Biology subjects

Chowdhury, R.

Publications and source records attributed to Chowdhury, R..

50 records · Page 3Linked to original sources

bioRxiv2021

Oligomerization state of the functional bacterial twin arginine translocation (Tat) receptor complex

The twin-arginine translocation (Tat) system transports folded proteins across bacterial and plastid energy transducing membranes. Ion leaks are generally considered to be mitigated by the creation and destruction of the translocation conduit in a cargodependent manner, a mechanism that enables tight sealing around a wide range of cargo shapes and sizes. In contrast to the variable stoichiometry of the active translocon, the oligomerization state of the receptor complex is considered more consistently stable, but has proved stubbornly difficult to establish. Here, using a single molecule photobleaching analysis of individual inverted membrane vesicles, we demonstrate that Tat receptor complexes are tetrameric in native membranes with respect to both TatB and TatC. This establishes a maximal diameter for a resting state closed pore. A large percentage of Tat-deficient vesicles explains the typical low transport efficiencies observed. This individual reaction chamber approach will facilitate examination of the effects of stochastically distributed molecules.

biophysics↗

bioRxiv2021

Comparative analysis of mandible morphology in four ant species with different foraging and nesting habits

Mandibles of ants can be considered as one of the most vital tools for the survival and success of their colonies since these are extensively utilised for defence, nest maintenance and foraging activities. We hypothesised that mandibular design is strongly dependent on the respective ecological niche and foraging habit of an ant species. In the present study, we compared the external morphology and zinc content in the mandibles of four species of ants by using scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX). The ant mandible morphology varied significantly in accordance with their species-specific foraging and nesting strategies. The sickle-shaped mandibles of the strongly predaceous, Oecophylla smaragdina worker ants were characterised by a large number of pointed teeth which would be of immense utility for subduing the prey, while the shovel-shaped, highly sclerotized mandibles of Cataglyphus longipedem ants appear to be adaptations for the solitary scavenging habit and nest maintenance in arid habitats. The large-sized mandibles of Camponotus compressus ants and the stout mandibles of the predatory, Tetraponera. rufonigra forager ants, have apparently evolved for collection of sugary secretions by the former and for the solitary foraging and arboreal nesting habit of the latter. The mandibular zinc content was highest in T. rufonigra ants and the lowest in the mandibles of the sugar-loving Cm. compressus ants. The diversity in the arrangement of bristles and the type of mandibular concavities, have also evolved accordingly. Thus, this study might prove to be instrumental in evaluating the various physical mechanisms involved in the evolution of insect mandibles for their defined function.

zoology↗

bioRxiv2021

Single-sequence protein structure prediction using language models from deep learning

AlphaFold2 and related systems use deep learning to predict protein structure from co-evolutionary relationships encoded in multiple sequence alignments (MSAs). Despite dramatic, recent increases in accuracy, three challenges remain: (i) prediction of orphan and rapidly evolving proteins for which an MSA cannot be generated, (ii) rapid exploration of designed structures, and (iii) understanding the rules governing spontaneous polypeptide folding in solution. Here we report development of an end-to-end differentiable recurrent geometric network (RGN) able to predict protein structure from single protein sequences without use of MSAs. This deep learning system has two novel elements: a protein language model (AminoBERT) that uses a Transformer to learn latent structural information from millions of unaligned proteins and a geometric module that compactly represents C backbone geometry. RGN2 outperforms AlphaFold2 and RoseTTAFold (as well as trRosetta) on orphan proteins and is competitive with designed sequences, while achieving up to a 106-fold reduction in compute time. These findings demonstrate the practical and theoretical strengths of protein language models relative to MSAs in structure prediction.

bioinformatics↗

bioRxiv2021

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor

The association of the receptor binding domain (RBD) of SARS-CoV-2 viral spike with human angiotensin converting enzyme (hACE2) represents the first required step for viral entry. Amino acid changes in the RBD have been implicated with increased infectivity and potential for immune evasion. Reliably predicting the effect of amino acid changes in the ability of the RBD to interact more strongly with the hACE2 receptor can help assess the public health implications and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born electrostatic solvation, hydrogen-bonding, {pi}-{pi} packing and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity using the decomposed energy terms as descriptors. The computational base achieves an accuracy of 82.2% in terms of correctly classifying single amino-acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient r of 0.69 between predicted and experimentally calculated binding affinities. Both metrics are calculated using a 5-fold cross validation test. Our method thus sets up a framework for effectively screening binding affinity change with unknown single and multiple amino-acid changes. This can be a very valuable tool to predict host adaptation and zoonotic spillover of current and future SARS-CoV-2 variants.

biophysics↗

bioRxiv2021

Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutation.

Frontotemporal dementia (FTD) due to MAPT mutation causes pathological accumulation of tau and glutamatergic cortical neuronal death by unknown mechanisms. We used human induced pluripotent stem cell (iPSC)-derived cerebral organoids expressing tau-V337M and isogenic corrected controls to discover early alterations due to the mutation that precede neurodegeneration. At 2 months, mutant organoids show upregulated expression of MAPT, and glutamatergic signaling pathways and regulators including the RNA-binding protein ELAVL4. Over the following 4 months, mutant organoids accumulate splicing changes, disruption of autophagy function and build-up of tau and P-tau S396. By 6 months, tau-V337M organoids show specific loss of glutamatergic neurons of layers affected in patients. Mutant neurons are susceptible to glutamate toxicity which was rescued pharmacologically by treatment with the PIKFYVE kinase inhibitor apilimod. Our results demonstrate a sequence of events that precede cell death, revealing molecular pathways associated with glutamate signaling as potential targets for therapeutic intervention in FTD.

neuroscience↗

bioRxiv2020

Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes

Large-scale gene sequencing studies for complex traits have the potential to identify causal genes with therapeutic implications. We performed gene-based association testing of blood lipid levels with rare (minor allele frequency<1%) predicted damaging coding variation using sequence data from >170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels.

genetics↗

bioRxiv2020

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

We previously described the design of triacetic acid lactone (TAL) biosensor "AraC-TAL1", based on the AraC regulatory protein. While useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity, and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a "decoy" ligand during negative selection, resulting in isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the IPRO computational framework was employed, followed by two rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.

synthetic biology↗

bioRxiv2020

In-vivo evaluation of the anti-diarrheal effect of Lactococcus lactis subspecies lactis and Lactococcus piscium isolated from yogurt.

Lactobacillus and Lactococcus species found in the yogurt of different sources are most widely assayed and used all over the world as a probiotic agent. This study aimed to isolate and identify novel probiotic agents with therapeutic value against diarrhea. Initially, the probiotic properties of the isolated lactic acid bacteria from the yogurt samples of the Chittagong division, Bangladesh, were evaluated. All probiotic candidates inhibited the growth of selected pathogens, including Escheriachia coli, Serratia sp. Salmonella paratyphi, Streptococcus Group-B, Staphylococcus aureus, Haemophillus influenzae, Bacillus subtillis, and Klebsiella pneumoniae. Lactococcus lactis subsp lactis were found most useful in inhibiting all the selected pathogens. When the probiotics were applied against castor oil-induced diarrhea in the rat model, Lactococcus lactis subspecies lactis and Lactococcus piscium were found significantly effective relative to the controls indicating their potentiality as an alternative therapeutic against diarrhea. HighlightsO_LILactococcus lactis subspecies lactis and Lactococcus piscium has shown potentiality to be a therapeutic agent against castor-oil induced diarrhea in an animal model. C_LIO_LILactococcus lactis subspecies lactis and Lactococcus piscium inhibited the growth of specified pathogens. C_LI

microbiology↗

bioRxiv2020

De novo design of high-affinity antibody variable regions (scFv) against the SARS-CoV-2 spike protein

The emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral spike receptor binding domain (RBD) with the human angiotensin converting enzyme (hACE2). In an earlier paper1, we report on the specific residue interactions underpinning this event. Here we report on the de novo computational design of high affinity antibody variable regions through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike protein using the software tool OptMAVEn-2.02. Subsequently, we carry out computational affinity maturation of the designed prototype variable regions through point mutations for improved binding with the target epitope. Immunogenicity was restricted by preferring designs that match sequences from a 9-mer library of "human antibodies" based on H-score (human string content, HSC)3. We generated 106 different designs and report in detail on the top five that trade-off the greatest affinity for the spike RBD epitope (quantified using the Rosetta binding energies) with low H-scores. By grafting the designed Heavy (VH) and Light (VL) chain variable regions onto a human framework (Fc), high-affinity and potentially neutralizing full-length monoclonal antibodies (mAb) can be constructed. Having a potent antibody that can recognize the viral spike protein with high affinity would be enabling for both the design of sensitive SARS-CoV-2 detection devices and for their deployment as therapeutic antibodies.

immunology↗

bioRxiv2020

Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis

SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor - angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-causing SARS-CoV-1, SARS-CoV-2, and bat coronavirus RaTG13 using the Rosetta energy function. We find that the RBD of the spike protein of SARS-CoV-2 is highly optimized to achieve very strong binding with human ACE2 (hACE2) which is consistent with its enhanced infectivity. SARS-CoV-2 forms the most stable complex with hACE2 compared to SARS-CoV-1 (23% less stable) or RaTG13 (11% less stable) while occupying the greatest number of residues in the ATR1 binding site. Notably, the SARS-CoV-2 RBD out-competes the angiotensin 2 receptor type I (ATR1) which is the native binding partner of ACE2 by 35% in terms of the calculated binding affinity. Strong binding is mediated through strong electrostatic attachments with every fourth residue on the N-terminus alpha-helix (starting from Ser19 to Asn53) as the turn of the helix makes these residues solvent accessible. By contrasting the spike protein SARS-CoV-2 Rosetta binding energy with ACE2 of different livestock and pet species we find strongest binding with bat ACE2 followed by human, feline, equine, canine and finally chicken. This is consistent with the hypothesis that bats are the viral origin and reservoir species. These results offer a computational explanation for the increased infectivity of SARS-CoV-2 and allude to therapeutic modalities by identifying and rank-ordering the ACE2 residues involved in binding with the virus.

biophysics↗

bioRxiv2019

Learning in anticipation of reward and punishment: Perspectives across the human lifespan

Pavlovian biases influence the interaction between action and valence by coupling reward seeking to action invigoration and punishment avoidance to action suppression. In this study we used an orthogonalised go/no-go task to investigate learning in 247 individuals across the human lifespan (7-80 years) to demonstrate that all participants, independently of age, demonstrated an influence of Pavlovian control. Computational modeling revealed peak performance in young adults was attributable to greater sensitivity to both rewards and punishment. However in children and adolescents an increased bias towards action but not reward sensitivity was observed. In contrast, reduced learning in midlife and older adults was accompanied with decreased reward sensitivity and especially punishment sensitivity. These findings reveal distinct learning capabilities across the human lifespan that cannot be probed using conventional go/reward no-go/punishment style paradigms that have important implications in life-long education.

neuroscience↗

bioRxiv2018

Detection of acute TLR-7 agonist-induced hemorrhagic myocarditis in mice by refined multi-parametric quantitative cardiac MRI.

BACKGROUNDHemorrhagic myocarditis is a potentially fatal complication of excessive levels of systemic inflammation. It has been reported in viral infection, but is also possible in systemic autoimmunity. Cardiac magnetic resonance (CMR) imaging is the current gold standard for non-invasive detection of suspected inflammatory damage to the heart and changes in T1 and T2 relaxation times are commonly used to detect edema associated with immune cell infiltration and fibrosis. These measurements also form the basis of the Lake Louise Criteria, which define a framework for the CMR-based diagnosis of myocarditis. However, they do not take into account the possibility of hemorrhage leading to tissue iron deposition which strongly influences T1 and T2 measurements and may complicate interpretation based on these two parameters only.\n\nMETHODSSystemic inflammation was induced in CFN mice by application of the TLR-7 agonist Resiquimod. Histopathology was performed on heart sections to assess immune cell infiltration (Hematoxylin & Eosin), fibrosis (PicoSirius Red) and tissue iron deposition (Perls Prussian Blue). A multi-parametric cardiac MRI tissue mapping approach measuring T1, T2, and T2* relaxation times was established to non-invasively identify these parameters in this small rodent model.\n\nRESULTSResiquimod-treated mice developed severe thrombocytopenia and hemorrhagic myocarditis. We identified patches of cardiac hemorrhage based on the presence of two major MRI phenotypes. Increased T2 with normal T1 and T2* values correlated with infiltration/edema only, while decreased T1, T2, and T2* values identify areas with infiltration/edema in the presence of iron indicating hemorrhagic myocarditis.\n\nCONCLUSIONWe show that over-activation of the TLR-7 pathway by Resiquimod treatment of CFN mice induces an early immune response reminiscent of excessive systemic inflammation due to viral infection. This causes internal bleeding which manifests most prominently as severe hemorrhagic myocarditis. We optimized a comprehensive noninvasive in vivo MRI approach based on quantitative measurement of T1, T2 and T2* to demonstrate the presence of diffuse myocardial edema, infiltration and iron deposition without the need of contrast agent administration. We propose that adding quantitative T2* mapping to CMR protocols for detection of myocarditis will improve diagnostic sensitivity and interpretation of disease mechanisms.

physiology↗

bioRxiv2017

Electron microscopy reveals unique nano forms of bacterial spores

Endospore formation under environmental stress conditions is a well-established phenomenon for members of bacterial phylum Firmicutes, among which the most well studied ones belong to genus Bacillus and Clostridium. So far, known sizes of the spores are all larger than 500 nm. Nano-forms of bacteria have been reported but the notion still remains controversial. In this study, we provide visual evidences of living nano-entities (named here as nano-spores) formed by a bacterial species Bacillus cereus under prolonged stress, which are capable of escaping though standard sterile filtration procedure. The existence of nano-forms of bacteria was initially identified in a yeast ribosome preparation. We further demonstrate the transformation of the nano-spores into mature cells upon nutrient supply. Our study not only demonstrates the ability of bacteria to get transformed into yet-unknown form in order to survive under harsh environment, but also brings to light the existence of the smallest possible form of life.

microbiology↗

bioRxiv2017

Switchable amplification of fluoresence from a photosynthetic microbe

One known attribute of the photosynthetic apparatus is photon capture and generation of metabolic energy. The thermodynamic implications of fluorescence, invariably associated with the photosynthetic components is however poorly understood. In this paper we report a density dependent amplification of such fluorescence which can be interpreted as a thermodynamic strategy of controlled energy release by the cell. We show in support of this hypothesis that prolonged photo-exitation of cell free extract of Rhodobacter capsulatus SB1003 at 395 nm, induces fluorescence emission amplifying with time as long as the fluorophore density is above a critical level. The fact that the amplification disappears at low temperature and at dilute condition, is in accordance with the thermodynamic interpretation that energy is released as per requirement. Live cell imaging is also validation of the phenomenon even at the cellular level. Single cells of Rhodobacter capsulatus SB1003 shows time dependent loss of fluorescence, the process being reversed for cellular clusters. To explain the mechanism of this bistable fluorescence (F) amplification, variation of the scale free kinetic constant k=1/F (dF/dt) is studied at varying temperatures in presence and absence of static magnetic field. The sign of k shifts from positive to negative if T is lowered or if the system is diluted. But at low T, k again switches from negative to positive value, if static magnetic field is applied. The chain of events can be explained by a simple model assuming excretion of a porphyrin by the microbe and possible photon dependent aggregation behavior of such porphyrin complex, differential temperature and magnetic field sensitivity of the monomeric or aggregated forms of porphyrin being reported earlier.

biophysics↗