Scientific Reports Biology Table of Contents e-alert: January 2013

02 January 2013      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports                 We've got something to share with you   Access the latest scientific news and research when and where you want it. Download the latest issues to browse at your convenience, zoom in on figures and images, save your searches and synchronize your bookmarks across devices.   Tap in to find out more .                 Biological Sciences               C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes ▶     Pietro Fratta, Sarah Mizielinska, Andrew J. Nicoll et al.     Large expansions of a non-coding GGGGCC-repeat in the first intron of the C9orf72 gene are a common cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia …             Gene direction in living organisms ▶     Xiu-Qing Li, Donglei Du     Gene direction, which is important for function, has not been subjected to statistical testing for randomness and for the degree of evolutionary changes. We analyzed 747 sequenced …             Mega-Bites: Extreme jaw forces of living and extinct piranhas (Serrasalmidae) ▶     Justin R. Grubich, Steve Huskey, Stephanie Crofts et al.     Here, we document in-vivo bite forces recorded from wild piranhas. Integrating this empirical data with allometry, bite simulations, and FEA, we have reconstructed the bite …             Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions ▶     Vincent VanBuren, Hailin Chen     The complexity of biomolecular interactions and influences is a major obstacle to their comprehension and elucidation. Visualizing knowledge of biomolecular interactions increases …             PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy ▶     Kahori Shiba-Fukushima, Yuzuru Imai, Shigeharu Yoshida et al.     Parkinson's disease genes PINK1 and parkin encode kinase and ubiquitin ligase, respectively. The gene products PINK1 and Parkin are implicated in mitochondrial autophagy, or …             Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections ▶     Javier Carrera, Santiago F. Elena     The molecular mechanisms underlying viral pathogenesis are yet poorly understood owed to the large number of factors involved and the complexity of their interactions. Could we …             Iron and bismuth bound human serum transferrin reveals a partially-opened conformation in the N-lobe ▶     Nan Yang, Hongmin Zhang, Minji Wang et al.     Human serum transferrin (hTF) binds Fe(III) tightly but reversibly, and delivers it to cells via a receptor-mediated endocytosis process. The metal-binding and release result in …             Retention of potentially mobile radiocesium in forest surface soils affected by the Fukushima nuclear accident ▶     Jun Koarashi, Koichi Moriya, Mariko Atarashi-Andoh et al.     The fate of 137Cs derived from the Fukushima nuclear accident fallout and associated radiological hazards are largely dependent on its mobility in the surface soils of forest …             Digit patterning during limb development as a result of the BMP-receptor interaction ▶     Amarendra Badugu, Conradin Kraemer, Philipp Germann et al.     Turing models have been proposed to explain the emergence of digits during limb development. However, so far the molecular components that would give rise to Turing patterns are …             Interplay between distribution of live cells and growth dynamics of solid tumours ▶     Edoardo Milotti, Vladislav Vyshemirsky, Michela Sega et al.     Experiments show that simple diffusion of nutrients and waste molecules is not sufficient to explain the typical multilayered structure of solid tumours, where an outer rim of …             Stability of miRNA 5′terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy ▶     Naoki Hibio, Kimihiro Hino, Eigo Shimizu et al.     MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly …             Helicobacter pylori colonization critically depends on postprandial gastric conditions ▶     Roland Bücker, Marina Azevedo-Vethacke, Claudia Groll et al.     The risk of Helicobacter pylori infection is highest in childhood, but the colonization process of the stomach mucosa is poorly understood. We used anesthetized Mongolian gerbils …             Growth patterns for acervuli in human pineal gland ▶     Jinkyung Kim, Hyun-Wook Kim, Soeun Chang et al.     Acervuli are calcified concretions in the pineal gland (PG). Particularly interesting are their incidence and size, which are believed to affect neurological disorders and many …             Cdc42-dependent structural development of auditory supporting cells is required for wound healing at adulthood ▶     Tommi Anttonen, Anna Kirjavainen, Ilya Belevich et al.     Cdc42 regulates the initial establishment of cytoskeletal and junctional structures, but only little is known about its role at later stages of cellular differentiation. We …             ERRATUM: Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome ▶     Bai Jiang, Xujun Liang, Yang Chen et al.                 Force and scleraxis synergistically promote the commitment of human ES cells derived MSCs to tenocytes ▶     Xiao Chen, Zi Yin, Jia-lin Chen et al.     As tendon stem/progenitor cells were reported to be rare in tendon tissues, tendons as vulnerable targets of sports injury possess poor self-repair capability. Human ESCs (hESCs) …             Endogenous Cardiac Troponin T Modulates Ca2+-Mediated Smooth Muscle Contraction ▶     Shunichi Kajioka, Fumi Takahashi-Yanaga, Nouval Shahab et al.     Mechanisms linked to actin filaments have long been thought to cooperate in smooth muscle contraction, although key molecules were unclear. We show evidence that cardiac troponin …             Nuclear localization of folate receptor alpha: a new role as a transcription factor ▶     Vanda Boshnjaku, Kyu-Won Shim, Takao Tsurubuchi et al.     Folic acid (FA) has traditionally been associated with prevention of neural tube defects; more recent work suggests that it may also be involved in in the prevention of adult …             IL-27 increases BST-2 expression in human monocytes and T cells independently of type I IFN ▶     Christina Guzzo, Masany Jung, Ashley Graveline et al.     IL-27 modulates inflammatory responses by influencing cytokine secretion and CD4 T cell differentiation. Recently, IL-27 was demonstrated to inhibit HIV replication by inducing …             Molecular genetic basis of the human Forssman glycolipid antigen negativity ▶     Miyako Yamamoto, Emili Cid, Fumiichiro Yamamoto     Forssman heterophilic glycolipid antigen has structural similarity to the histo-blood group A antigen, and the GBGT1 gene encoding the Forssman glycolipid synthetase (FS) is …             Early Indicators of Disease in Ferrets Infected with a High Dose of Avian Influenza H5N1 ▶     James P. Long, Eric M. Vela, Gregory V. Stark et al.     Avian influenza viruses are widespread in birds, contagious in humans, and are categorized as low pathogenicity avian influenza or highly pathogenic avian influenza. Ferrets are …             Metformin limits the tumourigenicity of iPS cells without affecting their pluripotency ▶     Alejandro Vazquez-Martin, Sílvia Cufi, Eugeni Lopez-Bonet et al.     The antidiabetic drug metformin efficiently circumvents the dilemma that in reducing the tumourigenicity of stem cells, their essence, specifically their pluripotency, must also …             Organic carbon hidden in urban ecosystems ▶     Jill L. Edmondson, Zoe G. Davies, Nicola McHugh et al.     Urbanization is widely presumed to degrade ecosystem services, but empirical evidence is now challenging these assumptions. We report the first city-wide organic carbon (OC) budget …             Flow-dependent double-nanohole optical trapping of 20 nm polystyrene nanospheres ▶     Ana Zehtabi-Oskuie, Jarrah Gerald Bergeron, Reuven Gordon     We study the influence of fluid flow on the ability to trap optically a 20 nm polystyrene particle from a stationary microfluidic environment and then hold it against flow. …             Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes ▶     Adrian Reyes-Prieto, Ahmed Moustafa     Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacteria involved the recruitment of non-cyanobacterial proteins. Our phylogenetic …             Centenarians, but not octogenarians, up-regulate the expression of microRNAs ▶     Eva Serna, Juan Gambini, Consuelo Borras et al.     Centenarians exhibit extreme longevity and a remarkable compression of morbidity. They have a unique capacity to maintain homeostatic mechanisms. Since small non-coding RNAs …             Interpersonal body and neural synchronization as a marker of implicit social interaction ▶     Kyongsik Yun, Katsumi Watanabe, Shinsuke Shimojo     One may have experienced his or her footsteps unconsciously synchronize with the footsteps of a friend while walking together, or heard an audience's clapping hands naturally …             DNA based identification of medicinal materials in Chinese patent medicines ▶     Rong Chen, Juan Dong, Xin Cui et al.     Chinese patent medicines (CPM) are highly processed and easy to use Traditional Chinese Medicine (TCM). The market for CPM in China alone is tens of billions US dollars annually …             Non-destructive Inhibition of Metallofullerenol Gd@C82(OH)22 on WW domain: Implication on Signal Transduction Pathway ▶     Seung-gu Kang, Tien Huynh, Ruhong Zhou     Endohedral metallofullerenol Gd@C82(OH)22 has recently been shown to effectively inhibit tumor growth; however, its potential adverse bioeffects remain to be understood before its …             DJ-1 isoforms in whole blood as potential biomarkers of Parkinson disease ▶     Xiangmin Lin, Travis J. Cook, Cyrus P. Zabetian et al.     DJ-1 is a multifunctional protein that plays an important role in oxidative stress, cell death, and synucleinopathies, including Parkinson disease. Previous studies have …             Discovery and verification of panels of T-lymphocyte proteins as biomarkers of Parkinson's disease ▶     Tiziana Alberio, Agnese C. Pippione, Maurizio Zibetti et al.     The diagnosis of Parkinson's disease (PD) is currently based on the clinical evaluation of extrapyramidal signs with a considerable error rate. The identification of specific …             Multiple roles of the ER stress sensor IRE1 demonstrated by gene targeting in rice ▶     Yuhya Wakasa, Shimpei Hayashi, Kenjirou Ozawa et al.     The endoplasmic reticulum (ER) stress sensor, IRE1, contains a kinase domain and a ribonuclease domain. Ribonuclease mediates the unconventional splicing of mRNA encoding the …             Two distinct knockout approaches highlight a critical role for p53 in rat development ▶     Masaki Kawamata, Takahiro Ochiya     Gene targeting in embryonic stem cells (ESCs) has become the principal technology for generating knockout models. Although numerous studies have predicted that the disruption of …             Doublesex target genes in the red flour beetle, Tribolium castaneum ▶     Jayendra Nath Shukla, Subba Reddy Palli     Sex determination cascade in insects terminates with the production of sex-specific protein, Doublesex (Dsx). We identified the dsx homolog (Tcdsx) in Tribolium castaneum. The …             Structural properties of the tubular appendage spinae from marine bacterium Roseobacter sp. strain YSCB ▶     A. Bernadac, L.-F. Wu, C.-L. Santini et al.     Spinae are tubular surface appendages broadly found in Gram-negative bacteria. Little is known about their architecture, function or origin. Here, we report structural …             Expression of a fungal sterol desaturase improves tomato drought tolerance, pathogen resistance and nutritional quality ▶     Ayushi Kamthan, Mohan Kamthan, Mohammad Azam et al.     Crop genetic engineering mostly aims at improving environmental stress (biotic and abiotic) tolerance as well as nutritional quality. Empowering a single crop with multiple traits …             Cross-sensory transfer of sensory-motor information: visuomotor learning affects performance on an audiomotor task, using sensory-substitution ▶     Shelly Levy-Tzedek, Itai Novick, Roni Arbel et al.     Visual-to-auditory sensory-substitution devices allow users to perceive a visual image using sound. Using a motor-learning task, we found that new sensory-motor information was …             Identifying critical transitions and their leading biomolecular networks in complex diseases ▶     Rui Liu, Meiyi Li, Zhi-Ping Liu et al.     Identifying a critical transition and its leading biomolecular network during the initiation and progression of a complex disease is a challenging task, but holds the key to early …             Concentration of 3H in plants around Fukushima Dai-ichi Nuclear Power Station ▶     Hideki Kakiuchi, Naofumi Akata, Hidenao Hasegawa et al.     A large amount of radionuclides was released from the Fukushima Dai-ichi Nuclear Power Station (FDNPS) following the damage caused by the tsunami due to the Great East Japan …             Structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen ▶     Nethaji Thiyagarajan, Tram T. K. Pham, Brittany Stinson et al.     Histo-blood group antigens (HBGAs) are a source of antigenic variation between individuals that modulates resistance and susceptibility to pathogens and is a barrier to the spread …             Bone regeneration by polyhedral microcrystals from silkworm virus ▶     Goichi Matsumoto, Takayo Ueda, Junko Shimoyama et al.     Bombyx mori cypovirus is a major pathogen which causes significant losses in silkworm cocoon harvests because the virus particles are embedded in micrometer-sized protein crystals …             Prevalent Glucocorticoid and Androgen Activity in US Water Sources ▶     Diana A. Stavreva, Anuja A. George, Paul Klausmeyer et al.     Contamination of the environment with endocrine disrupting chemicals (EDCs) is a major health concern. The presence of estrogenic compounds in water and their deleterious effect …             Distinct Feedforward and Intrinsic Neurons in Posterior Inferotemporal Cortex Revealed by in Vivo Connection Imaging ▶     Noritaka Ichinohe, Elena Borra, Kathleen Rockland     We investigated circuits for object recognition in macaque anterior (TE) and posterior inferotemporal cortex (TEO), using a two-step method with in vivo anatomical imaging. In …             Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome ▶     Bai Jiang, Xujun Liang, Yang Chen et al.     Tongue diagnosis is a unique method in traditional Chinese medicine (TCM). This is the first investigation on the association between traditional tongue diagnosis and the tongue …             Statistical patterns of visual search for hidden objects ▶     Heitor F. Credidio, Elisângela N. Teixeira, Saulo D. S. Reis et al.     The movement of the eyes has been the subject of intensive research as a way to elucidate inner mechanisms of cognitive processes. A cognitive task that is rather frequent in our …             ERRATUM: Gene Set Enrichment Analysis Identifies LIF as a Negative Regulator of Human Th2 Cell Differentiation ▶     Ubaid Ullah, Parul Tripathi, Naresh Sahoo et al.                 Fast and accurate low-dimensional reduction of biophysically detailed neuron models ▶     Addolorata Marasco, Alessandro Limongiello, Michele Migliore     Realistic modeling of neurons are quite successful in complementing traditional experimental techniques. However, their networks require a computational power beyond the …             A medium-chain fatty acid as an alternative energy source in mouse preimplantation development ▶     Mitsutoshi Yamada, Kazumi Takanashi, Toshio Hamatani et al.     To further optimize the culturing of preimplantation embryos, we undertook metabolomic analysis of relevant culture media using capillary electrophoresis time-of-flight mass …             The importance of serine 776 in Ataxin-1 partner selection: A FRET Analysis ▶     Rajesh P. Menon, Daniel Soong, Cesira de Chiara et al.     Anomalous expansion of a polymorphic tract in Ataxin-1 causes the autosomal dominant spinocerebellar ataxia type 1. In addition to polyglutamine expansion, requirements for …             Disparate roles of marrow- and parenchymal cell-derived TLR4 signaling in murine LPS-induced systemic inflammation ▶     Justin E. Juskewitch, Jeffrey L. Platt, Bruce E. Knudsen et al.     Systemic inflammatory response syndrome (SIRS) occurs in a range of infectious and non-infectious disease processes. Toll-like receptors (TLRs) initiate such responses. We have …             PMA-induced dissociation of Ku86 from the promoter causes transcriptional up-regulation of histamine H1 receptor ▶     Hiroyuki Mizuguchi, Kohei Miyagi, Takuma Terao et al.     Histamine H1 receptor (H1R) gene is up-regulated in patients with allergic rhinitis, and its expression level strongly correlates with the severity of symptoms. However, the …             Accelerated crossing of fitness valleys through division of labor and cheating in asexual populations ▶     Natalia L. Komarova, Erin Urwin, Dominik Wodarz     Complex traits can require the accumulation of multiple mutations that are individually deleterious. Their evolution requires a fitness valley to be crossed, which can take …                         Scientific Reports is accepting submissions from all scientific fields. 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