Biology subjects

Singh, A. K.

Publications and source records attributed to Singh, A. K..

10 recordsLinked to original sources

bioRxiv2018

Effect of light intensity and nutritional value of food resources on flight response of adult parasitoid, Cotesia plutellae (Kurdjumov) (Hymenoptera: Braconidae)

Cotesia plutellae (Kurdjumov) (Hymenoptera: Braconidae) is the major larval parasitoid of Plutella xylostella (L) (Lepidoptera: Plutellidae), which is a serious pest of cruciferous plants throughout the world. We evaluated the influence of light intensities and feeding conditions on the vertical angle of flight in freshly emerged wasps in a cylinder having diameter 15cm and height 30cm. Light intensity was found to directly affects the flight activity. Increase in light intensity causes increase in vertical flight of the female wasps. However, Increase in light intensity did not influence the inclination of vertical flight in males. Feeding condition was also found to affect the vertical flight of the wasps. Honey odour, from below the flight chamber, arrested the flight of unfed or sucrose fed wasps. However, flight of honey fed wasps was not affected by honey odour. Male flight response was also influenced by feeding condition and light intensity but the response was not as higher as shown by females. The present study is useful for selecting suitable food prior to inundative release of parasitoid in the field at suitable time period of the day.

animal behavior and cognition↗

bioRxiv2018

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required in nuclear processes of gene expression

UPF1 is an RNA helicase that is required for efficient nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm and that it has multiple functions in the nucleus. It is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary gland and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNA transcripts, and cells depleted of UPF1 show defects in several nuclear processes essential to correct gene expression - most strikingly, the release of mRNAs from transcription sites and mRNA export from the nucleus.

cell biology↗

bioRxiv2018

Emergence of Multidrug-Resistant Uropathogens harboring ESBL, Carbapenem, Aminoglycosides and AmpC resistant genes from Northern India

Extended-spectrum {beta}-lactamase (ESBL) producing bacteria acts as a serious threat, and its co-existence with other antibiotic resistant gene makes the clinical scenario worse nowadays. Therefore in this study, we investigated the occurrence of ESBL genes coexisting with carbapenem, AmpC and aminoglycoside resistance gene in uropathogens. Out of 1516 urine samples, 454 showed significant bacteriuria with a prevalence rate of 29.94 %. Escherichia coli (n=340) were found to be the most predominant uropathogen followed by Klebsiella pneumoniae (n=92), Pseudomonas aeruginosa (n=10) and Proteus mirabilis (n=9). Among the total uropathogens, sixty-three ESBL-producers were identified which included blaCTX-M-15 (n=32), followed by blaCTX-M-15 + blaOXA-2 (n=15), blaCTX-M-15 + blaOXA-2 + blaTEM (n=6), blaOXA-2 (n=5), bla OXA-2 + bla SHV-76 (n=1), bla TEM+SHV-76 (n= 1) and bla TEM (n=1). All ESBL genes were found on plasmid incompatibility types: HI1, I1, FIA+FIB, FIA and Y and were horizontally transferable. Among 63 ESBL-producers, 59 isolates harboured carbapenem-resistant genes which included blaNDM-5 (n=48), blaNDM-5 + blaOXA-48 (n=5), blaNDM-5 + blaIMP (n=5) and blaNDM-5 + blaIMP + blaVIM (n=1). The ESBL producing uropathogens also harbored 16S rRNA methylase genes which included rmtB (n=9), rmtA (n=4), rmtC (n=1) and ArmA (n=1) followed by AmpC genes which includes CIT (n=8) and DHA-1 (n=1) genes. Imipenem and gentamicin were found to be more effective. We speculating, this is the first report showing the prevalence of multidrug-resistant uropathogens in this area demanding regular surveillance for such resistance mechanisms which will be useful for health personnel to treat ESBL infection and its co-existence with another antibiotic resistance gene.

microbiology↗

bioRxiv2018

BCG overexpressing an endogenous STING agonist provides enhanced protection against pulmonary tuberculosis

Stimulator of interferon genes (STING) has emerged as a key signaling receptor that induces proinflammatory cytokines, and small molecule STING agonists are being developed as anticancer and antiviral agents. Here we report a strategy of delivering a STING agonist from within live BCG. We generated a recombinant BCG (BCG-disA-OE) that overexpresses the endogenous mycobacterial diadenylate cyclase gene and releases high levels of the STING agonist c-di-AMP. In macrophages BCG-disA-OE elicited statistically significantly stronger TNF-, IL-6, IL-1{beta}, IRF3, and IFN-{beta} levels than BCG-WT. In a 24-week guinea pig vaccination-Mtb challenge model, BCG-disA-OE reduced lung weights, pathology scores, and Mtb CFU counts in lungs by 28% (p<0.05), 34%, and 2.0 log10 CFU units (p < 0.5) compared with BCG-WT, respectively. Overproduction of the STING agonist c-di-AMP significantly enhanced the protective efficacy of BCG against pulmonary and extrapulmonary tuberculosis. Our findings support the development of BCG-vectored STING agonists as a TB vaccine strategy.

microbiology↗

bioRxiv2018

Integrating genotype and weather variables for soybean yield prediction using deep learning

Realized performance of complex traits is dependent on both genetic and environmental factors, which can be difficult to dissect due to the requirement for multiple replications of many genotypes in diverse environmental conditions. To mediate these problems, we present a machine learning framework in soybean (Glycine max (L.) Merr.) to analyze historical performance records from Uniform Soybean Tests (UST) in North America, with an aim to dissect and predict genotype response in multiple envrionments leveraging pedigree and genomic relatedness measures along with weekly weather parameters. The ML framework of Long Short Term Memory - Recurrent Neural Networks works by isolating key weather events and genetic interactions which affect yield, seed oil, seed protein and maturity enabling prediction of genotypic responses in unseen environments. This approach presents an exciting avenue for genotype x environment studies and enables prediction based systems. Our approaches can be applied in plant breeding programs with multi-environment and multi-genotype data, to identify superior genotypes through selection for commercial release as well as for determining ideal locations for efficient performance testing.

bioinformatics↗

bioRxiv2018

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

Water quality of a region directly corroborates with the health index of people. People in the Himalayan hills mainly depend upon the spring water for potability. To determine the microbial ecology of the spring waters of Sikkim, the variable region of 16S rRNA has been sequenced using Illumina MiSeq. Phylum wise annotation showed the East and North district are mostly dominated by Proteobacteria (41% and 35.80%), whereas West and South district is dominated by Planctomycetes (38.46%) and Verrucomicrobia (33%). The consistent dominance phyla in the all the four districts were Bacteriodetes (34-24%) which was highest dominancy in North district and lowest in wets district. Genus wise distribution showed the abundance of Brevifolis, Flavobacterium, Verrucomicrobia subdivision3, Emticica, Cytophaga, Prosthecobacter, Planctomycetes, Varivorax, Arcicella, Isosphera, Sedimunibacterium etc. The East district showed highest dominancy of genus Emticicia whereas Planctomycetes in the West district. The North district was mainly dominated by genus Arcicella and Brevifollis in the South district. North on the antonymous showed totally different sets of microbial diversity. North district showed an abundance of Arcicella, Planctomycetes, Schlerensia and Azohydromonas. The heat map produced by Bray Curtis distance method produced three clusters which showed the close relationship between West and East district microbiome that further related to South district. The sample of North district formed out group that showed different community structure from other three districts. The principle component analysis was showed that the east and South district samples are closely related and distantly correlated to the west Sikkim, but the North district showed completely different microbial community. The canonical correspondence analysis showed correlation between bacterial diversity and hydrochemistry and it was found that the bacterial diversity was influenced by the concentration of different metallic ions like sodium, calcium, barium and iron. This is a first report from the Eastern Himalayan region of India and it largely enhances our knowledge about the microbial structure of potable spring water of Eastern Himalayan. This study is useful for Government of India as well as the state government to adopt the different strategic treatment procedures to improve the quality of water that is supplied to the community resides in the Himalayan regions and solely dependent on this untreated spring water.

microbiology↗

bioRxiv2018

Single-nucleotide and Copy-number variance related to severity of Hypospadias

The genetic association of Hypospadias-risk studies has been conducted in Caucasians, Chinese-Han populations and few in Indian populations. Although no comprehensive approach has been followed to assess genetic involvement in the severity of the disorder. The study evaluated to establish the correlation between genotyped SNPs/CNVs and Hypospadias-severity by an association in a total 30 SNPs in genes related to sex hormone-biosynthesis and metabolism; embryonic-development and Phospholipase-D-signalling pathways on 138 surgery-confirmed hypospadias-cases from North-India (84 Penile and 28 cases of Penoscrotal-Hypospadias compared against 31 cases of Glanular+Coronal), and analyzed and identified copy number variants (CNVs) in four Familial samples (18 members) and three paired-sporadic cases (6 samples) using array-based comparative-genomic-hybridization and validated in 32 Hypospadias samples by TaqMan assay. Based on Odds Ratio at 95% CI, Z Statistic and Significance Levels, STS gene-rs17268974 was associated with Penile-Hypospadias and 9-SNPs (seven-SNPs (rs5934740; rs5934842; rs5934913; rs6639811; rs3923341; rs17268974; rs5934937) of STS gene; rs7562326-SRD5A2 and rs1877031-STARD3 were associated with Penoscrotal-Hypospadias. On aggregate analysis with p <0.001, we identified homozygous-loss of Ch7:q34 (PRSS3P2, PRSS2). On validation in previously CNV-characterized and new (32-hypospadias-cases), we identified PRSS3P2-loss in most of the grade 3 and 4 hypospadias. Hence, Grade 1 and 2 (coronal and granular) show no-PRSS3P2-loss and no-association with SNPs in STS; SRD5A2; STARD3-gene but Grade 3 and 4 (Penile and Penoscrotal) show PRSS3P2-loss accompanied with the association of SNPs in STS; SRD5A2; STARD3. Hence, homozygous-loss of PRSS3P2 accompanied with the association of STS; SRD5A2; STARD3 may link to the severity of the disease.

genomics↗

bioRxiv2018

Prevalence of Antibiotic Resistance in Commensal Escherichia Coli among the Children in Rural Hill Communities of North East India

Commensal bacteria are the representative of the reservoir of antibiotic resistance genes present in a community. Merely a few community-based studies on the prevalence of antibiotic resistance in commensal bacteria have been conducted so far in Southeast Asia and other parts of India. Northeastern India is still untapped regarding the surveillance of antibiotic-resistant genes and prevalence in commensal bacteria. In the present work, the prevalence of antibiotic resistance in commensal Escherichia coli was investigated along with the associated demographic factors in pre-school and school going children in rural areas of Sikkim. A total of 550 fecal E. coli isolates were obtained from children of the age 1-14 years living in different villages at various altitudes of Sikkim from July 2015 to June 2017. Standard antibiotic susceptibility testing of these isolates was performed. A structured questionnaire was designed to study the factors associated with carriage of antibiotic resistance in commensal E. coli isolates among children. Descriptive statistics analysis and a logistic regression model were used to identify the effect of external factors on antibiotic resistance pattern. High prevalence of resistance was found against commonly used antibiotics ampicillin (92%), ceftazidime (90%), cefoxitin (88%), streptomycin (40%) and tetracycline (36%) among the samples examined in our present study. No resistance to chloramphenicol was recorded. Fifty-two percent of the isolates were resistant to the combination of penicillin and quinolone group of antibiotics. Children living in nuclear families showed higher incidence of resistance to ampicillin (63.15%, OR 0.18,95% CI:0.11 - 0.28, p<0.01) while children of mothers having education up to school level displayed higher incidence of ceftazidime (59.27% OR 0.75, 95% CI:0.55 - 1.02, p<0.02). Our study demonstrates a high prevalence of antibiotic-resistant commensal E. coli against the commonly used antibiotics among children in the study area. A close association between different demographic factors and the pattern of carriage of antibiotic-resistant isolates was observed suggesting a concern over misuse of antibiotics and warrants a future threat of emerging multidrug resistant isolates.

microbiology↗

bioRxiv2017

Swapping Of Transmembrane Domains In The Epithelial Calcium Channel TRPV6

Tetrameric ion channels have either swapped or non-swapped arrangements of the S1-S4 and pore domains. Here we show that mutations in the transmembrane domain of TRPV6 can result in conversion from a domain-swapped to non-swapped fold. These results reveal structural determinants of domain swapping and raise the possibility that a single ion channel subtype can fold into either arrangement in vivo, affecting its function in normal or disease states.

biochemistry↗

bioRxiv2016

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remains a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 publicly available 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of bacterial communities of the same. We have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. We have identified essential metabolic signatures and also showed that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

microbiology↗