Biology subjects

Kumar, S.

Publications and source records attributed to Kumar, S..

At least 397 records · Page 22Linked to original sources

bioRxiv2022

Scream's roughness confers a privileged access to the brain during sleep

During sleep, recognizing threatening signals is crucial to know when to wake up and when to continue vital sleep functions. Screaming is perhaps the most salient and efficient signal for communicating danger at a distance or in conditions of limited visibility. Beyond the intensity or the pitch of the sound, rapid modulations of sound pressure in the so-called roughness range (i.e. 30-150 Hz) are particularly powerful in capturing attention and accelerating reactions. Roughness is an acoustic feature that characterizes alarm signals such as screams. However, whether rough sounds are also processed in a privileged manner during sleep is unknown. We tested this hypothesis by stimulating sleeping human participants with low-intensity screams and neutral calls. We found that screams trigger more reliable and better time-locked responses in wakefulness and NREM sleep. In addition, screams boosted sleep spindles, suggesting elevated stimulus salience. The increase in sleep spindle power was linearly proportional to the roughness of vocalizations, but not to their pitch. These findings demonstrate that, even at low sound intensity, screams roughness conveys stimulus relevance and enhances processing in both the waking and sleeping states. Preserved differential neural responses based on stimulus salience may ensure adaptive reactions -and ultimately survival- in a state where the brain is mostly disconnected from external inputs.

neuroscience↗

bioRxiv2022

FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome

Large-scale whole genome sequencing (WGS) studies and biobanks are rapidly generating a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries or are unable to functionally annotate the genotype data of large WGS studies and biobanks for downstream analysis. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive online multi-faceted portal with summarization and visualization of all possible 9 billion single nucleotide variants (SNVs) across the genome, and allows for rapid variant-, gene-, and region-level online queries. It integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, a scalable annotation tool, FAVORannotator, is provided for functionally annotating and efficiently storing the genotype and variant functional annotation data of a large-scale sequencing study in an annotated GDS file format to facilitate downstream analysis. FAVOR and FAVORannotator are available at https://favor.genohub.org.

genetics↗

bioRxiv2022

Local RNA Structure, Ion Hydration Shell and the Energy Barrier for Water Exchange from the Ion Hydration Shell Determine the Mechanism of Ion Condensation on Specific RNA Sites

RNA folding and functioning require the binding of metal ions in specific cavities of the folded structure. This property is critical to the functioning of riboswitches that especially regulate the metal ions concentration in bacteria. However, the fundamental principles governing the specific binding of metal ions in RNA are unclear. We probed the condensation mechanism of biologically relevant alkali (Na+ and K+), alkaline earth (Mg2+ and Ca2+), and transition metals (Mn2+, Co2+, Ni2+ and Zn2+) on a part of the Ni2+ and Co2+ (NiCo) sensing riboswitch aptamer domain using computer simulations. The selected structure has multiple secondary structural elements and a single site for the specific binding of a metal ion. We show that three factors primarily determine the binding of a metal ion to an RNA site - (1) The varying structural constraints from different RNA secondary structural elements strongly influence the metal ion binding. The mode of ion binding depends on the local structure around the RNAs ion-binding pocket. (2) The arrangement of water molecules in the ion hydration shell, and (3) the energy barrier for the ion to lose a water molecule from its hydration shell and transition from an outer to an inner shell interaction, which is primarily influenced by the metal ion charge density. These results have implications for designing biocompatible sensors using riboswitches to probe the concentration of intracellular metal ions.

biophysics↗

bioRxiv2022

Exploiting the Nonlinear Structure of the Antithetic Integral Controller to Enhance Dynamic Performance

The design of biomolecular feedback controllers has been identified as an important goal across a broad range of biological applications spanning synthetic biology, cell therapy, metabolic engineering, etc. This originates from the need to regulate various cellular processes in a robust and timely fashion. Recently, antithetic integral controllers found their way into synthetic biology due to the Robust Perfect Adaptation (RPA) property they endow -- the biological analogue of robust steady-state tracking. The antithetic integral motif hinges on a sequestration reaction between two molecules that annihilates their function. Here, we demonstrate that the complex resulting from the nonlinear sequestration reaction can be leveraged as an inhibitor to enhance the dynamic performance while maintaining the RPA property. We establish that this additional inhibition by the sequestration complex gives rise to a filtered Proportional-Integral (PI) controller thus offering more flexibility in shaping the dynamic response and reducing cell-to-cell variability. Furthermore, we explore the effect of various biological inhibitory mechanisms on the overall performance. The various analyses in the paper are carried out using analytical tools and are supported by numerical simulations. Finally, an experimental validation is performed using the cyberloop -- a hybrid platform where the controller is implemented in silico to control a genetic circuit in vivo.

synthetic biology↗

bioRxiv2022

Specialized Tfh cell subsets driving type-1 and type-2 humoral responses in lymphoid tissue

Effective antibody responses are essential to generate protective humoral immunity. Different inflammatory signals polarize T cells towards an appropriate effector phenotype during an infection or immunization. Th1 and Th2 cells have been associated with the polarization of humoral responses for several decades. However, it is now established that T follicular helper cells (Tfh) have a unique ability to access the B cell follicle and support the Germinal Centre (GCs) responses by providing help to B cells. We investigated the specialization of Tfh cells induced under type-1 and type-2 conditions. We first studied homogenous Tfh cell populations generated by adoptively transferred TCR-transgenic T cells in mice immunized with type-1 and type-2 adjuvants. Using a machine learning approach, we established a gene expression signature that discriminates Tfh cells polarized towards type-1 and type-2 response, defined as Tfh1 and Tfh2 cells. The Tfh1 and Tfh2 distinct signature was validated against datasets of Tfh cells induced following LCMV or helminth infection. Using single-cell transcriptomics, we also dissected the heterogeneity of Tfh cells from the two immunizing conditions. Our results show that Tfh cells acquire a specialized function under distinct types of immune responses, but with the coexistence of a small population of Tfh cells of the alternative type. Furthermore, the specific molecular hallmarks of Tfh1 and Tfh2 cells identified herein offer putative new targets for tuning humoral responses.

immunology↗

bioRxiv2022

De-differentiation and Proliferation of Artery Endothelial Cells Drive Coronary Collateral Development

Collateral arteries act as natural bypasses which re-route blood flow to ischemic regions and facilitate tissue regeneration. In an injured heart, neonatal artery endothelial cells orchestrate a systematic series of cellular events, which includes their outward migration, proliferation, and coalescence into fully functional collateral arteries. This process, called Artery Reassembly, aids complete cardiac regeneration in neonatal hearts, but is absent in adults. The reason for this age-dependent disparity in artery cell response is completely unknown. In this study, we investigated if regenerative potential of coronary arteries, like in cardiomyocytes, is dictated by their ability to de-differentiate. We performed single cell RNA sequencing of coronary endothelial cells and identified differences in molecular profiles of neonatal and adult endothelial cells. Neonates show significant increase in actively cycling artery cells that expressed prominent de-differentiation markers. Using both, in silico pathway analyses and in vivo experiments, we show that cell cycle re-entry of pre-existing artery cells, subsequent collateral artery formation and cardiac function is dependent on arterial VegfR2. This sub-population of de-differentiated and proliferating artery cells is absent in non-regenerative P7 or adult hearts. Together, our data indicate that adult artery endothelial cells fail to drive collateral artery development due to their limited ability to de-differentiate and proliferate.

developmental biology↗

bioRxiv2022

Effect of Single Nucleotide Polymorphisms on the structure of long noncoding RNAs and their interaction with RNA Binding Proteins

Long non-coding RNAs (lncRNA) are emerging as a new class of regulatory RNAs with remarkable potential to be utilized as therapeutic targets against many human diseases. Several genome-wide association studies (GWAS) have catalogued Single Nucleotide Polymorphisms (SNPs) present in the noncoding regions of the genome, transcribing lncRNAs. In this study, we have selected 67 lncRNAs with GWAS-tagged SNPs and have also investigated their role in affecting the local secondary structures. The majority of the SNPs lead to changes in the secondary structure of lncRNA to a different extent by altering the base pairing patterns. These structural changes in lncRNA are also manifested in form of alteration in the binding site for RNA binding proteins (RBPs) along with affecting their binding efficacies. Ultimately, these structural modifications may influence the transcriptional and post-transcriptional pathways of these RNAs, leading to the causation of diseases. Hence, it is important to understand the possible underlying mechanism of RBPs in association with GWAS-tagged SNPs in human diseases.

bioinformatics↗

bioRxiv2022

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

genomics↗

bioRxiv2022

What drives prey selection? Assessment of tiger food habits across the Terai-Arc landscape, India

Large carnivores strongly shape ecological interactions within their respective ecosystems, but experience significant conflicts with human across their range due to their specific ecological resource requirements. The tiger (Panthera tigris) typifies the challenges faced by the large carnivore communities globally. India retains majority of the global tiger population with significant numbers outside protected areas (PAs) that are involved in conflicts from livestock predation and human/tiger death. To understand the prey selection patterns and spatio-temporal patterns of livestock predation-related conflict issues we investigated tiger food habits across the Indian part of the Terai-Arc Landscape (TAL), a globally-important tiger conservation landscape in India. We used 510 genetically-confirmed tiger faeces collected across the landscape and ascertained 10 wild and livestock as major prey species. Large-bodied species (sambar, swamp deer, nilgai, chital, wild pig and livestock) comprised ~94% of tiger diet, with sambar, chital and livestock were the major prey species. Habitat-specific (Shivalik-Bhabar and Terai) analyses show significantly different pattern of prey selections determined by abundance and prey body weight. Results also suggest that PA and non-PAs of Terai habitat are more prone to livestock depredation-related conflicts, and careful management interventions and community involvements are required to reduce such threats. We suggest long-term plans including population estimation of tigers and prey outside PAs, reducing grazing pressures and cattle enumeration, detailed investigation of tiger deaths etc. to ensure future tiger sustainability across this habitat.

ecology↗

bioRxiv2022

Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation

We present a robust, "real-time" optical autofocus system for microscopy that provides high accuracy (<230 nm) and long range ([~]130 {micro}m) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of {+/-}37.5 {micro}m and can also operate as a 2-step process up to {+/-}68 {micro}m. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.

bioengineering↗

bioRxiv2022

Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies

T-cell receptor-mimetic antibodies (TCRms) targeting disease-associated peptides presented by Major Histocompatibility Complexes (pMHCs) are set to become a major new drug modality. However, we lack a general understanding of how TCRms engage pMHC targets, which is crucial for predicting their specificity and safety. Several new structures of TCRm:pMHC complexes have become available in the past year, providing sufficient initial data for a holistic analysis of TCRms as a class of pMHC binding agents. Here, we profile the complete set of TCRm:pMHC complexes against representative TCR:pMHC complexes to quantify the TCR-likeness of their pMHC engagement. We find that intrinsic molecular differences between antibodies and TCRs lead to fundamentally different roles for their heavy/light chains and Complementarity-Determining Region loops during antigen recognition. The idiotypic properties of antibodies may increase the likelihood of TCRms engaging pMHCs with less peptide selectivity than TCRs. However, the pMHC recognition features of some TCRms, including the two TCRms currently in clinical trials, can be remarkably TCR-like. The insights gained from this study will aid in the rational design and optimisation of next-generation TCRms.

immunology↗

bioRxiv2022

A 2D Fragment-Assisted Protein Mimetic Approach to Rescue α-Synuclein Aggregation Mediated Early and Post-Disease Parkinsons Phenotypes

We have developed a Oligopyridylamide (OP) based 2-Dimensional Fragment-Assisted Structure-based Technique (2D-FAST) to identify potent antagonists of -Synuclein (S) aggregation, a process central to Parkinsons disease (PD). The 2D-FAST utilizes a fragment-based screening of large chemical space in OPs, which led to the identification of NS132 as an antagonist of the multiple facets of S aggregation. We also identified a better cell permeability analog (NS163) without sacrificing activity. OPs rescue S aggregation mediated PD phenotypes in muscle cells and dopaminergic (DA) neurons in C. elegans models. OPs prevent the progression of PD phenotypes in a novel post-disease onset PD model. This is one of the first examples of a synthetic mimetic-based 2D-FAST to identify antagonists of toxic S self-assembly. We envision that 2D-FAST will have tremendous potential as it is expandable for other oligoamide scaffolds and for a much larger chemical space to identify lead therapeutics for various diseases.

biochemistry↗

bioRxiv2022

The nucleoporin Nup170 mediates subtelomeric gene silencing through the Ctf18-RFC complex and PCNA

The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. The inner ring nucleoporin Nup170 has been implicated in chromatin organization and the maintenance of gene silencing in subtelomeric regions. To gain insight into how Nup170 regulates this process, we used protein-protein interaction, genetic interaction, and transcriptome correlation analyses to identify the Ctf18-RFC complex, an alternative proliferating cell nuclear antigen (PCNA) loader, as a facilitator of the gene regulatory functions of Nup170. The Ctf18-RFC complex is recruited to a subpopulation of NPCs that lack the nuclear basket proteins Mlp1 and Mlp2. In the absence of Nup170, PCNA levels on DNA are reduced, resulting in the loss of silencing of subtelomeric genes. Increasing PCNA levels on DNA by removing Elg1, which is required for PCNA unloading, rescues subtelomeric silencing defects in nup170{Delta}. The NPC therefore mediates subtelomeric gene silencing by regulating PCNA levels on DNA.

cell biology↗

bioRxiv2022

Phagosomal RNA sensing through TLR8 controls susceptibility to tuberculosis

Genetic determinants of susceptibility to Mycobacterium tuberculosis (Mtb) are poorly understood but could provide insights into critical pathways involved in infection, informing host-directed therapies and enabling risk stratification at individual and population levels. Through a genome-wide forward genetic screen, we identify the Toll-like Receptor 8 (TLR8), as a key regulator of intracellular killing of Mtb. Pharmacological TLR8 activation enhances killing of phylogenetically diverse clinical isolates of drug-susceptible and multidrug-resistant Mtb by macrophages and during in vivo infection in mice. TLR8 is activated by phagosomal mycobacterial RNA released by extracellular membrane vesicles, and enhances xenophagy-dependent Mtb killing. We find that the TLR8 variant, M1V, common in far eastern populations, enhances intracellular killing of Mtb through preferential signal-dependent trafficking to phagosomes. TLR8 signalling may therefore both regulate susceptibility to tuberculosis and provide novel drug targets. Single sentence summaryRNA released from Mycobacterium tuberculosis in the macrophage phagosome is sensed by the pattern recognition receptor TLR8 controlling host susceptibility to tuberculosis and revealing a druggable pathway for host-directed therapy.

immunology↗

bioRxiv2022

Dynamic cybergenetic control of bacterial co-culturecomposition via optogenetic feedback

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. Additionally, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.

synthetic biology↗

bioRxiv2022

Reconstructing the cascade of language processing in the brain using the internal computations of a transformer-based language model

Humans use complex linguistic structures to transmit ideas to one another. The brain is thought to deploy specialized computations to process these structures. Recently, a new class of artificial neural networks based on the Transformer architecture has revolutionized the field of language modeling, attracting attention from neuroscientists seeking to understand the neurobiology of language in silico. Transformers integrate information across words via multiple layers of structured circuit computations, forming increasingly contextualized representations of linguistic content. Prior work has focused on the internal representations (the "embeddings") generated by these circuits. In this paper, we instead analyze the circuit computations directly: we deconstruct these computations into functionally-specialized "transformations" to provide a complementary window onto linguistic computations in the human brain. Using functional MRI data acquired while participants listened to naturalistic spoken stories, we first verify that the transformations account for considerable variance in brain activity across the cortical language network. We then demonstrate that the emergent syntactic computations performed by individual, functionally-specialized "attention heads" differentially predict brain activity in specific cortical regions. These heads fall along gradients corresponding to different layers, contextual distances, and syntactic dependencies in a low-dimensional cortical space. Our findings indicate that large language models and the cortical language network may converge on similar trends of functional specialization for processing natural language.

neuroscience↗

bioRxiv2022

The amino acid transporter pfaat1 modulates chloroquine resistance and fitness in malaria parasites

Malaria parasites break down host hemoglobin into peptides and amino acids in the digestive vacuole for export to the parasite cytoplasm for growth: interrupting this process is central to the mode of action of several antimalarial drugs. Mutations in the chloroquine (CQ) resistance transporter, pfcrt, located in the digestive vacuole membrane, confer CQ resistance in Plasmodium falciparum, but typically affect parasite fitness. However, the role of other parasite loci in the evolution of CQ resistance is unclear. Here we use a combination of population genomics, genetic crosses and gene editing to demonstrate that a second vacuolar transporter plays a key role in both resistance and compensatory evolution. Longitudinal genomic analyses of the Gambian parasites revealed temporal signatures of selection on an amino acid transporter (pfaat1) S258L variant which increased from 0-87% in frequency between 1984 and 2014 in parallel with pfcrt1 K76T. Parasite genetic crosses then identified a chromosome 6 quantitative trait locus containing pfaat1 that is selected by CQ treatment. Gene editing demonstrated that pfaat1 S258L potentiates CQ-resistance but at a cost of reduced fitness, while pfaat1 F313S, a common Southeast Asian polymorphism, reduces CQ-resistance while restoring fitness. Our analyses reveal hidden complexity in CQ-resistance evolution, suggesting that pfaat1 may underlie regional differences in the dynamics of resistance evolution, and modulate parasite resistance or fitness by manipulating the balance between both amino acid and drug transport.

genomics↗

bioRxiv2022

Comparative genomic insights into the evolution of Halobacteria-associated "Candidatus Nanohaloarchaeota"

The phylum "Candidatus Nanohaloarchaeota" is a representative halophilic lineage within DPANN superphylum. They are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear for the lack of genomes located at the transition stage. Here, we performed a comparative genomic analysis of "Ca. Nanohaloarchaeota". We propose a novel family "Candidatus Nanoanaerosalinaceae" represented by five de-replicated metagenome-assembled genomes obtained from hypersaline sediments and the enrichment cultures of soda-saline lakes. Phylogeny analysis reveals that the novel family are placed at the root of the family "Candidatus Nanosalinaceae" including the well-researched taxa. Most members of "Ca. Nanoanaerosalinaceae" contain lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae", while they maintain moderately acidic proteomes for hypersaline adaptation of "salt-in" strategy, suggesting that "Ca. Nanoanaerosalinaceae" have not established an intimate association with Halobacteria, and may descend from an intermediate stage. Functional prediction discloses that they exhibit divergent potentials in carbohydrate and organic acids metabolism, and environmental responses. Historical events reconstruction illustrates that the involved genes acquired at the putative ancestors possibly drive the evolutionary and symbiotic divergences. Globally, this research on the new family "Ca. Nanoanaerosalinaceae" enriches the taxonomic and functional diversity of "Ca. Nanohaloarchaeota", and provides insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. ImportanceDPANN superphylum is a group of archaea widely distributing in various habitats. They generally have small cells, and perform a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is important to understand microbial community. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, hypersaline adaptation, functional potentials, and historical events of "Ca. Nanohaloarchaeota", a representative phylum within the DPANN superphylum, we report a novel family descending from an intermediate stage, and we illustrate the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Furthermore, we find the acquired genes involved in carbohydrate and organic acids metabolism and environmental responses possibly drive the evolutionary and symbiotic divergences. Altogether, this research helps in understanding the evolution of the archaeal symbiosis, and provides a model for the evolution of the other DPANN lineages.

microbiology↗