bluuebunny/crossref_metadata_2025_split huggingface dataset:
Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes
Authors: Mayr Magdalena J , Zimmermann Matthias , Guggenheim Carole , Brand Andreas , Bürgmann Helmut 
Published: October 2019

AbstractLakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen–methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen–methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen–methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen–methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.
Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation
Authors: Fan Peixin , Bian Beilei , Teng Lin , Nelson Corwin D , Driver J , Elzo Mauricio A , Jeong Kwangcheol C 
Published: October 2019

Abstract
Multiple synergistic factors affect the development and composition of mammalian gut microbiota, but effects of host genetics remain unclear. To illuminate the role of host genetics on gut microbiota, we employed animals with a graduated spectrum of genetic variation with minimal environmental influences. We bred 228 calves with linearly varying breed composition from 100% Angus (Bos taurus) to 100% Brahman (Bos indicus), as a proxy for genetic variation, and then raised the offspring in the same environment with identical diets. We hypothesized each breed would harbor distinct gut microbiota due to genetic influence. We found that the gut microbiota of preweaning calves at 3 months old is significantly affected by host genetics, profoundly by paternal genome. We also demonstrate that single nucleotide polymorphisms in host mucin-encoding genes, critical for gut mucosal health, are significantly correlated with both breed composition and mucin-degrading gut bacteria. We further demonstrate host genetics indirectly changes gut microbiota composition via microbe–microbe interactions. These findings indicate a strong contribution by host genetics in shaping the gut microbiota during early life stages, shedding light on impact of animal breeding on gut microbiota, which is associated with animal growth and health.
Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species
Authors: Massoni Julien , Bortfeld-Miller Miriam , Jardillier Ludwig , Salazar Guillem , Sunagawa Shinichi , Vorholt Julia A 
Published: October 2019

Abstract
Bacteria colonizing the aerial parts of plants (phyllosphere) are linked to the biology of their host. They impact plant–pathogen interactions and may influence plant reproduction. Past studies have shown differences in composition and structure of the leaf, flower, and host microbiota, but an investigation of the impact of individual taxa on these variations remains to be tested. Such information will help to evaluate disparities and to better understand the biology and evolution of the plant–microbe associations. In the present study, we investigated the community structure, occupancy of host and organ, and the prevalence of phyllosphere bacteria from three host species collected at the same location. Almost all (98%) of bacterial taxa detected in the phyllosphere were not only shared across leaves and flowers, or different plant species but also had a conserved prevalence across sub-environments of the phyllosphere. We also found nonrandom associations of the phylogenetic diversity of phyllosphere bacteria. These results suggest that the phyllosphere microbiota is more conserved than previously acknowledged, and dominated by generalist bacteria adapted to environmental heterogeneity through evolutionary conserved traits.
Attention-deficit hyperactivity disorder shares copy number variant risk with schizophrenia and autism spectrum disorder
Authors: Gudmundsson Olafur O. , Walters G. Bragi , Ingason Andres , Johansson Stefan , Zayats Tetyana , Athanasiu Lavinia , Sonderby Ida Elken , Gustafsson Omar , Nawaz Muhammad S. , Jonsson Gudbjorn F. , Jonsson Lina , Knappskog Per-Morten , Ingvarsdottir Ester , Davidsdottir Katrin , Djurovic Srdjan , Knudsen Gun Peggy Strømstad , Askeland Ragna Bugge , Haraldsdottir Gyda S. , Baldursson Gisli , Magnusson Pall , Sigurdsson Engilbert , Gudbjartsson Daniel F. , Stefansson Hreinn , Andreassen Ole A. , Haavik Jan , Reichborn-Kjennerud Ted , Stefansson Kari 
Published: October 2019

AbstractAttention-deficit/hyperactivity disorder (ADHD) is a highly heritable common childhood-onset neurodevelopmental disorder. Some rare copy number variations (CNVs) affect multiple neurodevelopmental disorders such as intellectual disability, autism spectrum disorders (ASD), schizophrenia and ADHD. The aim of this study is to determine to what extent ADHD shares high risk CNV alleles with schizophrenia and ASD. We compiled 19 neuropsychiatric CNVs and test 14, with sufficient power, for association with ADHD in Icelandic and Norwegian samples. Eight associate with ADHD; deletions at 2p16.3 (NRXN1), 15q11.2, 15q13.3 (BP4 & BP4.5–BP5) and 22q11.21, and duplications at 1q21.1 distal, 16p11.2 proximal, 16p13.11 and 22q11.21. Six of the CNVs have not been associated with ADHD before. As a group, the 19 CNVs associate with ADHD (OR = 2.43, P = 1.6 × 10−21), even when comorbid ASD and schizophrenia are excluded from the sample. These results highlight the pleiotropic effect of the neuropsychiatric CNVs and add evidence for ADHD, ASD and schizophrenia being related neurodevelopmental disorders rather than distinct entities.
Clinical-learning versus machine-learning for transdiagnostic prediction of psychosis onset in individuals at-risk
Authors: Fusar-Poli Paolo , Stringer Dominic , M. S. Durieux Alice , Rutigliano Grazia , Bonoldi Ilaria , De Micheli Andrea , Stahl Daniel 
Published: October 2019

AbstractPredicting the onset of psychosis in individuals at-risk is based on robust prognostic model building methods including a priori clinical knowledge (also termed clinical-learning) to preselect predictors or machine-learning methods to select predictors automatically. To date, there is no empirical research comparing the prognostic accuracy of these two methods for the prediction of psychosis onset. In a first experiment, no improved performance was observed when machine-learning methods (LASSO and RIDGE) were applied—using the same predictors—to an individualised, transdiagnostic, clinically based, risk calculator previously developed on the basis of clinical-learning (predictors: age, gender, age by gender, ethnicity, ICD-10 diagnostic spectrum), and externally validated twice. In a second experiment, two refined versions of the published model which expanded the granularity of the ICD-10 diagnosis were introduced: ICD-10 diagnostic categories and ICD-10 diagnostic subdivisions. Although these refined versions showed an increase in apparent performance, their external performance was similar to the original model. In a third experiment, the three refined models were analysed under machine-learning and clinical-learning with a variable event per variable ratio (EPV). The best performing model under low EPVs was obtained through machine-learning approaches. The development of prognostic models on the basis of a priori clinical knowledge, large samples and adequate events per variable is a robust clinical prediction method to forecast psychosis onset in patients at-risk, and is comparable to machine-learning methods, which are more difficult to interpret and implement. Machine-learning methods should be preferred for high dimensional data when no a priori knowledge is available.
Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy
Authors: Cheung Chantal Hoi Yin , Hsu Chia-Lang , Tsuei Chao-Yin , Kuo Tzu-Ting , Huang Chen-Tsung , Hsu Wen-Ming , Chung Yun-Hsien , Wu Hsin-Yi , Hsu Cheng-Chih , Huang Hsuan-Cheng , Juan Hsueh-Fen 
Published: October 2019

AbstractMYCN-amplified (MNA) neuroblastoma is an aggressive neural crest-derived pediatric cancer. However, MYCN is indispensable for development and transcriptionally regulates extensive network of genes. Integrating anti-MYCN ChIP-seq and gene expression profiles of neuroblastoma patients revealed the metabolic enzymes, MTHFD2 and PAICS, required for one-carbon metabolism and purine biosynthesis were concomitantly upregulated, which were more susceptible to metastatic neuroblastoma. Moreover, we found that MYCN mediated the folate cycle via MTHFD2, which contributed one-carbon unit to enhance purine synthesis, and further regulated nucleotide production by PAICS in response to cancer progression. Dual knockdown of the MYCN-targeted gene pair, MTHFD2 and PAICS, in MNA neuroblastoma cells synergically reduced cell proliferation, colony formation, migration ability, and DNA synthesis. By systematically screening the compound perturbagens, the gene expression levels of MTHFD2 and PAICS were specifically suppressed by anisomycin and apicidin across cell lines, and our co-treatment results also displayed synergistic inhibition of MNA neuroblastoma cell proliferation. Collectively, targeting a combination of MYCN-targeted genes that interrupts the interconnection of metabolic pathways may overcome drug toxicity and improve the efficacy of current therapeutic agents in MNA neuroblastoma.
Disordered zero-index metamaterials based on metal-induced crystallization
Authors: Galinski Henning , Wyss Andreas , Seregni Mattia , Ma Huan , Schnabel Volker , Sologubenko Alla , Spolenak Ralph 
Published: October 2019

AbstractZero-index (ZI) materials are synthetic optical materials with a vanishing effective permittivity and/or permeability at a given design frequency. Recently, it has been shown that the permeability of a zero-index host material can be deterministically tuned by adding photonic dopants. Here, we apply metal-induced crystallization (MIC) in quasi-random metal–semiconductor composites to fabricate large-area zero-index materials. Using Ag–Si as a model system, we demonstrate that the localized crystallization of the semiconductor at the metal/semiconductor interface can be used as a design parameter to control light interaction in such a disordered system. The induced crystallization generates new zero-index states corresponding to a hybridized plasmonic mode emerging from selective coupling of light to the Ångstrom-sized crystalline shell of the semiconductor. Photonic doping can be used to enhance the transmission in these disordered metamaterials, as shown by simulations. Our results establish novel large-area zero-index materials for wafer-scale applications and beyond.
Enhanced spin orbit interaction of light in highly confining optical fibers for mode division multiplexing
Authors: Gregg P. , Kristensen P. , Rubano A. , Golowich S. , Marrucci L. , Ramachandran S. 
Published: October 2019

AbstractLight carries both orbital angular momentum (OAM) and spin angular momentum (SAM), related to wavefront rotation and polarization, respectively. These are usually approximately independent quantities, but they become coupled by light’s spin-orbit interaction (SOI) in certain exotic geometries and at the nanoscale. Here we reveal a manifestation of strong SOI in fibers engineered at the micro-scale and supporting the only known example of propagating light modes with non-integer mean OAM. This enables propagation of a record number (24) of states in a single optical fiber with low cross-talk (purity > 93%), even as tens-of-meters long fibers are bent, twisted or otherwise handled, as fibers are practically deployed. In addition to enabling the investigation of novel SOI effects, these light states represent the first ensemble with which mode count can be potentially arbitrarily scaled to satisfy the exponentially growing demands of high-performance data centers and supercomputers, or telecommunications network nodes.
UHRF1 suppresses retrotransposons and cooperates with PRMT5 and PIWI proteins in male germ cells
Authors: Dong Juan , Wang Xiaoli , Cao Congcong , Wen Yujiao , Sakashita Akihiko , Chen Si , Zhang Jin , Zhang Yue , Zhou Liquan , Luo Mengcheng , Liu Mingxi , Liao Aihua , Namekawa Satoshi H. , Yuan Shuiqiao 
Published: October 2019

AbstractDNA methylation, repressive histone marks, and PIWI-interacting RNA (piRNA) are essential for the control of retrotransposon silencing in the mammalian germline. However, it remains unknown how these repressive epigenetic pathways crosstalk to ensure retrotransposon silencing in the male germline. Here, we show that UHRF1 is responsible for retrotransposon silencing and cooperates with repressive epigenetic pathways in male germ cells. Conditional loss of UHRF1 in postnatal germ cells causes DNA hypomethylation, upregulation of retrotransposons, the activation of a DNA damage response, and switches in the global chromatin status, leading to complete male sterility. Furthermore, we show that UHRF1 interacts with PRMT5, an arginine methyltransferase, to regulate the repressive histone arginine modifications (H4R3me2s and H3R2me2s), and cooperates with the PIWI pathway during spermatogenesis. Collectively, UHRF1 regulates retrotransposon silencing in male germ cells and provides a molecular link between DNA methylation, histone modification, and the PIWI pathway in the germline.
Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation
Authors: Klein Brianna J. , Jang Suk Min , Lachance Catherine , Mi Wenyi , Lyu Jie , Sakuraba Shun , Krajewski Krzysztof , Wang Wesley W. , Sidoli Simone , Liu Jiuyang , Zhang Yi , Wang Xiaolu , Warfield Becka M. , Kueh Andrew J. , Voss Anne K. , Thomas Tim , Garcia Benjamin A. , Liu Wenshe R. , Strahl Brian D. , Kono Hidetoshi , Li Wei , Shi Xiaobing , Côté Jacques , Kutateladze Tatiana G. 
Published: October 2019

AbstractAcetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.
Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
Authors: Wang Kun , Wang Dehe , Zheng Xiaomin , Qin Ai , Zhou Jie , Guo Boyu , Chen Yanjun , Wen Xingpeng , Ye Wen , Zhou Yu , Zhu Yuxian 
Published: October 2019

AbstractCotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
The evolution of parental care diversity in amphibians
Authors: Furness Andrew I. , Capellini Isabella 
Published: October 2019

AbstractParental care is extremely diverse across species, ranging from simple behaviours to complex adaptations, varying in duration and in which sex cares. Surprisingly, we know little about how such diversity has evolved. Here, using phylogenetic comparative methods and data for over 1300 amphibian species, we show that egg attendance, arguably one of the simplest care behaviours, is gained and lost faster than any other care form, while complex adaptations, like brooding and viviparity, are lost at very low rates, if at all. Prolonged care from the egg to later developmental stages evolves from temporally limited care, but it is as easily lost as it is gained. Finally, biparental care is evolutionarily unstable regardless of whether the parents perform complementary or similar care duties. By considering the full spectrum of parental care adaptations, our study reveals a more complex and nuanced picture of how care evolves, is maintained, or is lost.
Correlation between manganese dissolution and dynamic phase stability in spinel-based lithium-ion battery
Authors: Liu Tongchao , Dai Alvin , Lu Jun , Yuan Yifei , Xiao Yinguo , Yu Lei , Li Matthew , Gim Jihyeon , Ma Lu , Liu Jiajie , Zhan Chun , Li Luxi , Zheng Jiaxin , Ren Yang , Wu Tianpin , Shahbazian-Yassar Reza , Wen Jianguo , Pan Feng , Amine Khalil 
Published: October 2019

AbstractHistorically long accepted to be the singular root cause of capacity fading, transition metal dissolution has been reported to severely degrade the anode. However, its impact on the cathode behavior remains poorly understood. Here we show the correlation between capacity fading and phase/surface stability of an LiMn2O4cathode. It is revealed that a combination of structural transformation and transition metal dissolution dominates the cathode capacity fading. LiMn2O4exhibits irreversible phase transitions driven by manganese(III) disproportionation and Jahn-Teller distortion, which in conjunction with particle cracks results in serious manganese dissolution. Meanwhile, fast manganese dissolution in turn triggers irreversible structural evolution, and as such, forms a detrimental cycle constantly consuming active cathode components. Furthermore, lithium-rich LiMn2O4with lithium/manganese disorder and surface reconstruction could effectively suppress the irreversible phase transition and manganese dissolution. These findings close the loop of understanding capacity fading mechanisms and allow for development of longer life batteries.
Targeting the mTOR pathway uncouples the efficacy and toxicity of PD-1 blockade in renal transplantation
Authors: Esfahani Khashayar , Al-Aubodah Tho-Alfakar , Thebault Pamela , Lapointe Réjean , Hudson Marie , Johnson Nathalie A. , Baran Dana , Bhulaiga Najwa , Takano Tomoko , Cailhier Jean-François , Piccirillo Ciriaco A. , Miller Wilson H. 
Published: October 2019

AbstractImmune checkpoint inhibitor (ICI) use remains a challenge in patients with solid organ allografts as most would undergo rejection. In a melanoma patient in whom programmed-death 1 (PD-1) blockade resulted in organ rejection and colitis, the addition of the mTOR inhibitor sirolimus resulted in ongoing anti-tumor efficacy while promoting allograft tolerance. Strong granzyme B+, interferon (IFN)-γ+ CD8+ cytotoxic T cell and circulating regulatory T (Treg) cell responses were noted during allograft rejection, along with significant eosinophilia and elevated serum IL-5 and eotaxin levels. Co-treatment with sirolimus abated cytotoxic T cell numbers and eosinophilia, while elevated Treg cell numbers in the peripheral blood were maintained. Interestingly, numbers of IFN-γ+ CD4+ T cells and serum IFN-γ levels increased with the addition of sirolimus treatment likely promoting ongoing anti-PD-1 efficacy. Thus, our results indicate that sirolimus has the potential to uncouple anti-PD-1 therapy toxicity and efficacy.
Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation
Authors: Annavajhala Medini K. , Gomez-Simmonds Angela , Macesic Nenad , Sullivan Sean B. , Kress Anna , Khan Sabrina D. , Giddins Marla J. , Stump Stephania , Kim Grace I. , Narain Ryan , Verna Elizabeth C. , Uhlemann Anne-Catrin 
Published: October 2019

AbstractInfections by multidrug-resistant bacteria (MDRB) remain a leading cause of morbidity and mortality after liver transplantation (LT). Gut dysbiosis characteristic of end-stage liver disease may predispose patients to intestinal MDRB colonization and infection, in turn exacerbating dysbiosis. However, relationships between MDRB colonization and dysbiosis after LT remain unclear. We prospectively recruited 177 adult patients undergoing LT at a single tertiary care center. 16 S V3-V4 rRNA sequencing was performed on 723 fecal samples collected pre-LT and periodically until one-year post-LT to test whether MDRB colonization was associated with decreased microbiome diversity. In multivariate linear mixed-effect models, MDRB colonization predicts reduced Shannon α-diversity, after controlling for underlying liver disease, antibiotic exposures, and clinical complications. Importantly, pre-LT microbial markers predict subsequent colonization by MDRB. Our results suggest MDRB colonization as a major, previously unrecognized, marker of persistent dysbiosis. Therapeutic approaches accounting for microbial and clinical factors are needed to address post-transplant microbiome health.