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Abstract Microbes are pervasive and their interaction with each other and the environment can impact fields as diverse as health and agriculture. While network inference and related algorithms that use abundance data from pyrosequencing can infer microbial interaction networks, the ambiguity surrounding the actual underlying networks hampers the validation of these algorithms. This study introduces a generative model to synthesize both the underlying interactive network and observable abundance data, serving as a test bed for the existing and future network inference algorithms. We tested our generative model with four typical network inference algorithms; our results suggest that none of these algorithms demonstrate adequate accuracy for inferring ecologies of non-commensalistic species, either mutualistic or competitive. We further explored the potential for predictability by combining existing algorithms with an oracle algorithm built by fusing the results of several existing algorithms. The oracle algorithm reveals promising improvements in predictability, although it falls short when applied to networks characterized by dense interspecies taxa interactions. Our work underscores the need for the continued development and validation of algorithms to unravel the intricacies of microbial interaction networks.

Abstract Loss-of-function mutations in CLN3 cause juvenile Batten disease, featuring neurodegeneration and early-stage neuroinflammation. How loss of CLN3 function leads to early neuroinflammation is not yet understood. Here, we have comprehensively studied microglia from Cln3 ∆ex7/8 mice, a genetically accurate disease model. Loss of CLN3 function in microglia leads to lysosomal storage material accumulation and abnormal morphology of subcellular organelles. Moreover, pathological proteomic signatures are indicative of defects in lysosomal function and abnormal lipid metabolism. Consistent with these findings, CLN3-deficient microglia are unable to efficiently turnover myelin and metabolize the associated lipids, showing defects in lipid droplet formation and cholesterol accumulation. Accordingly, we also observe impaired myelin integrity in aged Cln3 ∆ex7/8 mouse brain. Autophagy inducers and cholesterol-lowering drugs correct the observed microglial phenotypes. Taken together, these data implicate a cell-autonomous defect in CLN3-deficient microglia that impacts their ability to support neuronal cell health, suggesting microglial targeted therapies should be considered for CLN3 disease.

Abstract Detergent-induced vesicle interactions, critical for applications including virus inactivation, varies according to the detergent type and membrane composition, but the underlying mechanistic details remain underexplored. Here, we use a lipid mixing assay based on Förster resonance energy transfer (FRET), and single-vesicle characterization approaches to identify that sub-micron-sized vesicles are induced to fuse by the non-ionic detergent Triton-X-100. We demonstrate that the process is a multi-step mechanism, characterized by discrete values of FRET efficiency between membrane-embedded fluorophores, and involves permeabilization, vesicle docking, hemi-fusion and full lipid mixing at sub-solubilizing detergent concentrations. We also dissect the kinetics of vesicle fusion to surface-tethered vesicles using a label-free quartz-crystal microbalance with dissipation monitoring approach, opening a platform for biotechnology applications. The presented strategies provide mechanistic insight into the dynamics of vesicle fusion and have implications for applications including drug delivery and sensor development where transport and manipulation of encapsulated cargo is essential.

Abstract The objective of study was to characterize HPV in vaginal samples from women being seen at the Center for Reproductive Medicine and Infertility at Weill Cornell Medicine before and following ovarian stimulation. A total of 29 women made samples available for analysis by viral metagenomics. Eighteen women were HPV-positive, six (33.3%) at their initial visit and 15 (83.3%) following hormone stimulation (p = 0.0059). Pairwise comparison of nucleotide sequences and phylogenetic analysis showed the classification sequences into two genera: Alphapapillomavirus and Gammapapillomavirus. Sequences were from 8 HPV types: HPV 51 (n = 2), HPV 68 (n = 1), HPV 83 (n = 9), HPV 84 (n = 2), HPV 121 (n = 6), HPV 175 (n = 1) and HPV 190 (n = 1). Additionally, C16b and C30 likely represent new types. In summary, multiple HPV types are present in the vagina of reproductive age women and are induced by hormone used to stimulate ovulation.

Abstract Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

Abstract Background Clostridium autoethanogenum is an acetogenic bacterium that autotrophically converts carbon monoxide (CO) and carbon dioxide (CO2) gases into bioproducts and fuels via the Wood–Ljungdahl pathway (WLP). To facilitate overall carbon capture efficiency, the reaction stoichiometry requires supplementation of hydrogen at an increased ratio of H2:CO to maximize CO2 utilization; however, the molecular details and thus the ability to understand the mechanism of this supplementation are largely unknown. Results In order to elucidate the microbial physiology and fermentation where at least 75% of the carbon in ethanol comes from CO2, we established controlled chemostats that facilitated a novel and high (11:1) H2:CO uptake ratio. We compared and contrasted proteomic and metabolomics profiles to replicate continuous stirred tank reactors (CSTRs) at the same growth rate from a lower (5:1) H2:CO condition where ~ 50% of the carbon in ethanol is derived from CO2. Our hypothesis was that major changes would be observed in the hydrogenases and/or redox-related proteins and the WLP to compensate for the elevated hydrogen feed gas. Our analyses did reveal protein abundance differences between the two conditions largely related to reduction–oxidation (redox) pathways and cofactor biosynthesis, but the changes were more minor than we would have expected. While the Wood–Ljungdahl pathway proteins remained consistent across the conditions, other post-translational regulatory processes, such as lysine-acetylation, were observed and appeared to be more important for fine-tuning this carbon metabolism pathway. Metabolomic analyses showed that the increase in H2:CO ratio drives the organism to higher carbon dioxide utilization resulting in lower carbon storages and accumulated fatty acid metabolite levels. Conclusions This research delves into the intricate dynamics of carbon fixation in C. autoethanogenum, examining the influence of highly elevated H2:CO ratios on metabolic processes and product outcomes. The study underscores the significance of optimizing gas feed composition for enhanced industrial efficiency, shedding light on potential mechanisms, such as post-translational modifications (PTMs), to fine-tune enzymatic activities and improve desired product yields.

Abstract The erosion of marine sediments is a pressing issue for coastal areas worldwide. Established methods to mitigate coastal erosion fail to provide lasting and sustainable solutions to protect marine ecosystems. Here we demonstrate the application of mild electrical stimulations to precipitate calcareous mineral binders from seawater in the pores of marine soils via electrodeposition, an alternative approach to mitigating coastal erosion. Results of electrochemical laboratory experiments unveil that the polymorphs, precipitation sites, intrusion mechanisms, and effects of electrodeposited minerals in marine sands vary as a function of the magnitude and duration of applied voltage, soil relative density, and electrolyte ionic concentration. Surprisingly, in addition to the precipitation of calcium carbonate and magnesium hydroxide, the formation of hydromagnesite is also observed due to electrically driven fluctuations in the local $${pH}$$ p H . These electrodeposits lead to enhanced mechanical and hydraulic properties of the marine sands, indicating that electrodeposition routes could be developed to reinforce marine soils in coastal areas that more closely mimic natural systems.

Abstract The bacterial genus Salmonella includes diverse isolates with multiple variations in the structure of the main polysaccharide component (O antigen) of membrane lipopolysaccharides. In addition, some isolates produce a transient (T) antigen, such as the T1 polysaccharide identified in the 1960s in an isolate of Salmonella enterica Paratyphi B. The structure and biosynthesis of the T1 antigen have remained enigmatic. Here, we use biophysical, biochemical and genetic methods to show that the T1 antigen is a complex linear glycan containing tandem homopolymeric domains of galactofuranose and ribofuranose, linked to lipid A–core, like a typical O antigen. T1 is a phase-variable antigen, regulated by recombinational inversion of the promoter upstream of the T1 genetic locus through a mechanism not observed for other bacterial O antigens. The T1 locus is conserved across many Salmonella isolates, but is mutated or absent in most typhoidal serovars and in serovar Enteritidis.

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Pollen transfer efficiency (PTE; the proportion of pollen removed from flowers that reaches conspecific stigmas) is expected to vary with the type of pollinator and flower morphology, and to influence male siring success. Many species in the genus Erica are pollinated by bees (which consume pollen and should thus lower PTE) but during its radiation in the Cape, several independent shifts to both sunbird and long-proboscid fly (LP fly) pollinators, which do not consume pollen have taken place. Improvements in PTE could be one of the factors driving these pollinator shifts. PTE data for 15 Erica species (five for each of the three pollinator types) were collected and compared in relation to type of pollinator and anther exsertion. LP fly- and bird-pollinated species had higher PTE in comparison with bee-pollinated species. Species with inserted anthers had higher PTE than those with exserted anthers. This suggests that sunbirds and LP flies are more efficient pollinators than bees. Additionally, the study suggests that insertion of anthers within the corolla tube can reduce pollen losses.

Abstract Background The phenolic polymer lignin is one of the primary chemical constituents of the plant secondary cell wall. Due to the inherent plasticity of lignin biosynthesis, several phenolic monomers have been shown to be incorporated into the polymer, as long as the monomer can undergo radicalization so it can participate in coupling reactions. In this study, we significantly enhance the level of incorporation of monolignol ferulate conjugates into the lignin polymer to improve the digestibility of lignocellulosic biomass. Results Overexpression of a rice Feruloyl-CoA Monolignol Transferase (FMT), OsFMT1, in hybrid poplar (Populus alba x grandidentata) produced transgenic trees clearly displaying increased cell wall-bound ester-linked ferulate, p-hydroxybenzoate, and p-coumarate, all of which are in the lignin cell wall fraction, as shown by NMR and DFRC. We also demonstrate the use of a novel UV–Vis spectroscopic technique to rapidly screen plants for the presence of both ferulate and p-hydroxybenzoate esters. Lastly we show, via saccharification assays, that the OsFMT1 transgenic p oplars have significantly improved processing efficiency compared to wild-type and Angelica sinensis-FMT-expressing poplars. Conclusions The findings demonstrate that OsFMT1 has a broad substrate specificity and a higher catalytic efficiency compared to the previously published FMT from Angelica sinensis (AsFMT). Importantly, enhanced wood processability makes OsFMT1 a promising gene to optimize the composition of lignocellulosic biomass.

Abstract Background The SARS-CoV-2 virus activates maternal and placental immune responses. Such activation in the setting of other infections during pregnancy is known to impact fetal brain development. The effects of maternal immune activation on neurodevelopment are mediated at least in part by fetal brain microglia. However, microglia are inaccessible for direct analysis, and there are no validated non-invasive surrogate models to evaluate in utero microglial priming and function. We have previously demonstrated shared transcriptional programs between microglia and Hofbauer cells (HBCs, or fetal placental macrophages) in mouse models. Methods and results We assessed the impact of maternal SARS-CoV-2 on HBCs isolated from 24 term placentas (N = 10 SARS-CoV-2 positive cases, 14 negative controls). Using single-cell RNA-sequencing, we demonstrated that HBC subpopulations exhibit distinct cellular programs, with specific subpopulations differentially impacted by SARS-CoV-2. Assessment of differentially expressed genes implied impaired phagocytosis, a key function of both HBCs and microglia, in some subclusters. Leveraging previously validated models of microglial synaptic pruning, we showed that HBCs isolated from placentas of SARS-CoV-2 positive pregnancies can be transdifferentiated into microglia-like cells (HBC-iMGs), with impaired synaptic pruning behavior compared to HBC models from negative controls. Conclusion These findings suggest that HBCs isolated at birth can be used to create personalized cellular models of offspring microglial programming.

Not available.

Spatial ability tests measure capacity for mentally understanding and interpreting three-dimensional images. Such skills have been found to be predictive for anatomical learning success and proficiency in human and veterinary medical students. Veterinarians in the radiology and surgery field develop high levels of three-dimensional topographic anatomic understanding through exposure to anatomy portions of the veterinary curriculum, followed by highly specialized residency programs. Validated testing tools were used to compare spatial and general non-verbal reasoning abilities in veterinarians in the field of radiology (radiology group, RG) and veterinarians in the field of surgery (surgery group, SG). These tests were: Guay’s Visualization of Views Test: Adapted Version (GVVT), the Mental Rotation Test (MRT), and Raven’s Advanced Progressive Matrices Test, short form (APMT). Results showed a significant difference for GVVT scores in favor of the RG (15.2 ± 0.3 and 12.3 ± 0.4, respectively, p

Background: Right heart catheterization (RHC) is the gold standard for diagnosing pulmonary hypertension (PH) in patients with interstitial lung disease (ILD). However, discrepancies between pulmonary arterial wedge pressure (PAWP) and left ventricular end-diastolic pressure (LVEDP) remain understudied in this population. Methods: We conducted a retrospective analysis of data from ILD patients who underwent RHC and had concomitant LVEDP measurements. Pulmonary vascular resistance (PVR) was calculated using both PAWP and LVEDP. Patients were categorized based on PAWP and LVEDP values using a threshold of 15 mmHg and PVR values using a threshold of 2 or 3 Wood Units. After that patients were categorized as concordant or discordant if both values were on the same or opposite sides of these thresholds, respectively. A discordantly higher PAWP group (left atrial dysfunction, LAD) was defined as patients with a PAWP-LVEDP difference of more than 3 mmHg. Results: Among 87 ILD patients, 9 patients (10.3%) showed discordance between PAWP and LVEDP. LAD was observed in 12 patients (13.8%) and was associated with lower forced vital capacity (Odd ratio [OR]: 0.956, p = 0.049) and a larger left atrium diameter (OR: 3.205, p = 0.033). Discordance in PVR values was also noted, with potential treatment targets for PH-specific therapy differing in 9 patients (22.0%) depending on whether PAWP or LVEDP was used. Conclusions: This study highlights the clinical significance of PAWP-LVEDP discrepancies in suspected PH-ILD patients, emphasizing the need for comprehensive assessments incorporating LVEDP and clinical context for accurate diagnosis, risk stratification, and treatment decisions.

Abstract The Dynamic Albedo of Neutrons (DAN) instrument on the Mars Science Laboratory Curiosity rover primarily measures neutrons that have undergone interactions with rocks and materials in the rover's local environment. As the rover ascends Aeolis Mons, it may encounter more extreme local topography (e.g., cliffs, gullies, canyons). We present three parts of the rover's traverse in which local topography, expressed as the average local relief relative to the rover, is moderately to strongly correlated with an increase in passive thermal neutron count rates. These increases in count rates are consistent with results from radiation transport models of the instrument's performance near simulated topographic features. Additional DAN measurements in areas of high average local relief (>0.25 m) within 5 m of the instrument could bolster this correlation. DAN's sensitivity to topography in its passive mode could be utilized as a new measurement capability and has implications for the operation of future landed missions carrying neutron spectrometers (e.g., VIPER, MoonRanger, Lunar‐VISE).

Abstract The transition from acute kidney injury (AKI) to chronic kidney disease (CKD) is a critical clinical issue. Although previous studies have suggested macrophages as a key player in promoting inflammation and fibrosis during this transition, the heterogeneity and dynamic characterization of macrophages are still poorly understood. Here, we used integrated single‐cell RNA sequencing and spatial transcriptomic to characterize the spatiotemporal heterogeneity of macrophages in murine AKI‐to‐CKD model of unilateral ischemia‐reperfusion injury. A marked increase in macrophage infiltration at day 1 was followed by a second peak at day 14 post AKI. Spatiotemporal profiling revealed that injured tubules and macrophages co‐localized early after AKI, whereas in late chronic stages had spatial proximity to fibroblasts. Further pseudotime analysis revealed two distinct lineages of macrophages in this transition: renal resident macrophages differentiated into the pro‐repair subsets, whereas infiltrating monocyte‐derived macrophages contributed to chronic inflammation and fibrosis. A novel macrophage subset, extracellular matrix remodeling‐associated macrophages (EAMs) originating from monocytes, linked to renal fibrogenesis and communicated with fibroblasts via insulin‐like growth factors (IGF) signalling. In sum, our study identified the spatiotemporal dynamics of macrophage heterogeneity with a unique subset of EAMs in AKI‐to‐CKD transition, which could be a potential therapeutic target for preventing CKD development.

Abstract Intensified production of stocker‐size tilapia can be accomplished using the biofloc technology production system. Stocker‐size tilapia (ca. 10–200 g/fish) are raised for subsequent stocking for grow‐out to market size. The relationship between stocking rate and the production of stocker‐size hybrid tilapia (Oreochromis aureus × O. niloticus) was evaluated in two studies in outdoor mixotrophic biofloc tanks. Hybrid tilapia were stocked in 18.6‐m2 (15.7‐m3) tanks at 50–150 fish/m2 (59–178 fish/m3) in 25 fish/m2 (30 fish/m3) increments in Study 1 and grown for 141–143 days. Stocking rates evaluated in 4.7‐m2 (3.6‐m3) tanks during Study 2 over 78–79 days ranged from 100 to 300 fish/m2 (132–396 fish/m3) in 25 fish/m2 (33 fish/m3) increments. Linear regression models best described growth to stocker size in both studies. Fish yield increased linearly with stocking rate and ranged from 20.1 to 38.3 kg/m3. Individual weight at harvest was inversely related to stocking rate and ranged from 389.8 to 163.4 g/fish and 155.2 to 81.4 g/fish in Studies 1 and 2, respectively. Partial budget analyses suggested positive net changes in profit with incremental increases in stocking rate for producing a 75‐g stocker. Water quality concentrations were impacted directly by daily feed ration and total feed fed, which increased linearly with stocking rate. In Study 2, whole‐body dry matter, protein, protein retention, and lipid were unaffected by stocking rate, whereas whole‐body ash increased with stocking rate. Whole‐body energy retention significantly decreased with stocking rate. The outdoor mixotrophic biofloc production system is well suited for intensive production of hybrid tilapia stockers. However, additional replicated research and economic analysis are needed to evaluate stocking rate and culture duration to produce specific‐sized stocker hybrid tilapia.

BackgroundChildren and adolescents with type 1 diabetes require frequent outpatient evaluation to assess glucose trends, modify insulin doses, and screen for comorbidities. Continuous glucose monitoring (CGM) provides a detailed glycemic control assessment. Telemedicine has been increasingly used since the COVID-19 pandemic. ObjectiveTo investigate CGM profile parameter improvement immediately following pediatric outpatient diabetes visits and determine if visit modality impacted these metrics, completion of screening laboratory tests, or diabetic emergency occurrence. MethodsA dual-center retrospective review of medical records assessed the CGM metrics time in range and glucose management indicator for pediatric outpatient diabetes visits during 2021. Baseline values were compared with those at 2 and 4 weeks post visit. Rates of completion of screening laboratory tests and diabetic emergencies following visits were determined. ResultsA total of 269 outpatient visits (41.2% telemedicine) were included. Mean time in range increased by 1.63% and 1.35% at 2 and 4 weeks post visit (P=.003 and .01, respectively). Mean glucose management indicator decreased by 0.07% and 0.06% at 2 and 4 weeks post visit (P=.003 and .02, respectively). These improvements in time in range and glucose management indicator were seen across both telemedicine visits and in-person visits without a significant difference. However, patients seen in person were 2.69 times more likely to complete screening laboratory tests (P=.03). Diabetic emergencies occurred too infrequently to analyze. ConclusionsOur findings demonstrate an immediate improvement in CGM metrics following outpatient visits, regardless of modality. While statistically significant, the magnitude of these changes was small; hence, multiple visits over time would be required to achieve clinically relevant improvement. However, completion of screening laboratory tests was found to be more likely after visits occurring in person. Therefore, we suggest a hybrid approach that allows patient convenience with telemedicine but also incorporates periodic in-person assessment.

IntroductionTo achieve and maintain adequate weight, people with cystic fibrosis (CF) May often consume energy-dense, nutrient-poor foods high in added sugars and refined carbohydrates; however, little is known about the glycemic and metabolic effects of dietary composition in this patient population. The objective of this pilot study was to investigate the safety and tolerability of a low glycemic load (LGL) diet in adults with CF and abnormal glucose tolerance (AGT).MethodsTen adults with CF and AGT completed this prospective, open-label pilot study. Mean age was 27.0 ± 2.1 years, 64% were female, and all had pancreatic insufficiency. Each participant followed his/her typical diet for 2 weeks, then transitioned to a LGL diet via meal delivery service for 8 weeks. The primary outcome was change in weight from baseline to study completion, with safety established if no significant decline was noted. Other key safety outcomes included change in hypoglycemia measured by patient report and continuous glucose monitoring (CGM). Exploratory outcomes included changes in other CGM measures, body composition by dual energy X-ray absorptiometry (DXA), and patient reported outcomes.ResultsThere were no significant changes in weight or in subjectively-reported or objectively-measured hypoglycemia. Favorable non-significant changes were noted in CGM measures of hyperglycemia and glycemic variability, DXA measures of fat mass, and gastrointestinal symptom surveys.DiscussionA LGL dietary intervention was safe and well tolerated in adults with CF and AGT. These results lay the groundwork for future trials investigating the impact of low-glycemic dietary interventions on metabolic outcomes in the CF population.

Summary: Background: Bacterial biofilm communities are embedded in a protective extracellular matrix comprised of various components, with its' integrity largely owed to a 3-dimensional lattice of extracellular DNA (eDNA) interconnected by Holliday Junction (HJ)-like structures and stabilised by the ubiquitous eubacterial DNABII family of DNA-binding architectural proteins. We recently showed that the host innate immune effector High Mobility Group Box 1 (HMGB1) protein possesses extracellular anti-biofilm activity by destabilising these HJ-like structures, resulting in release of biofilm-resident bacteria into a vulnerable state. Herein, we showed that HMGB1's anti-biofilm activity was completely contained within a contiguous 97 amino acid region that retained DNA-binding activity, called ‘mB Box-97’. Methods: We engineered a synthetic version of this 97-mer and introduced a single amino acid change which lacked any post-translational modifications, and tested its activity independently and in combination with a humanised monoclonal antibody that disrupts biofilms by the distinct mechanism of DNABII protein sequestration. Findings: mB Box-97 disrupted and prevented biofilms, including those formed by the ESKAPEE pathogens, and importantly reduced measurable proinflammatory activity normally associated with HMGB1 in a murine lung infection model. Interpretation: Herein, we discuss the value of targeting the ubiquitous eDNA-dependent matrix of biofilms via mB Box-97 used singly or in a dual host-augmenting/pathogen-targeted cocktail to resolve bacterial biofilm infections. Funding: This work was supported by NIH/NIDCD R01DC011818 to L.O.B. and S.D.G. and NIH/NIAID R01AI155501 to S.D.G.

ABSTRACT: Vitamin D3 (25-hydroxyvitamin D3 (VD)) and vitamin E (VE) have proven to have immunomodulatory and antioxidant functions along with capacities to improve the reproductive function in chickens. Coccidiosis in laying hens at different stages of growth has been shown to negatively affect performance, immune response, and oxidative status, thus increasing the cost of production. A study was conducted to evaluate the influence of dietary VD or VE on performance, gut health, immune response, and oxidative status of laying hens at peak production. Laying hens (23 wk-of-age, n = 225) were randomly allocated into 5 treatment groups (n = 9 hens/replicate) with 5 replicate groups each: 1) unchallenged control (UC), 2) pair-fed control (PF), 3) challenged control (CC), 4) challenged control top-dressed with 5,000 IU of 25-hydroxyvitamin D3 (VD) per kg of diet, and 5) challenged control top-dressed with 100 IU of DL-α-tocopherol (VE). At 25 wk-of-age, hens grouped in CC, VD, and VE were challenged with mixed Eimeria spp. to induce coccidiosis. VD or VE supplemented hens did not impact bird body weight; however, egg production increased by 10.36% and 13.77%, respectively (P < 0.0001). Furthermore, the gut health of the hens was improved with either VD or VE supplementation, as indicated by lowered gut permeability and intestinal lesion scores (P < 0.05). VE significantly reduced the heterophil count (P = 0.0490) alongside numerically increasing the peripheral CD4+ and CD8+ T cells and monocyte counts (P > 0.05). Both VD or VE increased the TAC at 14 DPI compared to UC (P

Background: During the preoperative evaluation of a patient being considered for spinal surgery, Dual-energy x-ray absorptiometry (DEXA) has been traditionally used to diagnose poor bone mineral density (BMD) as a risk factor. As ordering a DEXA can add cost and delay diagnosis, spine surgeons have more recently began to use Hounsfield Units (HU) measured on computed tomography scans (CT) as a measure of BMD. The aim of our study was to evaluate associations between DEXA and HU on lumbar spine CT scans. Methods: Forty-two patients (32 female, 10 male, mean age = 67.7 years) with DEXA and lumbar spine CT scans performed within one year of each other were identified. DEXA T-scores were collected from the hip, forearm and L1-L4. HU was determined using the maximum region of interest within the cancellous area in the mid-vertebral body from L1-L4 in the sagittal and axial planes. Results: Using the lowest T-score, 8 (19 %) cases were osteoporotic and 25 (60 %) were osteopenic. Statistically significant differences in HU were seen in osteoporotic cases (Axial HU = 59.2, Sagittal HU = 61.1, p = 0.006) compared to osteopenic (Axial HU = 119.8, Sagittal HU = 122.9) and normal cases (Axial HU = 141.2, Sagittal HU = 142.3). There were moderate associations between the spine T-scores and CT HUs (Axial HU:r2 = 0.50, Sagittal HU:r2 = 0.49, p

Abstract Background Musculoskeletal injuries are a common occurrence in sport. The goal of sport injury epidemiology is to study these injuries at a population level to inform their prevention and treatment. Main body This review provides an overview of musculoskeletal sport injuries and the musculoskeletal system from a biological and epidemiologic perspective, including injury mechanism, categorizations and types of sport injuries, healing, and subsequent injuries. It is meant to provide a concise introductory substantive background of musculoskeletal sport injuries for epidemiologists who may not have formal training in the underlying anatomy and pathophysiology. Conclusion An understanding of sport injuries is important for researchers in sport injury epidemiology when determining how to best define and assess their research questions and measures.

Abstract The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

Abstract A plutonium-rich carbide, (U,Pu)(Al,Fe)3C3, was discovered in a hot particle from the Maralinga nuclear testing site in South Australia. The particle was produced between 1960 and 1963 and has been exposed to ambient conditions since then. The new phase belongs to a group of ternary carbides known as 'derivative-MAX phases'. It formed at high temperature within an explosion cloud via rapid eutectic crystallisation from a complex Al–Fe–U–Pu–C–O melt, and is the major Pu host in this particle. Despite signs of volume expansion due to radiation damage, (U,Pu)(Al,Fe)3C3 remains highly X-ray crystalline 60 years after its formation, with no evidence of Pu leaching from the crystals. Our results highlight that the high-energy conditions of (sub-)critical explosions can create unexpected species. Even micro-particles of a derivative-MAX phase can effectively retain low-valence (metallic-like character) Pu under environmental conditions; the slow physical and chemical weathering of these particles may contribute to the slow release of radionuclides over decades, explaining constant low-levels of radionuclides observed in fauna. This study further suggests that rapidly quenched eutectic melts may be engineered to stabilise actinides in nuclear waste products, removing the need for hydrometallurgical processing.

Abstract Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.

Background: A six-minute walk test (6MWT) is a reproducible, easily performed test, and is widely used to determine functional exercise capacity in patients with idiopathic pulmonary fibrosis (IPF). However, there is currently a paucity of data on the clinical significance of baseline and serial 6-minute walk tests in patients with IPF, especially in Asian patients. Objectives: We aimed to investigate the clinical significance of serial 6MWT in patients with IPF, especially in Asian patients. Design: This is a single-center retrospective cohort study. Methods: Clinical data of patients diagnosed with IPF at a tertiary center in Korea were retrospectively analyzed. IPF diagnosis was defined according to the clinical guidelines of the American Thoracic Society (ATS)/European Respiratory Society (ERS)/Japanese Respiratory Society/Latin American Thoracic Association. Results: There were 216 patients diagnosed with IPF from December 2012 to January 2022, of whom 198 had a baseline of 6MWT data. The mean age of the cohort was 66.9 ± 8.6, and 89% were male. The non-survivors showed significantly lower six-minute walk distance (6MWD), minimum saturation of peripheral oxygen (SpO 2 ) during 6MWT, forced vital capacity, and diffusing capacity of the lung for carbon monoxide than survivors at baseline. A multivariate Cox analysis demonstrated that lower minimum SpO 2 was independently associated with increased mortality rates (Hazard ratio (HR): 1.081, 95% confidence interval (CI): 1.024–1.142, p = 0.005). Higher mortality rates were also associated with echocardiographic-determined pulmonary hypertension (HR: 2.466, 95% CI: 1.149–5.296, p = 0.021) at diagnosis. Among 144 patients with 6MWT results at 12 months, patients with a decline of 50 m or more in the 6MWD showed poorer overall survival than others (median survival: 45.0 months vs 58.0 months, p

The different structures and behaviors of UO2+x observed in crystallographic and local structure measurements were examined by extended X-ray absorption fine structure (EXAFS) measurements of pristine UO2.0, p+ and He2+ irradiated UO2.0, and, at multiple temperatures, bulk U4O9 and U3O7 and thin film U4O9-δ on an epitaxial substrate. The disorder caused by irradiation is mostly limited to increased widths of the existing U–O/U pair distributions, with any new neighbor shells being minor. As has been previously reported, the disorder caused by oxidative addition to U4O9 and U3O7 is much more extensive, resulting in multisite U–O distributions and greater reduction of the U–U amplitude with different distributions in bulk and thin-film U4O9. This includes the significant spectral feature near R = 1.2 Å for all U4O9 and U3O7 samples fit with a U-oxo type moiety with a U–O distance around 1.7 Å. In addition to indicating that these anomalies only occur in mixed valence materials, this work confirms the continuous rearrangement of the U–O distributions from 10 to 250 K. Although these variations of the structure are not observed in crystallography, their prominence in the EXAFS indicates that the dynamic structure underlying these effects is an essential factor of these materials.

In recent years, numerous examples of food system dashboards have been developed with the goal of offering users the opportunity to monitor or assess (their) national food systems. One of the many challenges faced by these initiatives has been to strike an acceptable balance between the complexity, local-specificity, and multi-sectoral nature of these food systems while also ensuring that the information remains accessible and usable for decision-makers. Perhaps even more critical, yet rarely discussed or implemented in most of the current food system dashboard initiatives, is the imperative of co-constructing these initiatives with local stakeholders. The case presented in this study puts participation at the center of the design and construction of a food systems’ monitoring dashboard. Using a replicable yet rigorous methodology, we demonstrate the feasibility of co-creating food system dashboards that integrate comprehensive and multi-sectoral inputs from national stakeholders while ensuring these dashboards are functional, evidence-based, and reflective of the country’s specific features. The approach is illustrated with the empirical cases of three pilot countries within the low-and middle-income countries group (Bangladesh, Ethiopia, and Honduras), where the methodology was tested between 2021 and 2022. We conclude by succinctly examining the ongoing challenges in constructing actionable food system dashboards.

Background. A prior single-center, retrospective cohort study identified baseline lung allograft dysfunction (BLAD) as a risk factor for death in bilateral lung transplant recipients. In this multicenter prospective cohort study, we test the association of BLAD with death in bilateral lung transplant recipients, identify clinical risk factors for BLAD, and assess its association with allograft injury on the molecular level. Methods. This multicenter, prospective cohort study included 173 bilateral lung transplant recipients that underwent serial pulmonary function testing and plasma collection for donor-derived cell-free DNA at prespecified time points. BLAD was defined as failure to achieve ≥80% predicted for both forced expiratory volume in 1 s and forced vital capacity after lung transplant, on 2 consecutive measurements at least 3 mo apart. Results. BLAD was associated with increased risk of death (hazard ratio, 1.97; 95% confidence interval [CI], 1.05-3.69; P = 0.03) but not chronic lung allograft dysfunction alone (hazard ratio, 1.60; 95% CI, 0.87-2.95; P = 0.13). Recipient obesity (odds ratio, 1.69; 95% CI, 1.15-2.80; P = 0.04) and donor age (odds ratio, 1.03; 95% CI, 1.02-1.05; P = 0.004) increased the risk of developing BLAD. Patients with BLAD did not demonstrate higher log10(donor-derived cell-free DNA) levels compared with no BLAD (slope [SE]: –0.0095 [0.0007] versus –0.0109 [0.0007]; P = 0.15). Conclusions. BLAD is associated with an increased risk of death following lung transplantation, representing an important posttransplant outcome with valuable prognostic significance; however, early allograft specific injury on the molecular level does not increase the risk of BLAD, supporting further mechanistic insight into disease pathophysiology.

Summary: Many techniques exist for the identification of protein interaction networks. We present a protocol that relies on an affinity purification-mass spectrometry (AP-MS) approach to detect proteins that co-purify with a tagged bait of interest from Drosophila melanogaster larval muscles using the GAL4/upstream activating sequence (UAS) expression system. We also describe steps for the isolation and identification of protein complexes, followed by streamlined bioinformatics analysis for rapid and reproducible results. This protocol can be extended to investigate protein interactions in other tissues.For complete details on the use and execution of this protocol, please refer to Guo et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Columnaris disease is a prevalent disease in freshwater environments caused by the ubiquitous aquatic pathogen Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Demonstrated here and in previous research, the hybrid striped bass (Morone chrysops x M. saxatilis), a prominent United States aquaculture product, is more susceptible to infection with F. covae than the maternal white bass (M. chrysops) parental species. To further elucidate the mechanisms underlying differences in resistance between these fish we examined gill gene expression profiles using RNA sequencing at different timepoints after F. covae infection. Patterns of differential gene expression and association with key enrichment terms indicate the effective immune response observed in white bass includes the up-regulation of multiple cytokines (IL-1β, IL-17C, TNF-α, G-CSF, IL-8, CCL16, CXCL9), hepcidins (HAMP and HAMP2), ribosomal subunit components (e.g., RPL13), and, interestingly, the down-regulation of leptin (LEPA) during initial (1 – 4 h) stages of infection. Conversely, up-regulation of the same genes was not detected in hybrid striped bass until 24 h after infection, indicating a delay in immune response mechanisms that is ultimately ineffective in protecting the host, as this was concurrent with the onset of mortality in these fish. Collectively, the presented results include several putative pathways and candidate genes for further investigation toward characterizing immune defense mechanisms underlying the resistance (white bass) and susceptibility (hybrid striped bass) for selective breeding efforts and/or biotechnological intervention.

Objectives There is little evidence guiding the management of grade I–II traumatic splenic injuries with contrast blush (CB). We aimed to analyze the failure rate of nonoperative management (NOM) of grade I–II splenic injuries with CB in hemodynamically stable patients.Methods A multicenter, retrospective cohort study examining all grade I–II splenic injuries with CB was performed at 21 institutions from January 1, 2014, to October 31, 2019. Patients >18 years old with grade I or II splenic injury due to blunt trauma with CB on CT were included. The primary outcome was the failure of NOM requiring angioembolization/operation. We determined the failure rate of NOM for grade I versus grade II splenic injuries. We then performed bivariate comparisons of patients who failed NOM with those who did not.Results A total of 145 patients were included. Median Injury Severity Score was 17. The combined rate of failure for grade I–II injuries was 20.0%. There was no statistical difference in failure of NOM between grade I and II injuries with CB (18.2% vs 21.1%, p>0.05). Patients who failed NOM had an increased median hospital length of stay (p=0.024) and increased need for blood transfusion (p=0.004) and massive transfusion (p=0.030). Five patients (3.4%) died and 96 (66.2%) were discharged home, with no differences between those who failed and those who did not fail NOM (both p>0.05).Conclusion NOM of grade I–II splenic injuries with CB fails in 20% of patients.Level of evidence IV.

Abstract Otitis media (OM) is one of the most globally pervasive pediatric conditions. Translocation of nasopharynx-resident opportunistic pathogens like nontypeable Haemophilus influenzae (NTHi) assimilates into polymicrobial middle ear biofilms, which promote OM pathogenesis and substantially diminish antibiotic efficacy. Oral or tympanostomy tube (TT)-delivered antibiotics remain the standard of care (SOC) despite consequences including secondary infection, dysbiosis, and antimicrobial resistance. Monoclonal antibodies (mAb) against two biofilm-associated structural proteins, NTHi-specific type IV pilus PilA (anti-rsPilA) and protective tip-region epitopes of NTHi integration host factor (anti-tip-chimer), were previously shown to disrupt biofilms and restore antibiotic sensitivity in vitro. However, the additional criterion for clinical relevance includes the absence of consequential microbiome alterations. Here, nine chinchilla cohorts (n = 3/cohort) without disease were established to evaluate whether TT delivery of mAbs disrupted nasopharyngeal or fecal microbiomes relative to SOC-OM antibiotics. Cohort treatments included a 7d regimen of oral amoxicillin-clavulanate (AC) or 2d regimen of TT-delivered mAb, AC, Trimethoprim-sulfamethoxazole (TS), ofloxacin, or saline. Fecal and nasopharyngeal lavage (NPL) samples were collected before and several days post treatment (DPT) for 16S sequencing. While antibiotic-treated cohorts displayed beta-diversity shifts (PERMANOVA, P

Abstract Since the insights by Charles Darwin, heterostyly, a floral polymorphism with morphs bearing stigmas and anthers at reciprocal heights, has become a model system for the study of natural selection. Based on his archetypal heterostylous flower, including regular symmetry, few stamens and a tube, Darwin hypothesised that heterostyly evolved to promote outcrossing through efficient pollen transfer between morphs involving different areas of a pollinator’s body, thus proposing his seminal pollination-precision hypothesis. Here we update the number of heterostylous and other style-length polymorphic taxa to 247 genera belonging to 34 families, notably expanding known cases by 20%. Using phylogenetic and comparative analyses across the angiosperms, we show numerous independent origins of style-length polymorphism associated with actinomorphic, tubular flowers with a low number of sex organs, stamens fused to the corolla, and pollination by long-tongued insects. These associations provide support for the Darwinian pollination-precision hypothesis as a basis for convergent evolution of heterostyly across angiosperms.

Abstract Globalization of fishery products is playing a significant role in shaping the harvesting and use of aquatic foods, but a vigorous debate has focused on whether the trade is a driver of the inequitable distribution of aquatic foods. Here, we develop species-level mass balance and trophic level identification datasets for 174 countries and territories to analyze global aquatic food consumption patterns, trade characteristics, and impacts from 1976 to 2019. We find that per capita consumption of aquatic foods has increased significantly at the global scale, but the human aquatic food trophic level (HATL), i.e., the average trophic level of aquatic food items in the human diet, is declining (from 3.42 to 3.18) because of the considerable increase in low-trophic level aquaculture species output relative to that of capture fisheries since 1976. Moreover, our study finds that trade has contributed to increasing the availability and trophic level of aquatic foods in >60% of the world’s countries. Trade has also reduced geographic differences in the HATL among countries over recent decades. We suggest that there are important opportunities to widen the current focus on productivity gains and economic outputs to a more equitable global distribution of aquatic foods.

Rate splitting multiple access (RSMA) enables interference management trade-offs between space-division multiple access (SDMA) and non-orthogonal multiple access (NOMA) to serve multiple users in the multiple-input multiple-output (MIMO) broadcast channel. The design of RSMA beamforming, or precoding, to maximize typical rate performance is a non-convex optimization problem. In this paper, a parameterization of optimal beamforming directions for different performance maximization problems subject to a total power constraint is obtained for RSMA for systems with full column rank channel matrices. The performance evaluation function may be an arbitrary increasing function of split user rates. The proposed solution combines maximizing each stream’s signal-to-noise-ratio (SNR) and reducing interference on other streams for different objectives. Using the derived beamforming directions, the design is completed by solving a power allocation problem. Simulation results reveal that the proposed approach is able to provide attractive performance/complexity trade-offs compared to existing schemes.

We describe a method to estimate coefficients ${{{\bm{h}}}_{\bm{n}}}$ of a power spectral density of the form ${\bm{\Sigma}}{{{\bm{h}}}_{\bm{n}}}/{{{\bm{f}}}^{\bm{n}}}$ (${\bm{f}}\;{\bm{\ }}\text{is}$ the frequency and integer ${\bm{n}} \geq 0$) from corresponding measured time series with periodic gaps. This technique is applied to consistently estimate the amount of $1/{\bm{f}}$ noise present in weather system follow-on microwave microwave imager's (MWI) channels from the time-series data collected with different periodic gaps during prelaunch ground tests. The method assumes that the power spectrum of $1/{\bm{f}}$ noise present in MWI can be represented as a second-order frequency polynomial model of the form ${\bm{\Sigma}}{{{\bm{h}}}_{\bm{n}}}/{{{\bm{f}}}^{\bm{n}}}{\bm{\ }}$ and attempts to retrieve the true spectrum by solving for the ${{{\bm{h}}}_{\bm{n}}}$ coefficients using the power spectrum of the time-series data with periodic gaps. The method also assumes that the periodicity and duration of the data gaps are known and consistent for a given time series. The theoretical basis of the new technique is derived and tested using simulation and the new procedure is then applied to real test data to estimate the coefficients of the frequency polynomial. As a quantitative estimate for the $1/{\bm{f}}$ noise, the radiometer gain fluctuation (${\bm{\Delta}}{\bm{G}}/{\bm{G}}$) at 1 Hz is then solved from the frequency polynomial of the gain fluctuation power spectrum. The 1 Hz $( {{\bm{\Delta}}{\bm{G}}/{\bm{G}}} )$ values were compared between two sets of ground test data for the same MWI channels but with large (92%) and small (4.89%) duty cycles. The similarity of the 1 Hz $( {{\bm{\Delta}}{\bm{G}}/{\bm{G}}} )$ values extracted from these two disparate datasets establishes confidence in the method. The derived noise power spectrum is then used to simulate MWIs radiometric brightness temperature images and predict the level of unwanted striping in the flight data due to $1/{\bm{f}}$ noise content. This method may be applicable to solve for the polynomial coefficients of the power spectrum of any noise process, which can be modeled as a frequency polynomial, given the polynomial form is known a priori.

Abstract Mammalian pregnancy requires gradual yet extreme remodeling of the reproductive organs to support the growth of the embryos and their birth. After delivery, the reproductive organs return to their non-pregnant state. As pregnancy has traditionally been understudied, there are many unknowns pertaining to the mechanisms behind this remarkable remodeling and repair process which, when not successful, can lead to pregnancy-related complications such as maternal trauma, pre-term birth, and pelvic floor disorders. This study presents the first longitudinal imaging data that focuses on revealing anatomical alterations of the vagina, cervix, and uterine horns during pregnancy and postpartum using the mouse model. By utilizing advanced magnetic resonance imaging (MRI) technology, T1-weighted and T2-weighted images of the reproductive organs of three mice in their in vivo environment were collected at five time points: non-pregnant, mid-pregnant (gestation day: 9–10), late pregnant (gestation day: 16–17), postpartum (24–72 h after delivery) and three weeks postpartum. Measurements of the vagina, cervix, and uterine horns were taken by analyzing MRI segmentations of these organs. The cross-sectional diameter, length, and volume of the vagina increased in late pregnancy and then returned to non-pregnant values three weeks after delivery. The cross-sectional diameter of the cervix decreased at mid-pregnancy before increasing in late pregnancy. The volume of the cervix peaked at late pregnancy before shortening by 24–72 h postpartum. As expected, the uterus increased in cross-sectional diameter, length, and volume during pregnancy. The uterine horns decreased in size postpartum, ultimately returning to their average non-pregnant size three weeks postpartum. The newly developed methods for acquiring longitudinal in vivo MRI scans of the murine reproductive system can be extended to future studies that evaluate functional and morphological alterations of this system due to pathologies, interventions, and treatments.

Abstract Discrete symmetries play an important role in particle physics with violation of CP connected to the matter-antimatter imbalance in the Universe. We report the most precise test of P, T and CP invariance in decays of ortho-positronium, performed with methodology involving polarization of photons from these decays. Positronium, the simplest bound state of an electron and positron, is of recent interest with discrepancies reported between measured hyperfine energy structure and theory at the level of 10−4 signaling a need for better understanding of the positronium system at this level. We test discrete symmetries using photon polarizations determined via Compton scattering in the dedicated J-PET tomograph on an event-by-event basis and without the need to control the spin of the positronium with an external magnetic field, in contrast to previous experiments. Our result is consistent with QED expectations at the level of 0.0007 and one standard deviation.

National parks and other federally designated natural areas play critical roles in preserving unique habitats, communities, and biodiversity. However, in the United States, it is estimated that 80–90% of species diversity in national parks is presently unknown. Therefore, contemporary biodiversity inventories are critical for conservation, management and establishing baselines for future comparisons. Ongoing efforts to characterize lichen diversity highlight diverse and robust communities in a number of national parks in the USA. In arid regions of the western USA facing ecological transformations, lichens can play a pivotal role for monitoring these changes. Lichen diversity in Bryce Canyon National Park (BRCA) in southern Utah, USA remains nearly completely uncharacterized, despite nearly 100 years as a federally protected area. Our study aims to provide a critical perspective into the lichen diversity of BRCA. Using a metabarcoding community sampling approach, we documented 215 candidate lichen-forming fungal species distributed across ecologically distinct sites in BRCA. At each sampled site, species richness ranged from 104 to 133 species, with no more than 20% shared species among the three sites. The limited overlap between collection sites suggests that BRCA harbors greater diversity than initially thought. We document a number of sensitive lichens, particularly Usnea spp. and Ramalina sinensis , that should be monitored as air pollution, land use, and impacts of climate change affect biological communities in the park. The inventory also includes unknown species and other species that have not been documented in the western USA. While our DNA-based inventory highlights strikingly rich lichen diversity, future voucher-based collections will be essential for robust taxonomic determinations.

In allogeneic MSC implantation, the cells are isolated from a donor different from the recipient. When tested, allogeneic MSCs have several advantages over autologous ones: faster cell growth, sufficient cell concentration, and readily available cells for clinics. To ensure the safe and efficient use of allogeneic MSCs in clinics, the MSCs need to be first tested in vitro. With this study, we paved the way by addressing the in vitro aspects of canine adipose-derived MSCs, considering the limited studies on the clinical use of canine cells. We isolated cAD-MSCs from canine falciform ligament fat and evaluated their viability and proliferation using an MTS assay. Then, we characterized the MSC-specific antigens using immunophenotyping and immunofluorescence and demonstrated their potential for in vitro differentiation. Moreover, we established shipping and cryobanking procedures to lead the study to become an off-the-shelf therapy. During expansion, the cells demonstrated a linear increase in cell numbers, confirming their proliferation quantitatively. The cells showed viability before and after cryopreservation, demonstrating that cell viability can be preserved. From a clinical perspective, the established shipping conditions demonstrated that the cells retain their viability for up to 48 h. This study lays the groundwork for the potential use of allogeneic cAD-MSCs in clinical applications.

Background/Objectives: Peripheral nerve injuries (PNIs) are a debilitating problem, resulting in diminished quality of life due to the continued presence of both chronic and acute pain. The current standard of practice for the repair of PNIs larger than 10 mm is the use of autologous nerve grafts. Autologous nerve grafts have limitations that often result in outcomes that are not sufficient to remove motor and sensory impairments. Bio-mimetic nanocomposite scaffolds combined with mesenchymal stem cells (MSCs) represent a promising approach for PNIs. In this study, we investigated the potential of an electrospun wrap of polycaprolactone (PCL) + graphene oxide (GO), with and without xenogeneic human adipose tissue-derived MSCs (hADMSCs) to use as a platform for neural tissue engineering. Methods: We evaluated, in vitro and in vivo, the potential of the nerve wrap in providing support for axonal growth. To establish the rat sciatic nerve defect model, a 10 mm long limiting defect was created in the rat sciatic nerve of 18 Lewis rats. Rats treated with the nanocomposites were compared with autograft-treated defects. Gait, histological, and muscle analyses were performed after sacrifice at 12 weeks post-surgery. Results: Our findings demonstrate that hADMSCs had the potential to transdifferentiate into neural lineage and that the nanocomposite successfully delivered hADMSCs to the injury site. Histologically, we show that the PCL + GO nanocomposite with hADMSCs is comparable to the autologous nerve graft, to support and guide axonal growth. Conclusions: The novel PCL + GO nerve wrap and hADMSCs used in this study provide a foundation on which to build upon and generate future strategies for PNI repair.

Background: Smacovirus is a CRESS-DNA virus identified almost exclusively in transient fecal samples from various vertebrate species. Objective: We evaluated human vaginal samples for the presence and maintenance of Smacovirus. Methods: Viral metagenomics analysis was performed on vaginal samples collected from 28 apparently healthy women in New York City, USA. Twenty-one of the women provided duplicate samples over a 12–21-day interval. Results: Phylogenetic analysis identified two samples from the same individual, collected over a twelve-day interval, that were positive for the complete Smacovirus genome. All detected sequence contigs belonged to a single variant of CRESS-DNA. Conclusions: The continuous presence of Smacovirus in the human vagina over a twelve-day period was identified.

IntroductionApproximately 50% of melanomas harbor an activating BRAFV600E mutation. Standard of care involves a combination of inhibitors targeting mutant BRAF and MEK1/2, the substrate for BRAF in the MAPK pathway. PTEN loss-of-function mutations occur in ~40% of BRAFV600E melanomas, resulting in increased PI3K/AKT activity that enhances resistance to BRAF/MEK combination inhibitor therapy.MethodsTo compare the response of PTEN null to PTEN wild-type cells in an isogenic background, CRISPR/Cas9 was used to knock out PTEN in a melanoma cell line that harbors a BRAFV600E mutation. RNA sequencing, functional kinome analysis, and drug synergy screening were employed in the context of BRAF/MEK inhibition.ResultsRNA sequencing and functional kinome analysis revealed that the loss of PTEN led to an induction of FOXD3 and an increase in expression of the FOXD3 target gene, ERBB3/HER3. Inhibition of BRAF and MEK1/2 in PTEN null, BRAFV600E cells dramatically induced the expression of ERBB3/HER3 relative to wild-type cells. A synergy screen of epigenetic modifiers and kinase inhibitors in combination with BRAFi/MEKi revealed that the pan ERBB/HER inhibitor, neratinib, could reverse the resistance observed in PTEN null, BRAFV600E cells.ConclusionsThe findings indicate that PTEN null BRAFV600E melanoma exhibits increased reliance on ERBB/HER signaling when treated with clinically approved BRAFi/MEKi combinations. Future studies are warranted to test neratinib reversal of BRAFi/MEKi resistance in patient melanomas expressing ERBB3/HER3 in combination with its dimerization partner ERBB2/HER2.

ABSTRACTMicrobes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.