bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial variability in the mammalian gut captured by a single-cell synthetic oscillator
Authors: Riglar David T. , Richmond David L. , Potvin-Trottier Laurent , Verdegaal Andrew A. , Naydich Alexander D. , Bakshi Somenath , Leoncini Emanuele , Lyon Lorena G. , Paulsson Johan , Silver Pamela A. 
Published: October 2019

AbstractSynthetic gene oscillators have the potential to control timed functions
and periodic gene expression in engineered cells. Such oscillators have been refined
in bacteria in vitro, however, these systems have lacked the robustness and
precision necessary for applications in complex in vivo environments, such as the
mammalian gut. Here, we demonstrate the implementation of a synthetic oscillator
capable of keeping robust time in the mouse gut over periods of days. The
oscillations provide a marker of bacterial growth at a single-cell level enabling
quantification of bacterial dynamics in response to inflammation and underlying
variations in the gut microbiota. Our work directly detects increased bacterial
growth heterogeneity during disease and differences between spatial niches in the
gut, demonstrating the deployment of a precise engineered genetic oscillator in
real-life settings.
The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
Authors: Xu Peng , Xu Jian , Liu Guangjian , Chen Lin , Zhou Zhixiong , Peng Wenzhu , Jiang Yanliang , Zhao Zixia , Jia Zhiying , Sun Yonghua , Wu Yidi , Chen Baohua , Pu Fei , Feng Jianxin , Luo Jing , Chai Jing , Zhang Hanyuan , Wang Hui , Dong Chuanju , Jiang Wenkai , Sun Xiaowen 
Published: October 2019

AbstractCommon carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.
A chemically fueled non-enzymatic bistable network
Authors: Maity Indrajit , Wagner Nathaniel , Mukherjee Rakesh , Dev Dharm , Peacock-Lopez Enrique , Cohen-Luria Rivka , Ashkenasy Gonen 
Published: October 2019

AbstractOne of the grand challenges in contemporary systems chemistry research is to mimic life-like functions using simple synthetic molecular networks. This is particularly true for systems that are out of chemical equilibrium and show complex dynamic behaviour, such as multi-stability, oscillations and chaos. We report here on thiodepsipeptide-based non-enzymatic networks propelled by reversible replication processes out of equilibrium, displaying bistability. Accordingly, we present quantitative analyses of the bistable behaviour, featuring a phase transition from the simple equilibration processes taking place in reversible dynamic chemistry into the bistable region. This behaviour is observed only when the system is continuously fueled by a reducing agent that keeps it far from equilibrium, and only when operating within a specifically defined parameter space. We propose that the development of biomimetic bistable systems will pave the way towards the study of more elaborate functions, such as information transfer and signalling.
Mapping the increased minimum mortality temperatures in the context of global climate change
Authors: Yin Qian , Wang Jinfeng , Ren Zhoupeng , Li Jie , Guo Yuming 
Published: October 2019

AbstractMinimum mortality temperature (MMT) is an important indicator to assess the temperature–mortality relationship. It reflects human adaptability to local climate. The existing MMT estimates were usually based on case studies in data rich regions, and limited evidence about MMT was available at a global scale. It is still unclear what the most significant driver of MMT is and how MMT will change under global climate change. Here, by analysing MMTs in 420 locations covering six continents (Antarctica was excluded) in the world, we found that although the MMT changes geographically, it is very close to the local most frequent temperature (MFT) in the same period. The association between MFT and MMT is not changed when we adjust for latitude and study year. Based on the MFT~MMT association, we estimate and map the global distribution of MMTs in the present (2010s) and the future (2050s) for the first time.
Species abundance information improves sequence taxonomy classification accuracy
Authors: Kaehler Benjamin D. , Bokulich Nicholas A. , McDonald Daniel , Knight Rob , Caporaso J. Gregory , Huttley Gavin A. 
Published: October 2019

AbstractPopular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments.
Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis
Authors: Toledo Alejandro Gómez , Golden Gregory , Campos Alexandre Rosa , Cuello Hector , Sorrentino James , Lewis Nathan , Varki Nissi , Nizet Victor , Smith Jeffrey W. , Esko Jeffrey D. 
Published: October 2019

AbstractSepsis is a life-threatening condition triggered by a dysregulated host response to microbial infection resulting in vascular dysfunction, organ failure and death. Here we provide a semi-quantitative atlas of the murine vascular cell-surface proteome at the organ level, and how it changes during sepsis. Using in vivo chemical labeling and high-resolution mass spectrometry, we demonstrate the presence of a vascular proteome that is perfusable and shared across multiple organs. This proteome is enriched in membrane-anchored proteins, including multiple regulators of endothelial barrier functions and innate immunity. Further, we automated our workflows and applied them to a murine model of methicillin-resistant Staphylococcus aureus (MRSA) sepsis to unravel changes during systemic inflammatory responses. We provide an organ-specific atlas of both systemic and local changes of the vascular proteome triggered by sepsis. Collectively, the data indicates that MRSA-sepsis triggers extensive proteome remodeling of the vascular cell surfaces, in a tissue-specific manner.
Cis-regulatory CYP6P9b P450 variants associated with loss of insecticide-treated bed net efficacy against Anopheles funestus
Authors: Mugenzi Leon M. J. , Menze Benjamin D. , Tchouakui Magellan , Wondji Murielle J. , Irving Helen , Tchoupo Micareme , Hearn Jack , Weedall Gareth D. , Riveron Jacob M. , Wondji Charles S. 
Published: October 2019

AbstractElucidating the genetic basis of metabolic resistance to insecticides in malaria vectors is crucial to prolonging the effectiveness of insecticide-based control tools including long lasting insecticidal nets (LLINs). Here, we show that cis-regulatory variants of the cytochrome P450 gene, CYP6P9b, are associated with pyrethroid resistance in the African malaria vector Anopheles funestus. A DNA-based assay is designed to track this resistance that occurs near fixation in southern Africa but not in West/Central Africa. Applying this assay we demonstrate, using semi-field experimental huts, that CYP6P9b-mediated resistance associates with reduced effectiveness of LLINs. Furthermore, we establish that CYP6P9b combines with another P450, CYP6P9a, to additively exacerbate the reduced efficacy of insecticide-treated nets. Double homozygote resistant mosquitoes (RR/RR) significantly survive exposure to insecticide-treated nets and successfully blood feed more than other genotypes. This study provides tools to track and assess the impact of multi-gene driven metabolic resistance to pyrethroids, helping improve resistance management.
Breakdown of energy transfer gap laws revealed by full-dimensional quantum scattering between HF molecules
Authors: Yang Dongzheng , Huang Jing , Hu Xixi , Guo Hua , Xie Daiqian 
Published: October 2019

AbstractInelastic collisions involving molecular species are key to energy transfer in gaseous environments. They are commonly governed by an energy gap law, which dictates that transitions are dominated by those between initial and final states with roughly the same ro-vibrational energy. Transitions involving rotational inelasticity are often further constrained by the rotational angular momentum. Here, we demonstrate using full-dimensional quantum scattering on an ab initio based global potential energy surface (PES) that HF–HF inelastic collisions do not obey the energy and angular momentum gap laws. Detailed analyses attribute the failure of gap laws to the exceedingly strong intermolecular interaction. On the other hand, vibrational state-resolved rate coefficients are in good agreement with existing experimental results, validating the accuracy of the PES. These new and surprising results are expected to extend our understanding of energy transfer and provide a quantitative basis for numerical simulations of hydrogen fluoride chemical lasers.
Anthropogenic shift towards higher risk of flash drought over China
Authors: Yuan Xing , Wang Linying , Wu Peili , Ji Peng , Sheffield Justin , Zhang Miao 
Published: October 2019

AbstractFlash droughts refer to a type of droughts that have rapid intensification without sufficient early warning. To date, how will the flash drought risk change in a warming future climate remains unknown due to a diversity of flash drought definition, unclear role of anthropogenic fingerprints, and uncertain socioeconomic development. Here we propose a new method for explicitly characterizing flash drought events, and find that the exposure risk over China will increase by about 23% ± 11% during the middle of this century under a socioeconomic scenario with medium challenge. Optimal fingerprinting shows that anthropogenic climate change induced by the increased greenhouse gas concentrations accounts for 77% ± 26% of the upward trend of flash drought frequency, and population increase is also an important factor for enhancing the exposure risk of flash drought over southernmost humid regions. Our results suggest that the traditional drought-prone regions would expand given the human-induced intensification of flash drought risk.
Second messenger Ap4A polymerizes target protein HINT1 to transduce signals in FcεRI-activated mast cells
Authors: Yu Jing , Liu Zaizhou , Liang Yuanyuan , Luo Feng , Zhang Jie , Tian Cuiping , Motzik Alex , Zheng Mengmeng , Kang Jingwu , Zhong Guisheng , Liu Cong , Fang Pengfei , Guo Min , Razin Ehud , Wang Jing 
Published: October 2019

AbstractSignal transduction systems enable organisms to monitor their external environments and accordingly adjust the cellular processes. In mast cells, the second messenger Ap4A binds to the histidine triad nucleotide-binding protein 1 (HINT1), disrupts its interaction with the microphthalmia-associated transcription factor (MITF), and eventually activates the transcription of genes downstream of MITF in response to immunostimulation. How the HINT1 protein recognizes and is regulated by Ap4A remain unclear. Here, using eight crystal structures, biochemical experiments, negative stain electron microscopy, and cellular experiments, we report that Ap4A specifically polymerizes HINT1 in solution and in activated rat basophilic leukemia cells. The polymerization interface overlaps with the area on HINT1 for MITF interaction, suggesting a possible competitive mechanism to release MITF for transcriptional activation. The mechanism depends precisely on the length of the phosphodiester linkage of Ap4A. These results highlight a direct polymerization signaling mechanism by the second messenger.
Inflight leg cuff test does not identify the risk for orthostatic hypotension after long-duration spaceflight
Authors: Wood Katelyn N. , Murray Kevin R. , Greaves Danielle K. , Hughson Richard L. 
Published: October 2019

AbstractLanding day symptoms from orthostatic hypotension after prolonged spaceflight can be debilitating, but severity of these symptoms can be unpredictable and highly individual. We tested the hypothesis that an impaired baroreflex response to an inflight leg cuff test could predict orthostatic intolerance on return to Earth. Eight male astronauts (44 ± 7 years of age (mean ± SD); mean mission length: 167 ± 12 days) participated in a standardized supine-to-sit-to-stand test (5 min–30s–3 min) pre- and postflight, and a 3 min thigh cuff occlusion test pre- and inflight with continuous monitoring of heart rate and arterial blood pressure. The arterial baroreflex was not changed inflight as shown by similar reductions in mean arterial pressure (MAP) response to leg cuff deflation (preflight −19 ± 2 mmHg vs. inflight −18 ± 5 mmHg). With the sit/stand test, the nadir of MAP was lower postflight (−17 ± 9 mmHg) than preflight (−11 ± 6 mmHg, p < 0.05). A greater increase in heart rate (25 ± 7; 16 ± 3 bpm) and decrease in stroke volume (−24 ± 11; −6 ± 4 mL) occurred with sit/stand postflight than leg cuffs inflight (p < 0.001). Inflight testing was influenced by elevated cardiac output resulting in a smaller drop in total peripheral resistance. Two of eight subjects exhibited orthostatic hypotension during the postflight stand test; their responses were not predicted by the inflight leg cuff deflation test. These results suggest that the baroreflex response examined by inflight leg cuff deflation was not a reliable indicator of postflight stand responses.
Quantitative Histopathology of Stained Tissues using Color Spatial Light Interference Microscopy (cSLIM)
Authors: Majeed Hassaan , Keikhosravi Adib , Kandel Mikhail E. , Nguyen Tan H. , Liu Yuming , Kajdacsy-Balla Andre , Tangella Krishnarao , Eliceiri Kevin W. , Popescu Gabriel 
Published: October 2019

AbstractTissue biopsy evaluation in the clinic is in need of quantitative disease markers for diagnosis and, most importantly, prognosis. Among the new technologies, quantitative phase imaging (QPI) has demonstrated promise for histopathology because it reveals intrinsic tissue nanoarchitecture through the refractive index. However, a vast majority of past QPI investigations have relied on imaging unstained tissues, which disrupts the established specimen processing. Here we present color spatial light interference microscopy (cSLIM) as a new whole-slide imaging modality that performs interferometric imaging on stained tissue, with a color detector array. As a result, cSLIM yields in a single scan both the intrinsic tissue phase map and the standard color bright-field image, familiar to the pathologist. Our results on 196 breast cancer patients indicate that cSLIM can provide stain-independent prognostic information from the alignment of collagen fibers in the tumor microenvironment. The effects of staining on the tissue phase maps were corrected by a mathematical normalization. These characteristics are likely to reduce barriers to clinical translation for the new cSLIM technology.
Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates
Authors: Rawi Reda , Mall Raghvendra , Shen Chen-Hsiang , Farney S. Katie , Shiakolas Andrea , Zhou Jing , Bensmail Halima , Chun Tae-Wook , Doria-Rose Nicole A. , Lynch Rebecca M. , Mascola John R. , Kwong Peter D. , Chuang Gwo-Yu 
Published: October 2019

AbstractBroadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have promising utility in prevention and treatment of HIV-1 infection, and several are currently undergoing clinical trials. Due to the high sequence diversity and mutation rate of HIV-1, viral isolates are often resistant to specific bNAbs. Currently, resistant isolates are commonly identified by time-consuming and expensive in vitro neutralization assays. Here, we report machine learning classifiers that accurately predict resistance of HIV-1 isolates to 33 bNAbs. Notably, our classifiers achieved an overall prediction accuracy of 96% for 212 clinical isolates from patients enrolled in four different clinical trials. Moreover, use of gradient boosting machine – a tree-based machine learning method – enabled us to identify critical features, which had high accordance with epitope residues that distinguished between antibody resistance and sensitivity. The availability of an in silico antibody resistance predictor should facilitate informed decisions of antibody usage and sequence-based monitoring of viral escape in clinical settings.
Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean
Authors: Lin Yanhui , Li Wei , Zhang Yanwei , Xia Changjian , Liu Yun , Wang Caijie , Xu Ran , Zhang Lifeng 
Published: October 2019

AbstractFlooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.
Cadmium and High-Fat Diet Disrupt Renal, Cardiac and Hepatic Essential Metals
Authors: Young Jamie L. , Yan Xiaofang , Xu Jianxiang , Yin Xinmin , Zhang Xiang , Arteel Gavin E. , Barnes Gregory N. , States J. Christopher , Watson Walter H. , Kong Maiying , Cai Lu , Freedman Jonathan H. 
Published: October 2019

AbstractExposure to the environmental toxicant cadmium (Cd) contributes to the development of obesity-associated diseases. Obesity is a risk factor for a spectrum of unhealthy conditions including systemic metabolic dyshomeostasis. In the present study, the effects of whole-life exposure to environmentally-relevant concentrations of Cd on systemic essential metal distribution in adult mice fed a high-fat diet (HFD) were examined. For these studies, male and female mice were exposed to Cd-containing drinking water for >2 weeks before breeding. Pregnant mice and dams with offspring were exposed to Cd-containing drinking water. After weaning, offspring were continuously exposed to the same Cd concentration as their parents, and divided into HFD and normal (low) fat diet (LFD) groups. At 10 and 24 weeks, mice were sacrificed and blood, liver, kidney and heart harvested for metal analyses. There were significant concentration dependent increases in Cd levels in offspring with kidney > liver > heart. Sex significantly affected Cd levels in kidney and liver, with female animals accumulating more metal than males. Mice fed the HFD showed > 2-fold increase in Cd levels in the three organs compared to similarly treated LFD mice. Cadmium significantly affected essential metals levels in blood, kidney and liver. Additionally, HFD affected essential metal levels in these three organs. These findings suggest that Cd interacts with HFD to affect essential metal homeostasis, a phenomenon that may contribute to the underlying mechanism responsible for the development of obesity-associated pathologies.
Carbon and Water Use Efficiencies: A Comparative Analysis of Ten Terrestrial Ecosystem Models under Changing Climate
Authors: El Masri Bassil , Schwalm Christopher , Huntzinger Deborah N. , Mao Jiafu , Shi Xiaoying , Peng Changhui , Fisher Joshua B. , Jain Atul K. , Tian Hanqin , Poulter Benjamin , Michalak Anna M. 
Published: October 2019

AbstractTerrestrial ecosystems carbon and water cycles are tightly coupled through photosynthesis and evapotranspiration processes. The ratios of carbon stored to carbon uptake and water loss to carbon gain are key ecophysiological indicators essential to assess the magnitude and response of the terrestrial plant to the changing climate. Here, we use estimates from 10 terrestrial ecosystem models to quantify the impacts of climate, atmospheric CO2 concentration, and nitrogen (N) deposition on water use efficiency (WUE), and carbon use efficiency (CUE). We find that across models, WUE increases over the 20th Century particularly due to CO2 fertilization and N deposition and compares favorably to experimental studies. Also, the results show a decrease in WUE with climate for the last 3 decades, in contrasts with up-scaled flux observations that demonstrate a constant WUE. Modeled WUE responds minimally to climate with modeled CUE exhibiting no clear trend across space and time. The divergence between simulated and observationally-constrained WUE and CUE is driven by modeled NPP and autotrophic respiration, nitrogen cycle, carbon allocation, and soil moisture dynamics in current ecosystem models. We suggest that carbon-modeling community needs to reexamine stomatal conductance schemes and the soil-vegetation interactions for more robust modeling of carbon and water cycles.