Biology subjects

Kumar, K.

Publications and source records attributed to Kumar, K..

61 records · Page 4Linked to original sources

bioRxiv2020

Structural Features and Oligomeric Nature of Human Podocin Domain

Podocytes are crucial cells of the glomerular filtration unit and playing a vital role at the interface of the blood-urine barrier. Podocyte slit-diaphragm is a modified tight junction that facilitates size and shape-dependent permselectivity. Several proteins including podocin, nephrin, CD2AP, and TRPC6 form a macromolecular assembly and constitute the slit-diaphragm. Podocin is an integral membrane protein attached to the inner membrane of the podocyte via a short transmembrane region (101-125). The cytosolic N- and C-terminus help podocin to attain a hook-like structure. Podocin shares 44% homology with stomatin family proteins and similar to the stomatin proteins, podocin was shown to associate into higher-order oligomers at the site of slit-diaphragm. However, the stoichiometry of the homo-oligomers and how it partakes in the macromolecular assemblies with other slit-diaphragm proteins remains elusive. Here we investigated the oligomeric propensity of a truncated podocin construct (residues:126-350). We show that the podocin domain majorly homo-oligomerize into a 16mer. Circular dichroism and fluorescence spectroscopy suggest that the 16mer oligomer has considerable secondary structure and moderate tertiary packing.

biophysics↗

bioRxiv2020

Analysis of Pan-Omics Data in Human Interactome Network (APODHIN)

Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-interactome networks consisting of human protein-protein interactions, miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships, respectively. In its first module, APODHIN maps proteins/genes/miRNAs from different omics data in its meta-interactome network and extracts the network of biomolecules that are differentially altered in the given scenario. Using this context specific, filtered interaction network, APODHIN identifies topologically important nodes (TINs) implementing graph theory based network topology analysis and further justifies their role via pathway and disease marker mapping. These TINs could be used as prospective diagnostic and/or prognostic biomarkers and/or potential therapeutic targets. In its second module, APODHIN attempts to identify cross pathway regulatory and protein-protein interaction (PPI) links connecting signaling proteins, transcription factors, and miRNAs to metabolic enzymes via utilization of single-omics and/or pan-omics data and implementation of mathematical modeling. Interconnections between regulatory components such as signaling proteins/TFs/miRNAs and metabolic pathways need to be elucidated more elaborately in order to understand the role of oncogene and tumor suppressors in regulation of metabolic reprogramming during cancer. APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links. Tabular, graphical and 3D network representations of the identified TINs and cross-pathway links are provided for better appreciation. Additionally, this platform also provides a database part where cancer specific, single and/or multi omics dataset centric meta-interactome networks, TINs, and cross-pathway links are provided for cervical, ovarian, and breast cancers, respectively. APODHIN platform is freely available at http://www.hpppi.iicb.res.in/APODHIN/home.html.

bioinformatics↗

bioRxiv2020

PresRAT: A server for identification of bacterial small-RNA sequences and their targets with probable binding region.

Bacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform named PresRAT (Prediction of sRNA and their Targets). PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on identification of the probable sRNA-mRNA binding regions. Using PresRAT we have identified a total of 60,518 potential sRNA sequences from 54 bacterial genomes and 2447 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets and their corresponding 3D models with structural dynamics information.

bioinformatics↗

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

Rat bone marrow derived mesenchymal stem cells differentiate to germ cell like cells

Summary StatementThe in vitro differentiation of rMSCs provides an excellent model for studying cell commitment and their potential in stem cell technology. We have demonstrated that rat bone marrow derived MSCs are able to differentiate into germ-line cells in vitro which has an enormous scope in the advancement of fertility research. In future, this technique can be utilized in different domestic animal species for propagation of elite germ plasm.\n\nAbstractGerm cells undergo distinctive male or female pathways to produce spermatozoa or oocyte respectively essential for sexual reproduction. Mesenchymal stem cells (MSCs) have the capacity of trans-differentiation to form the multiple lineages of cells of mesoderm, endoderm, and ectoderm origin. Herein, MSCs were isolated from rat bone marrow and characterized by their morphological features, expression of surface markers by immunophenotyping and molecular biology tools as well as self renewal and differentiation capability. Thereafter, by inducing these cells with retinoic acid we could able to show that bone marrow derived MSCs are able to trans-differentiate into male germ cell-like cells which were further characterized by the expressions of germ cell specific markers. This in vitro study for the generation of germ-like cells suggests that bone marrow MSCs can be a potential source of germ cells that could be a sustainable source of sperm / oocyte production for potential therapeutic applications in future. Moreover, this technique can be applied in different domestic animal species for propagation of elite germ plasm.

cell biology↗

bioRxiv2017

Multi-modal brain fingerprinting: a manifold approximation based framework

This work presents an efficient framework, based on manifold approximation, for generating brain fingerprints from multi-modal data. The proposed framework represents images as bags of local features, which are used to build a subject proximity graph. Compact fingerprints are obtained by projecting this graph in a low-dimensional manifold, using spectral embedding. Experiments using the T1/T2-weighted MRI, diffusion MRI, and resting state fMRI data of 945 Human Connectome Project subjects demonstrate the benefit of combining multiple modalities, with multi-modal fingerprints more discriminative than those generated from individual modalities. Results also highlight the link between fingerprint similarity and genetic proximity, monozygotic twins having more similar fingerprints than dizygotic or non-twin siblings. This link is also reflected in the differences of feature correspondences between twin/sibling pairs, occurring in major brain structures and across hemispheres. The robustness of the proposed framework to factors like image alignment and scan resolution, as well as the reproducibility of results on retest scans, suggest the potential of multi-modal brain fingerprinting for characterizing individuals in a large cohort analysis. In addition, taking inspiration from the computer vision community, the proposed rank retrieval evaluation based on the task of twin/sibling identification and using Mean Average Precision (MAP) can be used for a standardized comparison of future brain fingerprints.

neuroscience↗

bioRxiv2017

Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data

Herpes simplex virus 2 is a human herpesvirus found worldwide that causes genital lesions and more rarely causes encephalitis. This pathogen is most common in Africa, and particularly in central and east Africa, an area of particular significance for the evolution of modern humans. Unlike HSV1, HSV2 has not simply co-speciated with humans from their last common ancestor with primates. HSV2 jumped the species barrier between 1.4 and 3 MYA, most likely through an intermediate but unknown hominin species.\n\nIn this paper, we use probability-based network analysis to determine the probable path between intermediate hosts of HSV2, from chimpanzees to modern humans, using paleoenvironmental data on the distribution of African tropical rainforest over the last 3 million years and data on the age and distribution of fossil species of hominin present in Africa between 1.4 and 3 MYA. Our model identifies Homo rudolfensis as the most likely intermediate host of HSV2

evolutionary biology↗