Biology subjects

Roberts, A.

Publications and source records attributed to Roberts, A..

At least 19 recordsLinked to original sources

bioRxiv2026

How body size and microclimate determine when solar absorptivity matters for insect body temperature

1. The net effect of solar absorption on body temperature is difficult to intuit because it depends on nonlinear interactions between the traits of organisms and their immediate environment. 2. We used biophysical modelling to quantify solar absorption effects for Australian jewel beetles across their wide natural range of solar absorptivity (0.67-0.93), mass (more than 2 orders of magnitude) and shape under naturally co-occurring combinations of microclimatic conditions across Australia. 3. Under hot, calm conditions, solar absorptivity could increase steady-state body temperature by 2.3{degrees}C on average. Higher wind reduced this effect by more than half, whereas increasing shortwave radiation amplified it. Transient simulations indicated substantial damping of these effects at a time scale of one minute. 4. Across daylight hours during the spring-early summer period when adult jewel beetles are active, the absorptivity effect averaged 0.36{degrees}C across Australia. Under locally extreme high-radiation, low-wind conditions, the effect reached 5.69{degrees}C in the largest beetles and was more than twice as large at maximum as at minimum body mass. 5. Whether solar absorptivity is of biological significance to heat budgets is therefore highly contextual. Experiments to infer the adaptive significance of insect colour for heat budgets should account for transient responses under realistic environmental combinations.

ecology↗

bioRxiv2026

Targeting the APRIL-BAFF axis in IgA nephropathy: preclinical insights from influenza challenge and single-cell spatial profiling

BackgroundAPRIL and BAFF are TNF superfamily cytokines that regulate B-cell development, survival, and antibody production, and are emerging therapeutic targets for IgA nephropathy (IgAN). Selective APRIL and dual APRIL/BAFF inhibitors both reduce IgA and proteinuria in IgAN clinical trials, but whether their broader immunological consequences differ has not been systematically characterized. MethodsWe compared selective APRIL and dual APRIL/BAFF inhibition using influenza vaccination and lethal challenge, KLH immunization, serological profiling, and flow cytometry in mice, alongside human B-cell survival assays in vitro. Single-cell CITE-seq and in situ spatial transcriptomics were applied to characterize molecular and tissue-level changes in the spleen. ResultsBoth modes of inhibition reduced serum IgA by [≥]60% in mice. However, dual APRIL/BAFF inhibition nearly abolished vaccine-mediated protection against lethal influenza challenge (10% versus 70% survival in controls; p < 0.01), whereas selective APRIL inhibition had limited impact on protective immunity. This functional divergence was underpinned by broad cellular disruption under dual blockade, including >80% depletion of splenic B cells, loss of T follicular helper cells, and impaired antigen-specific IgM and IgG responses. Selective APRIL inhibition left these populations and responses largely intact. Consistent with these findings, human B-cell survival in vitro was dependent on BAFF, not APRIL. Single-cell and spatial transcriptomics revealed that dual blockade collapsed follicular architecture, eliminated germinal centers, and disrupted chemokine organization, whereas these structures remained intact under selective APRIL inhibition. At the molecular level, dual blockade, but not selective APRIL inhibition, downregulated NF-{kappa}B survival signaling and antigen presentation programs and shifted surviving germinal center B cells toward a pro-apoptotic state. ConclusionsSelective APRIL and dual APRIL/BAFF inhibition both reduce IgA, the pathologically relevant isotype in IgAN, but only dual blockade disrupts B-cell maturation, germinal center function, tissue architecture, and protective immunity. These findings inform the benefit-risk assessment of chronic B cell-targeting therapies in IgAN.

immunology↗

bioRxiv2025

Distinct cellular and transcriptional mechanisms mediate an antioxidant therapeutic response in 22q11-deleted upper layer cortical projection neurons

We characterized cellular and molecular mechanisms underlying the therapeutic response in vitro and in vivo to the antioxidant N-acetyl cysteine (NAC), which in the LgDel 22q11.2 Deletion Syndrome mouse model restores growth and connectivity of upper layer cortical projection neurons (Layer 2/3 PNs) and improves cognitive performance. NAC treatment of primary cultured LgDel L 2/3 PNs does not restore these neurons to a wild type (WT) state. Rather than returning to the bimodal dendrite and axon size distribution seen in WT, LgDel L 2/3 PN dendrite and axon growth in vitro increases unimodally in response to NAC. In parallel, altered expression of 22q11-deleted genes and presumed downstream targets are unchanged. Instead, novel antioxidant defense and neuronal growth genes are differentially expressed: some generally NAC-regulated, others responsive only in the context of 22q11 deletion. Apparently, NAC ameliorates L 2/3 PN developmental pathology without restoring WT cell states or typical expression of mutant genes or their downstream targets. NAC also elicits differential expression of antioxidant defense genes in 22q11-deleted L 2/3 PNs--but not L 5/6 counterparts--in the developing postnatal LgDel mouse cortex, rather than modulating 22q11 genes or downstream targets. These NAC-dependent, L 2/3 PN-selective in vivo cellular and transcriptional changes differ substantially from those in primary culture. Thus, despite some in vitro and in vivo parallels, the NAC therapeutic response that diminishes oxidative stress-related L 2/3 PN circuit and behavioral pathology due to 22q11 deletion has a unique in vivo signature.

neuroscience↗

bioRxiv2025

Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies

BackgroundMajor depressive disorder (MDD), bipolar disorder (BP), and schizophrenia (SCZ) involve learning impairments with poorly understood mechanisms. Understanding both the similarities and differences in these mechanisms is important to guide the development of new, targeted interventions. Methods255 participants diagnosed with MDD (n=54), BP (n=47), SCZ (n=67) or without any diagnoses (CTRL; n=87) performed an associative learning task. Computational modeling quantified the mechanistic interplay between working memory (WM) and reinforcement learning (RL). The latent RL and WM signatures in the EEG dynamics showed shared and distinct neurocognitive mechanisms underlying learning. ResultsAll clinical groups showed learning impairments at the behavioral level. Model-based EEG analyses linked these impairments to distinct patterns in the dynamic interplay between latent RL and WM mechanisms, contrasting with the typical patterns observed in CTRL. SCZ was characterized by reduced neural markers of WM, weakening the cooperative influence of WM onto RL (reduced WM recruitment), and reduced integration of negative feedback. Conversely, MDD was characterized by reduced reciprocal influence of RL onto WM, reducing the tendency to upregulate WM contribution with reward history (impaired WM management). Finally, BP was characterized by deficits in both WM and RL recruitment, along with higher WM decay. ConclusionsBehavioral learning impairments that appear similar across clinical groups can be linked to distinct neurocognitive mechanisms via integrative neurocomputational modeling. Our approach provides insights into the interplay of underlying learning mechanisms and how they manifest differently across psychopathologies. CitationThis manuscript is a preprint version of the later manuscript accepted for publication in Biological Psychiatry: Global Open Science. The content may differ from the final published version following peer review and editorial revisions. Ging-Jehli, N.R., Rac-Lubashevsky, R., Bera, K., Roberts, A., Loder, A., Boudewyn, M.A., Carter, C.S., Erickson, M., Gold, J., Luck, S.J., Ragland, J.D., Yonelinas, A.P., MacDonald III, A.W., Barch, D.M., & Frank, M.J. (2025). Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies. Preprint at bioRxiv.

pathology↗

bioRxiv2025

Mouse Models Uniformly Featuring Human-like Lesions Harboring Drug-tolerant Mycobacterium tuberculosis

Mouse models have been key to studies of tuberculosis pathogenesis and drug efficacy, but many, such as those employing BALB/c mice, fail to reproduce the full range of heterogenous microniches observed in well-structured human lesions, which feature hypoxic caseous cores of necrotic debris surrounded by infected foamy macrophages. The granuloma presents a variety of environments differing in levels of oxygen, ions, nutrients, and intra versus extracellular residence, which determine the physiological state of the infecting bacillus and its susceptibility to immune or drug control. Recently, alternative mouse strains such as C3HeB/FeJ have allowed the study of infection and treatment in the context of these varied environments but exhibit substantial inconsistency in development of human-like lesions, both within and between individual mice. Building on the observation that inducible nitric oxide synthase (Nos2)-deficient mice consistently develop hypoxic necrotic lesions, we have established two simplified models with infection by the aerosol route. The first uses the slightly attenuated M. tuberculosis R1Rv strain, which produces a progressive infection that is contained at a high stable burden by an adaptive immune response. In the second model, vaccination with the attenuated {Delta}RD1, pantothenate auxotroph mc2 6230 protects from an otherwise lethal infection with virulent M. tuberculosis Erdman. This model reflects most contemporary tuberculosis infections, which take place in the context of a pre-existing immune response from vaccination. Both variations uniformly develop well-structured hypoxic necrotic lesions harboring drug tolerant bacteria. These refined models will be useful in studies of M. tuberculosis infection and treatment.

microbiology↗

bioRxiv2025

Cortical myelination networks reflect neuronal gene expression and track adolescent age in marmosets

Structural similarity provides a powerful framework for measuring coordinated macro- and microstructural variation across the cortex of a single brain. Similarity networks derived from myelin-sensitive MRI sequences undergo marked reorganisation during adolescence, linked to psychosocial outcomes in humans and rodents. However, the cellular mechanisms of myelination similarity and its development in non-human primate cortex remain unexplored. Here, we used myelin-sensitive T1w/T2w ratio images from a cross-sectional sample of 446 common marmosets (aged 0.62 to 12.75 years) to estimate cortical similarity networks in individual animals. Cortical areas with similar myeloarchitecture showed highly similar patterns of gene co-expression in glutamatergic neurons and PV+ and VIP+ interneurons, reflecting the activity dependence of myelination. A reliable age-based signal exists within network features, with coordinated developmental trajectories observed across the cortical hierarchy from primary to transmodal association cortices - a pattern that mirrors findings in human cortex. Taken together, marmosets demonstrate phylogenetically conserved patterns of myelination network development, potentially underpinned by key neuronal cell types that shape the functional specialisation of cortical areas.

neuroscience↗

bioRxiv2025

Evidence of ecosystem process recovery across a large-scale coral reef restoration programme using AI accelerated soundscape analysis

1.Coral reef restoration efforts are on the increase globally. However, reporting on the ecological outcomes of these efforts is rare and typically focuses on coral related metrics. As a result, understanding of whether restoration can recover broader aspects of reef functioning remains limited. In this study we use passive acoustic monitoring coupled with human-in-the-loop artificial intelligence to analyse >12 months of soundscape recordings from 45 sites across five biogeographically independent regions to investigate the impact of active restoration on reef functioning. We trained and rigorously evaluated machine learning models to identify 34 biological sound types within this data, generating >912,000 high-confidence detections. These detections were used to infer four key functions across healthy, degraded, early-stage (<3 months) and mid-stage (32-53 months) restored reefs. Restoration significantly enhanced: (i) biological sounds at night, key to recruiting juvenile fish; (ii) diversity of biological sounds, an indicator of fish community diversity; and (iii) snapping shrimp activity, an indicator of bioturbation. However, effects varied by region, and audible parrotfish grazing, key to algal control and bioerosion, did not differ among habitat types in four of the five regions. Our findings provide evidence that restoration can support recovery of broader ecosystem functioning when carefully implemented in the right contexts. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/678197v4_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@7d5462org.highwire.dtl.DTLVardef@2efa7dorg.highwire.dtl.DTLVardef@3f4b9eorg.highwire.dtl.DTLVardef@17d829c_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Hypoxia-induced metastatic heterogeneity in pancreatic cancer

In most solid tumors, hypoxia constitutes a defining microenvironmental feature that reprograms malignant cells into a highly metastatic state by driving cellular plasticity and exacerbating chromosomal instability (CIN). However, the mechanisms by which cancer cells concurrently co-opt these elements of hypoxic adaptation to promote metastasis remains poorly understood. Here, we report that hypoxia promotes metastasis by suppressing the JmjC-containing histone lysine demethylase Kdm8. CRISPR/Cas9-mediated targeting of Kdm8 in a Kras;Trp53-driven mouse model of pancreatic ductal adenocarcinoma (PDA) robustly rewires the malignant cell transcriptomic programs, leading to a profound loss of the epithelial morphology and widespread metastatic disease. In PDA patients, a high KDM8-induced gene signature is associated with reduced metastatic burden and better survival in advanced disease. Notably, Kdm8 suppression in normoxia recapitulates key aspects of the global epigenetic and transcriptomic rewiring, mitotic spindle defects, and CIN induced by hypoxia. Moreover, disruption of Kdm8s demethylase activity phenocopies Kdm8 loss, whereas expression of hypermorphic Kdm8 variants resistant to hypoxic suppression markedly reduces metastasis beyond the levels achieved by the wildtype protein. Through the suppression of Kdm8 demethylase function, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and CIN.

cell biology↗

bioRxiv2025

The microbial tryptophan metabolite indole acts on the gastrointestinal tract to improve glucose homeostasis by enhancing GLP-1 secretion and L-cell differentiation

Aims/hypothesisGrowing evidence implicates gut microbiota-derived metabolites in metabolic homeostasis. Indole, a microbial tryptophan metabolite, has been reported to enhance Glucagon-like peptide-1 (GLP-1) secretion in vitro, and its derivatives have been inversely associated with risk of type 2 diabetes (T2D). We hypothesised that indole acts via the gastrointestinal tract to modulate glucose homeostasis, and aimed to test this hypothesis using in vitro and in vivo models. MethodsThe acute effects of indole on GLP-1 secretion in vitro, and on glucose tolerance and hormone secretion in mice, were determined. Subsequently, the effects of indole on intestinal epithelial cell fate and L-cell differentiation in murine ileal organoids and in vivo were studied. Finally, the utility of chronic indole administration in a murine model of T2D was explored. ResultsIndole stimulated in vitro GLP-1 secretion in a concentration-dependent manner, and improved acute glucose control in vivo. Additionally, we demonstrate that indole drives enteroendocrine L-cell differentiation in murine ileal organoids, resulting in increased L-cell density and longer-term glucoregulatory benefits in vivo. Finally, sub-chronic indole administration improved glucose tolerance and insulin sensitivity in diabetic mice. Conclusions/interpretationOur findings identify indole as an anti-diabetic molecule that acts on the gut, and raise the possibility of incorporating indole into nutraceutical supplements to aid in the treatment or prevention of T2D. This highlights the importance of gut microbiota-derived metabolites in metabolic health and opens new avenues for developing novel strategies to combat T2D. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIGut microbiota-derived metabolites play a role in metabolic homeostasis. C_LIO_LIIndole, a microbial tryptophan metabolite, enhances GLP-1 secretion in vitro. C_LIO_LIIndole derivatives are inversely associated with type 2 diabetes (T2D) risk. C_LI What is the key question?O_LIDoes indole act on the gut to modulate glucose homeostasis? C_LI What are the new findings?O_LIIndole stimulates GLP-1 secretion and improves acute glucose control in vivo. C_LIO_LIIndole drives enteroendocrine L-cell differentiation in murine ileal organoids, increasing L-cell density and long-term glucoregulatory benefits. C_LIO_LISub-chronic indole administration improves glucose tolerance and insulin sensitivity in mice with type 2 diabetes, showing the potential of gut microbiota-derived metabolites as therapeutic targets. C_LI How might this impact clinical practice in the foreseeable future?O_LIIndole could be incorporated into nutraceutical supplements for T2D prevention or treatment. C_LI

physiology↗

bioRxiv2025

Accumulation of SA-βGal High Cells in Human Naive T Cell Compartments Reveals a Stress-Adapted, Senescent-Like State

Aging is associated with a decline in immune function termed immunosenescence, characterized by accumulation of senescent-like immune cells and chronic inflammation, known as inflammaging. While senescence-associated {beta}-galactosidase (SA-{beta}Gal) activity is a well-established senescence marker, its functional significance and the precise cellular subsets affected within the T cell compartment remain unclear. Here, we identify and characterize a previously unrecognized subset of naive CD4 and CD8 T cells displaying high SA-{beta}Gal activity that significantly increases with age. Despite exhibiting hallmark features of senescence such as DNA damage, nuclear envelope disruption, loss of heterochromatin, and pronounced dysregulation of autophagy and lysosomal pathways, these SA-{beta}Gal-high naive T cells notably lack the canonical senescence marker p21CIP1 and retain robust proliferative capacity upon activation. Remarkably, naive CD4 SA-{beta}Gal-high T cells acquire cytotoxic properties including NK-like features, granzyme secretion, and the ability to induce paracrine DNA damage in endothelial cells. Mechanistically, we demonstrate that impaired autophagic flux contributes significantly to this phenotype. Our findings address critical knowledge gaps regarding the nature and functional plasticity of senescence-like states in naive T cells, highlighting a novel link between lysosomal-autophagic dysfunction, cellular stress adaptation, and inflammaging. Understanding this unique T cell population provides important insights into immune aging and offers potential targets to mitigate age-associated immune dysfunction and chronic inflammation.

immunology↗

bioRxiv2025

Benchmarking Genomic Variant Calling Tools in Inbred Mouse Strains: Recommendations and Considerations

With the growing affordability of whole genome sequencing, variant identification has become an increasingly common task, but there are many challenges due to both technical and biological factors. In recent years, the number of software packages available for variant calling has rapidly increased. Understanding the benefits and drawbacks of different tools is important in setting leading practices and highlighting limitations. These considerations are crucial in model organism research, as many variant calling programs assume outbred genomes and implicit heterozygosity, which may not apply to inbred laboratory models. Here, we present an analysis of variant calling tools and their performance in the simulated genomes of the C57BL/6J inbred laboratory mouse and nine non-reference laboratory strains. Our findings reveal a tradeoff between the recall and precision of tools. Balancing these considerations, we show that an optimal call set is obtained by using an ensemble approach, but specific variant calling recommendations vary by strain and analytical goals. Further, we highlight filters improving the performance of different variant calling tools, both for the discovery of rare variants and in the discovery of strain polymorphisms. In summary, our work provides best practices for calling and filtering genomic variants in inbred organisms, particularly laboratory mice. Article SummaryIdentifying mutations and rare genetic variants is a central task for modern genomics. Many computational tools exist for variant detection, but their performance varies across diverse applications. Further, few variant calling tools have been benchmarked against inbred genomes, which are commonly used for research. To address this, we evaluated five variant calling tools using simulated data from ten diverse inbred mouse strains. We show that variant detection, recall, and precision vary across tools and mouse strains, and that an ensemble approach improves confidence in detected mutations. Our findings offer a set of best practices for variant calling in inbred organisms across diverse analytical applications.

bioinformatics↗

bioRxiv2025

Multiplexed Targeted Spatial Mass Spectrometry Imaging Assays to monitor lipids and NAD+ metabolites in CD38 knockout mice exhibiting improved metabolism.

Mass spectrometry imaging (MSI) is a rapidly advancing technology that provides mapping of the spatial molecular landscape of tissues for a variety of analytes. Matrix-assisted laser desorption/ionization (MALDI)-MSI is commonly employed, however, confident in situ identification and accurate quantification of analytes remain challenging. We present a novel imaging methodology combining trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) with MALDI ionization for targeted imaging parallel reaction monitoring (iprm-PASEF). We investigated the spatial distribution of lipids and metabolites in liver tissues from male wild-type and CD38 knockout mice (CD38-/-). CD38, an enzyme involved in nicotinamide adenine dinucleotide (NAD) metabolism, significantly influences liver metabolic function and contributes to age-related NAD decline. Although CD38 deletion previously was linked to improved metabolic phenotypes, the underlying spatial metabolic mechanisms are poorly understood. The spatial iprm-PASEF workflow enabled confident identification and differentiation of lipid isomers at the MS2 fragment ion level and confirmed increased NAD+ and decreased adenosine diphosphate ribose (ADPR), a by-product of NAD+ hydrolysis, in CD38-/- livers. This approach provided confident, specific, and robust MS2-based identification and quantification of fragment ions in spatial MSI experiments. Additionally, the innovative iprm-PASEF opens unprecedented opportunities for spatial metabolomics and lipidomics, offering spatially resolved insights into molecular mechanisms.

cell biology↗

bioRxiv2025

Prex1 controls glucose homeostasis by limiting glucose uptake and mitochondrial metabolism in liver through GEF-independent regulation of Gpr21

We investigated the roles of Rac guanine-nucleotide factor (Rac-GEF) Prex1 in glucose homeostasis using Prex1-/- and catalytically-inactive Prex1GD mice. Prex1 maintains fasting blood glucose levels and insulin sensitivity through its Rac-GEF activity but limits glucose clearance independently of its catalytic activity, throughout ageing. Prex1-/-mice on high-fat diet are protected from developing diabetes. The increased glucose clearance in Prex1-/- mice stems from constitutively enhanced hepatic glucose uptake. Prex1 limits Glut2 surface levels, mitochondrial membrane potential and mitochondrial ATP production, and controls mitochondrial morphology in hepatocytes, independently of its catalytic activity. Prex1 limits GPCR trafficking through an adaptor function, and we identify here the inhibitory orphan GPCR Gpr21 as a Prex1 target. The Gpr21-mediated blockade of glucose uptake and mitochondrial ATP production in hepatocytes requires Prex1. We propose that Prex1 limits glucose clearance by maintaining Gpr21 at the hepatocyte surface, thus limiting hepatic glucose uptake and metabolism. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/648781v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@110e660org.highwire.dtl.DTLVardef@84c0c3org.highwire.dtl.DTLVardef@18b8319org.highwire.dtl.DTLVardef@4bfde0_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Biological Drivers of Early Childhood Caries in Preschool Children of Northern Arizona and Hawaii

Early childhood caries (ECC) is the most prevalent chronic childhood disease, disproportionately affecting children from specific racial/ethnic groups. While ECC is a multifactorial disease influenced by demographic, behavioral, and environmental factors, it is also widely associated with the presence of Streptococcus mutans in the oral microbiome. To better understand the interplay between demographic and microbial factors and ECC risk, we collected saliva samples from 408 preschool children aged 1-6 years, including 266 from northern Arizona and 142 from Hawaii, representing racially and geographically diverse populations. Logistic regression showed that the odds of developing ECC increased 80.09% with each year of age, and that compared to White children, the odds were significantly higher for Native Hawaiian/Pacific Islander (330.94%), Native American (282.35%), and Hispanic (245.22%) children. Oral S. mutans colonization increased odds by 360.49%. The S. mutans-positive samples were genotyped using a multiplexed targeted amplicon sequencing assay. Phylogenetic analysis showed high genetic diversity in S. mutans between and within populations, with no geographic clustering. Some S. mutans clades were associated with up to a 33-fold increase in ECC odds. Only Native Hawaiian/Pacific Islander children were more likely to carry S. mutans strains from higher-risk clades. Markers associated with high risk S. mutans strains were identified in genes involved in carbohydrate metabolism, pH regulation, and biofilm formation. This study underscores the multifaceted nature of ECC, linking demographic disparities with strain-specific features of S. mutans and identifies new genetic markers that may play a role in S. mutans virulence.

microbiology↗

bioRxiv2024

Longitudinal prevalence and co-carriage of pathogens associated with nursing home acquired pneumonia in three long-term care facilities

Nursing home acquired pneumonia (NHAP), and its subset - aspiration-associated pneumonia, is a leading cause of morbidity and mortality among residents in long-term care facilities (LTCFs). Understanding colonization dynamics of respiratory pathogens in LTCF residents is essential for effective infection control. This study examines the longitudinal trends in prevalence, persistence, bacterial load, and co-colonization patterns of five respiratory pathogens in three LTCFs in Phoenix, Arizona. Anterior nares and oral swabs were collected every other week and tested using qPCR for Haemophilus influenzae, Pseudomonas aeruginosa, Streptococcus pneumoniae, Staphylococcus aureus, and Chlamydia pneumoniae. Weekly average positivity rates were 17.75% for H. influenzae (0% - 39.39%), 9.95% for P. aeruginosa (0% - 37.74%), 31.89% for S. pneumoniae (1.79% - 41.67%), and for 28.00% for S. aureus (0% - 55.36%). C. pneumoniae was not detected. H. influenzae and S. pneumoniae predominantly colonized the oral cavity, while P. aeruginosa and S. aureus predominantly colonized the nasal cavity. S. pneumoniae and S. aureus colonizations were significantly more persistent than H. influenzae and P. aeruginosa, with persistence correlating with significantly higher bacterial loads. Co-colonization did occur in [~]20% of positive samples, but appeared to be due to random chance. This study reveals distinct colonization patterns among respiratory pathogens in LTCF residents, highlighting differences in site-specific prevalence, persistence, and bacterial load. These findings underscore the importance of longitudinal monitoring to inform targeted infection control strategies in LTCFs.

microbiology↗

bioRxiv2024

High-throughput targeted amplicon screening tool for characterizing intrahost diversity in Staphylococcus aureus directly from sample

A significant proportion of people are asymptomatic carriers of Staphylococcus aureus (SA), an important risk factor for development of opportunistic infections. SA colonization is dynamic, appearing and disappearing, with strains evolving and potentially shifting in composition over time and between body sites. These changes make detection challenging and the numerous potential sources of reintroduction from other people and even other body site reservoirs preclude efficient efforts to prevent transmission and spread. Identifying typical sources is therefore critical for mitigation. Whole-genome sequencing (WGS), ideally of multiple colonies from multiple body sites, is the gold standard for characterizing SA strains and confirming transmission. However, this is often too resource-intensive for initial assessments of transmission and not feasible for large-scale studies involving various body sites from multiple individuals over time. To address these challenges, we developed a low-cost, custom, species-specific amplicon sequencing (AmpSeq) assay, optimized to provide high resolution discrimination of SA genotypes directly from samples. We tested this approach on a subset of samples that were a part of a large-scale longitudinal study of SA carriage. Oral and nasal samples were collected from 9 participants every two weeks for up to 18 weeks and qPCR positive samples were analyzed using our AmpSeq assay directly from the sample without culturing. The longitudinal sampling strategy enabled us to characterize changes in SA colonization patterns over time, detect potential strain mixtures, and identify rare variants that may serve as signatures of transmission between different body sites or among individuals. Without using WGS, we were able to rapidly eliminate the possibility of transmission between sampled residents. Participants that had positive oral and nasal samples had no fixed SNP differences between the two body sites, suggesting likely within-person spread. In these cases, we were able to infer the most likely direction of spread (nasal to oral sites) by analyzing segregating rare variants. While WGS can be used to provide higher resolution to colonization patterns and validate these findings, our amplicon sequencing approach offers a rapid, cost-effective, direct-from-sample method for species-specific screening intended for population-level characterization that allows researchers to characterize strain types, identify or eliminate likely transmission cases, and identify potential reservoirs before resorting to more expensive WGS methods. Authors summaryColonizing opportunistic pathogens like Staphylococcus aureus present a unique challenge for disease study because rather than causing acute infections upon transmission, they persist asymptomatically for long periods of time allowing the bacterial population to evolve and differentiate. Characterizing the diversity within these populations is important for choosing correct treatments, quantifying the risk of horizontal gene transfer, and understanding paths of transmission between people and spread to different body sites. The gold-standard approach for characterizing population diversity is through culturing and whole-genome sequencing of multiple colonies per sample which is labor-intensive and expensive for any large-scale study. Using a custom-designed species-specific amplicon sequencing assay, we offer a cost-effective method for characterizing the diversity in Staphylococcus aureus populations directly from samples without the need for labor-intensive culturing or whole-genome sequencing. Our small-scale study highlights how this method provides a scalable tool for large epidemiological studies ideal for systematically exploring broader patterns of carriage and transmission.

genomics↗

bioRxiv2024

Longitudinal evidence for the emergence of multiple intelligences in assistance dog puppies

Cognitive test batteries suggest that adult dogs have different types of cognitive abilities that vary independently. In the current study, we tested puppies repeatedly over a crucial period of development to explore the timing and rate at which these different cognitive skills develop. Service dog puppies (n = 113), raised using two different socialization strategies, were either tested longitudinally (n =91) or at a single time point (n = 22). Subjects tested longitudinally participated in the battery every two weeks during and just beyond their final period of rapid brain growth (from approximately 8-20 weeks of age). Control puppies only participated in the test battery once, which allowed us to evaluate the impact of repeated testing. In support of the multiple intelligences hypothesis (MIH), cognitive skills emerged at different points across the testing period, not simultaneously. Maturational patterns also varied between cognitive skills, with puppies showing adult-like performance on some tasks only weeks after a skill emerged, while never achieving adult performance in others. Differences in rearing strategy did not lead to differences in developmental patterns while, in some cases, repeated testing did. Overall, our findings provide strong support for the MIH by demonstrating differentiated development across the cognitive abilities tested.

animal behavior and cognition↗

bioRxiv2024

Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocytederived hormones

Observations that intestinal microbes can beneficially impact host physiology have prompted investigations into the therapeutic usage of such microbes in a range of diseases. For example, the human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments including colic, infection, and inflammation as well as non- intestinal ailments including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses in the gut, we postulated that L. reuteri may also regulate hormones of the gastrointestinal tract to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as being produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones which are produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promotes the secretion of several enteric hormones including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.

microbiology↗