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Biology subjects

Ahmed, S.

Publications and source records attributed to Ahmed, S..

At least 91 records · Page 5Linked to original sources

Wat1/mLst8, a TOR complex protein regulates mitochondrial integrity and calcium ion homeostasis in fission yeast S. pombe

The mTOR complexes play a fundamental role in mitochondrial biogenesis and cellular homeostasis. Wat1, an ortholog of mammalian Lst8 is an important component of TOR complex and is essential for the regulation of downstream signaling. Earlier we reported the role of Wat1 in oxidative stress response. Here, we show that the inactivation of wat1 leads to respiratory defects and mitochondrial depolarization leading to decrease in ATP production. The confocal and electron microscopy in wat1{Delta} cells revealed the fragmented mitochondrial morphology implying its role in mitochondrial fission. Furthermore, we also showed its role in autophagy and the maintenance of calcium ion homeostasis. Additionally, tor2-287 mutant cells also exhibit defects in mitochondrial integrity indicating the TORC1-dependent involvement of Wat1 in the maintenance of mitochondrial homeostasis. The interaction studies of Wat1 and Tor2 with Por1 and Mmm1 proteins revealed a cross-talk between mitochondria and endoplasmic reticulum through the Mitochondria-associated membranes (MAM) and endoplasmic reticulum-mitochondria encounter structure (ERMES) complex, involving TORC1. Taken together, this study demonstrates involvement of Wat1/mLst8 in harmonizing various mitochondrial functions, redox status, and Ca2+ homeostasis.

cell biology↗

NTpred: A robust and precise machine learningframework for in-silico identification of Tyrosine nitration sites in protein sequences

Post-translational modifications (PTMs) either enhance a proteins activity in various sub-cellular processes, or degrade their activity which leads towards failure of intracellular processes. Tyrosine nitration (NT) modification degrades proteins activity that initiate and propagate various diseases including Neurodegenerative, Cardiovascular, Autoimmune diseases, and Carcinogenesis. Identification of NT modification support development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming, and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches remain fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. The paper in hand presents NTpred framework competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, that is utilized to train a Logistic Regression classifier. On BD1 benchmark dataset, the proposed framework outperform existing best performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on BD2 benchmark dataset, the proposed framework outperform existing best performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC.

bioinformatics↗

Molecular Investigation of TSHR gene in Bangladeshi Congenital Hypothyroid patients

The disorder of thyroid gland development or thyroid dysgenesis (TH) accounts for 80-85% cases of congenital hypothyroidism (CH). Hence, the understanding of molecular etiology of TH is prerequisite. Mutations in TSHR gene is mostly associated with thyroid dysgenesis, prevent or disrupt normal development of the gland. The current study detects two nonsynonymous mutations (p.Ser508Leu, p.Asp727Glu) in transmembrane (TM)-region (Exon 10) of TSHR gene in 21 patients with dysgenesis by sequencing-based analysis. Later, transmembrane (TM)-region of TSHR protein is modelled by homology modeling. Transmembrane (TM)-region of TSHR protein is targeted by small molecules thyrogenic drugs, MS437 and MS438 to perceive the effect of mutations. The damaging effect in drug-protein complexes of mutants were envisaged by molecular docking and interactions. The binding affinity of wild type protein was much higher than the mutant cases for both of the ligands (MS437 and MS438). Molecular dynamics simulates dynamic behavior of wild type and mutant complexes. MS437-TSHR368-764MT2 and MS438-TSHR368-764MT1 show stable conformations in biological environments. Finally, PCA reveals structural and energy profile discrepancies. TSHR368-764MT1 exhibits much variations than TSHR368-764WT and TSHR368-764MT2, emphasizing more damaging pattern in TSHR368-764MT1. The study might be helpful to understand molecular etiology of thyroid dysgenesis (TH) exploring the mutational impact on TSHR protein to the interaction with agonists.

genetics↗

Discovery of highly potent small molecule pan-coronavirus fusion inhibitors

The unprecedented pandemic of COVID-19, caused by a novel coronavirus, SARS-CoV-2, has led to massive human suffering, death, and economic devastation worldwide. The virus is mutating fast to more transmissible and infectious variants. The Delta variant (B.1.617.2), initially identified in India, and the omicron variant (BA.4 and BA.5) have spread worldwide. In addition, recently alarming antibody evasive SARS-CoV-2 subvariants, BQ and XBB, have been reported. These new variants may pose a substantial challenge to controlling the spread of this virus. Therefore, the continued development of novel drugs having pan-coronavirus inhibition to treat and prevent infection of COVID-19 is urgently needed. These drugs will be critically important in dealing with new pandemics that will emerge in the future. We report the discovery of several highly potent small molecule pan-coronavirus inhibitors. One of which, NBCoV63, showed low nM potency against SARS-CoV-2 (IC50: 55 nM), SARS-CoV (IC50: 59 nM), and MERS-CoV (IC50: 75 nM) in pseudovirus-based assays with excellent selectivity indices (SI: as high as > 900) demonstrating its pan-coronavirus inhibition. NBCoV63 showed equally effective antiviral potency against SARS-CoV-2 mutant (D614G) and several variants of concerns (VOCs) such as B.1.617.2 (Delta), B.1.1.529/BA.1 and BA.4/BA.5 (Omicron) and K417T/E484K/N501Y (Gamma). NBCoV63 also showed similar efficacy profiles to Remdesivir against authentic SARS-CoV-2 (Hong Kong strain) and two of its variants (Delta and Omicron) by plaque reduction in Calu3 cells. Additionally, we show that NBCoV63 inhibits virus-mediated cell-to-cell fusion in a dose-dependent manner. Furthermore, the Absorption, distribution, metabolism, and excretion (ADME) data of NBCoV63 demonstrated drug-like properties.

pharmacology and toxicology↗

Susceptible bacteria survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

In vitro systems have provided great insight into the mechanisms of antibiotic resistance. Yet, in vitro approaches cannot reflect the full complexity of what transpires within a host. As the mammalian gut is host to trillions of resident bacteria and thus a potential breeding ground for antibiotic resistance, we sought to better understand how gut bacteria respond to antibiotic treatment in vivo. Here, we colonized germ-free mice with a genetically barcoded antibiotic pan-susceptible Escherichia coli clinical isolate and then administered the antibiotic cefepime via programmable subcutaneous pumps which allowed for closer emulation of human parenteral antibiotic pharmacokinetics/dynamics. After seven days of antibiotics, we were unable to culture E. coli from feces. We were, however, able to recover barcoded E. coli from harvested gastrointestinal (GI) tissue, despite high GI tract and plasma cefepime concentrations. Strikingly, these E. coli isolates were not resistant to cefepime but had acquired mutations - most notably in the wbaP gene, which encodes an enzyme required for the initiation of the synthesis of the polysaccharide capsule and lipopolysaccharide O antigen - that increased their ability to invade and survive within intestinal cells, including cultured human colonocytes. Further, these E. coli mutants exhibited a persister phenotype when exposed to cefepime, allowing for greater survival to pulses of cefepime treatment when compared to the wildtype strain. Our findings highlight a mechanism by which bacteria in the gastrointestinal tract can adapt to antibiotic treatment by increasing their ability to persist during antibiotic treatment and invade intestinal epithelial cells where antibiotic concentrations are substantially reduced.

microbiology↗

Individual Decision-Making Underlying the Tragedy of the Commons

Group decision-making is common in everyday life, whether a family is sharing a meal or a corporation is dividing profits. Research in economics on group decision-making has coalesced into a theory known as the tragedy of the commons, which states that resources are inevitably overused when shared by a group. However, even while multiple approaches to mitigating overuse of common resources have been put forward, notable counterexamples to the tragedy of the commons exist such that groups are ultimately able to avoid resource overuse. Development of a computerized paradigm amenable to behavioral modeling and simulation analyses could allow for exploration of whether resources will be overused in a given group of individuals and allow for the rapid testing of behavioral interventions designed to reduce instances of resource overuse. Using a newly developed group decision-making task, we studied how participants made decisions to utilize shared resources for the potential to receive a larger amount of money or conserve resources for a smaller amount of money. Using behavioral modeling, we found that valuation of resource overuse is most impacted only when an exceptionally small amount of resources are remaining. Using computational analyses, we were able to differentiate individual participants by both group earnings and self-reported social attitudes in ways that correlated with their willingness to utilize resources. These results signify the importance of individual differences in group composition regarding the tragedy of the commons, emphasizing the impact of the attitudes and behaviors of individual group members in predicting shared resource use.

animal behavior and cognition↗

A hydrogel-based model of aortic stiffness reveals that microtubules are novel regulators of smooth muscle cell hypertrophy

During ageing, the extracellular matrix of the aortic wall becomes more rigid. In response, VSMCs generate enhanced contractile forces. Our previous findings demonstrate that VSMC volume is enhanced in response to increased matrix rigidity, but our understanding of mechanisms regulating this process remain incomplete. In this current study, we show that microtubule stability in VSMCs is reduced in response to enhanced matrix rigidity via piezo1-mediated Ca2+ influx. Moreover, VSMC volume and Ca2+ flux was regulated by microtubule dynamics; microtubule stabilising agents reduced both VSMC volume and Ca2+ flux on rigid hydrogels, whereas microtubule destabilising agents increased VSMC volume and Ca2+ flux on pliable hydrogels. Finally, we show that disruption of the microtubule deacetylase HDAC6 uncoupled these processes and increased K40 alpha tubulin acetylation, VSMC volume and Ca2+ flux on pliable hydrogels, but did not alter VSMC microtubule stability. These findings uncover a microtubule stability switch that controls VSMC volume by regulating Ca2+ flux. Together, these data demonstrate that manipulation of microtubule stability can modify VSMC matrix rigidity response.

cell biology↗

SiRNA Molecules as Potential RNAi Therapeutics to Silence RdRP Region and N-Gene of SARS-CoV-2: An In Silico Approach

COVID-19 pandemic keeps pressing onward and effective treatment option against it is still far-off. Since the onslaught in 2020, 13 different variants of SARS-CoV-2 have been surfaced including 05 different variants of concern. Success in faster pandemic handling in the future largely depends on reinforcing therapeutics along with vaccines. As a part of RNAi therapeutics, here we developed a computational approach for predicting siRNAs, which are presumed to be intrinsically active against two crucial mRNAs of SARS-CoV-2, the RNA-dependent RNA polymerase (RdRp), and the nucleocapsid phosphoprotein gene (N gene). Sequence conservancy among the alpha, beta, gamma, and delta variants of SARS-CoV-2 was integrated in the analyses that warrants the potential of these siRNAs against multiple variants. We preliminary found 13 RdRP-targeting and 7 N gene-targeting siRNAs using the siDirect V.2.0. These siRNAs were subsequently filtered through different parameters at optimum condition including macromolecular docking studies. As a result, we selected 4 siRNAs against the RdRP and 3 siRNAs against the N-gene as RNAi candidates. Development of these potential siRNA therapeutics can significantly synergize COVID-19 mitigation by lessening the efforts, furthermore, can lay a rudimentary base for the in silico design of RNAi therapeutics for future emergencies.

bioinformatics↗

Compartmentation of putrescine synthesis in plants

Three plant pathways for the synthesis of putrescine have been described to date. These are the synthesis of putrescine from ornithine, by ornithine decarboxylase (ODC); and the synthesis of putrescine from arginine by arginine decarboxylase, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (NLP1); or arginine decarboxylase and agmatinase. Several enzymes associated with putrescine synthesis have yet to be localized. Here we showed that ODC in soybeans and rice was localized to the ER. In rice, agmatinase is localized to the mitochondria. In A. thaliana there are five isoforms of AIH and three isoforms of NLP1. Stable GFP-tagged transformants of the longest isoforms of AIH and NLP1 showed that both proteins were localized to the ER in leaves and roots of A. thaliana. Four of the isoforms of AIH and all of the isoforms of NLP1 were localized to the ER. However, AIH1.4 was localized to both the ER and the chloroplast. Combining these results with other published data, reveal that putrescine synthesis is excluded from the cytoplasm and is spatially localized to the chloroplast, ER and likely the mitochondria. Synthesis of putrescine in the ER may facilitate cell to cell transport via plasmodesmata, or secretion via vesicles. Differential expression of these pathways may enable putrescine-mediated activation of hormone-responsive genes.

plant biology↗

RTEL-1 and DNA polymerase theta promote subtelomeric DNA synthesis and telomere fusion in C. elegans

Interstitial telomere sequences (ITS) are degenerate telomere tracts scattered along chromosome arms whose functions are not well understood. We found that critically shortened telomeres of C. elegans telomerase mutants initiate DNA synthesis within ITS tracts that were close to or far from a telomere. Some ITS tracts were targeted recurrently. RTEL-1 dismantles T-loops and recombination intermediates, and DNA polymerase theta (POLQ-1) promotes end-joining using short segments of microhomology. In telomerase mutants, RTEL-1 and POLQ-1 promoted telomere fusion and DNA synthesis at subtelomeric ITS tracts. RTEL-1 is known to suppress homologous recombination, and we found that RTEL-1 similarly suppressed POLQ-1-mediated double-strand break repair. Mutation signatures characteristic of repair by POLQ-1 occurred during initiation of subtelomeric DNA synthesis and at subsequent template shifting events. We propose that RTEL-1 and POLQ-1 play distinct essential roles in subtelomeric DNA synthesis, a process that may contribute significantly to telomere fusion and tumor genome evolution.

genetics↗

CryoEM structure of QacA, an antibacterial efflux transporter from Staphylococcus aureus

Efflux of antibacterial compounds is a major mechanism for developing antimicrobial resistance. In the Gram-positive pathogen Staphylococcus aureus, QacA, a 14 transmembrane (TM) helix containing major facilitator superfamily antiporter, mediates proton-coupled efflux of mono and divalent cationic antibacterial compounds. In this study, we report the cryoEM structure of QacA, with a single mutation D411N that improves homogeneity and retains efflux activity against divalent cationic compounds like dequalinium and chlorhexidine. The structure of substrate-free QacA, complexed to two single-domain camelid antibodies, was elucidated to a resolution of 3.6 [A]. The structure displays an outward-open conformation with an extracellular hairpin loop, which is conserved in a subset of DHA2 transporters and its deletion causes a loss of function in the transporter. Modeling and simulations of QacAs cytosol-facing and occluded conformations reveal asymmetry in the rocker-switch mode of QacAs conformational shifts, providing new insights into the organization and structural dynamics of DHA2 members.

biochemistry↗

svCapture: Efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing

Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to strategies for comparable detection of rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from cell samples with known SV properties, we demonstrate that Duplex Sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of even single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and the high base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of sub-clonal and newly created SVs, suggesting end joining as a predominant formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.

genomics↗

Mechanoregulatory role of TRPV4 in prenatal skeletal development

Biophysical cues are essential for guiding skeletal development, but the mechanisms underlying the physical regulation of cartilage and bone formation are unknown. TRPV4 is a cell membrane ion channel responsible for transducing mechanical stimuli as a means of regulating skeletal cell homeostatic processes. Dysregulation of TRPV4 is associated with several skeletal developmental pathologies, indicating its involvement in cartilage and bone development, potentially in a mechanosensing capacity. In this study, we test the hypothesis that mechanically mediated prenatal skeletogenesis depends on TRPV4 activity. We first validate a novel model where we establish that dynamically loading embryonic mouse hindlimb explants cultured ex vivo promotes joint cartilage growth and morphogenesis, but not diaphyseal mineralization. We next reveal that TRPV4 protein expression is mechanically regulated and spatially localized to patterns of high biophysical stimuli in the femoral condyles of cultured limbs. Finally, we demonstrate that TRPV4 activity is crucial for the mechanical regulation of joint cartilage growth and shape, mediated via the control of cell proliferation and matrix biosynthesis, indicating a mechanism by which mechanical loading could direct morphogenesis during joint formation. We conclude that the regulatory pathways initiated by TRPV4 mechanotransduction are essential for the for the cartilage response to physical stimuli during skeletal development. Therefore, TRPV4 may be a valuable target for the development of therapeutic skeletal disease modifying drugs and developmentally-inspired tissue engineering strategies for skeletal repair.

developmental biology↗

Mechanical loading due to muscle movement regulates establishment of the collagen network in the developing murine skeleton

Mechanical loading is critical for collagen network maintenance and remodelling in adult skeletal tissues, but the role of loading in collagen network formation during development is poorly understood. We test the hypothesis that mechanical loading is necessary for the onset and maturation of spatial localisation and structure of collagens in prenatal cartilage and bone, using in vivo and in vitro mouse models of altered loading. The majority of collagens studied were aberrant in structure or localisation, or both, when skeletal muscle was absent in vivo. Using in vitro bioreactor culture system, we demonstrate that mechanical loading directly modulates the spatial localisation and structure of collagens II and X. Furthermore, we show that mechanical loading in vitro rescues aspects of collagens II and X development from the effects of fetal immobility. In conclusion, our findings show that mechanical loading is a critical determinant of collagen network establishment during prenatal skeletal development. Teaser (One line)Mechanical loading is required for normal establishment and maturation of key collagens during prenatal skeletal development.

developmental biology↗

Metabolic Implications of Birth via Cesarean Section in Prairie Vole (Microtus ochrogaster)

Throughout the United States the rates of performed cesarean section (CS) have increased. The scientific community has observed an association between birth by cesarean and the offsprings increased weight at maturity (Masukume, 2019). Studies are being conducted to better understand the relationship between cesarean delivery and offspring metabolism (Kozhimannil, 2013; Kenkel, 2020). To test this potential connection, a diet intervention study has been used to test vaginal delivery (VD) vs CS birth subjects weight gain using a prairie vole model. Vole diets were either supplemented with a high-fat alternative mixed chow (MC) or fed standard vole chow (VC) to induce weight gain. Through this study, we collected sucrose preference, home cage, food consumption data from both birth mode groups and diet conditions. At sacrifice, we collected measures of weight, length, and adipose tissue to analyze for post-mortem body composition in adulthood of each group. CS voles gained more weight than VD voles, despite having lower food consumption and greater locomotive activity. Body composition analysis found that CS animals were longer and heavier than their VD counterparts. Additionally, CS animals were found to have a larger percent brown adipose tissue relative to body weight compared to VD counterparts. Future studies will target the variables contributing to this weight gain among CS offspring by examining factors like muscle mass, and total adiposity through advanced imaging data. Future studies will incorporate exogenous oxytocin administration to examine the impact of birth mode on body weight, metabolism, adiposity, and later life development to determine the possible mechanisms impacting the metabolic outcomes seen in this study.

physiology↗

Ter-Seq: A high-throughput method to stabilize transient ternary complexes and measure associated kinetics

Regulation of biological processes by proteins often involves the formation of transient, multimeric complexes whose characterisation is mechanistically important but challenging. The bacterial toxin CcdB binds and poisons DNA Gyrase. The corresponding antitoxin CcdA extracts CcdB from its complex with Gyrase through formation of a transient ternary complex, thus rejuvenating Gyrase. We describe a high throughput methodology called Ter-Seq to stabilize probable ternary complexes and measure associated kinetics using the CcdA-CcdB-GyrA14 ternary complex as a model system. The method involves screening a YSD saturation mutagenesis library of one partner (CcdB) for mutants that show enhanced ternary complex formation. We also isolated CcdB mutants that were either resistant or sensitive to rejuvenation, and used SPR with purified proteins to validate the kinetics measured using surface display. Positions where CcdB mutations lead to slower rejuvenation rates are largely involved in CcdA-binding, though there were several notable exceptions. Mutations at these positions reduce the affinity towards CcdA, thereby slowing down the rejuvenation process. Mutations at GyrA14-interacting positions significantly enhanced rejuvenation rates, either due to reduced affinity or complete loss of CcdB binding to GyrA14. We examined the effect of different parameters (CcdA affinity, GyrA14 affinity, surface accessibilities, evolutionary conservation) on the rate of rejuvenation. Finally, we further validated the Ter-Seq results by monitoring kinetics of ternary complex formation for individual CcdB mutants in solution by FRET studies.

biophysics↗

Immunopharmacological evaluation of adjuvant efficacy of Monophosphoryl lipid-A and CpG ODN with SARS-CoV-2 RBD antigen

SARS-CoV-2 infection has made the mankind to witness most sever and serious pandemic situation in the history. Millions of people have suffered and are still suffering with this infection which has caused a mass mortality in the past three years. Development of an effective vaccine to control the spread of infection and to prevent this viral infection is need of the hour. Adjuvanted vaccines have proven their efficacy in controlling many other viral infections like flu, keeping this context in view we have evaluated the immunopharmacological efficacy of two adjuvants MPL-A and CpG ODN in combination with MF59 emulsion against SARS-CoV-2 antigen. From the data obtained we can infer that both the adjuvants were capable of eliciting a potent antibody response against antigen alone and MF59 groups. Comparatively MPL-A was eliciting a Th1 polarized response in terms of IgG2a and cytokine production. Both the adjuvants were capable of enhancing the CD 4, 8 and 19 cell populations. Overall the pre clinical evaluation has given a clue of the effectiveness of MPL-A and CpG adjuvants against SARS-CoV-2 antigen.

immunology↗

Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies Against Delta and Omicron in Mice

As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We have previously developed highly thermo-tolerant monomeric and trimeric receptor binding domain derivatives that can withstand 100{degrees}C for 90 minutes and 37{degrees}C for four weeks, and help eliminate cold chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations, and 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for the upcoming Phase I human clinical trials, and that there is potential for increasing efficacy with vaccine matching to improve responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions which show that while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible, and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.

immunology↗