Biology subjects

Singh, S. K.

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

At least 55 records · Page 3Linked to original sources

bioRxiv2020

New insights of zoogeographical distribution of Himalayan goral (Naemorhedus goral) from Indian Himalayan Region

In the present study, we explored the intraspecific genetic variation and phylogeographic relationship among all the reported species in the genus Naemorhedus distributed in a wide range of habitats. The Bayesian based phylogeny demonstrated that Himalayan goral, is a highly diverged species from the other reported species of gorals. We claim the presence of two valid sub-species of Himalayan goral, i.e. N. g. bedfordi and N. g. goral, distributed in the western and central Himalaya, respectively. The comparative analysis with the inclusion of data available from different ranges, suggests the presence of plausibly six species of gorals across the distribution with a few valid subspecies. Further, we report that N. griseus is a valid species and not the synonyms of N. goral considering the observed discrepancy in the available sequences. We recommend all the sub-species present at distant locations may be considered as Evolutionary Significant Units (ESUs) and, therefore, appeal to provide them special attention for long term conservation and management.

genetics↗

bioRxiv2020

Integrated genomic view of SARS-CoV-2 in India

India first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

microbiology↗

bioRxiv2020

Multi-Antigenic Virus-like Particle of SARS CoV-2 produced in Saccharomyces cerevisiae as a vaccine candidate

Spike, Envelope and Membrane proteins from the SARS CoV-2 virus surface coat are important vaccine targets. We hereby report recombinant co-expression of the three proteins (Spike, Envelope and Membrane) in a engineered Saccharomyces cerevisiae platform (D-Crypt) and their self-assembly as Virus-like particle (VLP). This design as a multi-antigenic VLP for SARS CoV-2 has the potential to be a scalable vaccine candidate. The VLP is confirmed by transmission electron microscopy (TEM) images of the SARS CoV-2, along with supportive HPLC, Dynamic Light Scattering (DLS) and allied analytical data. The images clearly outline the presence of a "Corona" like morphology, and uniform size distribution.

biochemistry↗

bioRxiv2020

A cell competition-based drug screen identifies a novel compound that induces dual c-Myc degradation and p53 activation

BCR-Abl is a driver oncogene that causes chronic myeloid leukemia and a subset of acute lymphoid leukemias. Although tyrosine kinase inhibitors provide an effective treatment for these diseases, they generally do not kill leukemic stem cells. Leukemic stem cells are cancer-initiating cells that compete with normal hematopoietic stem cells for the bone marrow niche. Using BCR-Abl as a model oncogene, we performed a drug screen based on competition between isogenic untransformed cells and BCR-Abl-transformed cells, and identified several compounds that selectively target BCR-Abl-transformed cells. Systems-level analysis of one of these novel compounds, DJ34, revealed that it induced depletion of c-Myc and activation of p53. c-Myc depletion occurred in a wide range of tumor types, including leukemia, lymphoma, lung, glioblastoma and breast cancer. Further analyses revealed that DJ34 interferes with c-Myc synthesis at the level of transcription, and we provide data showing that DJ34 is a DNA intercalator and topoisomerase II inhibitor. Physiologically, DJ34 induced apoptosis, cell cycle arrest and cell differentiation, and primary leukemic stem cells were particularly sensitive to DJ34. Taken together, we have identified a novel compound that dually targets c-Myc and p53 in a wide variety of cancers, and with particularly strong activity against leukemic stem cells.

cancer biology↗

bioRxiv2020

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.

genomics↗

bioRxiv2020

Latent defense response to non-pathogenic microbial factors impairs plant-rhizobacteria mutualism

Unlike pathogens that trigger plant defense responses, commensal or beneficial microbes are compatible with plants and do not elicit a defense response. An assumption underlying the compatibility is that plants are inert in mounting a defense response to non-pathogenic microbial factors. However, the mechanisms underlying this inertness in defense are unknown. Here a forward genetic screen led to the isolation of an Arabidopsis mutant displaying a new type of immunity which we named as latent defense response (LDR) to a beneficial rhizobacterium. The mutant, known as gp1 for Growth-Promotion 1, is impaired in rhizobacteria-induced plant growth-promotion due to disrupted oleic acid homeostasis and consequent activation of defense responses. Several bacterial volatile compounds trigger LDR in gp1 but not wild type plants. GP1 dysfunction strongly represses colonization of the beneficial rhizobacterium and alters root-associated microbiota. Our findings reveal a hidden layer of plant defense, LDR, which is suppressed by GP1 to allow mutualistic association between plants and beneficial rhizobacteria. One Sentence SummaryA hidden layer of host immunity against non-pathogenic microbes leads to plant incompatibility with beneficial rhizobacteria.

plant biology↗

bioRxiv2020

Semecarpus anacardium Linn. leaf extract exhibits activities against breast cancer and prolongs the survival of tumor bearing mice

Semecarpus anacardium Linn. is commonly used in various traditional medicines from ancient times. The nuts have been described in Ayurveda medication systems to treat numerous clinical ailments. However, isolating phytochemical constituents from nuts remains challenging and exhibits cytotoxic effects on other cells. In this study, we have standardized procedures for isolating phytochemicals from the leaf extract. The ethyl acetate leaf extract selectively affects cancer cells in a dose-dependent manner (IC50: 0.57 g/ml in MCF-7 cells) in various cancer cell lines. Next, we examined if the extract incubation could induce cell cycle arrest and suppress cell migration in the cell culture model. Consistent with this idea, the leaf extract could potentially affect the aggressive migration nature of cancer cells. Moreover, oral administration of extract significantly restored tumor growth in mice. Together, these observations suggest the anti-cancer activities of S. anacardium leaf potential for both in vitro and in vivo models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/898940v3_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@3fefborg.highwire.dtl.DTLVardef@594510org.highwire.dtl.DTLVardef@c525d2org.highwire.dtl.DTLVardef@1362978_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2020

Virtaul screening of MAP-Tau protein inhibitors from Semecarpus anacardium Linn. leaf extract for cancer prevention

Semecarpus anacardium is a well known Indian medicinal plant with various medicinal properties like hypoglycemic, antioxidant, anticancer, anti-inflammatory, anti-geriatric, antimicrobial and hair growth promoter, etc. The molecular mechanism of metabolites from fruiting bodies of S. anacardium against cancer has been described but anticancerous properties in its leaves are still unknown. The leaves were extracted in petroleum ether, ethyl acetate and methanol and assayed for anticancer activity using MTT assay. The active extract was evaluated for mode of cell death induction using EtBr-AO double staining and analyzed for phytochemical constituents using GC-MS, followed by molecular docking studies for exploration of possibility for anticancer agents and Drugability. In this study, ethyl acetate extract of leaf was found potent cytotoxic in MCF-7 cells and also induced apoptosis. It has also found the SLE is safe for normal cells. The molecular docking studies were done to explore the probable mechanism of action of the extract which showed 9 compounds are targeting the microtubule-associated protein tau (MAPT). MAPT promotes assembling and prevents disassembling to arrest the cell cycle. The overexpression of MAPT induces chemoresistance to cancerous cells against conventional drugs like paclitaxel. We have identified 17 compounds from ethyl acetate extract of S. anacardium leaves and drawn its chemical structure by using chembiodraw software to transform into pdb format. Further, the compounds have been subjected for molecular docking study to investigate its interactive efficiency with MAPT protein. The compound 13 had higher interactive potential to MAPT with binding energy -31.75 kcal/mol and lowest binding energy (-15.44 kcal/mol) was observed in compound 6. The present study suggested that the compounds from leaves of S. anacardium could be alternative approach of conventional drug for cancer treatment with cost effective and less side effect.

bioinformatics↗

bioRxiv2019

A Novel Chloroplast Super-Complex Consisting of the ATP Synthase and Photosystem I Reaction Center

Several super-complexes of individual hetero-oligomeric membrane protein complexes, whose function is to facilitate intra-membrane electron and proton transfer and harvesting of light energy, have been previously characterized in the mitochondrial cristae and chloroplast thylakoid membranes. The latter membrane is reported here to also be the location of an intra-membrane super-complex which is dominated by the ATP-synthase and photosystem I (PSI) reaction-center complexes, defined by mass spectrometry, clear-native PAGE and Western Blot analyses. This is the first documented presence of ATP synthase in a super-complex with the PSI reaction-center located in the non-appressed stromal domain of the thylakoid membrane.

biochemistry↗

bioRxiv2019

Signature activities of 20S proteasome include degradation of the ubiquitin-tag with the protein under hypoxia

Careful removal of unwanted proteins is necessary for cell survival. The primary constitutive intracellular protease is the 26S proteasome complex, often found in equilibrium with its free catalytic subcomplex- the 20S core particle. Protein degradation by 26S is tightly regulated by prior ubiquitination of substrates, whereas 20S is amenable to substrates with an unstructured segment. Differentiating their contributions to intracellular proteolysis is challenging due to their common catalytic sites. Here, by chemically synthesizing a synoptic set of homogenous ubiquitinated proteins, we ascribe signature features to 20S function and demonstrate a unique property: degrading the ubiquitin-tag along with the target protein. Cryo-EM confirms that a ubiquitinated substrate can induce asymmetric conformational changes to 20S. Mass-spectrometry of intracellular peptidome under hypoxia and in human failing heart identifies the signature properties of 20S in cells. Moreover, the ability of 20S proteasome to clear toxic proteins rapidly, contributes to better survival under these conditions.

biochemistry↗

bioRxiv2019

Structure and activation mechanism of the BBSome membrane-protein trafficking complex

Bardet-Biedl syndrome (BBS) is an incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS assemble into the BBSome, a master regulator of the ciliary membrane proteome. We report the electron cryomicroscopy (cryo-EM) structures of the native bovine BBSome in inactive and active states at 3.1 and 3.5 [A] resolution, respectively. In the active state, the BBSome is bound to an Arf-family GTPase (ARL6/BBS3) that recruits the BBSome to ciliary membranes. ARL6 recognizes a composite binding site formed by BBS1 and BBS7 that is occluded in the inactive state. Activation requires an unexpected swiveling of the {beta}-propeller domain of BBS1, the key subunit implicated in substrate recognition, which widens a central cavity of the BBSome. Structural mapping of disease-causing mutations suggests that pathogenesis predominantly results from disruption of autoinhibition and activation.

biophysics↗

bioRxiv2019

Computational insights into mechanism of AIM4-mediated inhibition of aggregation of TDP-43 protein implicated in ALS and evidence for in vitro inhibition of liquid-liquid phase separation (LLPS) of TDP-432C-A315T by AIM4.

TDP-43 is an RNA/DNA-binding protein of versatile physiological functions and it is also implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS) disease in addition to several other implicated proteins such as mutant SOD1 and FUS etc. Cytoplasmic mis-localization, liquid-liquid phase separation (LLPS) due to RNA depletion and aggregation of TDP-43 are suggested to be important TDP-43-toxicity causing mechanisms for the ALS manifestation. So far, therapeutic options for ALS are extremely minimal and ineffective therefore, multi-faceted approaches such as treating the oxidative stress and inhibiting the TDP-43s aggregation are being actively pursued. In our recent study, an acridine imidazolium derivative compound, AIM4, has been identified to have anti-TDP-43 aggregation propensity however, its mechanism of inhibition is not deciphered. In this study, we have utilized computational methods to examine binding site(s) of AIM4 in the TDP-43 structure and have also compared its binding efficiency with several other relevant compounds. We find that AIM4 has a binding site in the C-terminal amyloidogenic core region of amino acids aa: 288-319, which coincides with one of the key residue motifs that could potentially mediate liquid-liquid phase separation (LLPS) of TDP-43. Importantly, alike to the previously reported effects exerted by RNA molecules, we found that AIM4 could also inhibit the in vitro LLPS of a recombinantly purified C-terminal fragment TDP-432C bearing an A315T familial mutation. Antagonistic effects of AIM4 towards LLPS which is believed as the precursor process to the TDP-43s aggregation and the in silico prediction of a binding site of AIM4 on TDP-43 occurring in the same region, assert that AIM4 could be an important molecule for further investigations on TDP-43s anti-aggregation effects with relevance to the ALS pathogenesis.

bioinformatics↗

bioRxiv2019

Machine learnt image processing to predict weight and size of rice kernels

Accurate measurement of rice kernel sizes after milling is critical to design, develop and optimize rice milling operations. The size and mass of the individual rice kernels are important parameters typically associated with rice quality attributes, particularly head rice yield. In this study, we propose a novel methodology that combines image processing and machine learning (ML) ensemble to accurately measure the size and mass of several rice kernels simultaneously. We have developed an image processing algorithm with the help of recursive method to identify the individual rice kernels from an image and estimate the size of the kernels based on the pixels a kernel occupies. The number of pixels representing a rice kernel has been used as its digital fingerprint in order to predict its size and mass. We have employed a number of popular machine learning models to build a stacked ensemble model (SEM), which can predict the mass of the individual rice kernels based on the features derived from the pixels of the individual kernels in the image. The prediction accuracy and robustness of our image processing and SEM are quantified using uncertainty quantification. The uncertainty quantification showed 3.6%, 2.5%, and 2.4% for mean errors in estimating the kernel length of small-grain (Calhikari-202), medium-grain (Jupiter), and long-grain (CL153) rice, respectively. Similarly, mean errors associated with predicting the 1000 grain weight are 4.1%, 2.9%, and 4.3% for Calhikari-202, Jupiter, and CL153, respectively. Use of the developed algorithm in rice imaging analyzers could facilitate head rice yield quantifications and promote quicker rice quality appraisals.

bioengineering↗

bioRxiv2019

Size and mass prediction of almond kernels using machine learning image processing

After harvesting almond crop, accurate measurement of almond kernel sizes is a significant specification to plan, develop and enhance almond processing operations. The size and mass of the individual almond kernels are vital parameters usually associated with almond quality, particularly head almond yield. In this study, we propose a novel methodology that combines image processing and machine-learning ensemble that accurately measures the size and mass of whole raw almond kernels (classification - Nonpareil) simultaneously. We have developed an image-processing algorithm using recursive method to identify the individual almond kernels from an image and estimate the size of the kernels based on the occupied pixels by a kernel. The number of pixels representing an almond kernel was used as its digital fingerprint to predict its size and mass. Various popular machine learning (ML) models were implemented to build a stacked ensemble model (SEM), predicting the mass of the individual almond kernels based on the features derived from the pixels of the individual kernels in the image. The prediction accuracy and robustness of image processing and SEM were analyzed using uncertainty quantification. The mean error in estimating the average length of 1000 almond kernel was 3.12%. Similarly, mean errors associated with predicting the 1000 kernel mass were 0.63%. The developed algorithm in almond imaging in this study can be used to facilitate a rapid almond yield and quality appraisals.

bioengineering↗

bioRxiv2019

Molecular Insights on exquisitely Selective SrtA inhibitors towards active site loop forming open/close lid conformations in SrtA from Bacillus anthracis

The present study clearly explains the dependency of inhibitory activities in SrtA inhibitors is closely related to protein conformational changes of SrtA from Bacillus anthracis B. anthracisSortase A (SrtA) protein anchors proteins by recognizing a cell wall sorting signal containing the amino acid sequence LPXTG In order to analyze conformational changes and the role of SrtA enzyme, especially the loop motions which situated proximal to the active site molecular dynamic simulation was carried out for 100ns. Particular loop is examined for its various conformations from the MD trajectories and the open/close lid conformations are considered for the enzyme activity validations. Experimentally verified SrtA inhibitors activity was analyzed through 3D-QSAR and Molecular docking approaches. Results indicate that, biological activity of SrtA inhibitors is closely related to the closed lid conformation of SrtA from Bacillus anthracis. This work may lead to a better understanding of the mechanism of action and aid to design a novel and more potent SrtA inhibitors.

bioinformatics↗

bioRxiv2019

Anti-oxidant, anti-apoptotic, anti-hypoxic and anti-inflammatory conditions induced by PTY-2 against STZ-induced stress in islets

Background and AimEarlier assessment of Pueraria tuberosa tubers has shown anti-diabetic effects through incretin mimetic action and DPP-IV inhibition. The aim of this work was to further explore the protective role of aqueous extract of Pueraria tuberosa against streptozotocin (STZ)-induced pancreatic stress in rats.\n\nMethodsDiabetes was induced with STZ (65 mg/kg body weight) in Charles foster male rats. After 60 days of STZ administration, animals with blood glucose levels > 200 g/dL were considered as diabetic. All the rats were later divided into three groups: Group-1 (STZ untreated normal rats), Group-2 (Diabetic control), and Group-3 (PTY-2 [50 mg/100 g bw treatment for next 10 days to diabetic rats). The rats were then sacrificed at the 10th day of treatment accordingly.\n\nResultsSTZ treatment led to an increase in expression of MMP-9, Tnf , HIF-1, VEGF, IL-6, PKC {varepsilon}, NF-kB, and Caspase-3. Reverse transcriptase Polymerase Chain Reaction (PCR), IHC and western blot analysis showed an increase in the expressions of superoxide dismutase (SOD) and Nephrin, and a decrease in the expressions of NF-kB, PKC {varepsilon}, TNF- MMP-9, HIF-1, VEGF, Caspase 3 and IL-6 after 10 days of PTY-2 treatment.\n\nConclusionThe results show that PTY-2 favorably changed the expression of NF-kB, PKC {varepsilon}, TNF , MMP 9, HIF-1, VEGF, IL-6, Caspase3, Nephrin and SOD in cases of STZ-induced pancreatic stress. Further evaluation of PTY-2 might be helpful in establishing its role in the management of diabetes mellitus.\n\nHighlightsO_LIPTY 2 act as a protective herbal drug against STZ induced islet stress.\nC_LIO_LIPTY 2 upregulates protective and downregulates harmful markers.\nC_LIO_LIThis study composed of four pathway through which PTY 2 acts on pancreas.\nC_LI\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC=\"FIGDIR/small/670364v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (69K):\norg.highwire.dtl.DTLVardef@14b1f18org.highwire.dtl.DTLVardef@e6a1f2org.highwire.dtl.DTLVardef@19225b0org.highwire.dtl.DTLVardef@1e87bf5_HPS_FORMAT_FIGEXP M_FIG Mechanism of action of PTY 2 against STZ induced islet stress.\n\nC_FIG

pharmacology and toxicology↗

bioRxiv2019

PTY 2 As DPP-IV Inhibitor Prevents Intestinal Cell’s Apoptosis

Enhanced DPP-IV expression is found to get enhanced in various intestinal diseases. PTY-2 has already been known to have DPP-IV inhibitory potential. This inhibition has not yet been studied at mRNA level. Increased incretin secretion due to DPP-IV inhibition could lead to suppression of stress & intestinal cells apoptosis. Through histological analysis, we have found morphological damage of intestine after STZ injection (65 mg/kg bw) to male Charles foster rats. mRNA expressions were analyzed by PCR and apoptosis of cells was checked through tunnel assay & Bcl 2 expression. The number and length of villi get reduced in STZ induced diabetic control, but these damages have been getting reversed after the PTY-2 treatment for 10 days. The expression of SOD was found to get reduced while that of DPP-IV was enhanced in diabetic control group along with significant intestinal cell apoptosis. PTY-2 treatment reduces the stress by upregulating the expression of SOD and through downregulation of DPP-IV mRNA expression. These recoveries by PTY-2 leads to suppression of intestinal cells apoptosis. These short studies explain the protective action of PTY-2 against STZ induced intestinal damage. Hence, PTY-2 could be taken as an herbal treatment against intestinal disorders in case of chronic diabetes.

pharmacology and toxicology↗

bioRxiv2019

Larval growth and survival in Indian Butter Catfish, Ompok bimaculatus (Bloch): effect of light intensity and photoperiod

Two sequential indoor rearing trials each of 21 days duration were conducted to investigate the effect of light intensity and photoperiod respectively on the growth and survival of Ompok bimaculatus larvae. In first trial, five different light intensities viz. 0, 300, 500, 900, 1200 lx were applied randomly to 800 larvae (0.003 g; 0.51 cm) stocked in triplicate following a completely randomized design into aquarium (30.0 x 15.0 x 15.0 cm) tanks. Sequentially, in second trial, five photoperiod cycles (light: dark, L: D) namely, 24L: 0D, 16L: 8D, 12L: 12D, 8L: 16D and 0L: 24D in combination with the best performing light intensity (300 lx) as observed from the first trial were employed in triplicates in similar set up. From the first trial, significantly higher survival was observed in 0 and 300 lx, whereas growth was highest in 900 lx (P < 0.05). In the second trial, survival was higher in continuous darkness (0L: 24D), whereas, maximum growth was recorded in 24L: 0D and 16L: 8D groups (P < 0.05). Performance index (PI) showed no significant difference (P > 0.05) among 0 and 300 lx light intensities, but were reduced at higher light intensities. The lowest PI was found in 12L: 12D and 8L: 16D condition but did not have any effect in other photoperiod cycles. Overall, from the present study it can be concluded that growth of the larvae is found to be higher in higher light intensity (900lx) and longer photoperiodic cycles (24L: 0D and 16L: 8D), however, better survival was recorded in total dark conditions suggesting that continuous dark condition is recommended for better hatchery performance of the larvae.

animal behavior and cognition↗