Biology subjects

Manikandan, A.

Publications and source records attributed to Manikandan, A..

6 recordsLinked to original sources

bioRxiv2026

Junb acts downstream of the Il-11/Stat3 signaling axis to limit tissue damage induced fibro-inflammation during regeneration

Inflammation is essential for regeneration yet can also drive fibroinflammatory remodeling; what determines these opposing outcomes remains unclear. Comparative transcriptomic analyses revealed that injured mouse hearts activated a broad inflammatory program, whereas zebrafish hearts mounted a restricted response characterized by selective il11 induction. This divergence extended across tissues and species: the non-regenerative mammalian injuries examined shared an inflammatory signature distinct from regenerative vertebrate contexts. We identified the AP-1 transcription factor Junb as an Il-11-Stat3-dependent regulator that restrains inflammation during fin fold regeneration. Combined loss of junba and junbb amplified a mammalian-like inflammatory program, increased neutrophil recruitment and fibroinflammatory gene expression, and reduced proliferation and regenerative outgrowth. Strikingly, dexamethasone or ibuprofen substantially restored regeneration in Junb deficient zebrafish larvae, demonstrating that hyperinflammation is a major determinant of regenerative failure. Thus, the Il-11-Stat3-Junb axis maintains a regeneration permissive inflammatory state preventing a regenerative response from shifting toward mammalian-like fibroinflammation.

immunology↗

bioRxiv2025

Machine learning-based structural classification of lytic polysaccharide monooxygenases

Lytic polysaccharide monooxygenase (LPMO) is a copper-dependent redox enzyme and according to CAZy is classified either as cellulolytic or chitinolytic. According to CAZy, there are eight families of LPMO namely AA9, AA10, AA11, AA13, AA14, AA15, AA16, and AA17, where AA stands for Auxiliary Activity. Previously, using the sequence information machine learning-based functional annotation was successfully completed using neural network and LSTM models. This was done for AA9 and AA10 as the number of sequences was large enough to train a model with high-performance indices. Here, the goal is to use existing 3D structures and AI-based models of the remaining LPMO sequences and train a machine learning model to identify and classify LPMO with the help of structural features by performing either a neural network algorithm or other suitable methods. Using the features of LPMO such as surface depth, accessible area, electrostatic charge distribution, and geometric features (independent features that define the shape and are not based on enzyme reaction mechanism) we will identify the features with high signal-to-noise ratio/significance using ensemble feature selection method. The features were extracted using Pymol, MdTraj, Biopython, Open3d, and Bio3D tools from OBJ and STL format. The model thus trained using structural features will enable identifying and annotating newer LPMO sequences belonging to one of the eight AA families.

bioinformatics↗

bioRxiv2023

Role of Tyrosine Phosphorylation in PTP-PEST

We study the influence of tyrosine phosphorylation on PTP-PEST, a cytosolic protein tyrosine phosphatase. Utilizing a combination of experimental data and computational modeling, specific tyrosine sites, notably Y64 and Y88, are identified for potential phosphorylation. Phosphorylation at these sites affects loop dynamics near the catalytic site, altering interactions among key residues and modifying the binding pockets size. This, in turn, impacts substrate binding, as indicated by changes in binding energy. Our findings provide insights into the structural and functional consequences of tyrosine phosphorylation on PTP-PEST, enhancing our understanding of its effects on substrate binding and catalytic conformation.

biophysics↗

bioRxiv2022

In-silico identification of Tyr232 in AMPKα2 as a dephosphorylation site for the protein tyrosine phosphatase PTP-PEST

The AMP-activated protein kinase (AMPK) is known to be activated by the protein tyrosine phosphatase non-receptor type 12 (PTP-PEST) under hypoxic conditions. This activation is mediated by tyrosine dephosphorylation of the AMPK subunit. However, the identity of the phosphotyrosine residues remains unknown. In this study we first predicted the structure of the complex of the AMPK2 subunit and PTP-PEST catalytic domain using bioinformatics tools and further confirm the stability of the complex using molecular dynamics simulations. Evaluation of the protein-protein interfaces indicates that residue Tyr232 is the most likely site of dephosphorylation on AMPK2. In addition, we explored the effect of phosphorylation of PTP-PEST residue Tyr64 on the stability of the complex. The phosphorylation of Tyr64, an interface residue, enhances the stability of the complex via the rearrangement of a network of electrostatic interactions in conjunction with conformational changes in the catalytic WPD loop. Our findings present a plausible structural basis of AMPK regulation mediated by PTP-PEST and shows how phosphorylation of PTP-PEST could be involved in its activation.

biochemistry↗

bioRxiv2020

Dynamics of the COVID -19 Related Publications

BackgroundThis study aims to analyze the dynamics of the published articles and preprints of Covid-19 related literature from different scientific databases and sharing platforms. MethodsThe PubMed, Elsevier, and Research Gate (RG) databases were under consideration in this study over a specific time. Analyses were carried out on the number of publications as (a) function of time (day), (b) journals and (c) authors. Doubling time of the number of publications was analyzed for PubMed "all articles" and Elsevier published articles. Analyzed databases were (1A) PubMed "all articles" (01/12/2019-12/06/2020) (1B) PubMed Review articles (01/12/2019-2/5/2020) and (1C) PubMed Clinical Trials (01/01/2020-30/06/2020) (2) Elsevier all publications (01/12/2019-25/05/2020) (3) RG (Article, Pre Print, Technical Report) (15/04/2020-30/4/2020). FindingsTotal publications in the observation period for PubMed, Elsevier, and RG were 23000, 5898 and 5393 respectively. The average number of publications/day for PubMed, Elsevier and RG were 70.0 {+/-}128.6, 77.6{+/-}125.3 and 255.6{+/-}205.8 respectively. PubMed shows an avalanche in the number of publication around May 10, number of publications jumped from 6.0{+/-}8.4/day to 282.5{+/-}110.3/day. The average doubling time for PubMed, Elsevier, and RG was 10.3{+/-}4 days, 20.6 days, and 2.3{+/-}2.0 days respectively. In PubMed average articles/journal was 5.2{+/-}10.3 and top 20 authors representing 935 articles are of Chinese descent. The average number of publications per author for PubMed, Elsevier, and RG was 1.2{+/-}1.4, 1.3{+/-}0.9, and 1.1{+/-}0.4 respectively. Subgroup analysis, PubMed review articles mean and median review time for each article were <0|17{+/-}17|77> and 13.9 days respectively; and reducing at a rate of-0.21 days (count)/day. InterpretationAlthough the disease has been known for around 6 months, the number of publications related to the Covid-19 until now is huge and growing very fast with time. It is essential to rationalize the publications scientifically by the researchers, authors, reviewers, and publishing houses. FundingNone

scientific communication and education↗

bioRxiv2020

Protein tyrosine phosphatase-PEST (PTP-PEST) mediates hypoxia-induced endothelial autophagy and angiogenesis through AMPK activation

Global and endothelial loss of PTP-PEST is associated with impaired cardiovascular development and embryonic lethality. Although hypoxia is implicated in vascular morphogenesis and remodelling, its effect on PTP-PEST remains unexplored. Here we report that hypoxia (1% oxygen)increases protein levels and catalytic activity of PTP-PEST in primary endothelial cells. Immunoprecipitation followed by mass spectrometry (LC/MS/MS) revealed that AMP-activated protein kinase alpha subunits (AMPK 1 and 2) interact with PTP-PEST under normoxia but not in hypoxia. Co-immunoprecipitation experiments confirmed this observation and determined that AMPK subunits interact with the catalytic domain of PTP-PEST. Knock-down of PTP-PEST abrogated hypoxia mediated tyrosine dephosphorylation and activation of AMPK (Thr172 phosphorylation). Absence of PTP-PEST also blocked hypoxia-induced autophagy (measured as LC3 degradation and puncta formation) which was rescued by AMPK activator, metformin (500{micro}M). Since endothelial autophagy is a pre-requisite for angiogenesis, knock-down of PTP-PEST also attenuated endothelial cell migration and capillary tube formation with autophagy inducer rapamycin (200nM) rescuing these effects. In conclusion, this work identifies for the first time PTP-PEST as a regulator of hypoxia-induced AMPK activation and endothelial autophagy to promote angiogenesis.

cell biology↗