Biology subjects

Prakash, A.

Publications and source records attributed to Prakash, A..

67 records · Page 4Linked to original sources

bioRxiv2021

Implementing the re-use of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.

bioinformatics↗

bioRxiv2021

Berberine as siderophore from Talaromyces trachyspermus: augmentation and characterization".

In the present study, a siderophore compound produced by an endophytic fungus, Talaromyces trachyspermus was optimized for maximum production, 88.9 % SU by applying Plackett-Burman design and Response Surface Methodology through Central Composite Design that showed the succinic acid (1.141 g/L), sucrose (31.028 g/L) and temperature (27.475 {degrees}C) as significant factors. On scale up, a further increase in siderophore yield was obtained (by 3%) The compound was extracted, purified and detected chemically as catecholate siderophore showing max. {lambda} absorbance at 279nm. Contained of hydroxy benzene as shown by GC-MS analysis and further identified as berberine by HRLC-MS studies. The compound berberine is clinically a very important drug with several ethnobotanical properties. This is rare to report fungal catecholate and first to report the production of berberine from Talaromyces species.

microbiology↗

bioRxiv2020

Lung Immune Tone Regulation by the Gut-Lung Immune Axis: Short-chain Fatty Acid Receptors FFAR2 and FFAR3, and IL-1β Expression Profiling in Mouse and Human Lung

Microbial metabolites produced by the gut microbiome, such as short-chain fatty acids (SCFA), can influence both local intestinal and distant lung physiology and response to injury. However, how lung immune activity is regulated by SCFAs is unknown. We examined fresh human lung tissue and observed the presence of SCFAs with large inter-individual and even intra-lobe variability. In vitro, SCFAs were capable of modifying the metabolic programming in both resting and LPS-exposed alveolar macrophages (AM). Additionally, since we hypothesized that lung immune tone could be defined through priming of the inflammasome (aka signal 1), we interrogated naive mouse lungs for pro-IL-1{beta} message and localized its presence within the alveolar space in situ, specifically in AM subsets, and in close proximity to alveolar type 2 epithelial (AT2) cells. We established that metabolically active gut microbiota, that produce SCFAs, can transmit LPS and SCFAs to the lung (potential sources of signal 1), and thereby could regulate lung immune tone and metabolic programming. To understand how murine lung cells sensed and upregulated IL-1{beta} in response to gut-microbiome factors, we determined that in vitro, AM and AT2 cells expressed SCFA receptors, FFAR2, FFAR3, and IL-1{beta} but with different expression patterns and LPS-inducibility. Finally, we observed that IL-1{beta}, FFAR2 and FFAR3 were expressed both in isolated human AM and AT2 cells ex-vivo, but in fresh human lung sections in situ, only AM expressed IL-1{beta} at rest and after LPS challenge. Together, this translational study using mouse and human lung tissue and cells supports an important role for the gut microbiome and SCFAs in regulating lung immune tone.

immunology↗

bioRxiv2020

Modulation of macrophage defense responses by Mycobacterial persistence protein MprA (Rv0981) in human THP-1 cells: effect of single amino acid variation on host-pathogen interactions

M. tuberculosis is one of the most successful human pathogens causing tuberculosis that leads to highest daily morbidity worldwide. The evasion of the host immune responses is an important strategy that M. tuberculosis adopts. MprA (Rv0981), the response regulator of two component system is known for DNA binding activity in the pathogen and its role in persistent infection in the host. MprA is recognized as a late stage antigen during infection. A variant form of the protein MprA with G70S polymorphism (MprA*) is observed in one of our local and in several global clinical isolates of M. tuberculosis. Here we report the nuclear localization of MprA and MprA* in differentiated macrophages. MprA and MprA* increase the expression of TGF-{beta} and IL-10, the immune suppressive cytokines in THP-1 derived macrophage cells. Concurrently the phago-lysosome fusion is significantly reduced as shown by infection with M.bovis BCG. We show that single nucleotide variation in clinical isolates lead to quantitative variations resulting in host immune suppression and support the survival and persistence of the pathogen.

microbiology↗

bioRxiv2019

Long-term metabolic consequences of acute dioxin exposure differ between male and female mice

Exposure to environmental pollutants is consistently associated with increased diabetes risk in humans. In male mice, acute dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin; TCDD) exposure supresses insulin secretion. This study investigated the long-term effects of a single TCDD injection (20 {micro}g/kg) on glucose metabolism and beta cell function in male and female mice. TCDD-exposed males displayed modest fasting hypoglycemia for [~]4 weeks post-injection, reduced fasting insulin levels for up to 6 weeks, increased insulin sensitivity, and decreased beta cell area. TCDD-exposed females also had long-term suppressed basal plasma insulin levels, and abnormal insulin secretion for up to 6 weeks. Unlike males, TCDD did not impact insulin sensitivity or beta cell area in females, but did cause transient glucose intolerance 4 weeks post-exposure. Our results show that a single exposure to dioxin can supress basal insulin levels long-term in both sexes, but effects on metabolism are sex-dependent.

pharmacology and toxicology↗

bioRxiv2019

BASAL RESISTANCE AGAINST A PATHOGEN IS MORE BENEFICIAL THAN IMMUNE PRIMING RESPONSES IN FLOUR BEETLES

In insects, basal pathogen resistance and immune priming can evolve as mutually exclusive strategies, with distinct infection outcomes. However, the evolutionary drivers of such diverse immune functions remain poorly understood. Here, we addressed this key issue by systematically analyzing the differential fitness costs and benefits of priming vs. resistance evolution in Tribolium beetle populations infected with Bacillus thuringiensis. Surprisingly, resistant beetles had increased post-infection reproduction and a longer lifespan under both starving as well as fed conditions, with no other measurable costs. In contrast, priming reduced offspring early survival, development rate and reproduction. Priming did improve post-infection survival of offspring, but this added trans-generational benefit of immune priming might not compensate for its pervasive costs. Resistance was thus consistently more beneficial. Our work represents the first report of experimentally evolved trans-generational priming, and a detailed comparison of the complex fitness consequences of evolved priming vs resistance. HIGHLIGHTSO_LIDivergent costs and benefits of experimentally evolved immune priming vs resistance C_LIO_LIIncreased reproduction and lifespan in resistant populations C_LIO_LINo other hidden costs of resistance C_LIO_LIIn contrast, reduced juvenile fitness and reproduction in primed populations C_LIO_LIFirst evidence for experimentally evolved trans-generational immune priming C_LI

evolutionary biology↗

bioRxiv2019

Doublesex mediates the development of sex-specific pheromone organs in Bicyclus butterflies via multiple mechanisms

The Bicyclus lineage of satyrid butterflies exhibits male-specific traits, the scent organ complex, used for chemical communication during courtship. This complex consists of tightly packed brush-like scales (hair-pencils) that rub against scent patches to disperse pheromones, but the evolution and molecular basis of the organs male-limited development remains unknown. Here, we examine the evolution of the number and location of the scent patches and hair-pencils within 53 species of Bicyclus butterflies, and the involvement of the sex determinant gene doublesex (dsx) in scent organ development in Bicyclus anynana using CRISPR/Cas9. We show that scent patches and hair-pencils arose via multiple, independent gains, in a correlated manner. Further, an initially non-sex-specific Dsx protein expression pattern in developing wing discs becomes male-specific and spatially refined to areas that develop the scent organ complex over the course of development. Functional perturbations of dsx show that this gene is required for male patch development whereas hair-pencils can develop in both sexes without Dsx input. Dsx in females is, instead, required to repress hair-pencils. These findings suggest that the patches and hair-pencils evolve as correlated composite organs that are sex-limited via the spatial regulation of dsx. Divergence in the function of dsx isoforms occurs in both sexes, where the male isoform promotes patch development in males and the female isoform represses hair-pencil development in females, both leading to the development of male-limited traits. Furthermore, evolution in number and location of patches, but not of hair-pencils, appears to be regulated by spatial regulation of dsx.

evolutionary biology↗

bioRxiv2018

Development and Application of a High-Content Virion Display Human GPCR Array

G protein-coupled receptors (GPCRs) comprise the largest membrane protein family in humans and can respond to a wide variety of ligands and stimuli. Like other multi-pass membrane proteins, the biochemical properties of GPCRs are notoriously difficult to study because they must be embedded in lipid bilayers to maintain their native conformation and function. To enable an unbiased, high-throughput platform to profile biochemical activities of GPCRs in native conformation, we individually displayed 315 human non-odorant GPCRs (>85% coverage) in the envelope of human herpes simplex virus-1 and immobilized on glass to form a high-content Virion Display (VirD) array. Using this array, we found that 50% of the tested commercial anti-GPCR antibodies (mAbs) is ultra-specific, and that the vast majority of those VirD-GPCRs, which failed to be recognized by the commercial mAbs, could bind to their canonical ligands, indicating that they were folded correctly. Next, we used the VirD-GPCR arrays to examine binding specificity of two known peptide ligands and recovered expected interactions, as well as new off-target interactions, three of which were confirmed with real-time kinetics measurements. Finally, we explored the possibility of discovering novel pathogen targets by probing VirD-GPCR arrays with live group B Streptococcus (GBS), a common Gram-positive bacterium causing neonatal meningitis. Using cell invasion assays and a mouse model of hematogenous meningitis, we showed that inhibition of one of the five newly identified GPCRs, CysLTR1, greatly reduced GBS penetration in brain-derived endothelial cells and in mouse brains. Therefore, our work demonstrated that the VirD-GPCR array holds great potential for high-throughput, unbiased screening for small molecule drugs, affinity reagents, and deorphanization.

pharmacology and toxicology↗

bioRxiv2018

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes, and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs), and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.

molecular biology↗

bioRxiv2018

Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles

In many insects, individuals primed with low doses of pathogens live longer after being exposed to the same pathogen later in life. Yet, our understanding of the evolutionary and ecological history of priming of immune response in natural insect populations is limited. Previous work demonstrated population-, sex- and- stage specific variation in the survival benefit of priming response in flour beetles (Tribolium castaneum) infected with their natural pathogen Bacillus thuringiensis. However, the evolutionary forces responsible for this natural variation remained unclear. Here, we tested whether the strength of the priming response (measured as the survival benefit after priming and subsequent infection relative to unprimed controls) was associated with multiple fitness parameters across 10 flour beetle populations. Our results suggest two major selective pressures that may explain the observed inter-population variation in priming: (A) Basal pathogen susceptibility - populations that were more susceptible to infection produced a stronger priming response, and (B) Reproductive success - populations where primed females produced more offspring had lower survival benefit, suggesting a trade-off between priming response and reproduction. Our work is the first empirical demonstration of multiple selective pressures that may govern the adaptive evolution of immune priming in the wild. We hope that this motivates further experiments to establish the role of pathogen-imposed selection and fitness costs in the evolution of priming in natural insect populations.

evolutionary biology↗

bioRxiv2017

Experimental Evolution Of Insect Immune Memory Vs. Pathogen Resistance

Under strong pathogen pressure, insects often evolve resistance to infection. Many insects are also protected via immune memory ( immune priming), whereby sub-lethal exposure to a pathogen enhances survival after secondary infection. To understand the evolution and consequences of these immune responses, we imposed strong pathogen selection on flour beetles (Tribolium castaneum), infecting them with Bacillus thuringiensis (Bt) for 11 generations. Populations injected first with heat-killed and then live Bt each generation evolved high basal resistance against multiple Bt strains. In contrast, all populations injected only with a high dose of live Bt evolved less effective but strain-specific priming response. Control populations injected with heat-killed Bt did not evolve priming; and in the ancestor, priming was effective only against a low Bt dose. Thus, pathogens can select for rapid modulation of insect priming ability, leading to divergent immune strategies (generalized resistance vs. specific immune priming) with distinct mechanisms and adaptive benefits.

evolutionary biology↗

bioRxiv2017

apterous A Specifies Dorsal Wing Patterns And Sexual Traits In Butterflies

Butterflies have evolved different color patterns on their dorsal and ventral wing surfaces to serve different signaling functions, yet the developmental mechanisms controlling surface-specific patterning are still unknown. Here, we mutate both copies of the transcription factor apterous in Bicyclus anynana butterflies using CRISPR/Cas9 and show that apterous A functions both as a repressor and modifier of ventral wing color patterns, as well as a promoter of dorsal sexual ornaments in males. We propose that the surface-specific diversification of wing patterns in butterflies proceeded via the co-option of apterous A into various gene regulatory networks involved in the differentiation of discrete wing traits. Further, interactions between apterous and sex-specific factors such as doublesex may have contributed to the origin of sexually dimorphic surface-specific patterns. Finally, we discuss the evolution of eyespot pattern diversity in the family Nymphalidae within the context of developmental constraints due to apterous regulation.\n\nSignificance statementButterflies have evolved different wing patterns on their dorsal and ventral wing surfaces that serve different signaling functions. We identify the transcription factor, apterous A, as a key regulator of this surface-specific differentiation in butterflies. We also show a role for apterous A in restricting the developmental origin of a novel trait, eyespots, to just the ventral wing surface. Dorsal-ventral differentiation of tissues is not just restricted to butterfly wings but occurs in many other organs and organisms from arthropods to humans. Thus, we believe that our work will be of interest to a diverse group of biologists and layman alike interested in the role of development in shaping biodiversity.

developmental biology↗

bioRxiv2017

FEMALE CHEMICAL WARFARE DRIVES FITNESS EFFECTS OF GROUP SEX RATIO

In animals, skewed sex ratios can affect individual fitness either via sexual interactions (e.g. intersexual conflict or intrasexual mate competition) or non-sexual interactions (e.g. sex-specific resource competition). Because most analyses of sex ratio focus on sexual interactions, the relative importance of these mechanisms remains unclear. We addressed this problem using the flour beetle Tribolium castaneum, where male-biased sex ratios increase female fitness relative to unbiased or female-biased groups. Although flour beetles show both sexual and non-sexual (resource) competition, we found that sexual interactions did not explain female fitness. Instead, female fecundity was dramatically reduced even after a brief exposure to flour conditioned by other females. Earlier studies suggested that quinones (secreted toxins) might mediate density-dependent population growth in flour beetles. We identified ethyl- and methyl-benzoquinone (EBQ and MBQ) as the primary components of adult stink glands that regulate female fecundity. In female-biased groups (i.e. at high female density), females upregulated quinones and suppressed each others reproduction. In male-biased groups, low female density lead to low quinone levels, allowing higher fecundity. Thus, quinones serve both as indicators and mediators of female competition, resulting in the observed fitness decline in female-biased groups. Our results underscore the importance of non-sexual interference competition that may often underlie the fitness consequences of skewed sex ratios.

evolutionary biology↗