bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osteoclast-derived microRNA-containing exosomes selectively inhibit osteoblast activity
Authors: Sun Weijia , Zhao Chenyang , Li Yuheng , Wang Liang , Nie Guangjun , Peng Jiang , Wang Aiyuan , Zhang Pengfei , Tian Weiming , Li Qi , Song Jinping , Wang Cheng , Xu Xiaolong , Tian Yanhua , Zhao Dingsheng , Xu Zi , Zhong Guohui , Han Bingxing , Ling Shukuan , Chang Yan-Zhong , Li Yingxian 
Published: May 2016

AbstractMicroRNAs have an important role in bone homeostasis. However, the detailed mechanism of microRNA-mediated intercellular communication between bone cells remains elusive. Here, we report that osteoclasts secrete microRNA-enriched exosomes, by which miR-214 is transferred into osteoblasts to inhibit their function. In a coculture system, inhibition of exosome formation and secretion prevented miR-214 transportation. Exosomes specifically recognized osteoblasts through the interaction between ephrinA2 and EphA2. In osteoclast-specific miR-214 transgenic mice, exosomes were secreted into the serum, and miR-214 and ephrinA2 levels were elevated. Therefore, these exosomes have an inhibitory role in osteoblast activity. miR-214 and ephrinA2 levels in serum exosomes from osteoporotic patients and mice were upregulated substantially. These exosomes may significantly inhibit osteoblast activity. Inhibition of exosome secretion via Rab27a small interfering RNA prevented ovariectomized-induced osteoblast dysfunction in vivo. Taken together, these findings suggest that exosome-mediated transfer of microRNA plays an important role in the regulation of osteoblast activity. Circulating miR-214 in exosomes not only represents a biomarker for bone loss but could selectively regulate osteoblast function.
Fasting induces a subcutaneous-to-visceral fat switch mediated by microRNA-149-3p and suppression of PRDM16
Authors: Ding Hanying , Zheng Shasha , Garcia-Ruiz Daniel , Hou Dongxia , Wei Zhe , Liao Zhicong , Li Limin , Zhang Yujing , Han Xiao , Zen Ke , Zhang Chen-Yu , Li Jing , Jiang Xiaohong 
Published: May 2016

AbstractVisceral adiposity is strongly associated with metabolic disease risk, whereas subcutaneous adiposity is comparatively benign. However, their relative physiological importance in energy homeostasis remains unclear. Here, we show that after 24-h fasting, the subcutaneous adipose tissue of mice acquires key properties of visceral fat. During this fast-induced ‘visceralization’, upregulation of miR-149-3p directly targets PR domain containing 16 (PRDM16), a key coregulatory protein required for the ‘browning’ of white fat. In cultured inguinal preadipocytes, overexpression of miR-149-3p promotes a visceral-like switch during cell differentiation. Mice deficient in miR-149-3p display an increase in whole-body energy expenditure, with enhanced thermogenesis of inguinal fat. However, a visceral-like adipose phenotype is observed in inguinal depots overexpressing miR-149-3p. These results indicate that in addition to the capacity of ‘browning’ to defend against hypothermia during cold exposure, the subcutaneous adipose depot is also capable of ‘whitening’ to preserve energy during fasting, presumably to maintain energy balance, via miR-149-3p-mediated regulation of PRDM16.
Genome-wide association study identifies 8p21.3 associated with persistent hepatitis B virus infection among Chinese
Authors: Li Yuanfeng , Si Lanlan , Zhai Yun , Hu Yanling , Hu Zhibin , Bei Jin-Xin , Xie Bobo , Ren Qian , Cao Pengbo , Yang Fei , Song Qingfeng , Bao Zhiyu , Zhang Haitao , Han Yuqing , Wang Zhifu , Chen Xi , Xia Xia , Yan Hongbo , Wang Rui , Zhang Ying , Gao Chengming , Meng Jinfeng , Tu Xinyi , Liang Xinqiang , Cui Ying , Liu Ying , Wu Xiaopan , Li Zhuo , Wang Huifen , Li Zhaoxia , Hu Bo , He Minghui , Gao Zhibo , Xu Xiaobing , Ji Hongzan , Yu Chaohui , Sun Yi , Xing Baocai , Yang Xiaobo , Zhang Haiying , Tan Aihua , Wu Chunlei , Jia Weihua , Li Shengping , Zeng Yi-Xin , Shen Hongbing , He Fuchu , Mo Zengnan , Zhang Hongxing , Zhou Gangqiao 
Published: May 2016

AbstractHepatitis B virus (HBV) infection is a common infectious disease. Here we perform a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci involved in persistent HBV infection. GWAS scan is performed in 1,251 persistently HBV infected subjects (PIs, cases) and 1,057 spontaneously recovered subjects (SRs, controls), followed by replications in four independent populations totally consisting of 3,905 PIs and 3,356 SRs. We identify a novel locus at 8p21.3 (index rs7000921, odds ratio=0.78, P=3.2 × 10−12). Furthermore, we identify significant expression quantitative trait locus associations for INTS10 gene at 8p21.3. We demonstrate that INST10 suppresses HBV replication via IRF3 in liver cells. In clinical plasma samples, we confirm that INST10 levels are significantly decreased in PIs compared with SRs, and negatively correlated with the HBV load. These findings highlight a novel antiviral gene INTS10 at 8p21.3 in the clearance of HBV infection.
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
Authors: Foote Andrew D. , Vijay Nagarjun , Ávila-Arcos María C. , Baird Robin W. , Durban John W. , Fumagalli Matteo , Gibbs Richard A. , Hanson M. Bradley , Korneliussen Thorfinn S. , Martin Michael D. , Robertson Kelly M. , Sousa Vitor C. , Vieira Filipe G. , Vinař Tomáš , Wade Paul , Worley Kim C. , Excoffier Laurent , Morin Phillip A. , Gilbert M. Thomas P. , Wolf Jochen B.W. 
Published: May 2016

AbstractAnalysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.
Non-thermal Plasma Exposure Rapidly Attenuates Bacterial AHL-Dependent Quorum Sensing and Virulence
Authors: Flynn Padrig B. , Busetti Alessandro , Wielogorska Ewa , Chevallier Olivier P. , Elliott Christopher T. , Laverty Garry , Gorman Sean P. , Graham William G. , Gilmore Brendan F. 
Published: May 2016

AbstractThe antimicrobial activity of atmospheric pressure non-thermal plasma has been exhaustively characterised, however elucidation of the interactions between biomolecules produced and utilised by bacteria and short plasma exposures are required for optimisation and clinical translation of cold plasma technology. This study characterizes the effects of non-thermal plasma exposure on acyl homoserine lactone (AHL)-dependent quorum sensing (QS). Plasma exposure of AHLs reduced the ability of such molecules to elicit a QS response in bacterial reporter strains in a dose-dependent manner. Short exposures (30–60 s) produce of a series of secondary compounds capable of eliciting a QS response, followed by the complete loss of AHL-dependent signalling following longer exposures. UPLC-MS analysis confirmed the time-dependent degradation of AHL molecules and their conversion into a series of by-products. FT-IR analysis of plasma-exposed AHLs highlighted the appearance of an OH group. In vivo assessment of the exposure of AHLs to plasma was examined using a standard in vivo model. Lettuce leaves injected with the rhlI/lasI mutant PAO-MW1 alongside plasma treated N-butyryl-homoserine lactone and n-(3-oxo-dodecanoyl)-homoserine lactone, exhibited marked attenuation of virulence. This study highlights the capacity of atmospheric pressure non-thermal plasma to modify and degrade AHL autoinducers thereby attenuating QS-dependent virulence in P. aeruginosa.
Exogenous NAD+ decreases oxidative stress and protects H2O2-treated RPE cells against necrotic death through the up-regulation of autophagy
Authors: Zhu Ying , Zhao Ke-ke , Tong Yao , Zhou Ya-li , Wang Yi-xiao , Zhao Pei-quan , Wang Zhao-yang 
Published: May 2016

AbstractIncreased oxidative stress, which can lead to the retinal pigment epithelium (RPE) cell death by inducing ATP depletion and DNA repair, is believed to be a prominent pathology in age-related macular degeneration (AMD). In the present study, we showed that and 0.1 mM nicotinamide adenine dinucleotide (NAD+) administration significantly blocked RPE cell death induced by 300 μM H2O2. Further investigation showed that H2O2 resulted in increased intracellular ROS level, activation of PARP-1 and subsequently necrotic death of RPE cells. Exogenous NAD+ administration significantly decreased intracellular and intranuclear ROS levels in H2O2-treated RPE cells. In addition, NAD+ administration to H2O2-treated RPE cells inhibited the activation of PARP-1 and protected the RPE cells against necrotic death. Moreover, exogenous NAD+ administration up-regulated autophagy in the H2O2-treated RPE cells. Inhibition of autophagy by LY294002 blocked the decrease of intracellular and intranuclear ROS level. Besides, inhibition of autophagy by LY294002 abolished the protection of exogenous NAD+ against H2O2-induced cell necrotic death. Taken together, our findings indicate that that exogenous NAD+ administration suppresses H2O2-induced oxidative stress and protects RPE cells against PARP-1 mediated necrotic death through the up-regulation of autophagy. The results suggest that exogenous NAD+ administration might be potential value for the treatment of AMD.
Soil fungal community development in a high Arctic glacier foreland follows a directional replacement model, with a mid-successional diversity maximum
Authors: Dong Ke , Tripathi Binu , Moroenyane Itumeleng , Kim Woosung , Li Nan , Chu Haiyan , Adams Jonathan 
Published: May 2016

AbstractDirectional replacement and directional non-replacement models are two alternative paradigms for community development in primary successional environments. The first model emphasizes turnover in species between early and late successional niches. The second emphasizes accumulation of additional diversity over time. To test whether the development of soil fungal communities in the foreland of an Arctic glacier conforms to either of these models, we collected samples from the Midtre Lovénbreen Glacier, Svalbard, along a soil successional series spanning >80 years. Soil DNA was extracted, and fungal ITS1 region was amplified and sequenced on an Illumina Miseq. There was a progressive change in community composition in the soil fungal community, with greatest fungal OTU richness in the Mid Stage (50–80 years). A nestedness analysis showed that the Early Stage (20–50 years) and the Late Stage (>80 years) fungal communities were nested within the Mid Stage communities. These results imply that fungal community development in this glacier succession follows a directional replacement model. Soil development processes may initially be important in facilitating arrival of additional fungal species, to give a mid-successional diversity maximum that contains both early- and late-successional fungi. Competition may then decrease the overall diversity due to the loss of early successional species.
Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine
Authors: Hong Xutao , Chen Jing , Liu Lin , Wu Huan , Tan Haiqin , Xie Guangfa , Xu Qian , Zou Huijun , Yu Wenjing , Wang Lan , Qin Nan 
Published: May 2016

AbstractChinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on the quality of CRW, high throughput sequencing was performed for 110 wine samples on bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by our finding that wine spoilage resulted from a high proportion of genusLactobacillus. Subsequently, based onLactobacillusabundance of an early stage, a model was constructed to predict final wine quality. In addition, three batches of 20 representative wine samples selected from a pool of 110 samples were further analyzed in metagenomics. The results revealed that wine spoilage was due to rapid growth ofLactobacillus brevisat the early stage of fermentation. Gene functional analysis indicated the importance of some pathways such as synthesis of biotin, malolactic fermentation and production of short-chain fatty acid. These results led to a conclusion that metabolisms of microbes influence the wine quality. Thus, nurturing of beneficial microbes and inhibition of undesired ones are both important for the mechanized brewery.
Bioengineered kidney tubules efficiently excrete uremic toxins
Authors: Jansen J. , Fedecostante M. , Wilmer M. J. , Peters J. G. , Kreuser U. M. , van den Broek P. H. , Mensink R. A. , Boltje T. J. , Stamatialis D. , Wetzels J. F. , van den Heuvel L. P. , Hoenderop J. G. , Masereeuw R. 
Published: May 2016

AbstractThe development of a biotechnological platform for the removal of waste products (e.g. uremic toxins), often bound to proteins in plasma, is a prerequisite to improve current treatment modalities for patients suffering from end stage renal disease (ESRD). Here, we present a newly designed bioengineered renal tubule capable of active uremic toxin secretion through the concerted action of essential renal transporters, viz. organic anion transporter-1 (OAT1), breast cancer resistance protein (BCRP) and multidrug resistance protein-4 (MRP4). Three-dimensional cell monolayer formation of human conditionally immortalized proximal tubule epithelial cells (ciPTEC) on biofunctionalized hollow fibers with maintained barrier function was demonstrated. Using a tailor made flow system, the secretory clearance of human serum albumin-bound uremic toxins, indoxyl sulfate and kynurenic acid, as well as albumin reabsorption across the renal tubule was confirmed. These functional bioengineered renal tubules are promising entities in renal replacement therapies and regenerative medicine, as well as in drug development programs.
Pcdh19 Loss-of-Function Increases Neuronal Migration In Vitro but is Dispensable for Brain Development in Mice
Authors: Pederick Daniel T. , Homan Claire C. , Jaehne Emily J. , Piltz Sandra G. , Haines Bryan P. , Baune Bernhard T. , Jolly Lachlan A. , Hughes James N. , Gecz Jozef , Thomas Paul Q. 
Published: May 2016

AbstractProtocadherin 19 (Pcdh19) is an X-linked gene belonging to the protocadherin superfamily, whose members are predominantly expressed in the central nervous system and have been implicated in cell-cell adhesion, axon guidance and dendrite self-avoidance. Heterozygous loss-of-function mutations in humans result in the childhood epilepsy disorder PCDH19 Girls Clustering Epilepsy (PCDH19 GCE) indicating that PCDH19 is required for brain development. However, understanding PCDH19 function in vivo has proven challenging and has not been studied in mammalian models. Here, we validate a murine Pcdh19 null allele in which a β-Geo reporter cassette is expressed under the control of the endogenous promoter. Analysis of β-Geo reporter activity revealed widespread but restricted expression of PCDH19 in embryonic, postnatal and adult brains. No gross morphological defects were identified in Pcdh19+/β-Geo and Pcdh19Y/β-Geo brains and the location of Pcdh19 null cells was normal. However, in vitro migration assays revealed that the motility of Pcdh19 null neurons was significantly elevated, potentially contributing to pathogenesis in patients with PCDH19 mutations. Overall our initial characterization of Pcdh19+/β-Geo, Pcdh19β-Geo/β-Geo and Pcdh19Y/β-Geomice reveals that despite widespread expression of Pcdh19 in the CNS and its role in human epilepsy, its function in mice is not essential for brain development.
Analysis of the dynamic co-expression network of heart regeneration in the zebrafish
Authors: Rodius Sophie , Fournier Anna , Götz Lou , Liechti Robin , Crespo Isaac , Merz Susanne , Nazarov Petr V. , de Klein Niek , Jeanty Céline , González-Rosa Juan M. , Muller Arnaud , Bernardin Francois , Niclou Simone P. , Vallar Laurent , Mercader Nadia , Ibberson Mark , Xenarios Ioannis , Azuaje Francisco 
Published: May 2016

AbstractThe zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.
Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure
Authors: Nayak Ashok K. , Mishra Aseem , Jena Bhabani S. , Mishra Barada K. , Subudhi Umakanta 
Published: May 2016

AbstractControlled conversion of right-handed B-DNA to left-handed Z-DNA is one of the greatest conformational transitions in biology. Recently, the B-Z transition has been explored from nanotechnological points of view and used as the driving machinery of many nanomechanical devices. Using a combination of CD spectroscopy, fluorescence spectroscopy and PAGE, we demonstrate that low concentration of lanthanum chloride can mediate B-to-Z transition in self-assembled Y-shaped branched DNA (bDNA) structure. The transition is sensitive to the sequence and structure of the bDNA. Thermal melting and competitive dye binding experiments suggest that La3+ ions are loaded to the major and minor grooves of DNA and stabilize the Z-conformation. Our studies also show that EDTA and EtBr play an active role in reversing the transition from Z-to-B DNA.
GC Preps: Fast and Easy Extraction of Stable Yeast Genomic DNA
Authors: Blount Benjamin A. , Driessen Maureen R. M. , Ellis Tom 
Published: May 2016

AbstractExisting yeast genomic DNA extraction methods are not ideally suited to extensive screening of colonies by PCR, due to being too lengthy, too laborious or yielding poor quality DNA and inconsistent results. We developed the GC prep method as a solution to this problem. Yeast cells from colonies or liquid cultures are lysed by vortex mixing with glass beads and then boiled in the presence of a metal chelating resin. In around 12 minutes, multiple samples can be processed to extract high yields of genomic DNA. These preparations perform as effectively in PCR screening as DNA purified by organic solvent methods, are stable for up to 1 year at room temperature and can be used as the template for PCR amplification of fragments of at least 8 kb.
Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China
Authors: Yang Wen , Jeelani Nasreen , Leng Xin , Cheng Xiaoli , An Shuqing 
Published: May 2016

AbstractThe role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community.
Assessment of polygenic effects links primary open-angle glaucoma and age-related macular degeneration
Authors: Cuellar-Partida Gabriel , Craig Jamie E. , Burdon Kathryn P. , Wang Jie Jin , Vote Brendan J. , Souzeau Emmanuelle , McAllister Ian L. , Isaacs Timothy , Lake Stewart , Mackey David A. , Constable Ian J. , Mitchell Paul , Hewitt Alex W. , MacGregor Stuart 
Published: May 2016

AbstractPrimary open-angle glaucoma (POAG) and age-related macular degeneration (AMD) are leading causes of irreversible blindness. Several loci have been mapped using genome-wide association studies. Until very recently, there was no recognized overlap in the genetic contribution to AMD and POAG. At genome-wide significance level, only ABCA1 harbors associations to both diseases. Here, we investigated the genetic architecture of POAG and AMD using genome-wide array data. We estimated the heritability for POAG (h2g = 0.42 ± 0.09) and AMD (h2g = 0.71 ± 0.08). Removing known loci for POAG and AMD decreased the h2g estimates to 0.36 and 0.24, respectively. There was evidence for a positive genetic correlation between POAG and AMD (rg = 0.47 ± 0.25) which remained after removing known loci (rg = 0.64 ± 0.31). We also found that the genetic correlation between sexes for POAG was likely to be less than 1 (rg = 0.33 ± 0.24), suggesting that differences of prevalence among genders may be partly due to heritable factors.