Biology subjects

Das, T.

Publications and source records attributed to Das, T..

43 records · Page 3Linked to original sources

bioRxiv2020

Expression of Toll like Receptor 4 in the ductal epithelial cells of the Breast tumor microenvironment is correlated with the invasiveness of the tumor

Toll like receptors are expressed by variety of cells, mainly immune cells and also found to have role in the tumor microenvironment. Among them, Toll like receptors-4 is found to modulate tumor progression. But definitive action of TLR4 in tumor progression is not well understood. In the present study, in breast tumor samples, expression of TLR4 was studied by immunohistochemistry method while MMP2 and MMP9 expression were studied by gelatin zymography. Kaplan Meier plotter was used to test survivability. Breast cancer cells - MCF7, MDA MB 231, T47D were studied in the presence of TLR4 lignd LPS, with the help of MTT assay, BrdU incorporation assay, scratch wound healing assay and invasion assay. Activation of TLR4 in MCF7 which is TP53 wild type has no significant effect in proliferative rate, adhesiveness and invasiveness. While in MDA-MB-231 and T47D which are TP53 mutant, there were a significant increase in adhesiveness and migratory ability, observed., TLR4 had been expressed in breast tumor of invasive ductal carcinoma (IDC) and was found to be significantly correlated with lymph node involvement. Kaplan Meier plotter analysis revealed that high TLR4 expression might serve as an immune-protectant in invading cancer cells of TP53 wild state. It has been revealed that activation of TLR4 in breast cancer cells leads to higher expression of EMT related genes along with matrix metalloproteinases helping in migration and invasion of cells. Kaplan Meier plotter analysis revealed that TP53 wild status of the patient along with high TLR4 expression has a good overall survival of the patients.

cancer biology↗

bioRxiv2019

Glutamate and Dysconnection in the Salience Network: Neurochemical, Effective-connectivity, and Computational Evidence in Schizophrenia

In the dysconnection hypothesis, psychosis is caused by NMDA hypofunction resulting in aberrant network connectivity. Combining a cognitive-control task, functional magnetic resonance spectroscopy, and functional magnetic resonance imaging, we tested this hypothesis in the salience network of 20 first-episode psychosis (FEP) and 20 healthy control (HC) subjects. Across groups, glutamate concentration in the dorsal anterior cingulate cortex (dACC) was associated with higher and lower inhibitory connectivity in the dACC and in the anterior insula (AI) respectively. Crucially, glutamate concentration correlated negatively with the inhibitory influence on the excitatory neuronal population in the dACC of FEP subjects. Furthermore, aberrant computational parameters of the cognitive-control task performance were associated with aberrant inhibitory connections. Finally, the strength of connections from the dACC to the AI correlated negatively with severity of social withdrawal. These findings support a link between glutamate-mediated cortical disinhibition, deficits in effective connectivity, and computational performance in psychosis.

neuroscience↗

bioRxiv2019

eMED-DNA: An in silico operating system for clinical medical data storage within the human genome

The propitious developments in molecular biology and next generation sequencing have enabled the possibility for DNA storage technologies. However, the full application and power of our genomic revolution have not been fully utilized in clinical medicine given a lack of transition from research to real world clinical practice. This has identified an increasing need for an operating system which allows for the transition from research to clinical use. We present eMED-DNA, an in silico operating system for archiving and managing all forms of electronic health records (EHRs) within ones own copy of the sequenced genome to aid in the application and integration of genomic medicine within real world clinical practice. We incorporated an efficient and sophisticated in-DNA file management system for the lossless management of EHRs within a genome. This represents the first in silico integrative system which would bring closer the utopian ideal for integrating genotypic data with phenotypic clinical data for future medical practice.

bioinformatics↗

bioRxiv2019

Polarity protein distribution on the metaphase furrow regulates hexagon dominated plasma membrane organization in syncytial Drosophila embryos

Epithelial cells have a polarised distribution of protein complexes on the lateral membrane and are present as a polygonal array dominated by hexagons. Metazoan embryogenesis enables the study of temporal formation of the polygonal array and mechanisms that regulate its distribution. The plasma membrane of the syncytial Drosophila blastoderm embryo is organized as a polygonal array during cortical division cycles with an apical membrane and lateral furrow in between adjacent nuclei. We find that polygonal plasma membrane organization arises in syncytial division cycle 11 and hexagon dominance occurs with increase in furrow length in cycle 12. This is coincident with DE-cadherin and Bazooka enrichment at edges and the septin, Peanut enrichment at vertices of the base of the furrow. DE-cadherin depletion leads to loss of hexagon dominance. Bazooka and Peanut depletion leads to a delay in occurrence of hexagon dominance from nuclear cycle 12 to 13. Hexagon dominance in Bazooka and Peanut mutants occurs with furrow extension and correlates with increase in DE-cadherin in syncytial cycle 13. We conclude that a change in polarity complex distribution leads to loss of furrow stability thereby changing the polygonal organization of the blastoderm embryo.\n\nHighlight Summary for TOCMetazoan embryogenesis starts with the formation of polygonal epithelial-like cells. We show that hexagon dominance in polygonal epithelial-like plasma membrane organization occurs in nuclear cycle 12 in the syncytial blastoderm Drosophila embryo. DE-cadherin and Bazooka distribution along the lateral furrow regulates this hexagon dominance.

developmental biology↗

bioRxiv2019

STELAR: A statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency

BackgroundSpecies tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets.\n\nResultsWe present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees. We formalized the constrained triplet consensus (CTC) problem and showed that the solution to the CTC problem is a statistically consistent estimate of the species tree under the multi-species coalescent (MSC) model. STELAR is an efficient dynamic programming based solution to the CTC problem which is highly accurate and scalable. We evaluated the accuracy of STELAR in comparison with SuperTriplets, which is an alternate fast and highly accurate triplet-based supertree method, and with MP-EST and ASTRAL - two of the most popular and accurate coalescent-based methods. Experimental results suggest that STELAR matches the accuracy of ASTRAL and improves on MP-EST and SuperTriplets.\n\nConclusionsTheoretical and empirical results (on both simulated and real biological datasets) suggest that STELAR is a valuable technique for species tree estimation from gene tree distributions.

bioinformatics↗

bioRxiv2018

Regulation of Exocytosis and Mitochondrial Relocalization by Alpha-Synuclein in a Mammalian Cell Model

We characterized phenotypes in RBL-2H3 mast cells transfected with human alpha synuclein (a-syn) using stimulated exocytosis of recycling endosomes as a proxy for similar activities of synaptic vesicles in neurons. We found that low expression of a-syn inhibits stimulated exocytosis and that higher expression causes slight enhancement. NMR measurements of membrane interactions correlate with these functional effects: they are eliminated differentially by mutants that perturb helical structure in the helix 1 (A30P) or NAC/helix-2 (V70P) regions of membrane-bound a-syn, but not by other PD-associated mutants or C-terminal truncation. We further found that a-syn (but not A30P or V70P mutants) associates weakly with mitochondria, but this association increases markedly under conditions of cellular stress. These results highlight the importance of specific structural features of a-syn in regulating vesicle release, and point to a potential role for a-syn in perturbing mitochondrial function under pathological conditions.

cell biology↗

bioRxiv2018

A randomised exploratory investigation of the effects of Attention vs Working Memory Training on cognitive performance and everyday functioning following stroke.

Difficulties with attention are common following stroke and are associated with poor outcome. Home-based online cognitive training may have to the potential to provide an efficient and effective way to improve attentional functions in such patients. Little work has been carried out to assess the efficacy of this approach in stroke patients, and the lack of studies with active control conditions and rigorous evaluations of cognitive functioning pre and post training means understanding is limited as to whether and how such interventions may be effective. Here we compare the effects of 20 days of active cognitive training using either novel Selective Attention Training (SAT) or commercial Working Memory Training (WMT) programme, versus a waitlist control group, on a wide range of attentional and working memory tasks, as well as on self-reported everyday functioning. We demonstrate separable effects of each of the active training conditions, with SAT leading to improvements in both spatial and non-spatial aspects of attention and WMT leading to improvements only on very closely related working memory tasks. Both training groups reported improvements in everyday functioning, which were associated with improvements in attentional functions, suggesting that improving attention may be of particular importance in maximising functional recovery in this patient group.

clinical trials↗