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

02 December 2013      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports         A systems engineering perspective on homeostasis and disease (open access) In this article from Frontiers in Bioengineering and Biotechnology, Ioannis P Androulakis and colleagues draw analogies between concepts in systems engineering and conceptual models of health and disease; establish connections between these concepts and physiologic modelling; and describe how these mirror onto the physiological counterparts of engineered systems.           Biological Sciences               Development of novel DNA vaccine for VEGF in murine cancer model ▶     Mariko Kyutoku, Hironori Nakagami, Hiroshi Koriyama et al.     We developed DNA vaccine for vascular endothelial growth factor (VEGF), which may provide the therapeutic option instead of anti-VEGF antibody, bevacizumab. Plasmid containing …             CORRIGENDUM: GSTM1 and GSTT1 null polymorphisms and male infertility risk: an updated meta-analysis encompassing 6934 subjects ▶     Wei Wu, Jing Lu, Qiuqin Tang et al.                 Heart rates increase after hatching in two species of natricine snakes ▶     Fabien Aubret     Experimental studies have shown heart rates to decrease from embryo to hatchling stage in turtles, remain steady in skinks, and increase in birds. However, no snake species has …             Cell electrofusion using nanosecond electric pulses ▶     Lea Rems, Marko Ušaj, Maša Kandušer et al.     Electrofusion is an efficient method for fusing cells using short-duration high-voltage electric pulses. However, electrofusion yields are very low when fusion partner cells …             Auraptenol attenuates vincristine-induced mechanical hyperalgesia through serotonin 5-HT1A receptors ▶     Yunfei Wang, Shu-e Cao, Jianmin Tian et al.     Common chemotherapeutic agents such as vincristine often cause neuropathic pain during cancer treatment in patients. Such neuropathic pain is refractory to common analgesics and …             Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity ▶     Tetsushi Sakuma, Hiroshi Ochiai, Takehito Kaneko et al.     Transcription activator-like effector (TALE) nuclease (TALEN) is a site-specific nuclease, which can be freely designed and easily constructed. Numerous methods of constructing …             Biomarker-guided translation of brain imaging into disease pathway models ▶     Erfan Younesi, Martin Hofmann-Apitius     The advent of state-of-the-art brain imaging technologies in recent years and the ability of such technologies to provide high-resolution information at both structural and …             Chitosan Coupling Makes Microbial Biofilms Susceptible to Antibiotics ▶     Amin Zhang, Haibo Mu, Wuxia Zhang et al.     Microbial biofilms, prevalent in nature and inherently resistant to both antimicrobial agents and host defenses, can cause serious problems in the chemical, medical and …             Identification of breast cancer patients based on human signaling network motifs ▶     Lina Chen, Xiaoli Qu, Mushui Cao et al.     Identifying breast cancer patients is crucial to the clinical diagnosis and therapy for this disease. Conventional gene-based methods for breast cancer diagnosis ignore gene-gene …             Plasma long-chain free fatty acids predict mammalian longevity ▶     Mariona Jové, Alba Naudí, Juan Carlos Aledo et al.     Membrane lipid composition is an important correlate of the rate of aging of animals and, therefore, the determination of their longevity. In the present work, the use of …             Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages ▶     Dáithí C. Murray, James Haile, Joe Dortch et al.     Highly fragmented and morphologically indistinct fossil bone is common in archaeological and paleontological deposits but unfortunately it is of little use in compiling faunal …             Sustained protection against Ebola virus infection following treatment of infected nonhuman primates with ZMAb ▶     Xiangguo Qiu, Jonathan Audet, Gary Wong et al.     Ebola virus (EBOV) is one of the most lethal filoviruses, with mortality rates of up to 90% in humans. Previously, we demonstrated 100% and 50% survival of EBOV-infected …             Anthocyanin-dependent anoxygenic photosynthesis in coloured flower petals? ▶     Vladimir Lysenko, Tatyana Varduny     Chlorophylless flower petals are known to be composed of non-photosynthetic tissues. Here, we show that the light energy storage that can be photoacoustically measured in flower …             Common and distinct structural features of Salmonella injectisome and flagellar basal body ▶     Akihiro Kawamoto, Yusuke V. Morimoto, Tomoko Miyata et al.     Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and injectisome export their component proteins for …             Mammalian Mon2/Ysl2 regulates endosome-to-Golgi trafficking but possesses no guanine nucleotide exchange activity toward Arl1 GTPase ▶     Divyanshu Mahajan, Boon Kim Boh, Yan Zhou et al.     Arl1 is a member of Arf family small GTPases that is essential for the organization and function of Golgi complex. Mon2/Ysl2, which shares significant homology with Sec7 family …             High-density distributed electrode network, a multi-functional electroporation method for delivery of molecules of different sizes ▶     Mengxi Wu, Deyao Zhao, Wenfeng Zhong et al.     We present a multi-functional electroporation method for delivery of biomolecule utilizing a high-density distributed electrode network (HDEN) under tri-phase electric …             Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture ▶     Carola Ingrid Weidner, Thomas Walenda, Qiong Lin et al.     Hematopoietic stem and progenitor cells (HPCs) can be maintained in vitro, but the vast majority of their progeny loses stemness during culture. In this study, we compared …             Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool ▶     Yasmine M. Mohamed, Mohamed A. Ghazy, Ahmed Sayed et al.     The Red Sea Atlantis II brine pool is an extreme environment that displays multiple harsh conditions such as high temperature, high salinity and high concentrations of multiple, …             The influence of the wind in the Schmallenberg virus outbreak in Europe ▶     Luigi Sedda, David J. Rogers     A model previously developed for the wind-borne spread by midges of bluetongue virus in NW Europe in 2006 is here modified and applied to the spread of Schmallenberg virus in …             Polymer-Free Optode Nanosensors for Dynamic, Reversible, and Ratiometric Sodium Imaging in the Physiological Range ▶     Timothy T. Ruckh, Ankeeta A. Mehta, J. Matthew Dubach et al.     This work introduces a polymer-free optode nanosensor for ratiometric sodium imaging. Transmembrane ion dynamics are often captured by electrophysiology and calcium imaging, but …             The oldest known communal latrines provide evidence of gregarism in Triassic megaherbivores ▶     Lucas E. Fiorelli, Martín D. Ezcurra, E. Martín Hechenleitner et al.     Defecation in communal latrines is a common behaviour of extant mammals widely distributed among megaherbivores. This behaviour has key social functions with important biological …             Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples ▶     Marie Renault, Laetitia Shintu, Martial Piotto et al.     High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. …             Cognitive factors correlating with the metacognition of the phenomenal properties of experience ▶     Ken Mogi     The awareness of the phenomenal qualities of one's experiences can be considered as an instance of metacognition. Although some people take qualia (sensory qualities such as the …             Generation of mutant mice by pronuclear injection of circular plasmid expressing Cas9 and single guided RNA ▶     Daisuke Mashiko, Yoshitaka Fujihara, Yuhkoh Satouh et al.     CRISPR/Cas mediated genome editing has been successfully demonstrated in mammalian cells and further applications for generating mutant mice were reported by injecting humanized …             C. elegans sensing of and entrainment along obstacles require different neurons at different body locations ▶     Seong-Won Nam, Chen Qian, So Hyun Kim et al.     We probe C. elegans mechanosensation using a microfabricated platform where worms encounter a linear array of asymmetric funnel-like barriers. We found that sensing of and moving …             Soluble expression of proteins correlates with a lack of positively-charged surface ▶     Pedro Chan, Robin A. Curtis, Jim Warwicker     Prediction of protein solubility is gaining importance with the growing use of protein molecules as therapeutics, and ongoing requirements for high level expression. We have …             New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis ▶     Yuji Tomaru, Kensuke Toyoda, Hidekazu Suzuki et al.     Diatoms are among the most abundant organisms in nature; however, their relationships with single-stranded DNA (ssDNA) viruses have not yet been defined in detail. We report the …             Modifying cellular properties using artificial aptamer-lipid receptors ▶     Meghan O. Altman, Yun Min Chang, Xiangling Xiong et al.     We demonstrate that artificial aptamer-lipid receptors (AR), which anchor on the surface of cells, can modify important cellular functions, including protein binding, enzymatic …             TSP1-producing B cells show immune regulatory property and suppress allergy-related mucosal inflammation ▶     Huan-Ping Zhang, Yingying Wu, Jiangqi Liu et al.     Specific immunotherapy (SIT) is the only specific remedy for the treatment of allergic diseases currently. B cells are important immune cells in the immunity. The role of B cells …             hERG1 channels modulate integrin signaling to trigger angiogenesis and tumor progression in colorectal cancer ▶     Olivia Crociani, Francesca Zanieri, Serena Pillozzi et al.     Angiogenesis is a potential target for cancer therapy. We identified a novel signaling pathway that sustains angiogenesis and progression in colorectal cancer (CRC). This pathway …             A novel platform to enable inhaled naked RNAi medicine for lung cancer ▶     Yu Fujita, Fumitaka Takeshita, Takayuki Mizutani et al.     Small interfering RNA (siRNA)-based therapeutics have been used in humans and offer distinct advantages over traditional therapies. However, previous investigations have shown …             Isolation, identification and expression of specific human CD133 antibodies ▶     Jing Xia, Ying Zhang, Jun Qian et al.     CD133, a 120 KDa glycoprotein is a transmembrane glycoprotein which has been recently used as a cancer stem cell (CSCs) marker in a variety of carcinomas. CD133 cells possess …             Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya ▶     Steffen Borrmann, Judith Straimer, Leah Mwai et al.     Early identification of causal genetic variants underlying antimalarial drug resistance could provide robust epidemiological tools for timely public health interventions. Using a …             Stationary distribution of self-organized states and biological information generation ▶     Hyung Jun Woo     Self-organization, where spontaneous orderings occur under driven conditions, is one of the hallmarks of biological systems. We consider a statistical mechanical treatment of the …             CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research ▶     Julie Sullivan, Kalpana Karra, Sierra A. T. Moxon et al.                 ERRATUM: Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions ▶     Shinsuke Ishigaki, Akio Masuda, Yusuke Fujioka et al.                 ERRATUM: FUS-regulated region- and cell-type-specific transcriptome is associated with cell selectivity in ALS/FTLD ▶     Yusuke Fujioka, Shinsuke Ishigaki, Akio Masuda et al.                 Effects of Bio-Au Nanoparticles on Electrochemical Activity of Shewanella oneidensis Wild Type and ΔomcA/mtrC Mutant ▶     Ranran Wu, Li Cui, Lixiang Chen et al.     Both Shewanella oneidensis MR-1 wild type and its mutant ΔomcA/mtrC are capable of transforming AuIII into Au nanoparticles (AuNPs). Cyclic voltammetry reveals a decrease in redox …             CORRIGENDUM: Nature of hardness evolution in nanocrystalline NiTi shape memory alloys during solid-state phase transition ▶     Abbas Amini, Chun Cheng                 Flood-tolerant rice reduces yield variability and raises expected yield, differentially benefitting socially disadvantaged groups ▶     Manzoor H. Dar, Alain de Janvry, Kyle Emerick et al.     Approximately 30% of the cultivated rice area in India is prone to crop damage from prolonged flooding. We use a randomized field experiment in 128 villages of Orissa India to …             Rediscovering the genus Lyticum, multiflagellated symbionts of the order Rickettsiales ▶     Vittorio Boscaro, Martina Schrallhammer, Konstantin A. Benken et al.     Among the bacterial symbionts harbored by the model organism Paramecium, many still lack a recent investigation that includes a molecular characterization. The genus Lyticum …             ERRATUM: Uniform magnetization transfer in chemical exchange saturation transfer magnetic resonance imaging ▶     Jae-Seung Lee, Prodromos Parasoglou, Ding Xia et al.                 HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor ▶     Kotaro Sakata, Mitsuko Hara, Takaho Terada et al.     Viruses sometimes mimic host proteins and hijack the host cell machinery. Hepatitis C virus (HCV) causes liver fibrosis, a process largely mediated by the overexpression of …             Specific Plasma Autoantibody Reactivity in Myelodysplastic Syndromes ▶     George I. Mias, Rui Chen, Yan Zhang et al.     Increased autoantibody reactivity in plasma from Myelodysplastic Syndromes (MDS) patients may provide novel disease signatures, and possible early detection. In a two-stage study …             Surface Charges and Shell Crosslinks Each Play Significant Roles in Mediating Degradation, Biofouling, Cytotoxicity and Immunotoxicity for Polyphosphoester-based Nanoparticles ▶     Mahmoud Elsabahy, Shiyi Zhang, Fuwu Zhang et al.     The construction of nanostructures from biodegradable precursors and shell/core crosslinking have been pursued as strategies to solve the problems of toxicity and limited …             Coexistence of sexual individuals and genetically isolated asexual counterparts in a thrips ▶     Kazuya Kobayashi, Jin Yoshimura, Eisuke Hasegawa     Sex is a paradoxical phenomenon because it is less efficient compared with asexual reproduction. To resolve this paradox we need a direct comparison between sexual and asexual …             Fluorescent silk cocoon creating fluorescent diatom using a “Water glass-fluorophore ferry” ▶     Tejas S. Kusurkar, Ishita Tandon, Niroj Kumar Sethy et al.     Fluorophores are ubiquitous in nature. Naturally occurring fluorophores are exceptionally stable and have high quantum yield. Several natural systems have acquired fluorescent …             Structure of the RecQ C-terminal Domain of Human Bloom Syndrome Protein ▶     Sun-Yong Kim, Toshio Hakoshima, Ken Kitano     Bloom syndrome is a rare genetic disorder characterized by genomic instability and cancer predisposition. The disease is caused by mutations of the Bloom syndrome protein (BLM). …             Fast targeted gene transfection and optogenetic modification of single neurons using femtosecond laser irradiation ▶     Maciej Antkowiak, Maria Leilani Torres-Mapa, Emily C. Witts et al.     A prevailing problem in neuroscience is the fast and targeted delivery of DNA into selected neurons. The development of an appropriate methodology would enable the transfection of …             Ocean acidification reverses competition for space as habitats degrade ▶     Mark I. McCormick, Sue-Ann Watson, Philip L. Munday     How marine communities are affected by CO2-induced climate change depends on the ability of species to tolerate or adapt to the new conditions, and how the altered characteristics …             AGO61-dependent GlcNAc modification primes the formation of functional glycans on α-dystroglycan ▶     Hirokazu Yagi, Naoki Nakagawa, Takuya Saito et al.     Dystroglycanopathy is a major class of congenital muscular dystrophy that is caused by a deficiency of functional glycans on α-dystroglycan (α-DG) with laminin-binding activity. A …             Ingested plastic transfers hazardous chemicals to fish and induces hepatic stress ▶     Chelsea M. Rochman, Eunha Hoh, Tomofumi Kurobe et al.     Plastic debris litters aquatic habitats globally, the majority of which is microscopic (< 1 mm), and is ingested by a large range of species. Risks associated with such small …             Ternary Composite of Hemin, Gold Nanoparticles and Graphene for Highly Efficient Decomposition of Hydrogen Peroxide ▶     Xincong Lv, Jian Weng     A ternary composite of hemin, gold nanoparticles and graphene is prepared by a two-step process. Firstly, graphene-hemin composite is synthesized through π-π interaction and then …             DNA Translocation through Hydrophilic Nanopore in Hexagonal Boron Nitride ▶     Zhi Zhou, Ying Hu, Hao Wang et al.     Ultra-thin solid-state nanopore with good wetting property is strongly desired to achieve high spatial resolution for DNA sequencing applications. Atomic thick hexagonal boron …             Braess's Paradox in Epidemic Game: Better Condition Results in Less Payoff ▶     Hai-Feng Zhang, Zimo Yang, Zhi-Xi Wu et al.     Facing the threats of infectious diseases, we take various actions to protect ourselves, but few studies considered an evolving system with competing strategies. In view of that, …             Knockout of an endogenous mannosyltransferase increases the homogeneity of glycoproteins produced in Pichia pastoris ▶     Florian W. Krainer, Christoph Gmeiner, Lukas Neutsch et al.     The yeast Pichia pastoris is a common host for the recombinant production of biopharmaceuticals, capable of performing posttranslational modifications like glycosylation of …             Lipidomics analysis revealed the phospholipid compositional changes in muscle by chronic exercise and high-fat diet ▶     Naoko Goto-Inoue, Kenichiro Yamada, Akiko Inagaki et al.     Although it is clear that lipids are responsible for insulin resistance, it is poorly understood what types of lipids are involved. In this study, we verified the characteristic …             Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy ▶     Clara Sousa, Ângela Novais, Ana Magalhães et al.     We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from …             DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells ▶     Anna M. Sokol, Séverine Cruet-Hennequart, Philippe Pasero et al.     Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of …             CORRIGENDUM: Lab on a Biomembrane: Rapid prototyping and manipulation of 2D fluidic lipid bilayer circuits ▶     Alar Ainla, Irep Gözen, Bodil Hakonen et al.                 Glutathionylation potentiates benign superoxide dismutase 1 variants to the toxic forms associated with amyotrophic lateral sclerosis ▶     Luke McAlary, Justin J. Yerbury, J. Andrew Aquilina     Dissociation of superoxide dismutase 1 dimers is enhanced by glutathionylation, although the dissociation constants reported to date are imprecise. We have quantified the discreet …             Oral ‘hydrogen water’ induces neuroprotective ghrelin secretion in mice ▶     Akio Matsumoto, Megumi Yamafuji, Tomoko Tachibana et al.     The therapeutic potential of molecular hydrogen (H2) is emerging in a number of human diseases and in their animal models, including in particular Parkinson's disease (PD). H2 …             Biofuel Cell Based on Microscale Nanostructured Electrodes with Inductive Coupling to Rat Brain Neurons ▶     Viktor Andoralov, Magnus Falk, Dmitry B. Suyatin et al.     Miniature, self-contained biodevices powered by biofuel cells may enable a new generation of implantable, wireless, minimally invasive neural interfaces for neurophysiological in …             Multiple leading edge vortices of unexpected strength in freely flying hawkmoth ▶     L. Christoffer Johansson, Sophia Engel, Almut Kelber et al.     The Leading Edge Vortex (LEV) is a universal mechanism enhancing lift in flying organisms. LEVs, generally illustrated as a single vortex attached to the wing throughout the …             The Role of Shape Complementarity in the Protein-Protein Interactions ▶     Ye Li, Xianren Zhang, Dapeng Cao     We use a dissipative particle dynamic simulation to investigate the effects of shape complementarity on the protein-protein interactions. By monitoring different kinds of protein …             Cysteinyl leukotrienes regulate endothelial cell inflammatory and proliferative signals through CysLT2 and CysLT1 receptors ▶     Ernest Duah, Ravi K. Adapala, Nosayba Al-Azzam et al.     Cysteinyl leukotrienes (cys-LTs), LTC4, LTD4, LTE4 are potent inflammatory lipid mediators that act through two distinct G-protein-coupled receptors, CysLT1R and CysLT2R. Although …             Implantable fiber-optic interface for parallel multisite long-term optical dynamic brain interrogation in freely moving mice ▶     L. V. Doronina-Amitonova, I. V. Fedotov, O. I. Ivashkina et al.     Seeing the big picture of functional responses within large neural networks in a freely functioning brain is crucial for understanding the cellular mechanisms behind the higher …             Differences between chimpanzees and humans in visual temporal integration ▶     Tomoko Imura, Masaki Tomonaga     Humans have a superior ability to integrate spatially separate visual information into an entire image. In contrast, comparative cognitive studies have demonstrated that nonhuman …             Inflammation and Immune System Activation in Aging: A Mathematical Approach ▶     Jason B. Nikas     Memory and learning declines are consequences of normal aging. Since those functions are associated with the hippocampus, I analyzed the global gene expression data from …             The fungus-growing termite Macrotermes natalensis harbors bacillaene-producing Bacillus sp. that inhibit potentially antagonistic fungi ▶     Soohyun Um, Antoine Fraimout, Panagiotis Sapountzis et al.     The ancient fungus-growing termite (Mactrotermitinae) symbiosis involves the obligate association between a lineage of higher termites and basidiomycete Termitomyces cultivar …             Systematic reference sample generation for multiplexed serological assays ▶     Hannes Planatscher, Stefanie Rimmele, Gerd Michel et al.     Quality controls of serological assays have to contain defined amounts of human antibodies specific for the targeted antigen. A prevailing issue for array-based antigen assays is …             MafK positively regulates NF-κB activity by enhancing CBP-mediated p65 acetylation ▶     Yu-Jin Hwang, Eun-Woo Lee, Jaewhan Song et al.     Reactive oxygen species, produced by oxidative stress, initiate and promote many metabolic diseases through activation/suppression of redox-sensitive transcription factors. NF-κB …             In vivo pH monitoring using boron doped diamond microelectrode and silver needles: Application to stomach disorder diagnosis ▶     Stéphane Fierro, Ryo Seishima, Osamu Nagano et al.     This study presents the in vivo electrochemical monitoring of pH using boron doped diamond (BDD) microelectrode and silver needles for potential application in medical diagnosis. …             Modified nucleotides m2G966/m5C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon ▶     Irina V. Prokhorova, Ilya A. Osterman, Dmitry E. Burakovsky et al.     Ribosomes contain a number of modifications in rRNA, the function of which is unclear. Here we show – using proteomic analysis and dual fluorescence reporter in vivo assays – that …             Defining the expression hierarchy of latent T-cell epitopes in Epstein-Barr virus infection with TCR-like antibodies ▶     Adrian Chong Nyi Sim, Chien Tei Too, Min Zin Oo et al.     Epstein-Barr virus (EBV) is a gamma herpesvirus that causes a life-long latent infection in human hosts. The latent gene products LMP1, LMP2A and EBNA1 are expressed by …             Iron(II)-dependent dioxygenase and N-formylamide deformylase catalyze the reactions from 5-hydroxy-2-pyridone to maleamate ▶     Yuxiang Yao, Hongzhi Tang, Huixue Ren et al.     5-Hydroxy-2-pyridone (2,5-DHP) is a central metabolic intermediate in catabolism of many pyridine derivatives, and has been suggested as a potential carcinogen. 2,5-DHP is …             A molecular pathway for the egress of ammonia produced by nitrogenase ▶     Ian Dance     Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a …             mTOR plays critical roles in pancreatic cancer stem cells through specific and stemness-related functions ▶     Shyuichiro Matsubara, Qiang Ding, Yumi Miyazaki et al.     Pancreatic cancer is characterized by near-universal mutations in KRAS. The mammalian target of rapamycin (mTOR), which functions downstream of RAS, has divergent effects on stem …             Discovering disease-disease associations by fusing systems-level molecular data ▶     Marinka Žitnik, Vuk Janjić, Chris Larminie et al.     The advent of genome-scale genetic and genomic studies allows new insight into disease classification. Recently, a shift was made from linking diseases simply based on their …             Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation ▶     Kyuhyun Im, Daun Jeong, Jaehyun Hur et al.     Structural analysis of branched DNA molecules (BDM) is important as model systems for DNA junctions and also as building units for DNA assembly. Although there have been efforts …             Establishment of a Novel Lingual Organoid Culture System: Generation of Organoids Having Mature Keratinized Epithelium from Adult Epithelial Stem Cells ▶     Hiroko Hisha, Toshihiro Tanaka, Shohei Kanno et al.     Despite the strong need for the establishment of a lingual epithelial cell culture system, a simple and convenient culture method has not yet been established. Here, we report the …             Diapause, signal and molecular characteristics of overwintering Chilo suppressalis (Insecta: Lepidoptera: Pyralidae) ▶     Ming-Xing Lu, Shuang-Shuang Cao, Yu-Zhou Du et al.     Diapause is a complex and dynamic process. Chilo suppressalis, an important rice pest in Asia enters facultative diapause as larvae. Our results demonstrated in Yangzhou, China, …             к Opioids inhibit tumor angiogenesis by suppressing VEGF signaling ▶     Kohei Yamamizu, Sadayoshi Furuta, Yusuke Hamada et al.     Opioids are effective analgesics for the management of moderate to severe cancer pain. Here we show that κ opioid receptor (KOR) agonists act as anti-angiogenic factors in tumors. …             Zebularine inhibits tumorigenesis and stemness of colorectal cancer via p53-dependent endoplasmic reticulum stress ▶     Pei-Ming Yang, Yi-Ting Lin, Chia-Tung Shun et al.     Aberrant DNA hypermethylation is frequently found in tumor cells and inhibition of DNA methylation is an effective anticancer strategy. In this study, the therapeutic effect of …             Single-neuron criticality optimizes analog dendritic computation ▶     Leonardo L. Gollo, Osame Kinouchi, Mauro Copelli     Active dendritic branchlets enable the propagation of dendritic spikes, whose computational functions remain an open question. Here we propose a concrete function to the active …             The medaka mutation tintachina sheds light on the evolution of V-ATPase B subunits in vertebrates ▶     Claudia Müller, Ignacio Maeso, Joachim Wittbrodt et al.     Vacuolar-type H ATPases (V-ATPases) are multimeric protein complexes that play a universal role in the acidification of intracellular compartments in eukaryotic cells. We have …             A novel approach for separating bacteriophages from other bacteriophages using affinity chromatography and phage display ▶     Izabela Ceglarek, Agnieszka Piotrowicz, Dorota Lecion et al.     Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for …             The natural compound magnolol inhibits invasion and exhibits potential in human breast cancer therapy ▶     Ying Liu, Wei Cao, Bo Zhang et al.     Invasion and metastasis are the main causes of treatment failure and death in breast cancer. Thus, novel invasion-based therapies such as those involving natural agents are …             Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I ▶     Charanpreet Kaur, Anchal Vishnoi, Thilini Udayangani Ariyadasa et al.     Glyoxalase pathway plays an important role in stress adaptation and many clinical disorders. The first enzyme of this pathway, glyoxalase I (GlxI), uses methylglyoxal as a …             Integration of TiO2 into the diatom Thalassiosira weissflogii during frustule synthesis ▶     Yvonne Lang, Francisco del Monte, Brian J. Rodriguez et al.     Nature has inspired the design of complex hierarchical structures in the field of material science. Diatoms, unicellular algae with a hallmark intricate siliceous cell wall, have …             CORRIGENDUM: Nonlinear Growth Kinetics of Breast Cancer Stem Cells: Implications for Cancer Stem Cell Targeted Therapy ▶     Xinfeng Liu, Sara Johnson, Shou Liu et al.                 A DNA-based method for studying root responses to drought in field-grown wheat genotypes ▶     Chun Y. Huang, Haydn Kuchel, James Edwards et al.     Root systems are critical for water and nutrient acquisition by crops. Current methods measuring root biomass and length are slow and labour-intensive for studying root responses …             Characterization of the interaction between Toxoplasma gondii rhoptry neck protein 4 and host cellular β-tubulin ▶     Hitoshi Takemae, Tatsuki Sugi, Kyousuke Kobayashi et al.     Toxoplasma rhoptry neck protein 4 (TgRON4) is a component of the moving junction macromolecular complex that plays a central role during invasion. TgRON4 is exposed on the …             Cryptic speciation or global spread? The case of a cosmopolitan marine invertebrate with limited dispersal capabilities ▶     Pérez-Portela R., Arranz V., Rius M. et al.     The existence of globally-distributed species with low dispersal capabilities is a paradox that has been explained as a result of human-mediated transport and by hidden diversity …             Analyses of Interactions Between Heparin and the Apical Surface Proteins of Plasmodium falciparum ▶     Kyousuke Kobayashi, Ryo Takano, Hitoshi Takemae et al.     Heparin, a sulfated glycoconjugate, reportedly inhibits the blood-stage growth of the malaria parasite Plasmodium falciparum. Elucidation of the inhibitory mechanism is valuable …             Involvement of TrkB- and p75NTR-signaling pathways in two contrasting forms of long-lasting synaptic plasticity ▶     Shigeo Sakuragi, Keiko Tominaga-Yoshino, Akihiko Ogura     The repetition of experience is often necessary to establish long-lasting memory. However, the cellular mechanisms underlying this repetition-dependent consolidation of memory …             Molecular basis of wing coloration in a Batesian mimic butterfly, Papilio polytes ▶     Hideki Nishikawa, Masatoshi Iga, Junichi Yamaguchi et al.     Batesian mimicry protects animals from predators through resemblance with distasteful models in shape, color pattern, or behavior. To elucidate the wing coloration mechanisms …             Antitoxin MqsA Represses Curli Formation Through the Master Biofilm Regulator CsgD ▶     Valerie W. C. Soo, Thomas K. Wood     MqsA, the antitoxin of the MqsR/MqsA toxin/antitoxin (TA) system, is a global regulator that reduces expression of several stress response genes (e.g., mqsRA, cspD, and rpoS) by …             Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses ▶     Weipeng Zhang, Yong Wang, On On Lee et al.     Marine organisms in intertidal zones are subjected to periodical fluctuations and wave activities. To understand how microbes in intertidal biofilms adapt to the stresses, the …             Involvement of Mincle and Syk in the changes to innate immunity after ischemic stroke ▶     Yukiya Suzuki, Yusuke Nakano, Keisuke Mishiro et al.     Accumulating evidence shows that post-ischemic inflammation originated by Toll-like receptors (TLR) plays critical roles in ischemic stroke. However, the functions of other innate …             Live single cell functional phenotyping in droplet nano-liter reactors ▶     Tania Konry, Alexander Golberg, Martin Yarmush     While single cell heterogeneity is present in all biological systems, most studies cannot address it due to technical limitations. Here we describe a nano-liter droplet …             The importance of observation versus process error in analyses of global ungulate populations ▶     Farshid S. Ahrestani, Mark Hebblewhite, Eric Post     Population abundance data vary widely in quality and are rarely accurate. The two main components of error in such data are observation and process error. We used Bayesian state …             Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) ▶     Toshitsugu Fujita, Yoshinori Asano, Junko Ohtsuka et al.     Biochemical analysis of molecular interactions in specific genomic regions requires their isolation while retaining molecular interactions in vivo. Here, we report isolation of …             Antioxidant Induces DNA Damage, Cell Death and Mutagenicity in Human Lung and Skin Normal Cells ▶     Linda Y. Lu, Ning Ou, Qing-Bin Lu     Clinical trials have shown that antioxidant supplementation increased the risk of lung and skin cancers, but the underlying molecular mechanism is unknown. Here, we show that …             Enhanced transcription and translation in clay hydrogel and implications for early life evolution ▶     Dayong Yang, Songming Peng, Mark R. Hartman et al.     In most contemporary life forms, the confinement of cell membranes provides localized concentration and protection for biomolecules, leading to efficient biochemical reactions. …             Neural Mechanism for Sensing Fast Motion in Dim Light ▶     Ran Li, Yi Wang     Luminance is a fundamental property of visual scenes. A population of neurons in primary visual cortex (V1) is sensitive to uniform luminance. In natural vision, however, the …             Movement patterns of Tenebrio beetles demonstrate empirically that correlated-random-walks have similitude with a Lévy walk ▶     Andy M. Reynolds, Lisa Leprêtre, David A. Bohan     Correlated random walks are the dominant conceptual framework for modelling and interpreting organism movement patterns. Recent years have witnessed a stream of high profile …             A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras ▶     Hong Yan Liu, Xiaohu Gao     siRNA-aptamer chimeras have emerged as one of the most promising approaches for targeted delivery of siRNA due to the modularity of their diblock RNA structure, relatively lower …             Aggression and polymorphisms in AR, DAT1, DRD2, and COMT genes in Datoga pastoralists of Tanzania ▶     Marina L. Butovskaya, Vasiliy A. Vasilyev, Oleg E. Lazebny et al.     The aim of this study was to analyse the relationships between polymorphisms in four candidate genes (AR, DAT1, DRD2, and COMT) and aggression in men from a traditional society of …             Regulation of epithelial plasticity by miR-424 and miR-200 in a new prostate cancer metastasis model ▶     Jacqueline Banyard, Ivy Chung, Arianne M. Wilson et al.     Using an in vivo cycling strategy, we selected metastatic cancer cells from the lymph nodes (LN) of mice bearing orthotopic DU145 human prostate tumors. Repeated rounds of …             Homogeneous Expansion of Human T-Regulatory Cells Via Tumor Necrosis Factor Receptor 2 ▶     Yoshiaki Okubo, Toshiyuki Mera, Limei Wang et al.     T-regulatory cells (Tregs) are a rare lymphocyte subtype that shows promise for treating infectious disease, allergy, graft-versus-host disease, autoimmunity, and asthma. Clinical …             Analysis of an ethanol precipitate from ileal digesta: evaluation of a method to determine mucin ▶     Warren M. Miner-Williams, Paul J. Moughan, Malcolm F. Fuller     The precipitation of mucin using high concentrations of ethanol has been used by many researchers while others have questioned the validity of the technique. In this study, …             First Biosynthetic pathway of 1-hepten-3-one in Iporangaia pustulosa (Opiliones) ▶     Daniele F. O. Rocha, Felipe C. Wouters, Glauco Machado et al.     Arthropods produce a great variety of natural compounds, many of which have unexplored biosynthesis. Among the armored harvestmen (Arachnida: Opiliones) of the suborder …             The Retraction Penalty: Evidence from the Web of Science ▶     Susan Feng Lu, Ginger Zhe Jin, Brian Uzzi et al.     Scientific articles are retracted at increasing rates, with the highest rates among top journals. Here we show that a single retraction triggers citation losses through an …             Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection ▶     Akihisa Shimizu, Ai Kawana-Tachikawa, Atsushi Yamagata et al.     We investigated the crystal structure of an HLA-A*2402-restricted CTL epitope in the HIV-1 nef gene (Nef134-10) before (pHLA) or after TCR docking. The wild type epitope and two …             Microfluidic Preparation of Polymer-Nucleic Acid Nanocomplexes Improves Nonviral Gene Transfer ▶     Christopher L. Grigsby, Yi-Ping Ho, Chao Lin et al.     As the designs of polymer systems used to deliver nucleic acids continue to evolve, it is becoming increasingly apparent that the basic bulk manufacturing techniques of the past …             Modeling the effect of transient populations on epidemics in Washington DC ▶     Nidhi Parikh, Mina Youssef, Samarth Swarup et al.     Large numbers of transients visit big cities, where they come into contact with many people at crowded areas. However, epidemiological studies have not paid much attention to the …             Targeting human embryonic stem cells with quantum dot-conjugated phages ▶     Wenxiu Zhao, Lei Jin, Hang Yuan et al.     Targeting embryonic stem cells (ESCs) is important for ESC labeling, drug delivery and cell fate control. In this study, we identified twenty-two phage clones that bind …             Taxis Toward Hydrogen Gas by Methanococcus maripaludis ▶     Kristen A. Brileya, James M. Connolly, Carey Downey et al.     Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to …             Hydrogel-Stabilized Droplet Bilayers for High Speed Solution Exchange ▶     Shiv A. Acharya, Alexander Portman, Carl S. Salazar et al.     Many applications utilizing artificial lipid bilayers require the ability to exchange the bilayer's solution environment. However, because of the instability of the bilayer, the …             Production of Sry knockout mouse using TALEN via oocyte injection ▶     Tomoko Kato, Kohei Miyata, Miku Sonobe et al.     Recently developed transcription activator-like effector nuclease (TALEN) technology has enabled the creation of knockout mice, even for genes on the Y chromosome. In this study, …             Bitter melon extract attenuating hepatic steatosis may be mediated by FGF21 and AMPK/Sirt1 signaling in mice ▶     Yongmei Yu, Xian H. Zhang, Blake Ebersole et al.     We sought to evaluate the effects of Momordica charantia (bitter melon, BM) extract on insulin sensitivity, NAFLD, hepatic FGF21 and AMPK signaling in mice fed a high-fat diet. …             Ancient DNA and Population Turnover in Southern Levantine Pigs- Signature of the Sea Peoples Migration? ▶     Meirav Meiri, Dorothée Huchon, Guy Bar-Oz et al.     Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand …             Prohibitin is associated with antioxidative protection in hypoxia/reoxygenation-induced renal tubular epithelial cell injury ▶     Tian-Biao Zhou, Yuan-Han Qin, Feng-Ying Lei et al.     Prohibitin is an evolutionary conserved and pleiotropic protein that has been implicated in various cellular functions, including proliferation, tumour suppression, apoptosis, …             CDKAL1 gene rs7756992 A/G polymorphism and type 2 diabetes mellitus: a meta-analysis of 62,567 subjects ▶     Yan-yan Li, Lian-sheng Wang, Xin-zheng Lu et al.     The Cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like (CDKAL1) gene rs7756992 A/G polymorphism has been suggested to be associated with type 2 diabetes …             Horseradish Peroxidase Inactivation: Heme Destruction and Influence of Polyethylene Glycol ▶     Liang Mao, Siqiang Luo, Qingguo Huang et al.     Horseradish peroxidase (HRP) mediates efficient conversion of many phenolic contaminants and thus has potential applications for pollution control. Such potentially important …             Crosstalk between Second Messengers Predicts the Motility of the Growth Cone ▶     Takahiko Kobayashi, Fumiaki Nagase, Kohji Hotta et al.     Axon guidance involves multiple second messenger signal transduction pathways. Although each signal transduction pathway has been characterized, only a few studies have examined …             Temporal-spatial heterogeneity in animal-environment contact: Implications for the exposure and transmission of pathogens ▶     Shi Chen, Michael W. Sanderson, Brad J. White et al.     Contact structure, a critical driver of infectious disease transmission, is not completely understood and characterized for environmentally transmitted pathogens. In this study, …             Optical imaging to map blood-brain barrier leakage ▶     Hayder Jaffer, Isaac M. Adjei, Vinod Labhasetwar     Vascular leakage in the brain is a major complication associated with brain injuries and certain pathological conditions due to disruption of the blood-brain barrier (BBB). We …             Increased tissue levels of omega-3 polyunsaturated fatty acids prevents pathological preterm birth ▶     Aki Yamashita, Kei Kawana, Kensuke Tomio et al.     Omega-3 polyunsaturated fatty acids such as eicosapentaenoic acid (EPA) have anti-inflammatory effects. Preterm birth is an important problem in modern obstetrics and one of the …             ABCC3 as a marker for multidrug resistance in non-small cell lung cancer ▶     Yanbin Zhao, Hailing Lu, An Yan et al.     Multidrug resistance (MDR) contributes to the failure of chemotherapy and high mortality in non-small cell lung cancer (NSCLC). We aim to identify MDR genes that predict tumor …             ERRATUM: H+-type and OH−-type biological protonic semiconductors and complementary devices ▶     Yingxin Deng, Erik Josberger, Jungho Jin et al.                 Firmicutes dominate the bacterial taxa within sugar-cane processing plants ▶     Farhana Sharmin, Steve Wakelin, Flavia Huygens et al.     Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial …             TRPA1 detects environmental chemicals and induces avoidance behavior and arousal from sleep ▶     Toru Yonemitsu, Chiharu Kuroki, Nobuaki Takahashi et al.     Detecting threats and escaping before serious confrontations are important for animals to avoid danger and death. Transient receptor potential ankyrin 1 (TRPA1), a member of the …             Requirement for phosphorylation of P53 at Ser312 in suppression of chemical carcinogenesis ▶     Elizabeth A. Slee, Xin Lu     The p53 tumour suppressor is activated in response to a wide variety of genotoxic stresses, frequently via post-translational modification. Using a knock in mouse model with a …             Optical control of neuronal excitation and inhibition using a single opsin protein, ChR2 ▶     Holly Liske, Xiang Qian, Polina Anikeeva et al.     The effect of electrical stimulation on neuronal membrane potential is frequency dependent. Low frequency electrical stimulation can evoke action potentials, whereas high …             Flow Through Randomly Curved Manifolds ▶     M. Mendoza, S. Succi, H. J. Herrmann     We present a computational study of the transport properties of campylotic (intrinsically curved) media. It is found that the relation between the flow through a campylotic media, …             Ratcheted diffusion transport through crowded nanochannels ▶     Anna Lappala, Alessio Zaccone, Eugene M. Terentjev     The problem of transport through nanochannels is one of the major questions in cell biology, with a wide range of applications. In this paper we discuss the process of spontaneous …             Maternal depressive symptoms related to Epstein-Barr virus reactivation in late pregnancy ▶     Peng Zhu, Yu-Jiang Chen, Jia-Hu Hao et al.     We examined the relationship between maternal depressive symptoms in late pregnancy and Epstein-Barr virus reactivation before delivery. In this prospective observational study, …             Assessment of Genetically Modified Soybean in Relation to Natural Variation in the Soybean Seed Metabolome ▶     Joseph D. Clarke, Danny C. Alexander, Dennis P. Ward et al.     Genetically modified (GM) crops currently constitute a significant and growing part of agriculture. An important aspect of GM crop adoption is to demonstrate safety and …             Cytokinesis-required Cdc14 is a signaling hub of asexual development and multi-stress tolerance in Beauveria bassiana ▶     Jie Wang, Jing Liu, Yue Hu et al.     A dual-specificity, paralogue-free Cdc14 phosphatase was located in the nuclei of Beauveria bassiana (filamentous entomopathogen) and functionally characterized. Inactivation of …             A Simple Assay for Measuring Catalase Activity: A Visual Approach ▶     Tadayuki Iwase, Akiko Tajima, Shinya Sugimoto et al.     In this study, an assay that combines the ease and simplicity of the qualitative approach for measuring catalase activity was developed. The assay reagents comprised only hydrogen …             Proteomic analysis of the SIRT6 interactome: novel links to genome maintenance and cellular stress signaling ▶     Federica Simeoni, Luisa Tasselli, Shinji Tanaka et al.     The chromatin regulatory factor SIRT6 plays pivotal roles in metabolism, tumor suppression, and aging biology. Despite the fundamental roles of SIRT6 in physiology and disease, …             CD200R signaling inhibits pro-angiogenic gene expression by macrophages and suppresses choroidal neovascularization ▶     Shintaro Horie, Scott J. Robbie, Jian Liu et al.     Macrophages are rapidly conditioned by cognate and soluble signals to acquire phenotypes that deliver specific functions during inflammation, wound healing and angiogenesis. …             The Effect of Blood Flow on Magnetic Resonance Imaging of Non Thermal Irreversible Electroporation ▶     Mohammad Hjouj, Jacob Lavee, David Last et al.     To generate an understanding of the physiological significance of MR images of Non-Thermal Irreversible Electroporation (NTIRE) we compared the following MR imaging sequences: …             Identifcation of a Novel Mutation p.I240T in the FRMD7 gene in a Family with Congenital Nystagmus ▶     Yihua Zhu, Jianfu Zhuang, Xianglian Ge et al.     Congenital Nystagmus (CN) is a genetically heterogeneous ocular disease, which causes a significant proportion of childhood visual impairment. 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