Scientific Reports Biology Table of Contents e-alert: 29 September 2015

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29 September 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               Activated WNT signaling in postnatal SOX2-positive dental stem cells can drive odontoma formation ▶     Guilherme M. Xavier, Amanda L. Patist, Chris Healy et al.     In common with most mammals, humans form only two dentitions during their lifetime. Occasionally, supernumerary teeth develop in addition to the normal complement. Odontoma …             Ursolic acid exerts anti-cancer activity by suppressing vaccinia-related kinase 1-mediated damage repair in lung cancer cells ▶     Seong-Hoon Kim, Hye Guk Ryu, Juhyun Lee et al.     Many mitotic kinases have been targeted for the development of anti-cancer drugs, and inhibitors of these kinases have been expected to perform well for cancer therapy. Efforts …             Human Induced Pluripotent Stem Cell Derived Neuronal Cells Cultured on Chemically-Defined Hydrogels for Sensitive In Vitro Detection of Botulinum Neurotoxin ▶     Sabine Pellett, Michael P. Schwartz, William H. Tepp et al.     Botulinum neurotoxin (BoNT) detection provides a useful model for validating cell-based neurotoxicity screening approaches, as sensitivity is dependent on functionally competent …             Structural Mechanism for Regulation of Bcl-2 protein Noxa by phosphorylation ▶     Christine B. Karim, L. Michel Espinoza-Fonseca, Zachary M. James et al.     We showed previously that phosphorylation of Noxa, a 54-residue Bcl-2 protein, at serine 13 (Ser13) inhibited its ability to promote apoptosis through interactions with canonical …             Illusory Tactile Motion Perception: An Analog of the Visual Filehne Illusion ▶     Alessandro Moscatelli, Vincent Hayward, Mark Wexler et al.     We continually move our body and our eyes when exploring the world, causing our sensory surfaces, the skin and the retina, to move relative to external objects. In order to …             Antibody-mediated disruption of the mechanics of CS20 fimbriae of enterotoxigenic Escherichia coli ▶     Bhupender Singh, Narges Mortezaei, Bernt Eric Uhlin et al.     Preventive vaccines against enterotoxigenic Escherichia coli (ETEC) are being developed, many of which target common fimbrial colonization factors as the major constituent, based …             Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus ▶     Mi Liu, Xiang Zhao, Sha Hua et al.     The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution …             A peptide factor secreted by Staphylococcus pseudintermedius exhibits properties of both bacteriocins and virulence factors ▶     Benedykt Wladyka, Marcin Piejko, Monika Bzowska et al.     Staphylococcus pseudintermedius is a common commensal bacterium colonizing the skin and mucosal surfaces of household animals. However, it has recently emerged as a dangerous …             Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach ▶     Tunahan Çakır     A systems-based investigation of the effect of perturbations on metabolic machinery is crucial to elucidate the mechanism behind perturbations. One way to investigate the …             The arsenic hyperaccumulating Pteris vittata expresses two arsenate reductases ▶     Patrizia Cesaro, Chiara Cattaneo, Elisa Bona et al.     Enzymatic reduction of arsenate to arsenite is the first known step in arsenate metabolism in all organisms. Although the presence of one mRNA arsenate reductase (PvACR2) has …             Steric Interference of Adhesion Supports In-Vitro Chondrogenesis of Mesenchymal Stem Cells on Hydrogels for Cartilage Repair ▶     Revital Goldshmid, Shlomit Cohen, Yonatan Shachaf et al.     Recent studies suggest the presence of cell adhesion motifs found in structural proteins can inhibit chondrogenesis. In this context, the current study aims to determine if a …             Chronic TLR Stimulation Controls NLRP3 Inflammasome Activation through IL-10 Mediated Regulation of NLRP3 Expression and Caspase-8 Activation ▶     Prajwal Gurung, Bofeng Li, R. K. Subbarao Malireddi et al.     While the molecular mechanisms promoting activation of the Nod-like Receptor (NLR) family member NLRP3 inflammasome are beginning to be defined, little is known about the …             Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth ▶     Xueshu Xie, Daniel Backman, Albert T. Lebedev et al.     Sixty years after the seminal Miller-Urey experiment that abiotically produced a mixture of racemized amino acids, we provide a definite proof that this primordial soup, when …             Activating transcription factor 3 represses inflammatory responses by binding to the p65 subunit of NF-κB ▶     Ji-Woong Kwon, Hyuk-Kwon Kwon, Hyeon-Jun Shin et al.     Activating transcription factor 3 (ATF3) is induced by inflammatory responses, cell death, cytokines, and oxidative stress conditions. ATF3 is a negative regulator in the …             Genome wide discovery of long intergenic non-coding RNAs in Diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains ▶     Kayvan Etebari, Michael J. Furlong, Sassan Asgari     Long non-coding RNAs (lncRNAs) play important roles in genomic imprinting, cancer, differentiation and regulation of gene expression. Here, we identified 3844 long intergenic …             Evidence of a deep viral host switch event with beak and feather disease virus infection in rainbow bee-eaters (Merops ornatus) ▶     Subir Sarker, Kathy G. Moylan, Seyed A. Ghorashi et al.     Since the characterization of psittacine beak and feather disease (PBFD) in 1984, a wide range of avian circoviruses have been discovered with varying pathogenic effects amongst …             A generalized target theory and its applications ▶     Lei Zhao, Dong Mi, Bei Hu et al.     Different radiobiological models have been proposed to estimate the cell-killing effects, which are very important in radiotherapy and radiation risk assessment. However, most …             HMGA1 overexpression in adipose tissue impairs adipogenesis and prevents diet-induced obesity and insulin resistance ▶     Altamira Arce-Cerezo, Miquel García, Aida Rodríguez-Nuevo et al.     High-Mobility-Group-A1 (HMGA1) proteins are non-histone proteins that regulate chromatin structure and gene expression during embryogenesis, tumourigenesis and immune responses. …             Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents ▶     Yuri Kimura, Melissa T. R. Hawkins, Molly M. McDonough et al.     Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of …             Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods ▶     John C. Mu, Pegah Tootoonchi Afshar, Marghoob Mohiyuddin et al.     A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput …             Genomic and transcriptomic insights into the efficient entomopathogenicity of Bacillus thuringiensis ▶     Lei Zhu, Donghai Peng, Yueying Wang et al.     Bacillus thuringiensis has been globally used as a microbial pesticide for over 70 years. However, information regarding its various adaptions and virulence factors and their …             Cargo Delivery into the Brain by in vivo identified Transport Peptides ▶     Eduard Urich, Roland Schmucki, Nadine Ruderisch et al.     The blood-brain barrier and the blood-cerebrospinal fluid barrier prevent access of biotherapeutics to their targets in the central nervous system and therefore prohibit the …             O-GlcNAcylation regulates ischemia-induced neuronal apoptosis through AKT signaling ▶     Jianhua Shi, Jin-hua Gu, Chun-ling Dai et al.     Apoptosis plays an important role in neural development and neurological disorders. In this study, we found that O-GlcNAcylation, a unique protein posttranslational modification …             The determinant of periodicity in Mycoplasma pneumoniae incidence: an insight from mathematical modelling ▶     Ryosuke Omori, Yukihiko Nakata, Heidi L. Tessmer et al.     Until the early 1990s, incidences of Mycoplasma pneumoniae (MP) infection showed three to five year epidemic cycles in multiple countries, however, the mechanism for the MP …             Jagged-2 enhances immunomodulatory activity in adipose derived mesenchymal stem cells ▶     Zhu Xishan, Zhang Bin, Zhao Haiyue et al.     Adipose derived Mesenchymal stem cells (AMSCs) are able to expand in vitro and undergo differentiation into multiple cell lineages, yet have low immunogenicity while exhibiting …             PAK2 is an effector of TSC1/2 signaling independent of mTOR and a potential therapeutic target for Tuberous Sclerosis Complex ▶     Maria M. Alves, Gwenny M. Fuhler, Karla C.S. Queiroz et al.     Tuberous sclerosis complex (TSC) is caused by inactivating mutations in either TSC1 or TSC2 and is characterized by uncontrolled mTORC1 activation. Drugs that reduce mTOR …             Coronin7 regulates WASP and SCAR through CRIB mediated interaction with Rac proteins ▶     Karthic Swaminathan, Maria Stumpf, Rolf Müller et al.     Coronin7 (CRN7) stabilizes F-actin and is a regulator of processes associated with the actin cytoskeleton. Its loss leads to defects in phagocytosis, motility and development. It …             Functional Analyses of the Toxoplasma gondii DNA Gyrase Holoenzyme: A Janus Topoisomerase with Supercoiling and Decatenation Abilities ▶     Ting-Yu Lin, Soshichiro Nagano, Jonathan Gardiner Heddle     A number of important protozoan parasites including those responsible for toxoplasmosis and malaria belong to the phylum Apicomplexa and are characterised by their possession of …             Selective autophagic receptor p62 regulates the abundance of transcriptional coregulator ARIP4 during nutrient starvation ▶     Megumi Tsuchiya, Shin Isogai, Hiroaki Taniguchi et al.     Transcriptional coregulators contribute to several processes involving nuclear receptor transcriptional regulation. The transcriptional coregulator androgen receptor-interacting …             Ethyl acetate fraction of Amomum xanthioides improves bile duct ligation-induced liver fibrosis of rat model via modulation of pro-fibrogenic cytokines ▶     Hyeong-Geug Kim, Jong-Min Han, Jin-Seok Lee et al.     We investigated anti-hepatofibrotic effects of ethyl acetate fraction of Ammomum xanthoides (EFAX) using bile duct ligation (BDL)-induced hepatic fibrosis in a rat model. Male SD …             A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis ▶     Changzhen Liu, Yunfeng Zhao, Wen He et al.     Anti-cytokine therapeutic antibodies have been demonstrated to be effective in the treatment of several auto-immune disorders. However, The problems in antibody manufacture and …             Pharmacogenetics of Complement Factor H Y402H Polymorphism and Treatment of Neovascular AMD with Anti-VEGF Agents: A Meta-Analysis ▶     Guohai Chen, Radouil Tzekov, Wensheng Li et al.     The purpose of this study is to investigate whether the Y402H polymorphism (rs1061170, a T-to-C transition at amino acid position 402) in the complement factor H (CFH) gene have …             Renoprotective effect of long acting thioredoxin by modulating oxidative stress and macrophage migration inhibitory factor against rhabdomyolysis-associated acute kidney injury ▶     Kento Nishida, Hiroshi Watanabe, Shigeru Ogaki et al.     Rhabdomyolysis-associated acute kidney injury (AKI) is a serious life-threatening condition. As such, more effective strategies are needed for its prevention. Thioredoxin-1 …             Titanium dioxide nanoparticles stimulate sea urchin immune cell phagocytic activity involving TLR/p38 MAPK-mediated signalling pathway ▶     Annalisa Pinsino, Roberta Russo, Rosa Bonaventura et al.     Titanium dioxide nanoparticles (TiO2NPs) are one of the most widespread-engineered particles in use for drug delivery, cosmetics, and electronics. However, TiO2NP safety is still …             Metabolomics insights into chronic kidney disease and modulatory effect of rhubarb against tubulointerstitial fibrosis ▶     Zhi-Hao Zhang, Feng Wei, Nosratola D. Vaziri et al.     Chronic kidney disease (CKD) is a major public health problem worldwide. Rhubarb has been shown to have nephroprotective and anti-fibrotic activities in patients with CKD. …             Erratum: Musical training, individual differences and the cocktail party problem ▶     Jayaganesh Swaminathan, Christine R. Mason, Timothy M. Streeter et al.                 CRB2 completes a fully expressed Crumbs complex in the Retinal Pigment Epithelium ▶     Antonio E. Paniagua, Saúl Herranz-Martín, David Jimeno et al.     The CRB proteins CRB1, CRB2 and CRB3 are members of the cell polarity complex Crumbs in mammals that together with Scribble and Par complexes stablish the polarity of a variety …             Dynamic expression of chromatin modifiers during developmental transitions in mouse preimplantation embryos ▶     Peter Nestorov, Hans-Rudolf Hotz, Zichuan Liu et al.     During mouse preimplantation development, major changes in cell fate are accompanied by extensive alterations of gene expression programs. Embryos first transition from a …             Social Networks of Educated Nematodes ▶     Denis S. Willett, Hans T. Alborn, Larry W. Duncan et al.     Entomopathogenic nematodes are obligate lethal parasitoids of insect larvae that navigate a chemically complex belowground environment while interacting with their insect hosts, …             Cortical Folding Pattern and its Consistency Induced by Biological Growth ▶     Mir Jalil Razavi, Tuo Zhang, Tianming Liu et al.     Cortical folding, characterized by convex gyri and concave sulci, has an intrinsic relationship to the brain’s functional organization. Understanding the mechanism of the brain’s …             Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae ▶     Dong Yan, Yun Wang, Tatsuya Murakami et al.     The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still …             Decreased bilateral thalamic gray matter volume in first-episode schizophrenia with prominent hallucinatory symptoms: A volumetric MRI study ▶     Peng Huang, Yibin Xi, Zhong-Lin Lu et al.     Studies comparing gray matter (GM) volume of schizophrenic patients with or without auditory verbal hallucinations (AVHs) to that of normal controls remain controversial. This …             In situ biomarker discovery and label-free molecular histopathological diagnosis of lung cancer by ambient mass spectrometry imaging ▶     Tiegang Li, Jiuming He, Xinxin Mao et al.     Sensitive and spatial exploration of the metabolism of tumors at the metabolome level is highly challenging. In this study, we developed an in situ metabolomics method based on …             Molecular portraits revealing the heterogeneity of breast tumor subtypes defined using immunohistochemistry markers ▶     Xiaofeng Dai, Yang Li, Zhonghu Bai et al.     Breast cancer is highly heterogeneous. The subtypes defined using immunohistochemistry markers and gene expression profilings (GEP) are related but not equivalent, with …             Osmotic/ionic status of body fluids in the euryhaline cephalopod suggest possible parallel evolution of osmoregulation ▶     Tatsuya Sakamoto, Satoshi Ogawa, Yudai Nishiyama et al.     Acclimation from marine to dilute environments constitutes among the dramatic evolutionary transitions in the history of life. Such adaptations have evolved in multiple lineages, …             Recombinant human thrombopoietin promotes hematopoietic reconstruction after severe whole body irradiation ▶     Chao Wang, Bowen Zhang, Sihan Wang et al.     Recombinant human thrombopoietin (rHuTPO) is a drug that is used clinically to promote megakaryocyte and platelet generation. Here, we report the mitigative effect of rHuTPO …             Latitudinal variation of leaf stomatal traits from species to community level in forests: linkage with ecosystem productivity ▶     Ruili Wang, Guirui Yu, Nianpeng He et al.     To explore the latitudinal variation of stomatal traits from species to community level and their linkage with net primary productivity (NPP), we investigated leaf stomatal …             Isoform dependent regulation of human HCN channels by cholesterol ▶     Oliver Fürst, Nazzareno D’Avanzo     Cholesterol has been shown to regulate numerous ion channels. HCN channels represent the molecular correlate of If or Ih in sinoatrial node (SAN) and neuronal cells. Previous …             High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification ▶     Minghua Nie, Ajay A. Vashisht, James A. Wohlschlegel et al.     Covalent attachment of the small ubiquitin-like modifier (SUMO) to key targets in the proteome critically regulates the evolutionarily conserved processes of cell cycle control, …             Graph theoretic network analysis reveals protein pathways underlying cell death following neurotropic viral infection ▶     Sourish Ghosh, G. Vinodh Kumar, Anirban Basu et al.     Complex protein networks underlie any cellular function. Certain proteins play a pivotal role in many network configurations, disruption of whose expression proves fatal to the …             The synthesis of n-caproate from lactate: a new efficient process for medium-chain carboxylates production ▶     Xiaoyu Zhu, Yong Tao, Cheng Liang et al.     A unique microbiome that metabolizes lactate rather than ethanol for n-caproate production was obtained from a fermentation pit used for the production of Chinese strong-flavour …             Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas ▶     Yanhua Qu, Shilin Tian, Naijian Han et al.     Species that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a …             A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1 ▶     Mika Hayashi-Tsugane, Masahiko Maekawa, Kazuo Tsugane     A non-autonomous DNA transposon in rice, nDart1, is actively transposed in the presence of an autonomous element, aDart1, under natural conditions. The nDart1-promoted gene …             Angiotensin II receptor blockade promotes repair of skeletal muscle through down-regulation of aging-promoting C1q expression ▶     Chizuru Yabumoto, Hiroshi Akazawa, Rie Yamamoto et al.     Disruption of angiotensin II type 1 (AT1) receptor prolonged life span in mice. Since aging-related decline in skeletal muscle function was retarded in Atgr1a−/− mice, we …             The AP-1 transcription factor homolog Pf-AP-1 activates transcription of multiple biomineral proteins and potentially participates in Pinctada fucata biomineralization ▶     Xiangnan Zheng, Minzhang Cheng, Liang Xiang et al.     Activator protein-1 (AP-1) is an important bZIP transcription factor that regulates a series of physiological processes by specifically activating transcription of several genes, …             Structural basis of Ac-SDKP hydrolysis by Angiotensin-I converting enzyme ▶     Geoffrey Masuyer, Ross G. Douglas, Edward D. Sturrock et al.     Angiotensin-I converting enzyme (ACE) is a zinc dipeptidylcarboxypeptidase with two active domains and plays a key role in the regulation of blood pressure and electrolyte …             Coordinated vigilance provides evidence for direct reciprocity in coral reef fishes ▶     Simon J. Brandl, David R. Bellwood     Reciprocity is frequently assumed to require complex cognitive abilities. Therefore, it has been argued that reciprocity may be restricted to animals that can meet these demands. …             The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses ▶     Diego Forni, Giulia Filippi, Rachele Cagliani et al.     Middle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of the spike (S) …             Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation ▶     Sara L. Lawrence, Susanne C. Feil, Craig J. Morton et al.     Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural …             Transcriptome and gene expression analysis of DHA producer Aurantiochytrium under low temperature conditions ▶     Zengxin Ma, Yanzhen Tan, Guzhen Cui et al.     Aurantiochytrium is a promising docosahexaenoic acid (DHA) production candidate due to its fast growth rate and high proportions of lipid and DHA content. In this study, …             High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations ▶     Bryan T. Mott, Richard T. Eastman, Rajarshi Guha et al.     Drug resistance in Plasmodium parasites is a constant threat. Novel therapeutics, especially new drug combinations, must be identified at a faster rate. In response to the urgent …             Information content of contact-pattern representations and predictability of epidemic outbreaks ▶     Petter Holme     To understand the contact patterns of a population—who is in contact with whom, and when the contacts happen—is crucial for modeling outbreaks of infectious disease. Traditional …             The peptidylarginine deiminase gene is a conserved feature of Porphyromonas gingivalis ▶     Giorgio Gabarrini, Menke de Smit, Johanna Westra et al.     Periodontitis is an infective process that ultimately leads to destruction of the soft and hard tissues that support the teeth (the periodontium). Periodontitis has been proposed …             Microfluidic cytometric analysis of cancer cell transportability and invasiveness ▶     Zongbin Liu, Yeonju Lee, Joon hee Jang et al.     The extensive phenotypic and functional heterogeneity of cancer cells plays an important role in tumor progression and therapeutic resistance. Characterizing this heterogeneity …             Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography ▶     Juliana Martins de S. e Silva, Irene Zanette, Peter B. Noël et al.     Low inherent contrast in soft tissues has been limiting the use of X-ray absorption micro-computed tomography (micro-CT) to access high-resolution structural information of …             Role of the KATP channel in the protective effect of nicorandil on cyclophosphamide-induced lung and testicular toxicity in rats ▶     Lamiaa A. Ahmed, Shohda A. EL-Maraghy, Sherine M. Rizk     This study is the first to investigate the role of the KATP channel in the possible protection mediated by nicorandil against cyclophosphamide-induced lung and testicular …             Assessment of C-phycocyanin effect on astrocytes-mediated neuroprotection against oxidative brain injury using 2D and 3D astrocyte tissue model ▶     Seul Ki Min, Jun Sang Park, Lidan Luo et al.     Drugs are currently being developed to attenuate oxidative stress as a treatment for brain injuries. C-phycocyanin (C-Pc) is an antioxidant protein of green microalgae known to …             Corrigendum: Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution ▶     Michaela Liegertová, Jiří Pergner, Iryna Kozmiková et al.                 Translational compensation of genomic instability in neuroblastoma ▶     Erik Dassi, Valentina Greco, Viktoryia Sidarovich et al.     Cancer-associated gene expression imbalances are conventionally studied at the genomic, epigenomic and transcriptomic levels. Given the relevance of translational control in …             Integrative analysis of human protein, function and disease networks ▶     Wei Liu, Aiping Wu, Matteo Pellegrini et al.     Protein-protein interaction (PPI) networks serve as a powerful tool for unraveling protein functions, disease-gene and disease-disease associations. However, a direct strategy …             Optimization of neuronal cultures from rat superior cervical ganglia for dual patch recording ▶     Julien Amendola, Norah Boumedine, Marion Sangiardi et al.     Superior cervical ganglion neurons (SCGN) are often used to investigate neurotransmitter release mechanisms. In this study, we optimized the dissociation and culture conditions …             A Casparian strip domain-like gene, CASPL, negatively alters growth and cold tolerance ▶     Jinghua Yang, Changqing Ding, Baochen Xu et al.     A cold-induced transcript encoding a Casparian strip membrane domain (CASP)-like protein (ClCASPL) was identified in watermelon (Citrullus lanatus). Fluorescence microscopy …             Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir ▶     Sarah Knight, Steffen Klaere, Bruno Fedrizzi et al.     Many crops display differential geographic phenotypes and sensorial signatures, encapsulated by the concept of terroir. The drivers behind these differences remain elusive, and …             Enhanced nematicidal potential of the chitinase pachi from Pseudomonas aeruginosa in association with Cry21Aa ▶     Lin Chen, Huang Jiang, Qipeng Cheng et al.     Nematodes are known to be harmful to various crops, vegetables, plants and insects. The present study reports that, chitin upregulates the activity of chitinase (20%) and …             Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater ▶     Eelco Franz, Christiaan Veenman, Angela H. A. M. van Hoek et al.     To assess public health risks from environmental exposure to Extended-Spectrum β-Lactamases (ESBL)-producing bacteria, it is necessary to have insight in the proportion of …             Protein interaction patterns in different cellular environments are revealed by in-cell NMR ▶     Letizia Barbieri, Enrico Luchinat, Lucia Banci     In-cell NMR allows obtaining atomic-level information on biological macromolecules in their physiological environment. Soluble proteins may interact with the cellular environment …             Associations between interleukin and interleukin receptor gene polymorphisms and risk of gout ▶     Shiguo Liu, Zheng Zhou, Can Wang et al.     Gout is a self-limiting, auto-inflammatory arthritis induced by the deposition of monosodium urate crystals in the synovial fluid and periarticular tissues. The aim of this study …             Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil ▶     Souichiro Kato, Kanako Chino, Naofumi Kamimura et al.     Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation …             Starvation-Induced Dietary Behaviour in Drosophila melanogaster Larvae and Adults ▶     Muhammad Ahmad, Safee Ullah Chaudhary, Ahmed Jawaad Afzal et al.     Drosophila melanogaster larvae are classified as herbivores and known to feed on non-carnivorous diet under normal conditions. However, when nutritionally challenged these larvae …             Raster image cross-correlation analysis for spatiotemporal visualization of intracellular degradation activities against exogenous DNAs ▶     Akira Sasaki, Johtaro Yamamoto, Takashi Jin et al.     Reducing intracellular DNA degradation is critical to enhance the efficiency of gene therapy. Exogenous DNA incorporation into cells is strictly blocked by the defense machinery …             Opposite Effects of M1 and M2 Macrophage Subtypes on Lung Cancer Progression ▶     Ang Yuan, Yi-Jing Hsiao, Hsuan-Yu Chen et al.     Macrophages in a tumor microenvironment have been characterized as M1- and M2-polarized subtypes. Here, we discovered the different macrophages’ impacts on lung cancer cell A549. …             A novel adhesive factor contributing to the virulence of Vibrio parahaemolyticus ▶     Ming Liu, Sheng Chen     Bacterial adhesins play a pivotal role in the tight bacteria-host cells attachment to initiate the downstream processes and bacterial infection of hosts. In this study, we …             A quantitative study of 3D-scanning frequency and Δd of tracking points on the tooth surface ▶     Hong Li, Peijun Lyu, Yuchun Sun et al.     Micro-movement of human jaws in the resting state might influence the accuracy of direct three-dimensional (3D) measurement. Providing a reference for sampling frequency settings …             Arrhythmogenic effects of mutated L-type Ca2+-channels on an optogenetically paced muscular pump in Caenorhabditis elegans ▶     Christina Schüler, Elisabeth Fischer, Lior Shaltiel et al.     Cardiac arrhythmias are often associated with mutations in ion channels or other proteins. To enable drug development for distinct arrhythmias, model systems are required that …             How musical expertise shapes speech perception: evidence from auditory classification images ▶     Léo Varnet, Tianyun Wang, Chloe Peter et al.     It is now well established that extensive musical training percolates to higher levels of cognition, such as speech processing. However, the lack of a precise technique to …             Future climate effects on suitability for growth of oil palms in Malaysia and Indonesia ▶     R. Russell M. Paterson, Lalit Kumar, Subhashni Taylor et al.     The production of palm oil (PO) is highly profitable. The economies of the principal producers, Malaysia and Indonesia, and others, benefit considerably. Climate change (CC) will …             Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption ▶     Chelsea M. Rochman, Akbar Tahir, Susan L. Williams et al.     The ubiquity of anthropogenic debris in hundreds of species of wildlife and the toxicity of chemicals associated with it has begun to raise concerns regarding the presence of …             Longitudinal tracking of single live cancer cells to understand cell cycle effects of the nuclear export inhibitor, selinexor ▶     Joshua M. Marcus, Russell T. Burke, John A. DeSisto et al.     Longitudinal tracking is a powerful approach to understand the biology of single cells. In cancer therapy, outcome is determined at the molecular and cellular scale, yet …             DNAJB3/HSP-40 cochaperone improves insulin signaling and enhances glucose uptake in vitro through JNK repression ▶     Mohamed Abu-Farha, Preethi Cherian, Irina Al-Khairi et al.     Heat shock response (HSR) is an essential host-defense mechanism that is dysregulated in obesity-induced insulin resistance and type 2 diabetes (T2D). Our recent data …             Chronic multichannel neural recordings from soft regenerative microchannel electrodes during gait ▶     Katherine M. Musick, Jacopo Rigosa, Shreya Narasimhan et al.     Reliably interfacing a nerve with an electrode array is one of the approaches to restore motor and sensory functions after an injury to the peripheral nerve. Accomplishing this …             Inhibitory luminopsins: genetically-encoded bioluminescent opsins for versatile, scalable, and hardware-independent optogenetic inhibition ▶     Jack K. Tung, Claire-Anne Gutekunst, Robert E. Gross     Optogenetic techniques provide an unprecedented ability to precisely manipulate neural activity in the context of complex neural circuitry. Although the toolbox of optogenetic …             Designing new strategy for controlling DNA orientation in biosensors ▶     Chao Feng, Hong-ming Ding, Chun-lai Ren et al.     Orientation controllable DNA biosensors hold great application potentials in recognizing small molecules and detecting DNA hybridization. Though electric field is usually used to …             Targeted mutations in myostatin by zinc-finger nucleases result in double-muscled phenotype in Meishan pigs ▶     Lili Qian, Maoxue Tang, Jinzeng Yang et al.     Myostatin (MSTN) is a dominant inhibitor of skeletal muscle development and growth. Mutations in MSTN gene can lead to muscle hypertrophy or double-muscled (DM) phenotype in …             When fur and feather occur together: interclass transmission of avian influenza A virus from mammals to birds through common resources ▶     J. Jeffrey Root, Susan A. Shriner, Jeremy W. Ellis et al.     The potential role of wild mammals in avian influenza A virus (IAV) transmission cycles has received some attention in recent years and cases where birds have transmitted IAV to …             Low Expression of Slit2 and Robo1 is Associated with Poor Prognosis and Brain-specific Metastasis of Breast Cancer Patients ▶     Fengxia Qin, Huikun Zhang, Li Ma et al.     Brain metastasis is a significant unmet clinical problem in breast cancer treatment. It is always associated with poor prognosis and high morbidity. Recently, Slit2/Robo1 pathway …             Methylene Blue Inhibits Caspases by Oxidation of the Catalytic Cysteine ▶     Prateep Pakavathkumar, Gyanesh Sharma, Vikas Kaushal et al.     Methylene blue, currently in phase 3 clinical trials against Alzheimer Disease, disaggregates the Tau protein of neurofibrillary tangles by oxidizing specific cysteine residues. …             NIR-driven Smart Theranostic Nanomedicine for On-demand Drug Release and Synergistic Antitumour Therapy ▶     Pengfei Zhao, Mingbin Zheng, Zhenyu Luo et al.     Smart nanoparticles (NPs) that respond to external and internal stimulations have been developing to achieve optimal drug release in tumour. However, applying these smart NPs to …             Griffiths phases and localization in hierarchical modular networks ▶     Géza Ódor, Ronald Dickman, Gergely Ódor     We study variants of hierarchical modular network models suggested by Kaiser and Hilgetag [ Front. in Neuroinform., 4 (2010) 8] to model functional brain connectivity, using …             Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats ▶     Xu Zhang, Yufeng Zhao, Jia Xu et al.     Accumulating evidence suggests that the gut microbiota is an important factor in mediating the development of obesity-related metabolic disorders, including type 2 diabetes. …             A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation ▶     Wenguang Shao, Min Zhang, Henry Lam et al.     Shotgun proteomics is an emerging tool for bacterial identification and differentiation. However, the identification of the mass spectra of peptides to genome-derived peptide …             Entrainment of mouse peripheral circadian clocks to <24 h feeding/fasting cycles under 24 h light/dark conditions ▶     Yutaro Hamaguchi, Yu Tahara, Hiroaki Kuroda et al.     The circadian clock system in peripheral tissues can endogenously oscillate and is entrained by the light-dark and fasting-feeding cycles in mammals. Although the system’s range …             A Molecular Toolkit to Visualize Native Protein Assemblies in the Context of Human Disease ▶     Brian L. Gilmore, Carly E. Winton, Andrew C. Demmert et al.     We present a new molecular toolkit to investigate protein assemblies natively formed in the context of human disease. The system employs tunable microchips that can be decorated …             Arabidopsis VQ motif-containing proteins VQ12 and VQ29 negatively modulate basal defense against Botrytis cinerea ▶     Houping Wang, Yanru Hu, Jinjing Pan et al.     Arabidopsis VQ motif-containing proteins have recently been demonstrated to interact with several WRKY transcription factors; however, their specific biological functions and the …             Identification and Characterization of a Novel Gentisate 1,2-Dioxygenase Gene from a Halophilic Martelella Strain ▶     Ling Huang, Haiyang Hu, Hongzhi Tang et al.     Halophilic Martelella strain AD-3, isolated from highly saline petroleum-contaminated soil, can efficiently degrade polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene …             The C-terminus hot spot region helps in the fibril formation of bacteriophage-associated hyaluronate lyase (HylP2) ▶     Harish Shukla, Sudhir Kumar Singh, Amit Kumar Singh et al.     The bacteriophage encoded hyaluronate lyases (HylP and HylP2) degrade hyaluronan and other glycosaminoglycans. HylP2 forms a functional fibril under acidic conditions in which …             Comparative quantitative trait loci for silique length and seed weight in Brassica napus ▶     Ying Fu, Dayong Wei, Hongli Dong et al.     Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been …             A Drosera-bioinspired hydrogel for catching and killing cancer cells ▶     Shihui Li, Niancao Chen, Erin R. Gaddes et al.     A variety of bioinspired materials have been successfully synthesized to mimic the sophisticated structures or functions of biological systems. However, it is still challenging …             Enterovirus 71 2C Protein Inhibits NF-κB Activation by Binding to RelA(p65) ▶     Haiwei Du, Peiqi Yin, Xiaojie Yang et al.     Viruses evolve multiple ways to interfere with NF-κB signaling, a key regulator of innate and adaptive immunity. Enterovirus 71 (EV71) is one of primary pathogens that cause …             Conotoxin αD-GeXXA utilizes a novel strategy to antagonize nicotinic acetylcholine receptors ▶     Shaoqiong Xu, Tianlong Zhang, Shiva N. Kompella et al.     Nicotinic acetylcholine receptors (nAChRs) play essential roles in transmitting acetylcholine-mediated neural signals across synapses and neuromuscular junctions, and are also …             The effects of inhibitory control training for preschoolers on reasoning ability and neural activity ▶     Qian Liu, Xinyi Zhu, Albert Ziegler et al.     Inhibitory control (including response inhibition and interference control) develops rapidly during the preschool period and is important for early cognitive development. This …             Effects of concurrent caffeine and mobile phone exposure on local target probability processing in the human brain ▶     Attila Trunk, Gábor Stefanics, Norbert Zentai et al.     Millions of people use mobile phones (MP) while drinking coffee or other caffeine containing beverages. Little is known about the potential combined effects of MP irradiation and …             Dissecting the genetic structure and admixture of four geographical Malay populations ▶     Lian Deng, Boon-Peng Hoh, Dongsheng Lu et al.     The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide …             Reducing the stress of drug administration: implications for the 3Rs ▶     Sarah A. Stuart, Emma S.J. Robinson     Restraint in animals is known to cause stress but is used during almost all scientific procedures in rodents, representing a major welfare and scientific issue. Administration of …             Autophosphorylation of CaMKK2 generates autonomous activity that is disrupted by a T85S mutation linked to anxiety and bipolar disorder ▶     John W. Scott, Elizabeth Park, Ramona M. Rodriguiz et al.     Mutations that reduce expression or give rise to a Thr85Ser (T85S) mutation of Ca2+-CaM-dependent protein kinase kinase-2 (CaMKK2) have been implicated in behavioural disorders …             Expression profile of a Caenorhabditis elegans model of adult neuronal ceroid lipofuscinosis reveals down regulation of ubiquitin E3 ligase components ▶     Hannah V. McCue, Xi Chen, Jeff W. Barclay et al.     Cysteine string protein (CSP) is a chaperone of the Dnaj/Hsp40 family of proteins and is essential for synaptic maintenance. Mutations in the human gene encoding CSP, DNAJC5, …             Proteomic analysis of endoplasmic reticulum stress responses in rice seeds ▶     Dandan Qian, Lihong Tian, Leqing Qu     The defects in storage proteins secretion in the endosperm of transgenic rice seeds often leads to endoplasmic reticulum (ER) stress, which produces floury and shrunken seeds, …             Leveraging existing data sets to generate new insights into Alzheimer’s disease biology in specific patient subsets ▶     Kevin D. Fowler, Jason M. Funt, Maxim N. Artyomov et al.     To generate new insights into the biology of Alzheimer’s Disease (AD), we developed methods to combine and reuse a wide variety of existing data sets in new ways. We first …             Effects of nitrogen and phosphorus additions on soil microbial biomass and community structure in two reforested tropical forests ▶     Lei Liu, Per Gundersen, Wei Zhang et al.     Elevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N …             QIAD assay for quantitating a compound’s efficacy in elimination of toxic Aβ oligomers ▶     Oleksandr Brener, Tina Dunkelmann, Lothar Gremer et al.     Strong evidence exists for a central role of amyloid β-protein (Aβ) oligomers in the pathogenesis of Alzheimer’s disease. We have developed a fast, reliable and robust in vitro …             Nanoparticles modulate autophagic effect in a dispersity-dependent manner ▶     Dengtong Huang, Hualu Zhou, Jinhao Gao     Autophagy plays a key role in human health and disease, especially in cancer and neurodegeneration. Many autophagy regulators are developed for therapy. Diverse nanomaterials …             Enzyme renaturation to higher activity driven by the sol-gel transition: Carbonic anhydrase ▶     Vladimir V. Vinogradov, David Avnir     We describe a so-far unknown route for renaturing denatured enzymes, namely subjecting the denatured enzyme to an oxide sol-gel transition. The phenomenon was revealed in a …             Increased precision of orthotopic and metastatic breast cancer surgery guided by matrix metalloproteinase-activatable near-infrared fluorescence probes ▶     Chongwei Chi, Qian Zhang, Yamin Mao et al.     Advanced medical imaging technology has allowed the use of fluorescence molecular imaging-guided breast cancer surgery (FMI-guided BCS) to specifically label tumour cells and to …             Down-regulation of microRNA-144 in air pollution-related lung cancer ▶     Hong-Li Pan, Zhe-Sheng Wen, Yun-Chao Huang et al.     Air pollution has been classified as a group 1 carcinogen in humans, but the underlying tumourigenic mechanisms remain unclear. In Xuanwei city of Yunnan Province, the lung …             Electrospun SF/PLCL nanofibrous membrane: a potential scaffold for retinal progenitor cell proliferation and differentiation ▶     Dandan Zhang, Ni Ni, Junzhao Chen et al.     Biocompatible polymer scaffolds are promising as potential carriers for the delivery of retinal progenitor cells (RPCs) in cell replacement therapy for the repair of damaged or …             A whole-cell tumor vaccine modified to express fibroblast activation protein induces antitumor immunity against both tumor cells and cancer-associated fibroblasts ▶     Meihua Chen, Rong Xiang, Yuan Wen et al.     Cancer-associated fibroblasts (CAFs) are common components of the tumor-suppressive microenvironment, and are a major determinant of the poor outcome of therapeutic vaccination. …             Analyzing animal behavior via classifying each video frame using convolutional neural networks ▶     Ulrich Stern, Ruo He, Chung-Hui Yang     High-throughput analysis of animal behavior requires software to analyze videos. Such software analyzes each frame individually, detecting animals’ body parts. But the image …             Hyperactivation and in situ recruitment of inflammatory Vδ2 T cells contributes to disease pathogenesis in systemic lupus erythematosus ▶     Shanshan Yin, Yujia Mao, Xuemei Li et al.     In this study, we measured the proportion of peripheral Vδ2 T cells as well as the status and chemokine receptor expression profiles in SLE patients and healthy control (HC). In …             Zinc inhibits the reproductive toxicity of Zearalenone in immortalized murine ovarian granular KK-1 cells ▶     Yijia Li, Xiaoyun He, Xuan Yang et al.     Zearalenone (ZEA) mainly injures the reproductive system of mammals. In the present study, we aimed to explore the mechanism by which zinc inhibits ZEA-induced reproductive …             Investigation of the methylation of Numb by the SET8 protein lysine methyltransferase ▶     Sara Weirich, Denis Kusevic, Srikanth Kudithipudi et al.     It has been reported that the Numb protein is methylated at lysine 158 and 163 and that this methylation is introduced by the SET8 protein lysine methyltransferase [Dhami et al., …             Genome-wide homozygosity signature and risk of Hodgkin lymphoma ▶     Amit Sud, Rosie Cooke, Anthony J. Swerdlow et al.     Recent studies have reported that regions of homozygosity (ROH) in the genome are detectable in outbred populations and can be associated with an increased risk of malignancy. To …             Edges of human embryonic stem cell colonies display distinct mechanical properties and differentiation potential ▶     Kathryn A. Rosowski, Aaron F. Mertz, Samuel Norcross et al.     In order to understand the mechanisms that guide cell fate decisions during early human development, we closely examined the differentiation process in adherent colonies of human …             NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors ▶     Graciela Gonzalez-Gil, Ludivine Thomas, Abdul-Hamid Emwas et al.     Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical …             Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models ▶     Wenfei Zhu, Long Li, Zhigang Yan et al.     The ongoing avian H7N9 influenza outbreaks in China have caused significant human fatal cases and the virus is becoming established in poultry. Mutations with potential to …             Introduction of Methyl Groups at C2 and C6 Positions Enhances the Antiangiogenesis Activity of Curcumin ▶     Hyun-Jung Koo, Sarah Shin, Joon Young Choi et al.     Curcumin has diverse biological activities, but is known to undergo rapid metabolism via reduction of vinylic double bonds and phase II conjugation. To prevent reductive …             Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited ▶     C. O. S. Sorzano, M. Alcorlo, J. M. de la Rosa-Trevín et al.     Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in …             Self make-up: the influence of self-referential processing on attention orienting ▶     Shuo Zhao, Shota Uono, Sayaka Yoshimura et al.     For humans, both eye gaze and arrows serve as powerful signals for orienting attention. Recent studies have shown important differences between gaze and arrows in attention …             Lack of association of the iNOS gene polymorphism with risk of cancer: a systematic review and Meta-Analysis ▶     Jinghua Jiao, Jingyang Wu, Desheng Huang et al.     In order to investigate the association between the iNOS gene polymorphisms and susceptibility to cancer, a search of English papers was done using Pubmed, the Cochrane Library, …             Statin-activated nuclear receptor PXR promotes SGK2 dephosphorylation by scaffolding PP2C to induce hepatic gluconeogenesis ▶     Saki Gotoh, Masahiko Negishi     Statin therapy is known to increase blood glucose levels in humans. Statins utilize pregnane X receptor (PXR) and serum/glucocorticoid regulated kinase 2 (SGK2) to activate …             A comprehensive study on different modelling approaches to predict platelet deposition rates in a perfusion chamber ▶     Jordi Pallarès, Oriol Senan, Roger Guimerà et al.     Thrombus formation is a multiscale phenomenon triggered by platelet deposition over a protrombotic surface (eg. a ruptured atherosclerotic plaque). Despite the medical urgency …             Post-conflict affiliation as conflict management in captive bottlenose dolphins (Tursiops truncatus) ▶     Chisato Yamamoto, Tadamichi Morisaka, Keisuke Furuta et al.     Post-conflict affiliation between former opponents or between one of the former opponents and bystanders might have the function of conflict management, which reduces the costs …             An integrated insight into the response of sedimentary microbial communities to heavy metal contamination ▶     Huaqun Yin, Jiaojiao Niu, Youhua Ren et al.     Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To …             RBM45 homo-oligomerization mediates association with ALS-linked proteins and stress granules ▶     Yang Li, Mahlon Collins, Rachel Geiser et al.     The aggregation of RNA-binding proteins is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBM45 is an RNA-binding …             A novel microtubule de-stabilizing complementarity-determining region C36L1 peptide displays antitumor activity against melanoma in vitro and in vivo ▶     Carlos R. Figueiredo, Alisson L. Matsuo, Ricardo A. Azevedo et al.     Short peptide sequences from complementarity-determining regions (CDRs) of different immunoglobulins may exert anti-infective, immunomodulatory and antitumor activities …             Predictive diagnosis of the risk of breast cancer recurrence after surgery by single-particle quantum dot imaging ▶     Kohsuke Gonda, Minoru Miyashita, Hideo Higuchi et al.     In breast cancer, the prognosis of human epidermal growth factor receptor 2 (HER2)-positive patients (20–25%) has been dramatically improved by the clinical application of the …             Volatile codes: Correlation of olfactory signals and reception in Drosophila-yeast chemical communication ▶     Nicole H. Scheidler, Cheng Liu, Kelly A. Hamby et al.     Drosophila have evolved strong mutualistic associations with yeast communities that best support their growth and survival, resulting in the development of novel niches. It has …             Tumour-promoting role of SOCS1 in colorectal cancer cells ▶     William S. Tobelaim, Claudia Beaurivage, Audrey Champagne et al.     The SOCS1 (Suppressor Of Cytokine Signalling 1) protein is considered a tumour suppressor. Notably, the SOCS1 gene is frequently silenced in cancer by hypermethylation of its …             Fast and Precise 3D Fluorophore Localization based on Gradient Fitting ▶     Hongqiang Ma, Jianquan Xu, Jingyi Jin et al.     Astigmatism imaging approach has been widely used to encode the fluorophore’s 3D position in single-particle tracking and super-resolution localization microscopy. Here, we …             Simultaneous Fluorescence and Phosphorescence Lifetime Imaging Microscopy in Living Cells ▶     Karolina Jahn, Volker Buschmann, Carsten Hille     In living cells, there are always a plethora of processes taking place at the same time. Their precise regulation is the basis of cellular functions, since small failures can …             Lipoproteins/peptides are sepsis-inducing toxins from bacteria that can be neutralized by synthetic anti-endotoxin peptides ▶     Guillermo Martinez de Tejada, Lena Heinbockel, Raquel Ferrer-Espada et al.     Sepsis, a life-threatening syndrome with increasing incidence worldwide, is triggered by an overwhelming inflammation induced by microbial toxins released into the bloodstream …             In vitro discovery of promising anti-cancer drug combinations using iterative maximisation of a therapeutic index ▶     M. Kashif, C. Andersson, S. Hassan et al.     In vitro-based search for promising anti-cancer drug combinations may provide important leads to improved cancer therapies. 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