Biology subjects

Krishnan, J.

Publications and source records attributed to Krishnan, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

Enterococci are Gram-positive opportunistic pathogens responsible for a wide range of nosocomial infections. One enterococcocal species, Enterococcus faecium, is steadily increasing in prevalence and has been listed among major multidrug-resistant ESKAPE pathogens. To gain systems-level insights into its metabolism and support discovery of potential therapeutic targets, we constructed iDR478, a comprehensive manually curated genome-scale metabolic model (GEM) to serve as a digital twin for E. faecium TX0016 (strain DO). The reconstruction was based on extensive homology searches and literature evidence, and further refined and gap-filled through experimental validation. Phenotypic profiling using Biolog microarrays enabled assessment of carbon source utilization, while amino acid leave-out growth assays allowed the evaluation of auxotrophies. The final refined model accurately predicted 100% of amino acid auxotrophies and 85% of growth on sole carbon sources. Discrepancies between model predictions and experimental phenotypes identified specific knowledge gaps across metabolic pathways, including unresolved carbon source utilization phenotypes, e.g., psicose, sorbitol, and palatinose utilization. Those gaps will guide future experimental characterization. Additionally, we conducted gene essentiality analysis to evaluate the predictive capacity of iDR478. Since no experimental gene essentiality data are currently available for E. faecium, model predictions were compared against Tn-seq experimental results from E. faecalis MMH594. Under simulated unconstrained uptake conditions, iDR478 achieved 84.2% concordance with the experimental essentiality results of E. faecalis MMH594. iDR478 thus provides a framework for studying E. faecium, offers insights into its metabolic network, and serves as a source for guiding future research and identification of therapeutic targets.

systems biology↗

bioRxiv2025

Human heart organoids reveal a regenerative strategy for mitochondrial disease

The human heart is among the most complex tissues to replicate in vitro, with vascular, neuronal, and immune elements shaping its development and function. Here we describe cardiomorphs, self-organising human cardiac organoids that recapitulate the cellular diversity, structural organisation, vascularisation, and innervation of the myocardium and mature along a developmental trajectory from early cardiogenesis to adult tissue. Using patient-derived cardiomorphs, we establish the first three-dimensional human tissue model of Kearns-Sayre syndrome (KSS), a rare mitochondrial disorder characterised by large-scale mtDNA deletions. KSS-cardiomorphs faithfully reproduce disease-associated metabolic, contractile, and ultrastructural hallmarks. Leveraging this platform, we identify Betaxolol, an FDA-approved selective {beta}1-adrenergic antagonist, as a modulator of mitochondrial quality control. Betaxolol increases intracellular oxygenation, selectively eliminates dysfunctional mitochondria via mitophagy, and promotes biogenesis of functional organelles, restoring contractility in KSS tissues. This dual-action, mutation-agnostic mechanism suggests a therapeutic principle with broad relevance to mitochondrial disease, cardiac pathology, and age-associated decline.

cell biology↗

bioRxiv2025

Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains. We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a [~]8% increase to the available genomic data for P. putida. Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes such as PcaI and PcaJ revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

bioengineering↗

bioRxiv2025

Stimulation of cholesterol efflux inhibits herpesvirus nuclear egress

Cholesterol in herpesvirus envelopes and host membranes supports membrane fusion during virus entry. However, little is known about how cholesterol affects other aspects of the viral replication cycle. Here, using an infection model that begins with reactivation from latency, bypassing the entry step, we demonstrate that depleting intracellular cholesterol inhibits the production of infectious Kaposis sarcoma-associated herpesvirus (KSHV). Treatment of latently infected cells with the liver X receptor (LXR) agonist 22(R)-hydroxycholesterol (22OH) increased expression of sterol response genes, including the cholesterol efflux pump ATP binding cassette subfamily A member 1 (ABCA1), and reduced intracellular cholesterol. 22OH treatment initially enhanced lytic reactivation, but diminished viral protein accumulation during late replication, while altering accumulation of host proteins that regulate the cell cycle and innate immunity. Cholesterol efflux led to an increase in the proportion of capsids lacking viral genomes in the nucleus and a reduction in nucleocapsids accessing the cytoplasm. Next, we used a herpes simplex virus (HSV) infection model to explore if 22OH affected the conserved herpesvirus nuclear egress complex (NEC), comprised of two viral proteins that accumulate at the inner nuclear membrane and facilitate primary envelopment. We found that 22OH inhibited HSV-1 and HSV-2 replication and spread in plaque reduction assays and impaired localization of NEC proteins pUL31 and pUL34 to the nuclear periphery. These findings indicate that cholesterol efflux inhibits herpesvirus replication by interfering with the formation of nucleocapsids competent to complete nuclear egress. IMPORTANCECholesterol plays key roles in regulating the fluidity of cellular membranes and the trafficking and lateral diffusion of transmembrane proteins. Herpesviruses encode a variety of transmembrane proteins that traffic to different cellular compartments, while herpesvirus capsids and tegument proteins interact with nuclear and trans-Golgi network membranes throughout the primary and secondary envelopment process, respectively. This produces viral particles with cholesterol as an envelope component which is required to support membrane fusion during entry. Our discovery that cholesterol efflux inhibits KSHV nuclear egress suggests that cholesterol plays important supportive roles at this stage of lytic replication. Moreover, we observed that cholesterol efflux mediated by oxysterol treatment has widespread effects on host cell protein expression, resulting in a non-classical antiviral state. Cholesterol likely supports the proper trafficking of viral proteins to nuclear sites of virion assembly or is influencing the fluidity of nuclear membranes used for viral primary envelopment and de-envelopment during nuclear egress.

microbiology↗

bioRxiv2025

Investigation of V1016G kdr Mutation during Pyrethroid Insecticide Resistance in Aedes aegypti from Nagapattinam district of Tamil Nadu, India

BackgroundAedes aegypti is a primary vector of Dengue, Chikungunya, and Zika viruses, and its control relies heavily on pyrethroid insecticides. However, the development of resistance in mosquito populations poses a major challenge to effective vector control. This study aimed to investigate the presence of the V1016G knockdown resistance (kdr) mutation in Aedes aegypti collected from Nagapattinam district, Tamil Nadu, India. Where insecticide uses is common. MethodologyAedes immature were collected from selected field sites and subjected to insecticide susceptibility testing using World Health Organization (WHO) guidelines. Genomic DNA was extracted, and allele-specific PCR was performed to detect the V1016G mutation in the voltage-gated sodium channel gene (vgsc). Principal findingsThe analysis revealed the presence of the V1016G mutation in heterozygous form (VG) among the tested samples. No homozygous mutants (GG) were detected. The presence of heterozygous individuals indicates an early stage of resistance development, likely due to ongoing insecticide selection pressure. Bioassay results showed reduced susceptibility to pyrethroids in these populations, supporting the molecular findings. ConclusionThis study provides baseline data on the genetic mechanism of pyrethroid resistance in Aedes aegypti from Nagapattinam district. Regular monitoring of kdr mutations is essential to detect resistance early and guide insecticide use policies. Integrating molecular surveillance with conventional control measures will help delay the spread of resistance and improve the long-term success of vector management programs. The findings highlight the need for alternative control strategies and responsible insecticide use to maintain the effectiveness of current interventions.

molecular biology↗

bioRxiv2025

A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis

Sequenced genomes for thousands of strains of a bacterial species allow for a comprehensive analysis of its pangenome. We present a pangenome study of Escherichia colis metabolism by formulating gene-to-protein-to-reaction associations (GPRs) for about 2,700 metabolic reactions in 2,377 fully sequenced strains. On one hand, these GPRs reconstruct strain-specific networks that allow computational predictions (and experimental validation) of metabolic phenotypes, while on the other hand, they give the genetic basis for a given metabolic reaction in every strain. A pangenome-wide analysis of GPRs shows that: 1) We can reveal the genetic basis for a specific metabolic property at the species level; 2) The genetic basis for many metabolic reactions is diverse; 3) Many rare genes show variation in the genes genomic neighborhood which often contain genes from transposable elements, 4) Many rare genes show large-scale fragmentation and horizontal gene transfer (>11,000 rare genes in 2,377 strains); and 5) The aromatic amino acids and branched chain amino acids pathways are enriched with rare genes, with Acetolactate synthase having 29 distinct genes. Thus, analysis of GPRs across the pangenome reveals a complex dynamic evolutionary history of metabolism, revealing the role of conserved, fragmented, and horizontally transferred metabolic genes.

systems biology↗

bioRxiv2024

Deciphering the transcriptional regulatory network of Yarrowia lipolytica using machine learning

The transcriptional regulatory network (TRN) in Yarrowia lipolytica coordinates its cellular processes, including the response to various stimuli. The TRN has been difficult to study due to its complex nature. In industrial-size fermenters, environments are often not homogenous, resulting in Yarrowia experiencing fluctuating conditions during a fermentation. Compared with homogenous laboratory conditions, these fluctuations result in altered cellular states and behaviors due to the action of the TRN. Here, a machine learning approach was deployed to modularize the transcriptome to enable meaningful description of its changing composition. To provide a sufficiently broad dataset, a wide range of relevant fermentation conditions (nutrient limitations, growth rates, pH values, oxygen availability and CO2 stresses) were run and samples obtained for RNA-Seq generation. We thus significantly increased the number of publicly available transcriptomic dataset on Y. lipolytica W29. In total, 23 independently modulated gene sets (termed iModulons) were identified of which 9 could be linked to corresponding regulons in S. cerevisiae. Strong responses were found in relation to oxygen limitation and elevated CO2 concentrations represented by (i) altered ribosomal protein synthesis, (ii) cell cycle disturbances, (iii) respiratory gene expression, and (iv) redox homeostasis. These results provide a fine-grained systems-level understanding of the Y. lipolytica TRN in response to industrially meaningful stresses, providing engineering targets to design more robust production strains. Moreover, this study provides a guide to perform similar work with poorly characterized single-cellular eukaryotic organisms. Highlights- A large screening setup significantly expands the public RNA-Seq library on Y. lipolytica. - This work provides a systems-level understanding of the TRN in response to industrial stresses. - iModulon analysis can help accelerate bioprocess development. - Results can guide similar work on poorly characterized single-cellular eukaryotic organisms.

systems biology↗

bioRxiv2024

Extracellular Respiration is a Latent Energy Metabolism in Escherichia coli

Diverse microbial species utilize redox shuttles to exchange electrons with their environment through mediated extracellular electron transfer (EET). This process maintains redox homeostasis and supports anaerobic survival across diverse microbial communities. Although mediated EET has been extensively leveraged for bioelectrocatalysis and bioelectronics for decades, fundamental questions remain about how these redox shuttles are reduced within cells and their bioenergetic implications. This knowledge gap limits our understanding of the physiological roles of mediated EET in various microbes and hampers the development of efficient microbial electrochemical technologies. To address this, we developed a methodology integrating genome editing, electrochemistry, and systems biology to investigate the mechanism and bioenergetic implications of mediated EET in bacteria. Using this approach, we uncovered a mediated EET mechanism in Escherichia coli. In the absence of alternative electron sinks, the redox cycling of 2-hydroxy-1,4-naphthoquinone (HNQ) via a cytoplasmic nitroreductase enabled E. coli to respire and grow on an extracellular electrode. Genome-scale metabolic modeling suggested that HNQ- mediated EET offers a more energetically favorable route for supporting anaerobic growth than canonical fermentation. Transcriptome analysis revealed redox perturbations in response to HNQ and identified rapid metabolic adaptations that support growth. This work demonstrates that E. coli can grow independently of classical electron transport chains and fermentative pathways, unveiling a new type of anaerobic energy metabolism.

systems biology↗

bioRxiv2024

HIF1α controls adipose tissue growth through metabolic rechanneling

Excessive expansion of white adipose tissue occurs when energy intake exceeds demand. It creates a state of relative hypoxia that is directly linked to activation of the hypoxia-inducible factor (HIF) in obese human subjects and mouse models of obesity. Whether HIF1 function is important for the development of basal adiposity and diet-induced obesity remains unclear. In the present study, we genetically ablated Hif1 in adipocytes and analyzed the corresponding mice for both basal and diet-induced obesity-associated visceral white adipose tissue mass as well as parameters of systemic glucose homeostasis and peripheral insulin sensitivity. We found that inactivation of Hif1 in mouse adipocytes inhibited basal adiposity and suppressed nutrient-overload-induced adipose tissue growth. These changes in adiposity were associated with improved systemic glucose homeostasis and peripheral insulin sensitivity. Mechanistically, Hif1 mediated effects on adipocyte metabolism by re-routing glycolytic intermediates into the glycerolipid shunt, leading to increased de novo triacylglyceride synthesis in hypertrophic adipocytes. Our results have established key roles for HIif1 in controlling adipocyte growth and metabolism and adipose tissue expansion under basal conditions and in response to a high-fat diet, highlighting the central role of hypoxia and HIF1 in the development of obesity. Article HighlightsO_LIHif1 function is critical for basal adipose tissue mass expansion, and is also required for fat accumulation in response to high fat diet. C_LIO_LICo-option and co-activation of the glycerolipid biosynthetic pathway by glycolysis is an important modulator of visceral adiposity. C_LIO_LIThese findings reveal an important role of Hif1 in the adipose tissue through the coupling of glycolysis and lipid anabolism in response to HFD, which may provide a potential therapeutic target for type 2 diabetes in the future. C_LI

cell biology↗

bioRxiv2023

Immunoproteasomal Processing of Isolevuglandin Adducts in Hypertension

O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/536054v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1fc2367org.highwire.dtl.DTLVardef@787fcforg.highwire.dtl.DTLVardef@10f09f2org.highwire.dtl.DTLVardef@561978_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Isolevuglandins (isoLGs) are lipid aldehydes that form in the presence of reactive oxygen species (ROS) and drive immune activation. We found that isoLG-adducts are presented within the context of major histocompatibility complexes (MHC-I) by an immunoproteasome dependent mechanism. Pharmacologic inhibition of LMP7, the chymotrypsin subunit of the immunoproteasome, attenuates hypertension and tissue inflammation in the angiotensin II (Ang II) model of hypertension. Genetic loss of function of all immunoproteasome subunits or conditional deletion of LMP7 in dendritic cell (DCs) or endothelial cells (ECs) attenuated hypertension, reduced aortic T cell infiltration, and reduced isoLG-adduct MHC-I interaction. Furthermore, isoLG adducts structurally resemble double-stranded DNA and contribute to the activation of STING in ECs. These studies define a critical role of the immunoproteasome in the processing and presentation of isoLG-adducts. Moreover they define a role of LMP7 as a regulator of T cell activation and tissue infiltration in hypertension.

immunology↗

bioRxiv2023

Biphasic responses in cell signalling: A unified approach

Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signalling and post-translational modification systems and represent safeguards against over-activation or overexpression of species. In this paper we provide a unified theoretical synthesis of biphasic responses in cell signalling systems, by assessing signalling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models) we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signalling behaviour in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signalling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.

systems biology↗

bioRxiv2023

CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression

BackgroundCardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding. MethodsThe SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed. ResultsBy using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs. ConclusionsIGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.

genomics↗

bioRxiv2023

Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish

Circadian control of physiology and metabolism is pervasive throughout nature, with circadian disruption contributing to premature aging, neurodegenerative disease, and type 2 diabetes (Musiek et al. 2016; Panda, 2016). It has become increasingly clear that peripheral tissues, such as skeletal muscle, possess cell-autonomous clocks crucial for metabolic homeostasis (Gabriel et al. 2021). In fact, disruption of the skeletal muscle circadian rhythm results in insulin resistance, sarcomere disorganization, and muscle weakness in both vertebrates and non-vertebrates - indicating that maintenance of a functional muscle circadian rhythm provides an adaptive advantage. We and others have found that cavefish possess a disrupted central circadian rhythm and, interestingly, a skeletal muscle phenotype strikingly similar to circadian knock-out mutants; namely, muscle loss, muscle weakness, and insulin resistance (Olsen et al. 2022; Riddle et al. 2018; Mack et al. 2021). However, whether the cavefish muscle phenotype results from muscle-specific circadian disruption remains untested. To this point, we investigated genome-wide, circadian-regulated gene expression within the skeletal muscle of the Astyanax mexicanus - comprised of the river-dwelling surface fish and troglobitic cavefish - providing novel insights into the evolutionary consequence of circadian disruption on skeletal muscle physiology.

evolutionary biology↗

bioRxiv2022

The lncRNA Sweetheart regulates compensatory cardiac hypertrophy after myocardial injury

After myocardial infarction in the adult heart the remaining, non-infarcted tissue adapts to compensate the loss of functional tissue. This adaptation requires changes in gene expression networks, which are mostly controlled by transcription regulating proteins. Long non-coding transcripts (lncRNAs) are now recognized for taking part in fine-tuning such gene programs. We identified and characterized the cardiomyocyte specific lncRNA Sweetheart RNA (Swhtr), an approximately 10 kb long transcript divergently expressed from the cardiac core transcription factor coding gene Nkx2-5. We show that Swhtr is dispensable for normal heart development and function, but becomes essential for the tissue adaptation process after myocardial infarction. Re-expressing Swhtr from an exogenous locus rescues the Swhtr null phenotype. Genes depending on Swhtr after cardiac stress are significantly occupied, and therefore most likely regulated by NKX2-5. Our results indicate a synergistic role for Swhtr and the developmentally essential transcription factor NKX2-5 in tissue adaptation after myocardial injury.

developmental biology↗

bioRxiv2022

Genetic Regulators of Sputum Mucin Concentration and Their Associations with COPD Phenotypes

Hyper-secretion and/or hyper-concentration of mucus is a defining feature of multiple obstructive lung diseases, including chronic obstructive pulmonary disease (COPD). Mucus itself is composed of a mixture of water, ions, salt and proteins, of which the gel-forming mucins, MUC5AC and MUC5B, are the most abundant. Recent studies have linked the concentrations of these proteins in sputum to COPD phenotypes, including chronic bronchitis (CB) and acute exacerbations (AE). We sought to determine whether common genetic variants influence sputum mucin concentrations and whether these variants are also associated with COPD phenotypes, specifically CB and AE. We performed a GWAS to identify quantitative trait loci for sputum mucin protein concentration (pQTL) in the Sub-Populations and InteRmediate Outcome Measures in COPD Study (SPIROMICS, n=708 for total mucin, n=215 for MUC5AC, MUC5B). Subsequently, we tested for associations of mucin pQTL with CB and AE using regression modeling (n=822-1300). Replication analysis was conducted using data from COPDGene (n =5740) and by examining results from the UK Biobank. We identified one genome-wide significant pQTL for MUC5AC (rs75401036) and two for MUC5B (rs140324259, rs10001928). The strongest association for MUC5B, with rs140324259 on chromosome 11, explained 14% of variation in sputum MUC5B. Despite being associated with lower MUC5B, the C allele of rs140324259 conferred increased risk of CB (odds ratio (OR) = 1.42; 95% confidence interval (CI): 1.10-1.80) as well as AE ascertained over three years of follow up (OR=1.41; 95% CI: 1.02-1.94). Associations between rs140324259 and CB or AE did not replicate in COPDGene. However, in the UK Biobank, rs140324259 was associated with phenotypes that define CB, namely chronic mucus production and cough, again with the C allele conferring increased risk. We conclude that sputum MUC5AC and MUC5B concentrations are associated with common genetic variants, and the top locus for MUC5B may influence COPD phenotypes, in particular CB. Author SummaryChronic obstructive pulmonary disease (COPD) is characterized by presence of emphysema and/or chronic bronchitis. Excessive mucus production is a defining phenotype of chronic bronchitis, and is associated with several important features of COPD, including exacerbations and loss of lung function. Recent studies have demonstrated that the amount of mucus produced in COPD patients is an important marker of disease state. We investigated whether common genetic variants are associated with the concentration of two key proteins in mucus, MUC5AC and MUC5B, and whether the variants we identified are also associated with COPD outcomes. We identified multiple genetic variants that were associated with MUC5AC or MUC5B concentration. The strongest association we detected, for MUC5B on chromosome 11, was also associated with features of COPD, including chronic bronchitis and acute exacerbations, in one COPD study population but not another. Results from a much larger study, the UK Biobank, indicate that this variant is associated with chronic mucus production and chronic cough, which are key features of chronic bronchitis. Thus, we conclude that the concentration of key proteins in mucus are influenced by genetic variation, and that a variant on chromosome 11 that affects MUC5B may in turn alter COPD outcomes.

genetics↗

bioRxiv2022

Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation

Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with a comprehensive biochemical and molecular characterization of the cell lines, which reflects key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.

evolutionary biology↗

bioRxiv2021

Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity.

Nutrient availability varies seasonally and spatially in the wild. The resulting nutrient limitation or restricted access to nutrients pose a major challenge for every organism. While many animals, such as hibernating animals, evolved strategies to overcome periods of nutrient scarcity, the cellular mechanisms of these strategies are poorly understood. Cave environments represent an extreme example of nutrient deprived environments since the lack of sunlight and therefore primary energy production drastically diminishes the nutrient availability. Here, we used Astyanax mexicanus, which includes river-dwelling surface fish and cave adapted cavefish populations to study the genetic adaptation to nutrient limitations. We show that cavefish populations store large amounts of fat in different body regions when fed ad libitum in the lab. We found higher expression of lipogenesis genes in cavefish livers when fed the same amount of food as surface fish, suggesting an improved ability of cavefish to use lipogenesis to convert available energy into triglycerides for storage into adipose tissue. Moreover, the lipid metabolism regulator, Peroxisome proliferator-activated receptor {gamma} (Ppar{gamma}), is upregulated at both transcript and protein levels in cavefish livers. Chromatin Immunoprecipitation sequencing (ChIP seq) showed that Ppar{gamma} binds cavefish promoter regions of genes to a higher extent than surface fish. Finally, we identified two possible regulatory mechanisms of Ppar{gamma} in cavefish: higher amounts of ligands of the nuclear receptor, and nonsense mutations in per2, a known repressor of Ppar{gamma}. Taken together, our study reveals that upregulated Ppar{gamma} promotes higher levels of lipogenesis in the liver and contributes to higher body fat accumulation in cavefish populations, an important adaptation to nutrient limited environments.

evolutionary biology↗

bioRxiv2020

Decontamination of Common Healthcare Facility Surfaces Contaminated with SARS-CoV-2 using Peracetic Acid Dry Fogging

BackgroundThe SARS-Cov-2 pandemic has highlighted the urgent need for safe and effective surface decontamination methods, particularly in healthcare settings. MethodsThe effectiveness of peracetic acid (PAA) dry fogging in decontaminating common healthcare setting surfaces was evaluated after experimentally contaminating nine surfaces (stainless steel, latex painted wood, unsealed hardwood, melamine countertop, vinyl flooring, clear plastic, faux leather, computer keyboard button and smartphone touch screen) with more than 106 TCID50 of SARS-CoV-2. ResultsWhen fumigated with PAA dry fog for an hour, no infectious SARS-CoV-2 virus was recovered from experimentally inoculated coupons of representing nine different surface types. In contrast, high titer recovery of infectious virus was demonstrated for corresponding untreated drying controls of the same materials. ConclusionStandard surface decontaminating processes, including sprays and wipes, are laborious and often cannot completely decontaminate sensitive electronic equipment. The ease of use, low cost and overall effectiveness of a PAA dry fogging suggest it should be considered for decontaminating settings, particularly intensive care units where severely ill SARS-CoV-2 patients are cared for.

microbiology↗