bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional properties of flagellin as a stimulator of innate immunity
Authors: Lu Yuan , Swartz James R. 
Published: January 2016

AbstractWe report the development of a well-defined flagellin-based nanoparticle stimulator and also provide a new mechanism of action model explaining how flagellin-triggered innate immunity has evolved to favor localized rather than potentially debilitating systemic immune stimulation. Cell-free protein synthesis (CFPS) was used to facilitate mutational analysis and precisely orientated display of flagellin on Hepatitis B core (HBc) protein virus-like particles (VLPs). The need for product stability and an understanding of mechanism of action motivated investigations indicating that the D0 domain of flagellin is sensitive to amino acid sequence independent hydrolysis – apparently due to the need for structural flexibility during natural flagellin polymerization. When D0-stabilized flagellin was attached to HBc VLPs with the D0 domain facing outward, flagellin’s tendency to polymerize caused the VLPs to precipitate. However, attaching the D0 domain to the VLP surface produced a stable nanoparticle adjuvant. Surprisingly, attaching only 2 flagellins per VLP provided the same 1 pM potency as did VLPs with about 33 attached flagellins suggesting that the TLR5 receptor is highly effective in delivering its intracellular signal. These observations suggest that flagellin’s protease sensitivity, tendency to aggregate and very high affinity for TLR5 receptors limit its systemic distribution to favor localized immune stimulation.
Ammonia-induced miRNA expression changes in cultured rat astrocytes
Authors: Oenarto Jessica , Karababa Ayse , Castoldi Mirco , Bidmon Hans J. , Görg Boris , Häussinger Dieter 
Published: January 2016

AbstractHepatic encephalopathy is a neuropsychiatric syndrome evolving from cerebral osmotic disturbances and oxidative/nitrosative stress. Ammonia, the main toxin of hepatic encephalopathy, triggers astrocyte senescence in an oxidative stress-dependent way. As miRNAs are critically involved in cell cycle regulation and their expression may be regulated by oxidative stress, we analysed, whether astrocyte senescence is a consequence of ammonia-induced miRNA expression changes. Using a combined miRNA and gene microarray approach, 43 miRNA species which were downregulated and 142 genes which were upregulated by NH4Cl (5 mmol/l, 48 h) in cultured rat astrocytes were found. Ammonia-induced miRNA and gene expression changes were validated by qPCR and 43 potential miRNA target genes, including HO-1, were identified by matching upregulated mRNA species with predicted targets of miRNA species downregulated by ammonia. Inhibition of HO-1 targeting miRNAs which were downregulated by NH4Cl strongly upregulated HO-1 mRNA and protein levels and inhibited astrocyte proliferation in a HO-1-dependent way. Preventing ammonia-induced upregulation of HO-1 by taurine (5 mmol/l) as well as blocking HO-1 activity by tin-protoporphyrine IX fully prevented ammonia-induced proliferation inhibition and senescence. The data suggest that ammonia induces astrocyte senescence through NADPH oxidase-dependent downregulation of HO-1 targeting miRNAs and concomitant upregulation of HO-1 at both mRNA and protein level.
Cryopreservation of the gorgonian endosymbiont Symbiodinium
Authors: Chong Gabriella , Tsai Sujune , Wang Li-Hsueh , Huang Chih-Yang , Lin Chiahsin 
Published: January 2016

AbstractThe study focused on finding a suitable cryoprotectant (CPA) and an optimum freezing protocol for the cryopreservation of the endosymbiotic dinoflagellates (Symbiodinium, clade G) of Junceella fragilis wherein the success of experiments is crucial to both scientific and ecology studies. A two-step freezing technique was developed. The viability of the thawed dinoflagellates was assayed using the adenosine triphosphate (ATP) bioassay for the first time and was further confirmed through the culturing of dinoflagellates in vitro. The results suggested that 30 min was the most suitable holding time for the dinoflagellates and the samples produced highest viability when suspended at 5 cm from the surface of LN2. Results also showed that 1 M methanol with 0.4 M sucrose was the most effective CPA, yielding the highest viability (56.93%). Although cell densities of both cryopreserved and control group suffered an initial decline of culture, the cell densities were maintained throughout the remaining duration. In the present study, the cryopreservation of clade G endosymbiont algae was studied for the first time and the method described here could be applied for future studies on symbiotic algae cryopreservation.
Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate
Authors: Yu Hongyu , Duan Defang , Liu Hanyu , Yang Ting , Tian Fubo , Bao Kuo , Li Da , Zhao Zhonglong , Liu Bingbing , Cui Tian 
Published: January 2016

AbstractHigh-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation.
Enhanced air pollution via aerosol-boundary layer feedback in China
Authors: Petäjä T. , Järvi L. , Kerminen V.-M. , Ding A.J. , Sun J.N. , Nie W. , Kujansuu J. , Virkkula A. , Yang X. , Fu C.B. , Zilitinkevich S. , Kulmala M. 
Published: January 2016

AbstractSevere air pollution episodes have been frequent in China during the recent years. While high emissions are the primary reason for increasing pollutant concentrations, the ultimate cause for the most severe pollution episodes has remained unclear. Here we show that a high concentration of particulate matter (PM) will enhance the stability of an urban boundary layer, which in turn decreases the boundary layer height and consequently cause further increases in PM concentrations. We estimate the strength of this positive feedback mechanism by combining a new theoretical framework with ambient observations. We show that the feedback remains moderate at fine PM concentrations lower than about 200 μg m−3, but that it becomes increasingly effective at higher PM loadings resulting from the combined effect of high surface PM emissions and massive secondary PM production within the boundary layer. Our analysis explains why air pollution episodes are particularly serious and severe in megacities and during the days when synoptic weather conditions stay constant.
Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro
Authors: Purohit Nupur K. , Robu Mihaela , Shah Rashmi G. , Geacintov Nicholas E. , Shah Girish M. 
Published: January 2016

AbstractThe existing methodologies for studying robust responses of poly (ADP-ribose) polymerase-1 (PARP-1) to DNA damage with strand breaks are often not suitable for examining its subtle responses to altered DNA without strand breaks, such as UV-damaged DNA. Here we describe two novel assays with which we characterized the interaction of PARP-1 with UV-damaged DNA in vivo and in vitro. Using an in situ fractionation technique to selectively remove free PARP-1 while retaining the DNA-bound PARP-1, we demonstrate a direct recruitment of the endogenous or exogenous PARP-1 to the UV-lesion site in vivo after local irradiation. In addition, using the model oligonucleotides with single UV lesion surrounded by multiple restriction enzyme sites, we demonstrate in vitro that DDB2 and PARP-1 can simultaneously bind to UV-damaged DNA and that PARP-1 casts a bilateral asymmetric footprint from −12 to +9 nucleotides on either side of the UV-lesion. These techniques will permit characterization of different roles of PARP-1 in the repair of UV-damaged DNA and also allow the study of normal housekeeping roles of PARP-1 with undamaged DNA.
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution
Authors: Zhang Guo-Qiang , Xu Qing , Bian Chao , Tsai Wen-Chieh , Yeh Chuan-Ming , Liu Ke-Wei , Yoshida Kouki , Zhang Liang-Sheng , Chang Song-Bin , Chen Fei , Shi Yu , Su Yong-Yu , Zhang Yong-Qiang , Chen Li-Jun , Yin Yayi , Lin Min , Huang Huixia , Deng Hua , Wang Zhi-Wen , Zhu Shi-Lin , Zhao Xiang , Deng Cao , Niu Shan-Ce , Huang Jie , Wang Meina , Liu Guo-Hui , Yang Hai-Jun , Xiao Xin-Ju , Hsiao Yu-Yun , Wu Wan-Lin , Chen You-Yi , Mitsuda Nobutaka , Ohme-Takagi Masaru , Luo Yi-Bo , Van de Peer Yves , Liu Zhong-Jian 
Published: January 2016

AbstractOrchids make up about 10% of all seed plant species, have great economical value and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC*, involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.
Insight into the mechanical, thermodynamics and superconductor properties of NbRuB via first-principles calculation
Authors: Tian Wenyan , Chen Haichuan 
Published: January 2016

AbstractUsing the first-principles calculations, the electronic structure, chemical bonding, mechanical, thermodynamics and superconductor properties of NbRuB are investigated. The optimized lattice parameters were in good agreement with the experimental data. The analysis of the density of states and chemical bonding implies that the metallic behavior of NbRuB originates from the Ru and Nb and the bonding behaviors are a mixture of covalent-ionic bonds. The bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and hardness of NbRuB were calculated. The results reveal that the NbRuB is ductility and the Vickers hardness is 15.06 GPa. Moreover, the 3D dependences of reciprocals of Young’s modulus is also calculated and discussed, showing strong anisotropic character for NbRuB. Finally, the Debye temperature and superconducting transition temperature are obtained.
Dynamics of the Transcriptome during Human Spermatogenesis: Predicting the Potential Key Genes Regulating Male Gametes Generation
Authors: Zhu Zijue , Li Chong , Yang Shi , Tian Ruhui , Wang Junlong , Yuan Qingqing , Dong Hui , He Zuping , Wang Shengyue , Li Zheng 
Published: January 2016

AbstractMany infertile men are the victims of spermatogenesis disorder. However, conventional clinical test could not provide efficient information on the causes of spermatogenesis disorder and guide the doctor how to treat it. More effective diagnosis and treating methods could be developed if the key genes that regulate spermatogenesis were determined. Many works have been done on animal models, while there are few works on human beings due to the limited sample resources. In current work, testis tissues were obtained from 27 patients with obstructive azoospermia via surgery. The combination of Fluorescence Activated Cell Sorting and Magnetic Activated Cell Sorting was chosen as the efficient method to sort typical germ cells during spermatogenesis. RNA Sequencing was carried out to screen the change of transcriptomic profile of the germ cells during spermatogenesis. Differential expressed genes were clustered according to their expression patterns. Gene Ontology annotation, pathway analysis and Gene Set Enrichment Analysis were carried out on genes with specific expression patterns and the potential key genes such as HOXs, JUN, SP1 and TCF3 which were involved in the regulation of spermatogenesis, with the potential value serve as molecular tools for clinical purpose, were predicted.
RETRACTED ARTICLE: TRIM25 blockade by RNA interference inhibited migration and invasion of gastric cancer cells through TGF-β signaling
Authors: Zhu Zhenya , Wang Yong , Zhang Chunhui , Yu Shiyong , Zhu Qi , Hou Kun , Yan Bo 
Published: January 2016

AbstractTripartite Motif Containing 25 (TRIM25), a member of TRIM proteins, has been found abnormally expressed in cancers of female reproductive system. Here, TRIM25 was conspicuously expressed in human gastric cancer (GC) tissues in which its higher expression generally correlated with the poor prognosis of patients. Small interfering RNA (siRNA)-mediated knockdown of TRIM25 expression in MGC-803 and AGS cells had no effects on cell proliferation, whereas reduced cell migration and invasion. Gene set enrichment analysis on The Cancer Genome Atlas stomach adenocarcinoma (STAD) dataset revealed that several signaling pathways, including the migration, E-cadherin and transforming growth factor-β (TGF-β) pathways, were enriched in TRIM25 higher expression patients. Moreover, ectopic expression of TRIM25 in a GC cell line with lower expression of TRIM25 significantly promoted the migration and invasion. Further experiments with TGF-β inhibitor suggested that TRIM25 may exert its function through TGF-β pathway. In summary, our results indicate that TRIM25 acts as an oncogene in GC and thus presents a novel target for the detection and treatment of GC.
Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests
Authors: Wang Xiaoli , Wang Xiaoling , Zhang Weixin , Shao Yuanhu , Zou Xiaoming , Liu Tao , Zhou Lixia , Wan Songze , Rao Xingquan , Li Zhian , Fu Shenglei 
Published: January 2016

AbstractSoil bacteria may be influenced by vegetation and play important roles in global carbon efflux and nutrient cycling under global changes. Coniferous and broadleaved forests are two phyletically distinct vegetation types. Soil microbial communities in these forests have been extensively investigated but few studies have presented comparable data regarding the characteristics of bacterial communities in subtropical forests. We investigated soil bacterial biomass and community composition in three pairs of coniferous and broadleaved forests across a subtropical climatic gradient. We found that bacterial biomass differed between the coniferous and broadleaved forests across the subtropical climate gradient; however, this difference disappeared at some individual sites. In contrast, the same 90 bacterial genera were found in both forest types and their relative abundances didn’t differ between the forest types, with the exception of one genus that was more abundant in broadleaved forests. Soil nitrogen or moisture was associated with bacterial groups in the coniferous and broadleaved forests, respectively. Thus, we inferred that these forests can respond differently to future changes in nitrogen deposition or precipitation. This study highlights soil bacterial invariant community composition in contrasting subtropical forests and provides a new perspective on the potential response and feedback of forests to global changes.
Astrocyte-derived adenosine is central to the hypnogenic effect of glucose
Authors: Scharbarg Emeric , Daenens Marion , Lemaître Frédéric , Geoffroy Hélène , Guille-Collignon Manon , Gallopin Thierry , Rancillac Armelle 
Published: January 2016

AbstractSleep has been hypothesised to maintain a close relationship with metabolism. Here we focus on the brain structure that triggers slow-wave sleep, the ventrolateral preoptic nucleus (VLPO), to explore the cellular and molecular signalling pathways recruited by an increase in glucose concentration. We used infrared videomicroscopy on ex vivo brain slices to establish that glucose induces vasodilations specifically in the VLPO via the astrocytic release of adenosine. Real-time detection by in situ purine biosensors further revealed that the adenosine level doubles in response to glucose and triples during the wakefulness period. Finally, patch-clamp recordings uncovered the depolarizing effect of adenosine and its A2A receptor agonist, CGS-21680, on sleep-promoting VLPO neurons. Altogether, our results provide new insights into the metabolically driven release of adenosine. We hypothesise that adenosine adjusts the local energy supply to local neuronal activity in response to glucose. This pathway could contribute to sleep-wake transition and sleep intensity.
Systematic Analysis of Sex-Linked Molecular Alterations and Therapies in Cancer
Authors: Ma Jonathan , Malladi Sadhika , Beck Andrew H 
Published: January 2016

AbstractThough patient sex influences response to cancer treatments, little is known of the molecular causes and cancer therapies are generally given irrespective of patient sex. We assessed transcriptomic differences in tumors from men and women spanning 17 cancer types and we assessed differential expression between tumor and normal samples stratified by sex across 7 cancers. We used the LincsCloud platform to perform Connectivity Map analyses to link transcriptomic signatures identified in male and female tumors with chemical and genetic perturbagens and we performed permutation testing to identify perturbagens that showed significantly differential connectivity with male and female tumors. Our analyses predicted that females are sensitive and males are resistant to tamoxifen treatment of lung adenocarcinoma, a finding which is consistent with known male-female differences in lung cancer. We made several novel predictions, including that CDK1 and PTPN1 knockdown would be more effective in males with hepatocellular carcinoma and SMAD3 and HSPA4 knockdown would be more effective in females with head and neck squamous cell carcinoma. Our results provide a new resource for researchers studying male-female biological and treatment response differences in human cancer. The complete results of our analyses are provided at the website accompanying this manuscript (http://becklab.github.io/SexLinked).
Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup
Authors: Singh Sakshi , Singh Ashish , Rajkumar Raja , Sampath Kumar Katakam , Kadarkarai Samy Subburaj , Nizamuddin Sheikh , Singh Amita , Ahmed Sheikh Shahnawaz , Peddada Vidya , Khanna Vinee , Veeraiah Pandichelvam , Pandit Aridaman , Chaubey Gyaneshwer , Singh Lalji , Thangaraj Kumarasamy 
Published: January 2016

AbstractThe global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
Construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern
Authors: Xia Yuanyuan , Cui Wenjing , Liu Zhongmei , Zhou Li , Cui Youtian , Kobayashi Michihiko , Zhou Zhemin 
Published: January 2016

AbstractMetallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. The metal is usually transferred between different proteins. In this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (NHase). Various “activator proteins” mediate the trafficking of metal ions into NHases. We constructed fusion NHases by fusing the β- and α-subunits and/or the “activator proteins” of the NHase from Pseudomonas putida. The fusion NHases exhibited higher thermostability and tolerance to high concentrations of the product amide. The mechanism of the cobalt incorporation changed from a self-subunit swapping pattern to an apoprotein-specific molecular chaperone pattern in vivo and a metallochaperone pattern in vitro. Notably, the cobalt transfer occurred between the same α-subunit in the metallochaperone pattern. These results not only demonstrated the superiority of fusion-type NHases, but also revealed an innovative metal ion transfer pattern in metalloprotein biosynthesis.
Livestock-associated methicillin and multidrug resistant S. aureus in humans is associated with occupational pig contact, not pet contact
Authors: Ye Xiaohua , Fan Yanping , Wang Xiaolin , Liu Weidong , Yu Haifeng , Zhou Junli , Chen Sidong , Yao Zhenjiang 
Published: January 2016

AbstractThis study aimed to explore the association of livestock-associated S. aureus with occupational pig contact and pet contact. In this cross-sectional study, 1,422 participants (including 244 pig workers, 200 pet-owning workers and 978 control workers) responded to a questionnaire and provided a nasal swab for S. aureus analysis. Resulting isolates were tested for antibiotic susceptibility, the immune evasion cluster (IEC) genes and multilocus sequence type. Compared with controls, the pig workers demonstrated a greater prevalence of multidrug-resistant S. aureus (MDRSA) [prevalence ratio (PR) = 3.38; 95% CI: 2.07–5.53] and methicillin-resistant S. aureus (MRSA) (PR = 7.42; 95% CI: 3.71–14.83), but the prevalence of MDRSA and MRSA was similar in pet-owning workers and controls. There was a positive relation of frequency of pig contact with prevalence of MDRSA and MRSA carriage. Only pig workers carried MDRSA CC9 (16 isolates) and MRSA CC9 (16 isolates) and all of these isolates were tetracycline resistant and absent of IEC genes. These findings suggest that livestock-associated MRSA and MDRSA(CC9, IEC-negative, tetracycline-resistant) in humans is associated with occupational pig contact, not pet contact and support growing concern about antibiotics use in pig farms and raising questions about the potential for occupational exposure to opportunistic S. aureus.