Biology subjects

Thakur, S.

Publications and source records attributed to Thakur, S..

At least 19 recordsLinked to original sources

bioRxiv2026

PCNA-Pol κ-Polδ /USP18 axes stabilize replication fork and restart to reduce cisplatin cytotoxicity

Cisplatin and its analogues are valuable anti-cancer drugs that target the genome, block DNA replication, and induce apoptosis. As a counteractive response, cancer cells activate several mechanisms to maintain uninterrupted DNA replication, and those are yet to be fully elucidated. This study using head and neck squamous carcinoma cells (HNSCC) demonstrated the involvement of DNA polymerase Kappa (Pol{kappa}), a trans-lesion DNA synthesis (TLS) polymerase that primarily functions as a mismatch extender, in cisplatin resistance. Interestingly, the catalytic activity of Pol{kappa} plays a minimal role in adduct bypass; rather, tripartite interactions involving it, rewire and stabilize the stalled replication fork. While the Pol{kappa}-PCNA-Pol{delta} axis facilitates efficient proliferation of cisplatin-resistant cells, the Pol{kappa}-PCNA-USP18 axis stabilizes critical proteins of ATM-ATR, and HR and NHEJ pathways to protect replication fork, repair damage, and restart DNA synthesis under cisplatin-induced stress. In resistant cells, the efficiency of ubiquitin-mediated proteasomal degradation is low, which is further diminished by Pol{kappa}-recruited USP18 deubiquitinase, maintaining a cellular homeostasis. In conclusion, for the first time, we uncovered two critical Pol{kappa} axes crucial for regulating cisplatin toxicity in cells and provided foundation for future drug discovery against advance HNSCC by targeting this non-essential DNA polymerase.

cell biology↗

bioRxiv2026

Microporous Immune-Isolating Capsule with Improved Diffusion for Restored Dynamic Bidirectional Hormone Signaling in a Murine Model of Premature Ovarian Insufficiency

Pediatric cancer survivors treated with gonadotoxic chemotherapy or radiation face lifelong premature ovarian insufficiency (POI), leading to elevated risk of cardiovascular disease, osteoporosis, and metabolic dysfunction. Pharmacological hormone replacement therapy (HRT) cannot replicate the pulsatile, bidirectional signaling of the hypothalamic-pituitary-gonadal (HPG) axis, leaving a critical therapeutic gap. Immune-isolating hydrogel capsules offer a promising strategy for the implantation of donor ovarian tissue without immunosuppression yet they require optimization for human applications. Here, we engineer a microporous immune-isolating capsule by incorporating thermosensitive gelatin microgels as sacrificial porogens. Microfluidic fabrication yielded monodisperse microgels that dissolved at 37{degrees}C generating disconnected micropores within a non-degradable poly(ethylene glycol) (PEG) matrix. Critically, the diffusion of FSH-scale analogs (40 kDa) increased by almost two-fold through the microporous capsules relative to nanoporous controls, while antibody-scale molecules (150 kDa) were blocked, demonstrating size-discriminating permeability. In ovariectomized mice implanted with encapsulated ovarian xenografts for 20 weeks, microporous capsules restored dynamic HPG-axis signaling evidenced by elevated levels of estradiol and progesterone, FSH suppression, and fluctuating hormone levels that resembled physiological patterns. Microporosity also improved graft viability, increasing stromal cellularity and reducing follicular apoptosis. These findings support microporous immune-isolating capsules as a platform for physiologically authentic therapy for POI.

bioengineering↗

bioRxiv2026

Biological Evaluation of Novel 2-Benzimidazole Derivatives for Antibacterial Activity

Infectious diseases remain a persistent global health burden, with bacterial infections accounting for a substantial disease burden. The increasing prevalence of antimicrobial resistance has emphasised the need for the development of novel antibacterial drugs. In the present study, antibacterial activity of novel 2-substituted benzimidazole derivatives (NR-1 to NR-9) was evaluated against three bacteria, viz. M. smegmatis, B. subtilis and E. coli using estimation of Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Two (NR-4 and NR-5) exhibited inhibitory activity against M. smegmatis, while two (NR-5 and NR-7) were active against B. subtilis, with MICs ranging from 62.5 to 250 g/mL. Notably, NR-5 demonstrated antibacterial activity against both M. smegmatis and B. subtilis, with more efficacy against M. smegmatis (MIC: 62.5 g/mL) and bactericidal activity with an MBC/MIC ratio of 1. Cytotoxicity assessment in Vero cells indicated low toxicity for NR-4 and NR-5, and SwissADME evaluation suggested favourable physicochemical properties and drug-likeness. The growth kinetics profiling and time kill kinetics of the NR-5 Benzimidazole derivative demonstrated concentration-dependent activity, with complete growth suppression at 2x MIC. Additionally, checkerboard assay evaluation revealed a synergistic interaction of NR-5 with Rifampicin (FICI: 0.48), highlighting the enhanced antimycobacterial activity in combination. Molecular docking and binding-pocket analysis identified thymidylate kinase (tmk) as a potential target of NR-5. Thus, we have identified and characterised NR-5 as a promising benzimidazole-based antibacterial candidate that shows potent, low-toxicity antimycobacterial activity and works synergistically with rifampicin, making it a potential lead for future anti-tuberculosis drug development.

microbiology↗

bioRxiv2025

Epigenetic Reprogramming of Host Chromatin by the Transforming Parasite Theileria annulata

Theileria annulata, a transforming apicomplexan parasite, extensively reprograms the chromatin architecture of bovine leukocytes to facilitate infection and cellular transformation. To elucidate the underlying epigenetic mechanisms, we characterized the chromatin landscape of infected lymphocytes using integrated proteomic, imaging, and functional assays. Our findings reveal that T. annulata lacks the DNA damage marker {gamma}H2A.X and its associated SQ/TQ motif, indicating an evolutionary divergence from canonical DNA repair signalling pathways. High-resolution profiling of histone post-translational modifications (PTMs) demonstrated distinct nuclear compartmentalization, with host (H3K27me3, H3K9me1/2), parasite-predominant modifications (H3K4me3, H3K18me1, H3K27ac, H3K9ac, and H3K36me3), and shared modifications (e.g., H3K4me1/2, H3K36me2, H4K5/8/12/16ac, H3K9me3 and H4K91Ac) suggesting a coordinated epigenetic strategy driving host cell programs to sustain proliferation and survival. Our study delineates a novel host-parasite epigenetic interface, positioning T. annulata as a unique model of epigenetic parasitism. By bridging parasitology and cancer epigenetics, these findings unveil new therapeutic opportunities targeting chromatin vulnerabilities in parasite-induced transformation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/684985v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1bd0e05org.highwire.dtl.DTLVardef@e37ea4org.highwire.dtl.DTLVardef@18f78d5org.highwire.dtl.DTLVardef@460eb4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Understudied and underprotected: biodiversity and conservation challenges in the Konkan region of Maharashtra

In biodiversity hotspots, such as the Western Ghats, periodic synthesis of existing ecological research can help identify knowledge gaps and address critical threats to biodiversity. The Maharashtra part of the Konkan region, situated between the Sahyadri foothills and the west coast, with diverse tropical vegetation, harbours unique open ecosystems, such as lateritic plateaus, and supports a multitude of threatened species, including hornbills and tigers. However, the region remains relatively understudied and has not received adequate protection through state or national conservation policies and laws. The area is undergoing rapid human-driven land-use change. These activities can impact the regions biodiversity, necessitating an effort to identify knowledge gaps and critical threats. Through a combination of a literature review and focus group discussions with 44 participants from various institutions and non-governmental organisations, we synthesised existing published information on the Konkan region of Maharashtra and identified key research gaps and conservation challenges. Our review of 138 studies found that while agroforestry and human-wildlife interactions have received some research attention, the effects of climate change on the regions biodiversity remain poorly understood. Focus group discussions highlighted major threats, including land-use changes due to expanding monoculture plantations, clear-felling of forests, forest fires, environmental pollution, and rapid infrastructure development, which are leading to habitat loss and fragmentation. Some of these concerns were validated by publicly available regional data, which revealed a 30% increase in roads, a 14% expansion of cashew plantations, and associated forest loss. This synthesis offers valuable insights for government and non-governmental organisations to inform future research and conservation efforts in the region.

ecology↗

bioRxiv2025

Polymer dynamics reveal stage-wise unfolding and homologous pairing of chromosomes in S. pombe

During meiosis, the exchange of genetic material ("recombination") is essential to bring up the genetic variation in offspring. To carry out the recombination, homologous pairs of DNA have to come in proximity and align. In fission yeast, this is accomplished by the extensive nuclear oscillation that applies pulling force on the chromosomes. In this work, we investigate the competition between the pulling force that tries to facilitate the alignment and the intra-chromatin interactions that assist the chromatin folding. The crucial role played by the intra-chromatin interaction for a range of pulling forces and loci location is highlighted here. Upon comparing our results with the experimental findings, we not only reaffirm the enhancement of contact probability with loci-dependent pulling but also get a meaningful interpretation of the chromosome unfolding and pairing in different stages of movement.

biophysics↗

bioRxiv2025

Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs

Campylobacter spp. resistant to fluoroquinolones and macrolides are serious public health threats. Studies aiming to identify risk factors for drug-resistant Campylobacter have narrowly focused on antimicrobial use at the farm level. Using chain graphs, we quantified risk factors for fluoroquinolones- and macrolide-resistance in Campylobacter coli isolated from two distinctive swine production systems, conventional and antibiotic-free (ABF). The chain graphs were learned using genotypic and phenotypic resistance data from 1082 isolates and host exposures obtained through surveys for 18 cohorts of pigs. The gyrA T86I point mutation alone explained at least 58 % of the variance in ciprofloxacin minimum inhibitory concentration (MIC) for ABF and 79 % in conventional farms. For macrolides, genotype and host exposures explained similar variance in azithromycin and erythromycin MIC. Among host exposures, heavy metal exposures were identified as risk factors in both conventional and ABF. Chain graph models can generate insights into the complex epidemiology of antimicrobial resistance by characterizing context-specific risk factors and facilitating causal discovery. Author summaryAntimicrobial resistance is influenced by multiple factors, including exposures to selecting agents, such as antibiotics, antiseptics, or heavy metals, and factors affecting the transmission of resistant pathogens, such as biosecurity and hygiene measures. Understanding what specific factors are associated with resistance in a given context is challenging. We developed an approach based on probabilistic graphical models to investigate context-specific antimicrobial resistance risk factors. We applied the approach to Campylobacter coli isolated from pigs in antibiotic-free and conventional farms. We demonstrated how for fluoroquinolones, risk factors were similar across both types of farms, but risk factors for macrolides were different across settings.

microbiology↗

bioRxiv2024

Molecular and cell phenotype programs in oral epithelial cells directed by co-exposure to arsenic and smokeless tobacco

Chronic arsenic exposure can lead to various health issues, including cancer. Concerns have been mounting about the enhancement of arsenic toxicity through co-exposure to various prevalent lifestyle habits. Smokeless tobacco products are commonly consumed in South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the in vitro molecular and cellular responses to arsenic and/or smokeless tobacco, we performed temporal multi-omics analysis of the transcriptome and DNA methylome remodelling in exposed hTERT-immortalized human normal oral keratinocytes (NOK), as well as arsenic and/or smokeless tobacco genotoxicity and mutagenicity investigations in NOK cells and in human p53 knock-in murine embryonic fibroblasts (Hupki MEF). RNAseq results from acute exposures to arsenic alone and in combination with smokeless tobacco extract revealed upregulation of genes with roles in cell cycle changes, apoptosis and inflammation responses. This was in keeping with global DNA hypomethylation affecting genes involved in the same processes in response to chronic treatment in NOK cells. At the phenotypic level, we observed a dose-dependent decrease in NOK cell viability, induction of DNA damage, cell cycle changes and increased apoptosis, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. Live-cell imaging experiments indicated that the DNA damage likely resulted from induction of apoptosis, an observation validated by a lack of exome-wide mutagenesis in response to chronic exposure to arsenic and/or smokeless tobacco. In sum, our integrative omics study provides novel insights into the acute and chronic responses to arsenic and smokeless tobacco (co-)exposure, with both types of responses converging on several key mechanisms associated with cancer hallmark processes. The generated rich catalogue of molecular programs in oral cells regulated by arsenic and smokeless tobacco (co-)exposure may provide bases for future development of biomarkers for use in molecular epidemiology studies of exposed populations at risk of developing oral cancer.

cancer biology↗

bioRxiv2024

Genomic epidemiology and phenotypic characterisation of Salmonella entericaserovar Panama in Victoria, Australia

Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one of several serovars that causes invasive NTS disease (iNTS) in humans. S. Panama is an understudied pathogen, with its pathobiology poorly understood. It is a predominant iNTS serovar in Australia, a high-income country with high rates of salmonellosis, where S. Panama has been documented to have a high odds ratio for causing iNTS. This study investigates the genomic epidemiology and antimicrobial resistance profiles of all S. Panama isolates recovered in Victoria, Australia, between 2000 and 2020. We examined the infection dynamics of S. Panama in seven isolates, representing the genetic diversity of the study population. Two sub-lineages, encompassed within a previously described Asian lineage, were identified. Multi-drug resistance (resistance to [≥]3 drug classes) was detected in 46 (51.7%) Australian isolates. The plasmid-mediated colistin resistance gene, mcr1.1, was detected in one Australian S. Panama isolate, carried by an IncI plasmid previously reported in Salmonella and Escherichia coli isolates collected from poultry in South-East Asia. Examination of the intracellular replication dynamics of S. Panama isolates demonstrated diverse phenotypes. In THP-1 derived macrophages, despite low host cell uptake, S. Panama showed higher replication rates over time compared to S. enterica serovar Typhimurium. However, a causative genotype could not be identified to explain this observed phenotype. This study provides insights into the S. Panama isolates imported into Australia over two-decades, showing MDR was common in this iNTS serovar, and colistin resistance reported for the first time. It provides the first data on the host-pathogen interactions of S. Panama in Australia, which will aid our collective understanding of the pathobiology of S. Panama and iNTS serovars more broadly. Author SummaryIn Australia, non-typhoidal Salmonella (NTS) cases have been on the rise since the 1970s; characterised by self-limiting enteritis, some NTS infections can result in systemic infections called invasive NTS disease. Salmonella enterica serovar Panama is a leading iNTS serovar in Australia. This study characterised the genomic epidemiology of S. Panama, identifying two lineages circulating in Australia over two decades and placing them within a global context. It also investigated the antimicrobial resistance (AMR) mechanisms of S. Panama, with multi-drug resistance commonly observed. Further, it identified the first plasmid-mediated colistin-resistant S. Panama in Australia. We additionally examined the characteristics of S. Panama-mediated host-pathogen interactions in both epithelial and macrophage cells lines, providing the first insight into the infection dynamics of this understudied pathogen. Thus, this study combines genomics and in vitro infection experiments to understand the pathogenic behaviour of the neglected iNTS S. Panama.

microbiology↗

bioRxiv2024

Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra

Understanding the phenotypic consequences of naturally occurring genetic changes, as well as their impact on fitness, is fundamental to understanding how organisms adapt to an environment. This is critical when genetic variants have pleiotropic effects, as determining how each phenotype impacted by a gene contributes to fitness is essential to understand how and why traits have evolved. A striking example of a pleiotropic gene contributing to trait evolution is the oca2 gene, coding mutations in which underlie albinism and reductions of sleep in the blind Mexican cavefish, Astyanax mexicanus. Here, we characterize the effects of mutations in the oca2 gene on larval prey capture. We find that when conspecific surface fish with engineered mutations in the oca2 allele are hunting, they use cave-like, wide angle strikes to capture prey. However, unlike cavefish or surface fish in the dark, which rely on lateral line mediated hunting, oca2 mutant surface fish use vision when striking at prey from wide angles. Finally, we find that while oca2 mutant surface fish do not outcompete pigmented surface siblings in the dark, pigmented fish outcompete albino fish in the light. This raises the possibility that albinism is detrimental to larval feeding in a surface-like lighted environment, but does not have negative consequences for fish in cave-like, dark environments. Together, these results demonstrate that oca2 plays a role in larval feeding behavior in A. mexicanus. Further, they expand our understanding of the pleiotropic phenotypic consequences of oca2 in cavefish evolution.

animal behavior and cognition↗

bioRxiv2024

Guava cv. Allahabad Safeda Chromosome scale assembly and comparative genomics decodes breeder choice marker trait association for pink pulp colour

Deciphering chromosomal length genome assemblies has the potential to unravel an organisms evolutionary relationships and genetic mapping of traits of commercial importance. We assembled guava genome using a hybrid sequencing approach with [~]450x depth Illumina short reads, [~]35x PacBio long reads and Bionano maps to [~]594 MB Scaffold length on 11 pseudo chromosomes ([~]479 MB contig length). Maker pipeline predicted 17,395 genes, 23% greater from earlier draft produced in same cultivar Allahabad Safeda. The genome assembly clarified guava evolutionary history, for example revealing predominance of gene expansion by dispersed duplications, in particular contributing to abundance of monoterpene synthases; and supporting evidence of a whole genome duplication event in guava as in other Myrtaceae. Guava breeders have been aiming to reduce screening time for selecting pink pulp colour progenies using marker-trait associations, but a previous comparative transcriptomics and comparative genomics approach with draft genome assembly to identify the effector gene associated with pink pulp was unsuccessful. Here, genome re-sequencing with Illumina short reads at [~]25x depth of 20 pink fleshed and/or non-coloured guava cultivars and comprehensive analysis for genes in the carotenoid biosynthesis pathway identified structural variations in Phytoene Synthase 2. Further, ddRAD based association mapping in core-collection of 82 coloured and non-coloured genotypes from Indian sub-continent found strong association with the same causal gene. Subsequently, we developed PCR based Indel/SSR breeder friendly marker that can readily be scored in routine agarose gels and empowers accurate selection for seedlings that will produce fruits with pink pulp.

plant biology↗

bioRxiv2024

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop

Several types of molecular machines move along biopolymers like chromatin. However, the details about the microscopic activity of these machines and how to distinguish their modes of action are not well understood. We propose that the activity of such machines can be classified by studying looped chromatin under shear flow. Our simulations show that a chromatin-like polymer with two types of activities (constant or local curvature-dependent tangential forces) exhibits very different behavior under shear flow. We show that one can distinguish both activities by measuring the nature of a globule-to-extended coil transition, tank treading, and tumbling dynamics.

biophysics↗

bioRxiv2023

A mitochondrial quality control mechanism reverses the phagosome maturation arrest caused by Mycobacterium tuberculosis

Phagosome maturation arrest (PMA) imposed by Mycobacterium tuberculosis (Mtb) is a classic tool that helps Mtb evade macrophage anti-bacterial responses. The exclusion of RAB7, a small GTPase, from Mtb-phagosomes causes PMA. Here, we report an unexpected mechanism that triggers crosstalk between the mitochondrial quality control (MQC) and the phagosome maturation pathways that reverses the PMA. CRISPR-mediated p62/SQSTM1 depletion (p62KD) does not appear to impact mitochondrial quality. The p62KD cells are restrictive to Mtb growth, triggered by an increasingly oxidative environment and increased lysosomal targeting. The lysosomal targeting of Mtb is facilitated by enhanced TOM20+ mitochondria-derived vesicles (MDVs) biogenesis, a key MQC mechanism. In p62KD cells, TOM20+-MDVs biogenesis is MIRO1/MIRO2-dependent and gets delivered to lysosomes for degradation in a RAB7-dependent manner. Upon infection in p62KD cells, TOM20+-MDVs get extensively targeted to Mtb-phagosomes, inadvertently facilitating RAB7 recruitment, PMA reversal and lysosomal targeting of Mtb; the phenotype also replicated in p62/SQSTM1 knockout cells. Triggering MQC collapse in p62KDcells further diminishes Mtb survival, signifying cooperation between redox- and lysosome-mediated mechanisms. The MQC-anti-bacterial pathway crosstalk could be exploited for host-directed anti-tuberculosis therapies.

microbiology↗

bioRxiv2023

Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina

BackgroundEscherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS). MethodsRetail chicken (breast, n=96; giblets, n=24), turkey (n=96), and pork (n=96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree were generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type. ResultsOf 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as MDR ([≥]3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3)-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2=2.21, p =0.33). MDR was observed in isolates from meat products with labels indicating "no claims" (n=29; 69%), "no antibiotics ever" (n=9; 21.4%), and "organic" (n=4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates. ConclusionsE. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.

microbiology↗

bioRxiv2023

Computational fitness estimates of SARS-CoV-2 mutations affecting spike protein binding to antibodies and ACE2

Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogen. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein ([~]3,80,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.

bioinformatics↗

bioRxiv2022

Recurrent evolution of small body size and loss of the sword ornament in Northern Swordtail fish

Across the tree of life, species have repeatedly evolved similar phenotypes. While well-studied for ecological traits, there is also evidence for convergent evolution of sexually selected traits. Swordtail fish (Xiphophorus) are a classic model system for studying sexual selection, and female Xiphophorus exhibit strong mate preferences for large male body size and a range of sexually dimorphic ornaments. However, sexually selected traits have been lost multiple times in the genus. Phylogenetic relationships between species in this group have historically been controversial, likely as a result of prevalent gene flow, resulting in uncertainty over the number of losses of ornamentation and large body size. Here, we use whole-genome sequencing approaches to re-examine phylogenetic relationships within a Xiphophorus clade that varies in the presence and absence of sexually selected traits. Using wild-caught individuals, we determine the phylogenetic placement of a small, unornamented species, X. continens, confirming an additional loss of ornamentation and large body size in the clade. With these revised phylogenetic relationships, we analyze evidence for coevolution between body size and other sexually selected traits using a phylogenetically independent contrasts approach. These results provide insights into the evolutionary pressures driving the recurrent loss of suites of sexually selected traits.

evolutionary biology↗

bioRxiv2022

Uncovering Changes in Microbiome Profiles Across Commercial and Backyard Poultry Farming Systems

Environmental health and microbiome can affect poultry production in a variety of ways. Poor environmental conditions can lead to increased stress, disease, and mortality in poultry, resulting in reduced production. Poor environmental conditions can also reduce the diversity of microbial populations in the poultry microbiome, which can lead to an increased risk of disease and reduced production. Finally, microorganisms in the environment can be introduced to the poultry microbiome, which can increase the risk of disease and reduce production. Additionally, poultry production can have significant impacts on the environmental microbiome. Poultry farming can alter soil and water microbiomes through pollution from manure and other agricultural runoff. These changes can lead to increased concentrations of certain microbes as well as an altered balance between beneficial microorganisms. In this study, we investigated the changes in the microbiome profiles of commercial and backyard broiler farming systems at different time points. To explore the microbiome profiles, fecal, soil, litter samples, and swabs from feeders and waterers were collected three times over the production period from a single flock. Each backyard farm was sampled at three time points: 10, 31, and 52 days of production and days 10, 24, and 38 of production in commercial farms. Statistical and network analyses were performed using DADA2 and MicrobiomeAnalyst platforms. Our results show marked differences in alpha diversity, beta diversity, and relative abundance of taxa between commercial and backyard farms over time. The observed species index significantly differed between the backyard and commercial farms for the soil, litter, and waterer samples. In addition, the fecal samples from backyard farms were found to have more Firmicutes, Bacteriodota, Desulfobacteria, Synergitota, Fusobacteriota, and Campilobacterota. Moreover, clustering showed different patterns in commercial and backyard farms with distinct marker taxa for each production system. Furthermore, the microbiome profiles of commercial and backyard farms evolved differently over time.

microbiology↗

bioRxiv2022

Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding

The binding affinity of the SARS-CoV-2 spike (S)-protein {Delta}{Delta}Gbind to the human membrane protein ACE2 is critical for virus function and evolution. Computational structure-based screening of new S-protein mutations for ACE2 binding lends promise to rationalize virus function directly from protein structure and ideally aid early detection of potentially concerning variants. We used a computational protocol based on cryo-electron microscopy structures of the S-protein to estimate the ACE2-binding that gave good trend agreement with experimental ACE2 affinities. We then expanded predictions to all possible S-protein mutations in 21 different S-protein-ACE2 complexes (400,000 {Delta}{Delta}Gbind data points in total), using mutation group comparisons to reduce systematic errors. We show that mutations that have arisen in major variants as a group maintain ACE2 affinity significantly more than random mutations in the total protein, at the interface, and at evolvable sites, with differences between variant mutations being small relative to these effects. Omicron mutations as a group had a modest change in binding affinity compared to mutations in other major variants. The single-mutation effects are consistent with ACE2 binding being optimized and maintained in omicron, despite increased importance of other selection pressures (antigenic drift). As epistasis, glycosylation and in vivo conditions will modulate these effects, computational predictive SARS-CoV-2 evolution remains far from achieved, but the feasibility of large-scale computation is substantially aided by using many structures and comparison of mutation groups rather than single mutation effects, which are very uncertain. Our results demonstrate substantial challenges but indicate ways to improve the quality of computer models for assessing SARS-CoV-2 mutation effects.

biophysics↗