Biology subjects

Goswami, C.

Publications and source records attributed to Goswami, C..

12 recordsLinked to original sources

bioRxiv2024

DeepFocus: A Transnasal Approach for Optimized Deep Brain Stimulation of Reward Circuit Nodes

ObjectiveTranscranial electrical stimulation (TES) is an effective technique to modulate brain activity and treat diseases. However, TES is primarily used to stimulate superficial brain regions and is unable to reach deeper targets. The spread of injected currents in the head is affected by volume conduction and the additional spreading of currents as they move through head layers with different conductivities, as is discussed in [1]. In this paper, we introduce DeepFocus, a technique aimed at stimulating deep brain structures in the brains "reward circuit" (e.g. the orbitofrontal cortex, Brodmann area 25, amygdala, etc.). ApproachTo accomplish this, DeepFocus utilizes transnasal electrode placement (under the cribriform plate and within the sphenoid sinus) in addition to electrodes placed on the scalp, and optimizes current injection patterns across these electrodes. To quantify the benefit of DeepFocus, we develop the DeepROAST simulation and optimization platform. DeepROAST simulates the effect of complex skull-base bones geometries on the electric fields generated by DeepFocus configurations using realistic head models. It also uses optimization methods to search for focal and efficient current injection patterns, which we use in our simulation and cadaver studies. Main ResultsIn simulations, optimized DeepFocus patterns created larger and more focal fields in several regions of interest than scalp-only electrodes. In cadaver studies, DeepFocus patterns created large fields at the medial orbitofrontal cortex (OFC) with magnitudes comparable to stimulation studies, and, in conjunction with established cortical stimulation thresholds, suggest that the field intensity is sufficient to create neural response, e.g. at the OFC. SignificanceThis minimally invasive stimulation technique can enable more efficient and less risky targeting of deep brain structures to treat multiple neural conditions.

neuroscience↗

bioRxiv2024

TRPV4 modulation affects mitochondrial parameters in adipocytes and its inhibition upregulates lipid accumulation

Enhanced lipid-droplet formation by adipocytes is a complex process and relevant for obesity. Using knock-out animals, involvement of TRPV4, a thermosensitive ion channel in the obesity has been proposed. However, exact role/s of TRPV4 in adipogenesis and obesity remain unclear and contradictory. Here we used in vitro culture of 3T3L-1 preadipocytes and primary murine-mesenchymal stem cells as model systems, and a series of live-cell-imaging to analyse the direct involvement of TRPV4 exclusively at the adipocytes that are free from other complex signalling as expected in in-vivo condition. Functional TRPV4 is endogenously expressed in pre- and in mature-adipocytes. Pharmacological inhibition of TRPV4 enhances differentiation of preadipocytes to mature adipocytes, increases expression of adipogenic and lipogenic genes, enhances cholesterol, promotes bigger lipid-droplet formation and reduces the lipid droplet temperature. TRPV4 regulates mitochondrial-temperature, Ca2+-load, ATP, superoxides, cardiolipin, membrane potential ({Delta}{Psi}m), and lipid-mitochondrial contact sites. TRPV4 also regulates the extent of actin fibres, affecting the cells mechanosensing ability. These findings link TRPV4-mediated mitochondrial changes in the context of lipid-droplet formation involved in adipogenesis and confirms the direct involvement of TRPV4 in adipogenesis. These findings may have broad implication in treating adipogenesis and obesity in future. Summary StatementThermosensitive ion channel TRPV4 regulates adipogenesis and changes mitochondria metabolism to facilitate bigger lipid droplet formation

cell biology↗

bioRxiv2023

InGene: Finding influential genes from embeddings of nonlinear dimension reduction techniques

We introduce InGene, the first of its kind, fast and scalable non-linear, unsupervised method for analyzing single-cell RNA sequencing data (scRNA-seq). While non-linear dimensionality reduction techniques such as t-SNE and UMAP are effective at visualizing cellular sub-populations in low-dimensional space, they do not identify the specific genes that influence the transformation. InGene addresses this issue by assigning an importance score to each expressed gene based on its contribution to the construction of the low-dimensional map. InGene can provide insight into the cellular heterogeneity of scRNA-seq data and accurately identify genes associated with cell-type populations or diseases, as demonstrated in our analysis of scRNA-seq datasets.

bioinformatics↗

bioRxiv2020

Ratio of hydrophobic-hydrophilic and positive-negative residues at lipid-water-interface influences surface expression and channel-gating of TRPV1

During evolution, TRPV1 has lost, retained or selected certain residues at Lipid-Water-Interface (LWI) and formed specific patterns there. The ratio of "hydrophobic-hydrophilic" and "positive-negative charged" residues at the inner LWI remains conserved throughout vertebrate evolution and play important role in regulating TRPV1 trafficking, localization and functions. Arg575 is an important residue as Arg575Asp mutant has reduced Capsaicin-sensitivity, surface expression, colocalization with lipid-raft markers, cell area, and increased cell lethality. This lethality is due to the disruption of the ratio between positive-negative charges there. Such lethality can be rescued by either using TRPV1-specfic inhibitor 5-IRTX or by restoring the positive-negative charge ratio at that position, i.e. by introducing Asp576Arg mutation in Arg575Asp backbone. We propose that Arg575Asp mutant confers TRPV1 in a "constitutive-open-like" condition. These findings have broader implication in understanding the molecular basis of thermo-gating and channel-gating and the microenvironments involved in such process that goes erratic in different diseases.

cell biology↗

bioRxiv2020

The mechanics of Temporal Interference stimulation

We utilize single neuron models to understand mechanisms behind Temporal Interference (TI) stimulation (also called "Interferential Stimulation"). We say that a neuron exhibits TI stimulation if it does not fire for a high-frequency sinusoidal input, but fires when the input is a low-frequency modulation of the high-frequency sinusoid (specifically that generated by addition of two high frequency sinusoids with a small difference in their frequencies), while the maximum amplitude is kept the same in both cases. Our key observation - that holds for both FitzHugh-Nagumo and Hodgkin-Huxley neuron models - is that for neuron models that do exhibit TI stimulation, a high frequency pure sinusoidal input results in a current balance between inward and outward currents. This current balance leads to a subthreshold periodic orbit that keeps the membrane potential from spiking for sinusoidal inputs. However, the balance is disturbed when the envelope of the sinusoids is modulated with a high slope: the fast-changing envelope activates fast depolarizing currents without giving slow outward currents time to respond. This imbalance causes the membrane potential to build up, causing the neuron to fire. This mechanistic understanding can help design current waveforms for neurons that exhibit TI stimulation, and also help classify which neuron-types may or may not exhibit TI stimulation.

neuroscience↗

bioRxiv2020

Differential expression and localization of thermosensitive Transient Receptor Potential Vanilloid (TRPV) channels in the mature sperm of white pekin duck (Anas platyrhynchos)

Sperm cells have the ability of precise chemotactic and thermotactic movement which is crucial for fertilization, yet the key molecules involved in the detection of different chemical and physical stimuli and guide the sperm cells for proper navigation are not known. This aspect is more complex as each species have their own reproductive identity. Never-the-less, Ca2+-signaling and thus a series of Ca2+-channels seem to coordinate in order to regulate different functions mediated by sperm cells. However, such aspects are controlled by different Ca2+ channels and have species-specific differences. In this work we explored if TRPV channels are endogenously expressed in the mature spermatozoa obtained from avian species. We have used the sperm cells of white pekin duck (Anas platyrhynchos) as a representative avian species to explore the endogenous expression and localization of different TRPV channels. Western blot analysis (WB), flow cytometry, confocal imaging and super resolution imaging was performed for the characterization. Our results strongly suggest the expression and distinct localization of different TRPV channels in the sperm cells. All these TRPV channels are mainly absent in the head region. Only TRPV3 and TRPV4 are sparsely present in the neck region enriched with mitochondria. All these channels (TRPV1-6) are present in the tail region. The differential localization of TRPVs in duck sperm indicate their respective functions relevant in fertilization process of avian sperm. These findings may also have commercial importance in poultry production, cryopreservation of sperm as well as conservation of endangered species through artificial insemination.

cell biology↗

bioRxiv2019

TRPV2 activation reorganizes actin cytoskeleton, induces neurite initiation and branching by altering cAMP levels

Understanding of molecules and their role in neurite initiation and/or extension is not only helpful to prevent different neurodegenerative diseases but also can be important by which neuronal damages can be repaired. In this work we explored the role of TRPV2, a non-selective cation channel in the context of neurite functions. Using western blot, immunofluorescence, and live cell Ca2+-imaging; we confirm that functional TRPV2 is endogenously present in the F11 cell, a model system mimicking peripheral neuron. In F11 cells TRPV2 localizes in specific sub-cellular regions enriched with filamentous actin, such as in growth cone, filopodia, lamellipodia and in neurites. TRPV2 regulates actin cytoskeleton and also interacts with soluble actin. Ectopic expression of TRPV2-GFP but not GFP-only in F11 cell induces more primary and secondary neurites, confirming its role in neurite initiation, extension and branching events. TRPV2-mediated neuritogenesis is dependent on wild-type TRPV2 as cells expressing TRPV2 mutants reveal no neuritogenesis. However, TRPV2-mediated neuritogenesis is unperturbed by the chelation of intracellular Ca2+ by BAPTA-AM, and thus involves Ca2+-independent signaling events also. We demonstrate that pharmacological modulation of TRPV2 alters cellular cAMP levels. These findings are relevant to understand the sprouting of new neurites, neuroregeneration and neuronal plasticity at the cellular, subcellular and molecular level. Such understanding may have border implication in neurodegeneration and peripheral neuropathy.

neuroscience↗

bioRxiv2019

Transient Receptor Potential Ankyrin1 channel is endogenously expressed in T cells and regulates immune functions

Transient Receptor Potential channel subfamily A member 1 (TRPA1) is a non selective cationic channel, identified initially as a cold sensory receptor. TRPA1 responds to diverse exogenous and endogenous stimuli associated with pain and inflammation. However, the role of TRPA1 towards T cell responses remains scanty. In this work, we explored the endogenous expression of TRPA1 in T cells. By RT-PCR we confirmed the expression of TRPA1 in T cell at RNA level. Using confocal microscopy as well as flow cytometry, we demonstrated that TRPA1 is endogenously expressed in primary murine splenic T cells as well as in primary human T cells. The endogenous expression of TRPA1 is confirmed by using another antibody. TRPA1 was primarily located at the cell surface. TRPA1-specific activator namely AITC increases intracellular Ca2+-levels while two different inhibitors namely A-967079 as well as HC-030031 reduce intracellular Ca2+-levels in T cells. Such Ca2+-influx can also be influenced by chelation of intracellular Ca2+ as well as extracellular Ca2+. TRPA1 expression was found to be increased during CD3/CD28 (TCR) or ConA driven stimulation in T cells. TRPA1-specific inhibitor treatment prevented induction of CD25, CD69 in ConA/TCR stimulated T cells and secretion of cytokines like TNF, IFN-{gamma} and IL-2 suggesting that endogenous activity of TRPA1 may be involved in T cell activation. Collectively these results may have implication in T cell-mediated responses and possible role of TRPA1 in immunological disorders.

immunology↗

bioRxiv2018

A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage

Bacterial type III secretion systems (T3SS) play an important role in pathogenesis of Gram-negative infections. Enteropathogenic and enterohemorrhagic Escherichia coli contain a well-defined T3SS but in addition a second T3SS termed E. coli T3SS 2 (ETT2) has been described in a number of strains of E. coli. The majority of E. coli contain elements of a genetic locus encoding ETT2, but which has undergone significant mutational attrition rendering it without predicted function. Only a very few strains have been reported to contain an intact ETT2 locus. To investigate the occurrence of the ETT2 locus in strains of human pathogenic E. coli, we carried out genomic sequencing of 162 isolates obtained from patient blood cultures in Scotland. We found that all 26 ST69 isolates from this collection contained an intact ETT2 together with an associated eip locus which encodes putative secreted ETT2 effectors as well as eilA, a gene encoding a putative transcriptional regulator of ETT2 associated genes. Using a reporter gene for eilA activation, we defined conditions under which this gene was differentially activated. However, comparison of secreted proteins from ST69 strains under high and low eilA activation failed to identify any ETT2 secreted substrates. The conservation of the genes encoding ETT2 in human pathogenic ST69 strains strongly suggests it has functional importance in infection, although its exact functional role remains obscure.\n\nImportanceOne of the commonest bacteria causing bloodstream infections in humans is Escherichia coli, which has a significant morbidity and mortality. Better understating of the mechanisms by which this microbe can invade blood could lead to more effective prevention and treatment. One mechanism by which some strains cause disease is by elaboration of a specialized secretion system, the type III secretion system (T3SS), encoded by the locus of enterocyte effacement (LEE). In addition to this well-defined T3SS, a second T3SS has been found in some E. coli strains termed E. coli type III secretion system 2 (ETT2). Most strains carry elements of the ETT2 locus, but with significant mutational attrition rendering it functionless. The significance of our work is that we have discovered that human bloodstream isolates of E. coli of sequence type 69 contain a fully intact ETT2 and associated genes, strongly suggesting its functional importance in human infection.

microbiology↗

bioRxiv2018

TRPV4 interacts with mitochondrial proteins and acts as a mitochondrial structure-function regulator

TRPV4 has been linked with the development of sensory defects, neuropathic pain, neurodegenerative disorders such as Charcot Marie Tooth disease and various muscular dystrophies. In all these cases mitochondrial abnormalities were tagged as cellular hallmarks and such abnormalities have been reported as key factor for the pathophysiological conditions. Mitochondria also have the unique ability to sense and regulate their own temperature. Here, we demonstrate that TRPV4, a thermosensitive ion channels, localizes to a subpopulation of mitochondria in various cell lines, in primary cells and also in sperm cells. Improper expression and/or function of TRPV4 induce several mitochondrial abnormalities such as low oxidative potential, high Ca2+-influx and changes in electron transport chain functions. TRPV4 is also involved in regulation of mitochondrial morphology, smoothness, and fusion-fission events. The C-terminal cytoplasmic region of TRPV4 can localize it to mitochondria and interacts with mitochondrial proteins including Hsp60, Mfn1 and Mfn2. Regulation of mitochondria by TRPV4 may contribute to previously uncharacterized mitochondria-specific functions observed in various cell types. This discovery may help to link TRPV4-mediated channelopathies with mitochondria-mediated diseases.

cell biology↗

bioRxiv2018

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

Farm animals have been identified as reservoirs of Clostridium difficile PCR-ribotype 078 (RT078). Since 2005, the incidence of human clinical cases (frequently severe), with this genotype has increased. We aimed to understand this change, by studying the recent evolutionary history of RT078. Phylogenetic analysis of international genomes (isolates from 2006-2014) revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired different alleles of the tetracycline resistance gene tetM. Consequently, an unusually high proportion of RT078 genomes were tetM positive (76.5%). Additional tetracycline resistance determinants were also identified, some for the first time in C. difficile (efflux pump tet40). Each tetM-clonal expansion lacked geographic structure, indicating rapid international spread. Resistance determinants for C. difficile-infection-triggering antimicrobials including fluoroquinolones and clindamycin were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid spread via the food-chain may explain the increased RT078 prevalence in humans.

microbiology↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗