Scientific Reports Biology Table of Contents e-alert: 17 February 2015

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17 February 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               Effects of subconscious and conscious emotions on human cue–reward association learning ▶     Noriya Watanabe, Masahiko Haruno     Life demands that we adapt our behaviour continuously in situations in which much of our incoming information is emotional and unrelated to our immediate behavioural goals. Such …             A Novel Protocol for Model Calibration in Biological Wastewater Treatment ▶     Ao Zhu, Jianhua Guo, Bing-Jie Ni et al.     Activated sludge models (ASMs) have been widely used for process design, operation and optimization in wastewater treatment plants. However, it is still a challenge to achieve an …             Diverse fungi associated with partial irregular heartwood of Dalbergia odorifera ▶     Sisheng Sun, Xu Zeng, Dawei Zhang et al.     Dalbergia odorifera T. Chen is a medium-sized evergreen tree that produces purple-brown heartwood called JiangXiang in traditional Chinese medicine, the formation process of …             Double minute amplification of mutant PDGF receptor α in a mouse glioma model ▶     Hongyan Zou, Rui Feng, Yong Huang et al.     In primary brain tumors, oncogenes are frequently amplified and maintained on extrachromosomal DNA as double minutes (DM), but the underlying mechanisms remain poorly understood. …             hiPS-MSCs differentiation towards fibroblasts on a 3D ECM mimicking scaffold ▶     Ruodan Xu, Mehmet Berat Taskin, Marina Rubert et al.     Fibroblasts are ubiquitous cells that constitute the stroma of virtually all tissues and play vital roles in homeostasis. The poor innate healing capacity of fibroblastic tissues …             Lentivirus-mediated Inhibition of Tumour Necrosis Factor-α improves motor function associated with PRDX6 in spinal cord contusion rats ▶     Xiao Zhang, Lan-lan Shi, Xia Gao et al.     The recovery of motor function in rats is inhibited following contusion spinal cord injury (cSCI). However, the mechanism of tumour necrosis factor α (TNF-α) in motor function …             Defoliation of interior Douglas-fir elicits carbon transfer and stress signalling to ponderosa pine neighbors through ectomycorrhizal networks ▶     Yuan Yuan Song, Suzanne W. Simard, Allan Carroll et al.     Extensive regions of interior Douglas-fir (Pseudotsuga menziesii var. glauca, IDF) forests in North America are being damaged by drought and western spruce budworm (Choristoneura …             Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China ▶     Caiyun Yang, Yi Li, Benjamin Zhou et al.     Although phytoplankton are the major source of marine dissolved organic matter (DOM), their blooms are a global problem that can greatly affect marine ecological systems, …             An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape ▶     Hebing Chen, Hao Li, Feng Liu et al.     DNase I hypersensitive sites (DHSs) define the accessible chromatin landscape and have revolutionised the discovery of distinct cis-regulatory elements in diverse organisms. …             Carnival or football, is there a real risk for acquiring dengue fever in Brazil during holidays seasons? ▶     Maíra Aguiar, Filipe Rocha, José Eduardo Marques Pessanha et al.     More than 600,000 football fans, coming from all over the world, were expected to visit Brazil during the FIFA World Cup 2014. International travel can become a public health …             Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters ▶     Inka Vanwonterghem, Paul D. Jensen, Korneel Rabaey et al.     Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production …             ERRATUM: Establishment of a primed pluripotent epiblast stem cell in FGF4-based conditions ▶     Jin Young Joo, Hyun Woo Choi, Min Jung Kim et al.                 Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations ▶     Huiyong Sun, Sheng Tian, Shunye Zhou et al.     How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket …             A neuro-inspired model-based closed-loop neuroprosthesis for the substitution of a cerebellar learning function in anesthetized rats ▶     Roni Hogri, Simeon A. Bamford, Aryeh H. Taub et al.     Neuroprostheses could potentially recover functions lost due to neural damage. Typical neuroprostheses connect an intact brain with the external environment, thus replacing …             On forward inferences of fast and slow readers. An eye movement study ▶     Stefan Hawelka, Sarah Schuster, Benjamin Gagl et al.     Unimpaired readers process words incredibly fast and hence it was assumed that top-down processing, such as predicting upcoming words, would be too slow to play an appreciable …             An ESCRT module is required for neuron pruning ▶     Nicolas Loncle, Monica Agromayor, Juan Martin-Serrano et al.     Neural circuits are refined by both functional and structural changes. Structural remodeling by large-scale pruning occurs where relatively long neuronal branches are cut away …             S100A4 promotes pancreatic cancer progression through a dual signaling pathway mediated by Src and focal adhesion kinase ▶     Pulin Che, Youfeng Yang, Xiaosi Han et al.     S100A4 expression is associated with poor clinical outcomes of patients with pancreatic cancer. The effects of loss or gain of S100A4 were examined in pancreatic cancer cell …             Terahertz in-line digital holography of human hepatocellular carcinoma tissue ▶     Lu Rong, Tatiana Latychevskaia, Chunhai Chen et al.     Terahertz waves provide a better contrast in imaging soft biomedical tissues than X-rays, and unlike X-rays, they cause no ionisation damage, making them a good option for …             How deeply does your mutant sleep? Probing arousal to better understand sleep defects in Drosophila ▶     R. Faville, B. Kottler, G. J. Goodhill et al.     The fruitfly, Drosophila melanogaster, has become a critical model system for investigating sleep functions. Most studies use duration of inactivity to measure sleep. However, a …             ycf1, the most promising plastid DNA barcode of land plants ▶     Wenpan Dong, Chao Xu, Changhao Li et al.     A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid …             Differential regulation of the hmsCDE operon in Yersinia pestis and Yersinia pseudotuberculosis by the Rcs phosphorelay system ▶     Xiao-Peng Guo, Gai-Xian Ren, Hui Zhu et al.     Yersinia pestis, the agent of plague, forms a biofilm in its flea vector to enhance transmission. Y. pestis biofilm development is positively regulated by hmsT and hmsD, encoding …             Community structure of gut fungi during different developmental stages of the Chinese white pine beetle (Dendroctonus armandi) ▶     Xia Hu, Ming Li, Hui Chen     The Chinese white pine beetle is arguably the most destructive forest insect in the Qinling Mountains in Northern China. Little is known about the structure of the fungal …             The Epileptic Thalamocortical Network is a Macroscopic Self-Sustained Oscillator: Evidence from Frequency-Locking Experiments in Rat Brains ▶     J. L. Perez Velazquez, R. Guevara Erra, M. Rosenblum     The rhythmic activity observed in nervous systems, in particular in epilepsies and Parkinson's disease, has often been hypothesized to originate from a macroscopic self-sustained …             Winners and losers in a world where the high seas is closed to fishing ▶     U. Rashid Sumaila, Vicky W. Y. Lam, Dana D. Miller et al.     Fishing takes place in the high seas and Exclusive Economic Zones (EEZs) of maritime countries. Closing the former to fishing has recently been proposed in the literature and is …             Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation ▶     Yuebin Zhang, Huiyan Niu, Yan Li et al.     Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is …             A proof-of-principle study of multi-site real-time functional imaging at 3T and 7T: Implementation and validation ▶     Sebastian Baecke, Ralf Lützkendorf, Johannes Mallow et al.     Real-time functional Magnetic Resonance Imaging (rtfMRI) is used mainly for neurofeedback or for brain-computer interfaces (BCI). But multi-site rtfMRI could in fact help in the …             The metabolic responses to hepatitis B virus infection shed new light on pathogenesis and targets for treatment ▶     Hongde Li, Wandi Zhu, Leike Zhang et al.     Chronic infection caused by the hepatitis B virus (HBV), is strongly associated with hepatitis, fatty liver and hepatocellular carcinoma. To investigate the underlying …             A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator ▶     Ricky Bhajun, Laurent Guyon, Amandine Pitaval et al.     MiRNAs are key regulators of gene expression. By binding to many genes, they create a complex network of gene co-regulation. Here, using a network-based approach, we identified …             The miR-199a/Brm/EGR1 axis is a determinant of anchorage-independent growth in epithelial tumor cell lines ▶     Kazuyoshi Kobayashi, Kouhei Sakurai, Hiroaki Hiramatsu et al.     In epithelial cells, miRNA-199a-5p/-3p and Brm, a catalytic subunit of the SWI/SNF complex were previously shown to form a double-negative feedback loop through EGR1, by which …             Climate change as an unexpected co-factor promoting coral eating seastar (Acanthaster planci) outbreaks ▶     S. Uthicke, M. Logan, M. Liddy et al.     Coral reefs face a crisis due to local and global anthropogenic stressors. A large proportion of the ~50% coral loss on the Great Barrier Reef has been attributed to outbreaks of …             CORRIGENDUM: A Comparative Study of Fast-Track Versus Conventional Surgery in Patients Undergoing Laparoscopic Radical Cystectomy and Ileal Conduit Diversion: Chinese Experience ▶     Xiao Guan, Longfei Liu, Xiang Lei et al.                 Transcriptional response to petiole heat girdling in cassava ▶     Yang Zhang, Zehong Ding, Fangfang Ma et al.     To examine the interactions of starch and sugar metabolism on photosynthesis in cassava, a heat-girdling treatment was applied to petioles of cassava leaves at the end of the …             Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase ▶     Elena Formoso, Vittorio Limongelli, Michele Parrinello     Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead …             Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types ▶     Haidan Yan, Dongwei Zhang, Hongbo Liu et al.     DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain …             SIRT2 is involved in the modulation of depressive behaviors ▶     Rui Liu, Wei Dang, Ying Du et al.     Exposure to chronic stress produces negative effects on mood and hippocampus-dependent memory formation. SIRT2 alteration has been reported in mood disorders; however, the role …             CORRIGENDUM: Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria ▶     Pilar Martínez-Hidalgo, Purificación Galindo-Villardón, Martha E. Trujillo et al.                 Fear renewal preferentially activates ventral hippocampal neurons projecting to both amygdala and prefrontal cortex in rats ▶     Jingji Jin, Stephen Maren     Anxiety, trauma and stress-related disorders are often characterized by a loss of context-appropriate emotional responding. The contextual retrieval of emotional memory involves …             A genetic contribution from the Far East into Ashkenazi Jews via the ancient Silk Road ▶     Jiao-Yang Tian, Hua-Wei Wang, Yu-Chun Li et al.     Contemporary Jews retain a genetic imprint from their Near Eastern ancestry, but obtained substantial genetic components from their neighboring populations during their history. …             CORRIGENDUM: DNA methylome in spleen of avian pathogenic escherichia coli-challenged broilers and integration with mRNA expression ▶     Haiping Xu, Xuenong Zhu, Yongsheng Hu et al.                 Involvement of dachshund and Distal-less in distal pattern formation of the cricket leg during regeneration ▶     Yoshiyasu Ishimaru, Taro Nakamura, Tetsuya Bando et al.     Cricket nymphs have the remarkable ability to regenerate a functional leg following amputation, indicating that the regenerating blastemal cells contain information for leg …             Integrin-Linked Kinase links Dynactin-1/Dynactin-2 with cortical Integrin receptors to orient the mitotic spindle relative to the substratum ▶     Edward James Morris, Kiran Assi, Baljinder Salh et al.     Cells must divide strictly along a plane to form an epithelial layer parallel to the basal lamina. The axis of cell division is primarily governed by the orientation of the …             Crystal structure of VmoLac, a tentative quorum quenching lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia ▶     Julien Hiblot, Janek Bzdrenga, Charlotte Champion et al.     A new representative of the Phosphotriesterase-Like Lactonases (PLLs) family from the hyperthermophilic crenarchaeon Vulcanisaeta moutnovskia has been characterized and …             Circadian rhythm phase shifts and endogenous free-running circadian period differ between African-Americans and European-Americans ▶     Charmane I. Eastman, Christina Suh, Victoria A. Tomaka et al.     Successful adaptation to modern civilization requires the internal circadian clock to make large phase shifts in response to circumstances (e.g., jet travel and shift work) that …             A Green Strategy to Prepare Metal Oxide Superstructure from Metal-Organic Frameworks ▶     Yonghai Song, Xia Li, Changting Wei et al.     Metal or metal oxides with diverse superstructures have become one of the most promising functional materials in sensor, catalysis, energy conversion, etc. In this work, a novel …             Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation ▶     Theerthankar Das, Samuel K. Kutty, Roya Tavallaie et al.     Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum …             Down-Regulation of Human Enteric Antimicrobial Peptides by NOD2 during Differentiation of the Paneth Cell Lineage ▶     Gao Tan, Run-hua Li, Chen Li et al.     Ileal Crohn's disease (CD) arising from the alteration of intestinal homeostasis is characterized by two features, namely a decrease in Paneth cell-produced antimicrobial …             Inhibitors of glutamate release from breast cancer cells; new targets for cancer-induced bone-pain ▶     Jennifer Fazzari, Hanxin Lin, Cecilia Murphy et al.     Glutamate is an important signaling molecule in a wide variety of tissues. Aberrant glutamatergic signaling disrupts normal tissue homeostasis and induces several disruptive …             Fitness Profiling Links Topoisomerase II Regulation of Centromeric Integrity to Doxorubicin Resistance in Fission Yeast ▶     Thi Thuy Trang Nguyen, Julia Sze Lynn Lim, Richard Ming Yi Tang et al.     Doxorubicin, a chemotherapeutic agent, inhibits the religation step of topoisomerase II (Top2). However, the downstream ramifications of this action are unknown. Here we …             Ethanol extract of Remotiflori radix induces endoplasmic reticulum stress-mediated cell death through AMPK/mTOR signaling in human prostate cancer cells ▶     Aeyung Kim, Minju Im, Jin Yeul Ma     Remotiflori radix is the root of Mosidae, which has long been used as a traditional medicine to treat chills, fever, and phlegm discharge. The ethanol extract of Mosidae leaves …             The Genetics of POAG in Black South Africans: A Candidate Gene Association Study ▶     Susan E. I. Williams, Trevor R. Carmichael, R. Rand Allingham et al.     Multiple loci have been associated with either primary open angle glaucoma (POAG) or heritable ocular quantitative traits associated with this condition. This study examined the …             A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples ▶     Yuqing Huang, Zhiyong Zhang, Hao Chen et al.     NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in …             Aurora B-dependent phosphorylation of Ataxin-10 promotes the interaction between Ataxin-10 and Plk1 in cytokinesis ▶     Jie Tian, Chuan Tian, Yuehe Ding et al.     Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurologic disorder caused by ATTCT expansion in the ATXN10 gene. Previous investigations have identified that …             Attentional modulations of the early and later stages of the neural processing of visual completion ▶     Xiang Wu, Liang Zhou, Cheng Qian et al.     The brain effortlessly recognizes objects even when the visual information belonging to an object is widely separated, as well demonstrated by the Kanizsa-type illusory contours …             The tomato borer, Tuta absoluta, invading the Mediterranean Basin, originates from a single introduction from Central Chile ▶     Thomas Guillemaud, Aurélie Blin, Isabelle Le Goff et al.     The Lepidopteran pest of tomato, Tuta absoluta, is native to South America and is invasive in the Mediterranean basin. The species' routes of invasion were investigated. The …             Fast Super-Resolution Imaging with Ultra-High Labeling Density Achieved by Joint Tagging Super-Resolution Optical Fluctuation Imaging ▶     Zhiping Zeng, Xuanze Chen, Hening Wang et al.     Previous stochastic localization-based super-resolution techniques are largely limited by the labeling density and the fidelity to the morphology of specimen. We report on an …             FGF23 neutralization improves bone quality and osseointegration of titanium implants in chronic kidney disease mice ▶     Ningyuan Sun, Yuchen Guo, Weiqing Liu et al.     Chronic kidney disease (CKD) is a worldwide health problem. Serum levels of FGF23, a phosphaturic hormone, increase at the earliest stages of CKD, and have been found to be …             RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes ▶     Thomas Brettin, James J. Davis, Terry Disz et al.     The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software …             Quantitative analysis of injury-induced anterior subcapsular cataract in the mouse: a model of lens epithelial cells proliferation and epithelial-mesenchymal transition ▶     Wei Xiao, Xiaoyun Chen, Weihua Li et al.     The mouse lens capsular injury model has been widely used in investigating the mechanisms of anterior subcapsular cataract (ASC) and posterior capsule opacification (PCO), and …             The molecular architecture of dihydropyrindine receptor/L-type Ca2+ channel complex ▶     Hongli Hu, Zhao Wang, Risheng Wei et al.     Dihydropyridine receptor (DHPR), an L-type Ca2 channel complex, plays an essential role in muscle contraction, secretion, integration of synaptic input in neurons and synaptic …             CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes ▶     Hua Zhong, Yiyun Chen, Yumei Li et al.     The era of genomics has demanded the development of more efficient and timesaving approaches to validate gene function in disease. Here, we utilized the CRISPR-Cas9 system to …             Generation of retinal ganglion cells with functional axons from human induced pluripotent stem cells ▶     Taku Tanaka, Tadashi Yokoi, Fuminobu Tamalu et al.     We generated self-induced retinal ganglion cells (RGCs) with functional axons from human induced pluripotent stem cells. After development of the optic vesicle from the induced …             Piezo1 forms mechanosensitive ion channels in the human MCF-7 breast cancer cell line ▶     Chouyang Li, Simin Rezania, Sarah Kammerer et al.     Mechanical interaction between cells – specifically distortion of tensional homeostasis-emerged as an important aspect of breast cancer genesis and progression. We investigated …             Accuracy and efficiency of detection dogs: a powerful new tool for koala conservation and management ▶     Romane H. Cristescu, Emily Foley, Anna Markula et al.     Accurate data on presence/absence and spatial distribution for fauna species is key to their conservation. Collecting such data, however, can be time consuming, laborious and …             Extensive load of somatic CNVs in the human placenta ▶     Laura Kasak, Kristiina Rull, Pille Vaas et al.     Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective …             A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline ▶     Xin Chen, Shanshan Qin, Shuai Chen et al.     In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the …             Earth's Phosphides in Levant and insights into the source of Archean prebiotic phosphorus ▶     Sergey N. Britvin, Michail N. Murashko, Yevgeny Vapnik et al.     Natural phosphides - the minerals containing phosphorus in a redox state lower than zero – are common constituents of meteorites but virtually unknown on the Earth. Herein we …             IER3 is a crucial mediator of TAp73β-induced apoptosis in cervical cancer and confers etoposide sensitivity ▶     Hanyong Jin, Dae-Shik Suh, Tae-Hyoung Kim et al.     Infection with high-risk human papillomaviruses (HPVs) causes cervical cancer. E6 oncoprotein, an HPV gene product, inactivates the major gatekeeper p53. In contrast, its …             Strong effects of ionizing radiation from Chernobyl on mutation rates ▶     Anders Pape Møller, Timothy A. Mousseau     In this paper we use a meta-analysis to examine the relationship between radiation and mutation rates in Chernobyl across 45 published studies, covering 30 species. Overall …             Transferable neuronal mini-cultures to accelerate screening in primary and induced pluripotent stem cell-derived neurons ▶     Mark Niedringhaus, Raluca Dumitru, Angela M. Mabb et al.     The effort and cost of obtaining neurons for large-scale screens has limited drug discovery in neuroscience. To overcome these obstacles, we fabricated arrays of releasable …             Prion Amplification and Hierarchical Bayesian Modeling Refine Detection of Prion Infection ▶     A. Christy Wyckoff, Nathan Galloway, Crystal Meyerett-Reid et al.     Prions are unique infectious agents that replicate without a genome and cause neurodegenerative diseases that include chronic wasting disease (CWD) of cervids. …             Pseudomonas aeruginosa manipulates redox and iron homeostasis of its microbiota partner Aspergillus fumigatus via phenazines ▶     Benoit Briard, Perrine Bomme, Beatrix E. Lechner et al.     The opportunistic fungal pathogen Aspergillus fumigatus is increasingly found as a coinfecting agent along with Pseudomonas aeruginosa in cystic fibrosis patients. 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