Activity of forkhead box P2-positive neurons is associated with tadpole begging behaviour.

Motor function is a critical aspect of social behaviour in a wide range of taxa. The transcription factor forkhead box P2 (FoxP2) is well studied in the context of vocal communication in humans, mice and songbirds, but its role in regulating social behaviour in other vertebrate taxa is unclear. We examined the distribution and activity of FoxP2-positive neurons in tadpoles of the mimic poison frog (Ranitomeya imitator). In this species, tadpoles are reared in isolated plant nurseries and are aggressive to other tadpoles. Mothers provide unfertilized egg meals to tadpoles that perform a begging display by vigorously vibrating back and forth. We found that FoxP2 is widely distributed in the tadpole brain and parallels the brain distribution in mammals, birds and fishes. We then tested the hypothesis that FoxP2-positive neurons would have differential activity levels in begging or aggression contexts compared to non-social controls. We found that FoxP2-positive neurons showed increased activation in the striatum and cerebellum during begging and in the nucleus accumbens during aggression. Overall, these findings lay a foundation for testing the hypothesis that FoxP2 has a generalizable role in social behaviour beyond vocal communication across terrestrial vertebrates.

Single-Stage Bilateral Corneal Neurotization for Neurotrophic Keratopathy in Stüve-Wiedemann Syndrome: A Case Report and Literature Review.

The authors report the surgical management and outcomes of neurotrophic keratopathy in two patients with Stüve-Weidemann syndrome who underwent single-stage bilateral corneal neurotization. Both patients experienced improvement in corneal sensation based on Cochet-Bonnet aesthesiometry measurements or cotton tip testing in addition to clinical improvement in ocular surface health. [J Pediatr Ophthalmol Strabismus. 2024;61(5):e54-e58.].

Resting trabecular meshwork cells experience constitutive cation influx.

A quintessential sentinel of cell health, the membrane potential in nonexcitable cells integrates biochemical and biomechanical inputs, determines the driving force for ionic currents activated by input signals and plays critical functions in cellular differentiation, signaling, and pathology. The identity and properties of ion channels that subserve the resting potential in trabecular meshwork (TM) cells is poorly understood, which impairs our understanding of intraocular pressure regulation in healthy and diseased eyes. Here, we identified a powerful cationic conductance that subserves the TM resting potential. It disappears following Na+ removal or substitution with choline or NMDG+, is insensitive to TTX, verapamil, phenamil methanesulfonate, amiloride and GsMTx4, is substituted by Li+ and Cs+, and inhibited by Gd3+ and Ruthenium Red. Constitutive cation influx is thus not mediated by voltage-operated Na+, Ca2+, epithelial Na+ (ENaC) channels, Piezo channels or Na+/H+ exchange but may involve TRP-like channels. Transcriptional analysis detected expression of many TRP genes, with the transcriptome pool dominated by TRPC1 followed by expression of TRPV1, TRPC3, TRPV4 and TRPC5. Pyr3 and Pico1,4,5 did not affect the standing current whereas SKF96365 promoted rather than suppressed, Na+ influx. SEA-0400 induced a modest hyperpolarization, indicating residual contribution from Na+/Ca2+ exchange. The resting membrane potential in human TM cells is thus maintained by a constitutive monovalent cation leak current with properties not unlike those of TRP channels. This conductance is likely to influence conventional outflow by setting the homeostatic steady-state and by regulating the magnitude of pressure-induced currents in normotensive and hypertensive eyes.

Multiple mycotoxin exposure assessment through human biomonitoring in an esophageal cancer case-control study in the Arsi-Bale districts of Oromia region of Ethiopia.

BACKGROUND: Esophageal cancer (EC) is a malignancy with a poor prognosis and a five-year survival rate of less than 20%. It is the ninth most frequent cancer globally and the sixth leading cause of cancer-related deaths. The incidence of EC has been found to vary significantly by geography, indicating the importance of environmental and lifestyle factors along with genetic factors in the onset of the disease. In this work, we investigated mycotoxin exposure in a case-control study from the Arsi-Bale districts of Oromia regional state in Ethiopia, where there is a high incidence of EC while alcohol and tobacco use - two established risk factors for EC - are very rare. METHODS: Internal exposure to 39 mycotoxins and metabolites was assessed by liquid chromatography-tandem mass spectrometry in plasma samples of EC cases (n = 166) and location-matched healthy controls (n = 166) who shared similar dietary sources. Demographic and lifestyle data were collected using structured questionnaires. Principal Component Analysis and machine learning models were used to identify the most relevant demographic, lifestyle, and mycotoxin (co-)exposure variables associated with EC. Multivariate binary logistic regression analysis was used to assess EC risk. RESULT: Evidence of mycotoxin exposure was observed in all plasma samples, with 10 different mycotoxins being detected in samples from EC cases, while only 6 different mycotoxins were detected in samples from healthy controls. Ochratoxin A was detected in plasma from all cases and controls, while tenuazonic acid was detected in plasma of 145 (87.3%) cases and 71 (42.8%) controls. Using multivariable logistic regression analysis, exposure to tenuazonic acid (AOR = 1.88 [95% CI: 1.68-2.11]) and to multiple mycotoxins (AOR = 2.54 [95% CI: 2.10-3.07]) were positively associated with EC. CONCLUSION: All cases and controls were exposed to at least one mycotoxin. Cases were exposed to a statistically significantly higher number of mycotoxins than controls. Exposure to tenuazonic acid and to multiple mycotoxins were associated with increased risk of EC in the study population. Although aflatoxin B1-lysine and the ratio of sphinganine to sphingosine (as a biomarker of effect to fumonisin exposure) were not assessed in this study, our result emphasizes the need to characterize the effect of mycotoxin co-exposure as part of the exposome and include it in risk assessment, since the current mycotoxin safety levels do not consider the additive or synergistic effects of mycotoxin co-exposure. Moreover, a prospective study design with regular sampling should be considered in this high incidence area of EC in Ethiopia to obtain conclusive results on the role of mycotoxin exposure in the onset and development of the disease.

Increasing Contributions of Temperature-Dependent Oxygenated Organic Aerosol to Summertime Particulate Matter in New York City.

As part of the summer 2022 NYC-METS (New York City metropolitan Measurements of Emissions and TransformationS) campaign and the ASCENT (Atmospheric Science and Chemistry mEasurement NeTwork) observational network, speciated particulate matter was measured in real time in Manhattan and Queens, NY, with additional gas-phase measurements. Largely due to observed reductions in inorganic sulfate aerosol components over the 21st century, summertime aerosol composition in NYC has become predominantly organic (80-83%). Organic aerosol source apportionment via positive matrix factorization showed that this is dominated by secondary production as oxygenated organic aerosol (OOA) source factors comprised 73-76% of OA. Primary factors, including cooking-related organic aerosol (COA) and hydrocarbon-like organic aerosol (HOA) comprised minor fractions of OA, only 13-15% and 10-11%, respectively. The two sites presented considerable spatiotemporal variations in OA source factor concentrations despite similar average PM2.5 concentrations. The less- and more-oxidized OOA factors exhibited clear temperature dependences at both sites with increased concentrations and greater degrees of oxidation at higher temperatures, including during a heatwave. With strong temperature sensitivity and minimal changes in summertime concentrations since 2001, secondary OA poses a particular challenge for air quality policy in NYC that will very likely be exacerbated by continued climate change and extreme heat events.

Evaluating taste preference of different sources of Ascophyllum nodosum meal in dairy heifers.

We evaluated the supplementation of different sources of the brown seaweed Ascophyllum nodosum (ASCO) meal on taste preference in dairy heifers during a sequential elimination experiment. Six organic certified Jersey heifers averaging (mean ± standard deviation) 16 ± 1.15 wk of age and 92 ± 9.88 kg of body weight at the beginning of the study were used. Treatments consisted of a ground corn-based concentrate mash without seaweed supplementation (control), or this same concentrate mash supplemented with 57 g/d of ASCO meal obtained from Acadian Seaplants (Acadian Kelp), North American Kelp (SeaLife Kelp), or Thorvin Inc. (Thorvin for Animals). The experiment was conducted with 1 heifer enrolled at a time for 11 d each (n = 66 d total) with the feeding regimens distributed as follows: d 0-2 (adaptation phase), d 3-6 (feeding segment 1), d 7-9 (feeding segment 2), and d 10-11 (feeding segment 3). During feeding segment 1 (d 3-6), the control diet was the most consumed treatment resulting in a total dry matter intake of 22.6 kg followed by Acadian, Thorvin, and SeaLife with 17.7, 13.2, and 11.0 kg, respectively. However, Acadian was selected as the most preferred treatment during feeding segment 1 for a total of 11 d, with control, Thorvin, and SeaLife totaling 8, 3, and 2 d, respectively. In the final ranking of treatments, when all 3 feeding segments were included in the evaluation, Acadian was selected as the first choice by 4 heifers with a ranking of 1.67 points, on a scale ranging from 1 (most preferred) to 4 (least preferred), followed by control (2.50 points), Thorvin (2.67 points), and SeaLife (3.17 points). Overall, the treatments containing Acadian and SeaLife were the most and least preferred, respectively, indicating that heifers were able to distinguish different sources of the same seaweed species based on a taste preference sequential elimination experiment.

Hospitalised infections and rituximab administration among children and adolescents with systemic lupus erythematosus from 2009 to 2021.

BACKGROUND: Rituximab is associated with high infection rates, but studies of infections following rituximab in youth with childhood-onset SLE (cSLE) are limited. We conducted a retrospective longitudinal cohort study to assess the incidence of hospitalised infections following rituximab among children with cSLE and to assess changes in hospital-based rituximab administration over time. METHODS: Youth ages 2-21 years with an International Classification of Diseases (ICD) code for SLE who received rituximab during admission to a Pediatric Health Information System hospital from 2009 to 2021 were included. Incidence rates for infections requiring hospitalisation over the 12 months following first rituximab administration were calculated. Rituximab use by year of hospital discharge was tabulated. RESULTS: We identified 1567 children with cSLE who received rituximab. 219 children were admitted with an infection within 1 year after first rituximab administration, for an incidence rate of 140 cases per 1000 patient-years. Seven children (0.44%) died during a hospitalisation with an infection in the year following rituximab administration. The most common hospitalised infections were bacterial pneumonia, sepsis and cellulitis. 12 children were hospitalised with COVID-19, none of whom died. Hospitalisations with rituximab administered decreased from 2019 to 2021. CONCLUSIONS: In this cohort of patients with cSLE who received inpatient treatment with rituximab, we observed a 14% rate of hospitalisation with infection in the year following rituximab administration among youth with cSLE. Rituximab use declined during the COVID-19 pandemic. No fatalities with COVID-19 were observed. Given the lack of outpatient data, including doses of concomitant medications and disease activity measures, further research is needed to identify risk factors for infection following rituximab among children with cSLE.

Muscle Quality And Physical Function In Men With And Without Hiv.

BACKGROUND: People with HIV (PWH) experience faster physical decline than those without HIV (PWoH), despite antiretroviral therapy. We compared skeletal muscle density and area and their relationship with physical function among PWH and PWoH. METHODS: Quantitative computed tomography (CT) scans were performed at the L4-L5 spinal region and the thigh to evaluate muscle groups in Multicenter AIDS Cohort (MACS) participants at baseline. Using exploratory factor analysis, we summarized aggregated muscle measures based on factor loadings. Longitudinal associations between muscle area and density with gait speed and grip strength were examined using multivariable linear regression models with generalized estimating equations, adjusting for demographics, HIV serostatus, and other health metrics. RESULTS: We included 798 men (61% of PWH). The median age was 54 years (IQR: 49-59), 61% were White, 32% Black, and 10% Hispanic. Among them, 22% had a BMI over 30 kg/m2, and 14% had diabetes. Two factors emerged from the factor analysis explaining 55.9% of variance. Factor 1 (explained 32.5% of variance) encompassed all density measures. Factor 2 (explained 23.4% of variance) encompassed all area measures. Associations between muscle density and gait speed were more pronounced with aggregated measures than with individual ones. Specifically, each unit increase in overall muscle density correlated with a 0.028 meter/second increase in gait speed (95% confidence interval [CI]: 0.017, 0.038, p<0.01). Grip strength was associated with aggregated measures of both muscle density and area, with overall muscle density associated with a 1.88 kg increase in grip strength (95% CI: 1.29, 2.46, p<0.01), and overall muscle area with a 1.60 kg increase (95% CI: 1.02, 2.19, p<0.01). CONCLUSIONS: Aggregated muscle density and area measurements were significantly associated with physical function. These correlations underscore the importance of interventions to enhance skeletal muscle to improve healthy aging for PWH and PWoH.

The Discover In-Hospital Cardiac Arrest (Discover IHCA) Study: An Investigation of Hospital Practices After In-Hospital Cardiac Arrest.

IMPORTANCE: In-hospital cardiac arrest (IHCA) is a significant public health burden. Rates of return of spontaneous circulation (ROSC) have been improving, but the best way to care for patients after the initial resuscitation remains poorly understood, and improvements in survival to discharge are stagnant. Existing North American cardiac arrest databases lack comprehensive data on the post-resuscitation period, and we do not know current post-IHCA practice patterns. To address this gap, we developed the Discover In-Hospital Cardiac Arrest (Discover IHCA) study, which will thoroughly evaluate current post-IHCA care practices across a diverse cohort. OBJECTIVES: Our study collects granular data on post-IHCA treatment practices, focusing on temperature control and prognostication, with the objective of describing variation in current post-IHCA practice. DESIGN, SETTING, AND PARTICIPANTS: This is a multicenter, prospectively collected, observational cohort study of patients who have suffered IHCA and have been successfully resuscitated (achieved ROSC). There are 24 enrolling hospital systems (23 in the United States) with 69 individual enrolling hospitals (39 in the United States). We developed a standardized data dictionary, and data collection began in October 2023, with a projected 1000 total enrollments. Discover IHCA is endorsed by the Society of Critical Care Medicine. INTERVENTIONS, OUTCOMES, AND ANALYSIS: The study collects data on patient characteristics including pre-arrest frailty, arrest characteristics, and detailed information on post-arrest practices and outcomes. Data collection on post-IHCA practice was structured around current American Heart Association and European Resuscitation Council guidelines. Among other data elements, the study captures post-arrest temperature control interventions and post-arrest prognostication methods. Analysis will evaluate variations in practice and their association with mortality and neurologic function. CONCLUSIONS: We expect this study, Discover IHCA, to identify variability in practice and outcomes following IHCA, and be a vital resource for future investigations into best-practice for managing patients after IHCA.

Relationships Between Hepatic Steatosis and Frailty Differ by HIV Serostatus.

BACKGROUND: Frailty is associated with obesity-related comorbidities, but the relationship with nonalcoholic fatty liver disease (NAFLD) in people with HIV has been incompletely described. Our objective was to assess the associations between NAFLD and frailty. METHODS: Cross-sectional and longitudinal analysis of men in the Multicenter AIDS Cohort Study. NAFLD was defined as a liver/spleen ratio <1.0 on abdominal computed tomography scans; frailty was defined by the frailty phenotype as having 3 of the following: weakness, slowness, weight loss, exhaustion, and low physical activity. RESULTS: Men without (n = 200) and with HIV (n = 292) were included. NAFLD prevalence was 21% vs 16% and frailty 12% vs 17%, respectively. Among men with NAFLD, frailty was more prevalent in men without HIV (21% vs 11%). In multivariate analysis, NAFLD was significantly associated with frailty after controlling for significant variables. Men without HIV and NAFLD had 2.6 times higher probability [95% confidence interval (CI): 1.2- to 5.7] of frailty relative to men with neither HIV nor NAFLD. This association was not seen in men with HIV. The probability of frailty was higher among men without HIV with NAFLD (27% vs 10% in men without NAFLD) but lower among men with HIV with NAFLD (14% vs 19% in men without NAFLD). No significant relationships were found in longitudinal analyses. CONCLUSIONS: NAFLD was independently associated with frailty among men without HIV but not men with HIV, despite increased prevalence of frailty among men with HIV. The mechanisms of the muscle-liver-adipose tissue axis underlying NAFLD might differ by HIV serostatus.

Graph Fourier transform for spatial omics representation and analyses of complex organs.

Spatial omics technologies decipher functional components of complex organs at cellular and subcellular resolutions. We introduce Spatial Graph Fourier Transform (SpaGFT) and apply graph signal processing to a wide range of spatial omics profiling platforms to generate their interpretable representations. This representation supports spatially variable gene identification and improves gene expression imputation, outperforming existing tools in analyzing human and mouse spatial transcriptomics data. SpaGFT can identify immunological regions for B cell maturation in human lymph nodes Visium data and characterize variations in secondary follicles using in-house human tonsil CODEX data. Furthermore, it can be integrated seamlessly into other machine learning frameworks, enhancing accuracy in spatial domain identification, cell type annotation, and subcellular feature inference by up to 40%. Notably, SpaGFT detects rare subcellular organelles, such as Cajal bodies and Set1/COMPASS complexes, in high-resolution spatial proteomics data. This approach provides an explainable graph representation method for exploring tissue biology and function.

Applications of artificial intelligence to myeloproliferative neoplasms: a narrative review.

INTRODUCTION: Artificial intelligence (AI) is a rapidly growing field of computational research with the potential to extract nuanced biomarkers for the prediction of outcomes of interest. AI implementations for the prediction for clinical outcomes for myeloproliferative neoplasms (MPNs) are currently under investigation. AREAS COVERED: In this narrative review, we discuss AI investigations for the improvement of MPN clinical care utilizing either clinically available data or experimental laboratory findings. Abstracts and manuscripts were identified upon querying PubMed and the American Society of Hematology conference between 2000 and 2023. Overall, multidisciplinary researchers have developed AI methods in MPNs attempting to improve diagnostic accuracy, risk prediction, therapy selection, or pre-clinical investigations to identify candidate molecules as novel therapeutic agents. EXPERT OPINION: It is our expert opinion that AI methods in MPN care and hematology will continue to grow with increasing clinical utility. We believe that AI models will assist healthcare workers as clinical decision support tools if appropriately developed with AI-specific regulatory guidelines. Though the reported findings in this review are early investigations for AI in MPNs, the collective work developed by the research community provides a promising framework for improving decision-making in the future of MPN clinical care.

Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.

BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship. OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life. METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics. RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway. CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.

Diverse RNA viruses discovered in multiple seagrass species.

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.

Steroid profiling in human primary teeth via liquid chromatography-tandem mass spectrometry for long-term retrospective steroid measurement.

Steroid hormones are important modulators of many physiological processes, and measurements of steroids in blood, saliva, and urine matrices are widely used to assess endocrine pathologies and stress. However, these matrices cannot be used to retrospectively assess early-life stress and developmental endocrine pathologies, because they do not integrate steroid levels over the long term. A novel biological matrix in which to measure steroids is primary teeth (or "baby teeth"). Primary teeth develop early in life and accumulate various endogenous molecules during their gradual formation. Here, we developed and validated the first assay to measure steroids in human primary teeth using liquid chromatography-tandem spectrometry (LC-MS/MS). Our assay is highly sensitive, specific, accurate, and precise. It allows for the simultaneous quantification of 17 steroids in primary teeth (16 of which have not been examined previously in primary teeth). Overall, steroid levels in primary teeth were relatively low, and 8 steroids were quantifiable. Levels of dehydroepiandrosterone, cortisol, and progesterone were the highest of the 17 steroids examined. Next, we used this assay to perform steroid profiling in primary teeth from males and females. The same 8 steroids were quantifiable, and no sex differences were found. Levels of androgens (androstenedione and testosterone) were positively correlated, and levels of glucocorticoids (cortisol, cortisone, corticosterone, 11-dehydrocorticosterone) were also positively correlated. These data demonstrate that multiple steroids can be quantified by LC-MS/MS in human primary teeth, and this method potentially provides a powerful new way to retrospectively assess early-life stress and developmental endocrine pathologies.

Machine Learning Guided AQFEP: A Fast and Efficient Absolute Free Energy Perturbation Solution for Virtual Screening.

Structure-based methods in drug discovery have become an integral part of the modern drug discovery process. The power of virtual screening lies in its ability to rapidly and cost-effectively explore enormous chemical spaces to select promising ligands for further experimental investigation. Relative free energy perturbation (RFEP) and similar methods are the gold standard for binding affinity prediction in drug discovery hit-to-lead and lead optimization phases, but have high computational cost and the requirement of a structural analog with a known activity. Without a reference molecule requirement, absolute FEP (AFEP) has, in theory, better accuracy for hit ID, but in practice, the slow throughput is not compatible with VS, where fast docking and unreliable scoring functions are still the standard. Here, we present an integrated workflow to virtually screen large and diverse chemical libraries efficiently, combining active learning with a physics-based scoring function based on a fast absolute free energy perturbation method. We validated the performance of the approach in the ranking of structurally related ligands, virtual screening hit rate enrichment, and active learning chemical space exploration; disclosing the largest reported collection of free energy simulations to date.

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.

Background: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. Results: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes. Conclusions: Using shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.

BRCA1/BRC-1 and SMC-5/6 regulate DNA repair pathway engagement during Caenorhabditis elegans meiosis.

The preservation of genome integrity during sperm and egg development is vital for reproductive success. During meiosis, the tumor suppressor BRCA1/BRC-1 and structural maintenance of chromosomes 5/6 (SMC-5/6) complex genetically interact to promote high fidelity DNA double strand break (DSB) repair, but the specific DSB repair outcomes these proteins regulate remain unknown. Using genetic and cytological methods to monitor resolution of DSBs with different repair partners in Caenorhabditis elegans, we demonstrate that both BRC-1 and SMC-5 repress intersister crossover recombination events. Sequencing analysis of conversion tracts from homolog-independent DSB repair events further indicates that BRC-1 regulates intersister/intrachromatid noncrossover conversion tract length. Moreover, we find that BRC-1 specifically inhibits error prone repair of DSBs induced at mid-pachytene. Finally, we reveal functional interactions of BRC-1 and SMC-5/6 in regulating repair pathway engagement: BRC-1 is required for localization of recombinase proteins to DSBs in smc-5 mutants and enhances DSB repair defects in smc-5 mutants by repressing theta-mediated end joining (TMEJ). These results are consistent with a model in which some functions of BRC-1 act upstream of SMC-5/6 to promote recombination and inhibit error-prone DSB repair, while SMC-5/6 acts downstream of BRC-1 to regulate the formation or resolution of recombination intermediates. Taken together, our study illuminates the coordinated interplay of BRC-1 and SMC-5/6 to regulate DSB repair outcomes in the germline.

Impact of Partial Oil Removal on Energy Content of Distillers Grains Plus Solubles for Finishing Cattle.

Two experiments evaluated the impact of the reduction in the percentage of corn oil remaining in distillers grains plus solubles (DGS) after the ethanol plant de-oiling process or by adding corn oil back to DGS following de-oiling on finishing cattle performance and nutrient digestion. Experiment 1 utilized 320 yearling steers (initial BW = 413 kg; SD = 25 kg) fed in 32 pens (10 steers/pen) and assigned to one of four treatments (n = 8 pens/treatment). The four treatments consisted of a blended DRC:HMC corn control diet (CON), de-oiled modified distillers grains plus solubles included at 40% of diet DM (DODGS), de-oiled modified distillers grains plus solubles included at 38% of diet DM plus 2% added corn oil (DODGS + Oil), and full-fat modified distillers grains plus solubles included at 40% of diet DM (FFDGS). The DODGS product contained 8.9% fat while the FFDGS product contained 11.6% fat. Dry matter intake (DMI) was impacted by treatment (p = 0.01) with steers fed DODGS having the greatest DMI and steers fed CON, DODGS + Oil, and FFDGS having lower DMI. Dietary treatment tended to impact ADG (p = 0.06) with steers fed DODGS and DODGS + Oil having greater gains than CON, with FFDGS being an intermediate. As a result of increased ADG, G:F differed between treatments (p < 0.01) with the greatest feed efficiency observed for steers fed DODGS + Oil and FFDGS. Including MDGS in the diet improved G:F by 6 to 11% compared to feeding DRC:HMC corn blend, with an improvement in G:F of 4.9 and 1.2% for DODGS + Oil and FFDGS, respectively, compared to DODGS. Hot carcass weight was impacted by dietary treatment (HCW; p = 0.05), with DODGS- and DODGS + Oil-fed steers having the heaviest HCW, CON steers having the lightest HCW, and FFDGS being an intermediate. Experiment 2 was a 5 × 4 unbalanced Latin rectangle digestion experiment with four diets, five ruminally cannulated steers, and five periods that utilized the same treatments as Exp. 1. Dietary fat measured 4.2, 6.0, 7.9, and 7.1% for CON, DODGS, DODGS + Oil, and FFDGS, respectively. Intakes of DM, OM, and energy as well as total tract fat digestibility and DE (Mcal/d) were not impacted by dietary treatment (p ≥ 0.46). When corn oil was added back to de-oiled MDGS, there was a negative impact on digestibility of OM (p < 0.01) and NDF (p = 0.07) compared with DODGS, FFDGS, and CON. Partially removing oil from modified distillers grains plus solubles did not significantly impact cattle performance, carcass traits, energy content, or digestibility when MDGS was included at approximately 40% of diet DM.