Biology subjects

Chaturvedi, S.

Publications and source records attributed to Chaturvedi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Unmasking the large and highly repetitive genome of Phlox reveals a complex evolutionary history of speciation with gene flow

The large size and high repetitive content of many plant genomes have hindered elucidation of how the fundamental processes of evolution give rise to speciation. Here we present chromosome-level assemblies of 6 gigabase genomes for four closely related Phlox wildflower species. We generate extensive population genetic data for the three well-studied annual species P. drummondii, P. cuspidata, and P. roemeriana, including structural variation from whole-genome long-read resequencing data. The whole-genome assemblies reveal extensive differences in amount and distribution of genetic variation within and between species, reflective of differences in life-history strategies, mating systems, and edaphic specialization. The population genetic data exposes a history of widespread and consistent gene flow between all three annual Phlox species throughout their divergence and speciation. Our unmasking of structural variants and repetitive elements exposes rich and dynamic forms of genetic variation that show strong phylogenetic signal and pervasive patterns of gene flow. Our results lay a foundation for untangling the highly complex genomes of plants to make advancements in our understanding of the processes of speciation and divergence.

evolutionary biology↗

bioRxiv2026

Rapid and Specific Identification of Emerging Trichophyton mentagrophytes Genotype VII Using an In-House Developed and Validated Real-Time PCR Assay

Trichophyton mentagrophytes genotype VII (TmVII) is an emerging sexually transmitted dermatophyte that causes skin infections characterized by inflammatory, erythematous-squamous, painful, and persistent lesions. This genotype is part of the T. interdigitale/T. mentagrophytes Species Complex (TiTmSC), which comprises 28 genotypes. To enable rapid and specific differentiation of TmVII from other genotypes, a real-time polymerase chain reaction (rt-PCR) assay was developed targeting three unique single-nucleotide polymorphisms in the ITS1 region of TmVII. Assay specificity was further improved by introducing an additional mismatch at the 3 ends of both forward and reverse primers. The rt-PCR assay demonstrated high sensitivity, with a detection limit of 0.0002 ng of TmVII genomic DNA. The assay was highly specific, with no cross-reactivity observed with either closely or distantly related fungal pathogens when a cycle threshold (Ct) cutoff of 37 was applied. Among 497 mold isolates tested, 47 were confirmed as TmVII by rt-PCR, and the results were fully concordant with conventional ITS-PCR/Sanger sequencing. The rt-PCR assay demonstrated high sensitivity, specificity, reproducibility, and speed, with a turnaround time of one day after DNA extraction, compared with seven to ten days for Sanger sequencing. The first rapid molecular assay developed using TaqMan chemistry for TmVII identification is expected to enhance patient care and support infection control measures.

microbiology↗

bioRxiv2026

Genomic forecasts of maladptation in Lycaeides butterflies

Genomic forecasting approaches based on genotype-environment associations (GEAs) are increasingly used to estimate genomic offsets (GOs), which predict population maladaptation and extinction risk under current or future climatic conditions. Despite their widespread use, only a subset of studies have evaluated how accurately GOs predict (mal)adaptation, limiting their interpretation and application in policy and management. Here, we used GEA analyses to estimate GOs for past, present, and future climates in Lycaeides butterflies, focusing on the causes of variation in GOs among populations and their relationships with demographic parameters inferred from population genomic data. Using multivariate linear regression and genotyping-by-sequencing data from 42 Lycaeides populations (922 butterflies), we found that mean annual temperature, cumulative annual precipitation, and hybridization history together explained 47.6% of variation in genome-wide allele frequencies. Genomic offsets differed substantially among populations and across past, present, and future climates, with evidence for increasing maladaptation under more distant future climate scenarios. We found no relationship between GOs for present climates and contemporary effective population size. In contrast, genetic diversity, which reflects long-term effective population size, and local rates of gene flow together explained 27.3% of variation in contemporary GOs. Populations with higher genetic diversity and more gene flow exhibited lower GOs, consistent with the hypothesis that genetic diversity enhances adaptive capacity and that gene flow may introduce adaptive alleles. Overall, our results support the utility of GO predictions, particularly when validated with independent measures of adaptation, while cautioning against simplistic interpretations of GO as a direct measure of maladaptation in conservation and management contexts.

evolutionary biology↗

bioRxiv2026

A Knock-In Igfn1iCre transgenic mouse line provides partial developmental access to type-7 bipolar cells

1.Functional neuronal circuits in the vertebrate retina emerge through coordinated developmental events, yet the timeline by which bipolar cells acquire visual feature selectivity remains unclear. A major barrier is the limited genetic access to bipolar subtypes during early postnatal stages. Recent comprehensive transcriptomic study points to Igfn1 as a molecular marker for type-7 bipolar cells (BC 7), a subtype that exhibits direction-selective glutamate releases in adult. Here, we generated an Igfn1iCre knock-in mouse line and characterized Igfn1-positive cell morphology from postnatal day 4(P4) to adult using Cre-dependent tdTomato reporter mice. We found Igfn1-positive cells in the inner retina by P12-P15, predominantly labelling bipolar cells and some amacrine populations. At P15, about 71% of labelled bipolar cells stratified their axons in the S4 sublamina of the inner plexiform layer, consistent with BC 7 morphology. In adult retina, the widespread Igfn1-labelling appears slightly dominated in amacrine cells. To validate these observations, we analysed Igfn1 expression in the Mouse Retina Cell Atlas and confirmed strong Igfn1 enrichment in BC 7 and expression in additional retinal cell types, mirroring experimental results. Overall, these results reveal Igfn1iCre as a potential developmental tool for BC 7 access in the retina.

neuroscience↗

bioRxiv2024

Cisplatin resistance reversal with treatment of Citric acid in cisplatin-resistant cell lines

Gastric cancer (GC) is a prevalent and aggressive malignancy with significant morbidity and mortality rates, posing a major threat to human health globally. While surgery remains the preferred clinical treatment, chemotherapy continues to be the cornerstone for perioperative care, adjuvant therapy, and palliative treatment for patients with advanced stages of GC. Among the chemotherapeutic agents, cisplatin (DDP) has been widely used for decades as a first-line treatment for various solid tumors. However, its therapeutic efficacy is frequently undermined by the development of resistance, which is attributed to the complex interplay of multiple proteins and signaling pathways involved in the resistance mechanisms. In this study, the issue of cisplatin resistance is addressed by employing citric acid as a treatment in cell lines. The findings demonstrate that citric acid effectively reverses cisplatin resistance, suggesting the potential involvement of a novel DNA damage repair mechanism. These results pave the way for further investigation into innovative therapeutic approaches to enhance the efficacy of cisplatin in treating gastric cancer.

pharmacology and toxicology↗

bioRxiv2024

Identification and Pharmacological Characterization of Multiple Allosteric Binding Sites on the Free Fatty Acid 1 Receptor

Free fatty acid receptor 1 (FFA1 or GPR40), activated by medium- and long-chain fatty acids, amplifies glucose-stimulated insulin secretion, making it a promising target for type 2 diabetes. Radioligand studies revealed distinct binding sites for partial and full agonists, with full agonists showing positive cooperativity. Functional assays demonstrated positive cooperativity between agonists and varying interactions with the endogenous fatty acid DHA. These findings suggest three allosterically linked binding sites on FFA1, with activation influenced by key arginine residues. Potent ligands with strong cooperativity hold significant therapeutic potential.

pharmacology and toxicology↗

bioRxiv2024

Diabetes-Tuberculosis Comorbidity Characterized by Reduced Type-II Interferon and Elevated Th17 Responses.

Understanding the perturbed lung immune cells distribution and its functionality in tuberculosis (TB) is well documented; however, limited reports have covered their disruption, if any, in diabetes-tuberculosis (DM-TB) comorbid conditions. Here, we employed single-cell RNA-seq to investigate the molecular mechanisms that govern the heterogeneity in host immune response in DM-TB comorbid conditions. Diabetes is associated with chronic hyperinflammation and reduced lung-infiltrating immune cells, which delays the immune response to Mycobacterial infection. scRNA-seq of lung CD3 and CD11c cells revealed compromised adaptive and innate immunity, with decreased Th1 and M1 macrophage populations in DM-TB mice. A dampened immune response, marked by increased IL-16 signaling and reduced TNF and IFN-II responses, was observed in DM-TB. This study highlights chronic inflammation, hyperglycemia, and dyslipidemia associated with diabetes impairing anti-TB immunity. Selective inhibition of aberrant IL-16 secretion and Th17 cell activation might provide strategies for better managing DM-TB comorbidity.

immunology↗

bioRxiv2024

What makes Candida auris pan-drug resistant? Integrative insights from genomic, transcriptomic, and phenomic analysis of clinical strains resistant to all four major classes of antifungal drugs

The global epidemic of drug-resistant Candida auris continues unabated. We do not know what caused the unprecedented appearance of pan-drug resistant (PDR) Candida auris strains in a hospitalized patient in New York; the initial report highlighted both known and unique mutations in the prominent gene targets of azoles, amphotericin B, echinocandins, and flucytosine antifungal drugs. However, the factors that allow C. auris to acquire multi-drug resistance and pan-drug resistance are not known. Therefore, we conducted a comprehensive genomic, transcriptomic, and phenomic analysis to better understand PDR C. auris. Among 1,570 genetic variants in drug-resistant C. auris, 299 were unique to PDR strains. The whole genome sequencing results suggested perturbations in genes associated with nucleotide biosynthesis, mRNA processing, and nuclear export of mRNA. Whole transcriptome sequencing of PDR C. auris revealed two genes to be significantly differentially expressed - a DNA repair protein and DNA replication-dependent chromatin assembly factor 1. Of 59 novel transcripts, 12 candidate transcripts had no known homology among expressed transcripts found in other organisms. We observed no fitness defects among multi-drug resistant (MDR) and PDR C. auris strains grown in nutrient-deficient or - enriched media at different temperatures. Phenotypic profiling revealed wider adaptability to nitrogenous nutrients with an uptick in the utilization of substrates critical in upper glycolysis and tricarboxylic acid cycle. Structural modelling of 33-amino acid deletion in the gene for uracil phosphoribosyl transferase suggested an alternate route in C. auris to generate uracil monophosphate that does not accommodate 5-fluorouracil as a substrate. Overall, we find evidence of metabolic adaptations in MDR and PDR C. auris in response to antifungal drug lethality without deleterious fitness costs.

microbiology↗

bioRxiv2024

Complement Biosensors Identify a Classical Pathway Stimulus in Complement-Mediated Hemolytic Uremic Syndrome

Complement-mediated hemolytic uremic syndrome (CM-HUS) is a thrombotic microangiopathy characterized by germline variants or acquired antibodies to complement proteins and regulators. Building upon our prior experience with the modified Ham (mHam) assay for ex vivo diagnosis of complementopathies, we have developed an array of cell-based complement "biosensors by selective removal of complement regulatory proteins (CD55 and CD59, CD46, or a combination thereof) in an autonomously bioluminescent HEK293 cell line. These biosensors can be used as a sensitive method for diagnosing CM-HUS and monitoring therapeutic complement blockade. Using specific complement pathway inhibitors, this model identifies IgM-driven classical pathway stimulus during both acute disease and in many patients during clinical remission. This provides a potential explanation for ~50% of CM-HUS patients who lack an alternative pathway "driving" variant and suggests at least a subset of CM-HUS is characterized by a breakdown of IgM immunologic tolerance. Key PointsO_LICM-HUS has a CP stimulus driven by polyreactive IgM, addressing the mystery of why 40% of CM-HUS lack complement specific variants C_LIO_LIComplement biosensors and the bioluminescent mHam can be used to aid in diagnosis of CM-HUS and monitor complement inhibitor therapy C_LI

immunology↗

bioRxiv2024

A Dynamical Systems Approach to Optimal Foraging

Foraging for resources in an environment is a fundamental activity that must be addressed by any biological agent. Modelling this phenomenon in simulations can enhance our understanding of the characteristics of natural intelligence. In this work, we present a novel approach to model foraging in-silico using a continuous coupled dynamical system. The dynamical system is composed of three differential equations, representing the position of the agent, the agents control policy, and the environmental resource dynamics. Crucially, the control policy is implemented as a parameterized differential equation which allows the control policy to adapt in order to solve the foraging task. Using this setup, we show that when these dynamics are coupled and the controller parameters are optimized to maximize the rate of reward collected, adaptive foraging emerges in the agent. We further show that the internal dynamics of the controller, as a surrogate brain model, closely resemble the dynamics of the evidence accumulation mechanism, which may be used by certain neurons of the dorsal anterior cingulate cortex region in non-human primates, for deciding when to migrate from one patch to another. We show that by modulating the resource growth rates of the environment, the emergent behaviour of the artificial agent agrees with the predictions of the optimal foraging theory. Finally, we demonstrate how the framework can be extended to stochastic and multi-agent settings. Author SummaryIntelligence is a phenomenon that arises due to the interactions of an agents dynamics with the environments dynamics under the assumption that the agent seeks optimization of certain objective. Modelling both these dynamics as a single coupled dynamical system can shed light on patterns of intelligence that unfold in time. This report aims to provide a minimal in-silico framework that models the main components involved in natural phenomena, like optimal foraging, as a coupled dynamical system. Interestingly, we observe similarities between the surrogate brain dynamics of the artificial agent with the evidence accumulation mechanism that can be responsible for decision-making in certain non-human primates performing a similar foraging task. We also observe similarities between trends prescribed by theories prevalent in behavioural ecology such as the optimal foraging theory and those shown by the artificial agent. Such similarities can increase the predictability and explainability of artificial systems. We can now expect them to mimic these natural decision-making mechanisms by replicating such trends and we can thus understand the reasoning behind their actions. They can also increase the confidence of researchers to consider using such artificial agent models as simulation tools to make predictions and test hypotheses about aspects of natural intelligence.

animal behavior and cognition↗

bioRxiv2023

Neutrophil-derived IL-17 limits protective host responses and promotes tuberculosis pathogenesis

The protective correlates of Mycobacterium tuberculosis (Mtb) infection-elicited host immune responses are incompletely understood. Here, we report pro-pathogenic crosstalk involving Ly6G+granulocytes (Ly6G+Gra), IL-17 and COX2. We show that in the lungs of Mtb-infected wildtype mice, either BCG-vaccinated or not, most intracellular bacilli are Ly6G+Gra-resident four weeks post-infection onwards. In the genetically susceptible IFN{psi} -/- mice, excessive Ly6G+Gra infiltration correlates with severe bacteraemia. Neutralizing IL-17 (anti-IL17mAb) and COX2 inhibition by celecoxib reverse Ly6G+Gra infiltration, associated pathology and death in IFN{psi} -/- mice. Surprisingly, Ly6G+Gra also serves as the major source of IL-17 in the lungs of Mtb-infected WT or IFN{psi} -/- mice. The IL-17-COX2-Ly6G+Gra interplay also operates in WT mice. Inhibiting ROR{psi}t, the key transcription factor for IL-17 production or COX2, reduces the bacterial burden in Ly6G+Gra, leading to reduced bacterial burden and pathology in the lungs of WT mice. In the Mtb-infected WT mice, COX2 inhibition abrogates IL-17 levels in the lung homogenates and significantly enhances BCGs protective efficacy, mainly by targeting the Ly6G+Gra-resident Mtb pool, a phenotype also observed when IL-17 is blocked by ROR{psi}t inhibitor. Furthermore, in pulmonary TB patients, high neutrophil count and IL-17 correlated with adverse treatment outcomes. Together, our results suggest that IL-17 and PGE2 are the negative correlates of protection, and we propose targeting the pro-pathogenic IL-17-COX2-Ly6G+Gra axis for TB prevention and therapy.

immunology↗

bioRxiv2023

Antibodies against Elapidae and Viperidae snake venoms: in vivo neutralization and mechanistic insights

Snake envenomation results in a range of clinical sequelae, and effective therapy is yet to be discovered. Anti-snake venom antibodies are being considered as a potent strategy. We developed venom-neutralizing humanized antibody scFvs and elucidated biochemical and structural mechanisms associated with the inhibition of toxicity. Tomlinson I and J human antibody scFv libraries were screened against Naja naja and Echis carinatus venoms, and seven unique antibody scFvs were obtained. Further, specific toxins of snake venom interacting with each of these scFvs were identified, and phospholipase A2 (PLA2) was found to be prominently captured by the phage-anchored antibody scFvs. Proteomic analysis of whole venom also revealed PLA2 to be the most abundant toxin in both venom samples. The scFvs binding to PLA2 were used to perform in vivo survival assay using the mouse model and in vitro toxin inhibition assays. scFv N194, which binds to acidic PLA2, showed considerable survival in Naja naja venom-challenged mice and conferred up to 50% protection. A combination of two scFvs, E113 and E10, both interacting with basic PLA2, exhibited synergistically enhanced survival of 33% in Echis carinatus venom-challenged mice, compared to 16% survival conferred by an equal amount of individual scFvs. Furthermore, these scFvs demonstrated inhibition of venom-induced myotoxicity and hemolysis which corroborate the survival data. Structural studies highlighted possible modes of PLA2 neutralization by scFv through the engagement of CDRs with C-terminal myotoxic loop and interfacial region, which are crucial for PLA2 toxicity.

biochemistry↗

bioRxiv2023

Splenic T follicular helper cells compromise Mycobacterium tuberculosis clearance in aged C57BL/6 mice

Immunosenescence increases susceptibility to infectious diseases like tuberculosis (TB) in older subjects ([≥]60 years) and may impact containment of Mycobacterium tuberculosis (Mtb) during therapeutic intervention. A deeper understanding of cellular and molecular changes with age could inform new strategies to improve therapeutic outcomes. Here, we monitored the immunopathology, frequency and functionality of immune cells across extreme age groups of C57BL/6 mice following low aerosol dose infection (100-120 cfu) with Mtb H37Rv and treatment with rifampicin and isoniazid (RIF-INH). Up to 6 weeks of infection, tissue (lung, spleen and liver) mycobacterial load in old (17-19 months; M) and aged (31M) C57BL/6 mice was similar compared to young (2-4M) mice. However, at two weeks post-treatment, older mice showed a slower rate of Mtb clearance in the lungs. Old Mtb-infected mice had higher splenic T-follicular cytotoxic (TFC)-like cells and proteomic analysis of flow-sorted CD4+CD44+ T cells revealed deregulated mitochondrial proteins (4-hydroxy-2-oxoglutarate aldolase, aspartate aminotransferase and prostaglandin E synthase), pointing to impaired mitochondrial function. Collectively, these findings suggest that age-associated immune alterations may impair immunometabolic processes contributing to delayed Mtb clearance. These results highlight the potential importance of targeting immunometabolic dysfunction to improve TB treatment outcomes in older populations and reduce morbidity. SummaryThe elderly population is particularly susceptible to tuberculosis (TB), making it crucial to understand the cellular and molecular mechanisms contributing to the decline in immune responses with age. Evaluating the immunopathology, frequency and functionality of immune cells and Mtb-specific antibody responses across different age groups is essential for developing adjunct therapies for geriatric TB patients.

immunology↗

bioRxiv2022

A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters

The high transmissibility of SARS-CoV-2 is a primary driver of the COVID-19 pandemic. While existing interventions prevent severe disease, they exhibit mixed efficacy in preventing transmission, presumably due to their limited antiviral effects in the respiratory mucosa, whereas interventions targeting the sites of viral replication might more effectively limit respiratory virus transmission. Recently, intranasally administered RNA-based therapeutic interfering particles (TIPs) were reported to suppress SARS-CoV-2 replication, exhibit a high barrier to resistance, and prevent serious disease in hamsters. Since TIPs intrinsically target the tissues with the highest viral replication burden (i.e., respiratory tissues for SARS-CoV-2), we tested the potential of TIP intervention to reduce SARS-CoV-2 shedding. Here, we report that a single, post-exposure TIP dose lowers SARS-CoV-2 nasal shedding and at 5 days post-infection infectious virus shed is below detection limits in 4 out of 5 infected animals. Furthermore, TIPs reduce shedding of Delta variant or WA-1 from infected to uninfected hamsters. Co-housed contact animals exposed to infected, TIP-treated, animals exhibited significantly lower viral loads, reduced inflammatory cytokines, no severe lung pathology, and shortened shedding duration compared to animals co-housed with untreated infected animals. TIPs may represent an effective countermeasure to limit SARS-CoV-2 transmission. SignificanceCOVID-19 vaccines are exceptionally effective in preventing severe disease and death, but they have mixed efficacy in preventing virus transmission, consistent with established literature that parenteral vaccines for other viruses fail to prevent mucosal virus shedding or transmission. Likewise, small-molecule antivirals, while effective in reducing viral-disease pathogenesis, also appear to have inconsistent efficacy in preventing respiratory virus transmission including for SARS-CoV-2. Recently, we reported the discovery of a single-administration antiviral Therapeutic Interfering Particle (TIP) against SARS-CoV-2 that prevents severe disease in hamsters and exhibits a high genetic barrier to the evolution of resistance. Here, we report that TIP intervention also reduces SARS-CoV-2 transmission between hamsters.

microbiology↗

bioRxiv2022

Population genomic evidence of selection on structural variants in a natural hybrid zone

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.

genomics↗

bioRxiv2021

Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides butterfly populations maintain low contemporary (variance) effective population sizes (e.g., [~]200 individuals) and thus evolve rapidly by genetic drift. Contemporary effective sizes were consistent with local census populations sizes. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

evolutionary biology↗

bioRxiv2021

Reverse Transcriptase Real-Time PCR Assay for the Rapid Enumeration of Live Candida auris from the Healthcare Environment

Ongoing healthcare-associated outbreaks of multidrug-resistant yeast Candida auris have prompted development of several rapid DNA-based molecular diagnostic tests. These tests do not distinguish between live and dead C. auris cells, limiting their use for environmental surveillance and containment efforts. We addressed this critical gap by developing a reverse transcriptase (RT) real-time PCR assay for rapid detection of live C. auris in healthcare environments. The assay targets the internal transcribed spacer 2 (ITS2) cDNA of C. auris, amplified by obtaining pure RNA followed by reverse transcription and real-time PCR assay. The assay was highly sensitive, with the detection limit of ten colony-forming units (CFU) per RT real-time PCR reaction. In C. auris viability studies, ITS2 cDNA was detectable in heat- and ethanol-killed C. auris cells, but not bleach-killed cells. Validation studies showed no cycle threshold (Ct) values were obtained from samples on a sponge matrix spiked with either dead C. auris (105/ml) or other Candida species (105/ml), while most environmental samples spiked with 102 to 105 CFU of live C. auris yielded positive Ct values. Finally, 33 environmental samples positive for C. auris DNA but negative by culture were all negative by RT real-time PCR assay, confirming concordance between culture and the assay. The RT real-time PCR assay appears highly reproducible, robust, and specific for detecting live C. auris from environmental samples, and could be an invaluable tool in surveillance efforts to control the spread of live C. auris in healthcare environments.

molecular biology↗

bioRxiv2021

Refget: standardised access to reference sequences

Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations. https://w3id.org/ga4gh/refget.

bioinformatics↗