Biology subjects

N, S.

Publications and source records attributed to N, S..

5 recordsLinked to original sources

bioRxiv2023

Extremely oligotrophic and complex organic compounds degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2-limitation obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a [~]3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates genomes and the habitats metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment-cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains survival in the critically carbon-depleted layers below the explored sediment-depths (core-bottom organic carbon: 0.5-1.0 % w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously-reported sources such as Nitrosopumilus species.

microbiology↗

bioRxiv2022

Novel Computational Models of Evoked Dopamine Release In Vivo Measured by Fast Scan Cyclic Voltammetry Quantify the Regulation of Presynaptic Kinetics by Synucleins

Dopamine neurotransmission in the striatum is central to many normal and disease functions. Ventral midbrain dopamine neurons exhibit ongoing tonic firing that produce low extrasynaptic levels of dopamine below the detection of extrasynaptic electrochemical recordings ([~]10 - 20 nanomolar), with superimposed bursts that can saturate the dopamine uptake transporter and produce transient micromolar concentrations. The bursts have previously been shown to lead to presynaptic plasticity via multiple mechanisms, but analysis methods for these kinetic parameters are limited. To provide a deeper understanding of the mechanics of dopamine neurotransmission, we present three computational models of dopamine release with different levels of spatiotemporal complexity to analyze in vivo fast-scan cyclic voltammetry recordings from the dorsal striatum of mice. The models accurately fit to the cyclic voltammetry data and provide estimates of presynaptic dopamine facilitation/depression kinetics and dopamine transporter reuptake kinetics. We use the models to analyze the role of synuclein proteins in neurotransmission and quantify recent findings linking presynaptic protein -synuclein to the short-term facilitation and long-term depression of dopamine release.

neuroscience↗

bioRxiv2021

Eudesmol-A promising inhibitor for glucosyltransferase: Docking and Molecular dynamics study

The loss of natural teeth can be avoided by invoking the molecular signal behind teeth regeneration. The destruction of the connective tissues is mainly due to bacterial origin which reacts to dental caries, a multifactorial disease. Glycosyl transferase is the enzyme which is involved in the glycosidic linkage. Glucosyltransferase inactivation reduces dental caries. This enzyme is a crucial virulence factor of Streptococcus mutans, a major pathogen that causes dental caries. In this present work, screening was done with library of anti-oxidant and anti-inflammatory molecules against the crystal structure of the target protein. Based on the predicted binding affinities, small molecules were selected and evaluated for their activity. Further, attempts were done to evaluate the toxicity of the lead compounds and compounds with no toxicity and good binding affinity were subjected for simulation and compared with reference complex. The potential energy of Glycosyl transferase-Eudesmol (proposed compound) (-1500 kj/mol) indicates its higher stability as compared to Glycosyl tranferase-G43 (reference) complex (-1100kj/mol).The inactives and actives compound for Glycosyl transferase was predicted from DeepScreening server.

bioinformatics↗

bioRxiv2021

Activity in the dorsomedial striatum decreases with improvement in motor coordination

It has been suggested that the dorsomedial striatum (DMS) facilitates the early stages of motor learning for goal-directed actions, whereas at later stages, control is transferred to the dorsolateral striatum (DLS), which enables the motor actions to become a skill or habit. It is unknown whether these striatal regions are simultaneously active while expertise is acquired during skill learning. To address this question, we developed the "treadmill training task" to track changes in mouse locomotor coordination during practice at running that simultaneously provides a means to measure local neuronal activity using photometry. We analyzed body position and paw movement to evaluate changes in motor coordination over practice sessions on the treadmill using DeepLabCut and custom-built code. By correlating improvements in motor coordination during training with simultaneous neuronal calcium activity in the striatum, we found that DMS direct pathway neurons exhibited decreased activity as the mouse gains proficiency at running. In contrast, direct pathway activity in the DLS was similar throughout training and did not correlate with learned skill proficiency. Pharmacological blockade of D1 dopamine receptors in these subregions during task performance confirmed that dopamine neurotransmission in the DMS direct pathway activity is necessary for efficient motor coordination learning, while dopamine signalling in the DLS is important for both coordination learning and maintenance of the acquired skill. These results provide new tools to measure changes in fine motor skills during simultaneous recordings of brain activity, revealing fundamental features of the neuronal substrates of motor learning.

neuroscience↗

bioRxiv2019

Preparation of Organ Scaffolds by Decellularization of Pancreas and Re-functionalization

Extracellular matrix of each tissue is unique in composition, architecture and finer details that support the very identity of the organ by regulating the status/character of the cells within it. Tissue engineering centers around creating a niche similar to the natural one, with a purpose of developing an organ/oid. In this study, whole organ decellularization of pancreas was attempted followed by reseeding it with adult mesenchymal stem cells. Decellularization completely removes cells leaving behind extracellular matrix rich scaffold. After reseeding, mesenchymal stem cells differentiate into pancreas specific cells. Upon transplantation of recellularized pancreas in streptozotocin induced diabetic mice, this organ was capable of restoring its histomorphology and normal functioning. Restoration of endocrine islets, the exocrine acinar region, and vascular network was seen in transplanted pancreas. The entire process of functional recovery took about 20 days when the mice demonstrated glucoregulation, though none achieved gluconormalization. Transplanted mice upon feeding show insulin and c-peptide in circulation. This process demonstrates that natural scaffolds of soft organs can be refunctionalized using recipients cells to counter immune problems arising due to organ transplantation.

cell biology↗