bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
Authors: Tran Patricia Q. , Bachand Samantha C. , McIntyre Peter B. , Kraemer Benjamin M. , Vadeboncoeur Yvonne , Kimirei Ismael A. , Tamatamah Rashid , McMahon Katherine D. , Anantharaman Karthik 
Published: November 2019

AbstractLake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 m deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 21 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change which is predicted to bring increased stratification and anoxia to freshwater lakes.
A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects
Authors: Mefferd Chrisabelle C. , Bhute Shrikant S. , Phan Jacqueline R. , Villarama Jacob V. , Do Dung M. , Alarcia Stephanie , Abel-Santos Ernesto , Hedlund Brian P. 
Published: November 2019

AbstractClostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and 100% mortality, and a high-fat/low-protein, medium-chain triglyceride (MCT)-like diet inducing highly variable CDI outcomes. In contrast, mice fed a high-carbohydrate diet were protected from CDI, despite high refined carbohydrate and low fiber content. 28 members of the Lachnospiraceae and Ruminococcaceae decreased in abundance due to diet and/or antibiotic treatment; these organisms may compete with C. difficile for amino acids and protect healthy animals from CDI in the absence of antibiotics. Together, these data suggest that antibiotic treatment might lead to loss of C. difficile competitors and create a favorable environment for C. difficile proliferation and virulence that is intensified by high-fat/high-protein diets; in contrast, high-carbohydrate diets might be protective regardless of the source of carbohydrate.
Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provide insights into chromosomal evolution and rediploidization across salmonids
Authors: Blumstein Danielle M. , Campbell Matthew A. , Hale Matthew C. , Sutherland Ben J. G. , McKinney Garrett J. , Stott Wendylee , Larson Wesley A. 
Published: November 2019

AbstractWhole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.
The ocellate river stingray (Potamotrygon motoro) exploits vortices of sediment to bury into the substrate
Authors: Seamone S.G. , Syme D.A. 
Published: November 2019

ABSTRACTParticle image velocimetry and video analysis were employed to discern and describe the mechanism used by the stingrayPotamotrygon motoroto bury into the substrate.P. motororepeatedly and rapidly pumped the body up and down while folding the posterior portion of the pectoral fins up and over, drawing water in and suspending sediment beneath the pectoral disc. As the fins folded up and over, vortices of fluidized sediment travelled along the ventral surface of the fins toward the fin tips, and were then directed onto the dorsal surface of the fins and towards the dorsal midline of the fish, where they dissipated and the sediment settled over the dorsal surface of the ray. As displacement and speed of the body pumping and finbeat motions increased, the speed of the sediment translating across the dorsal surface increased, and accordingly, sediment coverage of the dorsal surface increased. Mean sediment coverage was 82.5% ± 3.0 S.E.M, and appeared to be selectively controlled, whereby the pectoral fins tended to bury more than the body, head and tail, and the body more than the head and the tail. In the most vigorous burying events, vortices of sediment shed from each fin collided at the midline and annihilated, reorienting the sediment flow and sending jets of sediment towards the head and the tail, covering these locations with sediment. Hence, this study demonstrates that the mechanism of burying employed byP. motoropermits effective control of sediment vortices and flows to modulate the extent of burying.
A causal role for mouse superior colliculus in visual perceptual decision-making
Authors: Wang Lupeng , McAlonan Kerry , Goldstein Sheridan , Gerfen Charles R. , Krauzlis Richard J. 
Published: November 2019

AbstractThe superior colliculus (SC) is arguably the most important visual structure in the mouse brain and is well-known for its involvement in innate responses to visual threats and prey items. In other species, the SC plays a central role in voluntary as well as innate visual functions, including crucial contributions to selective attention and perceptual decision-making. In the mouse, the possible role of the SC in voluntary visual choice behaviors has not been established. Here, we demonstrate that the mouse SC plays a causal role in visual perceptual decision-making by transiently inhibiting SC activity during an orientation-change detection task. First, unilateral SC inhibition induced spatially specific deficits in detection. Hit rates were reduced and reaction times increased for orientation changes in the contralateral but not ipsilateral visual field. Second, the deficits caused by SC inhibition were specific to a temporal epoch coincident with early visual burst responses in the SC. Inhibiting SC during this 100-ms period caused a contralateral detection deficit, whereas inhibition immediately before or after did not. Third, SC inhibition reduced visual detection sensitivity. Psychometric analysis revealed that inhibiting SC visual activity significantly increased detection thresholds for contralateral orientation changes. In addition, effects on detection thresholds and lapse rates caused by SC inhibition were larger in the presence of a competing visual stimulus, indicating a role for the mouse SC in visual target selection. Together, our results demonstrate that the mouse SC plays a crucial role in voluntary visual choice behaviors.Significance statementThe mouse superior colliculus has become a popular model for studying the circuit organization and development of the visual system. Although the SC is a fundamental component of the visual pathways in mice, its role in visual perceptual decision-making is not clear. By investigating how temporally precise SC inhibition influenced behavioral performance during a visually guided orientation change detection task, we identified a 100-ms temporal epoch of SC visual activity that is crucial for the ability of mice to detect behaviorally relevant visual changes. In addition, we found that SC inhibition also caused deficits in visual target selection. Thus, our findings highlight the importance of the SC for visual perceptual choice behavior in the mouse.
Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018
Authors: Arteaga Mónica , Velasco Juliana , Rodriguez Shelly , Vidal Maricel , Arellano Carolina , Silva Francisco , Carreño Leandro J. , Vidal Roberto , Montero David A. 
Published: November 2019

AbstractVibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains.DATA SUMMARYSequence data were submitted to GenBank under the accession number SRLP00000000. The authors confirm that all supporting data and protocols have been provided within the article or through supplementary data files.Data statementAll supporting data, code and protocols have been provided within the article or through supplementary data files. Four supplementary tables are available with the online version of this article.
The early local and systemic Type I interferon responses to ultraviolet B light exposure are cGAS dependent
Authors: Skopelja-Gardner Sladjana , An Jie , Tai Joyce , Tanaka Lena , Sun Xizhang , Hermanson Payton , Baum Rebecca , Kawasumi Masaoki , Green Richard , Gale Michael , Kalus Andrea , Werth Victoria P. , Elkon Keith B. 
Published: November 2019

AbstractMost systemic lupus erythematosus (SLE) patients are photosensitive and ultraviolet B light (UVB) exposure worsens cutaneous disease and precipitates systemic flares of disease. The pathogenic link between skin disease and systemic exacerbations in SLE remains elusive. In an acute model of UVB-triggered inflammation, we observed that a single UV exposure triggered a striking IFN-I signature not only in the skin, but also in the blood and kidneys. The early IFN-I signature was significantly higher in female compared to male mice. The early IFN-I response in the skin was almost entirely, and in the blood partly, dependent on the presence of cGAS, as was skin inflammatory cell infiltration. Inhibition of cGAMP hydrolysis augmented the UVB-triggered IFN-I response. UVB skin exposure leads to cGAS-activation and both local and systemic IFN-I signature and could contribute to acute flares of disease in susceptible subjects such as patients with SLE.
mir-71 mediates age-dependent opposing contributions of the stress activated kinase KGB-1 inCaenorhabditis elegans
Authors: Ruediger Cyrus , Shapira Michael 
Published: November 2019

ABSTRACTStudying the evolutionary processes that shaped aging offers a path for understanding the causes of aging. The Antagonistic Pleiotropy theory for the evolution of aging proposes that the inverse correlation between natural selection strength and aging allows positive selection of gene variants with early-life beneficial contributions to fitness in spite of detrimental late-life consequences. However, mechanistic understanding of how this principle manifests in aging is still lacking. We previously identified antagonistic pleiotropy in the function of theCaenorhabditis elegansJNK homolog KGB-1, which provided stress protection in developing larvae, but sensitized adults to stress and shortened their lifespan. To a large extent, KGB-1’s contributions depended on age-dependent and opposing regulation of the stress transcription factor DAF-16, but the underlying mechanisms remained unknown. Here we describe a role for the microRNA mir-71 in mediating effects of KGB-1 on DAF-16 and on downstream phenotypes. Fluorescent imaging along with genetic and survival analyses revealed age-dependent regulation ofmir-71expression by KGB-1 – upregulation in larvae, but downregulation in adults, and showed thatmir-71was required both for late-life effects of KGB-1 (infection sensitivity and shortened lifespan), as well as for early life resistance to cadmium. Whilemir-71disruption did not compromise development under protein folding stress (known to depend on KGB-1), disruption of the argonaute genealg-1, a central component of the microRNA machinery, did. These results suggest that microRNAs play a role in mediating age-dependent antagonistic contributions of KGB-1 to survival, with mir-71 playing a central role and additional microRNAs contributing redundantly.
Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies
Authors: Thibério Rangel L. , Fournier Gregory P. 
Published: November 2019

AbstractThe trimming of fast-evolving sites, often known as “slow-fast” analysis, is broadly used in microbial phylogenetic reconstruction under assumption that fast-evolving sites do not retain accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here we show that, contrary to this assumption, even the fastest evolving sites, present in conserved proteins often used in Tree of Life studies, contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site specific substitution-rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we additionally show that both slow-and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.Significance StatementIt is common practice among comprehensive microbial phylogenetic studies to trim fast-evolving sites from the source alignment in the expectation to increase the signal to noise ratio. Here we show that despite fast-evolving sites being more sensitive to parameter misspecifications than mid-rate evolving sites, such sensitivity is comparable, if not smaller, than what we observe among slow-evolving sites. Through the use of both empirical and simulated datasets we also show that, besides the lack of evidences regarding the noisy nature of fast-evolving sites, such sites are of core importance for the reliable the reconstruction of short-branched bipartitions. Such points are exemplified by the variations in the Eukarya+Archaea Tree of Life when subjective alignment trimming strategies are employed.
Identifying Integrative Molecular Pathways for Predictive Modeling of Infectious Disease
Authors: Schaper Charles D. 
Published: November 2019

AbstractThe signs and symptoms of infectious disease are similar in presentation, such as fever and fatigue, but differ in magnitude, duration, and sequence. Although observable responses of dysfunction are well characterized, the integrative system mechanisms driving such trajectories are poorly known, even during normative circumstances. Here, molecular pathways are presented that enable predictive modeling of autonomic dysfunction due to infectious agents, and that illustrate a coordinating integration of body system dynamics. To arrive at this result, a molecular model is presented which shows, for the first time, that the hormone cortisol (CORT) and prostaglandin E2 (PGE2) have approximately equivalent chemical affinity, as indicated by the positioning of functional groups in hydrogen bonding and hydrophobicity, with the ligand binding domain of the glucocorticoid receptor (GR). A mathematical model is developed to predict that the signs and symptoms of illnesses are associated with the competitive inhibition at the GR of CORT and PGE2 within the hypothalamus that prevents normal gene expression during DNA transcription. To validate the pathways and model, a case study is presented to analyze the cause and presentation of fever and fatigue over multiple days due to the injection of a pneumococcal vaccine as influenced by physical activity. The research provides quantitative understanding of the root causes of signs and symptoms of infectious disease, which for example can offer a quantitative explanation of common symptomatic concerns of illness, such as fever, and can result in optimal drug treatment plans to minimize the effects of ailments.Graphical Abstract
Individual differences in haemoglobin concentration influence BOLD fMRI functional connectivity and its correlation with cognition
Authors: Ward Phillip G. D. , Orchard Edwina R. , Oldham Stuart , Arnatkevičiūtė Aurina , Sforazzini Francesco , Fornito Alex , Storey Elsdon , Egan Gary F. , Jamadar Sharna D. 
Published: November 2019

AbstractResting-state connectivity measures the temporal coherence of the spontaneous neural activity of spatially distinct regions, and is commonly measured using BOLD-fMRI. The BOLD response follows neuronal activity, when changes in the relative concentration of oxygenated and deoxygenated haemoglobin cause fluctuations in the MRI T2* signal. Since the BOLD signal detects changes in relative concentrations of oxy/deoxy-haemoglobin, individual differences in haemoglobin levels may influence the BOLD signal-to-noise ratio in a manner independent of the degree of neural activity. In this study, we examined whether group differences in haemoglobin may confound measures of functional connectivity. We investigated whether relationships between measures of functional connectivity and cognitive performance could be influenced by individual variability in haemoglobin. Finally, we mapped the neuroanatomical distribution of the influence of haemoglobin on functional connectivity to determine where group differences in functional connectivity are manifest.In a cohort of 518 healthy elderly subjects (259 men) each sex group was median split into two groups with high and low haemoglobin concentration. Significant differences were obtained in functional connectivity between the high and low haemoglobin groups for both men and women (Cohen’s d 0.17 and 0.03 for men and women respectively). The haemoglobin connectome in males showed a widespread systematic increase in functional connectivity correlational scores, whilst the female connectome showed predominantly parietal and subcortical increases and temporo-parietal decreases. Despite the haemoglobin groups having no differences in cognitive measures, significant differences in the linear relationships between cognitive performance and functional connectivity were obtained for all 5 cognitive tests in males, and 4 out of 5 tests in females.Our findings confirm that individual variability in haemoglobin levels that give rise to group differences are an important confounding variable in BOLD-fMRI-based studies of functional connectivity. Controlling for haemoglobin variability as a potentially confounding variable is crucial to ensure the reproducibility of human brain connectome studies, especially in studies that compare groups of individuals, compare sexes, or examine connectivity-cognition relationships.HighlightsIndividual differences in haemoglobin significantly impact measures of functional connectivity in the elderly.Significant differences in connectivity-cognition relationships are shown between groups separated by haemoglobin values without accompanying cognitive differences.The influence of haemoglobin on functional connectivity differs between men and women.