Scientific Reports Biology Table of Contents e-alert: December 2012

03 December 2012      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports             Nature Reviews Immunology POSTER-THE IMMUNE RESPONSE TO HIV Authors: Nina Bhardwaj, Florian Hladik and Susan Moir www.nature.com/nri/posters/hiv Produced with support from STEMCELL Technologies               Biological Sciences               Age-dependent α-synuclein aggregation in the Microcebus murinus lemur primate ▶     Marie-Hélène Canron, Martine Perret, Anne Vital et al.     Since age-dependent deposition of Aβ-amyloid has been reported in the Microcebus murinus, we posited that this animal could as well be a model of age-related synucleinopathy. We …             Delineation of breast cancer cell hierarchy identifies the subset responsible for dormancy ▶     Shyam A. Patel, Shakti H. Ramkissoon, Margarette Bryan et al.     The bone marrow (BM) is a major organ of breast cancer (BC) dormancy and a common source of BC resurgence. Gap junctional intercellular communication (GJIC) between BC cells …             Target proteins of ganoderic acid DM provides clues to various pharmacological mechanisms ▶     Jie Liu, Kuniyoshi Shimizu, Akinobu Tanaka et al.     Ganoderma fungus (Ganodermataceae) is a multifunctional medicinal mushroom and has been traditionally used for the treatment of various types of disease. Ganoderic acid DM (1) is …             Amperometric post spike feet reveal most exocytosis is via extended kiss-and-run fusion ▶     Lisa J. Mellander, Raphaël Trouillon, Maria I. Svensson et al.     The basis for communication between nerve cells lies in the process of exocytosis, the fusion of neurotransmitter filled vesicles with the cell membrane resulting in release of …             Environmental toxins trigger PD-like progression via increased alpha-synuclein release from enteric neurons in mice ▶     Francisco Pan-Montojo, Mathias Schwarz, Clemens Winkler et al.     Pathological studies on Parkinson's disease (PD) patients suggest that PD pathology progresses from the enteric nervous system (ENS) and the olfactory bulb into the central …             Juxtanodin is an intrinsically disordered F-actin-binding protein ▶     Salla Ruskamo, Maryna Chukhlieb, Juha Vahokoski et al.     Juxtanodin, also called ermin, is an F-actin-binding protein expressed by oligodendrocytes, the myelin-forming cells of the central nervous system. While juxtanodin carries a …             Network rewiring is an important mechanism of gene essentiality change ▶     Jinho Kim, Inhae Kim, Seong Kyu Han et al.     Gene essentiality changes are crucial for organismal evolution. However, it is unclear how essentiality of orthologs varies across species. We investigated the underlying …             In vivo assessment of cancerous tumors using boron doped diamond microelectrode ▶     Stéphane Fierro, Momoko Yoshikawa, Osamu Nagano et al.     The in vitro and in vivo electrochemical detection of the reduced form of glutathione (L-γ-glutamyl-L-cysteinyl-glycine, GSH) using boron doped diamond (BDD) microelectrode for …             ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets ▶     Zhen Xia, Peter Clark, Tien Huynh et al.                 Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression ▶     Yi Li, Richard Moore, Michael Guinn et al.     The ability to conditionally rewire pathways in human cells holds great therapeutic potential. Transcription activator-like effectors (TALEs) are a class of naturally occurring …             Cellular Inclusion Bodies of Mutant Huntingtin Exon 1 Obscure Small Fibrillar Aggregate Species ▶     Steffen J. Sahl, Lucien E. Weiss, Whitney C. Duim et al.     The identities of toxic aggregate species in Huntington's disease pathogenesis remain ambiguous. While polyQ-expanded huntingtin (Htt) is known to accumulate in compact inclusion …             Pharmacological inhibition of TLR4-NOX4 signal protects against neuronal death in transient focal ischemia ▶     Yukiya Suzuki, Kozo Hattori, Junya Hamanaka et al.     Recent data have shown that TLR4 performs a key role in cerebral ischemia-reperfusion injury which serves as the origin of the immunological inflammatory reactions. However, the …             Ecology of cryptic invasions: latitudinal segregation among Watersipora (Bryozoa) species ▶     Joshua A. Mackie, John A. Darling, Jonathan B. Geller     Watersipora is an invasive genus of bryozoans, easily dispersed by fouled vessels. We examined Cytochrome c oxidase subunit I haplotypes from introduced populations on the US …             Architecture of the HCN selectivity filter and control of cation permeation ▶     Vincenzo Macri, Damiano Angoli, Eric A. Accili     Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) channels are similar in structure and function to voltage-gated potassium channels. Sequence similarity and …             A proton shelter inspired by the sugar coating of acidophilic archaea ▶     Xiumei Wang, Bei’er Lv, Guixin Cai et al.     The acidophilic archaeons are a group of single-celled microorganisms that flourish in hot acid springs (usually pH < 3) but maintain their internal pH near neutral. Although …             Safety-Information-Driven Human Mobility Patterns with Metapopulation Epidemic Dynamics ▶     Bing Wang, Lang Cao, Hideyuki Suzuki et al.     With the help of mass media, people receive information concerning the status of an infectious disease to guide their mobility. Herein, we develop a theoretical framework to …             Witnessing Quantum Coherence: from solid-state to biological systems ▶     Che-Ming Li, Neill Lambert, Yueh-Nan Chen et al.     Quantum coherence is one of the primary non-classical features of quantum systems. While protocols such as the Leggett-Garg inequality (LGI) and quantum tomography can be used to …             Who needs a referee? How incorrect basketball actions are automatically detected by basketball players' brain ▶     Alice Mado Proverbio, Nicola Crotti, Mirella Manfredi et al.     While the existence of a mirror neuron system (MNS) representing and mirroring simple purposeful actions (such as reaching) is known, neural mechanisms underlying the …             Spectral pattern of urinary water as a biomarker of estrus in the giant panda ▶     Kodzue Kinoshita, Mari Miyazaki, Hiroyuki Morita et al.     Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important …             A Hydration-Based Biophysical Index for the Onset of Soil Microbial Coexistence ▶     Gang Wang, Dani Or     Mechanistic exploration of the origins of the unparalleled soil microbial biodiversity represents a vast and uncharted scientific frontier. Quantification of candidate mechanisms …             Regulation of autophagy by nucleoporin Tpr ▶     Tatsuyoshi Funasaka, Eriko Tsuka, Richard W. Wong     The nuclear pore complex (NPC) consists of a conserved set of ~30 different proteins, termed nucleoporins, and serves as a gateway for the exchange of materials between the …             Fibrin Clots Are Equilibrium Polymers That Can Be Remodeled Without Proteolytic Digestion ▶     Irina N. Chernysh, Chandrasekaran Nagaswami, Prashant K. Purohit et al.     Fibrin polymerization is a necessary part of hemostasis but clots can obstruct blood vessels and cause heart attacks and strokes. The polymerization reactions are specific and …             Broadband and broadangle SPP antennas based on plasmonic crystals with linear chirp ▶     J.-S Bouillard, S. Vilain, W. Dickson et al.     Plasmonic technology relies on the coupling of light to surface electromagnetic modes on smooth or structured metal surfaces. While some applications utilise the resonant nature …             Hierarchical Modularity in ERα Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes ▶     Binhua Tang, Hang-Kai Hsu, Pei-Yin Hsu et al.     Recent genome-wide profiling reveals highly complex regulation networks among ERα and its targets. We integrated estrogen (E2)-stimulated time-series ERα ChIP-seq and gene …             TMV-Gate vectors: Gateway compatible tobacco mosaic virus based expression vectors for functional analysis of proteins ▶     Sateesh Kagale, Shihomi Uzuhashi, Merek Wigness et al.     Plant viral expression vectors are advantageous for high-throughput functional characterization studies of genes due to their capability for rapid, high-level transient expression …             Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7 ▶     Santosh Kumar, Suneel Kateriya, Vijay Shankar Singh et al.     Ever since the discovery of the role of bacteriophytochrome (BphP) in inducing carotenoid synthesis in Deinococcus radiodurans in response to light the role of BphPs in other …             Enhancing electrochemical detection on graphene oxide-CNT nanostructured electrodes using magneto-nanobioprobes ▶     Priyanka Sharma, Vijayender Bhalla, Vinayak Dravid et al.     Graphene and related materials have come to the forefront of research in electrochemical sensors during recent years due to the promising properties of these nanomaterials. …             Simulating spread of Bluetongue Virus by flying vectors between hosts on pasture ▶     Kaare Græsbøll, René Bødker, Claes Enøe et al.     Bluetongue is a disease of ruminants which reached Denmark in 2007. We present a process-based stochastic simulation model of vector-borne diseases, where host animals are not …             Cell Type-Specific Activation of AKT and ERK Signaling Pathways by Small Negatively-Charged Magnetic Nanoparticles ▶     Jens Rauch, Walter Kolch, Morteza Mahmoudi     The interaction of nanoparticles (NPs) with living organisms has become a focus of public and scientific debate due to their potential wide applications in biomedicine, but also …             A Bayesian explanation of the ‘Uncanny Valley’ effect and related psychological phenomena ▶     Roger K. Moore     There are a number of psychological phenomena in which dramatic emotional responses are evoked by seemingly innocuous perceptual stimuli. A well known example is the ‘uncanny …             DNA Nanostructure-based Interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA ▶     Yanli Wen, Hao Pei, Ye Shen et al.     MicroRNAs (miRNAs) have been identified as promising cancer biomarkers due to their stable presence in serum. As an alternative to PCR-based homogenous assays, surface-based …             Neural Correlates of Lyrical Improvisation: An fMRI Study of Freestyle Rap ▶     Siyuan Liu, Ho Ming Chow, Yisheng Xu et al.     The neural correlates of creativity are poorly understood. Freestyle rap provides a unique opportunity to study spontaneous lyrical improvisation, a multidimensional form of …             Transmission of Ebola virus from pigs to non-human primates ▶     Hana M. Weingartl, Carissa Embury-Hyatt, Charles Nfon et al.     Ebola viruses (EBOV) cause often fatal hemorrhagic fever in several species of simian primates including human. While fruit bats are considered natural reservoir, involvement of …             Development of Miniaturized Walking Biological Machines ▶     Vincent Chan, Kidong Park, Mitchell B. Collens et al.     The quest to ‘forward-engineer’ and fabricate biological machines remains a grand challenge. Towards this end, we have fabricated locomotive “bio-bots” from hydrogels and …             Consequences of replacing EGFR juxtamembrane domain with an unstructured sequence ▶     Lijuan He, Kalina Hristova     EGFR is the best studied receptor tyrosine kinase. Yet, a comprehensive mechanistic understanding of EGFR signaling is lacking, despite very active research in the field. In this …             Hkat, a novel nutritionally regulated transmembrane protein in adipose tissues ▶     Ren Zhang     White adipose tissue is an active endocrine organ regulating many aspects of whole body physiology and pathology. Adipogenesis, a process in which premature cells differentiate …             Lipid-coated hydrogel shapes as components of electrical circuits and mechanical devices ▶     K. Tanuj Sapra, Hagan Bayley     Recently, two-dimensional networks of aqueous droplets separated by lipid bilayers, with engineered protein pores as functional elements, were used to construct millimeter-sized …             Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells ▶     Andrew P. Rudhall, Maciej Antkowiak, Xanthi Tsampoula et al.     The use of ultrashort femtosecond pulsed lasers to effect membrane permeabilisation and initiate both optoinjection and transfection of cells has recently seen immense interest. …             APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells ▶     Masanobu Shinohara, Katsuhiro Io, Keisuke Shindo et al.     Human APOBEC3 proteins play pivotal roles in intracellular defense against viral infection by catalyzing deamination of cytidine residues, leading to base substitutions in viral …             Differential network entropy reveals cancer system hallmarks ▶     James West, Ginestra Bianconi, Simone Severini et al.     The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is …             MicroRNA-mediated mRNA Translation Activation in Quiescent Cells and Oocytes Involves Recruitment of a Nuclear microRNP ▶     S. S. Truesdell, R. D. Mortensen, M. Seo et al.     MicroRNAs can promote translation of specific mRNAs in quiescent (G0) mammalian cells and immature Xenopus laevis oocytes. We report that microRNA-mediated upregulation of target …             Dishevelled3 is a novel arginine methyl transferase substrate ▶     Rama Kamesh Bikkavilli, Sreedevi Avasarala, Michelle Vanscoyk et al.     Dishevelled, a phosphoprotein scaffold, is a central component in all the Wnt-sensitive signaling pathways. In the present study, we report that Dishevelled is …             GTPases IF2 and EF-G bind GDP and the SRL RNA in a mutually exclusive manner ▶     Vladimir A. Mitkevich, Viktoriya Shyp, Irina Yu. Petrushanko et al.     Translational GTPases (trGTPases) are involved in all four stages of protein biosynthesis: initiation, elongation, termination and ribosome recycling. The trGTPases Initiation …             The miR-290-295 cluster suppresses autophagic cell death of melanoma cells ▶     Yong Chen, Ruediger Liersch, Michael Detmar     We compared the expression levels of 307 miRNAs in six different B16F1 melanoma cell lines of differing malignant properties and found that the miR-290–295 cluster showed a strong …             The Evolution of Homophily ▶     Feng Fu, Martin A. Nowak, Nicholas A. Christakis et al.     Biologists have devoted much attention to assortative mating or homogamy, the tendency for sexual species to mate with similar others. In contrast, there has been little …             Effects of gestational age and surface modification on materno-fetal transfer of nanoparticles in murine pregnancy ▶     Hui Yang, Cuiji Sun, Zhenlin Fan et al.     Nanoparticle exposure in pregnancy may result in placental damage and fetotoxicity; however, the factors that determine fetal nanoparticle exposure are unclear. Here we have …             White Band Disease transmission in the threatened coral, Acropora cervicornis ▶     S. A. Gignoux-Wolfsohn, Christopher J. Marks, Steven V. Vollmer     The global rise in coral diseases has severely impacted coral reef ecosystems, yet often little is known about these diseases, including how they are transmitted. White Band …             Hapten Mediated Display and Pairing of Recombinant Antibodies Accelerates Assay Assembly for Biothreat Countermeasures ▶     Laura J. Sherwood, Andrew Hayhurst     A bottle-neck in recombinant antibody sandwich immunoassay development is pairing, demanding protein purification and modification to distinguish captor from tracer. We developed …             Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening ▶     Tao Zhou, Hang Zhang, Tongfei Lai et al.     Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of …             You mob my owl, I’ll mob yours: birds play tit-for-tat game ▶     Tatjana Krama, Jolanta Vrublevska, Todd M. Freeberg et al.     Reciprocity is fundamental to cooperative behaviour and has been verified in theoretical models. However, there is still limited experimental evidence for reciprocity in …             Quantitative, spectrally-resolved intraoperative fluorescence imaging ▶     Pablo A. Valdés, Frederic Leblond, Valerie L. Jacobs et al.     Intraoperative visual fluorescence imaging (vFI) has emerged as a promising aid to surgical guidance, but does not fully exploit the potential of the fluorescent agents that are …             Assignment and secondary structure of the YadA membrane protein by solid-state MAS NMR ▶     Shakeel A. Shahid, Stefan Markovic, Dirk Linke et al.     We report the complete solid-state MAS NMR resonance assignment of a medium-sized, trimeric membrane protein, YadA-M. The protein YadA (Yersinia adhesin A) is an important …             BDNF gene therapy induces auditory nerve survival and fiber sprouting in deaf Pou4f3 mutant mice ▶     H. Fukui, H. T. Wong, L. A. Beyer et al.     Current therapy for patients with hereditary absence of cochlear hair cells, who have severe or profound deafness, is restricted to cochlear implantation, a procedure that …             Biomaterial evolution parallels behavioral innovation in the origin of orb-like spider webs ▶     Todd A. Blackledge, Matjaž Kuntner, Mohammad Marhabaie et al.     Correlated evolution of traits can act synergistically to facilitate organism function. But, what happens when constraints exist on the evolvability of some traits, but not …             Obesity-induced endoplasmic reticulum stress causes chronic inflammation in adipose tissue ▶     Noritaka Kawasaki, Rie Asada, Atsushi Saito et al.     Adipose tissue plays a central role in maintaining metabolic homeostasis under normal conditions. Metabolic diseases such as obesity and type 2 diabetes are often accompanied by …             RETRACTION: A therapeutic method for the direct reprogramming of human liver cancer cells with only chemicals ▶     Hisashi Moriguchi, Yue Zhang, Makoto Mihara et al.                 RETRACTION: Successful cryopreservation of human ovarian cortex tissues using supercooling ▶     Hisashi Moriguchi, Yue Zhang, Makoto Mihara et al.                 Characterization of coagulation factor synthesis in nine human primary cell types ▶     Monireh Dashty, Vishtaseb Akbarkhanzadeh, Clark J. Zeebregts et al.     The coagulation/fibrinolysis system is essential for wound healing after vascular injury. According to the standard paradigm, the synthesis of most coagulation factors is …             A Novel Tumor suppressor network in squamous malignancies ▶     Clotilde Costa, Mirentxu Santos, Carmen Segrelles et al.     The specific ablation of Rb1 gene in stratified epithelia (RbF/F;K14cre) promotes proliferation and altered differentiation but is insufficient to produce spontaneous tumors. The …             Loss of Maternal Annexin A5 Increases the Likelihood of Placental Platelet Thrombosis and Foetal Loss ▶     Hiroshi Ueki, Tomona Mizushina, Titaree Laoharatchatathanin et al.     Antiphospholipid syndrome is associated with an increased risk of thrombosis and pregnancy loss. Annexin A5 (Anxa5) is a candidate autoantigen. It is not known, however, whether …             Autocrine stimulation of clear-cell renal carcinoma cell migration in hypoxia via HIF-independent suppression of thrombospondin-1 ▶     Raquel Bienes-Martínez, Angel Ordóñez, Mónica Feijoo-Cuaresma et al.     Thrombospondin-1 is a matricellular protein with potent antitumour activities, the levels of which determine the fate of many different tumours, including renal carcinomas. …             Sequential detection of temporal communities by estrangement confinement ▶     Vikas Kawadia, Sameet Sreenivasan     Temporal communities are the result of a consistent partitioning of nodes across multiple snapshots of an evolving network, and they provide insights into how dense clusters in a …             Nano-visualization of oriented-immobilized IgGs on immunosensors by high-speed atomic force microscopy ▶     Masumi Iijima, Masaharu Somiya, Nobuo Yoshimoto et al.     Oriented immobilization of sensing molecules on solid phases is an important issue in biosensing. In case of immunosensors, it is essential to scrutinize not only the direction …             Multimodal imaging of human cerebellum - merging X-ray phase microtomography, magnetic resonance microscopy and histology ▶     Georg Schulz, Conny Waschkies, Franz Pfeiffer et al.     Imaging modalities including magnetic resonance imaging and X-ray computed tomography are established methods in daily clinical diagnosis of human brain. Clinical equipment does …             Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device ▶     Paola Fanzio, Chiara Manneschi, Elena Angeli et al.     Several strategies have been developed for the control of DNA translocation in nanopores and nanochannels. However, the possibility to reduce the molecule speed is still …             ROCK/Cdc42-mediated microglial motility and gliapse formation lead to phagocytosis of degenerating dopaminergic neurons in vivo ▶     Carlos Barcia, Carmen María Ros, Valentina Annese et al.     The role of microglial motility in the context of adult neurodegeneration is poorly understood. In the present work, we investigated the microanatomical details of …             Loss of the respiratory enzyme citrate synthase directly links the Warburg effect to tumor malignancy ▶     Chin-Chih Lin, Tsung-Lin Cheng, Wen-Hui Tsai et al.     To investigate whether altered energy metabolism induces the Warburg effect and results in tumor malignancy, the respiratory enzyme citrate synthase (CS) was examined, silenced, …             A chemical genomic study identifying diversity in cell migration signaling in cancer cells ▶     Shigeyuki Magi, Etsu Tashiro, Masaya Imoto     The aim of this study was to analyze the diversity and consistency of regulatory signaling in cancer cell migration, using a chemical genomic approach. The effects of 34 small …             RRM2B Suppresses Activation of the Oxidative Stress Pathway and is Up-regulated by P53 During Senescence ▶     Mei-Ling Kuo, Alexander J. Sy, Lijun Xue et al.     RRM2B is the DNA damage-inducible small subunit of ribonucleotide reductase, the rate-limiting enzyme in de novo deoxyribonucleoside triphosphate synthesis. Although RRM2B is …             Characterisation of the organophosphate hydrolase catalytic activity of SsoPox ▶     Julien Hiblot, Guillaume Gotthard, Eric Chabriere et al.     SsoPox is a lactonase endowed with promiscuous phosphotriesterase activity isolated from Sulfolobus solfataricus that belongs to the Phosphotriesterase-Like Lactonase family. …             Targeted transcript profiling by sequencing ▶     Pawel Zajac, Afshin Ahmadian     In this work we present a targeted gene expression strategy employing trinucleotide threading (TnT) amplification and massive parallel sequencing. We have previously shown that …             Formylpeptide receptors are critical for rapid neutrophil mobilization in host defense against Listeria monocytogenes ▶     Mingyong Liu, Keqiang Chen, Teizo Yoshimura et al.     Listeria monocytogenes (Listeria) causes opportunistic infection in immunocompromised hosts with high mortality. Resistance to Listeria depends on immune responses and recruitment …             A functioning artificial secretory cell ▶     Lisa Simonsson, Michael E. Kurczy, Raphaël Trouillon et al.     We present an amperometric study of content release from individual vesicles in an artificial secretory cell designed with the minimal components required to carry out exocytosis. …             Fluorescence laser microdissection reveals a distinct pattern of gene activation in the mouse hippocampal region ▶     Wataru Yoshioka, Nozomi Endo, Akie Kurashige et al.     A histoanatomical context is imperative in an analysis of gene expression in a cell in a tissue to elucidate physiological function of the cell. In this study, we made technical …                         Scientific Reports is accepting submissions from all scientific fields. 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