma risk in the Pakistanipopulation. This marker may be an important indication in the molecular mechanism of asthma and can become a usefultool in risk assessment and help in designing strategy to combat disease.

• The rice OsSAG12-2 gene codes for a functional protease that negatively regulates stress-induced cell death

Senescence is the final stage of plant development. Although expression of most of the genes is suppressed duringsenescence, a set of genes referred as senescence-associated genes (SAGs) is induced. Arabidopsis thaliana SAG12(AtSAG12) is one such gene that has been mostly studied for its strict association with senescence. AtSAG12 encodes apapain-like cysteine protease, expressed predominantly in senescence-associated vacuoles. Rice genome containsmultiple AtSAG12 homologues (OsSAGs). OsSAG12-1, the closest structural homologue of AtSAG12, is a negativeregulator of developmental and stress-induced cell death. Proteolytic activity has not been established for any SAG12homologues in vitro. Here, we report that OsSAG12-2, the second structural homologue of AtSAG12 from rice, codesfor a functional proteolytic enzyme. The recombinant OsSAG12-2 protein produced in Escherichia coli undergoesautolysis to generate a functional protease. The matured OsSAG12-2 protein shows 27% trypsin-equivalent proteolyticactivity on azocasein substrate. Dark-induced senescence activates OsSAG12-2 expression. Down-regulation of

OsSAG12-2 in the transgenic artificial miRNA lines results in enhanced salt- and UV-induced cell death, even thoughit does not affect cell viability in the stress-free condition. Our results show that OsSAG12-2 codes for a functionalprotease that negatively regulates stress-induced cell death in rice.

• Identifying wrong assemblies in de novo short read primary sequence assembly contigs

With the advent of short-reads-based genome sequencing approaches, large number of organisms are being sequencedall over the world. Most of these assemblies are done using some de novo short read assemblers and other relatedapproaches. However, the contigs produced this way are prone to wrong assembly. So far, there is a conspicuousdearth of reliable tools to identify mis-assembled contigs. Mis-assemblies could result from incorrectly deleted orwrongly arranged genomic sequences. In the present work various factors related to sequence, sequencing andassembling have been assessed for their role in causing mis-assembly by using different genome sequencing data.Finally, some mis-assembly detecting tools have been evaluated for their ability to detect the wrongly assembledprimary contigs, suggesting a lot of scope for improvement in this area. The present work also proposes a simpleunsupervised learning-based novel approach to identify mis-assemblies in the contigs which was found performingreasonably well when compared to the already existing tools to report mis-assembled contigs. It was observed that theproposed methodology may work as a complementary system to the existing tools to enhance their accuracy.

• Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework

Horizontal Gene Transfer (HGT) events, initially thought to be rare in Mycobacterium tuberculosis, have recentlybeen shown to be involved in the acquisition of virulence operons in M. tuberculosis. We have developed a newpartitioning framework based HGT prediction algorithm, called Grid3M, and applied the same for the prediction ofHGTs in Mycobacteria. Validation and testing using simulated and real microbial genomes indicated better performanceof Grid3M as compared with other widely used HGT prediction methods. Specific analysis of the genesbelonging to dormancy/reactivation regulons across 14 mycobacterial genomes indicated that horizontal acquisition isspecifically restricted to important accessory proteins. The results also revealed Burkholderia species to be a probablesource of HGT genes belonging to these regulons. The current study provides a basis for similar analyses investigatingthe functional/evolutionary aspects of HGT genes in other pathogens. A database of Grid3M predicted HGTs incompletely sequenced genomes is available at https://metagenomics.atc.tcs.com/Grid3M/.

• Copper transporters and chaperones: Their function on angiogenesis and cellular signalling

Copper, although known as a micronutrient, has a pivotal role in modulating the cellular metabolism. Many studieshave reported the role of copper in angiogenesis. Copper chaperones are intracellular proteins that mediate coppertrafficking to various cell organelles. However, the role and function of copper chaperones in relation to angiogenesishas to be further explored. The intracellular copper levels when in excess are deleterious and certain mutations ofcopper chaperones have been shown to induce cell death and influence various cellular metabolisms. The study ofthese chaperones will be helpful in understanding the players in the cascade of events in angiogenesis and their role incellular metabolic pathways. In this review we have briefly listed the copper chaperones associated with angiogenicand metabolic signalling and their function.

• Therapeutic resistance and cancer recurrence mechanisms: Unfolding the story of tumour coming back

Cancer recurrence is believed to be one of the major reasons for the failure of cancer treatment strategies. Thisbiological phenomenon could arise from the incomplete eradication of tumour cells after chemo- and radiotherapy.Recent developments in the design of models reflecting cancer recurrence and in vivo imaging techniques have ledresearchers to gain a deeper and more detailed insight into the mechanisms underlying tumour relapse. Here, weprovide an overview of three important drivers of recurrence including cancer stem cells (CSCs), neosis, and phoenixrising. The survival of cancer stem cells is well recognized as one of the primary causes of therapeutic resistance inmalignant cells. CSCs have a relatively latent metabolism and show resistance to therapeutic agents through a varietyof routes. Neosis has proven to be as an important mechanism behind tumour self-proliferation after treatment whichgives rise to the expansion of tumour cells in the injured site via production of Raju cells. Phoenix rising is a prorecurrencepathway through which apoptotic cancer cells send strong signals to the neighbouring diseased cellsleading to their multiplication. The mechanisms involved in therapeutic resistance and tumour recurrence have not yetbeen fully understood and mostly remain unexplained. Without doubt, an improved understanding of the cellularmachinery contributing to recurrence will pave the way for the development of novel, sophisticated and effective antitumourtherapeutic strategies which can eradicate tumour without the threat of relapse.

• Galectin-9: From cell biology to complex disease dynamics

Galectins is a family of non-classically secreted, β-galactoside-binding proteins that has recently received considerableattention in the spatio-temporal regulation of surface ‘signal lattice’ organization, membrane dynamics, cell-adhesionand disease therapeutics. Galectin-9 is a unique member of this family, with two non-homologous carbohydraterecognition domains joined by a linker peptide sequence of variable lengths, generating isoforms with distinctproperties and functions in both physiological and pathological settings, such as during development, immunereaction, neoplastic transformations and metastasis. In this review, we summarize the latest knowledge on thestructure, receptors, cellular targets, trafficking pathways and functional properties of galectin-9 and discuss howgalectin-9-mediated signalling cascades can be exploited in cancers and immunotherapies.

• Application of aptamers in diagnostics, drug-delivery and imaging

Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity andaffinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety ofapplications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class ofbiomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. Inthis review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging.We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makesthem a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potentialdrug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs,nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable forRNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior overprotein-based binding molecules in terms of labelling and conjugation strategies.

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