bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts
Authors: Kikuchi Yoshitomo , Ohbayashi Tsubasa , Jang Seonghan , Mergaert Peter 
Published: March 2020

Abstract
In addition to abiotic triggers, biotic factors such as microbial symbionts can alter development of multicellular organisms. Symbiont-mediated morphogenesis is well-investigated in plants and marine invertebrates but rarely in insects despite the enormous diversity of insect-microbe symbioses. The bean bug Riptortus pedestris is associated with Burkholderia insecticola which are acquired from the environmental soil and housed in midgut crypts. To sort symbionts from soil microbiota, the bean bug develops a specific organ called the “constricted region” (CR), a narrow and symbiont-selective channel, located in the midgut immediately upstream of the crypt-bearing region. In this study, inoculation of fluorescent protein-labeled symbionts followed by spatiotemporal microscopic observations revealed that after the initial passage of symbionts through the CR, it closes within 12–18 h, blocking any potential subsequent infection events. The “midgut closure” developmental response was irreversible, even after symbiont removal from the crypts by antibiotics. It never occurred in aposymbiotic insects, nor in insects infected with nonsymbiotic bacteria or B. insecticola mutants unable to cross the CR. However, species of the genus Burkholderia and its outgroup Pandoraea that can pass the CR and partially colonize the midgut crypts induce the morphological alteration, suggesting that the molecular trigger signaling the midgut closure is conserved in this bacterial lineage. We propose that this drastic and quick alteration of the midgut morphology in response to symbiont infection is a mechanism for stabilizing the insect-microbe gut symbiosis and contributes to host-symbiont specificity in a symbiosis without vertical transmission.
CD73 promotes tumor metastasis by modulating RICS/RhoA signaling and EMT in gastric cancer
Authors: Xu Zhijun , Gu Chuncai , Yao Xingxing , Guo Weihong , Wang Huanan , Lin Tian , Li Fengping , Chen Da , Wu Jianhua , Ye Gengtai , Zhao Liying , Hu Yanfeng , Yu Jiang , Shi Jiaolong , Li Guoxin , Liu Hao 
Published: March 2020

AbstractTumor microenvironment plays vital roles in shaping cancer diversity, and CD73 (ecto-5′-nucleotidase; NT5E) is an emerging immune checkpoint in modulating cancer progression via conversion of immunostimulatory ATP into immunosuppressive adenosine. However, how the CD73 is regulated and how it functions in the progression of cancer are largely unknown. Here, we showed that CD73 was overexpressed and correlated with poor prognosis of gastric cancer. CD73 links adenosinergic signaling in microenvironment switching to induction of epithelial-to-mesenchymal transition phenotype in gastric cancer during metastasis. Further pathway and gene set enrichment analysis of transcriptome data revealed the modulation role of CD73 in RICS/RhoA signaling by its extracellular function in adenosinergic pathway, which subsequently inhibited phosphorylation of LIMK/cofilin and promoted β-catenin activation. Pharmacological inhibition of CD73 adenosinergic signaling was found to induce RICS dysfunction. Dissemination and hematogenous metastasis model showed that targeting CD73 in gastric cancer could suppress experimental metastasis. To conclude, it substantiates CD73 as a target for treatment of gastric cancer metastasis and verifies RICS as an intracellular functional molecule linking CD73/adenosinergic signaling switching to RhoA/LIMK/cofilin pathway.
8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer
Authors: Dupont William D. , Breyer Joan P. , Plummer W. Dale , Chang Sam S. , Cookson Michael S. , Smith Joseph A. ,   University of Washington Center for Mendelian Genomics, Blue Elizabeth , Bamshad Michael , Chong Jessica , Nickerson Deborah , Blue Elizabeth E. , Bamshad Michael J. , Smith Jeffrey R. 
Published: March 2020

AbstractThe 8q24 genomic locus is tied to the origin of numerous cancers. We investigate its contribution to hereditary prostate cancer (HPC) in independent study populations of the Nashville Familial Prostate Cancer Study and International Consortium for Prostate Cancer Genetics (combined: 2,836 HPC cases, 2,206 controls of European ancestry). Here we report 433 variants concordantly associated with HPC in both study populations, accounting for 9% of heritability and modifying age of diagnosis as well as aggressiveness; 183 reach genome-wide significance. The variants comprehensively distinguish independent risk-altering haplotypes overlapping the 648 kb locus (three protective, and four risk (peak odds ratios: 1.5, 4, 5, and 22)). Sequence of the near-Mendelian haplotype reveals eleven causal mutation candidates. We introduce a linkage disequilibrium-based algorithm discerning eight independent sentinel variants, carrying considerable risk prediction ability (AUC = 0.625) for a single locus. These findings elucidate 8q24 locus structure and correlates for clinical prediction of prostate cancer risk.
Universal three-dimensional crosslinker for all-photopatterned electronics
Authors: Kim Min Je , Lee Myeongjae , Min Honggi , Kim Seunghan , Yang Jeehye , Kweon Hyukmin , Lee Wooseop , Kim Do Hwan , Choi Jong-Ho , Ryu Du Yeol , Kang Moon Sung , Kim BongSoo , Cho Jeong Ho 
Published: March 2020

AbstractAll-solution processing of large-area organic electronics requires multiple steps of patterning and stacking of various device components. Here, we report the fabrication of highly integrated arrays of polymer thin-film transistors and logic gates entirely through a series of solution processes. The fabrication is done using a three-dimensional crosslinker in tetrahedral geometry containing four photocrosslinkable azide moieties, referred to as 4Bx. 4Bx can be mixed with a variety of solution-processable electronic materials (polymer semiconductors, polymer insulators, and metal nanoparticles) and generate crosslinked network under exposure to UV. Fully crosslinked network film can be formed even at an unprecedentedly small loading, which enables preserving the inherent electrical and structural characteristics of host material. Because the crosslinked electronic component layers are strongly resistant to chemical solvents, micropatterning the layers at high resolution as well as stacking the layers on top of each other by series of solution processing steps is possible.
Structural insights into catalytic mechanism and product delivery of cyanobacterial acyl-acyl carrier protein reductase
Authors: Gao Yu , Zhang Hongmei , Fan Minrui , Jia Chenjun , Shi Lifang , Pan Xiaowei , Cao Peng , Zhao Xuelin , Chang Wenrui , Li Mei 
Published: March 2020

AbstractLong-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Biosynthesis of alkanes is ubiquitous in many kinds of organisms. Cyanobacteria possess two enzymes, acyl-acyl carrier protein (acyl-ACP) reductase (AAR) and aldehyde-deformylating oxygenase (ADO), which function in a two-step alkane biosynthesis pathway. These two enzymes act in series and possibly form a complex that efficiently converts long chain fatty acyl-ACP/fatty acyl-CoA into hydrocarbon. While the structure of ADO has been previously described, structures of both AAR and AAR–ADO complex have not been solved, preventing deeper understanding of this pathway. Here, we report a ligand-free AAR structure, and three AAR–ADO complex structures in which AARs bind various ligands. Our results reveal the binding pattern of AAR with its substrate/cofactor, and suggest a potential aldehyde-transferring channel from AAR to ADO. Based on our structural and biochemical data, we proposed a model for the complete catalytic cycle of AAR.
Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions
Authors: Thompson Oliver , von Meyenn Ferdinand , Hewitt Zoe , Alexander John , Wood Andrew , Weightman Richard , Gregory Sian , Krueger Felix , Andrews Simon , Barbaric Ivana , Gokhale Paul J. , Moore Harry D. , Reik Wolf , Milo Marta , Nik-Zainal Serena , Yusa Kosuke , Andrews Peter W. 
Published: March 2020

AbstractThe occurrence of repetitive genomic changes that provide a selective growth advantage in pluripotent stem cells is of concern for their clinical application. However, the effect of different culture conditions on the underlying mutation rate is unknown. Here we show that the mutation rate in two human embryonic stem cell lines derived and banked for clinical application is low and not substantially affected by culture with Rho Kinase inhibitor, commonly used in their routine maintenance. However, the mutation rate is reduced by >50% in cells cultured under 5% oxygen, when we also found alterations in imprint methylation and reversible DNA hypomethylation. Mutations are evenly distributed across the chromosomes, except for a slight increase on the X-chromosome, and an elevation in intergenic regions suggesting that chromatin structure may affect mutation rate. Overall the results suggest that pluripotent stem cells are not subject to unusually high rates of genetic or epigenetic alterations.
Fungal kinases and transcription factors regulating brain infection in Cryptococcus neoformans
Authors: Lee Kyung-Tae , Hong Joohyeon , Lee Dong-Gi , Lee Minjae , Cha Suyeon , Lim Yu-Gyeong , Jung Kwang-Woo , Hwangbo Areum , Lee Yelin , Yu Shang-Jie , Chen Ying-Lien , Lee Jong-Seung , Cheong Eunji , Bahn Yong-Sun 
Published: March 2020

AbstractCryptococcus neoformans causes fatal fungal meningoencephalitis. Here, we study the roles played by fungal kinases and transcription factors (TFs) in blood-brain barrier (BBB) crossing and brain infection in mice. We use a brain infectivity assay to screen signature-tagged mutagenesis (STM)-based libraries of mutants defective in kinases and TFs, generated in the C. neoformans H99 strain. We also monitor in vivo transcription profiles of kinases and TFs during host infection using NanoString technology. These analyses identify signalling components involved in BBB adhesion and crossing, or survival in the brain parenchyma. The TFs Pdr802, Hob1, and Sre1 are required for infection under all the conditions tested here. Hob1 controls the expression of several factors involved in brain infection, including inositol transporters, a metalloprotease, PDR802, and SRE1. However, Hob1 is dispensable for most cellular functions in Cryptococcus deuterogattii R265, a strain that does not target the brain during infection. Our results indicate that Hob1 is a master regulator of brain infectivity in C. neoformans.
Infrared spectroscopy data- and physics-driven machine learning for characterizing surface microstructure of complex materials
Authors: Lansford Joshua L. , Vlachos Dionisios G. 
Published: March 2020

AbstractThere is a need to characterize complex materials and their dynamics under reaction conditions to accelerate materials design. Adsorbate vibrational excitations are selective to adsorbate/surface interactions and infrared (IR) spectra associated with activating adsorbate vibrational modes are accurate, capture details of most modes, and can be obtained operando. Current interpretation depends on heuristic peak assignments for simple spectra, precluding the possibility of obtaining detailed structural information. Here, we combine data-based approaches with chemistry-dependent problem formulation to develop physics-driven surrogate models that generate synthetic IR spectra from first-principles calculations. Using synthetic IR spectra of carbon monoxide on platinum, we implement multinomial regression via neural network ensembles to learn probability distributions functions (pdfs) that describe adsorption sites and quantify uncertainty. We use these pdfs to infer detailed surface microstructure from experimental spectra and extend this methodology to other systems as a first step towards characterizing complex interfaces and closing the materials gap.
Concurrent germline and somatic pathogenic BAP1 variants in a patient with metastatic bladder cancer
Authors: Tesch Megan E. , Pater Justin A. , Vandekerkhove Gillian , Wang Gang , Binnington Kristin , So Alan I. , Wyatt Alexander W. , Eigl Bernhard J. 
Published: March 2020

AbstractGermline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1 tumor predisposition syndrome (TPDS). BAP1 TPDS is associated with an increased risk of uveal and cutaneous melanoma, mesothelioma, renal cell carcinoma, and several other cancer subtypes. Here, we report a germline nonsense BAP1 variant (c.850G>T, p.Glu284Ter) in a patient with bladder cancer and a strong family history of malignancy. Concurrently, we identified a somatic frameshift BAP1 variant, and as expected, immunostaining validated the loss of BAP1 protein in patient-derived tumor specimens. Together, these data provide strong evidence of pathogenicity in this case. With the addition of bladder cancer to the tumor types reported with germline BAP1 mutations, our understanding of the BAP1 TPDS continues to evolve, and may affect future screening and surveillance guidelines.
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Authors: Kazer Samuel W. , Aicher Toby P. , Muema Daniel M. , Carroll Shaina L. , Ordovas-Montanes Jose , Miao Vincent N. , Tu Ang A. , Ziegler Carly G. K. , Nyquist Sarah K. , Wong Emily B. , Ismail Nasreen , Dong Mary , Moodley Amber , Berger Bonnie , Love J. Christopher , Dong Krista L. , Leslie Alasdair , Ndhlovu Zaza M. , Ndung’u Thumbi , Walker Bruce D. , Shalek Alex K. 
Published: March 2020

AbstractCellular immunity is critical for controlling intracellular pathogens, but individual cellular dynamics and cell–cell cooperativity in evolving human immune responses remain poorly understood. Single-cell RNA-sequencing (scRNA-seq) represents a powerful tool for dissecting complex multicellular behaviors in health and disease1,2 and nominating testable therapeutic targets3. Its application to longitudinal samples could afford an opportunity to uncover cellular factors associated with the evolution of disease progression without potentially confounding inter-individual variability4. Here, we present an experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and apply it to HIV infection. By performing scRNA-seq on peripheral blood mononuclear cells from four untreated individuals before and longitudinally during acute infection5, we were powered within each to discover gene response modules that vary by time and cell subset. Beyond previously unappreciated individual- and cell-type-specific interferon-stimulated gene upregulation, we describe temporally aligned gene expression responses obscured in bulk analyses, including those involved in proinflammatory T cell differentiation, prolonged monocyte major histocompatibility complex II upregulation and persistent natural killer (NK) cell cytolytic killing. We further identify response features arising in the first weeks of infection, for example proliferating natural killer cells, which potentially may associate with future viral control. Overall, our approach provides a unified framework for characterizing multiple dynamic cellular responses and their coordination.
Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus
Authors: Liu Xiao , Li Chao , Chen Min , Liu Bo , Yan Xiaojun , Ning Junhao , Ma Bin , Liu Guilong , Zhong Zhaoshan , Jia Yanglei , Shi Qiong , Wang Chunde 
Published: March 2020

AbstractThe two subspecies of Atlantic bay scallop (Argopecten irradians), A. i. irradians and A. i. concentricus, are economically important aquacultural species in northern and southern China. Here, we performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for A. i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7 Mb and 874.82 Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54 kb and 1.53 Mb for the A. i. irradians genome, and those for the A. i. concentricus genome were 63.73 kb and 1.25 Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for A. i. irradians and A. i. concentricus, respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding.
Detecting small and cryptic animals by combining thermography and a wildlife detection dog
Authors: Karp Denise 
Published: March 2020

AbstractSmall and cryptic species are challenging to detect and study in their natural habitat. Many of these species are of conservation concern, and conservation efforts may be hampered by the lack of basic information on their ecological needs. Brown hare (Lepus europaeus) leverets - one example of such a small, cryptic and endangered animal - are notoriously difficult to detect, and therefore data on wild leverets are virtually non-existent. Novel technologies and methods such as thermal imaging and the use of wildlife detection dogs represent suitable means for the detection of such species by overcoming the problem of camouflage, using heat or scent emission respectively. Our study on brown hare leverets provides information on how to apply these new techniques successfully for the detection of small and cryptic species, thus enabling the collection of data that was previously inaccessible (e.g. behavioural observation, radio tagging). We found that the choice of method should be made according to vegetative structure. While the handheld thermal imaging camera is best used in areas with no or low vegetative cover, the thermal drone can be used up to medium vegetative cover, whereas the detection dog method is best applied where vegetation is very dense and not suitable to be searched using thermography. Being able to search all sort of different vegetation types, our combined approach enables the collection of a balanced and unbiased dataset regarding habitat type and hence selection of study specimen. We hope that the use of these new techniques will encourage research on many cryptic species that formerly have been neglected because they could not be detected using conventional methodologies.
Alcohol pretreatment of stools effect on culturomics
Authors: Afouda Pamela , Hocquart Marie , Pham Thi-Phuong-Thao , Kuete Edmond , Ngom Issa Isaac , Dione Niokhor , Valles Camille , Bellali Sara , Lagier Jean-Christophe , Dubourg Grégory , Raoult Didier 
Published: March 2020

AbstractRecent studies have used ethanol stool disinfection as a mean of promoting valuable species’ cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.
Effect of anti-inflammatory treatment on systemic inflammation, immune function, and endometrial health in postpartum dairy cows
Authors: Pascottini O. Bogado , Van Schyndel S. J. , Spricigo J. F. W. , Carvalho M. R. , Mion B. , Ribeiro E. S. , LeBlanc S. J. 
Published: March 2020

AbstractSystemic inflammation (SI) is increasingly studied in several species because it may be central in many metabolic disturbances and be a risk factor for clinical disease. This proof-of-concept study evaluated the effects of the anti-inflammatory drug meloxicam on markers of SI and energy metabolism, polymorphonuclear neutrophil (PMN) function, and endometritis in clinically healthy postpartum dairy cows. Cows received meloxicam (0.5 mg/kg of body weight; n = 20) once daily for 4 days (10–13 days postpartum) or were untreated (n = 22). Blood samples were collected −7, 1, 3, 5, 7, 10, 11, 12, 13, 14, 18, 21, 28, and 35 days relative to calving to measure serum concentrations of metabolic and inflammatory markers. Function of peripheral blood PMN were evaluated at 5, 10, 14, and 21, and proportion of PMN in endometrial cytology were performed at 5, 10, 14, 21, 28 and 35 days postpartum. Meloxicam decreased serum haptoglobin from the second until the last day of treatment, and improved indicators of energy metabolism (lesser β-hydroxybutyrate and greater insulin-like growth factor-1 during treatment, and greater glucose at the end of treatment than control cows). This improved PMN function at 14 days postpartum, but the endometrial inflammatory status was not affected.
The effect of incorporating inorganic materials into quaternized polyacrylic polymer on its mechanical strength and adsorption behaviour for ibuprofen removal
Authors: Zhang Guang , Li Shuangshuang , Shuang Chendong , Mu Yunsong , Li Aimin , Tan Liang 
Published: March 2020

AbstractQuaternized polyacrylic polymer has many applications in water treatment because of its ion exchange effects, but its further industrial applications are largely restricted because of its poor mechanical strength. In this work, a magnetic anion exchange resin with a polyacrylic matrix (MAP) was prepared by incorporation of Fe3O4 and subsequent modification with tetraethyl orthosilicate (TEOS) to improve the mechanical strength and adsorption performance. The incorporation of Fe3O4 significantly enhanced the mechanical strength of the polymer and improved the sphericity rate after ball milling of the polyacrylic resin from 80.1% to 97.2% as a result of hydrogen bonding between the -OH groups on Fe3O4 and the -NH- groups on the resin matrix. Further TEOS modification could effectively prevent Fe3O4 particles from dislodging from the resins. The adsorption performance was evaluated by using ibuprofen as a model compound. The adsorption kinetics showed that adsorption equilibrium was reached in 150 min. XPS analysis indicated that hydrogen bonding greatly contributed to the adsorption of ibuprofen onto the MAP. Adsorption isotherm analysis indicated that the adsorption was endothermic.