Scientific Reports Biology Table of Contents e-alert: 10 March 2015

10 March 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports         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). Learn more at http://www.nature.com/npjsba           Biological Sciences               Novel inhibitor discovery and the conformational analysis of inhibitors of listeriolysin O via protein-ligand modeling ▶     Jianfeng Wang, Xuan Zhou, Shui Liu et al.     Increasing bacterial resistance to available antibiotics makes the discovery of novel efficacious antibacterial agents a priority. A previous report showed that listeriolysin O …             High dissolved organic carbon release by benthic cyanobacterial mats in a Caribbean reef ecosystem ▶     Hannah J. Brocke, Frank Wenzhoefer, Dirk de Beer et al.     Benthic cyanobacterial mats (BCMs) are increasing in abundance on coral reefs worldwide. However, their impacts on biogeochemical cycling in the surrounding water and sediment …             Rate perception adapts across the senses: evidence for a unified timing mechanism ▶     Carmel A. Levitan, Yih-Hsin A. Ban, Noelle R. B. Stiles et al.     The brain constructs a representation of temporal properties of events, such as duration and frequency, but the underlying neural mechanisms are under debate. One open question …             Vascular Normalization Induced by Sinomenine Hydrochloride Results in Suppressed Mammary Tumor Growth and Metastasis ▶     Huimin Zhang, Yu Ren, Xiaojiang Tang et al.     Solid tumor vasculature is characterized by structural and functional abnormality and results in a hostile tumor microenvironment that mediates several deleterious aspects of …             Wilms' tumor 1 (WT1) expression and prognosis in solid cancer patients: a systematic review and meta-analysis ▶     Xiao-wei Qi, Fan Zhang, Hong Wu et al.     Though proposed as a promising target antigen for cancer immunotherapy, the prognostic value of Wilms' tumor 1 (WT1) in solid tumors remains inconclusive. Here, we report a …             High incubation temperatures enhance mitochondrial energy metabolism in reptile embryos ▶     Bao-Jun Sun, Teng Li, Jing Gao et al.     Developmental rate increases exponentially with increasing temperature in ectothermic animals, but the biochemical basis underlying this thermal dependence is largely unexplored. …             Extreme variation in migration strategies between and within wandering albatross populations during their sabbatical year, and their fitness consequences ▶     Henri Weimerskirch, Karine Delord, Audrey Guitteaud et al.     Migratory behavior, routes and zones used during the non-breeding season are assumed to have been selected to maximize fitness, and can lead to genetic differentiation. Yet, here …             Visual Attention Model Based on Statistical Properties of Neuron Responses ▶     Haibin Duan, Xiaohua Wang     Visual attention is a mechanism of the visual system that can select relevant objects from a specific scene. Interactions among neurons in multiple cortical areas are considered …             Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study ▶     Hui Sun Lee, Yifei Qi, Wonpil Im     N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently …             Human iPSC-based Cardiac Microphysiological System For Drug Screening Applications ▶     Anurag Mathur, Peter Loskill, Kaifeng Shao et al.     Drug discovery and development are hampered by high failure rates attributed to the reliance on non-human animal models employed during safety and efficacy testing. A fundamental …             Tumor cell secretion of soluble factor(s) for specific immunosuppression ▶     Arihiro Kano     Studies of tumor models using syngeneic transplantation have advanced our understanding of tumor immunity, including both immune surveillance and evasion. Murine mammary …             Specific microRNAs Regulate Heat Stress Responses in Caenorhabditis elegans ▶     Camilla Nehammer, Agnieszka Podolska, Sebastian D. Mackowiak et al.     The ability of animals to sense and respond to elevated temperature is essential for survival. Transcriptional control of the heat stress response has been much studied, whereas …             Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment ▶     Pengju Zhang, Alvin Lo, Yurong Huang et al.     The interplay between host genetics, tumor microenvironment and environmental exposure in cancer susceptibility remains poorly understood. Here we assessed the genetic control of …             P38/MAPK contributes to endothelial barrier dysfunction via MAP4 phosphorylation-dependent microtubule disassembly in inflammation-induced acute lung injury ▶     Lingfei Li, Jiongyu Hu, Ting He et al.     Excessive activation of inflammation and the accompanying lung vascular endothelial barrier disruption are primary pathogenic features of acute lung injury (ALI). …             Extinction during memory reconsolidation blocks recovery of fear in adolescents ▶     D. C. Johnson, B. J. Casey     Adolescence is a time of intensified emotional experiences, during which anxiety and stress-related disorders peak. The most effective behavioral therapies for treating these …             Identification and characterization of a vitamin D3 decomposition product bactericidal againstHelicobacter pylori ▶     Kouichi Hosoda, Hirofumi Shimomura, Kiyofumi Wanibuchi et al.     This study demonstrated that the vitamin D3 decomposition product VDP1 exerts an antibacterial action against Helicobacter pylori but not against other bacteria. Treatment with …             Genetic Variability and Phylogenetic Analysis of Han Population from Guanzhong Region of China based on 21 non-CODIS STR Loci ▶     Yu-Dang Zhang, Xiao-Li Tang, Hao-Tian Meng et al.     In the present study, we presented the population genetic data and their forensic parameters of 21 non-CODIS autosomal STR loci in Chinese Guanzhong Han population. A total of …             Irisin – a myth rather than an exercise-inducible myokine ▶     Elke Albrecht, Frode Norheim, Bernd Thiede et al.     The myokine irisin is supposed to be cleaved from a transmembrane precursor, FNDC5 (fibronectin type III domain containing 5), and to mediate beneficial effects of exercise on …             A Dual-Reporter System for Real-Time Monitoring and High-throughput CRISPR/Cas9 Library Screening of the Hepatitis C Virus ▶     Qingpeng Ren, Chan Li, Pengfei Yuan et al.     The hepatitis C virus (HCV) is one of the leading causes of chronic hepatitis, liver cirrhosis and hepatocellular carcinomas and infects approximately 170 million people …             Statistical Thermodynamics of Irreversible Aggregation: The Sol-Gel Transition ▶     Themis Matsoukas     Binary aggregation is known to lead, under certain kinetic rules, to the coexistence of two populations, one consisting of finite-size clusters (sol), and one that contains a …             Testosterone regulates the autophagic clearance of androgen binding protein in rat Sertoli cells ▶     Yi Ma, Hao-Zheng Yang, Long-Mei Xu et al.     Dysregulation of androgen-binding protein (ABP) is associated with a number of endocrine and andrology diseases. However, the ABP metabolism in Sertoli cells is largely unknown. …             Pattern segmentation with activity dependent natural frequency shift and sub-threshold resonance ▶     E. Shtrahman, M. Zochowski     Understanding the mechanisms underlying distributed pattern formation in brain networks and its content driven dynamical segmentation is an area of intense study. We investigate …             A three-dimensional phase diagram of growth-induced surface instabilities ▶     Qiming Wang, Xuanhe Zhao     A variety of fascinating morphological patterns arise on surfaces of growing, developing or aging tissues, organs and microorganism colonies. These patterns can be classified …             Hematologic and immunological characteristics of Henoch-Schönlein purpura in rat and rabbit models induced with ovalbumin based on type III hypersensitivity ▶     Yanhong Li, Xiaochun Feng, Lan Huang et al.     Henoch-Schönlein purpura (HSP) is a common systemic vasculitis in children. Animal models of HSP are needed to better understand the mechanism of HSP. Here, we investigated …             In vivo Quantification of the Structural Changes of Collagens in a Melanoma Microenvironment with Second and Third Harmonic Generation Microscopy ▶     Pei-Chun Wu, Tsung-Yuan Hsieh, Zen-Uong Tsai et al.     Using in vivo second harmonic generation (SHG) and third harmonic generation (THG) microscopies, we tracked the course of collagen remodeling over time in the same melanoma …             CD47 Deficiency Protects Mice From Diet-induced Obesity and Improves Whole Body Glucose Tolerance and Insulin Sensitivity ▶     Hasiyeti Maimaitiyiming, Heather Norman, Qi Zhou et al.     CD47 is a transmembrane protein with several functions including self-recognition, immune cell communication, and cell signaling. Although it has been extensively studied in …             Src inhibitor reduces permeability without disturbing vascularization and prevents bone destruction in steroid-associated osteonecrotic lesions in rabbits ▶     Yi-Xin He, Jin Liu, Baosheng Guo et al.     To examine the therapeutic effect of Src inhibitor on the VEGF mediating vascular hyperpermeability and bone destruction within steroid-associated osteonecrotic lesions in …             Metabolomic identification of biochemical changes induced by fluoxetine and imipramine in a chronic mild stress mouse model of depression ▶     Jing Zhao, Yang-Hee Jung, Choon-Gon Jang et al.     Metabolomics was applied to a C57BL/6N mouse model of chronic unpredictable mild stress (CMS). Such mice were treated with two antidepressants from different categories: …             Paramagnetic Nanoparticles as a Platform for FRET-Based Sarcosine Picomolar Detection ▶     Zbynek Heger, Natalia Cernei, Sona Krizkova et al.     Herein, we describe an ultrasensitive specific biosensing system for detection of sarcosine as a potential biomarker of prostate carcinoma based on Förster resonance energy …             (Pro)renin receptor is crucial for Wnt/β-catenin-dependent genesis of pancreatic ductal adenocarcinoma ▶     Yuki Shibayama, Takayuki Fujimori, Genevieve Nguyen et al.     Although Wnt/β-catenin signaling is known to be aberrantly activated in PDAC, mutations of CTNNB1, APC or other pathway components are rare in this tumor type, suggesting …             Prolonged-acting, Multi-targeting Gallium Nanoparticles Potently Inhibit Growth of Both HIV and Mycobacteria in Co-Infected Human Macrophages ▶     Prabagaran Narayanasamy, Barbara L. Switzer, Bradley E. Britigan     Human immunodeficiency virus (HIV) infection and Mycobacterium tuberculosis (TB) are responsible for two of the major global human infectious diseases that result in significant …             A Lower pH Value Benefits Regeneration of Trichosanthes kirilowii by Somatic Embryogenesis, Involving Rhizoid Tubers (RTBs), a Novel Structure ▶     Ke-dong Xu, Yun-xia Chang, Ju Zhang et al.     A new approach was established for the regeneration of Trichosanthes kirilowii from root, stem, and leaf explants by somatic embryogenesis (SE), involving a previously unreported …             Angiotensin-converting enzymes modulate aphid–plant interactions ▶     Wei Wang, Lan Luo, Hong Lu et al.     Angiotensin-converting enzymes (ACEs) are key components of the renin–angiotensin system in mammals. However, the function of ACE homologs in insect saliva is unclear. Aphids …             Temporal frequency of events rather than speed dilates perceived duration of moving objects ▶     Daniel Linares, Andrei Gorea     In everyday life moving objects often follow irregular or repetitive trajectories for which distinctive events are potentially noticeable. It is known that the perceived duration …             Mice lacking the cerebral cortex develop normal song: Insights into the foundations of vocal learning ▶     Kurt Hammerschmidt, Gabriela Whelan, Gregor Eichele et al.     Mouse models play an increasingly important role in the identification and functional assessment of speech-associated genes, with a focus on genes involved in vocal production, …             A Novel Mechanism for Small Heat Shock Proteins to Function as Molecular Chaperones ▶     Kaiming Zhang, Anastasia N. Ezemaduka, Zhao Wang et al.     Small heat shock proteins (sHSPs) are molecular chaperones ubiquitously present in all forms of life, but their function mechanisms remain controversial. Here we show by …             The formation of electronically excited species in the human multiple myeloma cell suspension ▶     Marek Rác, Michaela Sedlářová, Pavel Pospíšil     In this study, evidence is provided on the formation of electronically excited species in human multiple myeloma cells U266 in the growth medium exposed to hydrogen peroxide (H2O2…             Functional interaction of nicotinic acetylcholine receptors and Na+/K+ ATPase from Locusta migratoria manilensis (Meyen) ▶     Haibo Bao, Huahua Sun, Youxin Xiao et al.     Associated proteins are important for the correct functioning of nicotinic acetylcholine receptors (nAChRs). In the present study, a neonicotinoid-agarose affinity column was …             NKX2-5 Mutations in an Inbred Consanguineous Population: Genetic and Phenotypic Diversity ▶     Ossama K. Abou Hassan, Akl C. Fahed, Manal Batrawi et al.     NKX2-5 mutations are associated with different forms of congenital heart disease. Despite the knowledge gained from molecular and animal studies, genotype-phenotype correlations …             Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia ▶     Dariush Nasrollahzadeh, Reza Malekzadeh, Alexander Ploner et al.     Observational studies revealed a relationship between changes in gastric mucosa and risk of esophageal squamous cell carcinoma (ESCC) which suggested a possible role for gastric …             An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game ▶     Moshe Hoffman, Sigrid Suetens, Uri Gneezy et al.     Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium …             Amphiregulin activates human hepatic stellate cells and is upregulated in non alcoholic steatohepatitis ▶     Chad McKee, Barbara Sigala, Junpei Soeda et al.     Amphiregulin (AR) involvement in liver fibrogenesis and hepatic stellate cells (HSC) regulation is under study. Non-alcoholic fatty liver disease (NAFLD) and its more severe form …             Renal progenitors derived from human iPSCs engraft and restore function in a mouse model of acute kidney injury ▶     Barbara Imberti, Susanna Tomasoni, Osele Ciampi et al.     Acute kidney injury (AKI) is one of the most relevant health issues, leading to millions of deaths. The magnitude of the phenomenon remarks the urgent need for innovative and …             Common marmosets show social plasticity and group-level similarity in personality ▶     Sonja E. Koski, Judith M. Burkart     The social environment influences animal personality on evolutionary and immediate time scales. However, studies of animal personality rarely assess the effects of the social …             Origin of 1/f noise in hydration dynamics on lipid membrane surfaces ▶     Eiji Yamamoto, Takuma Akimoto, Masato Yasui et al.     Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and …             New potential eukaryotic substrates of the mycobacterial protein tyrosine phosphatase PtpA: hints of a bacterial modulation of macrophage bioenergetics state ▶     Mariana Margenat, Anne-Marie Labandera, Magdalena Gil et al.     The bacterial protein tyrosine phosphatase PtpA is a key virulence factor released by Mycobacterium tuberculosis in the cytosol of infected macrophages. So far only two unrelated …             Parameterization of temperature sensitivity of spring phenology and its application in explaining diverse phenological responses to temperature change ▶     Huanjiong Wang, Quansheng Ge, This Rutishauser et al.     Existing evidence of plant phenological change to temperature increase demonstrates that the phenological responsiveness is greater at warmer locations and in early-season plant …             An evolutionary inspection game with labour unions on small-world networks ▶     Salahuddin M. Kamal, Yas Al-Hadeethi, Fouad A. Abolaban et al.     We study an evolutionary inspection game where agents can chose between working and shirking. The evolutionary process is staged on a small-world network, through which agents …             Outlier-resilient complexity analysis of heartbeat dynamics ▶     Men-Tzung Lo, Yi-Chung Chang, Chen Lin et al.     Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals …             Lipid droplets hypertrophy: a crucial determining factor in insulin regulation by adipocytes ▶     Bahram Sanjabi, Monireh Dashty, Behiye Özcan et al.     Lipid droplets (LDs) hypertrophy in adipocytes is the main cause of energy metabolic system dysfunction, obesity and its afflictions such as T2D. However, the role of adipocytes …             Paper and Flexible Substrates as Materials for Biosensing Platforms to Detect Multiple Biotargets▶     Hadi Shafiee, Waseem Asghar, Fatih Inci et al.     The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant interest in clinical applications for disease diagnosis and treatment monitoring …             Real-time Measurement of Biomagnetic Vector Fields in Functional Syncytium Using Amorphous Metal ▶     Shinsuke Nakayama, Tusyoshi Uchiyama     Magnetic field detection of biological electric activities would provide a non-invasive and aseptic estimate of the functional state of cellular organization, namely a syncytium …             3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance ▶     Santiago Vilar, Nicholas P. Tatonetti, George Hripcsak     Adverse drugs events (ADEs) detection constitutes a considerable concern in patient safety and public health care. For this reason, it is important to develop methods that …             Dietary Methionine Restriction in Mice Elicits an Adaptive Cardiovascular Response to Hyperhomocysteinemia ▶     Gene P. Ables, Amadou Ouattara, Thomas G. Hampton et al.     Dietary methionine restriction (MR) in rodents increased lifespan despite higher heart-to-body weight ratio (w/w) and hyperhomocysteinemia, which are symptoms associated with …             Whole exome sequencing reveals recurrent mutations in BRCA2 and FAT genes in acinar cell carcinomas of the pancreas ▶     Toru Furukawa, Hitomi Sakamoto, Shoko Takeuchi et al.     Acinar cell carcinoma of the pancreas is a rare tumor with a poor prognosis. Compared to pancreatic ductal adenocarcinoma, its molecular features are poorly known. We studied a …             Microrheology with Optical Tweezers: Measuring the relative viscosity of solutions ‘at a glance’ ▶     Manlio Tassieri, Francesco Del Giudice, Emma J. Robertson et al.     We present a straightforward method for measuring the relative viscosity of fluids via a simple graphical analysis of the normalised position autocorrelation function of an …             Transforming growth factor beta 3 involved in the pathogenesis of synovial chondromatosis of temporomandibular joint ▶     Yingjie Li, Loaye Abdelaziz El.Mozen, Hengxing Cai et al.     Synovial chondromatosis (SC) of temporomandibular joint is rare proliferative disorder featured by the formation of cartilaginous nodules in synovium and joint space. …             Emergence of infectious malignant thrombocytopenia in Japanese macaques (Macaca fuscata) by SRV-4 after transmission to a novel host ▶     Munehiro Okamoto, Takayuki Miyazawa, Shigeru Morikawa et al.     We discovered a lethal hemorrhagic syndrome arising from severe thrombocytopenia in Japanese macaques kept at the Primate Research Institute, Kyoto University. Extensive …             Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer ▶     Yongsheng Li, Yunpeng Zhang, Shengli Li et al.     Despite growing appreciation of the importance of epigenetics in breast cancer, our understanding of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancer remains …             The relationship between response inhibition and posttraumatic stress symptom clusters in adolescent earthquake survivors: An event-related potential study ▶     Jianhui Wu, Yiran Yuan, Chengqi Cao et al.     Posttraumatic stress disorder (PTSD) patients experience impaired response inhibition. Little is known about the relationship between response inhibition abnormalities and …             AKT and 14-3-3 Regulate Notch4 Nuclear Localization ▶     Gopalakrishnan Ramakrishnan, Gantulga Davaakhuu, Wen Cheng Chung et al.     Members of the Notch family of transmembrane receptors, Notch1-4 in mammals, are involved in the regulation of cell fate decisions and cell proliferation in various organisms. …             An efficient strategy for producing a stable, replaceable, highly efficient transgene expression system in silkworm, Bombyx mori ▶     Dingpei Long, Weijian Lu, Yuli Zhang et al.     We developed an efficient strategy that combines a method for the post-integration elimination of all transposon sequences, a site-specific recombination system, and an optimized …             Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans ▶     Hanhae Kim, Kwang-Woo Jung, Shinae Maeng et al.     Cryptococcus neoformans is an opportunistic human pathogenic fungus that causes meningoencephalitis. Due to the increasing global risk of cryptococcosis and the emergence of …             Evidences of adaptive traits to rocky substrates undermine paradigm of habitat preference of the Mediterranean seagrass Posidonia oceanica ▶     Fabio Badalamenti, Adriana Alagna, Silvio Fici     Posidonia oceanica meadows are acknowledged as one of the most valuable ecosystems of the Mediterranean Sea. P. oceanica has been historically described as a species typically …             Autoimmunity conferred by chs3-2D relies on CSA1, its adjacent TNL-encoding neighbour ▶     Fang Xu, Chipan Zhu, Volkan Cevik et al.     Plant innate immunity depends on the function of a large number of intracellular immune receptor proteins, the majority of which are structurally similar to mammalian …             Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake ▶     Eri Adams, Vitaly Chaban, Himanshu Khandelia et al.     High concentrations of cesium (Cs) inhibit plant growth but the detailed mechanisms of Cs uptake, transport and response in plants are not well known. In order to identify small …             Involvement of the left insula in the ecological validity of the human voice ▶     Yuri Tamura, Shinji Kuriki, Tamami Nakano     A subtle difference between a real human and an artificial object that resembles a human evokes an impression of a large qualitative difference between them. This suggests the …             Pathway and kinetics of cyhalothrin biodegradation by Bacillus thuringiensis strain ZS-19 ▶     Shaohua Chen, Yinyue Deng, Changqing Chang et al.     Cyhalothrin is a common environmental pollutant which poses increased risks to non-target organisms including human beings. This study reported for the first time a newly …             Centrosome maturation requires YB-1 to regulate dynamic instability of microtubules for nucleus reassembly ▶     Atsushi Kawaguchi, Masamitsu N. Asaka, Ken Matsumoto et al.     Microtubule formation from the centrosome increases dramatically at the onset of mitosis. This process is termed centrosome maturation. However, regulatory mechanisms of …             Acute ER stress regulates amyloid precursor protein processing through ubiquitin-dependent degradation ▶     Eun Sun Jung, HyunSeok Hong, Chaeyoung Kim et al.     Beta-amyloid (Aβ), a major pathological hallmark of Alzheimer's disease (AD), is derived from amyloid precursor protein (APP) through sequential cleavage by β-secretase and …             Natural high pCO2 increases autotrophy in Anemonia viridis (Anthozoa) as revealed from stable isotope (C, N) analysis ▶     Rael Horwitz, Esther M. Borell, Ruth Yam et al.     Contemporary cnidarian-algae symbioses are challenged by increasing CO2 concentrations (ocean warming and acidification) affecting organisms' biological performance. We examined …             Mechanism of Action of Thalassospiramides, A New Class of Calpain Inhibitors ▶     Liang Lu, Michael J. Meehan, Shuo Gu et al.     Thalassospiramides comprise a large family of lipopeptide natural products produced by Thalassospira and Tistrella marine bacteria. Here we provide further evidence of their …             Nanospheres of doxorubicin as cross-linkers for a supramolecular hydrogelation ▶     Qiang Xue, He Ren, Chao Xu et al.     In this study, we synthesized a peptide of Nap-GFFYGRGD, which could self-assemble into supramolecular nanofibers. The peptide itself could only form nanofibers but not hydrogels …             The effects of delayed auditory feedback revealed by bone conduction microphone in adult zebra finches ▶     Makoto Fukushima, Daniel Margoliash     Vocal control and learning are critically dependent on auditory feedback in songbirds and humans. Continuous delayed auditory feedback (cDAF) robustly disrupts speech fluency in …             Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records▶     Hyojung Paik, Ah-Young Chung, Hae-Chul Park et al.     Prediction of new disease indications for approved drugs by computational methods has been based largely on the genomics signatures of drugs and diseases. We propose a method for …             New Cyt-like δ-endotoxins from Dickeya dadantii: structure and aphicidal activity ▶     Karine Loth, Denis Costechareyre, Géraldine Effantin et al.     In the track of new biopesticides, four genes namely cytA, cytB, cytC and cytD encoding proteins homologous to Bacillus thuringiensis (Bt) Cyt toxins have been identified in the …             Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels ▶     Gustavo Arruda Bezerra, Elena Dobrovetsky, Alma Seitova et al.     The voltage-gated potassium channel family (Kv) constitutes the most diverse class of ion channels in the nervous system. Dipeptidyl peptidase 10 (DPP10) is an inactive peptidase …             MiR-181a regulates lipid metabolism via IDH1 ▶     Bo Chu, Ting Wu, Lin Miao et al.     Lipid metabolism is important for cellular energy homeostasis. Excessive cellular lipid accumulation is associated with various human diseases such as obesity, cardiovascular …             Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4 ▶     Jinguang Huang, Yanxiang Zhao, Huaian Liu et al.     PC4, a well-known general transcription cofactor, has multiple functions in transcription and DNA repair. Residue W89, is engaged in stacking interactions with DNA in PC4, but …             Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish ▶     Yu Hisano, Tetsushi Sakuma, Shota Nakade et al.     The CRISPR/Cas9 system provides a powerful tool for genome editing in various model organisms, including zebrafish. The establishment of targeted gene-disrupted zebrafish …             Double-scattering/reflection in a Single Nanoparticle for Intensified Ultrasound Imaging ▶     Kun Zhang, Hangrong Chen, Xiasheng Guo et al.     Ultrasound contrast agents (UCAs) designed by the conventional composition-based strategy, often suffer from relatively low ultrasound utilization efficiency. In this report, a …             FOXK2 Transcription Factor Suppresses ERα-positive Breast Cancer Cell Growth Through Down-Regulating the Stability of ERα via mechanism involving BRCA1/BARD1 ▶     Ying Liu, Xiang Ao, Zhaojun Jia et al.     Estrogen receptors (ERs) are critical regulators of breast cancer development. Identification of molecules that regulate the function of ERs may facilitate the development of …             New Compound Sets Identified from High Throughput Phenotypic Screening Against Three Kinetoplastid Parasites: An Open Resource ▶     Imanol Peña, M. Pilar Manzano, Juan Cantizani et al.     Using whole-cell phenotypic assays, the GlaxoSmithKline high-throughput screening (HTS) diversity set of 1.8 million compounds was screened against the three kinetoplastids most …             Lessons from Hepatocyte-Specific Cyp51 Knockout Mice: Impaired Cholesterol Synthesis Leads to Oval Cell-Driven Liver Injury ▶     Gregor Lorbek, Martina Perše, Jera Jeruc et al.     We demonstrate unequivocally that defective cholesterol synthesis is an independent determinant of liver inflammation and fibrosis. We prepared a mouse hepatocyte-specific …             Combination of angiotensin-(1–7) with perindopril is better than single therapy in ameliorating diabetic cardiomyopathy ▶     Panpan Hao, Jianmin Yang, Yanping Liu et al.     We recently found that overexpression of angiotensin (Ang)-converting enzyme 2, which metabolizes Ang-II to Ang-(1–7) and Ang-I to Ang-(1–9), may improve left ventricular …             Revealing bending and force in a soft body through a plant root inspired approach ▶     Chiara Lucarotti, Massimo Totaro, Ali Sadeghi et al.     An emerging challenge in soft robotics research is to reveal mechanical solicitations in a soft body. Nature provides amazing clues to develop unconventional components that are …             Excess of Rare Variants in Genes that are Key Epigenetic Regulators of Spermatogenesis in the Patients with Non-Obstructive Azoospermia ▶     Zesong Li, Yi Huang, Honggang Li et al.     Non-obstructive azoospermia (NOA), a severe form of male infertility, is often suspected to be linked to currently undefined genetic abnormalities. To explore the genetic basis …             Uterine artery impedance during the first eight postpartum weeks ▶     L. Guedes-Martins, A. R. Gaio, J. Saraiva et al.     The aim of this study was to construct reference ranges for the uterine artery (UtA) mean pulsatility (PI) and resistance (RI) indices from 1–8 weeks postpartum. A prospective, …             CORRIGENDUM: Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics ▶     Zhi-Yong Li, Yue-Zhu Wang, Li-Ming He et al.                 HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation ▶     Meng Zhang, River Charles, Huimin Tong et al.     Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density …             Tilt after-effect from high spatial-frequency patterns in the amblyopic eye of adults with anisometropic amblyopia ▶     Jiawei Zhou, Lin Li, Pan Zhang et al.     With abnormal visual cortical development, amblyopia is generally associated with high spatial frequency deficits in spatial vision. In this study, we aim to answer a critical …             Competition between cap and basal actin fiber orientation in cells subjected to contact guidance and cyclic strain ▶     Chiara Tamiello, Carlijn V. C. Bouten, Frank P. T. Baaijens     In vivo, adhesive cells continuously respond to a complex range of physical cues coming from the surrounding microenvironment by remodeling their cytoskeleton. Topographical and …             Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells ▶     Mikihiro Shibata, Takayuki Uchihashi, Toshio Ando et al.     Visualization of morphological dynamics of live cells with nanometer resolution under physiological conditions is highly desired, but challenging. It has been demonstrated that …             Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry ▶     Frederik Weiß, Anke Schnabel, Hannes Planatscher et al.     Immunoaffinity enrichment of proteotypic peptides, coupled with selected reaction monitoring, enables indirect protein quantification. However the lack of suitable antibodies …             N-butylidenephthalide Attenuates Alzheimer's Disease-Like Cytopathy in Down Syndrome Induced Pluripotent Stem Cell-Derived Neurons ▶     Chia-Yu Chang, Sheng-Mei Chen, Huai-En Lu et al.     Down syndrome (DS) patients with early-onset dementia share similar neurodegenerative features with Alzheimer's disease (AD). To recapitulate the AD cell model, DS induced …             Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies ▶     Pramod Kumar, Abhigyan Satyam, Xingliang Fan et al.     Therapeutic strategies based on the principles of tissue engineering by self-assembly put forward the notion that functional regeneration can be achieved by utilising the …             The Role of Binding Site on the Mechanical Unfolding Mechanism of Ubiquitin ▶     Penghui Cao, Gwonchan Yoon, Weiwei Tao et al.     We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied …             Comparison of the physiological characteristics of transgenic insect-resistant cotton and conventional lines ▶     Xiaogang Li, Changfeng Ding, Xingxiang Wang et al.     The introduction of transgenic insect-resistant cotton into agricultural ecosystems has raised concerns regarding its ecological effects. Many studies have been conducted to …             Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production ▶     Yoshihiko Onda, Keiichi Mochida, Takuhiro Yoshida et al.     Several plant species can generate enough heat to increase their internal floral temperature above ambient temperature. Among thermogenic plants, Arum concinnatum shows the …             Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling ▶     Hua Wang, Yan Fang, Lipeng Wang et al.     Heterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, …             Genome engineering and direct cloning of antibiotic gene clusters via phage ϕBT1 integrase-mediated site-specific recombination in Streptomyces ▶     Deyao Du, Lu Wang, Yuqing Tian et al.     Several strategies have been used to clone large DNA fragments directly from bacterial genome. Most of these approaches are based on different site-specific recombination systems …             Completing bacterial genome assemblies: strategy and performance comparisons ▶     Yu-Chieh Liao, Shu-Hung Lin, Hsin-Hung Lin     Determining the genomic sequences of microorganisms is the basis and prerequisite for understanding their biology and functional characterization. While the advent of low-cost, …             Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA ▶     Dmitriy A. Khodakov, Anastasia S. Khodakova, David M. Huang et al.     Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding …             Synchrotron x-ray imaging of pulmonary alveoli in respiration in live intact mice ▶     Soeun Chang, Namseop Kwon, Jinkyung Kim et al.     Despite nearly a half century of studies, it has not been fully understood how pulmonary alveoli, the elementary gas exchange units in mammalian lungs, inflate and deflate during …             Microscale Magnetic Field Modulation for Enhanced Capture and Distribution of Rare Circulating Tumor Cells ▶     Peng Chen, Yu-Yen Huang, Kazunori Hoshino et al.     Immunomagnetic assay combines the powers of the magnetic separation and biomarker recognition and has been an effective tool to perform rare Circulating Tumor Cells detection. …             MicroRNA-320a sensitizes tamoxifen-resistant breast cancer cells to tamoxifen by targeting ARPP-19 and ERRγ* ▶     Mingrong Lü, Keshuo Ding, Guofeng Zhang et al.     Tamoxifen represents a major adjuvant therapy to those patients with estrogen receptor-alpha positive breast cancer. However, tamoxifen resistance occurs quite often, either de …             Do Arctic breeding geese track or overtake a green wave during spring migration? ▶     Yali Si, Qinchuan Xin, Willem F. de Boer et al.     Geese breeding in the Arctic have to do so in a short time-window while having sufficient body reserves. Hence, arrival time and body condition upon arrival largely influence …             Microreactor Array Device ▶     Peter Wiktor, Al Brunner, Peter Kahn et al.     We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible …             Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication ▶     Qinghe Li, Yuanyuan Wang, Xiaoxiang Hu et al.     It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Us…             Repetitive genomic insertion of gene-sized dsDNAs by targeting the promoter region of a counter-selectable marker ▶     Jaehwan Jeong, Han Na Seo, Yu Kyung Jung et al.     Genome engineering can be used to produce bacterial strains with a wide range of desired phenotypes. However, the incorporation of gene-sized DNA fragments is often challenging …             Non-thermal plasma with 2-deoxy-D-glucose synergistically induces cell death by targeting glycolysis in blood cancer cells ▶     Neha Kaushik, Su Jae Lee, Tae Gyu Choi et al.     In this study, we show the selective and efficient anti-cancer effects of plasma (at a low dose) when cell metabolic modifiers are also included. 2-deoxy-D-glucose (2-DG), a …             βA3/A1-crystallin is a critical mediator of STAT3 signaling in optic nerve astrocytes ▶     Mallika Valapala, Malia Edwards, Stacey Hose et al.     We have previously reported that in the Nuc1 rat, which has a spontaneous mutation in Cryba1 (the gene encoding βA3/A1-crystallin), astrocytes exhibit decreased Notch signaling, …             Image-Guided Transcranial Focused Ultrasound Stimulates Human Primary Somatosensory Cortex ▶     Wonhye Lee, Hyungmin Kim, Yujin Jung et al.     Focused ultrasound (FUS) has recently been investigated as a new mode of non-invasive brain stimulation, which offers exquisite spatial resolution and depth control. We report on …             Analysis of accumulation patterns and preliminary study on the condensation mechanism of proanthocyanidins in the tea plant [Camellia sinensis] ▶     Xiaolan Jiang, Yajun Liu, Yahui Wu et al.     In the present study, proanthocyanidins were qualitatively and quantitatively identified using hydrolysis and thiolysis assays, NP-HPLC, HPLC-ESI-MS, MALDI-TOF-MS, 1H-NMR, and 13…             Identification of the optic recess region as a morphogenetic entity in the zebrafish forebrain ▶     Pierre Affaticati, Kei Yamamoto, Barbara Rizzi et al.     Regionalization is a critical, highly conserved step in the development of the vertebrate brain. Discrepancies exist in how regionalization of the anterior vertebrate forebrain …             Helicobacter pylori infection can affect energy modulating hormones and body weight in germ free mice ▶     Yalda Khosravi, Shih Wee Seow, Arlaine Anne Amoyo et al.     Helicobacter pylori, is an invariably commensal resident of the gut microbiome associated with gastric ulcer in adults. In addition, these patients also suffered from a low grade …             In1-ghrelin splicing variant is overexpressed in pituitary adenomas and increases their aggressive features ▶     Alejandro Ibáñez-Costa, Manuel D. Gahete, Esther Rivero-Cortés et al.     Pituitary adenomas comprise a heterogeneous subset of pathologies causing serious comorbidities, which would benefit from identification of novel, common molecular/cellular …             X-ray phase contrast tomography by tracking near field speckle ▶     Hongchang Wang, Sebastien Berujon, Julia Herzen et al.     X-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption …             Modeling Post-death Transmission of Ebola: Challenges for Inference and Opportunities for Control ▶     Joshua S. Weitz, Jonathan Dushoff     Multiple epidemiological models have been proposed to predict the spread of Ebola in West Africa. These models include consideration of counter-measures meant to slow and, …             Recent ecological transitions in China: greening, browning, and influential factors ▶     Yihe Lü, Liwei Zhang, Xiaoming Feng et al.     Ecological conservation and restoration are necessary to mitigate environmental degradation problems. China has taken great efforts in such actions. To understand the ecological …             Mesenchymal stem cells alleviate airway inflammation and emphysema in COPD through down-regulation of cyclooxygenase-2 via p38 and ERK MAPK pathways ▶     Wen Gu, Lin Song, Xiao-Ming Li et al.     Bone marrow-derived mesenchymal stem cells (MSCs) have been identified as one possible strategy for the treatment of chronic obstructive pulmonary disease (COPD). Our previous …             Supramolecular protein assembly supports immobilization of a cytochrome P450 monooxygenase system as water-insoluble gel ▶     Cheau Yuaan Tan, Hidehiko Hirakawa, Teruyuki Nagamune     Diverse applications of the versatile bacterial cytochrome P450 enzymes (P450s) are hampered by their requirement for the auxiliary proteins, ferredoxin reductases and …             Microbial communities on flower surfaces act as signatures of pollinator visitation ▶     Masayuki Ushio, Eri Yamasaki, Hiroyuki Takasu et al.     Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part …             Borna disease virus possesses an NF-ĸB inhibitory sequence in the nucleoprotein gene ▶     Akiko Makino, Kan Fujino, Nicholas F. Parrish et al.     Borna disease virus (BDV) has a non-segmented, negative-stranded RNA genome and causes persistent infection in many animal species. Previous study has shown that the activation …             Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases ▶     Stefanie Nicole Hamer, Stefan Cord-Landwehr, Xevi Biarnés et al.     Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may …             An effective biphase system accelerates hesperidinase-catalyzed conversion of rutin to isoquercitrin ▶     Jun Wang, An Gong, Cai-Feng Yang et al.     Isoquercitrin is a rare, natural ingredient with several biological activities that is a key precursor for the synthesis of enzymatically modified isoquercitrin (EMIQ). The …             C2 rs547154 polymorphism and polypoidal choroidal vasculopathy susceptibility: a meta-analysis▶     Xue Chen, Xiaoli Kang, Kanxing Zhao et al.     Previous studies have indicated the association between C2 rs547154 polymorphism and polypoidal choroidal vasculopathy (PCV) risk, while the results are controversial and …             Cumulus cells accelerate oocyte aging by releasing soluble Fas Ligand in mice ▶     Jiang Zhu, Jie Zhang, Hong Li et al.     Although previous studies have suggested that cumulus cells (CCs) accelerate oocyte aging by secreting soluble and heat-sensitive paracrine factors, the factors involved are not …             Distance-dependent patterns of molecular divergences in tuatara mitogenomes ▶     Sankar Subramanian, Elmira Mohandesan, Craig D. Millar et al.     Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that …             Endocytic pathway mediates refractoriness of insect Bactrocera dorsalis to RNA interference ▶     Xiaoxue Li, Xiaolong Dong, Cong Zou et al.     RNA interference (RNAi) is a powerful and convenient tool for sequence-specific gene silencing, and it is triggered by double-stranded RNA (dsRNA). RNAi can be easily achieved in …             Disentangling the impacts of outcome valence and outcome frequency on the post-error slowing▶     Lijun Wang, Dandan Tang, Yuanfang Zhao et al.     Post-error slowing (PES) reflects efficient outcome monitoring, manifested as slower reaction time after errors. Cognitive control account assumes that PES depends on error …             A microfluidic live cell assay to study anthrax toxin induced cell lethality assisted by conditioned medium ▶     Jie Shen, Changzu Cai, Zhilong Yu et al.     It is technically challenging to investigate the function of secreted protein in real time by supply of conditioned medium that contains secreted protein of interest. The …             Disrupted-in-schizophrenia-1 (DISC1) Regulates Endoplasmic Reticulum Calcium Dynamics ▶     Sung Jin Park, Jaehoon Jeong, Young-Un Park et al.     Disrupted-in-schizophrenia-1 (DISC1) has emerged as a convincing susceptibility gene for multiple mental disorders, but its mechanistic link to the pathogenesis of schizophrenia …             WNT-1 inducible signaling pathway protein-1 enhances growth and tumorigenesis in human breast cancer ▶     Kun-Chun Chiang, Chun-Nan Yeh, Li-Chuan Chung et al.     WNT1 inducible signaling pathway protein 1 (WISP1) plays a key role in many cellular functions in a highly tissue-specific manner; however the role of WISP1 in breast cancer is …             A reusable immobilization matrix for the biodegradation of phenol at 5000 mg/L ▶     Najun Li, Jun Jiang, Dongyun Chen et al.     Bacteria-mediated degradation of toxins has been reported as a practical technique for the innocuous removal of toxic organic compounds from water. Specifically, immobilized and …             Anthracycline-containing chemotherapy causes long-term impairment of mitochondrial respiration and increased reactive oxygen species release in skeletal muscle ▶     Gilles Gouspillou, Celena Scheede-Bergdahl, Sally Spendiff et al.     Anticancer treatments for childhood acute lymphoblastic leukaemia (ALL) are highly effective but are now implicated in causing impaired muscle function in long-term survivors. …             A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments ▶     Shihu Hu, Raymond J. Zeng, Mohamed F. Haroon et al.     This study investigates interactions between recently identified denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (anammox) processes in …             Protein phosphorylation detection using dual-mode field-effect devices and nanoplasmonic sensors ▶     Nikhil Bhalla, Mirella Di Lorenzo, Giordano Pula et al.     Phosphorylation by kinases is an important post-translational modification of proteins. It is a critical control for the regulation of vital cellular activities, and its …             All-optical broadband ultrasonography of single cells ▶     T. Dehoux, M. Abi Ghanem, O. F. Zouani et al.     Cell mechanics play a key role in several fundamental biological processes, such as migration, proliferation, differentiation and tissue morphogenesis. In addition, many diseased …             Massive expansion and functional divergence of innate immune genes in a protostome ▶     Linlin Zhang, Li Li, Ximing Guo et al.     The molecules that mediate innate immunity are encoded by relatively few genes and exhibit broad specificity. Detailed annotation of the Pacific oyster (Crassostrea gigas) …             A quantum protective mechanism in photosynthesis ▶     Adriana Marais, Ilya Sinayskiy, Francesco Petruccione et al.     Since the emergence of oxygenic photosynthesis, living systems have developed protective mechanisms against reactive oxygen species. During charge separation in photosynthetic …             Pre-activation of mesenchymal stem cells with TNF-α, IL-1β and nitric oxide enhances its paracrine effects on radiation-induced intestinal injury ▶     Hao Chen, Xiao-Hui Min, Qi-Yi Wang et al.     Conditioned medium from mesenchymal stem cells (MSC-CM) may represent a promising alternative to MSCs transplantation, however, the low concentrations of growth factors in …             Crystal structure of Gib2, a signal-transducing protein scaffold associated with ribosomes inCryptococcus neoformans ▶     Rya Ero, Valya Tenusheva Dimitrova, Yun Chen et al.     The atypical Gβ-like/RACK1 Gib2 protein promotes cAMP signalling that plays a central role in regulating the virulence ofCryptococcus neoformans. Gib2 contains a seven-bladed β …                 Don't let your data go to waste...  Scientific Data helps researchers make the most of their data, offering publication in a peer reviewed open access journal. 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