Scientific Reports Biology Table of Contents e-alert: 28 October 2014

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28 October 2014      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding ▶     Linling He, Devin Sok, Parisa Azadnia et al.     B-cell repertoire analysis using next-generation sequencing has become a valuable tool for interrogating the genetic record of humoral response to infection. However, key …             Besides neuro-imaging, the Thy1-YFP mouse could serve for visualizing experimental tumours, inflammation and wound-healing ▶     Katalin Jósvay, Zoltán Winter, Róbert L. Katona et al.     The B6.Cg-Tg(Thy1-YFP)16Jrs/J transgenic mouse strain, widely used to study neuronal development and regeneration, expresses the yellow fluorescent protein (YFP) in the …             Self-recognition in corals facilitates deep-sea habitat engineering ▶     S. J. Hennige, C. L. Morrison, A. U. Form et al.     The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting …             Correlations of amyloid-β concentrations between CSF and plasma in acute Alzheimer mouse model ▶     Soo Min Cho, Hyunjin Vincent Kim, Sejin Lee et al.     Amyloid-β (Aβ) is one of the few neuropathological biomarkers associated with transporters of the blood-brain barrier (BBB). Despite the well-characterized clinical indication of …             Reference genes for normalizing transcription in diploid and tetraploid Arabidopsis ▶     Haibin Wang, Jingjing Wang, Jiafu Jiang et al.     Published transcription data from a set of 19 diploid Arabidopsis thaliana and 5 tetraploid (3 allo- and 2 auto- tetraploid) Arabidopsis accessions were re-analysed to identify …             Dramatic improvement in genome assembly achieved using doubled-haploid genomes ▶     Hong Zhang, Engkong Tan, Yutaka Suzuki et al.     Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced …             A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model ▶     Wonki Min, Francesca Angileri, Haibin Luo et al.     Chaperonins mediate protein folding in a cavity formed by multisubunit rings. The human CCT has eight non-identical subunits and the His147Arg mutation in one subunit, CCT5, …             An MFC-Based Online Monitoring and Alert System for Activated Sludge Process ▶     Gui-Hua Xu, Yun-Kun Wang, Guo-Ping Sheng et al.     In this study, based on a simple, compact and submersible microbial fuel cell (MFC), a novel online monitoring and alert system with self-diagnosis function was established for …             Network Structure and Community Evolution on Twitter: Human Behavior Change in Response to the 2011 Japanese Earthquake and Tsunami ▶     Xin Lu, Christa Brelsford     To investigate the dynamics of social networks and the formation and evolution of online communities in response to extreme events, we collected three datasets from Twitter …             Lensfree optofluidic plasmonic sensor for real-time and label-free monitoring of molecular binding events over a wide field-of-view ▶     Ahmet F. Coskun, Arif E. Cetin, Betty C. Galarreta et al.     We demonstrate a high-throughput biosensing device that utilizes microfluidics based plasmonic microarrays incorporated with dual-color on-chip imaging toward real-time and …             Universality of fixation probabilities in randomly structured populations ▶     Ben Adlam, Martin A. Nowak     The stage of evolution is the population of reproducing individuals. The structure of the population is known to affect the dynamics and outcome of evolutionary processes, but …             Genomewide Analysis of Rat Periaqueductal Gray-Dorsal Horn Reveals Time-, Region- and Frequency-Specific mRNA Expression Changes in Response to Electroacupuncture Stimulation ▶     Ke Wang, Xiao-Hui Xiang, Nan Qiao et al.     Electroacupuncture (EA) has been widely applied for illness prevention, treatment or rehabilitation in the clinic, especially for pain management. However, the molecular events …             In vitro nanobody discovery for integral membrane protein targets ▶     Rupak Doshi, Beverly R. Chen, Cecile Rose T. Vibat et al.     Nanobodies (Nbs) or single-domain antibodies are among the smallest and most stable binder scaffolds known. In vitro display is a powerful antibody discovery technique used …             Mycobacterium hassiacum recovers from nitrogen starvation with up-regulation of a novel glucosylglycerate hydrolase and depletion of the accumulated glucosylglycerate ▶     Susana Alarico, Mafalda Costa, Marta S. Sousa et al.     Some microorganisms accumulate glucosylglycerate (GG) during growth under nitrogen deprivation. However, the molecular mechanisms underlying the role of GG and the regulation of …             A bHLH transcription factor regulates iron intake under Fe deficiency in chrysanthemum ▶     Min Zhao, Aiping Song, Peiling Li et al.     Iron (Fe) deficiency can represent a serious constraint on crop growth and productivity. A number of members of the bHLH transcription factor family are known to be involved in …             Whole-cell biotransformation systems for reduction of prochiral carbonyl compounds to chiral alcohol in Escherichia coli ▶     Bingjuan Li, Yuxia Li, Dongmei Bai et al.     Lactobacillus brevis alcohol dehydrogenase (Lb-ADH) catalyzes reduction of prochiral carbonyl compounds to chiral alcohol and meanwhile consumes its cofactor NADH into NAD, while …             Unconscious learning of auditory discrimination using mismatch negativity (MMN) neurofeedback ▶     Ming Chang, Hiroyuki Iizuka, Yasushi Naruse et al.     Neurofeedback is a strong direct training method for brain function, wherein brain activity patterns are measured and displayed as feedback, and trainees try to stabilize the …             Urinary metabolic profiling of rat models revealed protective function of scoparone against alcohol induced hepatotoxicity ▶     Aihua Zhang, Hui Sun, Xijun Wang     Alcohol-induced liver disease (ALD) is a leading cause of non-accident-related deaths in the world. Identification of an early specific signature of ALD would aid in therapeutic …             Calciphytoliths (calcium oxalate crystals) analysis for the identification of decayed tea plants (Camellia sinensis L.) ▶     Jianping Zhang, Houyuan Lu, Linpei Huang     The history of tea is poorly known, mainly due to the questionable identification of decayed tea plants in archaeological samples. This paper attempts to test the utility of …             A thermo-physical analysis of the proton pump vacuolar-ATPase: the constructal approach ▶     Umberto Lucia, Antonio Ponzetto, Thomas S. Deisboeck     Pumping protons across a membrane was a critical step at the origin of life on earth, and it is still performed in all living organisms, including in human cells. Proton pumping …             MOFzyme: Intrinsic protease-like activity of Cu-MOF ▶     Bin Li, Daomei Chen, Jiaqiang Wang et al.     The construction of efficient enzyme mimetics for the hydrolysis of peptide bonds in proteins is challenging due to the high stability of peptide bonds and the importance of …             Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces ▶     Gang Wang, Dani Or     The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent …             Identification of the role of a MAP kinase Tmk2 in Hypocrea jecorina (Trichoderma reesei) ▶     Mingyu Wang, Yanmei Dong, Qiushuang Zhao et al.     Despite the important role of MAPKs in signal transduction, their functions in the cellulase hyper-producing filamentous fungus Hypocrea jecorina haven't been studied except for …             Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life ▶     Zhongtao Zhao, Huiquan Liu, Yongping Luo et al.     Microtubules are essential for various cellular activities and β-tubulins are the target of benzimidazole fungicides. However, the evolution and molecular mechanisms driving …             Modeling how shark and dolphin skin patterns control transitional wall-turbulence vorticity patterns using spatiotemporal phase reset mechanisms ▶     Promode R. Bandyopadhyay, Aren M. Hellum     Many slow-moving biological systems like seashells and zebrafish that do not contend with wall turbulence have somewhat organized pigmentation patterns flush with their outer …             Microsatellite polymorphism among Chrysanthemum sp. polyploids: the influence of whole genome duplication ▶     Haibin Wang, Xiangyu Qi, Ri Gao et al.     Polyploidy is common among flowering plants, including the Asteraceae, a relatively recent angiosperm group. EST-SSRs were used to characterize polymorphism among 29 Chrysanthemum…             Sediment Type Affects Competition between a Native and an Exotic Species in Coastal China ▶     Hong-Li Li, Yong-Yang Wang, Shu-Qing An et al.     Different types of sediments in salt marsh have different physical and chemical characters. Thus sediment type plays a role in plant competition and growth in salt marsh …             Both developmental and adult vision shape body representations ▶     Elena Nava, Tineke Steiger, Brigitte Röder     Sense of body ownership and body representation are fundamental parts of human consciousness, but the contribution of the visual modality to their development remains unclear. We …             Mutagenic and antimutagenic effects of Heterotheca inuloides ▶     Nancy J. Ruiz-Pérez, Myriam Arriaga-Alba, Jaime Sánchez-Navarrete et al.     The antioxidant and hepatoprotective effects of Heterotheca inuloides have been reported before, nevertheless its use as a possible chemopreventive agent has not been documented. …             A Palindromic Motif in the −2084 to −2078 Upstream Region is Essential for ABCA12 Promoter Function in Cultured Human Keratinocytes ▶     Yoshitaka Shimizu, Yasushi Ogawa, Kazumitsu Sugiura et al.     ATP-binding cassette transporter family A member 12 (ABCA12) is a keratinocyte transmembrane lipid transporter that plays a critical role in preserving the skin permeability …             Integrative investigation on breast cancer in ER, PR and HER2-defined subgroups using mRNA and miRNA expression profiling ▶     Xiaofeng Dai, Ana Chen, Zhonghu Bai     Exploring the molecular difference among breast cancer subtypes is of crucial importance in understanding its heterogeneity and seeking its effective clinical treatment. For …             Disease-Targeted Sequencing of Ion Channel Genes identifies de novo mutations in Patients with Non-Familial Brugada Syndrome ▶     Jyh-Ming Jimmy Juang, Tzu-Pin Lu, Liang-Chuan Lai et al.     Brugada syndrome (BrS) is one of the ion channelopathies associated with sudden cardiac death (SCD). The most common BrS-associated gene (SCN5A) only accounts for approximately …             Biologically inspired flexible quasi-single-mode random laser: An integration of Pieris canidia butterfly wing and semiconductors ▶     Cih-Su Wang, Tsung-Yuan Chang, Tai-Yuan Lin et al.     Quasi-periodic structures of natural biomaterial membranes have great potentials to serve as resonance cavities to generate ecological friendly optoelectronic devices with low …             Breakdown into nanoscale of graphene oxide: Confined hot spot atomic reduction and fragmentation ▶     Gil Gonçalves, Mercedes Vila, Igor Bdikin et al.     Nano-graphene oxide (nano-GO) is a new class of carbon based materials being proposed for biomedical applications due to its small size, intrinsic optical properties, large …             Increased N-glycosylation of Asn88 in serum pancreatic ribonuclease 1 is a novel diagnostic marker for pancreatic cancer ▶     Daisuke Nakata     Alterations of carbohydrate structures in cancer cells are the most promising targets for developing clinical diagnostic reagents. Pancreatic cancer is one of the most difficult …             ERRATUM: Network Science and the Effects of Music Preference on Functional Brain Connectivity: From Beethoven to Eminem ▶     R. W. Wilkins, D. A. Hodges, P. J. Laurienti et al.                 Novel Adeno-associated Viruses Derived From Pig Tissues Transduce Most Major Organs in Mice ▶     Alexander Bello, Allan Chand, Jenna Aviles et al.     Recently, development of Adeno-associated virus (AAV) vectors has been focusing on expanding the genetic diversity of vectors from existing sequences via directed evolution or …             Quantitative proteomic analysis of thylakoid from two microalgae (Haematococcus pluvialis and Dunaliella salina) reveals two different high light-responsive strategies ▶     Wenhui Gu, Huan Li, Peipei Zhao et al.     Under high light (HL) stress, astaxanthin-accumulating Haematococcus pluvialis and β-carotene-accumulating Dunaliella salina showed different responsive patterns. To elucidate …             The biosynthetic pathway for a thousand-year-old natural food colorant and citrinin in Penicillium marneffei ▶     Patrick C. Y. Woo, Ching-Wan Lam, Emily W. T. Tam et al.     Monascorubrin and its derivatives are polyketides used as natural colorants for a wide range of food for more than one thousand years. Since the biosynthetic pathway for this …             Human iPS cell-engineered cardiac tissue sheets with cardiomyocytes and vascular cells for cardiac regeneration ▶     Hidetoshi Masumoto, Takeshi Ikuno, Masafumi Takeda et al.     To realize cardiac regeneration using human induced pluripotent stem cells (hiPSCs), strategies for cell preparation, tissue engineering and transplantation must be explored. …             Paclitaxel-induced hyposensitivity to nociceptive chemical stimulation in mice can be prevented by treatment with minocycline ▶     Willias Masocha     Development of peripheral neuropathy, which can present as painful neuropathy or loss of sensation, sometimes limit the use of paclitaxel in the treatment of solid tumors such as …             Lab-on-a-brain: Implantable micro-optical fluidic devices for neural cell analysis in vivo ▶     Hiroaki Takehara, Akira Nagaoka, Jun Noguchi et al.     The high-resolution imaging of neural cells in vivo has brought about great progress in neuroscience research. Here, we report a novel experimental platform, where the intact …             Unglycosylated recombinant human glutathione peroxidase 3 mutant from Escherichia coli is active as a monomer ▶     Jian Song, Yang Yu, Ruiqing Xing et al.     Glutathione peroxidase 3 (GPx3) is a glycosylated member of GPx family and can catalyze the reaction of different types of peroxides with GSH to form their corresponding alcohols …             Impairment of vesicular ATP release affects glucose metabolism and increases insulin sensitivity ▶     Shohei Sakamoto, Takaaki Miyaji, Miki Hiasa et al.     Neuroendocrine cells store ATP in secretory granules and release it along with hormones that may trigger a variety of cellular responses in a process called purinergic chemical …             (R,S)-Tetrahydropapaveroline production by stepwise fermentation using engineered Escherichia coli ▶     Akira Nakagawa, Chiaki Matsuzaki, Eitaro Matsumura et al.     Tetrahydropapaveroline (THP), a benzylisoquinoline alkaloid (BIA) found in diverse pharmaceutical compounds, is used as a starting material for the production of BIA. THP also …             Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis ▶     Yu Xia, Yubo Wang, Herbert H. P. Fang et al.     The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were …             The common functional FKBP5 variant rs1360780 is associated with altered cognitive function in aged individuals ▶     Takashi Fujii, Miho Ota, Hiroaki Hori et al.     The common single nucleotide polymorphism (SNP) rs1360780 (C/T) of the FK506 Binding Protein 5 (FKBP5) gene has been reported to be associated with an altered response of the …             Comparative characterization of two intracellular Ca2+-release channels from the red flour beetle, Tribolium castaneum ▶     Yaping Liu, Chengjun Li, Jingkun Gao et al.     Ryanodine receptors (RyRs) and inositol 1,4,5-trisphosphate receptors (IP3Rs) are members of a family of tetrameric intracellular Ca2-release channels (CRCs). While it is well …             A refined model of water and CO2 membrane diffusion: Effects and contribution of sterols and proteins ▶     Lei Kai, Ralf Kaldenhoff     Black lipid bilayers, a general model system for biomembranes were studied for diffusion rates of small molecules such as water or CO2 using advanced analysis techniques and cell …             Localized Opto-Mechanical Control of Protein Adsorption onto Carbon Nanotubes ▶     Dakota O'Dell, Xavier Serey, Pilgyu Kang et al.     Chemical reactions can be described by an energy diagram along a reaction coordinate in which an activation barrier limits the rate at which reactants can be transformed into …             Association study between XPG Asp1104His polymorphism and colorectal cancer risk in a Chinese population ▶     Haina Du, Xizhi Zhang, Mulong Du et al.     Previous studies have reported that the Asp1104His polymorphism in Xeroderma Pigmentosum complementation group G (XPG) was associated with the susceptibility to colorectal cancer …             Brachiopods hitching a ride: an early case of commensalism in the middle Cambrian Burgess Shale ▶     Timothy P. Topper, Lars E. Holmer, Jean-Bernard Caron     Ecological interactions, including symbiotic associations such as mutualism, parasitism and commensalism are crucial factors in generating evolutionary novelties and strategies. …                     • Careers & Jobs           naturejobs.com Science jobs of the week       Postdoctoral Researcher     University of Utah            Research Associate     King's College London            Senior Research Associate     University of East Anglia (UEA)            PhD Programme in Molecular Cell Biology     University College London (UCL)            Postdoctoral Research Scientist in Cancer Genetics and Evolution     Wellcome Trust Centre for Human Genetics            Research Assistant / Postdoc     Stanford University School of Medicine            Postdoctoral fellow     University Hospital of Cologne            PhD Student     University of Oulu, Faculty of Biochemistry and Molecular Medicine            Postdoctoral Researcher     Louisiana State University            Research Fellow     The University of Nottingham          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. 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