Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids

A mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate with highly adapted and evolved microbial consortia. The microbial residents within these organ systems are increasingly well characterized, yielding a good understanding of human microbiome composition, but we have yet to elucidate the full chemical impact the microbiome exerts on an animal and the breadth of the chemical diversity it contributes. A number of molecular families are known to be shaped by the microbiome including short-chain fatty acids, indoles, aromatic amino acid metabolites, complex polysaccharides, and host lipids; such as sphingolipids and bile acids. These metabolites profoundly affect host physiology and are being explored for their roles in both health and disease. Considering the diversity of the human microbiome, numbering over 40,000 operational taxonomic units, a plethora of molecular diversity remains to be discovered. Here, we use unique mass spectrometry informatics approaches and data mapping onto a murine 3D-model to provide an untargeted assessment of the chemical diversity between germ-free (GF) and colonized mice (specific-pathogen free, SPF), and report the finding of novel bile acids produced by the microbiome in both mice and humans that have evaded characterization despite 170 years of research on bile acid chemistry

Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids

A mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate with highly adapted and evolved microbial consortia. The microbial residents within these organ systems are increasingly well characterized, yielding a good understanding of human microbiome composition, but we have yet to elucidate the full chemical impact the microbiome exerts on an animal and the breadth of the chemical diversity it contributes. A number of molecular families are known to be shaped by the microbiome including short-chain fatty acids, indoles, aromatic amino acid metabolites, complex polysaccharides, and host lipids; such as sphingolipids and bile acids. These metabolites profoundly affect host physiology and are being explored for their roles in both health and disease. Considering the diversity of the human microbiome, numbering over 40,000 operational taxonomic units, a plethora of molecular diversity remains to be discovered. Here, we use unique mass spectrometry informatics approaches and data mapping onto a murine 3D-model to provide an untargeted assessment of the chemical diversity between germ-free (GF) and colonized mice (specific-pathogen free, SPF), and report the finding of novel bile acids produced by the microbiome in both mice and humans that have evaded characterization despite 170 years of research on bile acid chemistry

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation.

There is a poor understanding of how the physiology of polymicrobial communities in cystic fibrosis (CF) lungs contributes to pulmonary exacerbations and lung function decline. In this study, a microbial culture system based on the principles of the Winogradsky column (WinCF system) was developed to study the physiology of CF microbes. The system used glass capillary tubes filled with artificial sputum medium to mimic a clogged airway bronchiole. Chemical indicators were added to observe microbial physiology within the tubes. Characterization of sputum samples from seven patients showed variation in pH, respiration, biofilm formation and gas production, indicating that the physiology of CF microbial communities varied among patients. Incubation of homogenized tissues from an explant CF lung mirrored responses of a Pseudomonas aeruginosa pure culture, supporting evidence that end-stage lungs are dominated by this pathogen. Longitudinal sputum samples taken through two exacerbation events in a single patient showed that a two-unit drop in pH and a 30% increase in gas production occurred in the tubes prior to exacerbation, which was reversed with antibiotic treatment. Microbial community profiles obtained through amplification and sequencing of the 16S rRNA gene showed that fermentative anaerobes became more abundant during exacerbation and were then reduced during treatment where P. aeruginosa became the dominant bacterium. Results from the WinCF experiments support the model where two functionally different CF microbial communities exist, the persistent Climax Community and the acute Attack Community. Fermentative anaerobes are hypothesized to be the core members of the Attack Community and production of acidic and gaseous products from fermentation may drive developing exacerbations. Treatment targeting the Attack Community may better resolve exacerbations and resulting lung damage

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Rubella Immunization of Adult Females Using HPV-77 DK-12 Live Attenuated Rubella Virus

This study demonstrates the serologic response as measured by the HAl test and the side reactions of the HPV-77 DK-12 live rubella vaccine in a small group of adult females. One hundred percent seroconversion was obtained using this vaccine. The mean titers obtained in two separate time periods post-vaccination are higher than those reported for several other rubella virus vaccines. A 66% occurrence of joint symptomatology was recorded post-vaccination with a mean duration of 11.6 days; 24% of women who received placebo reported joint complaints which had a mean duration of 2.0 days. The difference between these two rates is somewhat greater than that reported for other HPV-77 strain vaccines and the average duration of these complaints is longer. The other symptoms reported postvaccination seemed insignificant when comparing both the placebo and the vaccine group. One woman became pregnant three months after vaccination and was subsequently therapeutically aborted. At the time of therapeutic abortion, attempts were unsuccessful to recover rubella virus from the products of conception and cervical swabs

Human epicardial adipose tissue expresses a pathogenic profile of adipocytokines in patients with cardiovascular disease

Introduction: Inflammation contributes to cardiovascular disease and is exacerbated with increased adiposity, particularly omental adiposity; however, the role of epicardial fat is poorly understood. Methods: For these studies the expression of inflammatory markers was assessed in epicardial fat biopsies from coronary artery bypass grafting (CABG) patients using quantitative RT-PCR. Further, the effects of chronic medications, including statins, as well as peri-operative glucose, insulin and potassium infusion, on gene expression were also assessed. Circulating resistin, CRP, adiponectin and leptin levels were determined to assess inflammation. Results: The expression of adiponectin, resistin and other adipocytokine mRNAs were comparable to that in omental fat. Epicardial CD45 expression was significantly higher than control depots (p < 0.01) indicating significant infiltration of macrophages. Statin treated patients showed significantly lower epicardial expression of IL-6 mRNA, in comparison with the control abdominal depots (p < 0.001). The serum profile of CABG patients showed significantly higher levels of both CRP (control: 1.28 ± 1.57 μg/mL vs CABG: 9.11 ± 15.7 μg/mL; p < 0.001) and resistin (control: 10.53 ± 0.81 ng/mL vs CABG: 16.8 ± 1.69 ng/mL; p < 0.01) and significantly lower levels of adiponectin (control: 29.1 ± 14.8 μg/mL vs CABG: 11.9 ± 6.0 μg/mL; p < 0.05) when compared to BMI matched controls. Conclusion: Epicardial and omental fat exhibit a broadly comparable pathogenic mRNA profile, this may arise in part from macrophage infiltration into the epicardial fat. This study highlights that chronic inflammation occurs locally as well as systemically potentially contributing further to the pathogenesis of coronary artery disease

Putting Quality Functional Assessment into Practice in Schools: A Research Agenda on Behalf of E/BD Students

The discipline provisions of the IDEA place emphasis on gaining an understanding of why the student is motivated to engage in problem behavior and to consider, when appropriate, positive behavioral interventions, strategies, and supports to address the behavior. These legislative mandates bring center stage a range of new duties and responsibilities for the IEP team. This article discusses the problems that school divisions across the country are encountering when implementing these requirements and recommends a course of research to address these issues

Public interest in hyaluronic acid injections for knee osteoarthritis in the United States and Europe: An international Google Trends analysis

BACKGROUND: Hyaluronic acid injections remain a common nonsurgical alternative for the treatment of knee osteoarthritis despite limited clinical evidence and varying global recommendations regarding its use. We used the Google Trends tool to provide a quantitative analysis of public interest in hyaluronic acid injections for knee osteoarthritis in the United States and Europe. METHODS: We customized Google Trends parameters to obtain search data from January 2009 to December 2019 in both the United States and Europe. Combinations of arthritis , osteoarthritis , hyaluronic acid , knee arthritis , knee osteoarthritis , and knee injection were entered into the Google Trends tool, and trend analyses were performed. RESULTS: The models generated to describe public interest in hyaluronic acid for knee injections in both the United States and Europe showed increased Google queries as time progressed ( CONCLUSIONS: Our results indicate a significant increase in Google queries related to hyaluronic acid injections for knee osteoarthritis since 2009 in both the United States and Europe. Our models suggest that despite mixed evidence supporting its use, orthopedic surgeons should expect continued public interest in hyaluronic acid for knee osteoarthritis. The results of our study may help to prepare surgeons for patient inquiries, inform the creation of evidence-based shared decision-making tools, and direct future research

Who is classified as untestable on brief cognitive screens in an acute stroke setting?

Full completion of cognitive screening tests can be problematic in the context of a stroke. Our aim was to examine the completion of various brief cognitive screens and explore reasons for untestability. Data were collected from consecutive stroke admissions (May 2016–August 2018). The cognitive assessment was attempted during the first week of admission. Patients were classified as partially untestable (≥1 test item was incomplete) and fully untestable (where assessment was not attempted, and/or no questions answered). We assessed univariate and multivariate associations of test completion with: age (years), sex, stroke severity (National Institutes of Health Stroke Scale (NIHSS)), stroke classification, pre-morbid disability (modified Rankin Scale (mRS)), previous stroke and previous dementia diagnosis. Of 703 patients admitted (mean age: 69.4), 119 (17%) were classified as fully untestable and 58 (8%) were partially untestable. The 4A-test had 100% completion and the clock-draw task had the lowest completion (533/703, 76%). Independent associations with fully untestable status had a higher NIHSS score (odds ratio (OR): 1.18, 95% CI: 1.11–1.26), higher pre-morbid mRS (OR: 1.28, 95% CI: 1.02–1.60) and pre-stroke dementia (OR: 3.35, 95% CI: 1.53–7.32). Overall, a quarter of patients were classified as untestable on the cognitive assessment, with test incompletion related to stroke and non-stroke factors. Clinicians and researchers would benefit from guidance on how to make the best use of incomplete test data