bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent production and tolerance among 107 woody species and divergent production between shrubs and trees
Authors: He Wei-Ming , Sun Zhen-Kai 
Published: February 2016

AbstractGreen leaves face two fundamental challenges (i.e., carbon fixation and stress tolerance) during their lifespan. However, the relationships between leaf production potential and leaf tolerance potential have not been explicitly tested with a broad range of plant species in the same environment. To do so, we conducted a field investigation based on 107 woody plants grown in a common garden and complementary laboratory measurements. The values, as measured by a chlorophyll meter, were significantly related to the direct measurements of chlorophyll content on a leaf area basis. Area-based chlorophyll content was positively correlated with root surface area, whole-plant biomass, leaf mass per area (LMA) and force to punch. Additionally, LMA had a positive correlation with force to punch. Shrubs had a higher leaf chlorophyll content than trees; however, shrubs and trees exhibited a similar leaf lifespan, force to punch and LMA. These findings suggest that the production potential of leaves and their tolerance to stresses may be convergent in woody species and that the leaf production potential may differ between shrubs and trees. This study highlights the possibility that functional convergence and divergence might be linked to long-term selection pressures and genetic constraints.
Difference in expression patterns of placental cholesterol transporters, ABCA1 and SR-BI, in Meishan and Yorkshire pigs with different placental efficiency
Authors: Hong Linjun , Xu Xiangdong , Huang Ji , Lei Minggang , Xu Dequan , Zhao Shuhong , Yu Mei 
Published: February 2016

AbstractCholesterol is a key cell membrane component and precursor of steroid hormones. The maternal cholesterol is an important exogenous cholesterol source for the developing embryos and its transportation is mediated by ABCA1 and SR-BI. Here we reported that during the peri-implantation period in pigs, ABCA1 was expressed by uterine luminal epithelium (LE) and interestingly, its expression was more abundantly in LE on mesometrial side of uterus. However, SR-BI was expressed primarily by LE, glandular epithelial cells (GE) and trophoblast cells (Tr). During the placentation period, the expression levels of ABCA1 and SR-BI proteins at epithelial bilayer and placental areolae were significantly higher in Chinese Meishan pigs compared to Yorkshire pigs. Consisitently, mRNA levels of HMGCR, the rate-limiting enzyme for cholesterol synthesis, were significantly higher in Meishan placentas than in Yorkshire placentas. Our findings revealed the routes of transplacental cholesterol transport mediated by ABCA1 and SR-BI in pigs and indicated that ABCA1 related pathway may participate in anchoring the conceptus to the mesometrial side of uterus. Additionally, an ABCA1 dependent compensatory mechanism related to the placental efficiency in response to the smaller placenta size in Meishan pigs was suggested.
Prostaglandins E2 signal mediated by receptor subtype EP2 promotes IgE production in vivo and contributes to asthma development
Authors: Gao Yuhan , Zhao Chunyan , Wang Wei , Jin Rong , Li Qian , Ge Qing , Guan Youfei , Zhang Yu 
Published: February 2016

AbstractProstaglandins E2 (PGE2) has been shown to enhance IgE production by B cells in vitro. The physiological and pathological relevance of this phenomenon and the underlying molecular mechanism, however, remain to be elucidated. B cells from wild type and EP2-deficient mice were compared in culture for their responses to PGE2 in terms of IgE class switching and production. Ovalbumin (OVA)-induced asthma models were used to evaluate the impact of EP2-deficiency on IgE responses and the development of asthma. PGE2 promoted IgE class switching, generation of IgE+ cells and secretion of IgE by B cells stimulated with LPS+IL4. These effects were much attenuated as a consequence of EP2 deficiency. Consistent with the in vitro data, EP2-deficient mice showed a markedly suppressed IgE antibody response and developed less pronounced airway inflammation in the OVA-induced asthma model. Mechanistic studies demonstrated that PGE2, in an EP2-depedent manner, enhanced STAT6 activation induced by IL-4, thereby promoting the expression of IgE germline and post switch transcripts and the transcription of activation-induced cytidine deaminase (AID). Collectively, these data support an important regulatory role of the PGE2-EP2-STAT6 signaling pathway in IgE response and allergic diseases.
Spectroscopy of carrier multiplication in nanocrystals
Authors: Bruhn Benjamin , Limpens Rens , Chung Nguyen Xuan , Schall Peter , Gregorkiewicz Tom 
Published: February 2016

AbstractCarrier multiplication in nanostructures promises great improvements in a number of widely used technologies, among others photodetectors and solar cells. The decade since its discovery was ridden with fierce discussions about its true existence, magnitude and mechanism. Here, we introduce a novel, purely spectroscopic approach for investigation of carrier multiplication in nanocrystals. Applying this method to silicon nanocrystals in an oxide matrix, we obtain an unambiguous spectral signature of the carrier multiplication process and reveal details of its size-dependent characteristics-energy threshold and efficiency. The proposed method is generally applicable and suitable for both solid state and colloidal samples, as well as for a great variety of different materials.
Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing
Authors: Zhou Qiang , Luo Dong , Ma Lichao , Xie Wengang , Wang Yu , Wang Yanrong , Liu Zhipeng 
Published: February 2016

AbstractSiberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.
The exploration of network motifs as potential drug targets from post-translational regulatory networks
Authors: Zhang Xiao-Dong , Song Jiangning , Bork Peer , Zhao Xing-Ming 
Published: February 2016

AbstractPhosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks between these two PTMs are involved in many diseases. In this work, we construct a post-translational regulatory network (PTRN) consists of phosphorylation and proteolysis processes, which enables us to investigate the regulatory interplays between these two PTMs. With the PTRN, we identify some functional network motifs that are significantly enriched with drug targets, some of which are further found to contain multiple proteins targeted by combinatorial drugs. These findings imply that the network motifs may be used to predict targets when designing new drugs. Inspired by this, we propose a novel computational approach called NetTar for predicting drug targets using the identified network motifs. Benchmarking results on real data indicate that our approach can be used for accurate prediction of novel proteins targeted by known drugs.
Impact of high CO2 on the geochemistry of the coralline algae Lithothamnion glaciale
Authors: Ragazzola F. , Foster L. C. , Jones C. J. , Scott T. B. , Fietzke J. , Kilburn M. R. , Schmidt D. N. 
Published: February 2016

AbstractCoralline algae are a significant component of the benthic ecosystem. Their ability to withstand physical stresses in high energy environments relies on their skeletal structure which is composed of high Mg-calcite. High Mg-calcite is, however, the most soluble form of calcium carbonate and therefore potentially vulnerable to the change in carbonate chemistry resulting from the absorption of anthropogenic CO2by the ocean. We examine the geochemistry of the cold water coralline algaLithothamnion glacialegrown under predicted future (year 2050) high pCO2(589 μatm) using Electron microprobe and NanoSIMS analysis. In the natural and control material, higher Mg calcite forms clear concentric bands around the algal cells. As expected, summer growth has a higher Mg content compared to the winter growth. In contrast, under elevated CO2no banding of Mg is recognisable and overall Mg concentrations are lower. This reduction in Mg in the carbonate undermines the accuracy of the Mg/Ca ratio as proxy for past temperatures in time intervals with significantly different carbonate chemistry. Fundamentally, the loss of Mg in the calcite may reduce elasticity thereby changing the structural properties, which may affect the ability ofL. glacialeto efficiently function as a habitat former in the future ocean.
The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome
Authors: Li Robert W. , Li Weizhong , Sun Jiajie , Yu Peng , Baldwin Ransom L. , Urban Joseph F. 
Published: February 2016

AbstractHaemonchus contortus is arguably the most injurious helminth parasite for small ruminants. We characterized the impact of H. contortus infection on the caprine abomasal microbiome. Fourteen parasite naive goats were inoculated with 5,000 H. contortus infective larvae and followed for 50 days. Six age-matched naïve goats served as uninfected controls. Reduced bodyweight gain and a significant increase in the abosamal pH was observed in infected goats compared to uninfected controls. Infection also increased the bacterial load while reducing the abundance of the Archaea in the abomasum but did not appear to affect microbial diversity. Nevertheless, the infection altered the abundance of approximately 19% of the 432 species-level operational taxonomic units (OTU) detected per sample. A total of 30 taxa displayed a significantly different abundance between control and infected goats. Furthermore, the infection resulted in a distinct difference in the microbiome structure. As many as 8 KEGG pathways were predicted to be significantly affected by infection. In addition, H. contortus-induced changes in butyrate producing bacteria could regulate mucosal inflammation and tissue repair. Our results provided insight into physiological consequences of helminth infection in small ruminants and could facilitate the development of novel control strategies to improve animal and human health.
An Engineered Rare Codon Device for Optimization of Metabolic Pathways
Authors: Wang You , Li Chunying , Khan Md. Rezaul Islam , Wang Yushu , Ruan Yunfeng , Zhao Bin , Zhang Bo , Ma Xiaopan , Zhang Kaisi , Zhao Xiwen , Ye Guanhao , Guo Xizhi , Feng Guoyin , He Lin , Ma Gang 
Published: February 2016

AbstractRare codons generally arrest translation due to rarity of their cognate tRNAs. This property of rare codons can be utilized to regulate protein expression. In this study, a linear relationship was found between expression levels of genes and copy numbers of rare codons inserted within them. Based on this discovery, we constructed a molecular device in Escherichia coli using the rare codon AGG, its cognate tRNA (tRNAArg (CCU)), modified tRNAAsp (GUC → CCU), and truncated aspartyl-tRNA synthetase (TDRS) to switch the expression of reporter genes on or off as well as to precisely regulate their expression to various intermediate levels. To underscore the applicability of our work, we used the rare codon device to alter the expression levels of four genes of the fatty acid synthesis II (FASII) pathway (i.e. fabZ, fabG, fabI, and tesA’) in E. coli to optimize steady-state kinetics, which produced nearly two-fold increase in fatty acid yield. Thus, the proposed method has potential applications in regulating target protein expression at desired levels and optimizing metabolic pathways by precisely tuning in vivo molar ratio of relevant enzymes.
Colorectal cancer characterization and therapeutic target prediction based on microRNA expression profile
Authors: Xu Peng , Zhu Yanliang , Sun Bo , Xiao Zhongdang 
Published: February 2016

AbstractColorectal cancer (CRC) is one of the most commonly diagnosed cancers and a major cause of cancer death. However, the molecular mechanisms underlying CRC initiation, growth and metastasis are poorly understood. In this study, based on our previous work for comprehensively analyzing miRNA sequencing data, we examined a series of colorectal cancer microRNAs expression profiles data. Results show that all these CRC samples share the same four pathways including TGF-beta signaling pathway, which is important in colorectal carcinogenesis. Twenty-one microRNAs that evolved in the four overlapped pathways were then discovered. Further analysis selected miR-21 as an important regulator for CRC through TGF-beta pathways. This study develops methods for discovering tumor specific miRNA cluster as biomarker and for screening new cancer therapy targets based on miRNA sequencing.
PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection
Authors: O’Halloran Damien M. 
Published: February 2016

AbstractPrimer design represents a widely employed gambit in diverse molecular applications including PCR, sequencing and probe hybridization. Variations of PCR, including primer walking, allele-specific PCR and nested PCR provide specialized validation and detection protocols for molecular analyses that often require screening large numbers of DNA fragments. In these cases, automated sequence retrieval and processing become important features and furthermore, a graphic that provides the user with a visual guide to the distribution of designed primers across targets is most helpful in quickly ascertaining primer coverage. To this end, I describe here, PrimerMapper, which provides a comprehensive graphical user interface that designs robust primers from any number of inputted sequences while providing the user with both, graphical maps of primer distribution for each inputted sequence and also a global assembled map of all inputted sequences with designed primers. PrimerMapper also enables the visualization of graphical maps within a browser and allows the user to draw new primers directly onto the webpage. Other features of PrimerMapper include allele-specific design features for SNP genotyping, a remote BLAST window to NCBI databases and remote sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely available without restriction.
Feature co-localization landscape of the human genome
Authors: Ng Siu-Kin , Hu Taobo , Long Xi , Chan Cheuk-Hin , Tsang Shui-Ying , Xue Hong 
Published: February 2016

AbstractAlthough feature co-localizations could serve as useful guide-posts to genome architecture, a comprehensive and quantitative feature co-localization map of the human genome has been lacking. Herein we show that, in contrast to the conventional bipartite division of genomic sequences into genic and inter-genic regions, pairwise co-localizations of forty-two genomic features in the twenty-two autosomes based on 50-kb to 2,000-kb sequence windows indicate a tripartite zonal architecture comprising Genic zones enriched with gene-related features and Alu-elements; Proximal zones enriched with MIR- and L2-elements, transcription-factor-binding-sites (TFBSs) and conserved-indels (CIDs); and Distal zones enriched with L1-elements. Co-localizations between single-nucleotide-polymorphisms (SNPs) and copy-number-variations (CNVs) reveal a fraction of sequence windows displaying steeply enhanced levels of SNPs, CNVs and recombination rates that point to active adaptive evolution in such pathways as immune response, sensory perceptions and cognition. The strongest positive co-localization observed between TFBSs and CIDs suggests a regulatory role of CIDs in cooperation with TFBSs. The positive co-localizations of cancer somatic CNVs (CNVT) with all Proximal zone and most Genic zone features, in contrast to the distinctly more restricted co-localizations exhibited by germline CNVs (CNVG), reveal disparate distributions of CNVTs and CNVGs indicative of dissimilarity in their underlying mechanisms.
A physical mechanism of cancer heterogeneity
Authors: Chen Cong , Wang Jin 
Published: February 2016

AbstractWe studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching and weaker stability.
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana
Authors: Zhao M. , Wang T. , Adamson K. J. , Storey K. B. , Cummins S. F. 
Published: February 2016

AbstractThe land snail Theba pisana is native to the Mediterranean region but has become one of the most abundant invasive species worldwide. Here, we present three transcriptomes of this agriculture pest derived from three tissues: the central nervous system, hepatopancreas (digestive gland), and foot muscle. Sequencing of the three tissues produced 339,479,092 high quality reads and a global de novo assembly generated a total of 250,848 unique transcripts (unigenes). BLAST analysis mapped 52,590 unigenes to NCBI non-redundant protein databases and further functional analysis annotated 21,849 unigenes with gene ontology. We report that T. pisana transcripts have representatives in all functional classes and a comparison of differentially expressed transcripts amongst all three tissues demonstrates enormous differences in their potential metabolic activities. The genes differentially expressed include those with sequence similarity to those genes associated with multiple bacterial diseases and neurological diseases. To provide a valuable resource that will assist functional genomics study, we have implemented a user-friendly web interface, ThebaDB (http://thebadb.bioinfo-minzhao.org/). This online database allows for complex text queries, sequence searches, and data browsing by enriched functional terms and KEGG mapping.
Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke
Authors: Yang Hui , Hu Jinxiang , Long Xiaohua , Liu Zhaopu , Rengel Zed 
Published: February 2016

AbstractThe interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0–20 cm soil layer vertically and 0–30 cm horizontally from the plant centre. Root concentrations of K+, Na+, Mg2+ and particularly Ca2+ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0–5 cm and 5–10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities.
Direct observation of charge state in the quasi-one-dimensional conductor Li0.9Mo6O17
Authors: Wu Guoqing , Ye Xiao-shan , Zeng Xianghua , Wu Bing , Clark W. G. 
Published: February 2016

AbstractThe quasi-one-dimensional conductor Li0.9Mo6O17 has been of great interest because of its unusual properties. It has a conducting phase with properties different from a simple Fermi liquid, a poorly understood “insulating” phase as indicated by a metal-“insulator” crossover (a mystery for over 30 years) and a superconducting phase which may involve spin triplet Cooper pairs as a three-dimensional (p-wave) non-conventional superconductor. Recent evidence suggests a density wave (DW) gapping regarding the metal-“insulator” crossover. However, the nature of the DW, such as whether it is due to the change in the charge state or spin state and its relationship to the dimensional crossover and to the spin triplet superconductivity, remains elusive. Here by performing 7Li-/95Mo-nuclear magnetic resonance (NMR) spectroscopy, we directly observed the charge state which shows no signature of change in the electric field gradient (nuclear quadrupolar frequency) or in the distribution of it, thus providing direct experimental evidences demonstrating that the long mysterious metal-“insulator” crossover is not due to the charge density wave (CDW) that was thought and the nature of the DW gapping is not CDW. This discovery opens a parallel path to the study of the electron spin state and its possible connections to other unusual properties.
Reactive oxygen species generated from skeletal muscles are required for gecko tail regeneration
Authors: Zhang Qing , Wang Yingjie , Man Lili , Zhu Ziwen , Bai Xue , Wei Sumei , Liu Yan , Liu Mei , Wang Xiaochuan , Gu Xiaosong , Wang Yongjun 
Published: February 2016

AbstractReactive oxygen species (ROS) participate in various physiological and pathological functions following generation from different types of cells. Here we explore ROS functions on spontaneous tail regeneration using gecko model. ROS were mainly produced in the skeletal muscle after tail amputation, showing a temporal increase as the regeneration proceeded. Inhibition of the ROS production influenced the formation of autophagy in the skeletal muscles, and as a consequence, the length of the regenerating tail. Transcriptome analysis has shown that NADPH oxidase (NOX2) and the subunits (p40phox and p47phox) are involved in the ROS production. ROS promoted the formation of autophagy through regulation of both ULK and MAPK activities. Our results suggest that ROS produced by skeletal muscles are required for the successful gecko tail regeneration.