Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres

The G + C content at synonymous codon positions (GC3s) in genes varies along chromosomes in most eukaryotes. In Saccharomyces cerevisiae, regions of high GC3s are correlated with recombination hot spots, probably due to biased gene conversion. Here we examined how GC3s differs among groups of related yeast species in the Saccharomyces and Candida clades. The chromosomal locations of GC3s peaks and troughs are conserved among four Saccharomyces species, but we find that there have been highly consistent small shifts in their GC3s values. For instance, 84% of all S. cerevisiae genes have a lower GC3s value than their S. bayanus orthologs. There are extensive interspecies differences in the Candida clade both in the median value of GC3s (ranging from 22% to 49%) and in the variance of GC3s among genes. In three species—Candida lusitaniae, Pichia stipitis, and Yarrowia lipolytica—there is one region on each chromosome in which GC3s is markedly reduced. We propose that these GC-poor troughs indicate the positions of centromeres because in Y. lipolytica they coincide with the five experimentally identified centromeres. In P. stipitis, the troughs contain clusters of the retrotransposon Tps5. Likewise, in Debaryomyces hansenii, there is one cluster of the retrotransposon Tdh5 per chromosome, and all these clusters are located in GC-poor troughs. Locally reduced G + C content around centromeres is consistent with a model in which G + C content correlates with recombination rate, and recombination is suppressed around centromeres, although the troughs are unexpectedly wide (100–300 kb)

No sex scandals please, we're French: French attitudes towards politicians' public and private conduct

The notion of distinct ‘public’ and ‘private’ spheres underpins much normative and practical engagement with political misconduct. What is less clear is whether citizens draw distinctions between misdemeanours in the ‘public’ and ‘private’ spheres, and whether they judge these in systematically different ways. This paper explores attitudes to political misconduct in France. French citizens are often said to be particularly relaxed about politicians’ private affairs, but there has been little empirical evidence for this proposition. Drawing on original survey data, this paper demonstrates clearly that French citizens draw a sharp distinction between politicians’ public and private transgressions, and are more tolerant of the latter

Perioperative mental health intervention bundle for older surgical patients: Protocol for an intervention development and feasibility study

INTRODUCTION: The perioperative period is high risk for older adults. Depression and anxiety are common perioperative problems, frequently coexisting with cognitive impairment. Older patients with these conditions are more likely than younger patients to experience postoperative delirium, long hospital stays, poor quality of life and rehospitalisation. These experiences can, in turn, exacerbate anxiety and depressive symptoms. Despite these risks, little is known about how to treat perioperative anxiety and depression among older adults. METHODS AND ANALYSIS: We designed a feasibility study of a perioperative mental health intervention bundle to improve perioperative mental health, specifically depression and anxiety. The overarching goals of this study are twofold: first, to adapt and refine an intervention bundle comprised of behavioural activation and medication optimisation to meet the needs of older adults within three surgical patient populations (ie, orthopaedic, oncological and cardiac); and second, to test the feasibility of study procedures and intervention bundle implementation. Quantitative data on clinical outcomes such as depression, anxiety, quality of life, delirium, falls, length of stay, hospitalisation and pain will be collected and tabulated for descriptive purposes. A hybrid inductive-deductive thematic approach will be employed to analyse qualitative feedback from key stakeholders. ETHICS AND DISSEMINATION: The study received approval from the Washington University Institutional Review Board. Results of this study will be presented in peer-reviewed journals, at professional conferences, and to our perioperative mental health advisory board. TRIAL REGISTRATION NUMBER: NCT05110690

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term ‘fermented’ led the panel to define fermented foods and beverages as “foods made through desired microbial growth and enzymatic conversions of food components”. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term ‘fermented’ led the panel to define fermented foods and beverages as “foods made through desired microbial growth and enzymatic conversions of food components”. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines

Interleukin-1 polymorphisms associated with increased risk of gastric cancer

Helicobacter pylori infection is associated with a variety of clinical outcomes including gastric cancer and duodenal ulcer disease. The reasons for this variation are not clear, but the gastric physiological response is influenced by the severity and anatomical distribution of gastritis induced by H. pylori. Thus, individuals with gastritis predominantly localized to the antrum retain normal (or even high) acid secretion, whereas individuals with extensive corpus gastritis develop hypochlorhydria and gastric atrophy, which are presumptive precursors of gastric cancer. Here we report that interleukin-1 gene cluster polymorphisms suspected of enhancing production of interleukin-1-beta are associated with an increased risk of both hypochlorhydria induced by H. pylori and gastric cancer. Two of these polymorphism are in near-complete linkage disequilibrium and one is a TATA-box polymorphism that markedly affects DNA-protein interactions in vitro. The association with disease may be explained by the biological properties of interleukin-1-beta, which is an important pro-inflammatory cytokine and a powerful inhibitor of gastric acid secretion. Host genetic factors that affect interleukin-1-beta may determine why some individuals infected with H. pylori develop gastric cancer while others do no

Artificial Stupidity

Public debate about AI is dominated by Frankenstein Syndrome, the fear that AI will become superhuman and escape human control. Although superintelligence is certainly a possibility, the interest it excites can distract the public from a more imminent concern: the rise of Artificial Stupidity (AS). This article discusses the roots of Frankenstein Syndrome in Mary Shelley’s famous novel of 1818. It then provides a philosophical framework for analysing the stupidity of artificial agents, demonstrating that modern intelligent systems can be seen to suffer from ‘stupidity of judgement’. Finally it identifies an alternative literary tradition that exposes the perils and benefits of AS. In the writings of Edmund Spenser, Jonathan Swift and E.T.A. Hoffmann, ASs replace, enslave or delude their human users. More optimistically, Joseph Furphy and Laurence Sterne imagine ASs that can serve human intellect as maps or as pipes. These writers provide a strong counternarrative to the myths that currently drive the AI debate. They identify ways in which even stupid artificial agents can evade human control, for instance by appealing to stereotypes or distancing us from reality. And they underscore the continuing importance of the literary imagination in an increasingly automated society

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary

Volume 01

Introduction from Dean Dr. Charles Ross Three Decades of Digging: Undergraduate Archeology at Longwood by Jessica Fields and Stephanie Neeley Interactions of Allelopathy and Heat Stress in Plants by Derek W. Hambright and Mary E. Lehman Inertial Electrostatic Confinement D-D Fusion Device: Construction and Simulation by Andrew R. Grzankowski Shackled Nim by Zachary Johnson Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Boone M. Prentice A Comparison of Image Analysis Methods in cDNA Microarrays by Ashley M. Swandby Perceived Sexual Activity of Short and Long-Term Relationships by Victoria Morgan and Katie Williamson Elderly Male Communication by Kristine G. Bender Three Poems: “Adam and Eve and an Orange Tree”, “The Name of Everything Before Dying”, and “The ‘Poet Voice’” by Katelyn N. Romaine There\u27s Nothing Like Dancing, After All : Marriage and Gender in the Dance Scenes of Jane Austen\u27s Novels by D. Nicole Swann Two Poems: “Age Nine with Mother” and “The Apple That Crawls Away From the Tree” by Jessica Fox Untitled by Mike McAteer Room 9 by Alex Grabiec Two Photographs: “Gracie” and “Emily” by Laura Nodtvedt Bowling Lanes Night by Nick Costa Two Paintings: “Can and Kettle” and “Scarecrow” by Rachel Wolfe Exploring Henrik Ibsen\u27s “Perr Gynt” by Zack Dalton Creative Writing Scholarship at Longwood University Music Scholarship at Longwood – Senior Recital Arianne K. Burrus Longwood University Theater – Peer Gyn

The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs

Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at similar to 24.5 degrees C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk