Scientific Reports Biology Table of Contents e-alert: 9 December 2014

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09 December 2014      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               A Tool Set to Map Allosteric Networks through the NMR Chemical Shift Covariance Analysis ▶     Stephen Boulton, Madoka Akimoto, Rajeevan Selvaratnam et al.     Allostery is an essential regulatory mechanism of biological function. Allosteric sites are also pharmacologically relevant as they are often targeted with higher selectivity …             Re-emergent Human Adenovirus Genome Type 7d Caused an Acute Respiratory Disease Outbreak in Southern China After a Twenty-one Year Absence ▶     Suhui Zhao, Chengsong Wan, Changwen Ke et al.     Human adenoviruses (HAdVs) are highly contagious pathogens causing acute respiratory disease (ARD), among other illnesses. Of the ARD genotypes, HAdV-7 presents with more severe …             Xanthohumol suppresses oestrogen-signalling in breast cancer through the inhibition of BIG3-PHB2 interactions ▶     Tetsuro Yoshimaru, Masato Komatsu, Etsu Tashiro et al.     Xanthohumol (XN) is a natural anticancer compound that inhibits the proliferation of oestrogen receptor-α (ERα)-positive breast cancer cells. However, the precise mechanism of …             Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods ▶     Yuhua Wu, Yulei Wang, Jun Li et al.     The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported …             Stability of Gut Enterotypes in Korean Monozygotic Twins and Their Association with Biomarkers and Diet ▶     Mi Young Lim, Mina Rho, Yun-Mi Song et al.     Studies on the human gut microbiota have suggested that human individuals could be categorized into enterotypes based on the compositions of their gut microbial communities. …             Standing-wave-excited multiplanar fluorescence in a laser scanning microscope reveals 3D information on red blood cells ▶     Rumelo Amor, Sumeet Mahajan, William Bradshaw Amos et al.     Standing-wave excitation of fluorescence is highly desirable in optical microscopy because it improves the axial resolution. We demonstrate here that multiplanar excitation of …             Super-resolution microscopy reveals LINC complex recruitment at nuclear indentation sites ▶     Marie Versaevel, Jean-Baptiste Braquenier, Maryam Riaz et al.     Increasing evidences show that the actin cytoskeleton is a key parameter of the nuclear remodeling process in response to the modifications of cellular morphology. However, …             Vertebrate Hedgehog is secreted on two types of extracellular vesicles with different signaling properties ▶     Neha Vyas, Ankita Walvekar, Dhananjay Tate et al.     Hedgehog (Hh) is a secreted morphogen that elicits differentiation and patterning in developing tissues. Multiple proposed mechanisms to regulate Hh dispersion includes …             Exhaled volatile organic compounds as lung cancer biomarkers during one-lung ventilation ▶     Changsong Wang, Ran Dong, Xiaoyang Wang et al.     In this study, single-lung ventilation was used to detect differences in the volatile organic compound (VOCs) profiles between lung tissues in healthy and affected lungs. In …             T2DM GWAS in the Lebanese population confirms the role of TCF7L2 and CDKAL1 in disease susceptibility ▶     Michella Ghassibe-Sabbagh, Marc Haber, Angelique K. Salloum et al.     Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are crucial to the understanding of Type 2 Diabetes Mellitus …             Capture-stabilize approach for membrane protein SPR assays ▶     Ruiyin Chu, David Reczek, William Brondyk     Measuring the binding kinetics of antibodies to intact membrane proteins by surface plasmon resonance has been challenging largely because of the inherent difficulties in …             Homotypic NK cell-to-cell communication controls cytokine responsiveness of innate immune NK cells ▶     Tae-Jin Kim, Miju Kim, Hye Mi Kim et al.     While stationary organ cells are in continuous contact with neighboring cells, immune cells circulate throughout the body without an apparent requirement for cell-cell contact to …             Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome ▶     Kim Sneppen, Szabolcs Semsey     The mismatch repair system (MMR) corrects replication errors that escape proofreading. Previous studies on extrachromosomal DNA in Escherichia coli suggested that MMR uses …             In Vivo Flow Mapping in Complex Vessel Networks by Single Image Correlation ▶     Laura Sironi, Margaux Bouzin, Donato Inverso et al.     We describe a novel method (FLICS, FLow Image Correlation Spectroscopy) to extract flow speeds in complex vessel networks from a single raster-scanned optical xy-image, acquired …             Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues ▶     Zhicheng Pan, Zexian Liu, Han Cheng et al.     Recent studies have indicated that different post-translational modifications (PTMs) synergistically orchestrate specific biological processes by crosstalks. However, the …             Nuclemeter: A Reaction-Diffusion Based Method for Quantifying Nucleic Acids Undergoing Enzymatic Amplification ▶     Changchun Liu, Mohamed M. Sadik, Michael G. Mauk et al.     Real-time amplification and quantification of specific nucleic acid sequences plays a major role in medical and biotechnological applications. In the case of infectious diseases, …             Construction of a Hypervirulent and Specific Mycoinsecticide for Locust Control ▶     Weiguo Fang, Hsiao-Ling Lu, Glenn F. King et al.     Locusts and grasshoppers (acridids) are among the worst pests of crops and grasslands worldwide. Metarhizium acridum, a fungal pathogen that specifically infects acridids, has …             Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons ▶     Jie Li, Qi Chen, Li-Juan Long et al.     Investigation of the response of coral microbial communities to seasonal ecological environment at the microscale will advance our understanding of the relationship between …             Inositol Polyphosphate-5-Phosphatase F (INPP5F) inhibits STAT3 activity and suppresses gliomas tumorigenicity ▶     Hong Sug Kim, Aiguo Li, Susie Ahn et al.     Glioblastoma (GBM), the most common type of primary malignant brain tumors harboring a subpopulation of stem-like cells (GSCs), is a fast-growing and often fatal tumor. Signal …             A multicolor panel of TALE-KRAB based transcriptional repressor vectors enabling knockdown of multiple gene targets ▶     Zhonghui Zhang, Elise Wu, Zhijian Qian et al.     Stable and efficient knockdown of multiple gene targets is highly desirable for dissection of molecular pathways. Because it allows sequence-specific DNA binding, transcription …             Spider silk gut: Development and characterization of a novel strong spider silk fiber ▶     Ping Jiang, Núria Marí-Buyé, Rodrigo Madurga et al.     Spider silk fibers were produced through an alternative processing route that differs widely from natural spinning. The process follows a procedure traditionally used to obtain …             fM to aM nucleic acid amplification for molecular diagnostics in a non-stick-coated metal microfluidic bioreactor ▶     Guoliang Huang, Qin Huang, Li Ma et al.     A sensitive DNA isothermal amplification method for the detection of DNA at fM to aM concentrations for pathogen identification was developed using a non-stick-coated metal …             Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase ▶     Tong Zhu, Tadashi Satoh, Koichi Kato     The endoplasmic reticulum (ER) possesses a protein quality control system that supports the efficient folding of newly synthesized glycoproteins. In this system, a series of N…             CORRIGENDUM: Hes1 is involved in the self-renewal and tumourigenicity of stem-like cancer cells in colon cancer ▶     Fei Gao, YuQin Zhang, ShengChun Wang et al.                 In-vivo Optical Tomography of Small Scattering Specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster ▶     Alicia Arranz, Di Dong, Shouping Zhu et al.     Even though in vivo imaging approaches have witnessed several new and important developments, specimens that exhibit high light scattering properties such as Drosophila …             Intervention-induced enhancement in intrinsic brain activity in healthy older adults ▶     Shufei Yin, Xinyi Zhu, Rui Li et al.     This study examined the effects of a multimodal intervention on spontaneous brain activity in healthy older adults. Seventeen older adults received a six-week intervention that …             Small effects of smoking on visual spatiotemporal processing ▶     Marina Kunchulia, Karin S. Pilz, Michael H. Herzog     Nicotine is an important stimulant that is involved in modulating many neuronal processes, including those related to vision. Nicotine is also thought to play a key role in …             Rigosertib as a selective anti-tumor agent can ameliorate multiple dysregulated signaling transduction pathways in high-grade myelodysplastic syndrome ▶     Feng Xu, Qi He, Xiao Li et al.     Rigosertib has demonstrated therapeutic activity for patients with high-risk myelodysplastic syndrome (MDS) in clinical trials. However, the role of rigosertib in MDS has not …             The homeobox gene DLX4 promotes generation of human induced pluripotent stem cells ▶     Naritaka Tamaoki, Kazutoshi Takahashi, Hitomi Aoki et al.     The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by defined transcription factors has been a well-established technique and will provide an …             Combining TGF-β signal inhibition and connexin43 silencing for iPSC induction from mouse cardiomyocytes ▶     Ping Dai, Yoshinori Harada, Hitoshi Miyachi et al.     The reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) can be achieved by ectopic expression of defined transcription factors (Oct3/4, Sox2, Klf4 …             Stem cell differentiation increases membrane-actin adhesion regulating cell blebability, migration and mechanics ▶     Kristina Sliogeryte, Stephen D. Thorpe, David A. Lee et al.     This study examines how differentiation of human mesenchymal stem cells regulates the interaction between the cell membrane and the actin cortex controlling cell behavior. …             Sevoflurane Postconditioning Protects Rat Hearts against Ischemia-Reperfusion Injury via the Activation of PI3K/AKT/mTOR Signaling ▶     Jing Zhang, Chen Wang, Shuchun Yu et al.     Phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway plays a key role in myocardial ischemia-reperfusion (I/R) injury. Mammalian target of rapamycin (mTOR), a …             Utilisation of adsorption and desorption for simultaneously improving protein crystallisation success rate and crystal quality ▶     Yun-Zhu Guo, Li-Hua Sun, Dominik Oberthuer et al.     High-quality protein crystals of suitable size are an important prerequisite for applying X-ray crystallography to determine the 3-dimensional structure of proteins. However, it …             Global connectivity of hub residues in Oncoprotein structures encodes genetic factors dictating personalized drug response to targeted Cancer therapy ▶     Venky Soundararajan, Murali Aravamudan     The efficacy and mechanisms of therapeutic action are largely described by atomic bonds and interactions local to drug binding sites. Here we introduce global connectivity …             Prion protein- and cardiac troponin T-marked interstitial cells from the adult myocardium spontaneously develop into beating cardiomyocytes ▶     Mariko Omatsu-Kanbe, Yuka Nishino, Nozomi Nozuchi et al.     Atypically-shaped cardiomyocytes (ACMs) constitute a novel subpopulation of beating heart cells found in the cultures of cardiac myocyte-removed crude fraction cells obtained …             AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping ▶     Zhiqiang Xia, Meiling Zou, Shengkui Zhang et al.     We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted …             Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase ▶     Kaoru Kumazaki, Toshiki Kishimoto, Arata Furukawa et al.     Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for …             Prosthetic ankle push-off work reduces metabolic rate but not collision work in non-amputee walking ▶     Joshua M. Caputo, Steven H. Collins     Individuals with unilateral below-knee amputation expend more energy than non-amputees during walking and exhibit reduced push-off work and increased hip work in the affected …             HER2 confers drug resistance of human breast cancer cells through activation of NRF2 by direct interaction ▶     Hyo Jin Kang, Yong Weon Yi, Young Bin Hong et al.     Overexpression and/or activation of HER2 confers resistance of cancer cells to chemotherapeutic drugs. NRF2 also gives drug resistance of cancer cells through induction of …             Overexpression of Toll-like receptor 8 correlates with the progression of podocyte injury in murine autoimmune glomerulonephritis ▶     Junpei Kimura, Osamu Ichii, Kosuke Miyazono et al.     Members of the Toll-like receptor (TLR) family serve as pathogen sensors and participate in local autoimmune responses. This study found a correlation between glomerular injury …             Interferon-Inducible Cholesterol-25-Hydroxylase Inhibits Hepatitis C Virus Replication via Distinct Mechanisms ▶     Yongzhi Chen, Shanshan Wang, Zhaohong Yi et al.     Cholesterol 25-hydroxylase (CH25H) as an interferon-stimulated gene (ISG) has recently been shown to exert broad antiviral activity through the production of …             Overexpression of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) delays Alzheimer's progression in vivo ▶     Mingming Zhang, Fang Cai, Shuting Zhang et al.     Deposition of amyloid β protein (Aβ) to form neuritic plaques in the brain is the pathological hallmark of Alzheimer's disease (AD). Aβ is produced by β- and γ-cleavages of …             A novel mechanism of protein thermostability: a unique N-terminal domain confers heat resistance to Fe/Mn-SODs ▶     Wei Wang, Ting Ma, Baoliang Zhang et al.     Superoxide dismutases (SODs), especially thermostable SODs, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent …             Increased cortical responses to forepaw stimuli immediately after peripheral deafferentation of hindpaw inputs ▶     D. Humanes-Valera, G. Foffani, J. Aguilar     Both central and peripheral injuries of the nervous system induce dramatic reorganization of the primary somatosensory cortex. We recently showed that spinal cord injuries at …             RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking ▶     Xiaosi Lin, Ting Yang, Shicong Wang et al.     The HOPS complex serves as a tethering complex with GEF activity for Ypt7p in yeast to regulate late endosomal membrane maturation. While the role of HOPS complex is well …             Regulation of synaptic plasticity and cognition by SUMO in normal physiology and Alzheimer's disease ▶     Linda Lee, Elena Dale, Agnes Staniszewski et al.     Learning and memory and the underlying cellular correlate, long-term synaptic plasticity, involve regulation by posttranslational modifications (PTMs). Here we demonstrate that …             Activation of NLRP3 inflammasome by crystalline structures via cell surface contact ▶     Aswin Hari, Yifei Zhang, Zhongyuan Tu et al.     Crystalline structures activate the NLRP3 inflammasome, leading to the production of IL-1β, however, the molecular interactions responsible for NLRP3 activation are not fully …             Bipolar/rod-shaped microglia are proliferating microglia with distinct M1/M2 phenotypes ▶     Wing Yip Tam, Chi Him Eddie Ma     Microglia are generally considered the resident immune cells in the central nervous system (CNS) that regulate the primary events of neuroinflammatory responses. Microglia also …             Pleiotropy of the de novo-originated gene MDF1 ▶     Dan Li, Zhihui Yan, Lina Lu et al.     MDF1 is a young de novo-originated gene from a non-coding sequence in baker's yeast, S. cerevisiae, which can suppress mating and promote vegetative growth. Our previous …             Unravelling crucial biomechanical resilience of myelinated peripheral nerve fibres provided by the Schwann cell basal lamina and PMP22 ▶     Gonzalo Rosso, Ivan Liashkovich, Burkhard Gess et al.     There is an urgent need for the research of the close and enigmatic relationship between nerve biomechanics and the development of neuropathies. 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