Scientific Reports Biology Table of Contents e-alert: 14 July 2015

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14 July 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports               Biological Sciences               Corrigendum: Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin ▶     Yasuhiro Arimura, Hiroshi Kimura, Takashi Oda et al.                 Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding ▶     C. Haris Saslis-Lagoudakis, Sam Bruun-Lund, Natalie E. Iwanycki et al.     The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum …             Cutting improves the productivity of lucerne-rich stands used in the revegetation of degraded arable land in a semi-arid environment ▶     Zi-Qiang Yuan, Kai-Liang Yu, Bin-Xian Wang et al.     Understanding the relationships between vegetative and environmental variables is important for revegetation and ecosystem management on the Loess Plateau, China. Lucerne (…             Erratum: The First Small-Molecule Inhibitors of Members of the Ribonuclease E Family ▶     Louise Kime, Helen A. Vincent, Deena M. A. Gendoo et al.                 Spinal mechanisms underlying potentiation of hindpaw responses observed after transient hindpaw ischemia in mice ▶     Tatsunori Watanabe, Mika Sasaki, Seiji Komagata et al.     Transient ischemia produces postischemic tingling sensation. Ischemia also produces nerve conduction block that may modulate spinal neural circuits. In the present study, reduced …             How warm is too warm for the life cycle of actinopterygian fishes? ▶     Ryosuke Motani, Peter C. Wainwright     We investigated the highest constant temperature at which actinopterygian fishes can complete their lifecycles, based on an oxygen supply model for cleavage-stage eggs. This …             Bombyx E75 isoforms display stage- and tissue-specific responses to 20-hydroxyecdysone ▶     Kang Li, Enen Guo, Muktadir S. Hossain et al.     Resulted from alternative splicing of the 5′ exons, the nuclear receptor gene E75 in the silkworm, Bombyx mori, processes three mRNA isoforms, BmE75A, BmE75B and BmE75C. From the …             Fe65 Suppresses Breast Cancer Cell Migration and Invasion through Tip60 Mediated Cortactin Acetylation ▶     Yuefeng Sun, Jianwei Sun, Panida Lungchukiet et al.     Fe65 is a brain-enriched adaptor protein known for its role in the action of the Aβ amyloid precursor protein in neuronal cells and Alzheimer’s disease, but little is known about …             Rapid intraoperative visualization of breast lesions with γ-glutamyl hydroxymethyl rhodamine green ▶     Hiroki Ueo, Yoshiaki Shinden, Taro Tobo et al.     We previously developed γ-glutamyl hydroxymethyl rhodamine green (gGlu-HMRG) as a tool to detect viable cancer cells, based on the fact that the enzyme γ-glutamyltranspeptidase …             Spatial distribution and ecological niches of non-breeding planktivorous petrels ▶     Joan Navarro, Laura Cardador, Ruth Brown et al.     According to niche theory, mechanisms exist that allow co-existence of organisms that would otherwise compete for the same prey and other resources. How seabirds cope with …             OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus ▶     Wei Hong, Dan Qian, Runhong Sun et al.     RNAi is a major antiviral defense response in plant and animal model systems. RNA-dependent RNA polymerase 6 (RDR6) is an essential component of RNAi, which plays an important …             Hypoxia inducible factor-1 mediates expression of miR-322: potential role in proliferation and migration of pulmonary arterial smooth muscle cells ▶     Yan Zeng, Hongtao Liu, Kang Kang et al.     There is growing evidence that microRNAs play important roles in cellular responses to hypoxia and in pulmonary hypertensive vascular remodeling, but the exact molecular …             Corrigendum: Chromatic acclimation and population dynamics of green sulfur bacteria grown with spectrally tailored light ▶     Semion K. Saikin, Yadana Khin, Joonsuk Huh et al.                 Corrigendum: Cocaine exposure impairs multilineage hematopoiesis of human hematopoietic progenitor cells mediated by the sigma-1 receptor ▶     Christopher C. Nixon, Brandon H. Schwartz, Dhaval Dixit et al.                 GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks ▶     Brian Law, Gary D. Bader     The increasing ease and accuracy of protein-protein interaction detection has resulted in the ability to map the interactomes of multiple species. We now have an opportunity to …             Resolving single membrane fusion events on planar pore-spanning membranes ▶     Lando L. G. Schwenen, Raphael Hubrich, Dragomir Milovanovic et al.     Even though a number of different in vitro fusion assays have been developed to analyze protein mediated fusion, they still only partially capture the essential features of the …             Homoharringtonine induces apoptosis and inhibits STAT3 via IL-6/JAK1/STAT3 signal pathway in Gefitinib-resistant lung cancer cells ▶     Wei Cao, Ying Liu, Ran Zhang et al.     Tyrosine kinase inhibitors (TKIs) are mostly used in non-small cell lung cancer (NSCLC) treatment. Unfortunately, treatment with Gefitinib for a period of time will result in …             Differential and coherent processing patterns from small RNAs ▶     Sachin Pundhir, Jan Gorodkin     Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm …             Atmospheric benzenoid emissions from plants rival those from fossil fuels ▶     P.K. Misztal, C.N. Hewitt, J. Wildt et al.     Despite the known biochemical production of a range of aromatic compounds by plants and the presence of benzenoids in floral scents, the emissions of only a few benzenoid …             Dynamic tensile forces drive collective cell migration through three-dimensional extracellular matrices ▶     Nikolce Gjorevski, Alexandra S. Piotrowski, Victor D. Varner et al.     Collective cell migration drives tissue remodeling during development, wound repair, and metastatic invasion. The physical mechanisms by which cells move cohesively through dense …             Radiofrequency treatment alters cancer cell phenotype ▶     Matthew J. Ware, Sophia Tinger, Kevin L. Colbert et al.     The importance of evaluating physical cues in cancer research is gradually being realized. Assessment of cancer cell physical appearance, or phenotype, may provide information on …             T2D and Depression Risk Gene Proteasome Modulator 9 is Linked to Insomnia ▶     Han Hao, Michael J. Haas, Rongling Wu et al.     Insomnia increases type-2 diabetes (T2D) risk. The 12q24 locus is linked to T2D, depression, bipolar disorder and anxiety. At the 12q24 locus, the Proteasome-Modulator 9 (PSMD9) …             Tumour Necrosis Factor-α Gene Polymorphism Is Associated with Metastasis in Patients with Triple Negative Breast Cancer ▶     Hui-Hui Li, Hui Zhu, Li-Sheng Liu et al.     Tumour necrosis factor-α (TNF-α) is critical in the regulation of inflammation and tumour progression. TNF-α-308G > A is associated with constitutively elevated TNF-α expression. …             Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data ▶     Michael Forster, Silke Szymczak, David Ellinghaus et al.     Several pathogenic viruses such as hepatitis B and human immunodeficiency viruses may integrate into the host genome. These virus/host integrations are detectable using …             An anti-inflammatory role for C/EBPδ in human brain pericytes ▶     Justin Rustenhoven, Emma L. Scotter, Deidre Jansson et al.     Neuroinflammation contributes to the pathogenesis of several neurological disorders and pericytes are implicated in brain inflammatory processes. Cellular inflammatory responses …             Assessing the Efficacy of Mdm2/Mdm4-Inhibiting Stapled Peptides Using Cellular Thermal Shift Assays ▶     Ban Xiong Tan, Christopher J. Brown, Fernando J. Ferrer et al.     Previous publications on stapled peptide inhibitors against Mdm2/Mdm4-p53 interactions have established that this new class of drugs have the potential to be easily optimised to …             Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance ▶     Thomas Nordahl Petersen, Simon Rasmussen, Henrik Hasman et al.     Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding …             The E3 Ubiquitin Ligase COP1 Regulates Thermosensory Flowering by Triggering GI Degradation in Arabidopsis ▶     Kiyoung Jang, Hong Gil Lee, Su-Jin Jung et al.     Floral transition is influenced by environmental factors such as light and temperature. Plants are capable of integrating photoperiod and ambient temperature signaling into their …             Escherichia coli as host for membrane protein structure determination: a global analysis ▶     Georges Hattab, Dror E. Warschawski, Karine Moncoq et al.     The structural biology of membrane proteins (MP) is hampered by the difficulty in producing and purifying them. A comprehensive analysis of protein databases revealed that 213 …             A Nanotechnology-Based Platform for Extending the Pharmacokinetic and Binding Properties of Anti-methamphetamine Antibody Fragments ▶     Nisha Nanaware-Kharade, Shraddha Thakkar, Guillermo A. Gonzalez III et al.     To address the need for effective medications to aid in the treatment of methamphetamine (METH) abuse, we used a nanotechnology approach to customize the in vivo behavior of an …             Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer ▶     Ying Wang, Chen-Yue Qian, Xiang-Ping Li et al.     In this study, we aimed to explore the long noncoding RNA expression pattern in squamous cell lung cancer (SQCC) on a genome-wide scale. Total RNAs were extracted from 16 lung …             Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes ▶     Sari Peura, Lucas Sinclair, Stefan Bertilsson et al.     Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently …             Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics ▶     Peng Zhang, Yu Shen, Jin-Song Guo et al.     In this work, proteins in extracellular polymeric substances extracted from anaerobic, anoxic and aerobic sludges of wastewater treatment plant (WWTP) were analyzed to probe …             CGMD: An integrated database of cancer genes and markers ▶     Jangampalli Adi Pradeepkiran, Sri Bhashyam Sainath, Konidala Kramthi Kumar et al.     Integrating cancer genes and markers with experimental evidence might provide valuable information for the further investigation of crosstalk between tumor genes and markers in …             Ancient DNA sequence revealed by error-correcting codes ▶     Marcelo M. Brandão, Larissa Spoladore, Luzinete C. B. Faria et al.     A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of …             Rapid fusion between mesenchymal stem cells and cardiomyocytes yields electrically active, non-contractile hybrid cells ▶     Ilya Y. Shadrin, Woohyun Yoon, Liqing Li et al.     Cardiac cell therapies involving bone marrow-derived human mesenchymal stem cells (hMSCs) have shown promising results, although their mechanisms of action are still poorly …             Conformational thermostabilisation of corticotropin releasing factor receptor 1 ▶     James Kean, Andrea Bortolato, Kaspar Hollenstein et al.     Recent technical advances have greatly facilitated G-protein coupled receptors crystallography as evidenced by the number of successful x-ray structures that have been reported …             Corrigendum: An evolutionary inspection game with labour unions on small-world networks ▶     Salahuddin M. Kamal, Yas Al-Hadeethi, Fouad A. Abolaban et al.                 Corrigendum: Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore ▶     Yong Wang, Bin-Quan Luan, Zhiyu Yang et al.                 Isolation, characterization and antifungal docking studies of wortmannin isolated from Penicillium radicum ▶     Vineeta Singh, Vandana Praveen, Divya Tripathi et al.     During the search for a potent antifungal drug, a cell-permeable metabolite was isolated from a soil isolate taxonomically identified as Penicillium radicum. The strain was found …             Integrative proteomics to understand the transmission mechanism of Barley yellow dwarf virus-GPV by its insect vector Rhopalosiphum padi ▶     Hui Wang, Keke Wu, Yan Liu et al.     Barley yellow dwarf virus-GPV (BYDV-GPV) is transmitted by Rhopalosiphum padi and Schizaphis graminum in a persistent nonpropagative manner. To improve our understanding of its …             Results of an abbreviated phase-II study with the Akt Inhibitor MK-2206 in Patients with Advanced Biliary Cancer ▶     Daniel H. Ahn, Junan Li, Lai Wei et al.     Biliary cancers (BC) are rare, chemoresistant and are associated with a poor prognosis. Targeting the Akt pathway is of significance in BC. We hypothesized that the allosteric …             Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept ▶     Nicholas Allec, Mina Choi, Nikhil Yesupriya et al.     Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, …             Oxytocin evokes a pulsatile PGE2 release from ileum mucosa and is required for repair of intestinal epithelium after injury ▶     Dawei Chen, Junhan Zhao, Haoyi Wang et al.     We measured the short-circuit current (Isc) in rat ileum mucosa to identify the effect of oxytocin (OT) on mucosal secretion in small intestine. We identified a COX-2-derived …             Spexin Enhances Bowel Movement through Activating L-type Voltage-dependent Calcium Channel via Galanin Receptor 2 in Mice ▶     Cheng-yuan Lin, Man Zhang, Tao Huang et al.     A novel neuropeptide spexin was found to be broadly expressed in various endocrine and nervous tissues while little is known about its functions. This study investigated the role …             GPR143 Gene Mutations in Five Chinese Families with X-linked Congenital Nystagmus ▶     Ruifang Han, Xiaojuan Wang, Dongjie Wang et al.     The ocular albinism type I (OA1) is clinically characterized by impaired visual acuity, nystagmus, iris hypopigmentation with translucency, albinotic fundus, and macular …             Differential protein folding and chemical changes in lung tissues exposed to asbestos or particulates ▶     Lorella Pascolo, Violetta Borelli, Vincenzo Canzonieri et al.     Environmental and occupational inhalants may induce a large number of pulmonary diseases, with asbestos exposure being the most risky. The mechanisms are clearly related to …             Proteomic analysis of murine testes lipid droplets ▶     Weiyi Wang, Suning Wei, Linghai Li et al.     Testicular Leydig cells contain abundant cytoplasmic lipid droplets (LDs) as a cholesteryl-ester store for releasing cholesterols as the precursor substrate for testosterone …             Phosphodiesterase-4D Knock-down in the Prefrontal Cortex Alleviates Chronic Unpredictable Stress-Induced Depressive-Like Behaviors and Memory Deficits in Mice ▶     Zhen-Zhen Wang, Wei-Xing Yang, Yi Zhang et al.     Phosphodiesterase 4 (PDE4) has four isoforms (PDE4A-D) with at least 25 splice variants. PDE4 subtype nonselective inhibitors produce potent antidepressant-like and …             Leptin administration restores the altered adipose and hepatic expression of aquaglyceroporins improving the non-alcoholic fatty liver of ob/ob mice ▶     Amaia Rodríguez, Natalia R. Moreno, Inmaculada Balaguer et al.     Glycerol is an important metabolite for the control of lipid accumulation in white adipose tissue (WAT) and liver. We aimed to investigate whether exogenous administration of …             Understanding Dengue Virus Capsid Protein Interaction with Key Biological Targets ▶     André F. Faustino, Ivo C. Martins, Filomena A. Carvalho et al.     Dengue virus (DENV) causes over 500,000 hospitalizations and 20,000 deaths worldwide every year. Dengue epidemics now reach temperate regions due to globalization of trade and …             Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers ▶     Chen-Ching Lin, Wei Jiang, Ramkrishna Mitra et al.     Transcription factors (TFs) and microRNAs (miRNAs) form a gene regulatory network (GRN) at the transcriptional and post-transcriptional level in living cells. However, this …             Inactivation of group II intron RmInt1 in the Sinorhizobium meliloti genome ▶     María Dolores Molina-Sánchez, Nicolás Toro     Group II introns are self-splicing catalytic RNAs that probably originated in bacteria and act as mobile retroelements. The dispersal and dynamics of group II intron spread …             DNA-dependent targeting of cell nuclei by a lupus autoantibody ▶     Richard H. Weisbart, Grace Chan, Gwen Jordaan et al.     A nuclear-penetrating lupus anti-DNA autoantibody, 3E10, has been found to inhibit DNA repair and selectively kill certain cancer cells that are highly vulnerable to DNA damage. …             The chemomodulatory effects of resveratrol and didox on herceptin cytotoxicity in breast cancer cell lines ▶     Ghada A. Abdel-Latif, Ahmed M. Al-Abd, Mariane G. Tadros et al.     Herceptin is considered an essential treatment option for double negative breast cancer. Resveratrol and didox are known chemopreventive agents with potential anticancer …             Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics ▶     Zhiqiang Hu, Hamish S. Scott, Guangrong Qin et al.     Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the …             Functional Roles of Aromatic Residues and Helices of Papiliocin in its Antimicrobial and Anti-inflammatory Activities ▶     Eunjung Lee, Jin-Kyoung Kim, Dasom Jeon et al.     A cecropin-like peptide, papiliocin, isolated from the swallowtail butterfly Papilio xuthus, possesses high selectivity against gram-negative bacteria. Since Trp2 and Phe5 are …             Large-scale Direct Targeting for Drug Repositioning and Discovery ▶     Chunli Zheng, Zihu Guo, Chao Huang et al.     A system-level identification of drug-target direct interactions is vital to drug repositioning and discovery. However, the biological means on a large scale remains challenging …             Mammalian ranges are experiencing erosion of natural darkness ▶     James P. Duffy, Jonathan Bennie, América P. Durán et al.     The continuous increase in the intensity and extent of anthropogenic artificial light has significantly shaped Earth’s nighttime environment. This environmental change has …             Both TALENs and CRISPR/Cas9 directly target the HBB IVS2–654 (C > T) mutation in β-thalassemia-derived iPSCs ▶     Peng Xu, Ying Tong, Xiu-zhen Liu et al.     β-Thalassemia is one of the most common genetic blood diseases and is caused by either point mutations or deletions in the β-globin (HBB) gene. The generation of patient-specific …             Efficient introgression of allelic variants by embryo-mediated editing of the bovine genome ▶     Jingwei Wei, Stefan Wagner, Dan Lu et al.     The recent development of designer nucleases allows for the efficient and precise introduction of genetic change into livestock genomes. Most studies so far have focused on the …             Building an organic computing device with multiple interconnected brains ▶     Miguel Pais-Vieira, Gabriela Chiuffa, Mikhail Lebedev et al.     Recently, we proposed that Brainets, i.e. networks formed by multiple animal brains, cooperating and exchanging information in real time through direct brain-to-brain interfaces, …             In vivo efficacy and molecular docking of designed peptide that exhibits potent antipneumococcal activity and synergises in combination with penicillin ▶     Cheng-Foh Le, Mohd Yasim Mohd Yusof, Mahmood Ameen Abdulla Hassan et al.     We have previously designed a series of antimicrobial peptides (AMPs) and in the current study, the in vivo therapeutic efficacy and toxicity were investigated. Among all the …             Computing Arm Movements with a Monkey Brainet ▶     Arjun Ramakrishnan, Peter J. Ifft, Miguel Pais-Vieira et al.     Traditionally, brain-machine interfaces (BMIs) extract motor commands from a single brain to control the movements of artificial devices. Here, we introduce a Brainet that …             Involvement of PrPC in kainate-induced excitotoxicity in several mouse strains ▶     Patricia Carulla, Franc Llorens, Andreu Matamoros-Angles et al.     The cellular prion protein (PrPC) has been associated with a plethora of cellular functions ranging from cell cycle to neuroprotection. Mice lacking PrPC show an increased …             CAR-Engineered NK Cells Targeting Wild-Type EGFR and EGFRvIII Enhance Killing of Glioblastoma and Patient-Derived Glioblastoma Stem Cells ▶     Jianfeng Han, Jianhong Chu, Wing Keung Chan et al.     Glioblastoma (GB) remains the most aggressive primary brain malignancy. Adoptive transfer of chimeric antigen receptor (CAR)-modified immune cells has emerged as a promising …             To brood or not to brood: Are marine invertebrates that protect their offspring more resilient to ocean acidification? ▶     Noelle Marie Lucey, Chiara Lombardi, Lucia DeMarchi et al.     Anthropogenic atmospheric carbon dioxide (CO2) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought …             Antibacterial property of Ag nanoparticle-impregnated N-doped titania films under visible light ▶     Ming-Show Wong, Chun-Wei Chen, Chia-Chun Hsieh et al.     Photocatalysts produce free radicals upon receiving light energy; thus, they possess antibacterial properties. Silver (Ag) is an antibacterial material that disrupts bacterial …             Galangin attenuates airway remodelling by inhibiting TGF-β1-mediated ROS generation and MAPK/Akt phosphorylation in asthma ▶     Ya-Nan Liu, Wang-Jian Zha, Yuan Ma et al.     Galangin, a natural flavonol, has attracted much attention for its potential anti-inflammatory properties. However, its role in the regulation of airway remodelling in asthma has …             Regulation of mTOR Signaling by Semaphorin 3F-Neuropilin 2 Interactions In Vitro and In Vivo ▶     Hironao Nakayama, Sarah Bruneau, Nora Kochupurakkal et al.     Semaphorin 3F (SEMA3F) provides neuronal guidance cues via its ability to bind neuropilin 2 (NRP2) and Plexin A family molecules. Recent studies indicate that SEMA3F has …             Demographic comparison of sweetpotato weevil reared on a major host, Ipomoea batatas, and an alternative host, I. triloba ▶     Gadi V. P. Reddy, Hisn Chi     In this study, we collected life table data for the sweetpotato weevil, Cylas formicarius, grown on Ipomoea batatas and Ipomoea triloba, and analyzed them using an age-stage, …             Membrane-less microfiltration using inertial microfluidics ▶     Majid Ebrahimi Warkiani, Andy Kah Ping Tay, Guofeng Guan et al.     Microfiltration is a ubiquitous and often crucial part of many industrial processes, including biopharmaceutical manufacturing. Yet, all existing filtration systems suffer from …             Esophageal Squamous Cell Carcinoma and Gastric Cardia Adenocarcinoma Shared Susceptibility Locus in C20orf54: Evidence from Published Studies ▶     Fujiao Duan, Shuli Cui, Chunhua Song et al.     This study aimed to determine whether C20orf54 rs13042395 polymorphism modify the risk of esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinomas (GCA) in …             Growth and reproduction of laboratory-reared neanurid Collembola using a novel slime mould diet ▶     Jessica L. Hoskins, Charlene Janion-Scheepers, Steven L. Chown et al.     Although significant progress has been made using insect taxa as model organisms, non-tracheated terrestrial arthropods, such as Collembola, are underrepresented as model …             Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions ▶     Dennis Versluis, Marco Maria D’Andrea, Javier Ramiro Garcia et al.     Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but …             Feeding on Beauveria bassiana-treated Frankliniella occidentalis causes negative effects on the predatory mite Neoseiulus barkeri ▶     Shengyong Wu, Yulin Gao, Xuenong Xu et al.     The entomopathogenic fungus Beauveria bassiana and the predatory mite Neoseiulus barkeri are both potential biocontrol agents for their shared host/prey Frankliniella occidentalis…             Study of Protein Expresion in Peri-Infarct Tissue after Cerebral Ischemia ▶     David Brea, Jesús Agulla, An Staes et al.     In this work, we report our study of protein expression in rat peri-infarct tissue, 48 h after the induction of permanent focal cerebral ischemia. Two proteomic approaches, gel …             Immune response and insulin signalling alter mosquito feeding behaviour to enhance malaria transmission potential ▶     Lauren J. Cator, Jose E. Pietri, Courtney C. Murdock et al.     Malaria parasites alter mosquito feeding behaviour in a way that enhances parasite transmission. This is widely considered a prime example of manipulation of host behaviour to …             Novel drug target identification for the treatment of dementia using multi-relational association mining ▶     Thanh-Phuong Nguyen, Corrado Priami, Laura Caberlotto     Dementia is a neurodegenerative condition of the brain in which there is a progressive and permanent loss of cognitive and mental performance. Despite the fact that the number of …             TGFβ1 secreted by cancer-associated fibroblasts induces epithelial-mesenchymal transition of bladder cancer cells through lncRNA-ZEB2NAT ▶     Junlong Zhuang, Qun Lu, Bing Shen et al.     Urinary bladder cancer (UBC) patients at muscle invasive stage have poor clinical outcome, due to high propensity for metastasis. Cancer-associated fibroblasts (CAFs), one of the …             A novel long non-coding natural antisense RNA is a negative regulator of Nos1 gene expression ▶     Sergei A. Korneev, Mark Maconochie, Souvik Naskar et al.     Long non-coding natural antisense transcripts (NATs) are widespread in eukaryotic species. Although recent studies indicate that long NATs are engaged in the regulation of gene …             Bio-imaging and Photodynamic Therapy with Tetra Sulphonatophenyl Porphyrin (TSPP)-TiO2 Nanowhiskers: New Approaches in Rheumatoid Arthritis Theranostics ▶     Chunqiu Zhao, Fawad Ur Rehman, Yanlong Yang et al.     Since Rheumatoid arthritis (RA) is one of the major human joint diseases with unknown etiology, the early diagnosis and treatment of RA remains a challenge. In this contribution …             Pathogenic diversity amongst serotype C VGIII and VGIV Cryptococcus gattii isolates ▶     Jéssica Rodrigues, Fernanda L. Fonseca, Rafael O. Schneider et al.     Cryptococcus gattii is one of the causative agents of human cryptococcosis. Highly virulent strains of serotype B C. gattii have been studied in detail, but little information is …             IL-17A and its homologs IL-25/IL-17E recruit the c-RAF/S6 kinase pathway and the generation of pro-oncogenic LMW-E in breast cancer cells ▶     Sarah Mombelli, Stéphanie Cochaud, Yacine Merrouche et al.     Pro-inflammatory IL-17 cytokines were initially described for their pathogenic role in chronic inflammatory diseases and subsequent accumulating evidence indicated their …             Azithromycin inhibits IL-1 secretion and non-canonical inflammasome activation ▶     Guido A. Gualdoni, Tilman Lingscheid, Klaus G. Schmetterer et al.     Deregulation of inflammasome activation was recently identified to be involved in the pathogenesis of various inflammatory diseases. Although macrolide antibiotics display well …             How ants use quorum sensing to estimate the average quality of a fluctuating resource ▶     Nigel R. Franks, Jonathan P. Stuttard, Carolina Doran et al.     We show that one of the advantages of quorum-based decision-making is an ability to estimate the average value of a resource that fluctuates in quality. By using a quorum …             Cortical dynamics and subcortical signatures of motor-language coupling in Parkinson’s disease ▶     Margherita Melloni, Lucas Sedeño, Eugenia Hesse et al.     Impairments of action language have been documented in early stage Parkinson’s disease (EPD). The action-sentence compatibility effect (ACE) paradigm has revealed that EPD …             Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification ▶     Yi Wang, Yan Wang, Ai-Jing Ma et al.     We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). …             Reinitiation at non-canonical start codons leads to leak expression when incorporating unnatural amino acids ▶     Tanja Kalstrup, Rikard Blunck     With the rapid development of a continuously growing selection of unnatural amino acids (UAAs), UAA insertion becomes increasingly popular for investigating proteins. However, it …             Creating Anti-icing Surfaces via the Direct Immobilization of Antifreeze Proteins on Aluminum ▶     Yunho Gwak, Ji-in Park, Minjae Kim et al.     Cryoprotectants such as antifreeze proteins (AFPs) and sugar molecules may provide a solution for icing problems. These anti-icing substances protect cells and tissues from …             RalB regulates contractility-driven cancer dissemination upon TGFβ stimulation via the RhoGEF GEF-H1 ▶     Marco Biondini, Guillaume Duclos, Nathalie Meyer-Schaller et al.     RalA and RalB proteins are key mediators of oncogenic Ras signaling in human oncogenesis. Herein we investigated the mechanistic contribution of Ral proteins to invasion of lung …             Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution ▶     Michaela Liegertová, Jiří Pergner, Iryna Kozmiková et al.     Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a well-developed visual …             Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases ▶     Junji Hayashi, Shota Inoue, Kwang Kim et al.     NAD(P)-dependent dehydrogenases differ according to their coenzyme preference: some prefer NAD, others NADP, and still others exhibit dual cofactor specificity. The structure of …             A novel crosstalk between TLR4- and NOD2-mediated signaling in the regulation of intestinal inflammation ▶     Hajeong Kim, Quanju Zhao, Hua Zheng et al.     Although Toll-like receptor 4 (TLR4)- and nucleotide-binding oligomerization domain 2 (NOD2)-mediated signaling mechanisms have been extensively studied individually, the …             Analyzing Arabidopsis thaliana root proteome provides insights into the molecular bases of enantioselective imazethapyr toxicity ▶     Haifeng Qian, Haiping Lu, Haiyan Ding et al.     Imazethapyr (IM) is a widely used chiral herbicide that inhibits the synthesis of branched-chain amino acids (BCAAs). IM is thought to exert its toxic effects on amino acid …             Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis ▶     Aisha N. Andrewin, Jose M. Rodriguez-Llanes, Debarati Guha-Sapir     Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We …             Yeast model identifies ENTPD6 as a potential non-obstructive azoospermia pathogenic gene ▶     Qian Wang, Chao Liu, Chaoming Tang et al.     Approximately ten percent of male infertility is caused by non-obstructive azoospermia (NOA), but the etiologies of many NOA remain elusive. Recently, a genome-wide association …             High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures ▶     Yu-Chih Chen, Xia Lou, Zhixiong Zhang et al.     Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional …             Compound 331 selectively induces glioma cell death by upregulating miR-494 and downregulating CDC20 ▶     Lei Zhang, Tianhui Niu, Yafei Huang et al.     Malignant gliomas are the most common malignant tumors in the central nervous system (CNS). Up to date, the prognosis of glioma is still very poor, effective therapy with less …             The elusive life cycle of scyphozoan jellyfish – metagenesis revisited ▶     Janja Ceh, Jorge Gonzalez, Aldo S. Pacheco et al.     Massive proliferations of scyphozoan jellyfish considerably affect human industries and irreversibly change food webs. Efforts to understand the role of jellyfish in marine …             Systematic Analysis of the Genetic Variability That Impacts SUMO Conjugation and Their Involvement in Human Diseases ▶     Hao-Dong Xu, Shao-Ping Shi, Xiang Chen et al.     Protein function has been observed to rely on select essential sites instead of requiring all sites to be indispensable. Small ubiquitin-related modifier (SUMO) conjugation or …             Cyclic AMP Mimics the Anti-ageing Effects of Calorie Restriction by Up-Regulating Sirtuin ▶     Zhuoran Wang, Lu Zhang, Yaru Liang et al.     Cyclic adenosine monophosphate (cAMP) plays an important role in many biological processes as a second messenger, and cAMP treatment has been reported to extend the lifespan of …             Light Effect on Water Viscosity: Implication for ATP Biosynthesis ▶     Andrei P. Sommer, Mike Kh. Haddad, Hans-Jörg Fecht     Previous work assumed that ATP synthase, the smallest known rotary motor in nature, operates at 100% efficiency. Calculations which arrive to this result assume that the water …             Angiotensin type 1a receptor deficiency decreases amyloid β-protein generation and ameliorates brain amyloid pathology ▶     Junjun Liu, Shuyu Liu, Yukino Matsumoto et al.     Alzheimer’s disease is characterized by neuronal loss and cerebral accumulation of amyloid-β protein (Aβ) and lowering the generation of Aβ is a pivotal approach in the strategy …             Proton-Detected Solid-State NMR Spectroscopy of Bone with Ultrafast Magic Angle Spinning ▶     Kamal H. Mroue, Yusuke Nishiyama, Manoj Kumar Pandey et al.     While obtaining high-resolution structural details from bone is highly important to better understand its mechanical strength and the effects of aging and disease on bone …             FGF21 does not require interscapular brown adipose tissue and improves liver metabolic profile in animal models of obesity and insulin-resistance ▶     Barbara Bernardo, Min Lu, Gautam Bandyopadhyay et al.     FGF21 is a key metabolic regulator modulating physiological processes and its pharmacological administration improves metabolic profile in preclinical species and humans. We used …             Metabolomics Approach Reveals Integrated Metabolic Network Associated with Serotonin Deficiency ▶     Rui Weng, Sensen Shen, Yonglu Tian et al.     Serotonin is an important neurotransmitter that broadly participates in various biological processes. While serotonin deficiency has been associated with multiple pathological …             Real sequence effects on the search dynamics of transcription factors on DNA ▶     Maximilian Bauer, Emil S. Rasmussen, Michael A. Lomholt et al.     Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs …             Bridging Links between Long Noncoding RNA HOTAIR and HPV Oncoprotein E7 in Cervical Cancer Pathogenesis ▶     Sweta Sharma, Paramita Mandal, Tamal Sadhukhan et al.     Human Papillomavirus (HPV) type 16 oncoprotein E7 plays a major role in cervical carcinogenesis by interacting with and functionally inactivating various host regulatory …             Synchronization to a bouncing ball with a realistic motion trajectory ▶     Lingyu Gan, Yingyu Huang, Liang Zhou et al.     Daily music experience involves synchronizing movements in time with a perceived periodic beat. It has been established for over a century that beat synchronization is less …             A High Throughput Micro-Chamber Array Device for Single Cell Clonal Cultivation and Tumor Heterogeneity Analysis ▶     Feng-Min Shen, Lian Zhu, Heng Ye et al.     Recently, single cell cloning techniques have been gradually developed benefited from their important roles in monoclonal antibody screening, tumor heterogeneity research fields, …             Metabonomic analysis of potential biomarkers and drug targets involved in diabetic nephropathy mice ▶     Tingting Wei, Liangcai Zhao, Jianmin Jia et al.     Diabetic nephropathy (DN) is one of the lethal manifestations of diabetic systemic microvascular disease. Elucidation of characteristic metabolic alterations during diabetic …             Intermediate monocytes in ANCA vasculitis: increased surface expression of ANCA autoantigens and IL-1β secretion in response to anti-MPO antibodies ▶     Eóin C. O’Brien, Wayel H. Abdulahad, Abraham Rutgers et al.     ANCA vasculitis encompasses several autoimmune conditions characterised by destruction of small vessels, inflammation of the respiratory tract and glomerulonephritis. Most …             Corrigendum: Regulation of synaptic plasticity and cognition by SUMO in normal physiology and Alzheimer’s disease ▶     Linda Lee, Elena Dale, Agnes Staniszewski et al.                 Trapped lipopolysaccharide and LptD intermediates reveal lipopolysaccharide translocation steps across the Escherichia coli outer membrane ▶     Xuejun Li, Yinghong Gu, Haohao Dong et al.     Lipopolysaccharide (LPS) is a main component of the outer membrane of Gram-negative bacteria, which is essential for the vitality of most Gram-negative bacteria and plays a …             Function of a p24 Heterodimer in Morphogenesis and Protein Transport in Penicillium oxalicum ▶     Fangzhong Wang, Kuimei Liu, Lijuan Han et al.     The lignocellulose degradation capacity of filamentous fungi has been widely studied because of their cellulase hypersecretion. The p24 proteins in eukaryotes serve important …             Quantitative and qualitative analysis of the novel antitumor 1,3,4-oxadiazole derivative (GLB) and its metabolites using HPLC-UV and UPLC-QTOF-MS ▶     Pu Li, Xin Wang, Jian Li et al.     Fructose-based 3-acetyl-2,3-dihydro-1,3,4-oxadiazole (GLB) is a novel antitumor agent and belongs to glycosylated spiro-heterocyclic oxadiazole scaffold derivative. This research …             Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites ▶     Shoukai Lin, Qi Song, Huan Tao et al.     Experimentally-determined or computationally-predicted protein phosphorylation sites for distinctive species are becoming increasingly common. In this paper, we compare the …             Who started first? Bird species visiting novel birdfeeders ▶     Piotr Tryjanowski, Federico Morelli, Piotr Skórka et al.     Adapting to exploit new food sources may be essential, particularly in winter, when the impact of food limitation on survival of individuals is critical. One of the most …             Transcriptome analysis of the biofilm formed by methicillin-susceptible Staphylococcus aureus ▶     Xiaojuan Tan, Nan Qin, Chunyan Wu et al.     Biofilm formation is regarded as one of the major determinants in the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) as pathogens of medical device-related …             Real-time Imaging of Rabies Virus Entry into Living Vero cells ▶     Haijiao Xu, Xian Hao, Shaowen Wang et al.     Understanding the mechanism of rabies virus (RABV) infection is vital for prevention and therapy of virulent rabies. However, the infection mechanism remains largely …             Scaffolding of a bacterial genome using MinION nanopore sequencing ▶     E. Karlsson, A. Lärkeryd, A. Sjödin et al.     Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical …             Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate ▶     Heng Song, Wen Hu, Nathchar Naowarojna et al.     Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond …             Green to red photoconversion of GFP for protein tracking in vivo ▶     Amirali Sattarzadeh, Reza Saberianfar, Warren R. Zipfel et al.     A variety of fluorescent proteins have been identified that undergo shifts in spectral emission properties over time or once they are irradiated by ultraviolet or blue light. …             Crystal structure of a COG4313 outer membrane channel ▶     Bert van den Berg, Satya Prathyusha Bhamidimarri, Mathias Winterhalter     COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function …             BBS4 and BBS5 show functional redundancy in the BBSome to regulate the degradative sorting of ciliary sensory receptors ▶     Qingwen Xu, Yuxia Zhang, Qing Wei et al.     Cilia harbor sensory receptors for various signaling cascades critical for vertebrate development. However, the mechanisms underlying the ciliary homeostasis of sensory receptors …             Two short sequences in OsNAR2.1 promoter are necessary for fully activating the nitrate induced gene expression in rice roots ▶     Xiaoqin Liu, Huimin Feng, Daimin Huang et al.     Nitrate is an essential nitrogen source and serves as a signal to control growth and gene expression in plants. In rice, OsNAR2.1 is an essential partner of multiple OsNRT2 …             Structural insights into the unique inhibitory mechanism of the silkworm protease inhibitor serpin18 ▶     Peng-Chao Guo, Zhaoming Dong, Ping Zhao et al.     Serpins generally serve as inhibitors that utilize a mobile reactive center loop (RCL) as bait to trap protease targets. Here, we present the crystal structure of serpin18 from …             Primary microRNA processing is functionally coupled to RNAP II transcription in vitro ▶     Shanye Yin, Yong Yu, Robin Reed     Previous studies in vivo reported that processing of primary microRNA (pri-miRNA) is coupled to transcription by RNA polymerase II (RNAP II) and can occur co-transcriptionally. …             Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-β-cyclodextrin: Involvement of p53 and Fas receptor ligand complex ▶     Naoshad Mohammad, Shivendra Vikram Singh, Parmanand Malvi et al.     Doxorubicin (DOX) is one of the preferred drugs for treating breast and liver cancers. However, its clinical application is limited due to severe side effects and the …             Trace element fingerprinting of cockle (Cerastoderma edule) shells can reveal harvesting location in adjacent areas ▶     Fernando Ricardo, Luciana Génio, Miguel Costa Leal et al.     Determining seafood geographic origin is critical for controlling its quality and safeguarding the interest of consumers. Here, we use trace element fingerprinting (TEF) of …             Corrigendum: Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean ▶     Estelle Pedneault, Pierre E. Galand, Marianne Potvin et al.                 Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle ▶     Fabrizio Capuani, Daniele De Martino, Enzo Marinari et al.     Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, …             A versatile snap chip for high-density sub-nanoliter chip-to-chip reagent transfer ▶     Huiyan Li, Jeffrey D. Munzar, Andy Ng et al.     The coordinated delivery of minute amounts of different reagents is important for microfluidics and microarrays, but is dependent on advanced equipment such as microarrayers. …             Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs ▶     Lu Jing, Ye Hou, Hui Wu et al.     Feed efficiency (FE) can be measured by feed conversion ratio (FCR) or residual feed intake (RFI). In this study, we measured the FE related phenotypes of 236 castrated purebred …             Functional characterization of the principal sigma factor RpoD of phytoplasmas via an in vitro transcription assay ▶     Chihiro Miura, Ken Komatsu, Kensaku Maejima et al.     Phytoplasmas (class, Mollicutes) are insect-transmissible and plant-pathogenic bacteria that multiply intracellularly in both plants and insects through host switching. Our …             A time frame permissive for Protein Kinase D2 activity to direct angiogenesis in mouse embryonic stem cells ▶     Martin Müller, Jana Schröer, Ninel Azoitei et al.     The protein kinase D isoenzymes PKD1/2/3 are prominent downstream targets of PKCs (Protein Kinase Cs) and phospholipase D in various biological systems. Recently, we identified …             Incorporation of a GPI-anchored engineered cytokine as a molecular adjuvant enhances the immunogenicity of HIV VLPs ▶     Hao Feng, Han Zhang, Jiusheng Deng et al.     HIV vaccines should elicit immune responses at both the mucosal portals of entry to block transmission and systemic compartments to clear disseminated viruses. Co-delivery of …             Hui and Walter’s latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data ▶     Mairead L. Bermingham, Ian G. Handel, Elizabeth J. Glass et al.     Diagnostic test sensitivity and specificity are probabilistic estimates with far reaching implications for disease control, management and genetic studies. In the absence of …             Survival in patchy landscapes: the interplay between dispersal, habitat loss and fragmentation ▶     Bernardo B. S. Niebuhr, Marina E. Wosniack, Marcos C. Santos et al.     Habitat loss and fragmentation are important factors determining animal population dynamics and spatial distribution. Such landscape changes can lead to the deleterious impact of …             miR-125a-3p and miR-483-5p promote adipogenesis via suppressing the RhoA/ROCK1/ERK1/2 pathway in multiple symmetric lipomatosis ▶     Ke Chen, Honghui He, Yanhong Xie et al.     Multiple symmetric lipomatosis (MSL) is a rare disease characterized by symmetric and abnormal distribution of subcutaneous adipose tissue (SAT); however, the etiology is largely …             In situ microscopic observation of chitin and fungal cells with chitinous cell walls in hydrothermal conditions ▶     Shigeru Deguchi, Kaoru Tsujii, Koki Horikoshi     Recent findings of intact chitin in fossil records suggest surprisingly high recalcitrance of this biopolymer during hydrothermal treatments. We also know in the experience of …             Dynamic transcriptome analysis and volatile profiling of Gossypium hirsutum in response to the cotton bollworm Helicoverpa armigera ▶     Xin-Zheng Huang, Jie-Yin Chen, Hai-Jun Xiao et al.     In response to insect herbivory, plants emit elevated levels of volatile organic compounds for direct and indirect resistance. However, little is known about the molecular and …             Increased RIPK4 expression is associated with progression and poor prognosis in cervical squamous cell carcinoma patients ▶     De-Qing Liu, Fang-Fang Li, Jiang-Bo Zhang et al.     Aberrant expression of receptor interacting protein kinase 4 (RIPK4), a crucial regulatory protein of Wnt/β-catenin signaling, has recently been reported to be involved in …             Protein alterations in women with chronic widespread pain – An explorative proteomic study of the trapezius muscle ▶     Patrik Olausson, Björn Gerdle, Nazdar Ghafouri et al.     Chronic widespread pain (CWP) has a high prevalence in the population and is associated with prominent negative individual and societal consequences. 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