Scientific Reports Biology Table of Contents e-alert: 2 June 2015

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02 June 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports       Nature Communications is now fully open access All new submissions if accepted, will be published open access and an article processing charge will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more on APC funding.         Biological Sciences               The infection of turkeys and chickens by reassortants derived from pandemic H1N1 2009 and avian H9N2 influenza viruses ▶     Honglei Sun, Weili Kong, Litao Liu et al.     Outbreaks of pandemic H1N1 2009 (pH1N1) in turkeys have been reported in several countries. Co-infection of pH1N1 and avian H9N2 influenza viruses in turkeys provide the …             Genome-Wide Mining, Characterization, and Development of Microsatellite Markers in Gossypium Species ▶     Qiong Wang, Lei Fang, Jiedan Chen et al.     Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite …             Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex ▶     Thomas Bourquard, Flavie Landomiel, Eric Reiter et al.     β-arrestins serve as signaling scaffolds downstream of G protein-coupled receptors, and thus play a crucial role in a plethora of cellular processes. Although it is largely …             Incubation temperature affects the immune function of hatchling soft-shelled turtles, Pelodiscus sinensis ▶     Wei Dang, Wen Zhang, Wei-Guo Du     Identifying how developmental temperature affects the immune system is critical for understanding how ectothermic animals defend against pathogens and their fitness in the …             Oxalic acid and sclerotial differentiation of Polyporus umbellatus ▶     Yong-Mei Xing, Wan-Qiang Yin, Meng-Meng Liu et al.     The present investigation aimed to uncover the effects of exogenous oxalic acid during the sclerotial formation of Polyporus umbellatus, with an emphasis on determining the …             Zinc disrupts central carbon metabolism and capsule biosynthesis in Streptococcus pyogenes ▶     Cheryl-lynn Y. Ong, Mark J. Walker, Alastair G. McEwan     Neutrophils release free zinc to eliminate the phagocytosed bacterial pathogen Streptococcus pyogenes (Group A Streptococcus; GAS). In this study, we investigated the mechanisms …             Automated Pipeline for Purification, Biophysical and X-Ray Analysis of Biomacromolecular Solutions ▶     Melissa A. Graewert, Daniel Franke, Cy M. Jeffries et al.     Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample …             Electroretinographic assessment of rod- and cone-mediated bipolar cell pathways using flicker stimuli in mice ▶     Naoyuki Tanimoto, Vithiyanjali Sothilingam, Mineo Kondo et al.     Mouse full-field electroretinograms (ERGs) are dominated by responses of photoreceptors and depolarizing (ON-) bipolar cells, but not much of hyperpolarizing (OFF-) bipolar cells …             Light scattering as an intrinsic indicator for pancreatic islet cell mass and secretion ▶     E. Ilegems, P. P. van Krieken, P. K. Edlund et al.     The pancreatic islet of Langerhans is composed of endocrine cells producing and releasing hormones from secretory granules in response to various stimuli for maintenance of blood …             A new target region for changing the substrate specificity of amine transaminases ▶     Li-Jun Guan, Jun Ohtsuka, Masahiko Okai et al.     (R)-stereospecific amine transaminases (R-ATAs) are important biocatalysts for the production of (R)-amine compounds in a strict stereospecific manner. An improved R-ATA, …             Hemocompatibility improvement of perfusion-decellularized clinical-scale liver scaffold through heparin immobilization ▶     Ji Bao, Qiong Wu, Jiu Sun et al.     Whole-liver perfusion-decellularization is an attractive scaffold–preparation technique for producing clinical transplantable liver tissue. However, the scaffold’s poor …             Nontoxic singlet oxygen generator as a therapeutic candidate for treating tauopathies ▶     Sahabudeen Sheik Mohideen, Yasutoyo Yamasaki, Yasuhiro Omata et al.     Methylene blue (MB) inhibits the aggregation of tau, a main constituent of neurofibrillary tangles. However, MB’s mode of action in vivo is not fully understood. MB treatment …             Catalytic subunits of the phosphatase calcineurin interact with NF-κB-inducing kinase (NIK) and attenuate NIK-dependent gene expression ▶     Miho Shinzawa, Hiroyasu Konno, Junwen Qin et al.     Nuclear factor (NF)-κB-inducing kinase (NIK) is a serine/threonine kinase that activates NF-κB pathways, thereby regulating a wide variety of immune systems. Aberrant NIK …             Some like it hot: Thermal tolerance and oxygen supply capacity in two eurythermal crustaceans ▶     Rasmus Ern, Do Thi Thanh Huong, Nguyen Thanh Phuong et al.     Thermal sensitivity of the cardiorespiratory oxygen supply capacity has been proposed as the cardinal link underlying the upper boundary of the temperature niche in aquatic …             Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores ▶     Alina Asandei, Mauro Chinappi, Jong-kook Lee et al.     Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a …             The Serum Profile of Hypercytokinemia Factors Identified in H7N9-Infected Patients can Predict Fatal Outcomes ▶     Jing Guo, Fengming Huang, Jun Liu et al.     The novel avian origin influenza A (H7N9) virus has caused severe diseases in humans in eastern China since the spring of 2013. Fatal outcomes of H7N9 infections are often …             Myo-inositol improves the host’s ability to eliminate balofloxacin-resistant Escherichia coli ▶     Xin-hai Chen, Bing-wen Zhang, Hui Li et al.     Antibiotic-resistant mechanisms are associated with fitness costs. However, why antibiotic-resistant bacteria usually show increasing adaptation to hosts is largely unknown, …             Burkholderia cenocepacia and Salmonella enterica ArnT proteins that transfer 4-amino-4-deoxy-l-arabinose to lipopolysaccharide share membrane topology and functional amino acids ▶     Faviola Tavares-Carreón, Kinnari B. Patel, Miguel A. Valvano     We recently demonstrated that incorporation of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of lipopolysaccharide (LPS) is required for transport of LPS to the …             3, 4-dihydroxyl-phenyl lactic acid restores NADH dehydrogenase 1 α subunit 10 to ameliorate cardiac reperfusion injury ▶     Xiao-Yuan Yang, Ke He, Chun-Shui Pan et al.     The present study aimed to detect the role of 3, 4-dihydroxyl-phenyl lactic acid (DLA) during ischemia/reperfusion (I/R) induced myocardial injury with emphasis on the underlying …             Molecular pathway of near-infrared laser phototoxicity involves ATF-4 orchestrated ER stress ▶     Imran Khan, Elieza Tang, Praveen Arany     High power lasers are used extensively in medicine while lower power applications are popular for optical imaging, optogenetics, skin rejuvenation and a therapeutic modality …             Gross primary production of global forest ecosystems has been overestimated ▶     Jianyong Ma, Xiaodong Yan, Wenjie Dong et al.     Coverage rate, a critical variable for gridded forest area, has been neglected by previous studies in estimating the annual gross primary production (GPP) of global forest …             Nonsurgical deep uterine transfer of vitrified, in vivo-derived, porcine embryos is as effective as the default surgical approach ▶     Emilio A. Martinez, Cristina A Martinez, Alicia Nohalez et al.     Surgical procedures are prevalent in porcine embryo transfer (ET) programs, where the use of vitrified embryos is quasi non-existent. This study compared the effectiveness of …             Mechanical competence of ovariectomy-induced compromised bone after single or combined treatment with high-frequency loading and bisphosphonates ▶     Camargos G. V., Bhattacharya P., van Lenthe G. H. et al.     Osteoporosis leads to increased bone fragility, thus effective approaches enhancing bone strength are needed. Hence, this study investigated the effect of single or combined …             Effects of CO2-induced pH reduction on the exoskeleton structure and biophotonic properties of the shrimp Lysmata californica ▶     Jennifer R. A. Taylor, Jasmine M. Gilleard, Michael C. Allen et al.     The anticipated effects of CO2-induced ocean acidification on marine calcifiers are generally negative, and include dissolution of calcified elements and reduced calcification …             Discovery of novel inhibitors of human S-adenosylmethionine decarboxylase based on in silico high-throughput screening and a non-radioactive enzymatic assay ▶     Chenzeng Liao, Yanlin Wang, Xiao Tan et al.     Natural polyamines are small polycationic molecules essential for cell growth and development, and elevated level of polyamines is positively correlated with various cancers. As …             Self-organized criticality in cortical assemblies occurs in concurrent scale-free and small-world networks ▶     Paolo Massobrio, Valentina Pasquale, Sergio Martinoia     The spontaneous activity of cortical networks is characterized by the emergence of different dynamic states. Although several attempts were accomplished to understand the origin …             Paracrine effects of haematopoietic cells on human mesenchymal stem cells ▶     Shuanhu Zhou     Stem cell function decline during ageing can involve both cell intrinsic and extrinsic mechanisms. Bone and blood formation are intertwined in bone marrow, therefore …             The Wnt5a-Ror2 axis promotes the signaling circuit between interleukin-12 and interferon-γ in colitis ▶     Akira Sato, Hisako Kayama, Kensaku Shojima et al.     Wnt5a, which regulates various cellular functions in Wnt signaling, is involved in inflammatory responses, however the mechanism is not well understood. We examined the role of …             Shedding dynamics of Morogoro virus, an African arenavirus closely related to Lassa virus, in its natural reservoir host Mastomys natalensis ▶     Benny Borremans, Raphaël Vossen, Beate Becker-Ziaja et al.     Arenaviruses can cause mild to severe hemorrhagic fevers. Humans mainly get infected through contact with infected rodents or their excretions, yet little is known about …             Sound can suppress visual perception ▶     Souta Hidaka, Masakazu Ide     In a single modality, the percept of an input (e.g., voices of neighbors) is often suppressed by another (e.g., the sound of a car horn nearby) due to close interactions of …             Transmission of Tomato Yellow Leaf Curl Virus by Bemisia tabaci as Affected by Whitefly Sex and Biotype ▶     Wenxi Ning, Xiaobin Shi, Baiming Liu et al.     Bemisia tabaci is a serious pest of vegetables and other crops worldwide. The most damaging and predominant B. tabaci biotypes are B and Q, and both are vectors of tomato yellow …             Signal detection analysis of blindsight in monkeys ▶     Masatoshi Yoshida, Tadashi Isa     Macaque monkeys with a unilateral lesion in V1 have been used as an animal model of blindsight. While objective proof of blindsight requires that the two aspects of blindsight …             The Bax inhibitor MrBI-1 regulates heat tolerance, apoptotic-like cell death, and virulence in Metarhizium robertsii ▶     Yixiong Chen, Zhibing Duan, Peilin Chen et al.     Bax inhibitor 1 (BI-1) is a highly conserved protein originally identified as a suppressor of the proapoptotic protein Bax to inhibit cell death in animals and plants. The …             Host species vary in infection probability, sub-lethal effects, and costs of immune response when exposed to an amphibian parasite ▶     Jon Bielby, Matthew C. Fisher, Frances C. Clare et al.     The amphibian parasite Batrachochytrium dendrobatidis (Bd) is regarded as an extreme generalist, infecting over 500 species, but amongst these hosts there exists a great deal of …             Triggering mitophagy with far-red fluorescent photosensitizers ▶     Cheng-Wei Hsieh, Chih-Hang Chu, Hsien-Ming Lee et al.     Cells identify defective mitochondria and eliminate them through mitophagy: this allows cells to rid themselves of unwanted stress to maintain health and avoid the activation of …             PAX6 does not regulate Nfia and Nfib expression during neocortical development ▶     Jens Bunt, Jonathan W. C. Lim, Lu Zhao et al.     The Nuclear factor I (NFI) family of transcription factors regulates proliferation and differentiation throughout the developing central nervous system. In the developing …             RiboTALE: A modular, inducible system for accurate gene expression control ▶     Navneet Rai, Aura Ferreiro, Alexander Neckelmann et al.     A limiting factor in synthetic gene circuit design is the number of independent control elements that can be combined together in a single system. Here, we present RiboTALEs, a …             Diabetic silkworms for evaluation of therapeutically effective drugs against type II diabetes ▶     Yasuhiko Matsumoto, Masaki Ishii, Yohei Hayashi et al.     We previously reported that sugar levels in the silkworm hemolymph, i.e., blood, increase immediately (within 1 h) after intake of a high-glucose diet, and that the …             Targeted mutagenesis in soybean using the CRISPR-Cas9 system ▶     Xianjun Sun, Zheng Hu, Rui Chen et al.     Genome editing is a valuable technique for gene function analysis and crop improvement. Over the past two years, the CRISPR-Cas9 system has emerged as a powerful tool for …             Activation of the TOR Signalling Pathway by Glutamine Regulates Insect Fecundity ▶     Yifan Zhai, Zhongxiang Sun, Jianqing Zhang et al.     The target of rapamycin (TOR) positively controls cell growth in response to nutrients such as amino acids. However, research on the specific nutrients sensed by TOR is limited. …             Polyphyly of nuclear lamin genes indicates an early eukaryotic origin of the metazoan-type intermediate filament proteins ▶     Martin Kollmar     The nuclear lamina is a protein meshwork associated with the inner side of the nuclear envelope contributing structural, signalling and regulatory functions. Here, I report on …             Resilience to orthostasis and haemorrhage: A pilot study of common genetic and conditioning mechanisms ▶     Dmitry M. Davydov, Renad I. Zhdanov, Vladimir G. Dvoenosov et al.     A major challenge presently is not only to identify the genetic polymorphisms increasing risk to diseases, but to also find out factors and mechanisms, which can counteract a …             Origin and evolution of lysyl oxidases ▶     Xavier Grau-Bové, Iñaki Ruiz-Trillo, Fernando Rodriguez-Pascual     Lysyl oxidases (LOX) are copper-dependent enzymes that oxidize primary amine substrates to reactive aldehydes. The best-studied role of LOX enzymes is the remodeling of the …             Follower ants in a tandem pair are not always naïve ▶     Patrick Schultheiss, Chloé A Raderschall, Ajay Narendra     In addition to foraging individually several species of ants guide nestmates to a goal by tandem running. We found that the Australian ant, Camponotus consobrinus, forages both …             Endotoxic shock-expanded murine CD11clowCD45RB+ regulatory dendritic cells modulate inflammatory T cell responses through multiple mechanisms ▶     Xiaoqian Wang, Qingyang Wang, Xueying Zhang et al.     Changes in the number and function of dendritic cells (DCs) have been reported to play an important role in endotoxin tolerance. It has been reported that expansion of splenic …             Irrelevant tactile stimulation biases visual exploration in external coordinates ▶     José P. Ossandón, Peter König, Tobias Heed     We evaluated the effect of irrelevant tactile stimulation on humans’ free-viewing behavior during the exploration of complex static scenes. Specifically, we address the questions …             The Cullin 4A/B-DDB1-Cereblon E3 Ubiquitin Ligase Complex Mediates the Degradation of CLC-1 Chloride Channels ▶     Yi-An Chen, Yi-Jheng Peng, Meng-Chun Hu et al.     Voltage-gated CLC-1 chloride channels play a critical role in controlling the membrane excitability of skeletal muscles. Mutations in human CLC-1 channels have been linked to the …             Drosophila Rif1 is an essential gene and controls late developmental events by direct interaction with PP1-87B ▶     Easwaran Sreesankar, Vellaichamy Bharathi, Rakesh K. Mishra et al.     Rif1, identified as a regulator of telomerase in yeast, is an evolutionarily conserved protein and functions in diverse processes including telomere length regulation, epigenetic …             Cross-species comparative analysis of Dicer proteins during Sindbis virus infection ▶     Erika Girardi, Mathieu Lefèvre, Béatrice Chane-Woon-Ming et al.     In plants and invertebrates RNA silencing is a major defense mechanism against virus infections. The first event in RNA silencing is dicing of long double stranded RNAs into …             Characterization of the antibody response against EV71 capsid proteins in Chinese individuals by NEIBM-ELISA ▶     Yingying Ding, Xuguang Chen, Baohua Qian et al.     Human enterovirus 71 (EV71) has become the major pathogen of hand, foot, and mouth disease (HFMD) worldwide, while the anti-EV71 antibody responses other than neutralizing …             Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress ▶     Antonis Giannakakis, Jingxian Zhang, Piroon Jenjaroenpun et al.     Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the …             The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery ▶     Yasmin Ahmad, Narendra K. Sharma, Mohammad Faiz Ahmad et al.     Exposure to high altitude induces physiological responses due to hypoxia. Lungs being at the first level to face the alterations in oxygen levels are critical to counter and …             Effects of Aβ exposure on long-term associative memory and its neuronal mechanisms in a defined neuronal network ▶     Lenzie Ford, Michael Crossley, Thomas Williams et al.     Amyloid beta (Aβ) induced neuronal death has been linked to memory loss, perhaps the most devastating symptom of Alzheimer’s disease (AD). Although Aβ-induced impairment of …             New breast cancer prognostic factors identified by computer-aided image analysis of HE stained histopathology images ▶     Jia-Mei Chen, Ai-Ping Qu, Lin-Wei Wang et al.     Computer-aided image analysis (CAI) can help objectively quantify morphologic features of hematoxylin-eosin (HE) histopathology images and provide potentially useful prognostic …             Lipidome and Transcriptome Profiling of Pneumolysin Intoxication Identifies Networks Involved in Statin-Conferred Protection of Airway Epithelial Cells ▶     Sarah Statt, Jhen-Wei Ruan, Chih-Ting Huang et al.     Pneumonia remains one of the leading causes of death in both adults and children worldwide. Despite the adoption of a wide variety of therapeutics, the mortality from …             Non-Linear Optical Flow Cytometry Using a Scanned, Bessel Beam Light-Sheet ▶     Bradley B. Collier, Samir Awasthi, Deborah K. Lieu et al.     Modern flow cytometry instruments have become vital tools for high-throughput analysis of single cells. However, as issues with the cellular labeling techniques often used in …             Molecularly Targeted Therapy of Human Hepatocellular Carcinoma Xenografts with Radio-iodinated Anti-VEGFR2 Murine-Human Chimeric Fab ▶     Jianfei Huang, Qi Tang, Changjun Wang et al.     Vascular endothelial growth factor receptor 2 (VEGFR2) is traditionally regarded as an important therapeutic target in a wide variety of malignancies, such as hepatocellular …             A Late Devonian Fertile Organ with Seed Plant Affinities from China ▶     Deming Wang, Le Liu, Yun Guo et al.     Seed plants underwent first major evolutionary radiation in the Late Devonian (Famennian), as evidenced by the numerous ovules described to date. However, the early pollen organs …             Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding ▶     Luciano A. Abriata, Matteo Dal Peraro     Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations …             A bioinspired peptide scaffold with high antibiotic activity and low in vivo toxicity ▶     Francesc Rabanal, Ariadna Grau-Campistany, Xavier Vila-Farrés et al.     Bacterial resistance to almost all available antibiotics is an important public health issue. A major goal in antimicrobial drug discovery is the generation of new chemicals …             A novel inhibitory mechanism of MRTF-A/B on the ICAM-1 gene expression in vascular endothelial cells ▶     Ken’ichiro Hayashi, Toshiyuki Murai, Hiroki Oikawa et al.     The roles of myocardin-related transcription factor A (MRTF-A) and MRTF-B in vascular endothelial cells are not completely understood. Here, we found a novel regulatory mechanism …             Biodistribution and function of extracellular miRNA-155 in mice ▶     Shashi Bala, Timea Csak, Fatemeh Momen-Heravi et al.     Circulating miRNAs can be found in extracellular vesicles (EV) and could be involved in intercellular communication. Here, we report the biodistribution of EV associated miR-155 …             SUMO1 Affects Synaptic Function, Spine Density and Memory ▶     Shinsuke Matsuzaki, Linda Lee, Erin Knock et al.     Small ubiquitin-like modifier-1 (SUMO1) plays a number of roles in cellular events and recent evidence has given momentum for its contributions to neuronal development and …             Structural transition in Bcl-xL and its potential association with mitochondrial calcium ion transport ▶     Sreekanth Rajan, Minjoo Choi, Quoc Toan Nguyen et al.     Bcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational …             A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering ▶     P. Roedig, I. Vartiainen, R. Duman et al.     At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered …             GABAB receptor upregulates fragile X mental retardation protein expression in neurons ▶     Wenhua Zhang, Chanjuan Xu, Haijun Tu et al.     Fragile X mental retardation protein (FMRP) is an RNA-binding protein important for the control of translation and synaptic function. The mutation or silencing of FMRP causes …             Direct Identification of On-Bead Peptides Using Surface-Enhanced Raman Spectroscopic Barcoding System for High-Throughput Bioanalysis ▶     Homan Kang, Sinyoung Jeong, Yul Koh et al.     Recently, preparation and screening of compound libraries remain one of the most challenging tasks in drug discovery, biomarker detection, and biomolecular profiling processes. …             Arginine methylation of hnRNPUL1 regulates interaction with NBS1 and recruitment to sites of DNA damage ▶     Gayathri Gurunathan, Zhenbao Yu, Yan Coulombe et al.     Arginine methylation is a post-translational modification required for the maintenance of genomic integrity. Cells deficient in protein arginine methyltransferase 1 (PRMT1) have …             Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? ▶     Tereza Ševčíková, Aleš Horák, Vladimír Klimeš et al.     Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history …             L-cystathionine inhibits oxidized low density lipoprotein-induced THP-1-derived macrophage inflammatory cytokine monocyte chemoattractant protein-1 generation via the NF-κB pathway ▶     Mingzhu Zhu, Junbao Du, Angie Dong Liu et al.     This study aimed to explore whether and how L-cystathionine had any regulatory effect on the inflammatory response in THP-1-derived macrophages cultured in vitro under oxidized …             Pictionary-based fMRI paradigm to study the neural correlates of spontaneous improvisation and figural creativity ▶     Manish Saggar, Eve-Marie Quintin, Eliza Kienitz et al.     A novel game-like and creativity-conducive fMRI paradigm is developed to assess the neural correlates of spontaneous improvisation and figural creativity in healthy adults. …             Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis ▶     Clelia Peano, Johannes Wolf, Julien Demol et al.     In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase “core enzyme” (E) to …             VoICE: A semi-automated pipeline for standardizing vocal analysis across models ▶     Zachary D. Burkett, Nancy F. Day, Olga Peñagarikano et al.     The study of vocal communication in animal models provides key insight to the neurogenetic basis for speech and communication disorders. Current methods for vocal analysis suffer …             Direct Correlation Between Ligand-Induced α-Synuclein Oligomers and Amyloid-like Fibril Growth ▶     Martin Nors Perdersen, Vito Foderà, Istvan Horvath et al.     Aggregation of proteins into amyloid deposits is the hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. The suggestion that intermediate …             The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape ▶     Begoña Dobon, Hisham Y. Hassan, Hafid Laayouni et al.     East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new …             Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH ▶     Sami Hocine, Maria Vera, Daniel Zenklusen et al.     Transcription is a highly regulated biological process, initiated through the assembly of complexes at the promoter that contain both the general transcriptional machinery and …             A compact photometer based on metal-waveguide-capillary: application to detecting glucose of nanomolar concentration ▶     Min Bai, Hui Huang, Jian Hao et al.     Trace analysis of liquid samples has wide applications in life science and environmental monitor. In this paper, a compact and low-cost photometer based on …             Fabrication and Cytocompatibility of In Situ Crosslinked Carbon Nanomaterial Films ▶     Sunny C. Patel, Gaurav Lalwani, Kartikey Grover et al.     Assembly of carbon nanomaterials into two-dimensional (2D) coatings and films that harness their unique physiochemical properties may lead to high impact energy capture/storage, …             iMSRC: converting a standard automated microscope into an intelligent screening platform ▶     Angel Carro, Manuel Perez-Martinez, Joaquim Soriano et al.     Microscopy in the context of biomedical research is demanding new tools to automatically detect and capture objects of interest. The few extant packages addressing this need, …             Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana ▶     Yasuhiro Higashi, Yozo Okazaki, Fumiyoshi Myouga et al.     Environmental stress causes membrane damage in plants. Lipid studies are required to understand the adaptation of plants to climate change. Here, LC-MS-based lipidomic and …             Live Cell Characterization of DNA Aggregation Delivered through Lipofection ▶     Stephen Mieruszynski, Candida Briggs, Michelle A. Digman et al.     DNA trafficking phenomena, such as information on where and to what extent DNA aggregation occurs, have yet to be fully characterised in the live cell. Here we characterise the …             A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data ▶     Qiongshi Lu, Yiming Hu, Jiehuan Sun et al.     Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through …             Enthalpy-entropy compensation at play in human copper ion transfer ▶     Moritz S. Niemiec, Artur P. G. Dingeldein, Pernilla Wittung-Stafshede     Copper (Cu) is an essential trace element but toxic in free form. After cell uptake, Cu is transferred, via direct protein-protein interactions, from the chaperone Atox1 to the …             Eye closure enhances dark night perceptions ▶     Stefan Brodoehl, Carsten M. Klingner, Otto W. Witte     We often close our eyes when we explore objects with our fingers to reduce the dominance of the visual system over our other senses. Here we show that eye closure, even in …             A transcription and translation-coupled DNA replication system using rolling-circle replication ▶     Yoshihiro Sakatani, Norikazu Ichihashi, Yasuaki Kazuta et al.     All living organisms have a genome replication system in which genomic DNA is replicated by a DNA polymerase translated from mRNA transcribed from the genome. The artificial …             Cyanamide is biosynthesized from l-canavanine in plants ▶     Tsunashi Kamo, Sakae Sakurai, Tatsuya Yamanashi et al.     Cyanamide had long been recognized as a synthetic compound but more recently has been found as a natural product from several leguminous plants. This compound’s biosynthetic …             Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging ▶     Jun Li, Daniel M. Czajkowsky, Xiaowei Li et al.     Recently developed tissue clearing techniques, where the tissue is embedded within a hydrogel, have revolutionized our ability to resolve fine cellular structures in nearly …             Detection of Composite Communities in Multiplex Biological Networks ▶     Laura Bennett, Aristotelis Kittas, Gareth Muirhead et al.     The detection of community structure is a widely accepted means of investigating the principles governing biological systems. Recent efforts are exploring ways in which multiple …             Circulating miR-497 and miR-663b in plasma are potential novel biomarkers for bladder cancer ▶     Mulong Du, Danni Shi, Lin Yuan et al.     MicroRNAs (miRNAs), abundant and highly stable in the plasma, have been widely reported. This greatly pursued us to investigate whether plasma miRNAs could be considered as …             Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics ▶     Maoda Pang, Jingwei Jiang, Xing Xie et al.     Outbreaks in fish of motile Aeromonad septicemia (MAS) caused by Aeromonas hydrophila have caused a great concern worldwide. Here, for the first time, we provide two complete …             The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress ▶     Ping Lu, Marieke H. Heineke, Anil Koul et al.     Targeting respiration and ATP synthesis has received strong interest as a new strategy for combatting drug-resistant Mycobacterium tuberculosis. Mycobacteria employ a respiratory …             Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus ▶     Sandra Marxen, Timo D. Stark, Andrea Rütschle et al.     Cereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate …             Scoring the correlation of genes by their shared properties using OScal, an improved overlap quantification model ▶     Hui Liu, Wei Liu, Ying Lin et al.     Scoring the correlation between two genes by their shared properties is a common and basic work in biological study. A prospective way to score this correlation is to quantify …             Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice ▶     Jingxu Zhang, Zuomei Lu, Weimin Dai et al.     Weedy rice infests paddy fields worldwide at an alarmingly increasing rate. There is substantial evidence indicating that many weedy rice forms originated from or are closely …             Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains ▶     Lihua Meng, Gang Chen, Zhonghu Li et al.     The formation of the Mekong-Salween Divide and climatic oscillations in Pleistocene were the main drivers for the contemporary diversity and genetic structure of plants in the …             Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis ▶     Xinyun Qiu, Feng Zhang, Xi Yang et al.     Intestinal fungi are increasingly believed to greatly influence gut health. However, the effects of fungi on intestinal inflammation and on gut bacterial constitution are not …             Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity ▶     Xiaojuan Jia, Yuhai Bi, Jing Li et al.     Porcine reproductive and respiratory syndrome (PRRS) has caused large economic losses in the swine industry in recent years. Current PRRS vaccines fail to effectively prevent and …             Exercise intolerance and developmental delay associated with a novel mitochondrial ND5 mutation ▶     Hezhi Fang, Hao Shi, Xiyuan Li et al.     The aim of this study was to evaluate the contribution of mitochondrial DNA (mtDNA) mutations in oxidative phosphorylation (OXPHOS) deficiency. The complete mitochondrial genomes …             Centrin-2 (Cetn2) mediated regulation of FGF/FGFR gene expression in Xenopus ▶     Jianli Shi, Ying Zhao, Tyson Vonderfecht et al.     Centrins (Cetns) are highly conserved, widely expressed, and multifunctional Ca2+-binding eukaryotic signature proteins best known for their roles in ciliogenesis and as critical …             Morphological and molecular characterization of a sexually reproducing colony of the booklouse Liposcelis bostrychophila (Psocodea: Liposcelididae) found in Arizona ▶     Qianqian Yang, Zuzana Kučerová, Steve J. Perlman et al.     The booklouse, Liposcelis bostrychophila, is a worldwide pest of stored products. For decades, only thelytokous parthenogenetic reproduction was documented in L. bostrychophila. …             Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology ▶     Victor D. Martinez, Emily A. Vucic, Kelsie L. Thu et al.     Human PIWI-interacting RNAs (piRNAs) are known to be expressed in germline cells, functionally silencing LINEs and SINEs. Their expression patterns in somatic tissues are largely …             Starvation-induced collective behavior in C. elegans ▶     Alexander B. Artyukhin, Joshua J. Yim, Mi Cheong Cheong et al.     We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their …             Nonautophagic cytoplasmic vacuolation death induction in human PC-3M prostate cancer by curcumin through reactive oxygen species -mediated endoplasmic reticulum stress ▶     Wei-Jiunn Lee, Ming-Hsien Chien, Jyh-Ming Chow et al.     The antiapoptotic and antiautophagic abilities of cancer cells constitute a major challenge for anticancer drug treatment. Strategies for triggering nonapoptotic or nonautophagic …             Fractal features of soil particle size distribution in newly formed wetlands in the Yellow River Delta ▶     Junbao Yu, Xiaofei Lv, Ma Bin et al.     The characteristic of particle size distribution (PSD) in the newly formed wetlands in coast has seldom been studied. We applied fractal-scaling theory in assessing soil particle …             SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains ▶     Yong-Heng Huang, Aleksander Jankowski, Kathryn S. E. Cheah et al.     The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural …             Habitat stability, predation risk and ‘memory syndromes’ ▶     S. Dalesman, A. Rendle, S.R.X. Dall     Habitat stability and predation pressure are thought to be major drivers in the evolutionary maintenance of behavioural syndromes, with trait covariance only occurring within …             Tumor Invasion Optimization by Mesenchymal-Amoeboid Heterogeneity ▶     Inbal Hecht, Yasmin Bar-El, Frederic Balmer et al.     Metastasizing tumor cells migrate through the surrounding tissue and extracellular matrix toward the blood vessels, in order to colonize distant organs. They typically move in a …             Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir ▶     Yuqi Yu, Jinan Wang, Qiang Shao et al.     Molecular dynamics simulations are performed to investigate the dynamic properties of wild-type HIV-1 protease and its two multi-drug-resistant variants (Flap …             Decreased LKB1 predicts poor prognosis in Pancreatic Ductal Adenocarcinoma ▶     Jian-Yu Yang, Shu-Heng Jiang, De-Jun Liu et al.     Liver kinase B1 (LKB1) has been identified as a critical modulator involved in cell proliferation and polarity. The purpose of the current study was to characterize the …             Cell Size Modulates Oscillation, Positioning and Length of Mitotic Spindles ▶     Hongyuan Jiang     Mitotic spindle is the main subcellular structure that accomplishes the chromosome segregation between daughter cells during cell division. However, how mitotic spindles sense …             Cooperative Transmembrane Penetration of Nanoparticles ▶     Haizhen Zhang, Qiuju Ji, Changjin Huang et al.     Physical penetration of lipid bilayer membranes presents an alternative pathway for cellular delivery of nanoparticles (NPs) besides endocytosis. NPs delivered through this …             The prognostic factors and multiple biomarkers in young patients with colorectal cancer ▶     Mo-Jin Wang, Jie Ping, Yuan Li et al.     The incidence of colorectal cancer (CRC) in young patients (≤50 years of age) appears to be increasing. However, their clinicopathological characteristics and survival are …             Exploiting lipopolysaccharide-induced deformation of lipid bilayers to modify membrane composition and generate two-dimensional geometric membrane array patterns ▶     Peter G. Adams, Kirstie L. Swingle, Walter F. Paxton et al.     Supported lipid bilayers have proven effective as model membranes for investigating biophysical processes and in development of sensor and array technologies. The ability to …             Microbiota prevents cholesterol loss from the body by regulating host gene expression in mice ▶     Chun-Yan Zhong, Wei-Wei Sun, Yinyan Ma et al.     We have previously observed that knockout of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol transporter essential for intestinal cholesterol absorption, reduces the output of dry …             Three-dimensional cage-like microscaffolds for cell invasion studies ▶     Barbara Spagnolo, Virgilio Brunetti, Godefroy Leménager et al.     Cancer cell motility is one of the major events involved in metastatic process. Tumor cells that disseminate from a primary tumor can migrate into the vascular system and, being …             An overhang-based DNA block shuffling method for creating a customized random library ▶     Kosuke Fujishima, Chris Venter, Kendrick Wang et al.     We present an overhang-based DNA block shuffling method to create a customized random DNA library with flexible sequence design and length. Our method enables the efficient and …             TP53 transcription factor for the NEDD9/HEF1/Cas-L gene: potential targets in Non-Small Cell Lung Cancer treatment ▶     Bénédicte ROUSSEAU, Catherine JACQUOT, Julie LE PALABE et al.     Lung cancer is a serious public health problem. Although there has been significant progress in chemotherapy, non-small cell lung cancer is still resistant to current treatments, …             CORRIGENDUM: The Evidence of Glioblastoma Heterogeneity ▶     Akio Soeda, Akira Hara, Takahiro Kunisada et al.                 Combined treatment with a pH-sensitive fusogenic peptide and cationic lipids achieves enhanced cytosolic delivery of exosomes ▶     Ikuhiko Nakase, Shiroh Futaki     Exosomes, which are approximately 100 nm vesicles secreted by cells, have been studied with respect to cell-to-cell communication, disease diagnosis, and intracellular delivery. …             Systematic Genome-wide Screening and Prediction of microRNAs in EBOV During the 2014 Ebolavirus Outbreak ▶     Yue Teng, Yuzhuo Wang, Xianglilan Zhang et al.     Recently, several thousand people have been killed by the Ebolavirus disease (EVD) in West Africa, yet no current antiviral medications and treatments are available. Systematic …             A novel highly differentially expressed gene in wheat endosperm associated with bread quality ▶     A. Furtado, P. C. Bundock, P. M. Banks et al.     Analysis of gene expression in developing wheat seeds was used to identify a gene, wheat bread making (wbm), with highly differential expression (~1000 fold) in the starchy …                 A new online, open access, multi- and cross- disciplinary journal dedicated to publishing the finest research on systems biology and all its approaches. Published by Nature Publishing Group in partnership with the Systems Biology Institute (SBI). 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