bluuebunny/crossref_metadata_2025_split huggingface dataset:
RocS drives chromosome segregation and nucleoid occlusion inStreptococcus pneumoniae
Authors: Mercy Chryslène , Lavergne Jean-Pierre , Slager Jelle , Ducret Adrien , Garcia Pierre Simon , Noirot-Gros Marie-Francoise , Dubarry Nelly , Nourikyan Julien , Veening Jan-Willem , Grangeasse Christophe 
Published: July 2018

AbstractSegregation of replicated chromosomes in bacteria is poorly understood outside some prominent model strains and even less is known about how it is coordinated with other cellular processes. Here we report that RocS is crucial for chromosome segregation in the opportunistic human pathogenStreptococcus pneumoniae. RocS is membrane-bound and interacts both with DNA and the chromosome partitioning protein ParB to properly segregate the origin of replication region to new daughter cells. In addition, we show that RocS interacts with the tyrosine-autokinase CpsD required for polysaccharide capsule biogenesis, which is crucial forS. pneumoniae’s ability to prevent host immune detection. Altering the RocS-CpsD interaction drastically hinders chromosome partitioning and cell division. Altogether, this work reveals that RocS is the cornerstone of an atypical nucleoid occlusion system ensuring proper cell division in coordination with the biogenesis of a protective capsular layer.
Mutation Vulnerability Characterizes Human Cancer Genes
Authors: Li Yong Fuga , Xin Fuxiao 
Published: July 2018

AbstractRecent studies by Tomasetti et al. revealed that the risk disparity among different types of cancer is mainly determined by inherent patterns in DNA replication errors rather than environmental factors. In this study we reveal that inherent patterns of DNA mutations plays a similar role in cancer at the molecular level. Cancer results from stochastic DNA mutations, yet non-random patterns of cancer mutations emerge when we look across hundreds of cancer genomes. Over 500 cancer genes have been identified to date as the hot spot genes of cancer mutations. It is generally believed that these gene are mutated more frequently because they reside in functionally important pathways and are hence selected during the somatic evolution process of tumor progression. This theory however does not explain why many genes in the same pathways of cancer genes are not mutated in cancer. In this study, we challenge this view by showing that the inherent patterns of spontaneous mutations of human genes not only distinguish cancer causing genes and non-cancer genes but also shapes the mutation profile of cancer genes at the sub-gene level.
Cross-task perceptual learning of object recognition in simulated retinal implant perception
Authors: Wang Lihui , Sharifian Fariba , Napp Jonathan , Nath Carola , Pollmann Stefan 
Published: July 2018

AbstractThe perception gained by retina implants (RI) is limited, which asks for a learning regime to improve patients’ visual perception. Here we simulated RI vision and investigated if object recognition in RI patients can be improved and maintained through training. Importantly, we asked if the trained object recognition can be generalized to a new task context, and to new viewpoints of the trained objects. For this purpose, we adopted two training tasks, a naming task where participants had to choose the correct label out of other distracting labels for the presented object, and a discrimination task where participants had to choose the correct object out of other distracting objects to match the presented label. Our results showed that, despite of the task order, recognition performance was improved in both tasks and lasted at least for a week. The improved object recognition, however, can be transferred only from the naming task to the discrimination task but not vice versa. Additionally, the trained object recognition can be transferred to new viewpoints of the trained objects only in the naming task but not in the discrimination task. Training with the naming task is therefore recommended for RI patients to achieve persistent and flexible visual perception.
Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions
Authors: Thyme Summer B. , Pieper Lindsey M. , Li Eric H. , Pandey Shristi , Wang Yiqun , Morris Nathan S. , Sha Carrie , Choi Joo Won , Soucy Edward R. , Zimmerman Steve , Randlett Owen , Greenwood Joel , McCarroll Steven A. , Schier Alexander F. 
Published: July 2018

SummaryGenomic studies have identified hundreds of candidate genes near loci associated with risk for schizophrenia. To define candidates and their functions, we mutated zebrafish orthologues of 132 human schizophrenia-associated genes and created a phenotype atlas consisting of whole-brain activity maps, brain structural differences, and profiles of behavioral abnormalities. Phenotypes were diverse but specific, including altered forebrain development and decreased prepulse inhibition. Exploration of these datasets identified promising candidates in more than 10 gene-rich regions, including the magnesium transportercnnm2and the translational repressorgigyf2, and revealed shared anatomical sites of activity differences, including the pallium, hypothalamus or tectum. Single-cell RNA sequencing uncovered an essential role for the understudied transcription factorznf536in the development of forebrain neurons implicated in social behavior and stress. This phenotypic landscape of schizophrenia-associated genes prioritizes more than 30 candidates for further study and provides hypotheses to bridge the divide between genetic association and biological mechanism.
Gut bacterial diversity and physiological traits ofAnastrepha fraterculusBrazilian-1 morphotype males are affected by antibiotic treatment
Authors: Juárez M. Laura , Pimper Lida E. , Bachmann Guillermo E. , Conte Claudia A. , Ruiz M. Josefina , Goane Lucía , Pereyra Pilar Medina , Castro Felipe , Salgueiro Julieta , Cladera Jorge L. , Fernández Patricia E. , Bourtzis Kostas , Lanzavecchia Silvia B. , Vera M. Teresa , Segura Diego F. 
Published: July 2018

AbstractBackgroundThe interaction between gut bacterial symbionts and Tephritidae became the focus of several studies that showed that bacteria contributed to the nutritional status and the reproductive potential of its fruit fly hosts.Anastrepha fraterculusis an economically important fruit pest in South America. This pest is currently controlled by insecticides, which prompt the development of environmentally friendly methods such as the sterile insect technique (SIT). For SIT to be effective, a deep understanding of the biology and sexual behavior of the target species is needed. Although many studies have contributed in this direction, little is known about the composition and role ofA. fraterculussymbiotic bacteria. In this study we tested the hypothesis that gut bacteria contribute to nutritional status and reproductive success ofA. fraterculusmales.MethodsWild and laboratory-reared males were treated with antibiotics (AB) and provided sugar (S) or sugar plus protein (S+P) as food sources. The effect of AB on the gut bacteria diversity was assessed through DGGE and sequencing of the V6-V9 variable region of the bacterial 16SrRNAgene.ResultsAB affected the bacterial community of the digestive tract ofA. fraterculus, in particular bacteria belonging to the Enterobacteriaceae family, which was the dominant bacterial group in the control flies (i.e., non-treated with AB). AB negatively affected parameters directly related to the mating success of laboratory males and their nutritional status. AB also affected males’ survival under starvation conditions. The effect of AB on the behaviour and nutritional status of the males depended on two additional factors: the origin of the males and the presence of a proteinaceous source in the diet.ConclusionsOur results suggest thatA. fraterculusmales gut contain symbiotic organisms that are able to exert a positive contribution onA. fraterculusmales’ fitness, although the physiological mechanisms still need further studies.
The age-dependent relationship between resting heart rate variability and functional brain connectivity
Authors: Kumral D. , Schaare H.L. , Beyer F. , Reinelt J. , Uhlig M. , Liem F. , Lampe L. , Babayan A. , Reiter A. , Erbey M. , Roebbig J. , Loeffler M. , Schroeter M.L. , Husser D. , Witte A.V. , Villringer A. , Gaebler M. 
Published: July 2018

AbstractResting heart rate variability (HRV), an index of parasympathetic cardioregulation and an individual trait marker related to mental and physical health, decreases with age. Previous studies have associated resting HRV with structural and functional properties of the brain – mainly in cortical midline and limbic structures. We hypothesized that HRV may alter its relationship with brain structure and function across the adult lifespan. In 388 healthy subjects of three age groups (140 younger: 26.0±4.2 years, 119 middle-aged: 46.3±6.2 years, 129 older: 66.9±4.7 years), gray matter structure (voxel-based morphometry) and resting-state functional connectivity (eigenvector centrality mapping and exploratory seed-based functional connectivity) were related to resting HRV, measured as the root mean square of successive differences (RMSSD). Confirming previous findings, resting HRV decreased with age. For HRV-related gray matter volume, there were no statistically significant differences between the age groups, nor similarities across all age groups. In whole-brain functional connectivity analyses, we found an age-dependent association between resting HRV and eigenvector centrality in the bilateral ventromedial prefrontal cortex (vmPFC), driven by the younger adults. Across all age groups, HRV was positively correlated with network centrality in bilateral posterior cingulate cortex. Seed-based functional connectivity analysis using the vmPFC cluster revealed an HRV-related cortico-cerebellar network in younger but not in middle-aged or older adults. Our results indicate that the decrease of HRV with age is accompanied by changes in functional connectivity along the cortical midline. This extends our knowledge of brain-body interactions and their changes over the lifespan.
The processing of color preference in the brain
Authors: Racey Chris , Franklin Anna , Bird Chris M. 
Published: July 2018

AbstractDecades of research has established that humans have preferences for some colors (e.g., blue) and a dislike of others (e.g., dark chartreuse), with preference varying systematically with variation in hue (e.g., Hurlbert & Owen, 2015). Here, we used functional MRI to investigate why humans have likes and dislikes for simple patches of color, and to understand the neural basis of preference, aesthetics and value judgements more generally. We looked for correlations of a behavioural measure of color preference with the blood oxygen level-dependent (BOLD) response when participants performed an irrelevant orientation judgement task on colored squares. A whole brain analysis found a significant correlation between BOLD activity and color preference in the posterior midline cortex (PMC), centred on the precuneus but extending into the adjacent posterior cingulate and cuneus. These results demonstrate that brain activity is modulated by color preference, even when such preferences are irrelevant to the ongoing task the participants are engaged. They also suggest that color preferences automatically influence our processing of the visual world. Interestingly, the effect in the PMC overlaps with regions identified in neuroimaging studies of preference and value judgements of other types of stimuli. Therefore, our findings extends this literature to show that the PMC is related to automatic encoding of subjective value even for basic visual features such as color.
Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane
Authors: Sforça Danilo Augusto , Vautrin Sonia , Cardoso-Silva Claudio Benicio , Mancini Melina Cristina , da Cruz María Victoria Romero , da Silva Pereira Guilherme , Conte Mônica , Bellec Arnaud , Dahmer Nair , Fourment Joelle , Rodde Nathalie , Van Sluys Marie-Anne , Vicentini Renato , Garcia Antônio Augusto Franco , Forni-Martins Eliana Regina , Carneiro Monalisa Sampaio , Hoffmann Hermann Paulo , Pinto Luciana Rossini , de Andrade Landell Marcos Guimarães , Vincentz Michel , Berges Helene , Souza Anete Pereira 
Published: July 2018

AbstractBackgroundSugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization betweenS. officinarumandS. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.ResultsThe hypotheticalHP600and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genesHP600andCENP-Cwere found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was aSorghum bicolorortholog with all haplotypes ofHP600andCENP- Cexpressed, butHP600exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications ofHP600andCENP-C(paralogs). This duplication occurred before theSaccharumgenus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressedHP600pseudogene and a recombined fusion version ofCENP-Cand orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.ConclusionAll these findings describe a low synteny region in sugarcane, formed by events occurring in all members of theSaccharumgenus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.
Hierarchical Domain Structure Reveals the Divergence of Activity among TADs and Boundaries
Authors: An Lin , Yang Tao , Yang Jiahao , Nuebler Johannes , Xiang Guanjue , Hardison Ross C. , Li Qunhua , Zhang Yu 
Published: July 2018

AbstractThe spatial organization of chromatin in the nucleus has been implicated in many aspects of regulated gene expression. Maps of high frequency interactions between different segments of chromatin have revealed Topologically Associating Domains (TADs), within which most of the regulatory interactions are thought to occur. Recent studies have shown that TADs are not homogeneous structural units, but rather they appear to be organized into a hierarchy. However, precise identification of hierarchical TAD structures remains a challenge. We present OnTAD, an Optimized Nested TAD caller from Hi-C data, to identify hierarchical TADs. Compared to existing methods, OnTAD has significantly improved accuracy and running speed. Results from OnTAD reveal new biological insights on the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. The software and documentation for OnTAD are available at:https://github.com/anlin00007/OnTAD
Whole Genome Sequencing of Antimicrobial-Resistant Shigella sonnei Associated with Infection Acquired from International and Domestic Settings Reveals Gene Allelic Variants that Predict Global Lineages
Authors: Abelman Rebecca L. , M’ikanatha Nkuchia M. , Dudley Edward G. 
Published: July 2018

AbstractShigella spp. are a major cause of gastroenteritis worldwide, and S. sonnei is the most common species isolated within the United States. Recently, advancements in technology have made whole genome sequencing (WGS) readily available, and as such, laboratories are moving to implement WGS in outbreak analysis, surveillance, and antimicrobial resistance (AMR) monitoring of major foodborne pathogens. Accordingly, our study examined a collection of 22 antimicrobial resistant S. sonnei isolates from patients who either acquired the infections within the United States or when travelling to international locations between 2009 to 2014. We applied WGS to investigate both the relatedness of these isolates and the genetic determinants of AMR to address the phenotypic differences seen in previous observations. We analyzed the phylogeny of these strains and observed segmentation based on the previously described Global Lineages of S. sonnei. Following these results, 17 gene sequences with lineage specific single nucleotide polymorphisms (SNPs) were identified and developed into a lineage prediction test to determine the Global Lineage of uncharacterized S. sonnei, which accurately predicted phylogenetic segmentation and additionally showed specificity for S. sonnei genomes (97% accuracy, 38/39 genomes). Lastly, to determine differences between either the international or domestic isolates or between the Global Lineages, the AMR determinants were identified. We found a variety of AMR determinants within the genomes, and while the international and domestic S. sonnei carried similar resistance determinants, differences between Global Lineages were observed.
Oxytocin promotes lying for personal gain in a genotype-dependent manner
Authors: Sindermann Cornelia , Luo Ruixue , Becker Benjamin , Kendrick Keith M , Montag Christian 
Published: July 2018

AbstractSociety values honesty, since it fosters trust in others. Although we have a strong moral aversion to lying, particularly when it is self-serving, we nevertheless lie quite frequently and the biological basis for this is poorly understood. The hypothalamic neuropeptide oxytocin has been implicated in a number of anti-social as well as pro-social behaviours, including lying to benefit in-group members or in competitive situations. The aim of the present study was to investigate the effects of oxytocin administration on self-serving lying behaviour and possible moderating effects of genetic underpinnings of the oxytocin receptor. A total of 161 adult men participated in a randomized double-blind placebo-controlled between-subject intranasal oxytocin administration (24 International Units) study where self-serving lying was assessed using the die-in-a-cup paradigm. Additionally, contributions of polymorphisms in the oxytocin receptor gene were investigated using a haplotype approach. Results showed that while placebo-treated subjects behaved honestly across three successive rounds, oxytocin administration promoted self-serving lying, particularly in the third / last round and only to a certain degree (not to the maximum). Moreover, this effect of oxytocin was strongest in carriers of the GCG individual haplotype (rs237887-rs2268491-rs2254298) and non-carriers of the GT individual haplotype (rs53576-rs2268498) on the oxytocin receptor gene. Overall our findings demonstrate that oxytocin administration can promote self-serving lying when subjects are given repeated opportunities to lie and that these effects are moderated by genetic underpinnings of the oxytocin receptor.
How to build a mycelium: tradeoffs in fungal architectural traits
Authors: Lehmann Anika , Zheng Weishuang , Soutschek Katharina , Rillig Matthias C. 
Published: July 2018

AbstractThe fungal mycelium represents the essence of the fungal lifestyle, and understanding how a mycelium is constructed is of fundamental importance in fungal biology and ecology. Previous studies have examined initial developmental patterns or focused on a few strains, often mutants of model species, and frequently grown under non-harmonized growth conditions; these factors currently collectively hamper systematic insights into rules of mycelium architecture. To address this, we here use a broader suite of fungi (31 species including members of the Ascomycota, Basidiomycota and Mucoromycotina), all isolated from the same soil, and test for ten architectural traits under standardized laboratory conditions.We find great variability in traits among the saprobic fungal species, and detect several clear tradeoffs in mycelial architecture, for example between internodal length and hyphal diameter. Within the constraints so identified, we document otherwise great versatility in mycelium architecture in this set of fungi, and there was no evidence of trait ‘syndromes’ as might be expected.Our results point to an important dimension of fungal properties with likely consequences for coexistence within local communities, as well as for functional complementarity (e.g. decomposition, soil aggregation).
Anti-CD137 monoclonal antibody enhances trastuzumab-induced, natural killer cell-mediated cytotoxicity against pancreatic cancer cell lines with low human epidermal growth factor-like receptor 2 expression
Authors: Masu Takushi , Atsukawa Masanori , Nakatsuka Katsuhisa , Shimizu Masumi , Miura Daishu , Arai Taeang , Harimoto Hirotomo , Kondo Chisa , Kaneko Keiko , Futagami Seiji , Kawamoto Chiaki , Takahashi Hidemi , Iwakiri Katsuhiko 
Published: July 2018

AbstractBackgroundBecause human epidermal growth factor-like receptor (HER) 2 is expressed on the surface of human pancreatic carcinoma cells to varying degrees, trastuzumab, an anti-HER2 monoclonal antibody (mAb), is expected to exert antibody-dependent, natural killer (NK) cell-mediated cytotoxicity (ADCC) against the cells. However, some reports found that the effect of trastuzumab against human pancreatic carcinoma cells was limited because most express only limited HER2.MethodsWe examined whether anti-CD137 stimulating mAb could enhance trastuzumab-mediated ADCC against Panc-1, a human pancreatic cancer cell line with low HER2 expression, in vitro.ResultsSupplementation of anti-CD137 mAb could improve trastuzumab-mediated ADCC against Panc-1 which was insufficient without this stimulating antibody. The ADCC differed in individual cells, and this was related to the expression of CD137 on the surface of NK cells after trastuzumab stimulation in association with the Fcγ-RIIIA polymorphism. NK cells with Fcγ-RIIIA-VV/VF showed high levels of ADCC against Panc-1, but those with Fcγ-RIIIA-FF did not show optimal ADCC. In addition, trastuzumab-mediated ADCC against the human pancreatic cancer cell line Capan-1 with high HER2 expression was generally high and not affected by the Fcγ-RIIIA polymorphism.ConclusionsThese results demonstrated that in Fcγ-RIIIA-VV/VF-carrying hosts, trastuzumab plus αCD137 mAb could induce effective ADCC against HER2-low-expressing pancreatic cancer cells. This also indicates the therapeutic potential for unresectable human pancreatic cancer, in which HER-2 expression is generally low.