Biology subjects

Nayak, A.

Publications and source records attributed to Nayak, A..

31 records · Page 2Linked to original sources

bioRxiv2024

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

Acute respiratory viral infections (ARVI), such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1) a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV EC50 = 3-46 nM, human metapneumovirus (hMPV) EC50 = 210 {+/-} 50 nM, human rhinovirus (RV) EC50 = 54-61 nM, and enterovirus (EV) EC50 = 83-90 nM. Prodrug optimization for cellular potency and lung cell metabolism identified the 5-methyl((S)-hydroxy(phenoxy)phosphoryl)-L-alaninate in combination with 2,3-diisobutyrate promoieties as optimal for high intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together these finding support additional evaluation of 1 and its analogs as a potential therapeutic for pneumo- and picornaviruses.

biochemistry↗

bioRxiv2024

Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers

Pathogenic germline TP53 alterations cause Li-Fraumeni Syndrome (LFS), and breast cancer is the most common cancer in LFS females. We performed first of its kind multimodal analysis of LFS breast cancer (LFS-BC) compared to sporadic premenopausal BC. Nearly all LFS-BC underwent biallelic loss of TP53 with no recurrent oncogenic variants except ERBB2 (HER2) amplification. Compared to sporadic BC, in situ and invasive LFS-BC exhibited a high burden of short amplified aneuploid segments (SAAS). Pro-apoptotic p53 target genes BAX and TP53I3 failed to be up-regulated in LFS-BC as was seen in sporadic BC compared to normal breast tissue. LFS-BC had lower CD8+ T-cell infiltration compared to sporadic BC yet higher levels of proliferating cytotoxic T-cells. Within LFS-BC, progression from in situ to invasive BC was marked by an increase in chromosomal instability with a decrease in proliferating cytotoxic T-cells. Our study uncovers critical events in mutant p53-driven tumorigenesis in breast tissue.

genetics↗

bioRxiv2024

Behavioral sequences across multiple animal species in the wild share common structural features

Animal behavior can be decomposed into a sequence of discrete activity bouts over time. Analyzing the statistical structure of such behavioral sequences can provide insights into the drivers of behavioral decisions. Laboratory studies, predominantly in invertebrates, have suggested that behavioral sequences exhibit multiple timescales and long-range memory, but whether these results can be generalized to other taxa and to animals in natural settings remains unclear. By analyzing accelerometer-inferred predictions of behavioral states in three species of social mammals (meerkats, white-nosed coatis, and spotted hyenas) in the wild, we discovered surprisingly consistent structuring of behavioral sequences across all behavioral states, all individuals, and all study species. Behavioral bouts were characterized by decreasing hazard functions, wherein the longer a behavioral bout had progressed, the less likely it was to end within the next instant. The predictability of an animals future behavioral state as a function of its present state always decreased as a truncated power-law for predictions made farther into the future, with very similar estimates for the power law exponent across all species. Finally, the distributions of bout durations were also heavy-tailed. Why such shared structural principles emerge remains unknown, and we explore multiple plausible explanations, including environmental non-stationarity, behavioral self-reinforcement, and the hierarchical nature of behavior. The existence of highly consistent patterns in behavioral sequences across our study species suggests that these phenomena could be widespread in nature, and points to the existence of fundamental properties of behavioral dynamics that could drive such convergent patterns. Significance statementThe study of animal behavior seeks to understand how and why animals do what they do. This pursuit of general principles governing behavior across species can be approached by first understanding when animals choose to change their behavioral states (e.g., switching from walking to standing, or to running). Using accelerometer-inferred behaviors of three social mammals, we uncover common structural long timescale patterns in their sequences of behavior. We explore two explanations, involving either positive feedbacks or the interaction of several independent time-scales, about how such common patterns arise.

animal behavior and cognition↗

bioRxiv2024

Sorafenib induces muscle wasting by disrupting the activity of distinct chromatin regulators

Adverse effects of chemotherapies can outweigh the benefits in cancer patients. Various chemotherapeutics are linked to muscle wasting or cachexia, drastically reducing the chance of survivability of cancer patients. Insights into the molecular basis of chemotherapy-induced cachexia is an unmet need to improve the treatment strategies. Here, we investigated the tyrosine kinase inhibitor class of chemotherapeutic agents for their effects on muscle function. Sorafenib, but not Nilotinib and Imatinib, triggered cachexia. System-wide transcriptome and proteome analyses revealed that Sorafenib alters the global transcriptional program and proteostasis in muscle cells. Mechanistically, Sorafenib treatment reduced active epigenetic mark H3K4 methylation on distinct muscle-specific genes due to the defective chromatin association of SET1/A, a catalytic component of the SET1/MLL complex. It favored transcriptionally incompetent chromatin, characterized by diminished association with RNA polymerase II. The transcriptional reorientation led to disrupted sarcomere organization, calcium homeostasis, and mitochondrial respiration. Consequently, the contractile ability of muscle cells was severely compromised. Collectively, we identified an unanticipated transcriptional mechanism underlying Sorafenib-induced cachexia. Our findings hold the potential to strategize therapy regimens to minimize chemotherapy-induced cachexia and improve treatment outcomes.

cell biology↗

bioRxiv2023

'Pscore' - A Novel Percentile-Based Metric to Accurately Assess Individual Deviations in Non-Gaussian Distributions of Quantitative MRI Metrics

BACKGROUNDQuantitative MRI metrics could be used in personalized medicine to assess individuals against normative distributions. Conventional Zscore analysis is inadequate in the presence of non-Gaussian distributions. Therefore, if quantitative MRI metrics deviate from normality, an alternative is needed. PURPOSETo confirm non-Gaussianity of diffusion MRI (dMRI) metrics on a publicly available dataset, and to propose a novel percentile-based method, Pscore to address this issue. STUDY TYPERetrospective cohort POPULATION961 healthy young-adults (age:22-35 years, Females:53%) from the Human Connectome Project FIELD STRENGTH/SEQUENCE3-T, spin-echo diffusion echo-planar imaging, T1-weighted: MPRAGE ASSESSMENTThe dMRI data were preprocessed using the TORTOISE pipeline. Forty-eight regions of interest (ROIs) from the JHU-atlas were redrawn on a study-specific diffusion tensor (DT) template and average values were computed from various DT and mean apparent propagator (MAP) metrics. For each ROI, percentile ranks across participants were computed to generate Pscores- which normalized the difference between the median and a participants value with the corresponding difference between the median and the 5th/95th percentile values. STATISTICAL TESTSROI-wise distributions were assessed using Log transformations, Zscore, and the Pscore methods. The percentages of extreme values above-95th and below-5th percentile boundaries (PEV>95(%),PEV<5(%)) were also assessed in the overall white matter. Bootstrapping was performed to test the reliability of Pscores in small samples (n=100) using 100 iterations. RESULTSThe dMRI metric distributions were systematically non-Gaussian, including positively skewed (e.g., mean and radial diffusivity) and negatively skewed (e.g., fractional and propagator anisotropy) metrics. This resulted in unbalanced tails in Zscore distributions (PEV>95=5%,PEV<5=5%) whereas Pscore distributions were symmetric and balanced (PEV>95=PEV<5=5%); even for small bootstrapped samples (average [Formula]. DATA CONCLUSIONThe inherent skewness observed for dMRI metrics may preclude the use of conventional Zscore analysis. The proposed Pscore method may help estimating individual deviations more accurately in skewed normative data, even from small datasets.

neuroscience↗

bioRxiv2023

Sinefungin, a natural nucleoside analog of S-adenosyl methionine, impairs the pathogenicity of Candida albicans

Candida albicans, an opportunistic fungal human pathogen, is a major threat to the healthcare system due to both infections in immunocompromised individuals and the emergence of antifungal resistance. Fungal infection caused by C. albicans, candidiasis, is a life-threatening condition in immunocompromised patients and the current treatments are mostly restricted to polyenes, azoles, and echinocandins. Use of these antifungals is limited by toxicity, drug-drug interactions, and the emergence of resistance, underscoring the importance of identifying novel therapeutic targets and the need for new treatment approaches. C. albicans can undergo a morphological transition from yeast to hyphae and this transition is central to C. albicans virulence. Here, we determine the impact of sinefungin, a natural nucleoside analog of S-adenosyl methionine, on the virulence of C. albicans strain SC5314 by evaluating treatment effects on the morphological transition, human epithelial cell adhesion, and biofilm formation. Our data indicate that sinefungin impairs pathogenic traits of C. albicans including hyphal lengthening, biofilm formation and the adhesion to the human epithelial cell lines, without adversely affecting human cells, therefore highlighting sinefungin as a potential avenue for therapeutic intervention. We determine that the formation of N6-methyladenosine (m6A) is particularly disturbed by sinefungin. More broadly, this study underscores the importance of considering the post-transcriptional control mechanisms of pathogenicity when designing therapeutic solutions to fungal infection.

biochemistry↗

bioRxiv2022

Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation

Viruses have evolved mechanisms to modulate cellular pathways to facilitate infection. One such pathway is the formation of stress granules (SG), which are ribonucleoprotein complexes that assemble during translation inhibition following cellular stress. Inhibition of SG assembly has been observed under numerous virus infections across species, suggesting a conserved fundamental viral strategy. However, the significance of SG modulation during virus infection is not fully understood. The 1A protein encoded by the model dicistrovirus, Cricket Paralysis Virus (CrPV), is a multifunctional protein that can bind to and degrade Ago-2 in an E3 ubiquitin ligase-dependent manner to block the antiviral RNA interference pathway and inhibit SG formation. Moreover, the R146 residue of 1A is necessary for SG inhibition and CrPV infection in both Drosophila S2 cells and adult flies. Here, we uncoupled CrPV-1As functions and provide insight into its underlying mechanism for SG inhibition. CrPV-1A mediated inhibition of SGs requires the E3 ubiquitin-ligase binding domain and the R146 residue, but not the Ago-2 binding domain. Wild-type but not mutant CrPV-1A R146A localizes to the nuclear membrane which correlates with nuclear enrichment of poly(A)+ RNA. Transcriptome changes in CrPV-infected cells are dependent on the R146 residue. Finally, Nup358/RanBP2 is targeted and degraded in CrPV-infected cells in an R146-dependent manner and the depletion of Nup358 blocks SG formation. We propose that CrPV utilizes a multiprong strategy whereby the CrPV-1A protein interferes with a nuclear event that contributes to SG inhibition in order to promote infection. AUTHOR SUMMARYViruses often inhibit a cellular stress response that leads to the accumulation of RNA and protein condensates called stress granules. How this occurs and why this would benefit virus infection are not fully understood. Here, we reveal a viral protein that can block stress granules and identify a key amino acid residue in the protein that inactivates this function. We demonstrate that this viral protein has multiple functions to modulate nuclear events including mRNA export and transcription to regulate stress granule formation. We identify a key host protein that is important for viral protein mediate stress granule inhibition, thus providing mechanistic insights. This study reveals a novel viral strategy in modulating stress granule formation to promote virus infection.

microbiology↗

bioRxiv2022

Cardiac ventricular myosin and slow skeletal myosin exhibit dissimilar chemo-mechanical properties despite the same myosin heavy chain isoform.

The myosin II motors are ATP-powered, force-generating machines driving cardiac and muscle contraction. Myosin II heavy chain isoform-beta ({beta}-MyHC) is primarily expressed in the ventricular myocardium and slow-twitch muscle fibers, such as in M. soleus. M. soleus-derived myosin II (SolM-II) is often used as an alternative to the ventricular {beta}-cardiac myosin ({beta}M-II); however, the direct assessment of detailed biochemical and mechanical features of the native myosins is limited. By employing the optical trapping method, we examined the mechanochemical properties of the native myosins isolated from rabbit heart ventricle and M. soleus muscles at the single-molecule level. Contrary to previous reports, the purified motors from the two tissue sources, despite the same MyHC isoform, displayed distinct motile and ATPase kinetic properties. {beta}M-II was [~]threefold faster in the actin filament-gliding assay than SolM-II. The maximum acto-myosin (AM) detachment rate derived in single-molecule assays was [~]threefold higher in {beta}M-II. The stroke size for both myosins was comparable. The stiffness of the AM rigor cross-bridge was also similar for both the motor forms. The stiffness of {beta}M-II was found to be determined by the nucleotide state of the actin-bound myosin. Our analysis revealed distinct kinetic differences, i.e., a higher AM detachment rate for the {beta}M-II, corresponding to the ADP release rates from the cross-bridge, thus elucidating the observed differences in the motility driven by {beta}M-II and SolM-II. These studies have important implications for the future choice of tissue sources to gain insights into cardiomyopathies

biophysics↗

bioRxiv2021

Ca2+-inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM

Activation of the intracellular Ca2+ channel ryanodine receptor (RyR) triggers a cytosolic Ca2+ surge, while elevated cytosolic Ca2+ inhibits the channel in a negative feedback mechanism. Cryo-EM carried out under partially inactivating Ca2+ conditions revealed two conformations of RyR1, an open state and an inactivated state, resolved at 4.0 and 3.3 [A] resolution, respectively. RyR1s were embedded in nanodiscs with two lipids resolved at each inter-subunit crevice. Ca2+ binding to the high affinity site engages the central (CD) and C-terminal domains (CTD) into a quasi-rigid unit, which separates the S6 four-helix bundle and opens the channel. Further out-of-plane rotation of the quasi-rigid unit pushes S6 towards the central axis, closing (inactivating) the channel. The inactivated conformation is characterized by a downward conformation of the cytoplasmic assembly, a tightly-knit subunit interface contributed by a fully occupied and partially remodeled Ca2+ activation site, and two salt bridges between the EF hand domain and the S2-S3 loop of the neighboring subunit validated by naturally-occurring diseasecausing mutations. Ca2+ also bound to ATP, mediating a tighter interaction between S6 and CTD. Our study suggests that the closed-inactivated is a distinctive state of the RyR1 and its transition to the closed-activable state is not a simple reverse of the Ca2+ mediated activation pathway.

physiology↗

bioRxiv2020

Inferring Toll-Like Receptor induced epitope subunit vaccine candidate against SARS-CoV-2: A Reverse Vaccinology approach

Toll-Like Receptors (TLRs) are a group of Pattern Recognition Receptors (PRRs) which bind to the exogenous pathogen associated molecular patterns (PAMPs) like other PRRs; hence the main function is to sense the harmness and mediate the innate immune response to pathogens. TLRs play an important role in innate immune responses to infection. The host has evolved to use other TLR and PAMP agonists as agents to stimulate a protective inflammatory immune response against infection. Because only a small number of doses are given, TLR agonists appear to have greater potential and fewer safety concerns than other uses as vaccine adjuvants. In the present days, development of peptides targeting immune response can be approved for survival in biological monitoring systems before vaccine exposures. Peptide vaccines are easy to synthesize, more stable and relatively safe. In addition, production of peptides becomes simple, easily reproducible, fast and cost effective. Getting vaccinated against Covid-19, which has become a pandemic in the human population, is the most practical way to control the outbreak. The new coronavirus does not contain a drug or vaccine to prevent it from spreading to humans. To getting a proper vaccine candidate against the novel coronavirus, the present study used the reverse vaccinology approach by using a complete set of SARS-CoV-2 proteins; such as: Spike, Envelope, Nucleocapsid, Membrane, NSPs, and ORFs to extract the antigenic elements that produce B-cell, T-cell and IFN positive epitopes. These epitopes with precise binding to the Toll-Like receptors (1-10) have developed epitope based vaccine candidates. We have prioritized a set of epitopes based on their antigenicity, allergenicity, sequence conservation and projected population coverage world-wide. The selected epitopes were employed for in-silico docking interactions with Toll-Like receptors and molecular dynamic simulation confirmed the stability of the vaccine candidates resulting epitope of spike proteins with both the TLR 7 and 8 shows the best binding affinity. We believe that this ideal epitope vaccine candidate could enhance the immune response of the host and reduce the reinfection risk.

bioinformatics↗

bioRxiv2020

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

genomics↗

bioRxiv2020

Single-molecule analysis reveals the role of regulatory light chains in fine-tuning skeletal myosin-II function

Myosin II is the main force generating motor during muscle contraction. Myosin II exists as different isoforms, involved in diverse physiological functions. The outstanding question is whether the myosin heavy chain (MHC) isoforms alone account for the distinct physiological properties. Unique sets of essential and regulatory light chains (RLCs) assembled with specific MHCs raises an interesting possibility of specialization of myosin functions via light chains (LCs). Here, we ask whether different RLCs contribute to the functional diversification. To investigate this, we generated chimeric motors by reconstituting MHC fast isoform (MyHC-IId) and slow isoform (MHC-I) with different light chain variants. As a result of RLCs swapping, actin filament sliding velocity increased by [~] 10 fold for the slow myosin and decreased by >3 fold for the fast myosin. Ensemble molecule solution kinetics and single molecule optical trapping measurements provided in-depth insights into altered chemo mechanical properties of the myosin motors, thereby affecting the sliding speed. We find that both slow and fast myosins mechanical output is sensitive to the RLC isoform and propose that RLCs are crucial in fine-tuning of the myosin function.

biophysics↗

bioRxiv2019

Molecular mechanisms of Evening Complex activity in Arabidopsis

The Evening Complex (EC), composed of the DNA-binding protein LUX ARRHYTHMO (LUX) and two additional proteins, EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment and regulates important clock output genes such as PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a key transcription factor involved in temperature dependent plant growth. These properties make the EC an attractive target for altering plant development through targeted mutations to the complex. However, the molecular basis for EC function was not known. Here we show that binding of the EC requires all three proteins and that ELF3 decreases the ability of LUX to bind DNA whereas the presence of ELF4 restores interaction with DNA. To be able to manipulate this complex, we solved the structure of the DNA-binding domain of LUX bound to DNA. Using structure-based design, a LUX variant was constructed that showed decreased in vitro binding affinity but retained specificity for its cognate sequences. This designed LUX allele modulates hypocotyl elongation and flowering. These results demonstrate that modifying the DNA-binding affinity of LUX can be used to titrate the repressive activity of the entire EC, tuning growth and development in a predictable manner.\n\nSignificance StatementCircadian gene expression oscillates over a 24 hr. period and regulates many genes critical for growth and development. In plants, the Evening Complex (EC), a three-protein repressive complex made up of LUX ARRYTHMO, EARLY FLOWERING 3 and EARLY FLOWERING 4, acts as a key component of the circadian clock and is a regulator of thermomorphogenic growth. However, the molecular mechanisms of complex formation and DNA-binding have not been identified. Here we determine the roles of each protein in the complex and present the structure of the LUX DNA-binding domain in complex with DNA. Based on these data, we used structure-based protein engineering to produce a version of the EC with altered in vitro and in vivo activity. These results demonstrate that the EC can be modified to alter plant growth and development at different temperatures in a predictable manner.

plant biology↗