Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 19 recordsLinked to original sources

bioRxiv2018

In vitro model of inflammatory, hypoxia, and cancer stem cell signaling in pancreatic cancer using heterocellular 3-dimensional spheroids

IntroductionAs one of the most aggressive cancers worldwide, pancreatic cancer is associated with an extremely poor prognosis. The pancreatic tumor microenvironment consists of cancer cells and other tumor associated cells. Cross-talk between these different cell types through various signaling molecules results in the development of a more aggressive and malignant phenotype. Additionally, due to the highly dysregulated vasculature of tumors, the inner tumor core becomes hypoxic and eventually necrotic. Therefore, there is a need for the development of a physiologically relevant in vitro model that recapitulates these dynamic cell-cell interactions and the 3-dimensional (3D) structure of pancreatic tumors.\n\nMethodsFour different 3D co-culture spheroid models using different combinations of Panc-1 tumor cells, J774.A1 macrophages, and NIH-3T3 fibroblast cell lines were reproducibly developed using the hanging drop technique in order to mimic the tumor microenvironment and to evaluate the differences in expression of various inflammatory, hypoxia, and cancer stem cell markers, including IL-8, TNF-, TGF-{beta}, HIF-1 HIF-2, SCF, and LDH-A. Additionally, immunofluorescence studies were employed to investigate whether these spheroids tested positive for a cancer stem cell population.\n\nResultsPronounced differences in morphology as well as expression of signalling markers were observed using qPCR, indicative of strong influences of co-culturing different cell lines. These models also tested positive for cancer stem cell (CSCs) markers based on immunofluorescence and qPCR analysis.\n\nConclusionOur results demonstrate the potential of 3D co-culture spheroid models to capture the inflammatory and hypoxic markers of pancreatic tumor microenvironment. We further demonstrate the presence of cancer cells with stem cell markers, similar to actual pancreatic cancer tumor. These spheroids present excellent in vitro system to study tumor-immune-stromal cell interactions as well as test deliverability of potential therapeutics in the tumor microenvironment with accurate physical and physiological barriers.

cancer biology↗

bioRxiv2018

Mutually exclusive locales for N-linked glycans and disorder in glycoproteins

Several post-translational modifications of proteins lie within regions of disorder, stretches of amino acid residues that exhibit a dynamic tertiary structure and resist crystallization. Such localization has been proposed to expand the binding versatility of the disordered regions, and hence, the repertoire of interacting partners for the proteins. However, investigating a dataset of 500 human N-linked glycoproteins, we observed that the sites of N-linked glycosylations, or N-glycosites, lay predominantly within the regions of predicted order rather than their unstructured counterparts. This mutual exclusivity between disordered stretches and N-glycosites could not be reconciled merely through asymmetry in distribution of asparagines, serines or threonines residues, which comprise the minimum-required signature for conjugation by N-linked glycans, but rather by a contextual enrichment of these residues next to each other within the ordered portions. In fact, N-glycosite neighborhoods and disordered stretches showed distinct sets of enriched residues suggesting their individualized roles in protein phenotype. N-glycosite neighborhood residues also showed higher phylogenetic conservation than disordered stretches within amniote orthologs of glycoproteins. However, a universal search for residue-combinations that are putatively domain-constitutive ranked the disordered regions higher than the N-glycosite neighborhoods. We propose that amino acid residue-combinations bias the permissivity for N-glycoconjugation within ordered regions, so as to balance the tradeoff between the evolution of protein stability, and function, contributed by the N-linked glycans and disordered regions respectively.

bioinformatics↗

bioRxiv2018

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, Voltron, that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 minutes of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

neuroscience↗

bioRxiv2018

Extrinsic Noise Suppression in Micro RNA Mediated Incoherent Feedforward Loops

MicroRNA mediated incoherent feed forward loops (IFFLs) are recurrent network motifs in mammalian cells and have been a topic of study for their noise rejection and buffering properties. Previous work showed that IFFLs can adapt to varying promoter activity and are less prone to noise than similar circuits without the feed forward loop. Furthermore, it has been shown that microRNAs are better at rejecting extrinsic noise than intrinsic noise. This work studies the biological mechanisms that lead to extrinsic noise rejection for microRNA mediated feed forward network motifs. Specifically, we compare the effects of microRNA-induced mRNA degradation and translational inhibition on extrinsic noise rejection, and identify the parameter regimes where noise is most efficiently rejected. In the case of static extrinsic noise, we find that translational inhibition can expand the regime of extrinsic noise rejection. We then analyze rejection of dynamic extrinsic noise in the case of a single-gene feed forward loop (sgFFL), a special case of the IFFL motif where the microRNA and target mRNA are co-expressed. For this special case, we demonstrate that depending on the time-scale of fluctuations in the extrinsic variable compared to the mRNA and microRNA decay rates, the feed forward loop can both buffer or amplify fluctuations in gene product copy numbers.

systems biology↗

bioRxiv2018

Pharmacophore-driven Identification of N-Methyl-D-Receptor Antagonists as Potent Neuroprotective Agents Validated Using In-Vivo Studies

Alzheimers disease (AD), the most widespread cause of dementia is delineated by progressive cognitive impairment in the elderly people. During its progression, N-Methyl-D-Aspartate receptor antagonists are known to play a key role in the mechanisms of learning and memory. Extensive side effects alongside other effects on learning and memory have limited the therapeutic significance of various blockers and antagonists of the NMDA receptor. In this study, we identify potential compounds targeted against NMDA. In order to reveal the essential structural features for NMDA receptor, three-dimensional pharmacophore models are constructed based on a set of known NMDA inhibitors. This is followed by virtual screening which results in novel chemical compounds having the potential to inhibit NMDA. The lead compounds are then subjected to molecular docking and assessed by a scoring function, which results in two compounds with high Libdock scores. These compounds also show interactions with important residues at the active site. The compounds are shortlisted on the basis of high estimated activity, fit values, LibDock score, no violation to Lipinskis and availability for procuring.\n\nOf the shortlisted compounds, one compound satisfying the entire aforementioned criterion is further tested using in-vivo studies on mice with the help of an eight-arm radial maze. The pharmacophore-based virtual screening protocol presented in this study pave the way forward to address the unmet medical need of Alzheimer disease.

bioinformatics↗

bioRxiv2018

Mycobacterium ulcerans in Mosquitoes and March flies captured from endemic areas of Northern Queensland, Australia

Mycobacterium ulcerans is the causative agent of Buruli ulcer (BU). This nontuberculous mycobacterial infection has been reported in over 33 countries worldwide. In Australia, the majority of cases of BU have been recorded in coastal Victoria and the Mossman-Daintree areas of north Queensland. Mosquitoes have been postulated as a vector of M. ulcerans in Victoria, however the specific mode of transmission of this disease is still far from being well understood. In the current study, we trapped and analysed 16,900 (allocated to 845 pools) mosquitoes and 296 March flies from the endemic areas of north Queensland to examine for the presence of M. ulcerans DNA by polymerase chain reaction. Seven of 845 pools of mosquitoes were positive on screening using the IS2404 PCR target but only one pool was positive for presence of M. ulcerans after confirmatory testing. None of the March fly samples were positive for the presence of M. ulcerans. M. ulcerans was detected on proboscises of deliberately exposed mosquitoes.\n\nAuthor SummaryThe causative agent of Buruli ulcer is Mycobacterium ulcerans. This destructive skin disease is characterized by extensive and painless necrosis of skin and underlying tissues usually on extremities of body due to production of toxin named mycolactone. The disease is prevalent in Africa and coastal Australia. The exact mode of transmission and potential environmental reservoir for the pathogen still remain obscure. Aquatic and biting insects have been identified as important niche in transmission and maintenance of pathogen in the environment. In this study we screened mosquitoes and march flies captured from endemic areas of northern Queensland for the presence of M. ulcerans. In addition, we conducted artificial blood feeding experiment to identify the role of mosquitoes in transmission of this pathogen. We found one pool of mosquito out of 845 pools positive for M. ulcerans and none of the March fly samples were positive. This could indicate a low burden of the bacteria in the environment coinciding with a comparatively low number of human cases of M. ulcerans infection seen during the trapping period of the study. Evidence to support mechanical transmission via mosquito proboscises was found.

microbiology↗

bioRxiv2018

Pooled optical screens in human cells

Large-scale genetic screens play a key role in the systematic discovery of genes underlying cellular phenotypes. Pooling of genetic perturbations greatly increases screening throughput, but has so far been limited to screens of enrichments defined by cell fitness and flow cytometry, or to comparatively low-throughput single cell gene expression profiles. Although microscopy is a rich source of spatial and temporal information about mammalian cells, high-content imaging screens have been restricted to much less efficient arrayed formats. Here, we introduce an optical method to link perturbations and their phenotypic outcomes at the singlecell level in a pooled setting. Barcoded perturbations are read out by targeted in situ sequencing following image-based phenotyping. We apply this technology to screen a focused set of 952 genes across >3 million cells for involvement in NF-{kappa}B activation by imaging the translocation of RelA (p65) to the nucleus, recovering 20 known pathway components and 3 novel candidate positive regulators of IL-1{beta} and TNF-stimulated immune responses.

genomics↗

bioRxiv2018

Resting state fMRI based target selection for personalized rTMS: stimulation over the left DLPFC temporarily alters the default mode network in healthy subjects

High frequency repetitive TMS (HF-rTMS) to the left dorsolateral prefrontal cortex (DLPFC) is an approved option for the treatment of depression, but there is also much variability in the resulting antidepressant response. This variability is believed to arise from various factors, an important one of which being the method by which rTMS is targeted to the optimal stimulation site in the left DLPFC. To more accurately target HF-rTMS at left DLPFC, we present a new method for target selection based on individual RS-fMRI data. We show in 23 healthy subjects that the new proposed method of target selection is reproducible and yields left DLPFC targets whose functional connectivity correlates more negatively with subgenual anterior cingulate cortex (sgACC) than targets based on standard MNI coordinates. Since previous work has highlighted higher negative connectivity with the sgACC as an important feature of targets for higher antidepressant effect of HF-rTMS, the targets selected by the new method can be expected to lead to a higher therapeutic response. Additionally, the mechanism of action of an entire single session of HF-rTMS (3000 pulses) in healthy subjects has not been reported. We show significant decreases in functional connectivity of the default mode network in sgACC and ventral striatum (vStr) regions, peaking at 27-32 minutes after stimulation. Also, we report a negative correlation between the magnitude of this decrease in the right sgACC and the harm avoidance domain measure from the Temperament and Character Inventory (TCI). This finding points towards the possibility of using the harm avoidance measure as a predictor of HF-rTMS response. In addition, the decreased functional connectivity of the default mode network in right nucleus accumbens (NAcc) correlates with a short-term decrease in self-rated negative emotions from the Positive and Negative Affect Schedule (PANAS) i.e. the lower the functional connectivity of right NAcc with the default mode network, the lower the reported perception of negative mood by the subjects. This suggests a mechanism by which changes induced by rTMS influence the perception of negative mood in recipients.

neuroscience↗

bioRxiv2018

Understanding the Liver Under Heat Stress With Statistical Learning: A Multiomics Computational Approach

We present results from a pipeline developed to integrate multi-omics data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress is a significant cause of productivity loss in the poultry industry, both in terms of increased livestock morbidity and its negative influence on average feed efficiency. This study focuses on the liver because it is an important regulator of metabolism, controlling many of the physiological processes impacted by prolonged heat stress. Using statistical learning methods, we identify genes and metabolites that may regulate the heat stress response in the liver and adaptations required to acclimate to prolonged heat stress. Our findings provide more detailed context for genomic studies and generates hypotheses about dietary interventions that can mitigate the negative influence of heat stress on the poultry industry.\n\nAbbreviation Term

genomics↗

bioRxiv2018

Identifying Mechanisms of Regulation to Model Carbon Flux During Heat Stress And Generate Testable Hypotheses

Understanding biological response to stimuli requires identifying mechanisms that coordinate changes across pathways. One of the promises of multi-omics studies is achieving this level of insight by simultaneously identifying different levels of regulation. However, computational approaches to integrate multiple types of data are lacking. An effective systems biology approach would be one that uses statistical methods to detect signatures of relevant network motifs and then builds metabolic circuits from these components to model shifting regulatory dynamics. For example, transcriptome and metabolome data complement one another in terms of their ability to describe shifts in physiology. Here, we extend a previously described method used to identify single nucleotide polymorphism (SNPs) associated with metabolic changes (Gieger et al., 2008). We apply this strategy to link changes in sulfur, amino acid and lipid production under heat stress by relating ratios of compounds to potential precursors and regulators. This approach provides integration of multi-omics data to link previously described, discrete units of regulation into functional pathways and hypothesizes novel biology relevant to the heat stress response.

genomics↗

bioRxiv2018

Identification of novel and structurally diverse N-Methyl-D-Aspartate Receptor Antagonists: Successful Application of Pharmacophore Modeling, Virtual Screening and Molecular Docking

In view of \"excitotoxic\" effects of glutamate, wherein excessive excitatory input causes increase in intracellular Ca2+ and ultimately cell death, NMDA receptor has emerged as an important target for treatment and prevention of several neurological disorders, like Alzheimer disease. Prompted by the successful application of in-silico pharmacophore-based virtual screening in lead identification, we have made an effort to implement in-silico protocols to identify novel NMDA receptor antagonist. A series of novel benzo[b]quinolizinium cations as NMDA receptor antagonists have been used as a starting point to develop prognostic pharmacophore models. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, one hydrogen bond acceptor, one hydrophobic and two ring aromatic, showed a correlation (r) of 0.89, root mean square of 0.259, and the cost difference of 43.01 bits between null and fixed cost. The model was thoroughly validated and subjected to a chemical database search, which lead to the identification of 400 hits from NCI and Maybridge databases which were checked for Lipinskis violation and predictive potency.\n\nThis reduced the list to 10 compounds, out of which, two most potent compounds were subjected to molecular docking using Libdock software and interestingly, all the docked conformations showed hydrogen bond interactions with important amino acids Tyr214, His88, Thr174, Val169 and Arg121. In summary, through our validated pharmacophore-based virtual screening protocol, we have identified two potent, structurally diverse, druggable and novel NMDA receptor antagonist which might be of great help to address the unmet medical need of Alzheimer disease.

bioinformatics↗

bioRxiv2018

Noise Analysis in Biochemical Complex Formation

Several biological functions are carried out via complexes that are formed via multimerization of either a single species (homomers) or multiple species (heteromers). Given functional relevance of these complexes, it is arguably desired to maintain their level at a set point and minimize fluctuations around it. Here we consider two simple models of complex formation - one for homomer and another for heteromer of two species - and analyze how important model parameters affect the noise in complex level. In particular, we study effects of (i) sensitivity of the complex formation rate with respect to constituting species abundance, and (ii) relative stability of the complex as compared with that of the constituents. By employing an approximate moment analysis, we find that for a given steady state level, there is an optimal sensitivity that minimizes noise (quantified by fano-factor; variance/mean) in the complex level. Furthermore, the noise becomes smaller if the complex is less stable than its constituents. Finally, for the heteromer case, our findings show that noise is enhanced if the complex is comparatively more sensitive to one constituent. We briefly discuss implications of our result for general complex formation processes.

systems biology↗

bioRxiv2018

Helicase Promotes Replication Re-initiation from an RNA Transcript

To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind the DNA, resulting in a gap in the newly replicated DNA. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances the fork, the DNAP also moves forward processively, via its association with the helicase. The presence of the DNAP, in turn, increases both helicases processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicases novel role in replication re-initiation, independent of replication restart proteins or primase.

biophysics↗

bioRxiv2018

Buffering gene expression noise by microRNA based feedforward regulation

Cells use various regulatory motifs, including feedforward loops, to control the intrinsic noise that arises in gene expression at low copy numbers. Here we study one such system, which is broadly inspired by the interaction between an mRNA molecule and an antagonistic microRNA molecule encoded by the same gene. The two reaction species are synchronously produced, individually degraded, and the second species (microRNA) exerts an antagonistic pressure on the first species (mRNA). Using linear-noise approximation, we show that the noise in the first species, which we quantify by the Fano factor, is sub-Poissonian, and exhibits a nonmonotonic response both to the species lifetime ratio and to the strength of the antagonistic interaction. Additionally, we use the Chemical Reaction Network Theory to prove that the first species distribution is Poissonian if the first species is much more stable than the second. Finally, we identify a special parametric regime, supporting a broad range of behaviour, in which the distribution can be analytically described in terms of the confluent hypergeometric limit function. We verify our analysis against large-scale kinetic Monte Carlo simulations. Our results indicate that, subject to specific physiological constraints, optimal parameter values can be found within the mRNA-microRNA motif that can benefit the cell by lowering the gene-expression noise.

systems biology↗

bioRxiv2018

Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics.

Tropical Calcific Pancreatitis (TCP) is a neglected juvenile form of chronic non-alcoholic pancreatitis. Cathepsin B (CTSB), a lysososmal protease involved in cellular degradation process, is recently been studied as a potential candidate gene in the pathogenesis of TCP. According to cathepsin B hypothesis, mutated CTSB can lead to premature intracellular activation of trypsinogen, which is a key regulatory mechanism in pancreatitis. So far, CTSB mutations have been studied in pancreatitis and neurodegenerative disorders but little is known about the structural and functional effect of variants in CTSB. In this study, we investigated the effect of single nucleotide variants (SNVs) associated with TCP, using molecular dynamics and simulation algorithms. There were two non-synonymous variants in the coding region (L26V and S53G) of CTSB, located in the propeptide region. We tried to predict the effect of these variants on structure and function using multiple algorithms: SIFT, Polyphen2, Panther, SDM sever, i-Mutant2.0 suite, mCSM algorithm and Vadar. Further, using databases like miRdbSNP, PolymiRTS and miRNASNP, two SNPs in 3UTR region were predicted to affect the miRNA binding sites. Structural mutated models of nsSNP mutants (L26V and S53G) were prepared by MODELLER v9.15 and evaluated using TM-Align, Verify 3D, ProSA and Ramachandran plot. The results showed that the models (L26V and S53G) were of high accuracy. The 3D mutated structures were simulated using GROMACS 5.0 to predict the impact of these SNPs on protein stability. The results from in silico analysis and molecular dynamics simulations suggested that these variants in the propeptide region of cathepsin B could lead to structural and functional changes in the protein. Hence, the structural and functional analysis results have given interim conclusions that these variants can have deleterious effect in TCP and thus should be screen in samples from all TCP patients to decipher its distribution in patient population.

bioinformatics↗

bioRxiv2018

Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing

It is challenging for RNA processing machineries to select exons within long intronic regions. We find that intronic LINE repeat sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins (RBPs). This includes MATR3, which promotes binding of PTBP1 to multivalent binding sites in LINEs. Both RBPs repress splicing and 3 end processing within and around LINEs, as demonstrated in cultured human cells and mouse brain. Notably, repressive RBPs preferentially bind to evolutionarily young LINEs, which are confined to deep intronic regions. These RBPs insulate both LINEs and surrounding regions from RNA processing. Upon evolutionary divergence, gradual loss of insulation diversifies the roles of LINEs. Older LINEs are located closer to exons, are a common source of tissue-specific exons, and increasingly bind to RBPs that enhance RNA processing. Thus, LINEs are hubs for assembly of repressive RBPs, and contribute to evolution of new, lineage-specific transcripts in mammals.

genomics↗

bioRxiv2018

Optimal feedback mechanisms for regulating cell numbers

How living cells employ counting mechanisms to regulate their numbers or density is a long-standing problem in developmental biology that ties directly with organism or tissue size. Diverse cells types have been shown to regulate their numbers via secretion of factors in the extracellular space. These factors act as a proxy for the number of cells and function to reduce cellular proliferation rates creating a negative feedback. It is desirable that the production rate of such factors be kept as low as possible to minimize energy costs and detection by predators. Here we formulate a stochastic model of cell proliferation with feedback control via a secreted extracellular factor. Our results show that while low levels of feedback minimizes random fluctuations in cell numbers around a given set point, high levels of feedback amplify Poisson fluctuations in secreted-factor copy numbers. This trade-off results in an optimal feedback strength, and sets a fundamental limit to noise suppression in cell numbers. Intriguingly, this fundamental limit depends additively on two variables: relative half-life of the secreted factor with respect to the cell proliferation rate, and the average number of factors secreted in a cells lifespan. We further expand the model to consider external disturbances in key physiological parameters, such as, proliferation and factor synthesis rates. Intriguingly, while negative feedback effectively mitigates disturbances in the proliferation rate, it amplifies disturbances in the synthesis rate. In summary, these results provide unique insights into the functioning of feedback-based counting mechanisms, and apply to organisms ranging from unicellular prokaryotes and eukaryotes to human cells.

systems biology↗

bioRxiv2018

The fungal ligand chitin directly binds and signals inflammation dependent on oligomer size and TLR2

Chitin is a highly abundant polysaccharide and linked to fungal infection and asthma. Unfortunately, its polymeric structure has hampered the identification of immune receptors directly binding chitin and signaling immune activation and inflammation, because purity, molecular structure and molarity are not well definable for a polymer typically extracted from biomass. Therefore, by using defined chitin (N-acetyl-glucosamine) oligomers, we identified six subunit long chitin chains as the smallest immunologically active motif and the innate immune receptor Toll-like receptor (TLR) 2 as the primary fungal chitin receptor on human and murine immune cells. Chitin oligomers directly bound TLR2 with nanomolar affinity and showed both overlapping and distinct signaling outcomes compared to known mycobacterial TLR2 ligands. Conversely, chitin oligomers shorter than 6 subunits were inactive or showed antagonistic effects on chitin/TLR2-mediated signaling, hinting to a size-dependent sensing/activation system unexpectedly conserved in plants and humans. Since blocking the chitin-TLR2 interaction effectively prevented chitin-mediated inflammation in vitro and in vivo, our study highlights the chitin TLR2 interaction as a potential target for developing novel therapies in chitin-related pathologies and fungal disease.

immunology↗