bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical evidence that Australopithecus sediba was limited in its ability to eat hard foods
Authors: Ledogar Justin A. , Smith Amanda L. , Benazzi Stefano , Weber Gerhard W. , Spencer Mark A. , Carlson Keely B. , McNulty Kieran P. , Dechow Paul C. , Grosse Ian R. , Ross Callum F. , Richmond Brian G. , Wright Barth W. , Wang Qian , Byron Craig , Carlson Kristian J. , de Ruiter Darryl J. , Berger Lee R. , Tamvada Kelli , Pryor Leslie C. , Berthaume Michael A. , Strait David S.
Published: February 2016

Australopithecus sediba has been hypothesized to be a close relative of the genus Homo. Here we show that MH1, the type specimen of A. sediba, was not optimized to produce high molar bite force and appears to have been limited in its ability to consume foods that were mechanically challenging to eat. Dental microwear data have previously been interpreted as indicating that A. sediba consumed hard foods, so our findings illustrate that mechanical data are essential if one aims to reconstruct a relatively complete picture of feeding adaptations in extinct hominins. An implication of our study is that the key to understanding the origin of Homo lies in understanding how environmental changes disrupted gracile australopith niches. Resulting selection pressures led to changes in diet and dietary adaption that set the stage for the emergence of our genus.
Genome-wide association study identifies multiple susceptibility loci for craniofacial microsomia
Authors: Zhang Yong-Biao , Hu Jintian , Zhang Jiao , Zhou Xu , Li Xin , Gu Chaohao , Liu Tun , Xie Yangchun , Liu Jiqiang , Gu Mingliang , Wang Panpan , Wu Tingting , Qian Jin , Wang Yue , Dong Xiaoqun , Yu Jun , Zhang Qingguo
Published: February 2016

Craniofacial microsomia (CFM) is a rare congenital anomaly that involves immature derivatives from the first and second pharyngeal arches. The genetic pathogenesis of CFM is still unclear. Here we interrogate 0.9 million genetic variants in 939 CFM cases and 2,012 controls from China. After genotyping of an additional 443 cases and 1,669 controls, we identify 8 significantly associated loci with the most significant SNP rs13089920 (logistic regression P=2.15 × 10−120) and 5 suggestive loci. The above 13 associated loci, harboured by candidates of ROBO1, GATA3, GBX2, FGF3, NRP2, EDNRB, SHROOM3, SEMA7A, PLCD3, KLF12 and EPAS1, are found to be enriched for genes involved in neural crest cell (NCC) development and vasculogenesis. We then perform whole-genome sequencing on 21 samples from the case cohort, and identify several novel loss-of-function mutations within the associated loci. Our results provide new insights into genetic background of craniofacial microsomia.
Common electronic origin of superconductivity in (Li,Fe)OHFeSe bulk superconductor and single-layer FeSe/SrTiO3 films
Authors: Zhao Lin , Liang Aiji , Yuan Dongna , Hu Yong , Liu Defa , Huang Jianwei , He Shaolong , Shen Bing , Xu Yu , Liu Xu , Yu Li , Liu Guodong , Zhou Huaxue , Huang Yulong , Dong Xiaoli , Zhou Fang , Liu Kai , Lu Zhongyi , Zhao Zhongxian , Chen Chuangtian , Xu Zuyan , Zhou X. J.
Published: February 2016

The mechanism of high-temperature superconductivity in the iron-based superconductors remains an outstanding issue in condensed matter physics. The electronic structure plays an essential role in dictating superconductivity. Recent revelation of distinct electronic structure and high-temperature superconductivity in the single-layer FeSe/SrTiO3 films provides key information on the role of Fermi surface topology and interface in inducing or enhancing superconductivity. Here we report high-resolution angle-resolved photoemission measurements on the electronic structure and superconducting gap of an FeSe-based superconductor, (Li0.84Fe0.16)OHFe0.98Se, with a Tc at 41 K. We find that this single-phase bulk superconductor shows remarkably similar electronic behaviours to that of the superconducting single-layer FeSe/SrTiO3 films in terms of Fermi surface topology, band structure and the gap symmetry. These observations provide new insights in understanding high-temperature superconductivity in the single-layer FeSe/SrTiO3 films and the mechanism of superconductivity in the bulk iron-based superconductors.
Optogenetic control of nuclear protein export
Authors: Niopek Dominik , Wehler Pierre , Roensch Julia , Eils Roland , Di Ventura Barbara
Published: February 2016

Active nucleocytoplasmic transport is a key mechanism underlying protein regulation in eukaryotes. While nuclear protein import can be controlled in space and time with a portfolio of optogenetic tools, protein export has not been tackled so far. Here we present a light-inducible nuclear export system (LEXY) based on a single, genetically encoded tag, which enables precise spatiotemporal control over the export of tagged proteins. A constitutively nuclear, chromatin-anchored LEXY variant expands the method towards light inhibition of endogenous protein export by sequestering cellular CRM1 receptors. We showcase the utility of LEXY for cell biology applications by regulating a synthetic repressor as well as human p53 transcriptional activity with light. LEXY is a powerful addition to the optogenetic toolbox, allowing various novel applications in synthetic and cell biology.
Lysophosphatidic acid activates Arf6 to promote the mesenchymal malignancy of renal cancer
Authors: Hashimoto Shigeru , Mikami Shuji , Sugino Hirokazu , Yoshikawa Ayumu , Hashimoto Ari , Onodera Yasuhito , Furukawa Shotaro , Handa Haruka , Oikawa Tsukasa , Okada Yasunori , Oya Mototsugu , Sabe Hisataka
Published: February 2016

Acquisition of mesenchymal properties by cancer cells is critical for their malignant behaviour, but regulators of the mesenchymal molecular machinery and how it is activated remain elusive. Here we show that clear cell renal cell carcinomas (ccRCCs) frequently utilize the Arf6-based mesenchymal pathway to promote invasion and metastasis, similar to breast cancers. In breast cancer cells, ligand-activated receptor tyrosine kinases employ GEP100 to activate Arf6, which then recruits AMAP1; and AMAP1 then binds to the mesenchymal-specific protein EPB41L5, which promotes epithelial–mesenchymal transition and focal adhesion dynamics. In renal cancer cells, lysophosphatidic acid (LPA) activates Arf6 via its G-protein-coupled receptors, in which GTP-Gα12 binds to EFA6. The Arf6-based pathway may also contribute to drug resistance. Our results identify a specific mesenchymal molecular machinery of primary ccRCCs, which is triggered by a product of autotaxin and it is associated with poor outcome of patients.
Noise Reduction in Complex Biological Switches
Authors: Cardelli Luca , Csikász-Nagy Attila , Dalchau Neil , Tribastone Mirco , Tschaikowski Max
Published: February 2016

Cells operate in noisy molecular environments via complex regulatory networks. It is possible to understand how molecular counts are related to noise in specific networks, but it is not generally clear how noise relates to network complexity, because different levels of complexity also imply different overall number of molecules. For a fixed function, does increased network complexity reduce noise, beyond the mere increase of overall molecular counts? If so, complexity could provide an advantage counteracting the costs involved in maintaining larger networks. For that purpose, we investigate how noise affects multistable systems, where a small amount of noise could lead to very different outcomes; thus we turn to biochemical switches. Our method for comparing networks of different structure and complexity is to place them in conditions where they produce exactly the same deterministic function. We are then in a good position to compare their noise characteristics relatively to their identical deterministic traces. We show that more complex networks are better at coping with both intrinsic and extrinsic noise. Intrinsic noise tends to decrease with complexity and extrinsic noise tends to have less impact. Our findings suggest a new role for increased complexity in biological networks, at parity of function.
Significant improvements in InGaN/GaN nano-photoelectrodes for hydrogen generation by structure and polarization optimization
Authors: Tao Tao , Zhi Ting , Liu Bin , Li Mingxue , Zhuang Zhe , Dai Jiangping , Li Yi , Jiang Fulong , Luo Wenjun , Xie Zili , Chen Dunjun , Chen Peng , Li Zhaosheng , Zou Zhigang , Zhang Rong , Zheng Youdou
Published: February 2016

The photoelectrodes based on III-nitride semiconductors with high energy conversion efficiency especially for those self-driven ones are greatly desirable for hydrogen generation. In this study, highly ordered InGaN/GaN multiple-quantum-well nanorod-based photoelectrodes have been fabricated by a soft UV-curing nano-imprint lithography and a top-down etching technique, which improve the incident photon conversion efficiency (IPCE) from 16% (planar structure) to 42% (@ wavelength = 400 nm). More significantly, the turn-on voltage is reduced low to −0.6 V, which indicates the possibility of achieving self-driven. Furthermore, SiO2/Si3N4 dielectric distributed Bragg reflectors are employed to further improve the IPCE up to 60%. And the photocurrent (@ 1.1 V) is enhanced from 0.37 mA/cm2 (original planar structure) to 1.5 mA/cm2. These improvements may accelerate the possible applications for hydrogen generation with high energy-efficiency.
Role of the Pinning Points in epitaxial Graphene Moiré Superstructures on the Pt(111) Surface
Authors: Martínez José I. , Merino Pablo , Pinardi Anna L. , Gonzalo Otero-Irurueta , López María F. , Méndez Javier , Martín-Gago José A.
Published: February 2016

The intrinsic atomic mechanisms responsible for electronic doping of epitaxial graphene Moirés on transition metal surfaces is still an open issue. To better understand this process we have carried out a first-principles full characterization of the most representative Moiré superstructures observed on the Gr/Pt(111) system and confronted the results with atomically resolved scanning tunneling microscopy experiments. We find that for all reported Moirés the system relaxes inducing a non-negligible atomic corrugation both, at the graphene and at the outermost platinum layer. Interestingly, a mirror “anti-Moiré” reconstruction appears at the substrate, giving rise to the appearance ofpinning-points. We show that these points are responsible for the development of the superstructure, while charge from the Pt substrate is injected into the graphene, inducing a localn-doping, mostly localized at these specificpinning-pointpositions.
Emotional states as mediators between tinnitus loudness and tinnitus distress in daily life: Results from the “TrackYourTinnitus” application
Authors: Probst Thomas , Pryss Rüdiger , Langguth Berthold , Schlee Winfried
Published: February 2016

The psychological process how tinnitus loudness leads to tinnitus distress remains unclear. This cross-sectional study investigated the mediating role of the emotional state “stress level” and of the two components of the emotional state “arousal” and “valence” with N = 658 users of the “TrackYourTinnitus” smartphone application. Stress mediated the relationship between tinnitus loudness and tinnitus distress in a simple mediation model and even in a multiple mediation model when arousal and valence were held constant. Arousal mediated the loudness-distress relationship when holding valence constant, but not anymore when controlling for valence as well as for stress. Valence functioned as a mediator when controlling for arousal and even when holding arousal and stress constant. The direct effect of tinnitus loudness on tinnitus distress remained significant in all models. This study demonstrates that emotional states affect the process how tinnitus loudness leads to tinnitus distress. We thereby could show that the mediating influence of emotional valence is at least equally strong as the influence of stress. Implications of the findings for future research, assessment and clinical management of tinnitus are discussed.
Extracellular matrix stiffness dictates Wnt expression through integrin pathway
Authors: Du Jing , Zu Yan , Li Jing , Du Shuyuan , Xu Yipu , Zhang Lang , Jiang Li , Wang Zhao , Chien Shu , Yang Chun
Published: February 2016

It is well established that extracellular matrix (ECM) stiffness plays a significant role in regulating the phenotypes and behaviors of many cell types. However, the mechanism underlying the sensing of mechanical cues and subsequent elasticity-triggered pathways remains largely unknown. We observed that stiff ECM significantly enhanced the expression level of several members of the Wnt/β-catenin pathway in both bone marrow mesenchymal stem cells and primary chondrocytes. The activation of β-catenin by stiff ECM is not dependent on Wnt signals but is elevated by the activation of integrin/ focal adhesion kinase (FAK) pathway. The accumulated β-catenin then bound to the wnt1 promoter region to up-regulate the gene transcription, thus constituting a positive feedback of the Wnt/β-catenin pathway. With the amplifying effect of positive feedback, this integrin-activated β-catenin/Wnt pathway plays significant roles in mediating the enhancement of Wnt signal on stiff ECM and contributes to the regulation of mesenchymal stem cell differentiation and primary chondrocyte phenotype maintenance. The present integrin-regulated Wnt1 expression and signaling contributes to the understanding of the molecular mechanisms underlying the regulation of cell behaviors by ECM elasticity.
Iron Pyrite/Titanium Dioxide Photoanode for Extended Near Infrared Light Harvesting in a Photoelectrochemical Cell
Authors: Wang Di-Yan , Li Cheng-Hung , Li Shao-Sian , Kuo Tsung-Rong , Tsai Chin-Ming , Chen Tin-Reui , Wang Ying-Chiao , Chen Chun-Wei , Chen Chia-Chun
Published: February 2016

The design of active and stable semiconducting composites with enhanced photoresponse from visible light to near infrared (NIR) is a key to improve solar energy harvesting for photolysis of water in photoelectrochemical cell. In this study, we prepared earth abundant semiconducting composites consisting of iron pyrite and Titanium oxide as a photoanode (FeS2/TiO2 photoanode) for photoelectrochemical applications. The detailed structure and atomic compositions of FeS2/TiO2 photoanode was characterized by high-resolution transmission electron microscopy (HRTEM), energy-dispersive X-ray spectroscopy (EDS), powder X-ray diffraction (XRD), inductively coupled plasma with atomic emission spectroscopy (ICPAES) and Raman spectroscopy. Through the proper sulfurization treatment, the FeS2/TiO2 photoanode exhibited high photoresponse from visible light extended to near infrared range (900 nm) as well as stable durability test for 4 hours. We found that the critical factors to enhance the photoresponse are on the elimination of surface defect of FeS2 and on the enhancement of interface charge transfer between FeS2 and TiO2. Our overall results open a route for the design of sulfur-based binary compounds for photoelectrochemical applications.
Production of Human papillomavirus pseudovirions in plants and their use in pseudovirion-based neutralisation assays in mammalian cells
Authors: Lamprecht Renate L , Kennedy Paul , Huddy Suzanne M , Bethke Susanne , Hendrikse Megan , Hitzeroth Inga I , Rybicki Edward P
Published: February 2016

Human papillomaviruses (HPV) cause cervical cancer and have recently also been implicated in mouth, laryngeal and anogenital cancers. There are three commercially available prophylactic vaccines that show good efficacy; however, efforts to develop second-generation vaccines that are more affordable, stable and elicit a wider spectrum of cross-neutralising immunity are still ongoing. Testing antisera elicited by current and candidate HPV vaccines for neutralizing antibodies is done using a HPV pseudovirion (PsV)-based neutralisation assay (PBNA). PsVs are produced by transfection of mammalian cell cultures with plasmids expressing L1 and L2 capsid proteins and a reporter gene plasmid, a highly expensive process. We investigated making HPV-16 PsVs in plants, in order to develop a cheaper alternative. The secreted embryonic alkaline phosphatase (SEAP) reporter gene and promoter were cloned into a geminivirus-derived plant expression vector, in order to produce circular dsDNA replicons. This was co-introduced into Nicotiana benthamiana plants with vectors expressing L1 and L2 via agroinfiltration and presumptive PsVs were purified. The PsVs contained DNA and could be successfully used for PBNA with anti-HPV antibodies. This is the first demonstration of the production of mammalian pseudovirions in plants and the first demonstration of the potential of plants to make DNA vaccines.
Easily doped p-type, low hole effective mass, transparent oxides
Authors: Sarmadian Nasrin , Saniz Rolando , Partoens Bart , Lamoen Dirk
Published: February 2016

Fulfillment of the promise of transparent electronics has been hindered until now largely by the lack of semiconductors that can be doped p-type in a stable way and that at the same time present high hole mobility and are highly transparent in the visible spectrum. Here, a high-throughput study based on first-principles methods reveals four oxides, namely X2SeO2, with X = La, Pr, Nd and Gd, which are unique in that they exhibit excellent characteristics for transparent electronic device applications – i.e., a direct band gap larger than 3.1 eV, an average hole effective mass below the electron rest mass and good p-type dopability. Furthermore, for La2SeO2 it is explicitly shown that Na impurities substituting La are shallow acceptors in moderate to strong anion-rich growth conditions, with low formation energy and that they will not be compensated by anion vacancies VO or VSe.
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

Green 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

Cholesterol 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

Prostaglandins 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

Carrier 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

Siberian 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

Phosphorylation 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

Coralline 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

Haemonchus 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

Rare 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

Colorectal 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

Primer 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

Although 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

We 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

The 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

The 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

The 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.
Correction: Corrigendum: Green synthesis of carbon-supported nanoparticle catalysts by physical vapor deposition on soluble powder substrates
Authors: Park Hee-Young , Jang Injoon , Jung Namgee , Chung Young-Hoon , Ryu Jaeyune , Cha In Young , Kim Hyoung-Juhn , Jang Jong Hyun , Yoo Sung Jong
Published: February 2016

Scientific Reports 5: Article number: 14245; published online: 18 September 2015; updated: 08 February 2016. The original version of this Article contained typographical errors in the spelling of the authors Jaeyune Ryu, Hyoung-Juhn Kim and Jong Hyun Jang, which were incorrectly given as Jae Yoon Ryu, Hyung Juhn Kim and Jong Hyung Jang.
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

Reactive 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.
Dopamine disruption increases negotiation for cooperative interactions in a fish
Authors: Messias João P. M. , Paula José R. , Grutter Alexandra S. , Bshary Redouan , Soares Marta C.
Published: February 2016

Humans and other animals use previous experiences to make behavioural decisions, balancing the probabilities of receiving rewards or punishments with alternative actions. The dopaminergic system plays a key role in this assessment: for instance, a decrease in dopamine transmission, which is signalled by the failure of an expected reward, may elicit a distinct behavioural response. Here, we tested the effect of exogenously administered dopaminergic compounds on a cooperative vertebrate’s decision-making process, in a natural setting. We show, in the Indo-Pacific bluestreak cleaner wrasse Labroides dimidiatus, that blocking dopamine receptors in the wild induces cleaners to initiate more interactions with and to provide greater amounts of physical contact to their client fish partners. This costly form of tactile stimulation using their fins is typically used to prolong interactions and to reconcile with clients after cheating. Interestingly, client jolt rate, a correlate of cheating by cleaners, remained unaffected. Thus, in low effective dopaminergic transmission conditions cleaners may renegotiate the occurrence and duration of the interaction with a costly offer. Our results provide first evidence for a prominent role of the dopaminergic system in decision-making in the context of cooperation in fish.
Model predictions of features in microsaccade-related neural responses in a feedforward network with short-term synaptic depression
Authors: Zhou Jian-Fang , Yuan Wu-Jie , Zhou Zhao , Zhou Changsong
Published: February 2016

Recently, the significant microsaccade-induced neural responses have been extensively observed in experiments. To explore the underlying mechanisms of the observed neural responses, a feedforward network model with short-term synaptic depression has been proposed [Yuan, W.-J., Dimigen, O., Sommer, W. and Zhou, C. Front. Comput. Neurosci. 7, 47 (2013)]. The depression model not only gave an explanation for microsaccades in counteracting visual fading, but also successfully reproduced several microsaccade-related features in experimental findings. These results strongly suggest that, the depression model is very useful to investigate microsaccade-related neural responses. In this paper, by using the model, we extensively study and predict the dependance of microsaccade-related neural responses on several key parameters, which could be tuned in experiments. Particularly, we provide a significant prediction that microsaccade-related neural response also complies with the property “sharper is better” observed in many contexts in neuroscience. Importantly, the property exhibits a power-law relationship between the width of input signal and the responsive effectiveness, which is robust against many parameters in the model. By using mean field theory, we analytically investigate the robust power-law property. Our predictions would give theoretical guidance for further experimental investigations of the functional role of microsaccades in visual information processing.
An integrative approach for analyzing hundreds of neurons in task performing mice using wide-field calcium imaging
Authors: Mohammed Ali I. , Gritton Howard J. , Tseng Hua-an , Bucklin Mark E. , Yao Zhaojie , Han Xue
Published: February 2016

Advances in neurotechnology have been integral to the investigation of neural circuit function in systems neuroscience. Recent improvements in high performance fluorescent sensors and scientific CMOS cameras enables optical imaging of neural networks at a much larger scale. While exciting technical advances demonstrate the potential of this technique, further improvement in data acquisition and analysis, especially those that allow effective processing of increasingly larger datasets, would greatly promote the application of optical imaging in systems neuroscience. Here we demonstrate the ability of wide-field imaging to capture the concurrent dynamic activity from hundreds to thousands of neurons over millimeters of brain tissue in behaving mice. This system allows the visualization of morphological details at a higher spatial resolution than has been previously achieved using similar functional imaging modalities. To analyze the expansive data sets, we developed software to facilitate rapid downstream data processing. Using this system, we show that a large fraction of anatomically distinct hippocampal neurons respond to discrete environmental stimuli associated with classical conditioning and that the observed temporal dynamics of transient calcium signals are sufficient for exploring certain spatiotemporal features of large neural networks.
Light adaptation does not prevent early retinal abnormalities in diabetic rats
Authors: Kur Joanna , Burian Michael A. , Newman Eric A.
Published: February 2016

The aetiology of diabetic retinopathy (DR), the leading cause of blindness in the developed world, remains controversial. One hypothesis holds that retinal hypoxia, exacerbated by the high O2 consumption of rod photoreceptors in the dark, is a primary cause of DR. Based on this prediction we investigated whether early retinal abnormalities in streptozotocin-induced diabetic rats are alleviated by preventing the rods from dark adapting. Diabetic rats and their non-diabetic littermates were housed in a 12:12 hour light-dim light photocycle (30 lux during the day and 3 lux at night). Progression of early retinal abnormalities in diabetic rats was assessed by monitoring the ERG b-wave and oscillatory potentials, Müller cell reactive gliosis, and neuronal cell death, as assayed by TUNEL staining and retinal thickness at 6 and 12 weeks after diabetes induction. Maintaining diabetic animals in a dim-adapting light did not slow the progression of these neuronal and glial changes when compared to diabetic rats maintained in a standard 12:12 hour light-dark photocycle (30 lux during the day and 0 lux at night). Our results indicate that neuronal and glial abnormalities in early stages of diabetes are not exacerbated by rod photoreceptor O2 consumption in the dark.