Scientific Reports Biology Table of Contents e-alert: 31 March 2015

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31 March 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               A phylogenetically informed delineation of floristic regions within a biodiversity hotspot in Yunnan, China ▶     Rong Li, Nathan J. B. Kraft, Jie Yang et al.     Traditional attempts to delineate floristic regions typically focus on species distributions, often ignoring the rich context that phylogenetic relationships can provide. In this …             Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites ▶     Yana Valasatava, Claudia Andreini, Antonio Rosato     Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new …             A novel method for furfural recovery via gas stripping assisted vapor permeation by a polydimethylsiloxane membrane ▶     Song Hu, Yu Guan, Di Cai et al.     Furfural is an important platform chemical with a wide range of applications. However, due to the low concentration of furfural in the hydrolysate, the conventional methods for …             Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses ▶     Geng Chen, Dianke Yu, Jiwei Chen et al.     Using RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic …             Spatial training preserves associative memory capacity with augmentation of dendrite ramification and spine generation in Tg2576 mice ▶     Xia Jiang, Gao-Shang Chai, Zhi-Hao Wang et al.     Alzheimer's disease (AD) is the most common neurodegenerative disorder and there is currently no efficient cure for this devastating disease. Cognitive stimulation can delay …             Sestrin2 inhibits mTORC1 through modulation of GATOR complexes ▶     Jeong Sig Kim, Seung-Hyun Ro, Myungjin Kim et al.     Sestrins are stress-inducible metabolic regulators that suppress a wide range of age- and obesity-associated pathologies, many of which are due to mTORC1 overactivation. Upon …             A novel high light-inducible carotenoid-binding protein complex in the thylakoid membranes of Synechocystis PCC 6803 ▶     Soumana Daddy, Jiao Zhan, Saowarath Jantaro et al.     Synechocystis sp. PCC 6803 is a model cyanobacterium extensively used to study photosynthesis. Here we reveal a novel high light-inducible carotenoid-binding protein complex …             Probing the protective mechanism of poly-ß-hydroxybutyrate against vibriosis by using gnotobiotic Artemia franciscana and Vibrio campbellii as host-pathogen model ▶     Kartik Baruah, Tran T. Huy, Parisa Norouzitallab et al.     The compound poly-ß-hydroxybutyrate (PHB), a polymer of the short chain fatty acid ß-hydroxybutyrate, was shown to protect experimental animals against a variety of bacterial …             PHY906(KD018), an adjuvant based on a 1800-year-old Chinese medicine, enhanced the anti-tumor activity of Sorafenib by changing the tumor microenvironment ▶     Wing Lam, Zaoli Jiang, Fulan Guan et al.     PHY906 (KD018) is a four-herb Chinese Medicine Formula. It has been shown to potentially enhance the therapeutic indices of different class anticancer agents in vivo. Here, …             The importance of sensory integration processes for action cascading ▶     Krutika Gohil, Ann-Kathrin Stock, Christian Beste     Dual tasking or action cascading is essential in everyday life and often investigated using tasks presenting stimuli in different sensory modalities. Findings obtained with …             Novel Role of Mitochondrial Manganese Superoxide Dismutase in STAT3 Dependent Pluripotency of Mouse Embryonic Stem Cells ▶     Preethi Sheshadri, Ashwathnarayan Ashwini, Sowmya Jahnavi et al.     Leukemia Inhibitory Factor (LIF)/Signal transducer and activator of transcription 3 (STAT3) signaling pathway maintains the stemness and pluripotency of mouse embryonic stem …             Interactome of the negative regulator of nuclear import BRCA1-binding protein 2 ▶     Shadma Fatima, Kylie M. Wagstaff, Kate L. Loveland et al.     Although the negative regulator of nuclear import (NRNI) BRCA1 binding protein 2 (BRAP2) is highly expressed in testis, its role is largely unknown. Here we address this question …             Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales ▶     Jing Luo, Huan Qiu, Guohong Cai et al.     The order Magnaporthales (Ascomycota, Fungi) includes devastating pathogens of cereals, such as the rice blast fungus Pyricularia (Magnaporthe) oryzae, which is a model in …             Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis ▶     Awawing A. Andongma, Lun Wan, Yong-Cheng Dong et al.     Bactrocera dorsalis is one of the most economically important fruit flies around the world. In this study, 454 pyrosequencing was used to identify the bacteria associated with …             A mobile biosafety microanalysis system for infectious agents ▶     Daniel R. Beniac, Shannon L. Hiebert, Christine G. Siemens et al.     Biological threats posed by pathogens such as Ebola virus must be quickly diagnosed, while protecting the safety of personnel. Scanning electron microscopy and microanalysis …             A large mimotonid from the Middle Eocene of China sheds light on the evolution of lagomorphs and their kin ▶     Łucja Fostowicz-Frelik, Chuankui Li, Fangyuan Mao et al.     Mimotonids share their closest affinity with lagomorphs and were a rare and endemic faunal element of Paleogene mammal assemblages of central Asia. Here we describe a new …             Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism ▶     Silvia Falcinelli, Simona Picchietti, Ana Rodiles et al.     The microbiome plays an important role in lipid metabolism but how the introduction of probiotic communities affects host lipid metabolism is poorly understood. Using a …             Multivalent Conjugation of Antibody to Dendrimers for the Enhanced Capture and Regulation on Colon Cancer Cells ▶     Jingjing Xie, Jichuang Wang, Hongning Chen et al.     Circulation tumor cells (CTCs) in the bloodstream of early-stage cancer patients carry the important information about valuable biomarkers and biological properties of primary …             Mechanical interplay between invadopodia and the nucleus in cultured cancer cells ▶     Or-Yam Revach, Allon Weiner, Katya Rechav et al.     Invadopodia are actin-rich membrane protrusions through which cells adhere to the extracellular matrix and degrade it. In this study, we explored the mechanical interactions of …             A novel PKD2L1 C-terminal domain critical for trimerization and channel function ▶     Wang Zheng, Shaimaa Hussein, JungWoo Yang et al.     As a transient receptor potential (TRP) superfamily member, polycystic kidney disease 2-like-1 (PKD2L1) is also called TRPP3 and has similar membrane topology as voltage-gated …             "Turn on" and label-free core−shell Ag@SiO2 nanoparticles-based metal-enhanced fluorescent (MEF) aptasensor for Hg2+ ▶     Yuanfeng Pang, Zhen Rong, Rui Xiao et al.     A turn on and label-free fluorescent apasensor for Hg2 with high sensitivity and selectivity has been demonstrated in this report. Firstly, core−shell Ag@SiO2 nanoparticles (NPs) …             Diagnostic Accuracy of Calretinin for Malignant Mesothelioma in Serous Effusions: a Meta-analysis ▶     Diandian Li, Bo Wang, Hongyu Long et al.     Numerous studies have investigated the utility of calretinin in differentiating malignant mesothelioma (MM) from metastatic carcinoma (MC) in serous effusions. However, the …             Conservation of writhe helicity under anti-parallel reconnection ▶     Christian E. Laing, Renzo L. Ricca, De Witt L. Sumners     Reconnection is a fundamental event in many areas of science, from the interaction of vortices in classical and quantum fluids, and magnetic flux tubes in magnetohydrodynamics and …             Causal relevance of circulating high-density lipoprotein cholesterol with cancer: a Mendelian randomization meta-analysis ▶     Chunhua Yang, Geng Tian, Jia Mi et al.     We summarized published data on the associations of apolipoprotein E (APOE) gene ε2/ε3/ε4 polymorphism with both cancer risk and circulating lipid profiles, aiming to examine the …             Downregulation of ubiquitin inhibits the proliferation and radioresistance of non-small cell lung cancer cells in vitro and in vivo ▶     Yiting Tang, Yangyang Geng, Judong Luo et al.     Radioresistance has been an important factor in restricting efficacy of radiotherapy for non-small cell lung cancer (NSCLC) patients and new approaches to inhibit cancer growth …             Inducible VEGF Expression by Human Embryonic Stem Cell-Derived Mesenchymal Stromal Cells Reduces the Minimal Islet Mass Required to Reverse Diabetes ▶     E. Hajizadeh-Saffar, Y. Tahamtani, N. Aghdami et al.     Islet transplantation has been hampered by loss of function due to poor revascularization. We hypothesize that co-transplantation of islets with human embryonic stem cell-derived …             In-line phase-contrast and grating-based phase-contrast synchrotron imaging study of brain micrometastasis of breast cancer ▶     Sheng Huang, Binquan Kou, Yayun Chi et al.     Current bio-medical imaging researches aim to detect brain micrometastasis in early stage for its increasing incidence and high mortality rates. Synchrotron phase-contrast …             The extent of inflammatory infiltration in primary cancer tissues is associated with lymphomagenesis in immunodeficient mice ▶     Lianhai Zhang, Yiqiang Liu, Xiaohong Wang et al.     Xenotransplantation of human cancers into immunodeficient mice is a very useful approach for studying human tumor biology. However, the occasional occurrence of lymphomagenesis …             Opposite rheological properties of neuronal microcompartments predict axonal vulnerability in brain injury ▶     Thomas Grevesse, Borna E. Dabiri, Kevin Kit Parker et al.     Although pathological changes in axonal morphology have emerged as important features of traumatic brain injury (TBI), the mechanical vulnerability of the axonal microcompartment …             Association of Body Mass Index with Chromosome Damage Levels and Lung Cancer Risk among Males ▶     Xiaoliang Li, Yansen Bai, Suhan Wang et al.     Epidemiological studies have shown an etiological link between body mass index (BMI) and cancer risk, but evidence supporting these observations is limited. This study aimed to …             Specificity of Hemodynamic Brain Responses to Painful Stimuli: A functional near-infrared spectroscopy study ▶     Meryem A. Yücel, Christopher M. Aasted, Mihayl P. Petkov et al.     Assessing pain in individuals not able to communicate (e.g. infants, under surgery, or following stroke) is difficult due to the lack of non-verbal objective measures of pain. …             Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation ▶     Yanqiong Zhang, Ming Bai, Bo Zhang et al.     Wu-tou decoction (WTD) has been extensively used for the treatment of rheumatoid arthritis (RA). Due to lack of appropriate methods, pharmacological mechanisms of WTD acting on …             Identification of proteins responsible for adriamycin resistance in breast cancer cells using proteomics analysis ▶     Zhipeng Wang, Shuang Liang, Xin Lian et al.     Chemoresistance is a poor prognostic factor in breast cancer and is a major obstacle to the successful treatment of patients receiving chemotherapy. However, the precise …             CORRIGENDUM: qPMS9: An Efficient Algorithm for Quorum Planted Motif Search ▶     Marius Nicolae, Sanguthevar Rajasekaran                 ERRATUM: Interlayer Water Regulates the Bio-nano Interface of a β-sheet Protein stacking on Graphene ▶     Wenping Lv, Guiju Xu, Hongyan Zhang et al.                 Toll-like receptor 4 contributes to the inhibitory effect of morphine on colonic motility in vitro and in vivo ▶     Aitak Farzi, Juraj Halicka, Raphaela Mayerhofer et al.     Opioids rank among the most potent analgesic drugs but gastrointestinal side effects, especially constipation, limit their therapeutic utility. The adverse effects of opioids …             Ancient inland human dispersals from Myanmar into interior East Asia since the Late Pleistocene ▶     Yu-Chun Li, Hua-Wei Wang, Jiao-Yang Tian et al.     Given the existence of plenty of river valleys connecting Southeast and East Asia, it is possible that some inland route(s) might have been adopted by the initial settlers to …             The modulation of nicotinic acetylcholine receptors on the neuronal network oscillations in rat hippocampal CA3 area ▶     Yang Wang, Zhan Wang, Jiangang Wang et al.     γ oscillations are associated with higher brain functions such as memory, perception and consciousness. Disruption of γ oscillations occur in various neuro-psychological …             Genetic variants in de novo lipogenic pathway genes predict the prognosis of surgically-treated hepatocellular carcinoma ▶     Hequn Jiang, Jingyao Dai, Xiaojun huang et al.     Over-expression of de novo lipogenesis (DNL) pathway genes is associated with the prognosis of various types of cancers. However, effects of single nucleotide polymorphisms …             GLI2-dependent c-MYC upregulation mediates resistance of pancreatic cancer cells to the BET bromodomain inhibitor JQ1 ▶     Krishan Kumar, Sania S. Raza, Lawrence M. Knab et al.     JQ1 and I-BET151 are selective inhibitors of BET bromodomain proteins that have efficacy against a number of different cancers. Since the effectiveness of targeted therapies is …             Hydrophobic mismatch demonstrated for membranolytic peptides, and their use as molecular rulers to measure bilayer thickness in native cells ▶     Ariadna Grau-Campistany, Erik Strandberg, Parvesh Wadhwani et al.     Hydrophobic mismatch is a well-recognized principle in the interaction of transmembrane proteins with lipid bilayers. This concept was extended here to amphipathic membranolytic …             OsKinesin-13A Is an Active Microtubule Depolymerase Involved in Glume Length Regulation via Affecting Cell Elongation ▶     Zhu Yun Deng, Ling Tong Liu, Tang Li et al.     Grain size is an important trait influencing both the yield and quality of rice and its major determinant is glume size. However, how glume size is regulated remains largely …             Reassortant Highly Pathogenic Influenza A H5N2 Virus Containing Gene Segments Related to Eurasian H5N8 in British Columbia, Canada, 2014 ▶     John Pasick, Yohannes Berhane, Tomy Joseph et al.     In late November 2014 higher than normal death losses in a meat turkey and chicken broiler breeder farm in the Fraser Valley of British Columbia initiated a diagnostic …             The effect of music performance on the transcriptome of professional musicians ▶     Chakravarthi Kanduri, Tuire Kuusi, Minna Ahvenainen et al.     Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several neuroscientific …             Investigating a new neuromodulation treatment for brain disorders using synchronized activation of multimodal pathways ▶     Craig D. Markovitz, Benjamin T. Smith, Cory D. Gloeckner et al.     Neuromodulation is an increasingly accepted treatment for neurological and psychiatric disorders but is limited by its invasiveness or its inability to target deep brain …             ADP-ribose/TRPM2-mediated Ca2+ signaling is essential for cytolytic degranulation and antitumor activity of natural killer cells ▶     So-Young Rah, Jae-Yong Kwak, Yun-Jo Chung et al.     Natural killer (NK) cells are essential for immunosurveillance against transformed cells. Transient receptor potential melastatin 2 (TRPM2) is a Ca2-permeable cation channel …             The loss of Tm7sf gene accelerates skin papilloma formation in mice ▶     I. Bellezza, L. Gatticchi, R. del Sordo et al.     The 3β-hydroxysterol Δ14-reductase, encoded by the Tm7sf2 gene, is an enzyme involved in cholesterol biosynthesis. Cholesterol and its derivatives control epidermal barrier …             Entrainment of heterogeneous glycolytic oscillations in single cells ▶     Anna-Karin Gustavsson, Caroline B. Adiels, Bernhard Mehlig et al.     Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling …             Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids ▶     Melissa Ilardo, Markus Meringer, Stephen Freeland et al.     Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial …             Abnormal pairing of X and Y sex chromosomes during meiosis I in interspecific hybrids of Phodopus campbelli and P. sungorus ▶     Satoshi Ishishita, Kazuma Tsuboi, Namiko Ohishi et al.     Hybrid sterility plays an important role in the maintenance of species identity and promotion of speciation. Male interspecific hybrids from crosses between Campbell's dwarf …             Endurance training facilitates myoglobin desaturation during muscle contraction in rat skeletal muscle ▶     Hisashi Takakura, Yasuro Furuichi, Tatsuya Yamada et al.     At onset of muscle contraction, myoglobin (Mb) immediately releases its bound O2 to the mitochondria. Accordingly, intracellular O2 tension (PmbO2) markedly declines in order to …             Annexin V-induced rat Leydig cell proliferation involves Ect2 via RhoA/ROCK signaling pathway ▶     Jun Jing, Li Chen, Hai-Yan Fu et al.     This study investigated the effect of annexin V on the proliferation of primary rat Leydig cells and the potential mechanism. Our results showed that annexin V promoted rat …             Reprogramming of orientation columns in visual cortex: a domino effect ▶     Lyes Bachatene, Vishal Bharmauria, Sarah Cattan et al.     Cortical organization rests upon the fundamental principle that neurons sharing similar properties are co-located. In the visual cortex, neurons are organized into orientation …             Circumferential electrocautery of the patella in primary total knee replacement without patellar replacement: a meta-analysis and systematic review ▶     Lihong Fan, Zhaogang Ge, Chen Zhang et al.     The purpose of this meta-analysis and systematic review was to identify and assess whether circumferential electrocautery is useful for improving outcomes after primary total …             HPIP is upregulated in colorectal cancer and regulates colorectal cancer cell proliferation, apoptosis and invasion ▶     Yingying Feng, Xiaojie Xu, Yunjing Zhang et al.     Hematopoietic pre-B cell leukemia transcription factor (PBX)-interacting protein (HPIP) was shown to play a role in cancer development and progression. However, the role of HPIP …             Brain self-regulation in criminal psychopaths ▶     Lilian Konicar, Ralf Veit, Hedwig Eisenbarth et al.     Psychopathic individuals are characterized by impaired affective processing, impulsivity, sensation-seeking, poor planning skills and heightened aggressiveness with poor …             Evaluation of extraction kits and RT-qPCR systems adapted to high-throughput platform for circulating miRNAs ▶     Geok Wee Tan, Alan Soo Beng Khoo, Lu Ping Tan     MicroRNAs regulate gene expression at the post-transcriptional level. Differential expression of miRNAs can potentially be used as biomarkers for early diagnosis and prediction …             Effects of the Fukushima Daiichi nuclear accident on goshawk reproduction ▶     Kaori Murase, Joe Murase, Reiko Horie et al.     Although the influence of nuclear accidents on the reproduction of top predators has not been investigated, it is important that we identify the effects of such accidents because …             Caught in Action: Selecting Peptide Aptamers Against Intrinsically Disordered Proteins in Live Cells ▶     Jacqueline D. Cobbert, Christopher DeMott, Subhabrata Majumder et al.     Intrinsically disordered proteins (IDPs) or unstructured segments within proteins play an important role in cellular physiology and pathology. Low cellular concentration, …             MicroRNA-26a prevents endothelial cell apoptosis by directly targeting TRPC6 in the setting of atherosclerosis ▶     Yong Zhang, Wei Qin, Longyin Zhang et al.     Atherosclerosis, a chronic inflammatory disease, is the major cause of life-threatening complications such as myocardial infarction and stroke. Endothelial apoptosis plays a …             Structure and function of a Clostridium difficile sortase enzyme ▶     Christopher J. Chambers, April K. Roberts, Clifford C. Shone et al.     Sortase enzymes are responsible for covalent anchoring of specific proteins to the peptidoglycan of the cell wall of gram-positive bacteria. In some gram-positive bacteria (e.g. …             Glucocorticoid receptors in the locus coeruleus mediate sleep disorders caused by repeated corticosterone treatment ▶     Zi-Jun Wang, Xue-Qiong Zhang, Xiang-Yu Cui et al.     Stress induced constant increase of cortisol level may lead to sleep disorder, but the mechanism remains unclear. Here we described a novel model to investigate stress mimicked …             Portable Microfluidic Integrated Plasmonic Platform for Pathogen Detection ▶     Onur Tokel, Umit Hakan Yildiz, Fatih Inci et al.     Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked …             Ethnic differences in the association of SERPING1 with age-related macular degeneration and polypoidal choroidal vasculopathy ▶     Ke Liu, Timothy Y. Y. Lai, Li Ma et al.     Neovascular age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV) are leading causes of irreversible blindness in developed countries. In this study, …             EphB2 activation is required for ependymoma development as well as inhibits differentiation and promotes proliferation of the transformed cell ▶     Phylip Chen, Nathan Rossi, Samuel Priddy et al.     Our intracranial implantation mouse model of ependymoma clearly demonstrates overexpression of the ephrin receptor EphB2 in Ink4a/Arf(−/−) supratentorial embryonic neural stem …             Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis ▶     Yongxin Li, Zhongrui Li, Kazuya Yamanaka et al.     Bacilli are ubiquitous low GC environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic …             Multiscale visualization of the structural and characteristic changes of sewage sludge biochar oriented towards potential agronomic and environmental implication ▶     Jining Zhang, Fan Lü, Hua Zhang et al.     Sewage sludge biochars were obtained at different pyrolysis temperatures from 300°C to 900°C and their macro- and microscale properties were analyzed. 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