bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer
Authors: An Ning , Yang Xue , Cheng Shujun , Wang Guiqi , Zhang Kaitai 
Published: December 2015

AbstractCarcinogenesis is an exceedingly complicated process, which involves multi-level dysregulations, including genomics (majorly caused by somatic mutation and copy number variation), DNA methylomics and transcriptomics. Therefore, only looking into one molecular level of cancer is not sufficient to uncover the intricate underlying mechanisms. With the abundant resources of public available data in the Cancer Genome Atlas (TCGA) database, an integrative strategy was conducted to systematically analyze the aberrant patterns of colorectal cancer on the basis of DNA copy number, promoter methylation, somatic mutation and gene expression. In this study, paired samples in each genomic level were retrieved to identify differentially expressed genes with corresponding genetic or epigenetic dysregulations. Notably, the result of gene ontology enrichment analysis indicated that the differentially expressed genes with corresponding aberrant promoter methylation or somatic mutation were both functionally concentrated upon developmental process, suggesting the intimate association between development and carcinogenesis. Thus, by means of random walk with restart, 37 significant development-related genes were retrieved from a priori-knowledge based biological network. In five independent microarray datasets, Kaplan–Meier survival and Cox regression analyses both confirmed that the expression of these genes was significantly associated with overall survival of Stage III/IV colorectal cancer patients.
Long-term Autophagy and Nrf2 Signaling in the Hippocampi of Developing Mice after Carbon Ion Exposure
Authors: Ye Fei , Zhao Ting , Liu Xiongxiong , Jin Xiaodong , Liu Xinguo , Wang Tieshan , Li Qiang 
Published: December 2015

AbstractTo explore charged particle radiation-induced long-term hippocampus damage, we investigated the expression of autophagy and antioxidant Nrf2 signaling-related proteins in the mouse hippocampus after carbon ion radiation. Heads of immature female Balb/c mice were irradiated with carbon ions of different LETs at various doses. Behavioral tests were performed on the mice after maturation. Acute and chronic expression of LC3-II, p62/SQSTM1, nuclear Nrf2, activated caspase-3 and the Bax/Bcl-2 ratio were measured in the hippocampi. Secondary X-ray insult was adopted to amplify potential damages. Long-term behavioral changes were observed in high-LET carbon ion-irradiated mice. There were no differences in the rates of LC3-II induction and p62/SQSTM1 degradation compared to the control group regardless of whether the mice received the secondary X-ray insult. A high nuclear Nrf2 content and low apoptosis level in hippocampal cells subjected to secondary X-rays were observed for the mice exposed to relatively low-LET carbon ions. Therefore, carbon ion exposure in the immature mouse led to an LET-dependent behavioral change after maturation. Although autophagy was intact, the persistently high nuclear Nrf2 content in the hippocampus might account for the unchanged behavioral pattern in mice exposed to the relatively low-LET carbon ions and the subsequent increased radioresistance of the hippocampus.
Novel kinase fusion transcripts found in endometrial cancer
Authors: Tamura Ryo , Yoshihara Kosuke , Yamawaki Kaoru , Suda Kazuaki , Ishiguro Tatsuya , Adachi Sosuke , Okuda Shujiro , Inoue Ituro , Verhaak Roel G. W. , Enomoto Takayuki 
Published: December 2015

AbstractRecent advances in RNA-sequencing technology have enabled the discovery of gene fusion transcripts in the transcriptome of cancer cells. However, it remains difficult to differentiate the therapeutically targetable fusions from passenger events. We have analyzed RNA-sequencing data and DNA copy number data from 25 endometrial cancer cell lines to identify potential therapeutically targetable fusion transcripts and have identified 124 high-confidence fusion transcripts, of which 69% are associated with gene amplifications. As targetable fusion candidates, we focused on three in-frame kinase fusion transcripts that retain a kinase domain (CPQ-PRKDC, CAPZA2-MET and VGLL4-PRKG1). We detected only CPQ-PRKDC fusion transcript in three of 122 primary endometrial cancer tissues. Cell proliferation of the fusion-positive cell line was inhibited by knocking down the expression of wild-type PRKDC but not by blocking the CPQ-PRKDC fusion transcript expression. Quantitative real-time RT-PCR demonstrated that the expression of the CPQ-PRKDC fusion transcript was significantly lower than that of wild-type PRKDC, corresponding to a low transcript allele fraction of this fusion, based on RNA-sequencing read counts. In endometrial cancers, the CPQ-PRKDC fusion transcript may be a passenger aberration related to gene amplification. Our findings suggest that transcript allele fraction is a useful predictor to find bona-fide therapeutic-targetable fusion transcripts.
Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth
Authors: Xiao Shijun , Wang Panpan , Zhang Yan , Fang Lujing , Liu Yang , Li Jiong-Tang , Wang Zhi-Yong 
Published: December 2015

AbstractThe genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker.
Sequence and gene expression evolution of paralogous genes in willows
Authors: Harikrishnan Srilakshmy L. , Pucholt Pascal , Berlin Sofia 
Published: December 2015

AbstractWhole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows.
Topological constraints on network control profiles
Authors: Campbell Colin , Ruths Justin , Ruths Derek , Shea Katriona , Albert Réka 
Published: December 2015

AbstractNetwork models are designed to capture properties of empirical networks and thereby provide insight into the processes that underlie the formation of complex systems. As new information concerning network structure becomes available, it becomes possible to design models that more fully capture the properties of empirical networks. A recent advance in our understanding of network structure is the control profile, which summarizes the structural controllability of a network in terms of source nodes, external dilations and internal dilations. Here, we consider the topological properties–and their formation mechanisms—that constrain the control profile. We consider five representative empirical categories of internal-dilation dominated networks and show that the number of source and sink nodes, the form of the in- and out-degree distributions and local complexity (e.g., cycles) shape the control profile. We evaluate network models that are sufficient to produce realistic control profiles and conclude that holistic network models should similarly consider these properties.
Defect-Mediated Lithium Adsorption and Diffusion on Monolayer Molybdenum Disulfide
Authors: Sun Xiaoli , Wang Zhiguo , Fu Y. Q. 
Published: December 2015

AbstractMonolayer Molybdenum Disulfide (MoS2) is a promising anode material for lithium ion batteries because of its high capacities. In this work, first principle calculations based on spin density functional theory were performed to investigate adsorption and diffusion of lithium on monolayer MoS2with defects, such as single- and few-atom vacancies, antisite and grain boundary. The values of adsorption energies on the monolayer MoS2with the defects were increased compared to those on the pristine MoS2. The presence of defects causes that the Li is strongly bound to the monolayer MoS2with adsorption energies in the range between 2.81 and 3.80 eV. The donation of Li 2selectron to the defects causes an enhancement of adsorption of Li on the monolayer MoS2. At the same time, the presence of defects does not apparently affect the diffusion of Li and the energy barriers are in the range of 0.25–0.42 eV. The presence of the defects can enhance the energy storage capacity, suggesting that the monolayer MoS2with defects is a suitable anode material for the Li-ion batteries.
Nobiletin enhances the efficacy of chemotherapeutic agents in ABCB1 overexpression cancer cells
Authors: Ma Wenzhe , Feng Senling , Yao Xiaojun , Yuan Zhongwen , Liu Liang , Xie Ying 
Published: December 2015

AbstractMultidrug resistance (MDR) is the major obstacle to the successful chemotherapy treatment of many cancers. Here we found that nobiletin, a citrus methoxyflavone, significantly sensitized ABCB1 overexpressing cells A2780/T and A549/T to chemotherapeutic agents such as paclitaxel (a 433-fold reversal of MDR to PTX at 9 μM), doxorubicin (DOX), docetaxel and dounorubicin. Nobiletin profoundly inhibited ABCB1 transporter activity since it significantly increased the intracellular accumulation of DOX and Flutax-2 in A2780/T cells and decreased the efflux of ABCB1 substrates in Caco2 cells without altering the mRNA and protein expression of ABCB1. Moreover, nobiletin stimulated ATPase activity and inhibited verapamil-stimulated ATPase activity in a concentration-dependent manner, indicating a direct interaction with the transporter. Consistent with these findings, molecular docking analysis also identified favorable binding of nobiletin with the transmemberane region site 1 of homology modeled human ABCB1 transporter. Moreover, the Nrf2 protein expression and phosphorylation levels of AKT/ERK were suppressed by co-treated with nobiletin and PTX at the reversal concentrations, suggesting that inhibition of the AKT/ERK/Nrf2 pathway was associated with the sensitizing effect of nobiletin. These findings encourage further animal and clinical MDR studies with the combination therapy of nobiletin and chemotherapeutic drugs.
Beneficial metabolic effects of selected probiotics on diet‐induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota
Authors: Alard Jeanne , Lehrter Véronique , Rhimi Moez , Mangin Irène , Peucelle Véronique , Abraham Anne‐Laure , Mariadassou Mahendra , Maguin Emmanuelle , Waligora‐Dupriet Anne‐Judith , Pot Bruno , Wolowczuk Isabelle , Grangette Corinne 
Published: December 2015

SummaryAlterations in gut microbiota composition and diversity were suggested to play a role in the development of obesity, a chronic subclinical inflammatory condition. We here evaluated the impact of oral consumption of a monostrain or multi‐strain probiotic preparation in high‐fat diet‐induced obese mice. We observed a strain‐specific effect and reported dissociation between the capacity of probiotics to dampen adipose tissue inflammation and to limit body weight gain. A multi‐strain mixture was able to improve adiposity, insulin resistance and dyslipidemia through adipose tissue immune cell‐remodelling, mainly affecting macrophages. At the gut level, the mixture modified the uptake of fatty acids and restored the expression level of the short‐chain fatty acid receptor GPR43. These beneficial effects were associated with changes in the microbiota composition, such as the restoration of the abundance of Akkermansia muciniphila and Rikenellaceae and the decrease of other taxa like Lactobacillaceae. Using an in vitro gut model, we further showed that the probiotic mixture favours the production of butyrate and propionate. Our findings provide crucial clues for the design and use of more efficient probiotic preparations in obesity management and may bring new insights into the mechanisms by which host–microbe interactions govern such protective effects.
Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes
Authors: Pechal Jennifer L. , Benbow M. Eric 
Published: December 2015

SummaryCarrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic–terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high‐throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass‐bearing streams and in non‐carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy‐driven networks respond to resource pulses with bottom‐up effects on consumer microbial structure, as revealed by shifting communities over space and time.
Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems
Authors: Bergkemper Fabian , Schöler Anne , Engel Marion , Lang Friederike , Krüger Jaane , Schloter Michael , Schulz Stefanie 
Published: December 2015

SummaryPhosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus but conversely also take up and immobilize P. Therefore, we analysed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic deoxyribonucleic acid. For inorganic P solubilization, a significantly higher microbial potential was detected in the P‐rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the data sets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P‐depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harboured by Rhizobiales, Actinomycetales and Acidobacteriales.
Identification of bypass reactions leading to the formation of one central steroid degradation intermediate in metabolism of different bile salts in Pseudomonas sp. strain Chol1
Authors: Holert Johannes , Yücel Onur , Jagmann Nina , Prestel Andreas , Möller Heiko M. , Philipp Bodo 
Published: December 2015

SummaryThe bile salts cholate, deoxycholate, chenodeoxycholate and lithocholate are released from vertebrates into soil and water where environmental bacteria degrade these widespread steroid compounds. It was investigated whether different enzymes are required for the degradation of these tri‐, di‐ and monohydroxylated bile salts in the model organism Pseudomonas sp. strain Chol1. Experiments with available and novel mutants showed that the degradation of the C5‐carboxylic side chain attached to the steroid skeleton is catalysed by the same set of enzymes. A difference was found for the degradation of partially degraded bile salts consisting of H‐methylhexahydroindanone‐propanoates (HIPs). With deoxycholate and lithocholate, which lack a hydroxy group at C7 of the steroid skeleton, an additional acyl‐coenzyme A (CoA) dehydrogenase was required for β‐oxidation of the C3‐carboxylic side chain attached to the methylhexahydroindanone moiety. The β‐oxidation of this side chain could be measured in vitro. With cholate and deoxycholate, a reductive dehydroxylation of the C12‐hydroxy group of HIP was required. Deletion of candidate genes for this reaction step revealed that a so‐far unknown steroid dehydratase and a steroid oxidoreductase were responsible for this CoA‐dependent reaction. These results showed that all bile salts are channelled into a common pathway via bypass reactions with 3'‐hydroxy‐HIP‐CoA as central intermediate.
Urban Citizenship and Right to the City: The Fragmentation of Claims
Authors: Blokland Talja , Hentschel Christine , Holm Andrej , Lebuhn Henrik , Margalit Talia 
Published: December 2015

AbstractIn this symposium, we explore how urban citizenship is about expressing, if not producing, difference, and how fragmentation of claims affects urban citizenship and right to the city movements with their universal, all‐inclusive ideals. Investigating social movements, political participation and conflicting diversities in public space in Tel Aviv and Berlin, we see a trend towards a diversification of interests, a weakening of movements, and even a competition over rights and resources rather than a development of mutual support and solidarities among various groups on the pathway to a livable city. This tension, we argue, deserves attention. Radical urban scholarship and politics need to better understand the historical and place‐specific contexts that structure the formation of citizenship claims and the courses that citizenship struggles take. Celebrations of urban citizenship as a more contextualized, community oriented, and bottom‐up framework (in comparison to national citizenship) should therefore be complemented by a careful investigation of their fragmented and fragmenting practices.
‘There are Really Two Cities Here’: Fragmented Urban Citizenship In Tel Aviv
Authors: Cohen Nir , Margalit Talia 
Published: December 2015

AbstractThe inflow of African migrants into Tel Aviv's southern neighborhoods has aroused much resentment from long‐term residents. Contesting the uneven burden sharing, which exacerbates already poor conditions at the local level, southern residents have aimed their grievances at municipal and national policymakers as well as the city's more affluent northern residents. In analyzing the contestation, this article challenges traditional conceptions of migrants as the binary opposition to residents of the host city, intruders on the shared and socio‐culturally homogenous urban arena. We build on recent theorizations of urban citizenship as an agency‐centered process to think through the ways in which city residents articulate their identities relationally and hierarchically against new and old ‘others’ and argue that international newcomers have destabilized long‐conceived social relations. Using narratives of long‐term southern residents, we illustrate how the uneven geographies of African migrants' settlement in Tel Aviv have (re)set in motion a process of urban citizenship formation by southern residents, thereby adding new layers of contention to what was already a highly stratified realm.
Investigation into Seasonal Scavenging Patterns of Raccoons on Human Decomposition,
Authors: Jeong Yangseung , Jantz Lee Meadows , Smith Jake 
Published: December 2015

AbstractAlthough raccoons are known as one of the most common scavengers in the U.S., scavenging by these animals has seldom been studied in terms of forensic significance. In this research, the seasonal pattern of raccoon scavenging and its effect on human decomposition was investigated using 178 human cadavers placed at the Anthropological Research Facility (ARF) of the University of Tennessee, Knoxville (UTK) between February 2011 and December 2013. The results reveal that (i) the frequency of scavenging increases during summer, (ii) scavenging occurs relatively immediately and lasts shorter in summer months, and (iii) scavenging influences the decomposition process by hollowing limbs and by disturbing insect activities, both of which eventually increases the chance of mummification on the affected body. This information is expected to help forensic investigators identify raccoon scavenging as well as make a more precise interpretation of the effect of raccoon scavenging on bodies at crime scenes.