Biology subjects

Peterson, C.

Publications and source records attributed to Peterson, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Impact of histone N-terminal domains and linker DNA on H2A.Z deposition by yeast SWR1C

ATP-dependent chromatin remodeling enzymes play a central role in governing the essential functions of the genome, and deficiencies in their catalytic function often lead to developmental disorders or disease. While most remodelers use the energy of ATP hydrolysis to either mobilize nucleosomes or evict histone octamers, yeast SWR1C catalyzes the ATP-dependent replacement of nucleosomal H2A/H2B dimers with variant H2A.Z/H2B dimers. The H2A.Z histone variant is conserved in all eukaryotes where it plays key roles in regulating gene transcription, DNA repair, and heterochromatin function. Consequently, the regulation of H2A.Z deposition by SWR1C is central to numerous genomic functions. Here, we use both quantitative fluorescence-based assays and gel-based, electrophoretic methods to dissect the roles of histone tails, histone acetylation, and linker DNA in SWR1C-mediated H2A.Z deposition in vitro. Unlike many other remodeling enzymes, we find that histone tails are largely dispensable for the catalytic activity of SWR1C, and histone acetylation by the NuA4 acetyltransferase has only a minor stimulatory impact on SWR1C activity. In contrast, we confirm previous studies that nucleosome-free, linker DNA stimulates SWR1C activity even under saturating enzyme levels. These insights provide a clearer understanding of the structural and regulatory determinants that guide H2A.Z deposition by SWR1C, offering potential new avenues to investigate its role in chromatin dynamics and genome stability.

biochemistry↗

bioRxiv2026

Multi-omic Longitudinal Analysis of Canine Osteosarcoma Identifies Inter-Patient Heterogeneity and Immune Enrichment in Metastatic Lesions

Osteosarcoma (OS) exhibits substantial genomic complexity and inter-patient heterogeneity, necessitating longitudinal, patient-matched analyses to understand acquired features of tumor evolution. However, most published OS data is limited to primary tumor samples, limiting insight into patient-specific resistance mechanisms. To address this, we characterized the genomic landscape of paired primary and metastatic tumor samples from dogs with spontaneous OS. Whole-genome and single-cell RNA sequencing reveal mutation and gene expression profiles that are predominantly organized by patient identity. Mutational burden and pathway alterations such as those involving PI3K, NOTCH, TP53, MAPK, RAS and epigenetic regulation differ between primary and metastatic samples. Variants present in tumor tissue are readily detectable in paired cfDNA samples, demonstrating the utility of this assay for identifying tumor-specific alterations associated with treatment resistance. Analysis of bulk RNA-seq data to estimate cell-type composition shows greater immune cell representation in metastases, underscoring the importance of immune signaling pathways in OS. These findings exemplify the presence of patient-specific alterations in genomic architecture over the course of tumor progression, linking CNV amplification, pathway reprogramming, and immune evasion in metastatic OS.

genomics↗

bioRxiv2025

The Acropora millepora microbiome is predicted by algal symbionts, host genetics, and environment

The coral microbiome is a critical component of coral health and resilience, yet it is unclear what factors drive coral microbiome composition, especially within the context of coral bleaching. Here, we use whole genome sequencing data combined with a machine learning approach (RDAforest) to assess predictors of the microbiome in 208 colonies of Acropora millepora from 12 reef sites in the Central Great Barrier Reef during a 2016 bleaching event. We characterized microbiome variation using k-mers. While some environmental variables, such as chlorophyll seasonal range and maximum degree heating weeks, were associated with microbiome composition, we find that host genetics and dominant photosymbionts were more powerful predictors. In contrast, bleaching score had negligible predictive power. The corals microbiome therefore correlates with dominant photosymbiont identity even during a bleaching event. The association of the microbiome with the environment suggests that the coral microbiome can serve as a proxy for environmental variation when environment cannot be measured directly, which may be especially useful in ancient DNA studies.

evolutionary biology↗

bioRxiv2025

Interstrain Recombinants of Human Cytomegalovirus Reveals Complex Genetic Correlates and Epistasis Influencing Glycoprotein Display, Virion Infectivity and Spread Characteristics.

Most of the nucleotide diversity in the human cytomegalovirus (HCMV) genome is due to approximately 17 genes with 2-14 alleles each. These allelic genes are interspersed among longer stretches of highly conserved sequences with signatures of extensive recombination that would shuffle the allelic genes into a vast number of allelic haplotypes. Bacterial artificial chromosome clones derived from 3 independent clinical isolates (TB40/e (TB), TR and Merlin (ME)) display dramatic differences in the abundance of entry-mediating glycoproteins gH/gL/gO and gH/gL/UL128-131, virion infectivity and efficiency of cell-free and cell-to-cell modes of spread. Of these, TB and ME are the most phenotypically different and share only 2 of the 17 allelic genes. A set of recombinant HCMV was generated by coinfecting cells with TB and ME and restriction fragment length polymorphism (RFLP) analyses demonstrated complex crossover patterns. Most recombinants were either "TB-like" with much more gH/gL/gO than gH/gL/UL128-131, or "ME-like" with much more gH/gL/UL128-131. This correlated with a TB or ME UL128 sequence, consistent with a G/T polymorphism affecting UL128 pre-mRNA splicing. One recombinant had a gH/gL/gO:gH/gL/UL128-131 ratio of 0.8, suggesting genetic determinants beyond UL128. Virion infectivity correlated with TB versus ME-like glycoprotein display, but intragroup variability indicated additional factors and variability in spread efficiency and the contribution of cell-free and cell-to-cell spread modes indicated an influence of characteristics beyond virion infectivity. Results suggest that the relationships among these three phenotypes are not strictly causal and that all three phenotypes are genetically complex and influenced by epistasis among polymorphic loci across the genome. IMPORTANCEThe emerging picture of the genetic diversity of HCMV in vivo prompts a reevaluation of how in vitro characterized viral phenotypes, such as the abundance of the various glycoproteins displayed on the virion envelope and tendency towards cell-free or direct cell-to-cell spread, reflect viral characteristics in vivo. A small sampling of the in vivo genetic diversity of HCMV has been examined in the laboratory and the genetic correlates of in vitro phenotypes are unclear. Engineered mutations can yield different phenotypic effects when introduced on to different genetic backgrounds, suggesting complex epistasis among polymorphic loci across the genome. By generating a set of recombinants derived from two phenotypically and genotypically distinct parental clones, this work offers an approach to characterize complex genetic correlates of viral phenotypes, which in turn may enhance efforts to link genomics data with in vivo viral behavior and clinical outcomes.

microbiology↗

bioRxiv2025

Therapeutic delivery of albumin-binding siRNA targeting IRS2 to diverse cell types reduces mammary tumor growth

Oligonucleotide therapeutics are a new class of drugs that enable robust and sustained modulation of gene expression. However, achieving efficient delivery of siRNAs to tumors is a challenge for therapy. Here, we demonstrate that fully chemically modified siRNAs conjugated with an albumin-binding dendrimer are efficiently delivered to both neoplastic and stromal/immune cells within primary TNBC mammary tumors. siRNAs were designed to selectively target IRS2, a signaling adaptor of insulin and insulin-like growth factor signaling that has been implicated in aggressive breast cancers. These siRNAs reduced Irs2 expression in tumor and stromal cells without causing hyperglycemia, resulting in reduced tumor growth that was associated with decreased vascularization and alterations in macrophage polarization and the expression of EMT proteins. This work demonstrates that siRNAs can be delivered to neoplastic and specific stromal populations in mammary tumors and that they can effectively and specifically silence a driver of aggressive breast cancer.

cancer biology↗

bioRxiv2025

Acute cold exposure in humans shifts the circulating proteome to a cardioprotective and anti-aging profile

Cold exposure has been proposed to provide a constellation of salutary effects, yet its molecular correlates remain largely unknown. Brown adipose tissue (BAT) is the main site of adaptive thermogenesis, and its prevalence is linked with cardiometabolic health. Since the benefits of BAT activation and cold exposure more generally may be mediated through blood-borne factors, we conducted an extensive analysis of the circulating proteome linked with an acute cold challenge in healthy adults. Our goal was to uncover early molecular changes triggered by cooling and establish their specific relationships with the human brown adipocyte secretome as well as various phenotypic traits. Based on comprehensive inter-cohort validations, we provide the first reproducible proteomic signature of cold exposure in humans. Our data demonstrate that cooling favorably modulates circulating mediators linked with chronological aging, as well as metabolic and cardiovascular diseases, providing new potential biochemical transducers of the benefits associated with cold therapy. HighlightsO_LICooling alters the plasma proteome with striking concordance in independent human cohorts. C_LIO_LICooling represses circulating proteins linked with type 2 diabetes, hypercholesterolemia, hypertension, coronary heart disease and heart failure. C_LIO_LIThe circulating signature of cooling resembles a cardioprotective and anti-aging profile. C_LI

physiology↗

bioRxiv2025

Apparent cooperativity between human CMV virions introduces errors in conventional methods of calculating multiplicity of infection

Whether infection of cells by individual virions occurs randomly or if there is some form(s) of competition or cooperativity between individual virions remains largely unknown for most virus-cell associations. Here we studied cooperativity/competition for three different strains of human cytomegalovirus (HCMV) on two different cell types (fibroblasts and epithelial cells). By titrating viral inocula concentrations in small steps over several orders of magnitude, and by using flow cytometry to precisely measure frequency of infected cells, we found that for most virus-cell associations, the frequency of cell infection increases faster than linear with an increasing inoculum concentration, indicating cooperativity between individual infecting virions. Mathematical modeling suggests that this apparent cooperativity cannot be explained by heterogeneity in either the infectivity of the individual virions or the resistance of individual cells to infection, or by simple aggregation/clumping of viral particles. Stochastic simulations of two additional alternative models that allow for i) reduction in cell resistance to infection when exposed to multiple virions, or ii) compensation in infectivity of poorly infectious virions when coinfecting cells with more infectious virions, resulted in apparent viral cooperativity. Analysis of other published datasets suggests presence of apparent viral cooperativity for HIV and vaccinia virus, infecting CRFK or HeLa cells, respectively, but not for tobacco mosaic virus forming plaques on plant leaves. We thus 1) propose a methodology to rigorously evaluate apparent cooperativity of viruses infecting target cells, and 2) demonstrate that knowing the degree of virus cooperativity for any given virus-cell combination is important for an accurate quantification of multiplicity of infection (MOI). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/650360v2_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@f4de20org.highwire.dtl.DTLVardef@2342dcorg.highwire.dtl.DTLVardef@fab722org.highwire.dtl.DTLVardef@d43bd_HPS_FORMAT_FIGEXP M_FIG C_FIG Infection Unit per cell (IU/Cell) and specific infectivity (Genome/IU) of human cytomegalovirus depend on the infecting dose (Genome/Cell). The data are for HCMV-TB infecting fibroblasts.

microbiology↗

bioRxiv2024

Pushing the Isotopic Envelope: When carrier channels pollute their neighbors signals

Individual cells are the foundational unit of biology, and understanding their functions and interactions is critical to advancing our understanding of health and disease. Single cell proteomics has seen intense interest from mass spectrometrists, with a goal of quantifying the proteome of single cells by adapting current techniques used in bulk samples. To date, most method optimizations research has worked towards increasing the proteome coverage of single cells. One prominent technique multiplexes many individual cells into a single data acquisition event using isobaric labels. Accompanying the single cells, one label is typically used for a mixed set of many cells, called a carrier or boost channel. Although this improves peptide identification rates, several groups have examined the impact on quantitative accuracy as more cells are included in the carrier channel, e.g. 100x or 500x. This manuscript explores how impurities in the multiplexing reagent can lead to inaccurate quantification observed as a measurable signal in the wrong channel. We discover that the severe abundance differential between carrier and single cell, combined with the reagent impurities, can overshadow several channels typically used for single cells. For carrier amounts 100x and above, this contamination can be as abundant as true signal from a single cell. Therefore, we suggest limiting the carrier channel to a minimal amount and balance the goals of identification and quantification.

bioinformatics↗

bioRxiv2023

T-cell commitment inheritance - an agent-based multi-scale model

T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations showed that the commitment is a three-step process over several cell generations where a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function two to three generations later which is when the decision to commit is taken. Finally, after another one to two generations, the cell becomes committed by transitioning to the DN2b state. Our results showed that there is inheritance in the commitment mechanism.

systems biology↗

bioRxiv2023

Sex differences in pharmacokinetics, central accumulation, and behavioural effects of oral cannabis consumption in male and female C57BL/6 mice.

BackgroundCannabis edibles are an increasingly popular form of cannabis consumption. Oral consumption of cannabis has distinct physiological and behavioural effects than injection or inhalation. An animal model is needed to understand the pharmacokinetics and physiological effects of oral cannabis consumption in rodents as a model for human cannabis edible use. MethodsAdult male and female C57BL/6 mice received a single dose of commercially available cannabis oil (5 mg/kg THC) by oral gavage. At 0.5-, 1-, 2-, 3-, and 6-hours post-exposure, plasma, hippocampus, and adipose tissue was collected for THC, 11-OH-THC, and THC-COOH measures. ResultsWe report delayed time to peak THC and 11-OH-THC concentrations in plasma, brain and adipose tissue, which is consistent with human pharmacokinetics studies. We also found sex differences in the cannabis tetrad: (1) female mice had a delayed hypothermic effect 6 hours post-consumption, which was not present in males; (2) females had stronger catalepsy than males; (3) males were less mobile following cannabis exposure, whereas female mice showed no difference in locomotion but an anxiogenic effect at 3h post exposure; and (4) male mice displayed a longer lasting antinociceptive effect of oral cannabis. ConclusionsOral cannabis consumption is a translationally relevant form of administration that produces similar physiological effects as injection or vaping administration and thus should be considered as a viable approach for examining the physiological effects of cannabis moving forward. Furthermore, given the strong sex differences in metabolism of oral cannabis, these factors should be carefully considered when designing animal studies on the effects of cannabis. Significance statementOral delivery of cannabis oil in mice is a translational model that increases plasma, hippocampal, and adipose cannabinoids. Furthermore, oral cannabis and produces lasting psychoactive effects including sex dependent effects on hypothermia, cataplexy, locomotor activity and nociception.

pharmacology and toxicology↗

bioRxiv2023

Short- and long-term high-fat diet exposure differentially alters phasic and tonic GABAergic signalling onto lateral orbitofrontal pyramidal neurons

The chronic consumption of caloric dense high-fat foods is a major contributor to increased body weight, obesity, and other chronic health conditions. The orbitofrontal cortex (OFC) is critical in guiding decisions about food intake and is altered with diet-induced obesity. Obese rodents have altered morphological and synaptic electrophysiological properties in the lateral orbitofrontal cortex (lOFC). Yet the time course by which exposure to a high-fat diet (HFD) induces these changes is poorly understood. Here male mice are exposed to either short- (7 day) or long-term (90 day) HFD. Long-term HFD exposure increases body weight, and glucose signaling compared to short-term HFD or a standard chow control diet (SCD). Both short and long-term HFD exposure increased the excitability of lOFC pyramidal neurons. However, phasic and tonic GABAergic signalling was differentially altered depending on HFD exposure length, such that tonic GABAergic signaling was decreased with early exposure to the HFD and phasic signaling was changed with long-term diet exposure. Furthermore, alterations in the short-term diet exposure were transient, as removal of the diet restored electrophysiological characteristics similar to mice fed SCD whereas long-term HFD electrophysiological changes were persistent and remained after HFD removal. Finally, we demonstrate that changes in reward devaluation occur early with diet exposure. Together, these results suggest that the duration of HFD exposure differentially alters lOFC function and provides mechanistic insights into the susceptibility of the OFC to impairments in outcome devaluation. Significant statementThis study provides mechanistic insight on the impact of short- and long-term high fat diet (HFD) exposure on GABAergic function in the lateral orbitofrontal cortex (lOFC), a region known to guide decision making. We find short-term HFD exposure induces transient changes in firing and tonic GABA action on lOFC pyramidal neurons, whereas long-term HFD induces obesity and has lasting changes on firing, tonic GABA and inhibitory synaptic transmission onto lOFC neurons. Given that GABAergic signaling in the lOFC can influence decision making around food, these results have important implications in present society as palatable energy dense foods are abundantly available.

neuroscience↗

bioRxiv2023

Cryo-EM structure of the human Sirtuin 6-nucleosome complex

Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56. TeaserThe structure of the SIRT6 deacetylase/nucleosome complex suggests how the enzyme acts on both histone H3 K9 and K56 residues.

biochemistry↗

bioRxiv2022

Cellular and Fibrillar Collagen Analyses in an Animal Model of Retinal Detachment-Related Proliferative Vitreoretinopathy Reveals a Defined Transition to Chronic Fibrosis

PurposeProliferative vitreoretinopathy (PVR) is the most common cause of failure of surgically repaired rhegmatogenous retinal detachment (RRD). Chemically-induced and cell-injection PVR models do not fully simulate the clinical characteristics of PVR in the post-RRD context. There is an unmet need for translational models in which to study mechanisms and treatments specific to RRD-PVR. MethodsRRD-PVR was induced in adult Dutch Belted rabbits. Posterior segments of enucleated globes were fixed or processed for RNA-Seq at 6 hours and 2, 7, 14, and 35 days post-induction. Histochemical staining and immunolabeling for glial fibrillary acidic protein (GFAP), alpha smooth muscle actin (SMA), vascular endothelial growth factor receptor 2 (VEGFR2), CD68, and retinal pigment epithelium 65 kDa protein (RPE65) were performed, and labeling intensity was scored. Single cell RNA sequencing was performed. ResultsAcute histopathologic changes included intravitreal and intraretinal hemorrhage, leukocytic vitritis, chorioretinitis, and retinal rarefaction. Chronic lesions showed retinal atrophy, gliosis, fibrotic subretinal membranes, and epiretinal fibrovascular proliferation. Fibrillar collagen was present in the fibrocellular and fibrovascular membranes in chronic lesions. Moderate to strong labeling of glia and vasculature was detected in chronic lesions. At day 14, most cells profiled by single cell sequencing were identified as Muller glia and microglia, consistent with immunolabeling. Expression of several fibrillar collagen genes were upregulated in chronic lesions. ConclusionsHistologic and transcriptional features of this rabbit model simulate important features of human RRD-PVR, including the transition to chronic intra and periretinal fibrosis. This high-fidelity in vivo model of RRD-PVR will enable further research on targeted treatment interventions.

pathology↗

bioRxiv2022

Primary cilia regulate Meibomian glands development and dimensions without impairing the lipid composition of the meibum

PurposePrimary cilia regulate the development of various ectoderm-derived tissues, including the corneal epithelium, skin, hair follicle and sebaceous glands. We aimed to investigate their role in meibomian gland (MG) development. MethodsPrimary cilium ablation in MGs was achieved by crossing a floxed Ift88 mouse (Ift88fl/fl) with a mouse expressing the Cre recombinase under the keratin 14 (K14) promoter, to generate K14-Cre;Ift88fl/fl mice. MG morphology was evaluated by histology and immunostaining, as well as lipid staining and 2-photon microscopy on whole mount tarsal plates. MG lipid profiles were assessed by chromatography. ResultsWe showed that most of MG cells are ciliated during early stages of MG development and that MG ciliated rate decreases throughout morphogenesis. In morphologically mature glands, only the MG central duct and ductules are ciliated, and meibocytes lose their cilia as they differentiate and become filled with lipids. Primary cilium ablation induces enlargement of MGs, dilation of the MG central duct, and an increased production of lipids, without dramatically changing the lipid profiles. In addition, primary cilia regulate MG elongation and the spatial distribution of proliferating and dying cells within MGs, without changing the total cell proliferation and death rates. ConclusionsThese findings indicate that primary cilia are not necessary for normal MG development. However, they promote MG enlargement and lipid production, suggesting that primary cilia could be an interesting target for treatments of ocular surface diseases involving MGs, like dry eye disease.

developmental biology↗

bioRxiv2022

Local adaptation and host specificity to copepod intermediate hosts by the Schistocephalus solidus tapeworm

We investigated if there was local adaptation and host specify in the tapeworm Schistocephalus solidus to its copepod first intermediate hosts. The tapeworm is locally adapted and host specific to its threespine stickleback second intermediate host. We exposed copepods from five lakes in Vancouver Island (BC, Canada) to local (i.e. same lake) and foreign tapeworms in a reciprocal exposure experiment. Results indicate that the tapeworm is not locally adapted to the copepods, but there was host specificity as a copepod genus was more parasitized than another genus.

evolutionary biology↗

bioRxiv2021

Single-cell RNA Sequencing Reveals Immunosuppressive Myeloid Cell Diversity and Restricted Cytotoxic Effector Cell Trafficking and Activation During Malignant Progression in Glioma

Low grade gliomas (LGG) account for about two-thirds of all glioma diagnoses in adolescents and young adults (AYA) and malignant progression of these patients leads to dismal outcomes. Recent studies have shown the importance of the dynamic tumor microenvironment in high-grade gliomas (HGG), yet its role is still poorly understood in low-grade glioma malignant progression. Here, we investigated the heterogeneity of the immune microenvironment using a platelet-derived growth factor (PDGF)-driven RCAS (replication-competent ASLV long terminal repeat with a splice acceptor) glioma model that recapitulates the malignant progression of low to high-grade glioma in humans and also provides a model system to characterize immune cell trafficking and evolution. To illuminate changes in the immune cell landscape during tumor progression, we performed single-cell RNA sequencing on immune cells isolated from animals bearing no tumor (NT), LGG and HGG, with a particular focus on the myeloid cell compartment, which is known to mediate glioma immunosuppression. LGGs demonstrated significantly increased infiltrating T cells, CD4 T cells, CD8 T cells, B cells, and natural killer cells in the tumor microenvironment, whereas HGGs significantly abrogated this infiltration. Our study identified two distinct macrophage clusters in the tumor microenvironment; one cluster appeared to be bone marrow-derived while another was defined by overexpression of Trem2, a marker of tumor associated macrophages. Our data demonstrates that these two distinct macrophage clusters show an immune-activated phenotype (Stat1, Tnf, Cxcl9 and Cxcl10) in LGG which evolves to an immunosuppressive state (Lgals3, Apoc1 and Id2) in HGG that restricts T cell recruitment and activation. We identified CD74 and macrophage migration inhibition factor (MIF) as potential targets for these distinct macrophage populations. Interestingly, these results were mirrored by our analysis of the TCGA dataset, which demonstrated a statistically significant association between CD74 overexpression and decreased overall survival in AYA patients with grade II gliomas. Targeting immunosuppressive myeloid cells and intra-tumoral macrophages within this therapeutic window may ameliorate mechanisms associated with immunosuppression before and during malignant progression.

cancer biology↗

bioRxiv2021

Performance Determinants of Unsupervised Clustering Methods for Microbiome Data

BackgroundIn microbiome data analysis, unsupervised clustering is often used to identify naturally occurring clusters, which can then be assessed for associations with characteristics of interest. In this work, we systematically compared beta diversity and clustering methods commonly used in microbiome analyses. We applied these to four published datasets where highly distinct microbiome profiles could be seen between sample groups. ResultsAlthough no single method outperformed the others consistently, we did identify key scenarios where certain methods can underperform. Specifically, the Bray Curtis metric resulted in poor clustering in a dataset where high-abundance OTUs were relatively rare. In contrast, the unweighted UniFrac metric clustered poorly when used on a dataset with a high prevalence of low-abundance OTUs. To test our proposition, we systematically modified properties of the poorly performing datasets and found that this approach resulted in improved Bray Curtis and unweighted UniFrac performance. Based on these observations, we rationally combined the Bray Curtis metric and the unweighted UniFrac metrics and found that this new beta diversity metric showed high performance across all datasets. We also evaluated our findings by examining a clinical dataset where clusters are less separated. ConclusionsOur systematic evaluation of clustering performance in these five datasets demonstrates that there is no existing clustering method that universally performs best across all datasets. We propose a combined metric of Bray Curtis and unweighted UniFrac that capitalizes on the complementary strengths of the two metrics.

microbiology↗

bioRxiv2020

Optimization of SARS-CoV-2 detection by RT-QPCR without RNA extraction

Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study we evaluated the reliability and the efficiency of a direct RT-QPCR method (without RNA extraction) using SeeGene Allplex 2019-nCoV RT-QPCR and the influence of swab storage media composition on further viral detection. We show that SeeGenes assay provides similar efficiency as the RealStar(R) SARS-CoV-2 RT-PCR kit (Altona Diagnostics), and that RNA extraction is not necessary nor advantageous if samples are stored in UTM or molecular water but is recommended if samples are stored in saline solution and in Hanks medium.

molecular biology↗