Biology subjects

Das, B.

Publications and source records attributed to Das, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2021

ProMoCell and ProModb: web services for analyzing interaction-based functionally localized protein modules in a cell

The modular organization of a cell which can be determined by its interaction network allows us to understand a mesh of cooperation among the functional modules. Therefore, cellular level identification of functional modules aids in understanding the functional and structural characteristics of the biological network of a cell and also assists in determining or comprehending the evolutionary signal. We develop ProFuM-Cell that performs real-time web scraping for generating clusters of the cellular level functional units of an organism. ProFuMCell constructs the Protein Locality Graphs and clusters the cellular level functional units of an organism by utilizing experimentally verified data from various online sources. Also, we develop ProModb, a database service that houses precomputed whole-cell protein-protein interaction network-based functional modules of an organism using ProFuMCell. Our web service is entirely synchronized with the KEGG pathway database and allows users to generate spatially localized protein modules for any organism belonging to the KEGG genome using its real-time web scraping characteristics. Hence, the server will host as many organisms as is maintained by the KEGG database. Our web services provide the users a comprehensive and integrated tool for an efficient browsing and extraction of the spatial locality-based protein locality graph and the functional modules constructed by gathering experimental data from several interaction databases and pathway maps. We believe that our web services will be beneficial in pharmacological research, where a novel research domain called modular pharmacology has initiated the study on the diagnosis, prevention, and treatment of deadly diseases using functional modules. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/446966v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@145374borg.highwire.dtl.DTLVardef@13121aeorg.highwire.dtl.DTLVardef@9a3681org.highwire.dtl.DTLVardef@707985_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2021

Protein Interaction Network-based Deep Learning Framework for Identifying Disease-Associated Human Proteins

Infectious diseases in humans appear to be one of the most primary public health issues. Identification of novel disease-associated proteins will furnish an efficient recognition of the novel therapeutic targets. Here, we develop a Graph Convolutional Network (GCN)-based model called PINDeL to identify the disease-associated host proteins by integrating the human Protein Locality Graph and its corresponding topological features. Because of the amalgamation of GCN with the protein interaction network, PINDeL achieves the highest accuracy of 83.45% while AUROC and AUPRC values are 0.90 and 0.88, respectively. With high accuracy, recall, F1-score, specificity, AUROC, and AUPRC, PINDeL outperforms other existing machine-learning and deep-learning techniques for disease gene/protein identification in humans. Application of PINDeL on an independent dataset of 24320 proteins, which are not used for training, validation, or testing purposes, predicts 6448 new disease-protein associations of which we verify 3196 disease-proteins through experimental evidence like disease ontology, Gene Ontology, and KEGG pathway enrichment analyses. Our investigation informs that experimentally-verified 748 proteins are indeed responsible for pathogen-host protein interactions of which 22 disease-proteins share their association with multiple diseases such as cancer, aging, chem-dependency, pharmacogenomics, normal variation, infection, and immune-related diseases. This unique Graph Convolution Network-based prediction model is of utmost use in large-scale disease-protein association prediction and hence, will provide crucial insights on disease pathogenesis and will further aid in developing novel therapeutics.

bioinformatics↗

bioRxiv2021

Deciphering biological evolution exploiting the topology of Protein Locality Graph

The conventional sequence comparison-based evolutionary studies ignore other evolutionary constraints like interaction among proteins, functions of proteins and genes etc. A lot of speculations exist in literature regarding the presence of species divergence at the level of the Protein Interaction Networks. Additionally, it has been conjectured that the intra-module connections stay conserved whereas the inter-module connections change during evolution. The most important components of the biological networks are the functional modules which are more conserved among the evolutionary closer species. Here, we demonstrate an alternative method to decipher biological evolution by exploiting the topology of a spatially localized Protein Interaction Network called Protein Locality Graph (PLG). Our lossless graph compression from PLG to a power graph called Protein Cluster Interaction Network (PCIN) results in a 90% size reduction and aids in improving computational time. Further, we exploit the topology of PCIN and demonstrate our capability of deriving the correct species tree by focusing on the cross-talk between the protein modules exclusively. Our results provide new evidence that traces of evolution are not only present at the level of the Protein-Protein Interactions, but are also very much present at the level of the inter-module interactions.

bioinformatics↗

bioRxiv2021

AMP-Kinase mediates regulation of glomerular volume and podocyte survival

We reported that Shroom3 knockdown, via Fyn inhibition, induced albuminuria with foot process effacement (FPE) without glomerulosclerosis (FSGS) or podocytopenia. Interestingly, knockdown mice had reduced podocyte volumes. Human minimal change disease, where podocyte Fyn inactivation was reported, also showed lower glomerular volumes than FSGS. We hypothesized that lower glomerular volume prevented the progression to podocytopenia. To test this hypothesis, we utilized unilateral- and 5/6th nephrectomy models in Shroom3 knockdown mice. Knockdown mice exhibited lower glomerular volume, and less glomerular and podocyte hypertrophy after nephrectomy. FYN-knockdown podocytes had similar reductions in podocyte volume, implying Fyn was downstream of Shroom3. Using SHROOM3- or FYN-knockdown, we confirmed reduced podocyte protein content, along with significantly increased phosphorylated AMP-kinase, a negative regulator of anabolism. AMP-Kinase activation resulted from increased cytoplasmic redistribution of LKB1 in podocytes. Inhibition of AMP-Kinase abolished the reduction in glomerular volume and induced podocytopenia in mice with FPE, suggesting a protective role for AMP-Kinase activation. In agreement with this, treatment of glomerular injury models with AMP-Kinase activators restricted glomerular volume, podocytopenia and progression to FSGS. In summary, we demonstrate the important role of AMP-Kinase in glomerular volume regulation and podocyte survival. Our data suggest that AMP-Kinase activation adaptively regulates glomerular volume to prevent podocytopenia in the context of podocyte injury.

systems biology↗

bioRxiv2021

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor

BackgroundCircadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. "Around-the-clock" active nurse ants are usually younger and, with age, transition into rhythmically active foragers. Moreover, ants can shift between these behavioral castes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity in Camponotus floridanus carpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains. ResultsWe found that nurse brains have three times fewer 24h oscillating genes than foragers. However, several hundred genes that oscillated every 24h in forager brains showed robust 8h oscillations in nurses, including the core clock genes Period and Shaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment pathway, and showed enrichments for functions related to metabolism, cellular communication and protein modification. We additionally found that Vitellogenin, known to regulate division of labor in social insects, showed robust 24h oscillations in nurse brains but not in foragers. Furthermore, the protein products of several genes that were differentially expressed between the two ant castes were previously found in the trophallactic fluid of C. floridanus. This suggests a putative role for trophallaxis in regulating behavioral division of labor through caste-specific gene expression. ConclusionWe provide a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify putative molecular mechanisms underlying plastic timekeeping. Several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found in C. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.

animal behavior and cognition↗

bioRxiv2021

The CTEXT complex in Saccharomyces cerevisiae plays a crucial role in degrading distinct sets of aberrant mRNAs by the nuclear exosome

In Saccharomyces cerevisiae, DRN (Decay of RNA in the Nucleus) requiring Cbc1/2p, Tif4631p, and Upf3p promotes the exosomal degradation of aberrantly long 3'-extended-, export-defective transcripts and a small group of normal (special) mRNAs. In this study, using a systematic proteomic analysis we show that each of the known components interacts with one another and they exist as a separate complex, which was dubbed CTEXT (CBC-Tif4631p-dependent EXosome Targeting). We also identified a DEAD-box RNA helicase Dbp2p as an additional novel component of CTEXT during this analysis which was further bolstered by the finding that genomic deletions of Dbp2p led to the stabilization of all the signature nuclear messages. Interestingly, the RRM domain of Tif4631p located at the extreme N-termini of this polypeptide was found to play a vital role in in mediating the interaction of the CTEXT with the core exosome complex. These inferences were substantiated by the finding that deletion of this domain led to the functional impairment of the CTEXT complex. Thus, the CTEXT constitutes an independent complex that assists the nuclear exosome in degrading the select classes of nuclear transcripts in Saccharomyces cerevisiae.

molecular biology↗

bioRxiv2020

Rrp6p/Rrp47p constitutes an independent nuclear turnover system of mature small non-coding RNAs in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the nuclear exosome/Rrp6p/TRAMP participates in the 3-end processing of several precursor non-coding RNAs. Here we demonstrate that the depletion of nucleus-specific 3[->]5 exoribonuclease Rrp6p and its cofactor, Rrp47p led to the specific and selective enhancement of steady-state levels of mature small non-coding RNAs (sncRNAs) that include 5S and 5.8S rRNAs, snRNAs and snoRNAs, but not 18S and 25S rRNAs. Most importantly, their steady-state enhancement does not require the exosome, TRAMP, CTEXT, or Rrp6p-associated Mpp6p. Rrp6p/47p-dependent enhancement of the steady-state levels of sncRNAs is associated with the diminution of their nuclear decay-rate and requires their polyadenylation before targeting by Rrp6p, which is catalyzed by both the canonical and non-canonical poly(A) polymerases, Pap1p and Trf4p. Consistent with this finding, we also demonstrated that Rrp6p and Rrp47p exist as an exosome-independent complex. Thus, Rrp6p-Rrp47p defines a core nuclear exosome-independent novel turnover system that targets the small non-coding RNAs.

molecular biology↗

bioRxiv2020

Stem cell basis of a host driven transmission of antigen packed aerosols: a novel mechanism of natural vaccination for tuberculosis

Natural vaccination against pathogens are known to be achieved by herd-immunity i.e. infected human host provide immunity to the community by spreading the pathogen. Whether, infected human hosts transmit vesicle packed aerosols of pathogens antigen for natural vaccination of the community has not yet been considered. We have explored a traditional healing method of aerosol-inoculation against small pox and tuberculosis in the Sualkuchi-Hajo cultural complex of Kamarupa, an ancient Indian region known for tantra-based healing and spirituality. In the aerosol-inoculation method against TB, selected persons with TB (later identified as smear negative TB subject) are encouraged to spread good nigudah in the community by Kirtan chanting; the good Nigudah are thought to be present within bad-nigudah or invisible krimis (tiny flesh eating living being mentioned in ancient Indias medicinal text Caraka Samhita and Atharva Veda). A 15-years of contact TB investigation study, as well as laboratory study of aerosol obtained from smear negative PTB (SN-PTB) subjects led to the identification of good Nigudah as extracellular vesicles (EVs) filled with Mtb-antigen ESAT-6. We then developed a mouse model of aerosol-inoculation using SN-PTB subject derived aerosol EVs, and identified Mtb infected mesenchymal stem cells (MSCs) of the lung as the putative source of the ESAT-6+ EVs. These Mtb infected MSCs reprogram to altruistic stem cell (ASC) phenotype, which then secrete ESAT-6+ EVs to the aerosols; healthy mice receiving the aerosol develop Mtb specific herd immunity. These results expedite our ongoing work on the innate defense mechanism of ASCs against pathogen, and provide a novel mechanism of natural vaccination, where the host extracts appropriate antigens from a pathogen, and then spread it in the community via aerosols.

immunology↗

bioRxiv2020

Aberrant Epithelial Differentiation Contributes to Pathogenesis in a Murine Model of Congenital Tufting Enteropathy

Background & AimsCongenital Tufting Enteropathy (CTE) is an intractable diarrheal disease of infancy caused by mutation of Epithelial Cell Adhesion Molecule (EpCAM). The cellular and molecular basis of CTE pathology has been elusive. We hypothesized that the loss of EpCAM in CTE results in altered lineage differentiation and defects in absorptive enterocytes thereby contributing to CTE pathogenesis. MethodsIntestine from CTE mice was evaluated for specific markers by RT-qPCR, western blotting and immunostaining. Body weight, blood glucose and intestinal enzyme activity were also investigated. A CTE enteroid model was used to assess whether the decreased census of secretory cells could be rescued. ResultsCTE mice exhibited alterations in brush-border function, disaccharidase activity and glucose absorption, potentially contributing to nutrient malabsorption and impaired weight gain. Altered cell differentiation in CTE mice led to decreased secretory cells and increased numbers of absorptive cells, though the absorptive enterocytes lacked key features, causing brush border malfunction. Further, treatment with Notch signaling inhibitor, DAPT, increased the numbers of major secretory cell types in CTE enteroids (Graphical abstract 1). ConclusionsAlterations in intestinal epithelial cell differentiation in CTE mice favor an increase in absorptive cells at the expense of secretory cells. Although the proportion of absorptive enterocytes is increased, they lack key functional properties. We conclude that these effects underlie pathogenic features of CTE such as malabsorption and diarrhea, and ultimately the failure to thrive seen in patients. The ability of DAPT to reverse aberrant differentiation suggests a possible therapeutic strategy. SynopsisA murine model of Congenital Tufting Enteropathy exhibits altered intestinal cell differentiation, leading to increased absorptive and decreased secretory cells, which can be reversed with DAPT. Absorptive enterocytes in these mice are also dysfunctional, contributing to disease pathogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/330522v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@6700d7org.highwire.dtl.DTLVardef@6855b9org.highwire.dtl.DTLVardef@1d41207org.highwire.dtl.DTLVardef@1eb9f05_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2020

Detection of 'relict' western lineage of citrus tristeza virus virulent genotype in declining Arunachal Wakro orange

Eastern Himalayan foothills are known to have optimal agro-climatic conditions for production of quality citrus fruits including oranges. Among the citrus growing regions of eastern Himalayas, Wakro in the far eastern state of Arunachal Pradesh is known for its superior quality oranges, popular as the Wakro orange or the Arunachal orange, which has been included in Geographical Indication Registry by the Government of India. However, during last few years, Arunachal orange orchards have been experiencing severe infestation of aphid associated with rapid decline disease, causing catastrophe to the farmers as well as state economy. Therefore, in 2015, an intensive survey of severely affected orange orchards was carried out to investigate the aetiological factors of citrus decline. RNA samples extracted from leaf and aphid specimens collected from Wakro orchards were subjected to CTV detection through 3-UTR specific RT-PCR. Subsequently, ORF1 and CP genetic regions were amplified and clonal-sequencing was performed. Although, BLAST search showed close homology of the present sequences with other virulent genotype VT sequences, detailed phylogenetic analysis demonstrated affinity and clustering of present sequences with VT sequences belonging to the western lineage. This finding is considerably distinct from CTV sequences reported from citrus growing orchards in India and other neighbouring countries. Additionally, low diversity of CP gene sequences, recombination patterns and presence of sequence segments identical to the present ones in other CTV genotypes was also revealed. Collectively, these observations indicate pristine and primeval nature of present CTV sequences, corroborating well with the proposed origin of CTV in this part of the globe. We here report our finding of western lineage of CTV virulent genotype VT, which is distinct from CTV molecular epidemiology in other parts of India and discuss the implications of these findings.

microbiology↗

bioRxiv2020

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS Model

Aggregation of Cu-Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, ALS. Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not correlated with disease pathophysiology. Here, we use multiple mutational variants of SOD1 to show that the absence of Zn, and not Cu, significantly impacts membrane attachment of SOD1 through two loop regions facilitating aggregation driven by lipid induced conformational changes. These loop regions influence both the primary (through Cu intake) and the gain of function (through aggregation) of SOD1 presumably through a shared conformational landscape. Combining experimental and theoretical frameworks using representative ALS disease mutants, we develop a co-factor derived membrane association model wherein mutational stress closer to the Zn (but not to the Cu) pocket is responsible for membrane association mediated toxic aggregation and survival time scale after ALS diagnosis.

biophysics↗

bioRxiv2020

Genoprotective effects of Chaga mushroom (Inonotus obliquus) polysaccharides in UVB-exposed embryonic zebrafish (Danio rerio) through coordinated expression of DNA repair genes

BackgroundChaga mushroom (Inonotus obliquus) is one of the most promising antioxidants with incredible health-promoting effects. Chaga polysaccharides (IOP) have been reported to enhance immune response and alleviate oxidative stress during development. However, the effects of IOP on the genotoxicity in model organisms are yet to be clarified. MethodsZebrafish embryos (12 hours post fertilization, hpf) were exposed to transient UVB (12 J/m2/s, 310 nm) for 10 secs using a UV hybridisation chamber, followed by IOP treatment (2.5 mg/mL) at 24 hpf for up to 7 days post fertilization (dpf). The genotoxic effects were assessed using acridine orange staining, alkaline comet assay, and qRT-PCR for screening DNA repair genes. ResultsWe found significant reduction in DNA damage and amelioration of the deformed structures in the IOP-treated zebrafish exposed to UVB (p < 0.05) at 5 dpf and thereafter. In addition, the relative mRNA expressions of XRCC-5, XRCC-6, RAD51, P53, and GADD45 were significantly upregulated in the IOP-treated UVB-exposed zebrafish. Pathway analysis demonstrated coordinated regulation of DNA repair genes, suggesting collective response during UVB exposure. ConclusionsOverall, IOP treatment ameliorated the genotoxic effects in UVB-exposed zebrafish embryos, which eventually assisted in normal development. The study suggested the efficacy of Chaga mushroom polysaccharides in mitigating UV-induced DNA damage.

molecular biology↗

bioRxiv2020

The Nrd1p-Nab3p-Sen1p complex constitutes a vital component of the nuclear mRNA surveillance in Saccharomyces cerevisiae

In all eukaryotes, selective nuclear degradation of aberrant mRNAs by nuclear exosome and its cofactors TRAMP, and CTEXT contribute to the fidelity of the gene expression pipeline. In the model eukaryote, Saccharomyces cerevisiae, the Nrd1p-Nab3p-Sen1p (NNS) complex, previously known to be involved in the transcription termination and matured 3-end formation of vast majority of non-coding and several coding RNAs, is demonstrated to universally participate in the nuclear decay of various kinds of faulty messages in this study. Consistently, nrd1-1/nrd1-2 mutant cells display impairment of the decay of all kinds of aberrant mRNAs, like the yeast mutants deficient in Rrp41p, Rrp6p, and Rrp4p. nrd1{Delta}CID mutation (consisting of Nrd1p lacking its CID domain thereby abrogating its interaction with RNAPII) however, abolishes the decay of aberrant messages generated during early phases of mRNP biogenesis (transcription elongation, splicing and 3-end maturation) without affecting the decay rate of the export-defective mRNAs. Mutation in the 3-end processing factor, Pcf11p, in contrast, displayed a selective abolition of the decay of the aberrant mRNAs, generated at the late phase of mRNP biogenesis (export-defective mRNAs) without influencing the faulty messages spawned in the early phase of mRNP biogenesis. Co-transcriptional recruitment of Nrd1p onto the faulty messages, which relies on RNAPII during transcription elongation and on Pcf11p post transcription, is vital for the exosomal decay of aberrant mRNAs, as Nrd1p deposition on the export-defective messages led to the Rrp6p recruitment and eventually, their decay. Thus, presence of the Nrd1p mark on aberrant mRNAs appears rate-limiting for the distinction of the aberrant messages from their normal functional counterparts. Authors SummaryAberrant/faulty mRNAs generated from the deficiencies in any of the mRNP biogenesis events are promptly eliminated by the nuclear exosome and its cofactors TRAMP and CTEXT complexes. These machineries work relentlessly in the nucleus to detect all kinds of aberrant mRNAs and selectively target them for destruction. However, initial detection of a minuscule amount of aberrant mRNA in the vast background of normal mRNAs is quite challenging and its mechanism remains elusive. In this work, we demonstrate that, the trimeric Nrd1p-Nab3p-Sen1p complex, previously implicated in the transcription termination of diverse non-coding RNAs and a handful of mRNAs, constitute an integral component of the nuclear mRNA surveillance mechanism in bakers yeast Saccharomyces cerevisiae. Major component of this complex, Nrd1p is demonstrated to be recruited selectively onto various classes of representative model aberrant messages either co-transcriptionally by RNA Polymerase II or post-transcriptionally by Pcf11p. Binding of Nrd1p to the export-defective special mRNAs further leads to the recruitment of Rrp6p on to them thereby leading to their degradation. NNS complex thus plays a vital role of initially recognizing the faulty messages and further assists in the recruitment of the nuclear exosome for their prompt elimination.

molecular biology↗

bioRxiv2020

Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic

We postulate that similar to bacteria, adult stem cells may also exhibit an innate defense mechanism to protect their niche. Here, we provide preliminary data on stem cell based innate defense against a mouse model of coronavirus, murine hepatitis virus-1 (MHV-1) infection. In a mouse model of mesenchymal stem cell (MSC) mediated Mycobacterium tuberculosis (Mtb) dormancy, MHV-1 infection in the lung exhibited 20 fold lower viral loads than the healthy control mice, suggesting the potential enhancement of an anti-MHV-1 defense by Mtb. This defense mechanism involves the in vivo expansion and reprogramming of CD271+MSCs in the lung to an enhanced stemness phenotype. The reprogrammed MSCs facilitate the activation of stemness genes, intracellular Mtb replication, and extracellular release of Mtb. The conditioned media of the reprogrammed MSCs exhibit direct anti-viral activity in an in vitro model of MHV-1 induced toxicity to type II alveolar epithelial cells. Thus, our data suggest that reprogrammed MSCs exert a unique innate defense against MHV-1 by activating dormant Mtb. The molecular details of this anti-viral defense mechanism against coronavirus could be further studied to develop a vaccine against COVID-19.

microbiology↗

bioRxiv2020

Genetic underpinnings of host manipulation by Ophiocordyceps as revealed by comparative transcriptomics

AO_SCPLOWBSTRACTC_SCPLOWThe ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior on to vegetation, positioning the manipulated ant in a site beneficial for fungal growth and transmission. Notably, across Ophiocordyceps species and other known host manipulators, the molecular mechanisms underlying behavioral changes remain largely unclear. We explored possible genetic underpinnings of host manipulation by: (i) producing a hybrid assembly of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of both O. camponoti-floridani and its host, Campontous floridanus, and (iii) using these data for a comparative analysis to similar work performed in Ophiocordyceps kimflemingiae and Camponotus castaneus. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may be the result of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting nutrition-sensing or caste-identity pathways.

genomics↗

bioRxiv2019

Biodegradation of Chlorpyrifos and 3,5,6-trichloro-2-pyridinol (TCP) by Ochrobactrum sp. CPD-03: Insights from genome analysis on organophosphorus pesticidesdegradation, chemotaxis and PGPR activity

Chlorpyrifos (CP) is one of the worlds most widely used organophosphorous pesticides (OPs) in agriculture, has led to contaminate soil and water ecosystems along with human species. Here, we report a newly isolated strain, Ochrobactrum sp. CPD-03 form a paddy field which could degrade CP and its metabolite TCP (3,5,6-trichloro-2-pyridinol) in 48 hours with an efficiency of 85-88% in minimal salt medium. GC-MS analysis revealed possible metabolites during CP degradation. Whole genome analysis indicated the presence of arylesterase and existence of other genes accountable for xenobiotic compounds degradation. CPD-03 exhibited chemotactic features towards CP along with other OPs suggesting its versatile role for possible mineralization of these toxicants. Further screening of CPD-03 also displayed plant growth promoting activities. Taken altogether, our results highlight the potentials of this new isolate Ochrobactrum sp. CPD-03 in bioremediation and application in OP-contaminated ecosystem.

microbiology↗

bioRxiv2019

Draft genome sequence of a popular Indian tea genotype TV-1

Camellia assamica L. (O). Kuntze. var. TV-1 from Assam, India is one of the most important tea cultivar of Indian Tea Industry which botanically belongs to Assam type and has distinct morphological as well as chemical constituent in leaf than China type of tea. We here present the first draft genome sequence of TV-1, assembled in 2.93 Gb size comprising of 14,824 scaffolds and covering 97.66% of the predicted genome size (3.0 Gb) as determined by flow cytometry. The N50 value, longest and average contig size for this draft genome was found to be as 538.96 Kb, 3.64 Mb and 197.99 Kb, respectively. There were 495,747 SSRs (Di- to Hexa-mers) in the genome and the repeat contents accounted for 71.87% of the genome. About 94.40% genome completeness was predicted with BUSCO, maximum among the published and reported tea genomes. The clustering of the assembled genome with Hi-C data resulted in 15 clusters ranging from the size of 631.46 Mb to 14.39 Mb and accounting 99.32% of assembled genome. This data will act as the starting point for unravelling the important genes and differentiating Indian tea from other commercially available tea varieties.

plant biology↗

bioRxiv2018

Locomotor response to acute stressors requires hypothalamic-pituitary-interrenal axis activation and glucocorticoid receptors in zebrafish

When vertebrates face acute stressors, their bodies rapidly undergo a repertoire of physiological and behavioral adaptations, which is termed the stress response (SR). Rapid physiological changes in heart rate and blood sugar levels occur via the interaction of glucocorticoids and their cognate receptors following hypothalamic-pituitary-adrenal (HPA) axis activation. These physiological changes are observed within minutes of encountering a stressor and the rapid time domain rules out genomic responses that require gene expression changes. Although behavioral changes corresponding to physiological changes are commonly observed, it is not clearly understood to what extent HPA axis activation dictates adaptive behavior. We hypothesized that rapid locomotor response to acute stressors in zebrafish requires HPI axis activation. In teleost fish, interrenal cells (I) are functionally homologous to the adrenal gland cortical layer. We derived 8 frameshift mutants in genes involved in HPI axis function: two mutants in exon 2 of mc2r (adrenocorticotropic hormone receptor), two in each of exon 2 and exon 5 of nr3c1 (glucocorticoid receptor), and two in exon 2 of nr3c2 (mineralocorticoid receptor). Exposing larval zebrafish to mild environmental stressors, acute changes in salinity or light illumination, results in a rapid locomotor response. We show here that this locomotor response requires a functioning HPI axis via the action of mc2r (adrenocorticotropic hormone receptor) and the canonical glucocorticoid receptor encoded by nr3c1 gene, but not mineralocorticoid receptor (nr3c2). Our rapid behavioral assay paradigm based on HPI axis biology may prove useful to screen for genetic, pharmacological, or environmental modifiers of the HPA axis.\n\nSignificanceAltered HPA axis activity is acknowledged as a causative and critical prognostic factor in many psychiatric disorders including depression. Nonetheless, genome wide association studies (GWAS) on depression have revealed conflicting findings about susceptibility loci, while identifying several genetic loci that warrant further investigations in the process. Such findings indicate that psychiatric disorders with complex genetic foundations require functional studies as well as genetic analyses. We developed a sensitive behavioral assay paradigm that leverages the genetic amenability and rapid development of zebrafish and demonstrated that our assay system reliably detects changes in HPA axis responsiveness. Our functional genetics and behavioral assay approach provides a useful platform to discover novel genetic, pharmacological, or environmental modifiers of the HPA axis.

neuroscience↗