bluuebunny/crossref_metadata_2025_split huggingface dataset:
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition
Authors: Cornuault Jeffrey K , Moncaut Elisabeth , Loux Valentin , Mathieu Aurélie , Sokol Harry , Petit Marie-Agnès , De Paepe Marianne 
Published: December 2019

Abstract
Despite an overall temporal stability in time of the human gut microbiota at the phylum level, strong variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses, which can evolve to become ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammal’s microbiota has been largely unexplored. Here we studied temperate phage–bacteria coevolution in gnotoxenic mice colonised with Roseburia intestinalis, a dominant symbiont of the human gut microbiota, and Escherichia coli, a sub-dominant member of the same microbiota. We show that R. intestinalis L1-82 harbours two active prophages, Jekyll and Shimadzu. We observed the systematic evolution in mice of ultravirulent Shimadzu phage mutants, which led to a collapse of R. intestinalis population. In a second step, phage infection drove the fast counter-evolution of host phage resistance mainly through phage-derived spacer acquisition in a clustered regularly interspaced short palindromic repeats array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize. Our results demonstrate that prophages are a potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.
Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems
Authors: Dai Zhongmin , Liu Guofei , Chen Huaihai , Chen Chengrong , Wang Jingkuan , Ai Shaoying , Wei Dan , Li Daming , Ma Bin , Tang Caixian , Brookes Philip C , Xu Jianming 
Published: December 2019

Abstract
Microorganisms play an important role in soil phosphorus (P) cycling and regulation of P availability in agroecosystems. However, the responses of the functional and ecological traits of P-transformation microorganisms to long-term nutrient inputs are largely unknown. This study used metagenomics to investigate changes in the relative abundance of microbial P-transformation genes at four long-term experimental sites that received various inputs of N and P nutrients (up to 39 years). Long-term P input increased microbial P immobilization by decreasing the relative abundance of the P-starvation response gene (phoR) and increasing that of the low-affinity inorganic phosphate transporter gene (pit). This contrasts with previous findings that low-P conditions facilitate P immobilization in culturable microorganisms in short-term studies. In comparison, long-term nitrogen (N) input significantly decreased soil pH, and consequently decreased the relative abundances of total microbial P-solubilizing genes and the abundances of Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria containing genes coding for alkaline phosphatase, and weakened the connection of relevant key genes. This challenges the concept that microbial P-solubilization capacity is mainly regulated by N:P stoichiometry. It is concluded that long-term N inputs decreased microbial P-solubilizing and mineralizing capacity while P inputs favored microbial immobilization via altering the microbial functional profiles, providing a novel insight into the regulation of P cycling in sustainable agroecosystems from a microbial perspective.
LncRNA ODIR1 inhibits osteogenic differentiation of hUC-MSCs through the FBXO25/H2BK120ub/H3K4me3/OSX axis
Authors: He Shiwei , Yang Sheng , Zhang Yanru , Li Xiaoling , Gao Dan , Zhong Yancheng , Cao Lihua , Ma Haotian , Liu Ying , Li Guiyuan , Peng Shuping , Shuai Cijun 
Published: December 2019

AbstractLong noncoding RNAs (lncRNAs) have been demonstrated to be important regulators during the osteogenic differentiation of mesenchymal stem cells (MSCs). We analyzed the lncRNA expression profile during osteogenic differentiation of human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) and identified a significantly downregulated lncRNA RP11-527N22.2, named osteogenic differentiation inhibitory lncRNA 1, ODIR1. In hUC-MSCs, ODIR1 knockdown significantly promoted osteogenic differentiation, whereas overexpression inhibited osteogenic differentiation in vitro and in vivo. Mechanistically, ODIR1 interacts with F-box protein 25 (FBXO25) and facilitates the proteasome-dependent degradation of FBXO25 by recruiting Cullin 3 (CUL3). FBXO25 increases the mono-ubiquitination of H2BK120 (H2BK120ub) which subsequently promotes the trimethylation of H3K4 (H3K4me3). Both H2BK120ub and H3K4me3 form a loose chromatin structure, inducing the transcription of the key transcription factor osterix (OSX) and increasing the expression of the downstream osteoblast markers, osteocalcin (OCN), osteopontin (OPN), and alkaline phosphatase (ALP). In summary, ODIR1 acts as a key negative regulator during the osteogenic differentiation of hUC-MSCs through the FBXO25/H2BK120ub/H3K4me3/OSX axis, which may provide a novel understanding of lncRNAs that regulate the osteogenesis of MSCs and a potential therapeutic strategy for the regeneration of bone defects.
G3BP1 inhibits RNA virus replication by positively regulating RIG-I-mediated cellular antiviral response
Authors: Yang Wenping , Ru Yi , Ren Jingjing , Bai Juncui , Wei Junshu , Fu Shaozu , Liu Xiangtao , Li Dan , Zheng Haixue 
Published: December 2019

AbstractRetinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor and is involved in the innate immune response against RNA viruses infection. Here, we demonstrate that the Ras-GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a positive regulator of the RIG-I-mediated signaling pathway. G3BP1-deficient cells inhibited RNA virus-triggered induction of downstream antiviral genes. Furthermore, we found that G3BP1 inhibited the replication of Sendai virus and vesicular stomatitis virus, indicating a positive regulation of G3BP1 to cellular antiviral responses. Mechanistically, G3BP1 formed a complex with RNF125 and RIG-I, leading to decreased RNF125 via its auto-ubiquitination; thus, promoting expression of RIG-I. Overall, the results suggest a novel mechanism for G3BP1 in the positive regulation of antiviral signaling mediated by RIG-I.
Analysis of laser radiation using the Nonlinear Fourier transform
Authors: Sugavanam Srikanth , Kopae Morteza Kamalian , Peng Junsong , Prilepsky Jaroslaw E. , Turitsyn Sergei K. 
Published: December 2019

AbstractModern high-power lasers exhibit a rich diversity of nonlinear dynamics, often featuring nontrivial co-existence of linear dispersive waves and coherent structures. While the classical Fourier method adequately describes extended dispersive waves, the analysis of time-localised and/or non-stationary signals call for more nuanced approaches. Yet, mathematical methods that can be used for simultaneous characterisation of localized and extended fields are not yet well developed. Here, we demonstrate how the Nonlinear Fourier transform (NFT) based on the Zakharov-Shabat spectral problem can be applied as a signal processing tool for representation and analysis of coherent structures embedded into dispersive radiation. We use full-field, real-time experimental measurements of mode-locked pulses to compute the nonlinear pulse spectra. For the classification of lasing regimes, we present the concept of eigenvalue probability distributions. We present two field normalisation approaches, and show the NFT can yield an effective model of the laser radiation under appropriate signal normalisation conditions.
Extracellular vesicles from symbiotic vaginal lactobacilli inhibit HIV-1 infection of human tissues
Authors: Ñahui Palomino Rogers A. , Vanpouille Christophe , Laghi Luca , Parolin Carola , Melikov Kamran , Backlund Peter , Vitali Beatrice , Margolis Leonid 
Published: December 2019

AbstractThe vaginal microbiota, dominated by Lactobacillus spp., plays a key role in preventing HIV-1 transmission. Here, we investigate whether the anti-HIV effect of lactobacilli is mediated by extracellular vesicles (EVs) released by these bacteria. Human cervico-vaginal and tonsillar tissues ex vivo, and cell lines were infected with HIV-1 and treated with EVs released by lactobacilli isolated from vaginas of healthy women. EVs released by L. crispatus BC3 and L. gasseri BC12 protect tissues ex vivo and isolated cells from HIV-1 infection. This protection is associated with a decrease of viral attachment to target cells and viral entry due to diminished exposure of Env that mediates virus-cell interactions. Inhibition of HIV-1 infection is associated with the presence in EVs of several proteins and metabolites. Our findings demonstrate that the protective effect of Lactobacillus against HIV-1 is, in part, mediated by EVs released by these symbiotic bacteria. If confirmed in vivo, this finding may lead to new strategies to prevent male-to-female sexual HIV-1 transmission.
Phagocytosis-like cell engulfment by a planctomycete bacterium
Authors: Shiratori Takashi , Suzuki Shigekatsu , Kakizawa Yukako , Ishida Ken-ichiro 
Published: December 2019

AbstractPhagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, ‘Candidatus Uab amorphum’, which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the ‘Ca. Uab amorphum’ genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this “phagotrophic” bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.
A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans
Authors: Casanova Miguel , Moscatelli Madeleine , Chauvière Louis Édouard , Huret Christophe , Samson Julia , Liyakat Ali Tharvesh Moideen , Rosspopoff Olga , Rougeulle Claire 
Published: December 2019

AbstractTransposable elements (TEs) have been proposed to play an important role in driving the expansion of gene regulatory networks during mammalian evolution, notably by contributing to the evolution and function of long non-coding RNAs (lncRNAs). XACT is a primate-specific TE-derived lncRNA that coats active X chromosomes in pluripotent cells and may contribute to species-specific regulation of X-chromosome inactivation. Here we explore how different families of TEs have contributed to shaping the XACT locus and coupling its expression to pluripotency. Through a combination of sequence analysis across primates, transcriptional interference, and genome editing, we identify a critical enhancer for the regulation of the XACT locus that evolved from an ancestral group of mammalian endogenous retroviruses (ERVs), prior to the emergence of XACT. This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.
Genetic determinants of the molecular portraits of epithelial cancers
Authors: Xia Youli , Fan Cheng , Hoadley Katherine A. , Parker Joel S. , Perou Charles M. 
Published: December 2019

AbstractThe ability to characterize and predict tumor phenotypes is crucial to precision medicine. In this study, we present an integrative computational approach using a genome-wide association analysis and an Elastic Net prediction method to analyze the relationship between DNA copy number alterations and an archive of gene expression signatures. Across breast cancers, we are able to quantitatively predict many gene signatures levels within individual tumors with high accuracy based upon DNA copy number features alone, including proliferation status and Estrogen-signaling pathway activity. We can also predict many other key phenotypes, including intrinsic molecular subtypes, estrogen receptor status, andTP53mutation. This approach is also applied to TCGA Pan-Cancer, which identify repeatedly predictable signatures across tumor types including immune features in lung squamous and basal-like breast cancers. These Elastic Net DNA predictors could also be called from DNA-based gene panels, thus facilitating their use as biomarkers to guide therapeutic decision making.
Single-molecule detection on a portable 3D-printed microscope
Authors: Brown James W. P. , Bauer Arnaud , Polinkovsky Mark E , Bhumkar Akshay , Hunter Dominic J. B. , Gaus Katharina , Sierecki Emma , Gambin Yann 
Published: December 2019

AbstractSingle-molecule assays have, by definition, the ultimate sensitivity and represent the next frontier in biological analysis and diagnostics. However, many of these powerful technologies require dedicated laboratories and trained personnel and have therefore remained research tools for specialists. Here, we present a single-molecule confocal system built from a 3D-printed scaffold, resulting in a compact, plug and play device called the AttoBright. This device performs single photon counting and fluorescence correlation spectroscopy (FCS) in a simple format and is widely applicable to the detection of single fluorophores, proteins, liposomes or bacteria. The power of single-molecule detection is demonstrated by detecting single α-synuclein amyloid fibrils, that are currently evaluated as biomarkers for Parkinson’s disease, with an improved sensitivity of >100,000-fold over bulk measurements.
An intravital window to image the colon in real time
Authors: Rakhilin Nikolai , Garrett Aliesha , Eom Chi-Yong , Chavez Katherine Ramos , Small David M. , Daniel Andrea R. , Kaelberer Melanie M. , Mejooli Menansili A. , Huang Qiang , Ding Shengli , Kirsch David G. , Bohórquez Diego V. , Nishimura Nozomi , Barth Bradley B. , Shen Xiling 
Published: December 2019

AbstractIntravital microscopy is a powerful technique to observe dynamic processes with single-cell resolution in live animals. No intravital window has been developed for imaging the colon due to its anatomic location and motility, although the colon is a key organ where the majority of microbiota reside and common diseases such as inflammatory bowel disease, functional gastrointestinal disorders, and colon cancer occur. Here we describe an intravital murine colonic window with a stabilizing ferromagnetic scaffold for chronic imaging, minimizing motion artifacts while maximizing long-term survival by preventing colonic obstruction. Using this setup, we image fluorescently-labeled stem cells, bacteria, and immune cells in live animal colons. Furthermore, we image nerve activity via calcium imaging in real time to demonstrate that electrical sacral nerve stimulation can activate colonic enteric neurons. The simple implantable apparatus enables visualization of live processes in the colon, which will open the window to a broad range of studies.
Interaction data from the Copenhagen Networks Study
Authors: Sapiezynski Piotr , Stopczynski Arkadiusz , Lassen David Dreyer , Lehmann Sune 
Published: December 2019

AbstractWe describe the multi-layer temporal network which connects a population of more than 700 university students over a period of four weeks. The dataset was collected via smartphones as part of the Copenhagen Networks Study. We include the network of physical proximity among the participants (estimated via Bluetooth signal strength), the network of phone calls (start time, duration, no content), the network of text messages (time of message, no content), and information about Facebook friendships. Thus, we provide multiple types of communication networks expressed in a single, large population with high temporal resolution, and over a period of multiple weeks, a fact which makes the dataset shared here unique. We expect that reuse of this dataset will allow researchers to make progress on the analysis and modeling of human social networks.
Defined factors to reactivate cell cycle activity in adult mouse cardiomyocytes
Authors: Judd Justin , Lovas Jonathan , Huang Guo N. 
Published: December 2019

AbstractAdult mammalian cardiomyocytes exit the cell cycle during the neonatal period, commensurate with the loss of regenerative capacity in adult mammalian hearts. We established conditions for long-term culture of adult mouse cardiomyocytes that are genetically labeled with fluorescence. This technique permits reliable analyses of proliferation of pre-existing cardiomyocytes without complications from cardiomyocyte marker expression loss due to dedifferentiation or significant contribution from cardiac progenitor cell expansion and differentiation in culture. Using this system, we took a candidate gene approach to screen for fetal-specific proliferative gene programs that can induce proliferation of adult mouse cardiomyocytes. Using pooled gene delivery and subtractive gene elimination, we identified a novel functional interaction between E2f Transcription Factor 2 (E2f2) and Brain Expressed X-Linked (Bex)/Transcription elongation factor A-like (Tceal) superfamily members Bex1 and Tceal8. Specifically, Bex1 and Tceal8 both preserved cell viability during E2f2-induced cell cycle re-entry. Although Tceal8 inhibited E2f2-induced S-phase re-entry, Bex1 facilitated DNA synthesis while inhibiting cell death. In sum, our study provides a valuable method for adult cardiomyocyte proliferation research and suggests that Bex family proteins may function in modulating cell proliferation and death decisions during cardiomyocyte development and maturation.
Radiomodifying action, Pharmacokinetic and Biodistribution of Ethyl 3, 4, 5-trihydroxybenzoate-Implication in development of radiomitigator
Authors: Pandey Pranav K , Ahmed B. , Prasad J. , Bala M. , Khan H. A. 
Published: December 2019

AbstractEthyl 3, 4, 5-trihydroxybenzoate (GAE) is a major bioactive constituent of Hippophae Rhamnoides L. leaves and extract prepared from H. rhamnoides leaves exhibited radioprotective and pharmacological activity. Radiomodifying properties of polyphenol compounds through free radical neutralizing have been reported earlier. However, to date pharmacokinetic (PK) and biodistribution of polyphenol compounds post 60Co-γ-irradiation (5 Gy) exposure have not been studied yet. The study aims to investigate the radio modifying and inflammatory action, PK and biodistribution of GAE at a radioprotective dose and changes, if any, induced after irradiation. Male C 57 BL/6 mice (28–30 g) were administered GAE (200 mg/kg b.wt) orally 15 minutes post to irradiation. Mice were sacrificed at 15, 30 min, 1,2,4,8 and 24 h. PK and biodistribution of GAE in plasma and tissues were studied. The radiomodifying potential was assessed in terms of mitigating NF-kB activity and SGOT, SGPT, urea and creatinine levels in liver and kidney post irradiation. Our study suggested the potential use of GAE as radiomodifying agent inhibits NF-kB expression and maintains the SGOT 24.10 ± 2.4, SGPT 36.01 ± 6.1 U/l, urea18.16 ± 0.003, and creatinine 1.05 ± 0.04 mg/dL upto 8 h in comparison to irradiated mice. Moreover, in biodistribution studies, showed that GAE crosses the blood-brain barrier and is found in brain tissue. Plasma level of GAE peaked at about 15 min, with Cmax 4390.85 ± 285.20 in GAE and in 3391.78 ± 78.13 ng/mL in radiation + GAE-treated animals, Biodistribution resulted in the highest concentration to be found in liver and kidney. These radiomodifying and pharmacokinetic result may be useful for study of the bioactive mechanism associated with radiation injury and to develop a potent formulation of GAE for clinical application.
Simplifying Weighted Heterogeneous Networks by Extracting h-Structure via s-Degree
Authors: Wang Ruby W. , Ye Fred Y. 
Published: December 2019

AbstractIn this study, we developed a method to extract the core structure of weighted heterogeneous networks by transforming the heterogeneous networks into homogeneous networks. Using the standardized z-score, we define the s-degree by summing all the z-scores of adjacent edges into base-nodes for a weighted heterogeneous network. Then, we rank all the s-degrees in decreasing order to obtain the core structure via the h-index of a base-homogeneous-network. After reducing all adjacent edges between the attribute nodes and base-nodes to the core structure, we obtain the heterogeneous core structure of the weighted network, which is called the h-structure. We find that the h-structure in a heterogeneous network contains less than 1% nodes and edges, which results in the construction of a highly effective simplification of a weighted heterogeneous network. Two practical cases, the citation network and the co-purchase network, were examined in this study.
Genetic engineering of parthenocarpic tomato plants using transient SlIAA9 knockdown by novel tissue-specific promoters
Authors: Kim Ji-Seong , Ezura Kentaro , Lee Jeongeun , Ariizumi Tohru , Ezura Hiroshi 
Published: December 2019

AbstractParthenocarpy is the development of an ovary into a seedless fruit without pollination. The ubiquitous downregulation of SlIAA9 induces not only parthenocarpic fruit formation but also an abnormal vegetative phenotype. To make parthenocarpic transgenic tomato plants without unwanted phenotypes, we found two genes, namely, Solyc03g007780 and Solyc02g067760, expressed in ovary tissue but not in vegetative tissues. Solyc03g007780 was expressed in developing ovaries and anthers. Solyc02g067760 mRNA was detected in whole-flower tissues. The promoters of Solyc03g007780 (Psol80) and Solyc02g067760 (Psol60) predominantly induced the expression of genes in the ovule, placenta, endocarp and pollen and in whole-flower tissues, respectively. Psol80/60-SlIAA9i lines, created for SlIAA9-RNA interference controlled by two promoters, successfully formed parthenocarpic fruits without pleiotropic effects in vegetative tissues. Downregulation of SlIAA9, responsible for parthenocarpic fruit formation, was observed in ovules rather than ovaries in the Psol80/60-SlIAA9i lines. Although the weight of parthenocarpic fruits of the Psol80/60-SlIAA9i lines was lower than the weight of pollinated fruits of the wild type (WT), the parthenocarpic fruits presented redder and more saturated colors and higher levels of total soluble solids and titratable acidity than the WT fruits.