Biology subjects

Singh, P.

Publications and source records attributed to Singh, P..

At least 145 records · Page 8Linked to original sources

bioRxiv2022

Structural, functional and evolutionary analysis of wheat WRKY45 protein: A combined bioinformatics and MD simulation approach

Bread wheat (Triticum aestivum L.) is the worlds second-most important cereal crop, as well as Indias. It is an allohexaploid composed of three homeologous sub-genomes (AA, BB, and DD), which is a constraint in determining the complete genome sequence. Several transcription factors have been implicated in both abiotic and biotic stress. WRKY transcription factors are among the best characterised in the context of pathogen defence mechanisms. Different members of the WRKY transcription factors have been shown to confer resistance to stress. But very little is known about the wheat WRKY transcription factors. In silico analysis of the TaWRKY45 protein was performed in the present study using several bioinformatics tools like motif scan, CD search, Netphos, NGlycos, GRAVY, and the SWISS MODEL. The study revealed that TaWRKY45 belongs to the group III family and contains hydrophilic proteins with 19 potential phosphorylation sites. TaWRKY45 protein was found to be orthologous to rice OsWRKY45 by phylogenetic analysis. The catalytic domain was analysed by motif scan which showed that TaWRKY45 has one WRKY domain and a C2-HC zinc finger motif. TaWRKY45s structure was determined to be more stable, more constrained, more compact, and have greater potential to interact with other molecules than OsWRKY45, according to MD simulation analysis. Thus, in silico analysis of transcription factors helps study protein function, interaction, and regulatory pathways.

bioinformatics↗

bioRxiv2022

A sterility-mortality tolerance trade-off leads to within-population variation in host tolerance.

While experimental studies have demonstrated within-population variation in host tolerance to parasitism, theoretical studies rarely predict for polymorphism to arise. However, most theoretical models do not consider the crucial distinction between tolerance to the effects of infection-induced deaths (mortality tolerance) and tolerance to the parasite-induced reduction in the reproduction of infected hosts (sterility tolerance). While some studies have examined trade-offs between host tolerance and resistance mechanisms, none has considered a correlation within different tolerance mechanisms. We assume that sterility tolerance and mortality tolerance are directly traded-off in a host population subjected to a pathogen and use adaptive dynamics to study their evolutionary behaviour. We find that such a trade-off between the two tolerance strategies can drive the host population to branch into dimorphic strains, leading to coexistence of strains with sterile hosts that have low mortality and fully fertile with high mortality rates. Further, we find a wider range of trade-off shapes allows branching at intermediate or high infected population size. Our other significant finding is that sterility tolerance is maximised (and mortality tolerance minimised) at an intermediate disease-induced mortality rate. Additionally, evolution entirely reverses the disease prevalence pattern corresponding to the recovery rate, compared to when no strategies evolve. We provide novel predictions on the evolutionary behaviour of two tolerance strategies concerning such a trade-off.

evolutionary biology↗

bioRxiv2022

Kinase Inhibitor Pulldown Assay (KiP) for Clinical Proteomics

Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential, but current approaches are inadequate. For breast cancer treatment for example, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers more quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of protein yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method.

biochemistry↗

bioRxiv2022

Gene expression profiling and protein-protein network analysis revealed prognostic hub biomarkers linking cancer risk in type 2 diabetic patients

Type 2 diabetes mellitus (T2DM) and cancer are highly prevalent diseases imposing major health burden globally. Several epidemiological studies indicate increased susceptibility to cancer in T2DM patients. However, genetic factors linking T2DM with cancer are poorly studied so far. We used computational approach on the raw gene expression data of peripheral blood mononuclear cells of Homo sapiens available at the gene expression omnibus (GEO) database, to identify shared differentially expressed genes (DEGs) in T2DM and three common cancer types namely, pancreatic (PC), liver (LC) and breast cancer (BC). Additional functional and pathway enrichment analysis of identified common DEGs highlighted involvement of important biological pathways including cell cycle events, immune system process, cell morphogenesis, gene expression and metabolism. Furthermore, we retrieved the PPI network for crucial DEGs obtained from above analysis to deduce molecular level interactions. Based on the result of network analysis, we found 8, 5 and 9 common hub genes in T2DM vs PC, T2DM vs LC and T2DM vs BC, respectively. Overall, our analysis identified important genetic markers potentially able to predict the chances of pancreatic, liver and breast cancer onset in T2DM patients.

bioinformatics↗

bioRxiv2022

Plasticity and interactions in the odor responses of maxillary palps neurons in Aedes aegypti

Maxillary palps, in addition to the antennae, are major olfactory organs in mosquitoes and play an important role in the detection of human hosts. The sensory neurons of the maxillary palps reside in the capitate peg sensilla, each of which contains three neurons. In Aedes aegypti, the neuron with the largest spike amplitude in the sensillum is known to detect carbon dioxide. However, the responses of the other two neurons and the functional consequences of the grouping of these neurons within sensilla are not well understood. Here we identify odorants that activate the other two neurons. We detect a short-term plasticity in the odor-evoked local field potential of the sensillum and show that it originates in the spiking responses of the smallest-amplitude neuron, even though all three neurons contribute to the local field potential. We also detect inhibitory interactions among these neurons within the sensillum. We further show that the plasticity and the lateral interactions are functionally important as they affect the responses of the downstream projection neurons in the antennal lobe.

neuroscience↗

bioRxiv2022

Transcriptional profiles of functionally distinct HLADR+CD38+ CD8 T cells subsets from acute febrile dengue patients

Previous studies showed that a discrete population of the CD8 T cells with HLADR+CD38+ phenotype expand massively during the acute febrile phase of dengue natural infection. Although about a third of these massively expanding HLADR+CD38+ CD8 T cells were of CD69high phenotype, only a small fraction of them produced IFN{gamma} upon in vitro peptide stimulation. What other cytokines/ chemokines do these peptides stimulated HLADR+CD38+ CD8 T cells express, what transcriptional profiles distinguish the CD69+IFN{gamma}+, CD69+IFN{gamma}-, and CD69-IFN{gamma}- subsets, and whether the expansion of the total HLADR+CD38+ CD8 T cells or the IFN{gamma} producing CD8 T cells differ depending on disease severity remained unclear. This study addresses these knowledge gaps. We find that the CD69+IFN{gamma}+ subset uniquely expressed key genes involved in protein translation, cellular metabolism, proliferation and dendritic cell cross talk. Both the CD69+IFN{gamma}+ and CD69+IFN{gamma}- subsets had an antigen responsive gene signature with genes involved in cytotoxic effector functions, regulation of T cell receptor signaling, signaling by MAPK, chemotaxis and T cell trafficking to inflamed tissues with the expression being more robust in the IFN{gamma}+ CD69+ subset. On the other hand, the CD69- IFN{gamma}- subset was biased towards expression of genes that both augment and dampen T cell responses. Lastly, the expansion of total HLADR+ CD38+ CD8 T cells and also the IFN{gamma} producing HLADR+ CD38+ CD8 T cells was similar in patients with different grades of disease. Taken together, this study provides valuable insights into the inherent diversity of the effector CD8 T cell response during dengue.

immunology↗

bioRxiv2022

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

Standards support synthetic biology research by enabling the exchange of component information. However, using formal representations, such as the Synthetic Biology Open Language (SBOL), typically requires either a thorough understanding of these standards or a suite of tools developed in concurrence with the ontologies. Since these tools may be a barrier for use by many practitioners, the Excel-SBOL Converter was developed to allow easier use of SBOL and integration into existing workflows. The converter consists of two Python libraries: one that converts Excel templates to SBOL, and another that converts SBOL to an Excel workbook. Both libraries can be used either directly or via a SynBioHub plugin. We illustrate the operation of the Excel-SBOL Converter with two case studies: uploading experimental data with the studys metadata linked to the measurements and downloading the Cello part repository. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/505873v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@c06d7aorg.highwire.dtl.DTLVardef@153724eorg.highwire.dtl.DTLVardef@1758791org.highwire.dtl.DTLVardef@11779c2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

HP1 deficiency results in De-Repression of Endogenous Retroviruses and Induction of Neurodegeneration via Complement

In aging cells and animal models of premature aging, heterochromatin loss coincides with transcriptional disruption including the activation of normally silenced endogenous retroviruses (ERVs). Here we show that loss of heterochromatin maintenance and de-repression of ERVs results in a chronic inflammatory environment characterized by neurodegeneration and cognitive decline. We discovered differential contributions of HP1 proteins to ERV silencing where HP1{gamma} is necessary and sufficient for H4K20me3 deposition and HP1{beta} deficiency causes aberrant DNA methylation. Combined loss of HP1{beta} and HP1{gamma} resulted in loss of DNA methylation at ERVK elements. Progressive ERV de-repression in HP1{beta}/{gamma} DKO mice was followed by stimulation of the integrated stress response, an increase of Complement 3+ reactive astrocytes and phagocytic microglia. This chronic inflammatory state coincided with age-dependent reductions in dendrite complexity and cognition. Our results demonstrate the importance of preventing loss of epigenetic maintenance, as this will be the only way postmitotic neuronal genomes can be protected and/or renewed. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/505641v4_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@f5feb7org.highwire.dtl.DTLVardef@25d73dorg.highwire.dtl.DTLVardef@5604a4org.highwire.dtl.DTLVardef@14ad84a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Combination therapy of glycation lowering compounds reduces caloric intake, improves insulin sensitivity and extends lifespan.

Non-enzymatic reactions in glycolysis lead to the accumulation of methylglyoxal (MGO), a reactive precursor to advanced glycation end-products (AGEs), which has been hypothesized to drive obesity, diabetes and aging-associated pathologies. A combination of nicotinamide, -lipoic acid, thiamine, pyridoxamine, and piperine (Gly-Low) lowered deleterious effects of glycation by reducing MGO and MGO-derived AGE, MG-H1, in mice. Gly-Low supplementation in the diet reduced food consumption, decreased body weight, improved insulin sensitivity, and increased survival in leptin receptor-deficient (Leprdb) and wild-type C57B6/J mice. Transcriptional, protein, and functional analyses demonstrated that Gly-Low inhibited appetite-stimulating ghrelin signaling and enhanced the appetite-satiating mTOR pathways within the hypothalamus. Consistent with these molecular findings, Gly-Low inhibited ghrelin-mediated hunger responses. When administered as a late-life intervention, Gly-Low slowed hypothalamic aging signatures, improved glucose homeostasis and motor coordination, and increased lifespan, suggesting its potential benefits in ameliorating age-associated decline. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=171 HEIGHT=200 SRC="FIGDIR/small/503411v3_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1beedc4org.highwire.dtl.DTLVardef@1ec1933org.highwire.dtl.DTLVardef@16a7ad2org.highwire.dtl.DTLVardef@1a5a608_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Resting-state aperiodic neural activity as a novel objective marker of daytime somnolence

Study ObjectivesCurrent assessment of excessive daytime somnolence (EDS) requires subjective measurements such as the Epworth Sleepiness Scale (ESS), and/or resource intensive sleep laboratory investigations. Recent work 1,2 has called for more non-performance-based measures of EDS. One promising non-performance-based measure of EDS is the aperiodic component of electroencephalography (EEG). Aperiodic (non-oscillatory) activity reflects excitation/inhibition ratios of neural populations and is altered in various states of consciousness, and thus may be a potential biomarker of hypersomnolence. MethodsWe retrospectively analysed EEG data from patients who underwent a Multiple Sleep Latency Test (MSLT) and determined whether aperiodic neural activity is predictive of EDS. Participants having undergone laboratory polysomnogram and next day MSLT were grouped into MSLT+ (n = 26) and MSLT- (n = 33) groups (mean sleep latency of < 8min and > 10min, respectively) and compared against a non-clinical (Control) group of participants (n = 26). ResultsWhile the MSLT+ and MSLT- groups did not differ in their aperiodic activity, the Control group had a significantly flatter slope and larger offset compared to both MSLT+ and MSLT- groups. Logistic regression machine learning predicted group status (i.e., symptomatic, non-symptomatic) with 90% accuracy based on the aperiodic slope while controlling for age. Slow oscillation-spindle coupling was also significantly stronger in the Control group relative to MSLT+ and MSLT- groups. ConclusionsOur results provide first evidence that aperiodic neural dynamics and sleep-based cross-frequency coupling is predictive of EDS, thereby providing a novel avenue for basic and applied research in the study of sleepiness.

neuroscience↗

bioRxiv2022

Cohesin is involved in transcriptional repression of stage-specific genes in the human malaria parasite

The most virulent human malaria parasite, Plasmodium falciparum, has a complex life cycle between its human host and mosquito vector. Each stage is driven by a specific transcriptional program, but with a relatively high ratio of genes to specific transcription factors, it is unclear how genes are activated or silenced at specific times. The P. falciparum genome is relatively euchromatic compared to the mammalian genome, except for specific genes that are uniquely heterochromatinized via HP1. There seems to be an association between gene activity and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome-organizing proteins found in metazoans, it does have all core components of the cohesin complex. In other eukaryotes, cohesin is involved in sister chromatid cohesion, transcription, and genome organization. To investigate the role of cohesin in P. falciparum, we combined genome editing, mass spectrometry, chromatin immunoprecipitation and sequencing (ChIP-seq), and RNA sequencing to functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown in early stages of the intraerythrocytic developmental cycle (IDC) resulted in significant upregulation of a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq of SMC3 revealed that over the IDC, enrichment at the promoter regions of these genes inversely correlates with their expression and chromatin accessibility levels. These data suggest that SMC3 binding helps to repress specific genes until their appropriate time of expression, revealing a new mode of stage-specific, HP1-independent gene repression in P. falciparum.

molecular biology↗

bioRxiv2022

The genome of Gynandropsis gynandra provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra, anchored onto 17 main super- scaffolds with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. We revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-), then an addition of a third genome (Th-, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3 T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the impact of gene duplication and gene retention on the evolution of C4 photosynthesis in Cleomaceae.

plant biology↗

bioRxiv2022

Penetratin inhibits α-synuclein fibrillation and improves locomotor functions in mice model of Parkinsons disease

Parkinsons disease (PD) is the second most common neurodegenerative disease. The presence of lewy bodies, primarily consisting of -synuclein (-syn) aggregates is one of the common features seen in the substantia nigra region of the brain in PD patients. The disease remains incurable and only symptomatic relief is available. We screened various cell-penetrating peptides and reveal that penetratin is a potent inhibitor of -syn aggregation in-vitro, and significantly improved locomotor coordination in mice models of PD in-vivo. The peptide inhibits -syn aggregation in vitro as well as in yeast, and C.elegans models. We further made a cyclic derivative of penetratin by disulfide coupling of N- and C-terminal cysteine residues. Both penetratin and its cyclized derivative interact with -syn. NMR studies show that both linear as well as cyclic derivative interact at the acidic C-terminal tail of the protein. Similar to penetratin, its cyclic derivative inhibited -syn aggregation in the C.elegans model of Parkinsons disease, and also improved worm motility. Molecular Dynamics studies show that penetratin interacts with -synuclein and prevents its conformational transition from disordered into {beta}-sheet rich structure. The therapeutic efficacy of penetratin was further confirmed in a transgenic mice model of the disease, wherein penetratin treatment over a period of 90 days improved locomotor coordination, and halted disease progression. Overall, the present work provides a potent therapeutic agent that could be further explored in the management of PD.

neuroscience↗

bioRxiv2022

Understanding the genome-wide transcription response to varying cAMP levels using phenomenological models in bacteria

Attempts to understand gene regulation by global transcription factors (TF) have largely been limited to expression studies under binary conditions of presence and absence of the TF. Studies addressing genome-wide transcriptional responses to changing TF concentration at high resolution are lacking. Here, we create a dataset containing the entire E.coli transcriptome as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hills model to accurately summarise individual gene responses into 3 intuitively understandable parameters - k, n and Emax reflecting the midpoint of dynamic range, non-linearity and sensitivity of a gene. cAMP-regulated genes show a small dynamic range with midpoints centred around wild-type cAMP concentrations, with genes activating in a switch-like fashion. Using this approach we show that cAMP-CRP affinity at promoters is well correlated to the sensitivity(Emax) of genes but not to the midpoints of dynamic range(k). Finally, genes belonging to different functional classes are tuned to different k, n and Emax. We show phenomenological models to be a better alternative for studying gene expression trends compared to classical clustering methods with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network.

bioinformatics↗

bioRxiv2022

Combinatorial encoding of odors in the mosquito antennal lobe

Among the cues that a mosquito uses to find a host for blood-feeding, the smell of the host plays an important role. Previous studies have shown that host odors contain hundreds of chemical odorants, which are detected by different receptors on the peripheral sensory organs of mosquitoes. But how individual odorants are encoded by downstream neurons in the mosquito brain is not known. We developed an in vivo preparation for patch-clamp electrophysiology to record from projection neurons and local neurons in the antennal lobe of Aedes aegypti. Combining intracellular recordings with dye-fills, morphological reconstructions, and immunohistochemistry, we identify different sub-classes of antennal lobe neurons and their putative interactions. Our recordings show that an odorant can activate multiple neurons innervating different glomeruli, and that the stimulus identity and its behavioral preference are represented in the population activity of the projection neurons. Our results provide the first detailed description of olfactory neurons in the central nervous system of mosquitoes and lay a foundation for understanding the neural basis of their olfactory behaviors.

neuroscience↗

bioRxiv2022

Deciphering Hematopoiesis at single-cell level through the lens of reduced dimensions

Hematopoiesis plays a critical role in maintaining a diverse pool of blood cells throughout human life. Despite recent efforts with single-cell data analyses, the nature of the early cell fate decisions and compartmentalization of progenitors remains contentious due to the sparsity and noise of the data. Using publically available single-cell RNA-Seq hematopoietic data from bone marrow, with three different matrix factorization approaches to recover associated gene modules from cell clusters reveals a tri-directional and hierarchically-structured transcriptional landscape of hematopoietic differentiation. We also devised a bootstrap method, which in combination with the above can better characterize the progenitor compartments and retrieve cellular hierarchies.

genomics↗

bioRxiv2022

The Drosophila attP40 docking site and derivatives are insertion mutations of MSP300

The {phi}C31 integrase system is widely used in Drosophila to allow transgene targeting to specific loci. Over the years, flies bearing any of more than 100 attP docking sites have been constructed. One popular docking site, termed attP40, is located close to the Nesprin-1 orthologue MSP300 and lies upstream of certain MSP300 isoforms and within the first intron of others. Here we show that attP40 causes larval muscle nuclear clustering, which is a phenotype also conferred by MSP300 mutations. We also show that flies bearing insertions within attP40 can exhibit decreased MSP300 transcript levels in third instar larvae. Finally, chromosomes carrying certain "transgenic RNAi project" (TRiP) insertions into attP40 can confer pupal or adult inviability, or infertility. These phenotypes do not require transcription from the insertions within attP40. These results demonstrate that attP40 and insertion derivatives act as MSP300 insertional mutations. These findings should be considered when interpreting data from attP40-bearing flies.

genetics↗

bioRxiv2022

Decoding The Nuclear Genome of The Human Pathogen Babesia duncani Shed Light on its Virulence, Drug Susceptibility and Evolution among Apicomplexa

Babesia species are tick-transmitted apicomplexan pathogens and the causative agents of babesiosis, a malaria-like disease of major medical and veterinary importance. Of the different species of Babesia reported so far, Babesia duncani causes severe to lethal infection in patients. Despite the highly virulent nature of this parasite and the risk it may pose as an emerging pathogen, little is known about its biology, metabolic requirements, and pathogenesis. B. duncani is unique among apicomplexan parasites that infect red blood cells in that it can be continuously cultured in vitro in human erythrocytes but can also infect mice leading to fulminant babesiosis infection and death. Here we have taken advantage of the recent advances in the propagation of this parasite in vitro and in vivo to conduct detailed molecular, genomic and transcriptomic analyses and to gain insights into its biology. We report the assembly, 3D structure, and annotation of the nuclear genome of this parasite as well as its transcriptomic profile and an atlas of its metabolism during its intraerythrocytic life cycle. Detailed examination of the B. duncani genome and comparative genomic analyses identified new classes of candidate virulence factors, suitable antigens for diagnosis of active infection, and several attractive drug targets. Translational analyses and efficacy studies identified highly potent inhibitors of B. duncani thus enriching the pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.

microbiology↗