Scientific Reports Biology Table of Contents e-alert: 2 December 2014

If you are unable to see the message below, click here to view.

02 December 2014      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports         Nature Collections RNA SEQUENCING QUALITY CONTROL (SEQC) Articles from Nature Biotechnology, Nature Communications and Scientific Data presents results from The RNA Sequencing Quality Control (SEQC) project. This is the second phase of a collaboration between government, academic and industry researchers as part of the MicroArray Quality Control (MAQC) consortium. Produced with support from the National Center for Toxicological Research (NCTR/FDA) and the State Key Laboratory of Genetic Engineering (SKLGE) at Fudan University           Biological Sciences               Cooperative protofilament switching emerges from inter-motor interference in multiple-motor transport ▶     David Ando, Michelle K. Mattson, Jing Xu et al.     Within living cells, the transport of cargo is accomplished by groups of molecular motors. Such collective transport could utilize mechanisms which emerge from inter-motor …             A novel method for synthetic vaccine construction based on protein assembly ▶     Zhida Liu, Hang Zhou, Wenjun Wang et al.     In the history of vaccine development, the synthetic vaccine is a milestone that is in stark contrast with traditional vaccines based on live-attenuated or inactivated …             A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia ▶     Feng Liu, Fei Sun, Jun Hong Xia et al.     Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of …             Natural killer T cells play a necessary role in modulating of immune-mediated liver injury by gut microbiota ▶     Jianing Chen, Yingfeng Wei, Jianqin He et al.     Gut microbiota are implicated in many liver diseases. Concanavalin A (ConA)-induced hepatitis is a well-characterized murine model of fulminant immunological hepatic injury. Oral …             Evaluation of benzaldehyde derivatives from Morinda officinalis as anti-mite agents with dual function as acaricide and mite indicator ▶     Ji-Yeon Yang, Min-Gi Kim, Jun-Hwan Park et al.     Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by SFTS virus with 12–30% fatality rate. Despite severity of the disease, any …             The role of dapoxetine hydrochloride on-demand for the treatment of men with premature ejaculation ▶     Cao De Hong, Liu Liang Ren, Huang Yu et al.     Premature ejaculation (PE) is the most common male sexual dysfunction. Dapoxetine hydrochloride, belonging to a class of drugs known as selective serotonin reuptake inhibitors …             Antinociceptive effects of sinomenine in a rat model of neuropathic pain ▶     Qing Zhu, Yuehua Sun, Jie Zhu et al.     Sinomenine is a principal ingredient of traditional Chinese medicine, Sinomenium Acutum, which has been reported to have various pharmacological effects including anti-rheumatism …             Ultrasensitive and fast detection of denaturation of milk by Coherent backscattering of light ▶     Manish Verma, Dilip K. Singh, P. Senthilkumaran et al.     In this work, Coherence backscattering (CBS) of light has been used to detect the onset of denaturation of milk. The CBS cone shape and its enhancement factor are found to be …             A Unifying Framework for Measuring Weighted Rich Clubs ▶     Jeff Alstott, Pietro Panzarasa, Mikail Rubinov et al.     Network analysis can help uncover meaningful regularities in the organization of complex systems. Among these, rich clubs are a functionally important property of a variety of …             Are polymorphisms of the immunoregulatory factor CD40LG implicated in acute transfusion reactions? ▶     Chaker Aloui, Caroline Sut, Antoine Prigent et al.     The CD40 ligand (CD40L/CD154), a member of TNF superfamily, is notably expressed on activated CD4 T-cells and stimulated platelets. CD40L is linked to a variety of pathologies …             Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar ▶     S. Wuchty, Peter Uetz     Only recently novel high-throughput binary interaction data in E. coli became available that allowed us to compare experimentally obtained protein-protein interaction networks of …             Sexual maturity in western Atlantic bluefin tuna ▶     Gilad Heinisch, Hanna Rosenfeld, Jessica M. Knapp et al.     We introduce a novel endocrine approach for assessing the unresolved matter of the timing of sexual maturation in western Atlantic bluefin tuna (ABFT), a highly migratory …             Non-antibiotic quorum sensing inhibitors acting against N-acyl homoserine lactone synthase as druggable target ▶     Chien-Yi Chang, Thiba Krishnan, Hao Wang et al.     N-acylhomoserine lactone (AHL)-based quorum sensing (QS) is important for the regulation of proteobacterial virulence determinants. Thus, the inhibition of AHL synthases offers …             Training improves visual processing speed and generalizes to untrained functions ▶     Maria Lev, Karin Ludwig, Sharon Gilaie-Dotan et al.     Studies show that manipulating certain training features in perceptual learning determines the specificity of the improvement. The improvement in abnormal visual processing …             Role of Bcl-2 -938 C>A polymorphism in susceptibility and prognosis of cancer: a meta-analysis ▶     Xiao Zhang, Wenhao Weng, Wen Xu et al.     The association between B-cell lymphoma 2 (Bcl-2) polymorphism and cancer is under debate and remains elusive. This meta-analysis was performed to evaluate the relationships of …             A dual character of flavonoids in influenza A virus replication and spread through modulating cell-autonomous immunity by MAPK signaling pathways ▶     Wenjuan Dong, Xiuli Wei, Fayun Zhang et al.     Flavonoids are well known as a large class of polyphenolic compounds, which have a variety of physiological activities, including anti-influenza virus activity. The influenza …             Breathing life into fisheries stock assessments with citizen science ▶     D. V. Fairclough, J. I. Brown, B. J. Carlish et al.     Citizen science offers a potentially cost-effective way for researchers to obtain large data sets over large spatial scales. However, it is not used widely to support biological …             Quantitative assessment of short amplicons in FFPE-derived long-chain RNA ▶     Hui Kong, Mengou Zhu, Fengyun Cui et al.     Formalin-fixed paraffin-embedded (FFPE) tissues are important resources for molecular medical research. However, long-chain RNA analysis is restricted in FFPE tissues due to high …             Angiotensin II acting on brain AT1 receptors induces adrenaline secretion and pressor responses in the rat ▶     Kumiko Nakamura, Takahiro Shimizu, Toshihiko Yanagita et al.     Angiotensin II (AngII) plays important roles in the regulation of cardiovascular function. Both peripheral and central actions of AngII are involved in this regulation, but …             Direct evidence of milk consumption from ancient human dental calculus ▶     C. Warinner, J. Hendy, C. Speller et al.     Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food …             A gigantic nothosaur (Reptilia: Sauropterygia) from the Middle Triassic of SW China and its implication for the Triassic biotic recovery ▶     Jun Liu, Shi-xue Hu, Olivier Rieppel et al.     The presence of gigantic apex predators in the eastern Panthalassic and western Tethyan oceans suggests that complex ecosystems in the sea had become re-established in these …             Net ammonium and nitrate fluxes in wheat roots under different environmental conditions as assessed by scanning ion-selective electrode technique ▶     Yangquanwei Zhong, Weiming Yan, Juan Chen et al.     Wheat is one of the most important food crops in the world, its availability affects global food security. In this study, we investigated variations in NH4 and NO3- fluxes in the …             Bio-mimicking of Proline-Rich Motif Applied to Carbon Nanotube Reveals Unexpected Subtleties Underlying Nanoparticle Functionalization ▶     Yuanzhao Zhang, Camilo A. Jimenez-Cruz, Jian Wang et al.     Here, we report computational studies of the SH3 protein domain interacting with various single-walled carbon nanotubes (SWCNT) either bare or functionalized by mimicking the …             Cis-mediated down-regulation of a trypsin gene associated with Bt resistance in cotton bollworm ▶     Chenxi Liu, Yutao Xiao, Xianchun Li et al.     Transgenic plants producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) are useful for pest control, but their efficacy is reduced when pests evolve …             IMP-1 encoded by a novel Tn402-like class 1 integron in clinical Achromobacter xylosoxidans, China ▶     Zhenhong Chen, Haihong Fang, Li Wang et al.     Achromobacter xylosoxidans strain A22732 is isolated from a pneumonia patient in China and produces carbapenemases OXA-114e and IMP-1, which are encoded by chromosome and …             Licochalcone A up-regulates of FasL in mesenchymal stem cells to strengthen bone formation and increase bone mass ▶     Leiguo Ming, Fang Jin, Ping Huang et al.     The role of bone marrow-derived mesenchymal stem cells(BMSCs)in the pathogenesis and therapy of osteoporosis has drawn increasing attention in recent years. In the development of …             A 3D approximate maximum likelihood solver for localization of fish implanted with acoustic transmitters ▶     Xinya Li, Z. Daniel Deng, Yannan Sun et al.     Better understanding of fish behavior is vital for recovery of many endangered species including salmon. The Juvenile Salmon Acoustic Telemetry System (JSATS) was developed to …             Anthrapyrazolone analogues intercept inflammatory JNK signals to moderate endotoxin induced septic shock ▶     Karothu Durga Prasad, Jamma Trinath, Ansuman Biswas et al.     Severe sepsis or septic shock is one of the rising causes for mortality worldwide representing nearly 10% of intensive care unit admissions. Susceptibility to sepsis is …             The role of different social contexts in shaping influenza transmission during the 2009 pandemic ▶     Marco Ajelli, Piero Poletti, Alessia Melegaro et al.     Evaluating the relative importance of different social contexts in which infection transmission occurs is critical for identifying optimal intervention strategies. Nonetheless, …             The potential reproductive contribution of Mediterranean migrating eels to the Anguilla anguilla stock ▶     Fabrizio Capoccioni, Corrado Costa, Emiliano Canali et al.     The European eel is a highly migratory fish. After the reproduction in the Sargasso Sea early larval-stages start a passive ocean migration towards European and Mediterranean …             Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis ▶     Seung Hee Choi, Do Young Hyeon, ll Hwan Lee et al.     Many of duplicated genes are enriched in signaling pathways. Recently, gene duplication of kinases has been shown to provide genetic buffering and functional diversification in …             The domestication of the probiotic bacterium Lactobacillus acidophilus ▶     Matthew J. Bull, Keith A. Jolley, James E. Bray et al.     Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. …             Integrating computational modeling and functional assays to decipher the structure-function relationship of influenza virus PB1 protein ▶     Chunfeng Li, Aiping Wu, Yousong Peng et al.     The influenza virus PB1 protein is the core subunit of the heterotrimeric polymerase complex (PA, PB1 and PB2) in which PB1 is responsible for catalyzing RNA polymerization and …             The Hippo pathway as a target of the Drosophila DRE/DREF transcriptional regulatory pathway ▶     Nicole Vo, Takeshi Horii, Hiroshi Yanai et al.     The DRE/DREF transcriptional regulatory system has been demonstrated to activate a wide variety of genes with various functions. In Drosophila, the Hippo pathway is known to …             Effects of histone deacetylase inhibitor valproic acid on skeletal myocyte development ▶     Qiao Li, Michelle Foote, Jihong Chen     The tight interaction between genomic DNA and histones, which normally represses gene transcription, can be relaxed by histone acetylation. This loosening of the DNA-histone …             CORRIGENDUM: Coralligenous and maërl habitats: predictive modelling to identify their spatial distributions across the Mediterranean Sea ▶     C. S. Martin, M. Giannoulaki, F. De Leo et al.                 Novel method for the high-throughput processing of slides for the comet assay ▶     Mahsa Karbaschi, Marcus S. Cooke     Single cell gel electrophoresis (the comet assay), continues to gain popularity as a means of assessing DNA damage. However, the assay's low sample throughput and laborious …             Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture ▶     Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan et al.     We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a …                 Nature Reviews Microbiology CRISPR CALENDAR 2015 One of the most exciting recent developments in microbiology has been the discovery and characterization of the CRISPR-Cas adaptive immune system in bacteria and archaea. This special Calendar brings together CRISPR related images from a range of Nature Publishing Group journals. Produced with support from OriGene, Your Gene Company         • Careers & Jobs           naturejobs.com Science jobs of the week       Postdoctoral Researcher     John Innes Centre (JIC)            Postdoctoral Research Associate     University of Virginia            Lab technician     University Hospital Basel, Department of Biomedicine            Postdoctoral Fellow     European Molecular Biology Laboratory (EMBL)            PhD Studentship     Cardiff University            Research Associate     University of Cambridge            Research Associate     Centre for Heart Lung Innovation            Postdoctoral Research Assistant     University of Bristol            Staff Scientist     The Scripps Research Institute (TSRI)          No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter.           • Scientific Reports events Directory featured events           natureevents directory featured events         2015 Conference on Advances in Cell Biology (CACB 2015)     20 March 2015 Virgina, USA         Natureevents Directory is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide.                 Your email address is in the Scientific Reports: Biology mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th floor | New York | NY 10013-1917 | USA Nature Publishing Group's offices: Principal offices: London - New York - Tokyo Worldwide offices: Basingstoke - Boston - Buenos Aires - Delhi - Hong Kong - Madrid - Melbourne - Munich - Paris - San Francisco - Seoul - Washington DC Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.