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

03 June 2013      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports                 Choose Scientific Reports for fast, efficient, open access publishing 93% of authors said they are likely or very likely to recommend Scientific Reports to their colleagues* 92% of authors would publish in Scientific Reports again* SUBMIT your paper today! *Nature Publishing Group author survey, data correct as of April 2013                 Biological Sciences               A non-invasive imaging for the in vivo tracking of high-speed vesicle transport in mouse neutrophils ▶     Kenji Kikushima, Sayaka Kita, Hideo Higuchi     Neutrophils play an essential role in the innate immune response. To understand neutrophil activity, the development of a new technique to observe neutrophils in situ is required. …             Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment ▶     Dong Xu, Yang Zhang     Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in …             Neurotoxic amyloid beta oligomeric assemblies recreated in microfluidic platform with interstitial level of slow flow ▶     Yoon Jung Choi, Sukyung Chae, Jeong Hun Kim et al.     Alzheimer's disease is accompanied by progressive, time-dependent changes of three moieties of amyloid beta. In vitro models therefore should provide same conditions for more …             Filling the gaps of dinosaur eggshell phylogeny: Late Jurassic Theropod clutch with embryos from Portugal ▶     Ricardo Araújo, Rui Castanhinha, Rui M. S. Martins et al.     The non-avian saurischians that have associated eggshells and embryos are represented only by the sauropodomorph Massospondylus and Coelurosauria (derived theropods), thus missing …             Electron beam-assisted healing of nanopores in magnesium alloys ▶     He Zheng, Yu Liu, Fan Cao et al.     Nanopore-based sensing has emerged as a promising candidate for affordable and powerful DNA sequencing technologies. Herein, we demonstrate that nanopores can be successfully …             PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer ▶     Teruyuki Sato, Atsushi Kaneda, Shingo Tsuji et al.     Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis. Expression array analysis of 23 SCLC cases and 42 normal tissues revealed that EZH2 and other PRC2 …             Digital optical phase conjugation for delivering two-dimensional images through turbid media ▶     Timothy R. Hillman, Toyohiko Yamauchi, Wonshik Choi et al.     Optical transmission through complex media such as biological tissue is fundamentally limited by multiple light scattering. Precise control of the optical wavefield potentially …             Skin Stem Cell Hypotheses and Long Term Clone Survival – Explored Using Agent-based Modelling ▶     X. Li, A. K. Upadhyay, A. J. Bullock et al.     Epithelial renewal in skin is achieved by the constant turnover and differentiation of keratinocytes. Three popular hypotheses have been proposed to explain basal keratinocyte …             A novel protocol for three-dimensional structure prediction of RNA-protein complexes ▶     Yangyu Huang, Shiyong Liu, Dachuan Guo et al.     Three-dimensional structures of RNA-protein complexes are crucial for understanding their diverse functions. However, the number of the RNA-protein complex structures solved by …             L-arginine-NO-cGMP signalling pathway in pancreatitis ▶     Igor Buchwalow, Jürgen Schnekenburger, Katharina Tiemann et al.     The role of nitric oxide (NO) in the human pancreas and in pancreatitis still remains controversial. Furthermore, conflicting conclusions have been reached by different …             A Method for accurate in vivo micro-Raman spectroscopic measurements under guidance of advanced microscopy imaging ▶     Hequn Wang, Anthony M. D. Lee, Harvey Lui et al.     The movement from the subjects during in vivo confocal Raman spectral measurements could change the measurement volume, leading to non-specific signals and inaccurate …             Complex social contagion makes networks more vulnerable to disease outbreaks ▶     Ellsworth Campbell, Marcel Salathé     Social network analysis is now widely used to investigate the dynamics of infectious disease spread. Vaccination dramatically disrupts disease transmission on a contact network, …             In vivo minimally invasive interstitial multi-functional microendoscopy ▶     Asaf Shahmoon, Shiran Aharon, Oded Kruchik et al.     Developing minimally invasive methodologies for imaging of internal organs is an emerging field in the biomedical examination research. This paper introduces a new …             Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study ▶     Mattia Prosperi, Nazle Veras, Taj Azarian et al.     Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA …             Chemical activation of RARβ induces post-embryonically bilateral limb duplication during Xenopus limb regeneration ▶     Rodrigo Cuervo, Jesús Chimal-Monroy     The anuran amphibian Xenopus laevis can regenerate its limbs for a limited time during the larval stage, while limbs are still developing. Using this regeneration model, we …             Temporal fractals in seabird foraging behaviour: diving through the scales of time ▶     Andrew J. J. MacIntosh, Laure Pelletier, Andre Chiaradia et al.     Animal behaviour exhibits fractal structure in space and time. Fractal properties in animal space-use have been explored extensively under the Lévy flight foraging hypothesis, but …             Addressable and unidirectional energy transfer along a DNA three-way junction programmed by pyrrole-imidazole polyamides ▶     Wu Su, Clive R. Bagshaw, Glenn A. Burley     We describe a photonic waveguide where FRET is routed uni-directionally along a double-stranded DNA track. The efficiency of FRET is modulated by the supramolecular control of …             Attachment-regulated signaling networks in the fibroblast-populated 3D collagen matrix ▶     Mark A. Carlson, Lynette M. Smith, Crystal M. Cordes et al.     Fibroblasts in the attached collagen matrix are in a pro-survival, pro-proliferative state relative to fibroblasts in the released collagen matrix, such that matrix cell number …             Measuring collective cell movement and extracellular matrix interactions using magnetic resonance imaging ▶     Yun Chen, Stephen J. Dodd, Michael A. Tangrea et al.     Collective cell behaviors in migration and force generation were studied at the mesoscopic-level using cells grown in a 3D extracellular matrix (ECM) simulating tissues. Magnetic …             Memory of plant communications for priming anti-herbivore responses ▶     Mohamed Ali, Koichi Sugimoto, Abdelaziz Ramadan et al.     The emission of a specific blend of volatiles in response to Mythimna separata (herbivore-induced plant volatiles, HIPVs) plays a great ecological role by priming neighbouring …             Basilar membrane vibration is not involved in the reverse propagation of otoacoustic emissions ▶     W. He, T. Ren     To understand how the inner ear-generated sound, i.e., otoacoustic emission, exits the cochlea, we created a sound source electrically in the second turn and measured basilar …             Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation ▶     Xin-Yue Cheng, Xue-Liang Tian, Yun-Sheng Wang et al.     Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we …             Leaf Selection by Two Bornean Colobine Monkeys in Relation to Plant Chemistry and Abundance ▶     Ikki Matsuda, Augustine Tuuga, Henry Bernard et al.     Focusing on the chemical basis of dietary selection while investigating the nutritional ecology of animals helps understand their feeding biology. It is also important to consider …             Mesothelin Binding to CA125/MUC16 Promotes Pancreatic Cancer Cell Motility and Invasion via MMP-7 Activation ▶     Shih-Hsun Chen, Wei-Chien Hung, Pu Wang et al.     Mesothelin (MSLN) and cancer antigen125/mucin 16 (CA125/MUC16) are potential biomarkers for pancreatic cancer (PC) that are co-overexpressed at the invading edges of PC tissues, and …             Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles ▶     Yi-Chung Chang, Chia-Ying Yang, Ruei-Lin Sun et al.     Staphylococcus aureus is one of the most important human pathogens, causing more than 500,000 infections in the United States each year. Traditional methods for bacterial culture …             A Novel Electrochemical Membrane Bioreactor as a Potential Net Energy Producer for Sustainable Wastewater Treatment ▶     Yun-Kun Wang, Guo-Ping Sheng, Bing-Jing Shi et al.     One possible way to address both water and energy shortage issues, the two of major global challenges, is to recover energy and water resource from wastewater. Herein, a novel …             IRGM1 regulates oxidized LDL uptake by macrophage via actin-dependent receptor internalization during atherosclerosis ▶     Fucan Xia, Rui Li, Chaodong Wang et al.     Macrophage derived foam cells are actively involved in the initial phase of atherosclerosis. Uptake of modified lipoprotein such as oxidized LDL (oxLDL) is a critical step for foam …             Plasmon-Enhanced Light Harvesting of Chlorophylls on Near-Percolating Silver Films via One-Photon Anti-Stokes Upconversion ▶     Ya-Lan Wang, Fan Nan, Xiao-Li Liu et al.     There exists a wealth of means of efficient utilization of solar energy in nature, with photosynthesis of chlorophylls as a prime example. Separately, artificially structured …             Transcriptome sequencing of neonatal thymic epithelial cells ▶     Charles St-Pierre, Sylvie Brochu, Juan Ruiz Vanegas et al.     In order to gain novel insights into thymus biology, we analysed the whole transcriptome of cortical and medullary thymic epithelial cells (cTECs and mTECs) and of skin epithelial …             Physiologically-Relevant Modes of Membrane Interactions by the Human Antimicrobial Peptide, LL-37, Revealed by SFG Experiments ▶     Bei Ding, Lauren Soblosky, Khoi Nguyen et al.     Antimicrobial peptides (AMPs) could become the next generation antibiotic compounds which can overcome bacterial resistance by disrupting cell membranes and it is essential to …             Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinoceros ▶     Marlene Spinner, Alexander Kovalev, Stanislav N. Gorb et al.     The West African Gaboon viper (Bitis rhinoceros) is a master of camouflage due to its colouration pattern. Its skin is geometrically patterned and features black spots that …             Vibration driven vehicle inspired from grass spike ▶     Suo Bai, Qi Xu, Yong Qin     Searching and detecting in some harsh environments such as collapsed buildings, pipes, small cracks are crucial for human rescue and industrial detection, military surveillance …             Highly Rapid Amplification-Free and Quantitative DNA Imaging Assay ▶     Tobias Klamp, Marta Camps, Benjamin Nieto et al.     There is an urgent need for rapid and highly sensitive detection of pathogen-derived DNA in a point-of-care (POC) device for diagnostics in hospitals and clinics. This device …             Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease ▶     Jinfeng Wang, Ji Qi, Hui Zhao et al.     Although attempts have been made to reveal the relationships between bacteria and human health, little is known about the species and function of the microbial community …             Extended Stokes Shift in Fluorescent Proteins: Chromophore–Protein Interactions in a Near-Infrared TagRFP675 Variant ▶     Kiryl D. Piatkevich, Vladimir N. Malashkevich, Kateryna S. Morozova et al.     Most GFP-like fluorescent proteins exhibit small Stokes shifts (10–45 nm) due to rigidity of the chromophore environment that excludes non-fluorescent relaxation to a ground …             Common and distinct mechanisms of activation of rhodopsin and other G protein-coupled receptors ▶     Sumire Nakamura, Takeshi Itabashi, Daisuke Ogawa et al.     Detailed and systematic examination of high-resolution structural data is a rational strategy for understanding the function of biological macromolecules. G protein-coupled …             DEVD-Based Hydrogelator Minimizes Cellular Apoptosis Induction ▶     An-Ming Tang, Wei-Juan Wang, Bin Mei et al.     Herein, we report the rational design of a DEVD-based heptapeptide hydrogelator 1 which is susceptible to caspase-3 (CASP3), and its isomeric control hydrogelator 2 with a …             Virus-based Photo-Responsive Nanowires Formed By Linking Site-Directed Mutagenesis and Chemical Reaction ▶     Murali Murugesan, Gopal Abbineni, Susan L. Nimmo et al.     Owing to the genetic flexibility and error-free bulk production, bio-nanostructures such as filamentous phage showed great potential in materials synthesis, however, their …             Microtubule Alterations Occur Early in Experimental Parkinsonism and The Microtubule Stabilizer Epothilone D Is Neuroprotective ▶     Daniele Cartelli, Francesca Casagrande, Carla Letizia Busceti et al.     The role of microtubule (MT) dysfunction in Parkinson's disease is emerging. It is still unknown whether it is a cause or a consequence of neurodegeneration. Our objective was to …             A Novel Vitreous Substitute of Using a Foldable Capsular Vitreous Body Injected with Polyvinylalcohol Hydrogel ▶     Songfu Feng, Han Chen, Yaqin Liu et al.     Hydrogels may be the ideal vitreous substitutes due to their wonderful physical features and biocompatibility. However, their drawbacks, short residence time, and biodegradation …             A Coarse-Grained Protein Model in a Water-like Solvent ▶     Sumit Sharma, Sanat K. Kumar, Sergey V. Buldyrev et al.     Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent …             Improved adeno-associated virus (AAV) serotype 1 and 5 vectors for gene therapy ▶     Dwaipayan Sen, Balaji Balakrishnan, Nishanth Gabriel et al.     Despite significant advancements with recombinant AAV2 or AAV8 vectors for liver directed gene therapy in humans, it is well-recognized that host and vector-related immune …             Patterning of Regional Gene Expression in Autism: New Complexity ▶     Matthew R. Ginsberg, Robert A. Rubin, Marvin R. Natowicz     Autism is a common and often severe neurodevelopmental disorder for which diverse pathophysiological processes have been proposed. Recent gene expression data comparing autistic …             Pan-neuronal maturation but not neuronal subtype differentiation of adult neural stem cells is mechanosensitive ▶     Albert J. Keung, Meimei Dong, David V. Schaffer et al.     Most past studies of the biophysical regulation of stem cell differentiation have focused on initial lineage commitment or proximal differentiation events. It would be valuable to …             Adjunctive immunotherapy with α-crystallin based DNA vaccination reduces Tuberculosis chemotherapy period in chronically infected mice ▶     Priyanka Chauhan, Ruchi Jain, Bappaditya Dey et al.     By employing modified Cornell model, we have evaluated the potential of adjunctive immunotherapy with DNA vaccines to shorten the tuberculosis chemotherapy period and reduce …             A six-plex proteome quantification strategy reveals the dynamics of protein turnover ▶     Fangjun Wang, Kai Cheng, Xiaoluan Wei et al.     MS1 full scan based quantification is one of the most popular approaches for large-scale proteome quantification. Typically only three different samples can be differentially …             Antigenically intact hemagglutinin in circulating avian and swine influenza viruses and potential for H3N2 pandemic ▶     Kannan Tharakaraman, Rahul Raman, Nathan W. Stebbins et al.     The 2009 swine-origin H1N1 influenza, though antigenically novel to the population at the time, was antigenically similar to the 1918 H1N1 pandemic influenza, and consequently was …             Microfluidic Chemotaxis Platform for Differentiating the Roles of Soluble and Bound Amyloid-β on Microglial Accumulation ▶     Hansang Cho, Tadafumi Hashimoto, Elisabeth Wong et al.     Progressive microglial accumulation at amyloid-β (Aβ) plaques is a well-established signature of the pathology of Alzheimer's disease, but how and why microglia accumulate in the …             Arctic-nesting birds find physiological relief in the face of trophic constraints ▶     Laura McKinnon, Erica Nol, Cédric Juillet     A climate-induced phenological mismatch between the timing of reproduction and the timing of food resource peaks is one of the key hypothesized effects of climate change on …             Adaptor protein complexes-1 and 3 are involved at distinct stages of flavivirus life-cycle ▶     Tanvi Agrawal, Peter Schu, Guruprasad R. Medigeshi     Intracellular protein trafficking pathways are hijacked by viruses at various stages of viral life-cycle. Heterotetrameric adaptor protein complexes (APs) mediate vesicular …             Aging-associated excess formaldehyde leads to spatial memory deficits ▶     Zhiqian Tong, Chanshuai Han, Wenhong Luo et al.     Recent studies show that formaldehyde participates in DNA demethylation/methylation cycle. Emerging evidence identifies that neuronal activity induces global DNA demethylation and …             S-nitrosylation of ERK inhibits ERK phosphorylation and induces apoptosis ▶     Xiujing Feng, Tingzhe Sun, Yuncheng Bei et al.     Extracellular signal-regulated kinase (ERK) belongs to the mitogen-activated protein kinases (MAPK) superfamily. Aberrant upregulation and activation of ERK cascades may often …             Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy ▶     Libo Yuan, Tian Tian, Yuqi Chen et al.     Existence of G-quadruplex DNA in vivo always attract widespread interest in the field of biology and biological chemistry. We reported our findings for the existence of …             Migrating Oligodendrocyte Progenitor Cells Swell Prior to Soma Dislocation ▶     Patrick Happel, Kerstin Möller, Nina K. Schwering et al.     The migration of oligodendrocyte progenitor cells (OPCs) to the white matter is an indispensable requirement for an intact brain function. The mechanism of cell migration in …             The benefits of selecting phenotype-specific variants for applications of mixed models in genomics ▶     Christoph Lippert, Gerald Quon, Eun Yong Kang et al.     Applications of linear mixed models (LMMs) to problems in genomics include phenotype prediction, correction for confounding in genome-wide association studies, estimation of …             Molecular evolution of human adenoviruses ▶     Christopher M. Robinson, Gurdeep Singh, Jeong Yoon Lee et al.     The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality …             Prominent role for T cell-derived Tumour Necrosis Factor for sustained control of Mycobacterium tuberculosis infection ▶     Nasiema Allie, Sergei I. Grivennikov, Roanne Keeton et al.     Tumour Necrosis Factor (TNF) is critical for host control of M. tuberculosis, but the relative contribution of TNF from innate and adaptive immune responses during tuberculosis …             DDA3 associates with microtubule plus ends and orchestrates microtubule dynamics and directional cell migration ▶     Liangyu Zhang, Hengyi Shao, Tongge Zhu et al.     Cell motility and adhesion involve orchestrated interaction of microtubules (MTs) with their plus-end tracking proteins (TIPs). However, the mechanisms underlying regulations of …             InterMOD: integrated data and tools for the unification of model organism research ▶     Julie Sullivan, Kalpana Karra, Sierra A. T. Moxon et al.     Model organisms are widely used for understanding basic biology, and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided …             An ab-initio Computational Method to Determine Dielectric Properties of Biological Materials ▶     Chathurika D. Abeyrathne, Malka N. Halgamuge, Peter M. Farrell et al.     Frequency dependent dielectric properties are important for understanding the structure and dynamics of biological materials. These properties can be used to study underlying …             Destruction of Tissue, Cells and Organelles in Type 1 Diabetic Rats Presented at Macromolecular Resolution ▶     Raimond B. G. Ravelli, Ruby D. Kalicharan, M. Cristina Avramut et al.     Finding alternatives for insulin therapy and making advances in etiology of type 1 diabetes benefits from a full structural and functional insight into Islets of Langerhans. …             A novel cognitive-neurophysiological state biomarker in premanifest Huntington's disease validated on longitudinal data ▶     Christian Beste, Ann-Kathrin Stock, Vanessa Ness et al.     In several neurodegenerative diseases, like Huntington's disease (HD), treatments are still lacking. To determine whether a treatment is effective, sensitive disease progression …             Dating human cultural capacity using phylogenetic principles ▶     J. Lind, P. Lindenfors, S. Ghirlanda et al.     Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term “cultural capacity”. The age of this capacity has for long …             Tetraspanin-13 modulates voltage-gated CaV2.2 Ca2+ channels ▶     Robert T. Mallmann, Thomas Wilmes, Lucia Lichvarova et al.     Integration of voltage-gated Ca2 channels in a network of protein-interactions is a crucial requirement for proper regulation of channel activity. In this study, we took advantage …             Muscular senescence in cetaceans: adaptation towards a slow muscle fibre phenotype ▶     Eva Sierra, Antonio Fernández, Antonio Espinosa de los Monteros et al.     Sarcopenia, or senile muscle atrophy, is the slow and progressive loss of muscle mass with advancing age that constitutes the most prevalent form of muscle atrophy. The effects of …             Bivalve network reveals latitudinal selectivity gradient at the end-Cretaceous mass extinction ▶     Daril A. Vilhena, Elisha B. Harris, Carl T. Bergstrom et al.     Biogeographic patterns of survival help constrain the causal factors responsible for mass extinction. To test whether biogeography influenced end-Cretaceous (K-Pg) extinction …             Discrete Event Simulation Model of Sudden Cardiac Death Predicts High Impact of Preventive Interventions ▶     Victor P. Andreev, Trajen Head, Neil Johnson et al.     Sudden Cardiac Death (SCD) is responsible for at least 180,000 deaths a year and incurs an average cost of $286 billion annually in the United States alone. Herein, we present a …             Diagnosis of schistosomiasis japonica with interfacial co-assembly-based multi-channel electrochemical immunosensor arrays ▶     Wangping Deng, Bin Xu, Haiyan Hu et al.     Schistosomiasis control remains to be an important and challenging task in the world. However, lack of quick, simple, sensitive and specific sero-diagnostic test is still a hurdle …             Deleterious effect of suboptimal diet on rest-activity cycle in Anastrepha ludens manifests itself with age ▶     Joanna C. Chiu, Kevin Kaub, Sige Zou et al.     Activity patterns and sleep-wake cycles are among the physiological processes that change most prominently as animals age, and are often good indicators of healthspan. In this …             High risk of extinction of benthic foraminifera in this century due to ocean acidification ▶     S. Uthicke, P. Momigliano, K. E. Fabricius     Increased atmospheric CO2 concentrations lead to decreased pH and carbonate availability in the ocean (Ocean Acidification, OA). Carbon dioxide seeps serve as ‘windows into the …             Antiproton induced DNA damage: proton like in flight, carbon-ion like near rest ▶     J. N. Kavanagh, F. J. Currell, D. J. Timson et al.     Biological validation of new radiotherapy modalities is essential to understand their therapeutic potential. Antiprotons have been proposed for cancer therapy due to enhanced dose …             Observation of mesenteric microcirculatory disturbance in rat by laser oblique scanning optical microscopy ▶     Yichen Ding, Yu Zhang, Tong Peng et al.     Ischemia-reperfusion (I/R) injury model has been widely applied to the study of microcirculation disturbance. In this work, we used laser oblique scanning optical microscopy …             Underground hibernation in a primate ▶     Marina B. Blanco, Kathrin H. Dausmann, Jean F. Ranaivoarisoa et al.     Hibernation in mammals is a remarkable state of heterothermy wherein metabolic rates are reduced, core body temperatures reach ambient levels, and key physiological functions are …             Relationship between container ship underwater noise levels and ship design, operational and oceanographic conditions ▶     Megan F. McKenna, Sean M. Wiggins, John A. Hildebrand     Low-frequency ocean ambient noise is dominated by noise from commercial ships, yet understanding how individual ships contribute deserves further investigation. This study …                         Scientific Reports is accepting submissions from all scientific fields. 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