Scientific Reports Biology Table of Contents e-alert: 06 October 2015

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06 October 2015      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports         npj Aging and Mechanisms of Disease - first articles published Publishing high-quality open access research on aging and age-related diseases, npj Aging and Mechanisms of Disease has now published its first content. Part of the Nature Partner Journals series, and published in partnership with the Japanese Society of Anti-Aging Medicine (JAAM), highlights include yeast genomics and dementia.             Biological Sciences               Corrigendum: A Novel Role of Numb as A Regulator of Pro-inflammatory Cytokine Production in Macrophages in Response to Toll-like Receptor 4 ▶     Patipark Kueanjinda, Sittiruk Roytrakul, Tanapat Palaga                 An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life ▶     Daniel Barry Roche, Thomas Brüls     Previous studies of protein fold space suggest that fold coverage is plateauing. However, sequence sampling has been -and remains to a large extent- heavily biased, focusing on …             Analysis of a transgenic Oct4 enhancer reveals high fidelity long-range chromosomal interactions ▶     Mingyang Cai, Fan Gao, Peilin Zhang et al.     Genome structure or nuclear organization has fascinated researchers investigating genome function. Recently, much effort has gone into defining relationships between specific …             Lysine Methyltransferase SETD7 (SET7/9) Regulates ROS Signaling through mitochondria and NFE2L2/ARE pathway ▶     Shuying He, Dafydd R. Owen, Scott A. Jelinsky et al.     Reactive oxygen species (ROS) homeostasis requires stringent regulation. ROS imbalance, especially ROS accumulation, has profound implications in various disease pathogenesis. …             p38 MAPK regulates PKAα and CUB-serine protease in Amphibalanus amphitrite cyprids ▶     Gen Zhang, Li-Sheng He, Yue Him Wong et al.     The MKK3-p38 MAPK pathway has been reported to mediate larval settlement in Amphibalanus (=Balanus) amphitrite. To clarify the underlying molecular mechanism, we applied …             Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection ▶     Jason P. Mooney, Kristen L. Lokken, Mariana X. Byndloss et al.     Childhood malaria is a risk factor for disseminated infections with non-typhoidal Salmonella (NTS) in sub-Saharan Africa. While hemolytic anemia and an altered cytokine …             A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect ▶     Danny Ionescu, Mina Bizic-Ionescu, Arzhang Khalili et al.     Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of …             Hypoionic shock treatment enables aminoglycosides antibiotics to eradicate bacterial persisters ▶     Liu Jiafeng, Xinmiao Fu, Zengyi Chang     Bacterial persisters, usually being considered as dormant cells that are tolerant to antibiotics, are an important source for recurrent infection and emergence of antibiotic …             Plasma membrane restricted RhoGEF activity is sufficient for RhoA-mediated actin polymerization ▶     Jakobus van Unen, Nathalie R. Reinhard, Taofei Yin et al.     The small GTPase RhoA is involved in cell morphology and migration. RhoA activity is tightly regulated in time and space and depends on guanine exchange factors (GEFs). However, …             Real-time Detection of Breast Cancer Cells Using Peptide-functionalized Microcantilever Arrays ▶     Hashem Etayash, Keren Jiang, Sarfuddin Azmi et al.     Ligand-directed targeting and capturing of cancer cells is a new approach for detecting circulating tumor cells (CTCs). Ligands such as antibodies have been successfully used for …             Corrigendum: Epigenetic regulation of the nuclear-coded GCAT and SHMT2 genes confers human age-associated mitochondrial respiration defects ▶     Osamu Hashizume, Sakiko Ohnishi, Takayuki Mito et al.                 Increasing prevalence of ciprofloxacin-resistant food-borne Salmonella strains harboring multiple PMQR elements but not target gene mutations ▶     Dachuan Lin, Kaichao Chen, Edward Wai-Chi Chan et al.     Fluoroquinolone resistance in Salmonella has become increasingly prevalent in recent years. To probe the molecular basis of this phenomenon, the genetic and phenotypic features …             Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.) ▶     Jiaqin Shi, Jiepeng Zhan, Yuhua Yang et al.     To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, …             Uncovering the sources of DNA found on the Turin Shroud ▶     Gianni Barcaccia, Giulio Galla, Alessandro Achilli et al.     The Turin Shroud is traditionally considered to be the burial cloth in which the body of Jesus Christ was wrapped after his death approximately 2000 years ago. Here, we report …             Coexistence of glutamatergic spine synapses and shaft synapses in substantia nigra dopamine neurons ▶     Miae Jang, Ki Bum Um, Jinyoung Jang et al.     Dopamine neurons of the substantia nigra have long been believed to have multiple aspiny dendrites which receive many glutamatergic synaptic inputs from several regions of the …             Corrigendum: Sound Packing DNA: packing open circular DNA with low-intensity ultrasound ▶     DongHee Park, Bong-Kwang Jung, Hyunjin Park et al.                 The role of putrescine in the regulation of proteins and fatty acids of thylakoid membranes under salt stress ▶     Sheng Shu, Yinghui Yuan, Jie Chen et al.     Polyamines can alleviate the inhibitory effects of salinity on plant growth by regulating photosynthetic efficiency. However, little information is available to explain the …             USP15 regulates SMURF2 kinetics through C-lobe mediated deubiquitination ▶     Prasanna Vasudevan Iyengar, Patrick Jaynes, Laura Rodon et al.     Ubiquitin modification of the TGF-β pathway components is emerging as a key mechanism of TGF-β pathway regulation. To limit TGF-β responses, TGF-β signaling is regulated through …             Differential Responses of Plasma Adropin Concentrations To Dietary Glucose or Fructose Consumption In Humans ▶     Andrew A. Butler, Marie-Pierre St-Onge, Emily A. Siebert et al.     Adropin is a peptide hormone encoded by the Energy Homeostasis Associated (ENHO) gene whose physiological role in humans remains incompletely defined. Here we investigated the …             mirPRo–a novel standalone program for differential expression and variation analysis of miRNAs ▶     Jieming Shi, Min Dong, Lei Li et al.     Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many …             Prenatal ethanol exposure increases osteoarthritis susceptibility in female rat offspring by programming a low-functioning IGF-1 signaling pathway ▶     Qubo Ni, Yang Tan, Xianrong Zhang et al.     Epidemiological evidence indicates that osteoarthritis (OA) and prenatal ethanol exposure (PEE) are both associated with low birth weight but possible causal interrelationships …             Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue ▶     Adil Mardinoglu, John T. Heiker, Daniel Gärtner et al.     Weight loss has been shown to significantly improve Adipose tissue (AT) function, however changes in AT gene expression profiles particularly in visceral AT (VAT) have not been …             Anthropogenic effects on a tropical forest according to the distance from human settlements ▶     Ananya Popradit, Thares Srisatit, Somboon Kiratiprayoon et al.     The protection of tropical forests is one of the most urgent issues in conservation biology because of the rapid deforestation that has occurred over the last 50 years. Even in …             The enhanced information flow from visual cortex to frontal area facilitates SSVEP response: evidence from model-driven and data-driven causality analysis ▶     Fali Li, Yin Tian, Yangsong Zhang et al.     The neural mechanism of steady-state visual evoked potentials (SSVEP) is still not clearly understood. Especially, only certain frequency stimuli can evoke SSVEP. Our previous …             Rapid low dose electron tomography using a direct electron detection camera ▶     Vadim Migunov, Henning Ryll, Xiaodong Zhuge et al.     We demonstrate the ability to record a tomographic tilt series containing 3487 images in only 3.5 s by using a direct electron detector in a transmission electron microscope. The …             Distinguishing time-delayed causal interactions using convergent cross mapping ▶     Hao Ye, Ethan R. Deyle, Luis J. Gilarranz et al.     An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made …             The importance of spatial heterogeneity and self-restraint on mutualism stability - a quantitative review ▶     Rui-Wu Wang, Derek W. Dunn, Jun Luo et al.     Understanding the factors that enable mutualisms to evolve and to subsequently remain stable over time, is essential to fully understand patterns of global biodiversity and for …             Endometrial gene expression profile of pregnant sows with extreme phenotypes for reproductive efficiency ▶     S. Córdoba, I. Balcells, A. Castelló et al.     Prolificacy can directly impact porcine profitability, but large genetic variation and low heritability have been found regarding litter size among porcine breeds. To identify …             Parturition failure in mice lacking Mamld1 ▶     Mami Miyado, Kenji Miyado, Momori Katsumi et al.     In mice, the onset of parturition is triggered by a rapid decline in circulating progesterone. Progesterone withdrawal occurs as a result of functional luteolysis, which is …             An ace-1 gene duplication resorbs the fitness cost associated with resistance in Anopheles gambiae, the main malaria mosquito ▶     Benoît S. Assogba, Luc S. Djogbénou, Pascal Milesi et al.     Widespread resistance to pyrethroids threatens malaria control in Africa. Consequently, several countries switched to carbamates and organophophates insecticides for indoor …             Pre-amyloid oligomers of the proteotoxic RepA-WH1 prionoid assemble at the bacterial nucleoid ▶     María Moreno-del Álamo, Susana Moreno-Díaz de la Espina, M. Elena Fernández-Tresguerres et al.     Upon binding to short specific dsDNA sequences in vitro, the N-terminal WH1 domain of the plasmid DNA replication initiator RepA assembles as amyloid fibres. These are bundles of …             An optogenetic system for interrogating the temporal dynamics of Akt ▶     Yoshihiro Katsura, Hiroyuki Kubota, Katsuyuki Kunida et al.     The dynamic activity of the serine/threonine kinase Akt is crucial for the regulation of diverse cellular functions, but the precise spatiotemporal control of its activity …             JBP485 promotes corneal epithelial wound healing ▶     Maho Nagata, Takahiro Nakamura, Yuiko Hata et al.     Proper wound healing is vital for maintenance of corneal integrity and transparency. Corneal epithelial damage is one of the most frequently observed ocular disorders. Because …             The recombinant expression and activity detection of MAF-1 fusion protein ▶     Ping Fu, Jianwei Wu, Song Gao et al.     This study establishes the recombinant expression system of MAF-1 (Musca domestica antifungal peptide-1) and demonstrates the antifungal activity of the expression product and …             An automated fitting procedure and software for dose-response curves with multiphasic features ▶     Giovanni Y. Di Veroli, Chiara Fornari, Ian Goldlust et al.     In cancer pharmacology (and many other areas), most dose-response curves are satisfactorily described by a classical Hill equation (i.e. 4 parameters logistical). Nevertheless, …             Experimental Validation of Bacillus anthracis A16R Proteogenomics ▶     Zhiqi Gao, Zhiqiang Wang, Kun Zhang et al.     Anthrax, caused by the pathogenic bacterium Bacillus anthracis, is a zoonosis that causes serious disease and is of significant concern as a biological warfare agent. Validating …             A robust screening method for dietary agents that activate tumour-suppressor microRNAs ▶     Keitaro Hagiwara, Luc Gailhouste, Ken Yasukawa et al.     Certain dietary agents, such as natural products, have been reported to show anti-cancer effects. However, the underlying mechanisms of these substances in human cancer remain …             NSAIDs Ibuprofen, Indometacin, and Diclofenac do not interact with Farnesoid X Receptor ▶     Jurema Schmidt, Franca-Maria Klingler, Ewgenji Proschak et al.     The nuclear farnesoid X receptor (FXR) is a ligand activated transcription factor and acts as cellular sensor for bile acids. In this role, FXR is a highly important liver …             Navigating through digital folders uses the same brain structures as real world navigation ▶     Yael Benn, Ofer Bergman, Liv Glazer et al.     Efficient storage and retrieval of digital data is the focus of much commercial and academic attention. With personal computers, there are two main ways to retrieve files: …             Anti-interleukin-6 therapy through application of a monogenic protein inhibitor via gene delivery ▶     Dieter Görtz, Gerald S. Braun, Yuichi Maruta et al.     Anti-cytokine therapies have substantially improved the treatment of inflammatory and autoimmune diseases. Cytokine-targeting drugs are usually biologics such as antibodies or …             Natural small molecule FMHM inhibits lipopolysaccharide-induced inflammatory response by promoting TRAF6 degradation via K48-linked polyubiquitination ▶     Ke-Wu Zeng, Li-Xi Liao, Hai-Ning Lv et al.     TNF receptor-associated factor 6 (TRAF6) is a key hub protein involved in Toll-like receptor-dependent inflammatory signaling pathway, and it recruits additional proteins to form …             Activation of the AMPK-ULK1 pathway plays an important role in autophagy during prion infection ▶     Xue-Yu Fan, Chan Tian, Hui Wang et al.     AMPK is a serine/threonine protein kinase that acts as a positive regulator of autophagy, by phosphorylating ULK1 at specific sites. A previous study demonstrated activation of …             Stable expression and functional characterisation of the diamondback moth ryanodine receptor G4946E variant conferring resistance to diamide insecticides ▶     Bartlomiej J. Troczka, Alan J. Williams, Martin S. Williamson et al.     Diamides, such as flubendiamide and chlorantraniliprole, belong to a new chemical class of insecticides that act as conformation-sensitive activators of insect ryanodine …             Volatile fragrances associated with flowers mediate host plant alternation of a polyphagous mirid bug ▶     Hongsheng Pan, Yanhui Lu, Chunli Xiu et al.     Apolygus lucorum (Hemiptera: Miridae) is an important insect pest of cotton and fruit trees in China. The adults prefer host plants at the flowering stage, and their populations …             MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq ▶     Yun Xiao, Fulong Yu, Lin Pang et al.     As the fifth base in mammalian genome, 5-methylcytosine (5 mC) is essential for many biological processes including normal development and disease. Methylated DNA …             Bridging the translational divide: identical cognitive touchscreen testing in mice and humans carrying mutations in a disease-relevant homologous gene ▶     J. Nithianantharajah, A. G. McKechanie, T. J. Stewart et al.     Development of effective therapies for brain disorders has been hampered by a lack of translational cognitive testing methods. We present the first example of using the identical …             MiR-125a-5p Decreases the Sensitivity of Treg cells Toward IL-6-Mediated Conversion by Inhibiting IL-6R and STAT3 Expression ▶     Dan Li, Chao Kong, Andy Tsun et al.     The transcription factor FOXP3 is essential for the differentiation and function of regulatory T cells (Treg). It is established that the transcription factor GATA-3 is induced …             Detailed classification of swimming paths in the Morris Water Maze: multiple strategies within one trial ▶     Tiago V. Gehring, Gediminas Luksys, Carmen Sandi et al.     The Morris Water Maze is a widely used task in studies of spatial learning with rodents. Classical performance measures of animals in the Morris Water Maze include the escape …             Resonant Scanning with Large Field of View Reduces Photobleaching and Enhances Fluorescence Yield in STED Microscopy ▶     Yong Wu, Xundong Wu, Rong Lu et al.     Photobleaching is a major limitation of superresolution Stimulated Depletion Emission (STED) microscopy. Fast scanning has long been considered an effective means to reduce …             Copy number variation in the region harboring SOX9 gene in dogs with testicular/ovotesticular disorder of sex development (78,XX; SRY-negative) ▶     Malgorzata Marcinkowska-Swojak, Izabela Szczerbal, Hubert Pausch et al.     Although the disorder of sex development in dogs with female karyotype (XX DSD) is quite common, its molecular basis is still unclear. Among mutations underlying XX DSD in …             Comparative proteomics reveals human pluripotent stem cell-derived limbal epithelial stem cells are similar to native ocular surface epithelial cells ▶     Alexandra Mikhailova, Antti Jylhä, Jochen Rieck et al.     Limbal epithelial stem cells (LESCs) are tissue-specific stem cells responsible for renewing the corneal epithelium. Acute trauma or chronic disease affecting LESCs may disrupt …             Mass spectrometric identification and toxicity assessment of degraded products of aflatoxin B1 and B2 by Corymbia citriodora aqueous extracts ▶     Wajiha Iram, Tehmina Anjum, Mazhar Iqbal et al.     This study explores the detoxification potential of Corymbia citriodora plant extracts against aflatoxin B1 and B2 (AFB1; 100 μg L−1 and AFB2; 50 μg L−1) in In vitro and In vivo …             Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions ▶     Stephanie I. Fraley, Pei-hsun Wu, Lijuan He et al.     Multiple attributes of the three-dimensional (3D) extracellular matrix (ECM) have been independently implicated as regulators of cell motility, including pore size, crosslink …             Elevated free fatty acid uptake via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma ▶     Aritro Nath, Irene Li, Lewis R. Roberts et al.     Hepatocellular carcinoma (HCC) is the second-leading cause of cancer-related death worldwide, and the factors influencing HCC progression are poorly understood. Here we reveal …             Diversifying crop rotations with pulses enhances system productivity ▶     Yantai Gan, Chantal Hamel, John T. O’Donovan et al.     Agriculture in rainfed dry areas is often challenged by inadequate water and nutrient supplies. Summerfallowing has been used to conserve rainwater and promote the release of …             Cognitive deficits and anxiety induced by diisononyl phthalate in mice and the neuroprotective effects of melatonin ▶     Ping Ma, Xudong Liu, Jiliang Wu et al.     Diisononyl phthalate (DINP) is a plasticizer that is frequently used as a substitute for other plasticizers whose use is prohibited in certain products. In vivo studies on the …             Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process ▶     Itaru Yanagi, Takeshi Ishida, Koji Fujisaki et al.     To improve the spatial resolution of solid-state nanopores, thinning the membrane is a very important issue. The most commonly used membrane material for solid-state nanopores is …             Seroepidemiology of mumps in the general population of Jiangsu province, China after introduction of a one-dose measles-mumps-rubella vaccine ▶     Yuanbao Liu, Ying Hu, Xiuying Deng et al.     The mumps surveillance data from 2004 to 2011 showed that the incidence of mumps remained high after the one-dose measles-mumps-rubella (MMR) vaccine was introduced in China in …             The lethal response to Cdk1 inhibition depends on sister chromatid alignment errors generated by KIF4 and isoform 1 of PRC1 ▶     Erik Voets, Judith Marsman, Jeroen Demmers et al.     Cyclin-dependent kinase 1 (Cdk1) is absolutely essential for cell division. Complete ablation of Cdk1 precludes the entry of G2 phase cells into mitosis, and is early embryonic …             Direct chemotherapeutic dual drug delivery through intra-articular injection for synergistic enhancement of rheumatoid arthritis treatment ▶     A Reum Son, Da Yeon Kim, Seung Hun Park et al.     The effectiveness of systemic rheumatoid arthritis (RA) treatments is limited by difficulties in achieving therapeutic doses within articular joints. We evaluated the ability of …             Risk of Adverse Vascular Events in Newly Diagnosed Glioblastoma Multiforme Patients Treated with Bevacizumab: a Systematic Review and Meta-Analysis ▶     Xiaoqing Li, Rongzhong Huang, Zhongye Xu     Previous evidence suggests that the humanized anti-VEGF antibody bevacizumab increases thrombosis risk in glioma patients. Here, we comprehensively assessed the risk of adverse …             Chronic mercury exposure in Late Neolithic/Chalcolithic populations in Portugal from the cultural use of cinnabar ▶     Steven D. Emslie, Rebecka Brasso, William P. Patterson et al.     Cinnabar is a natural mercury sulfide (HgS) mineral of volcanic or hydrothermal origin that is found worldwide. It has been mined prehistorically and historically in China, …             Synergistic algicidal effect and mechanism of two diketopiperazines produced by Chryseobacterium sp. strain GLY-1106 on the harmful bloom-forming Microcystis aeruginosa ▶     Xingliang Guo, Xianglong Liu, Jianliang Pan et al.     A potent algicidal bacterium isolated from Lake Taihu, Chryseobacterium sp. strain GLY-1106, produces two algicidal compounds: 1106-A (cyclo(4-OH-Pro-Leu)) and 1106-B …             Azo-Based Iridium(III) Complexes as Multicolor Phosphorescent Probes to Detect Hypoxia in 3D Multicellular Tumor Spheroids ▶     Lingli Sun, Guanying Li, Xiang Chen et al.     Hypoxia is an important characteristic of malignant solid tumors and is considered as a possible causative factor for serious resistance to chemo- and radiotherapy. The …             A diphtheria toxin resistance marker for in vitro and in vivo selection of stably transduced human cells ▶     Gabriele Picco, Consalvo Petti, Livio Trusolino et al.     We developed a selectable marker rendering human cells resistant to Diphtheria Toxin (DT). The marker (DTR) consists of a primary microRNA sequence engineered to downregulate the …             Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon ▶     Yusuke Kakei, Keiichi Mochida, Tetsuya Sakurai et al.     Brachypodium distachyon is a new model plant closely related to wheat and other cereals. In this study, we performed a comprehensive analysis of hormone-regulated genes in …             Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, enlarge the parasite’s food vacuole and alter drug sensitivities ▶     Serena Pulcini, Henry M. Staines, Andrew H. Lee et al.     Mutations in the Plasmodium falciparum chloroquine resistance transporter, PfCRT, are the major determinant of chloroquine resistance in this lethal human malaria parasite. Here, …             Pathogen infection drives patterns of nutrient resorption in citrus plants ▶     Jirong Cao, Chunzhen Cheng, Junjie Yang et al.     Nutrient resorption processes in the plants infected by pathogen remain poorly understood. Huanglongbing (HLB) is a destructive disease of citrus. HLB-pathogen ‘Candidatus …             Quantifying barcodes of dendritic spines using entropy-based metrics ▶     D. Viggiano, D. P. Srivastava, L. Speranza et al.     Spine motility analysis has become the mainstay for investigating synaptic plasticity but is limited in its versatility requiring complex, non automatized instrumentations. We …             Unravelling polar lipids dynamics during embryonic development of two sympatric brachyuran crabs (Carcinus maenas and Necora puber) using lipidomics ▶     Felisa Rey, Eliana Alves, Tânia Melo et al.     Embryogenesis is an important stage of marine invertebrates with bi-phasic life cycles, as it conditions their larval and adult life. Throughout embryogenesis, phospholipids (PL) …             DAMP production by human islets under low oxygen and nutrients in the presence or absence of an immunoisolating-capsule and necrostatin-1 ▶     Genaro A. Paredes-Juarez, Neha M. Sahasrabudhe, Reina S. Tjoelker et al.     In between the period of transplantation and revascularization, pancreatic islets are exposed to low-oxygen and low-nutrient conditions. In the present study we mimicked those …             Ikaros mediates the DNA methylation-independent silencing of MCJ/DNAJC15 gene expression in macrophages ▶     Nicolás Navasa, Itziar Martin-Ruiz, Estíbaliz Atondo et al.     MCJ (DNAJC15) is a mitochondrial protein that regulates the mitochondrial metabolic status of macrophages and their response to inflammatory stimuli. CpG island methylation in …             Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR) ▶     Xavier Gallart-Palau, Aida Serra, Andrew See Weng Wong et al.     Extracellular vesicles (EVs) such as exosomes and microvesicles mediate intercellular communication and regulate a diverse range of crucial biological processes. Host cells that …             Ginkgo biloba leaf extract induces DNA damage by inhibiting topoisomerase II activity in human hepatic cells ▶     Zhuhong Zhang, Si Chen, Hu Mei et al.     Ginkgo biloba leaf extract has been shown to increase the incidence in liver tumors in mice in a 2-year bioassay conducted by the National Toxicology Program. In this study, the …             Cdh2 stabilizes FGFR1 and contributes to primed-state pluripotency in mouse epiblast stem cells ▶     Toshiyuki Takehara, Takeshi Teramura, Yuta Onodera et al.     The cell adhesion molecule Cadherin 2 (Cdh2) plays important roles in somatic cell adhesion, proliferation and migration. Cdh2 is also highly expressed in mouse epiblast stem …             Characterization of DNA variants in the human kinome in breast cancer ▶     Divyansh Agarwal, Yuan Qi, Tingting Jiang et al.     Kinases play a key role in cancer biology, and serve as potential clinically useful targets for designing cancer therapies. We examined nucleic acid variations in the human …             A covalent homodimer probing early oligomers along amyloid aggregation ▶     Levon Halabelian, Annalisa Relini, Alberto Barbiroli et al.     Early oligomers are crucial in amyloid aggregation; however, due to their transient nature they are among the least structurally characterized species. We focused on the …             Mutual positive effects between shrubs in an arid ecosystem ▶     Reyes Tirado, Kari Anne Bråthen, Francisco I. Pugnaire     One-way facilitation in plants has been found in many harsh environments and their role as structural forces governing species composition in plant communities is now well …             The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase ▶     Ali Flayhan, Célia Bergé, Nathalie Baïlo et al.     Bacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are …             Robustness of cell cycle control and flexible orders of signaling events ▶     Hao Zhu, Yanlan Mao     The highly robust control of cell cycles in eukaryotes enables cells to undergo strictly ordered G1/S/G2/M phases and respond adaptively to regulatory signals; however the nature …             Endoplasmic reticulum protein 29 (ERp29) confers radioresistance through the DNA repair gene, O6-methylguanine DNA-methyltransferase, in breast cancer cells ▶     Shaohua Chen, Yu Zhang, Daohai Zhang     Resistance of cancer cells to radiotherapy is a major clinical problem in cancer treatment. Therefore, understanding the molecular basis of cellular resistance to radiotherapy …             Germ plasm localisation of the HELICc of Vasa in Drosophila: analysis of domain sufficiency and amino acids critical for localisation ▶     Szu-Chieh Wang, Hao-Jen Hsu, Gee-way Lin et al.     Formation of the germ plasm drives germline specification in Drosophila and some other insects such as aphids. Identification of the DEAD-box protein Vasa (Vas) as a conserved …             Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites ▶     Xia Liu, Bo Zhao, Hua-Jun Zheng et al.     Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and …             Amygdala and cingulate structure is associated with stereotype on sex-role ▶     Hikaru Takeuchi, Yasuyuki Taki, Atsushi Sekiguchi et al.     Sex-role egalitarianism (SRE) is the belief that the sex of an individual should not influence the perception of his or her rights, abilities, obligations, and opportunities. …             Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics ▶     Venkata R. Duvvuri, Andrea Granados, Paul Rosenfeld et al.     Human respiratory syncytial virus (RSV) A ON1 genotype, first detected in 2010 in Ontario, Canada, has been documented in 21 countries to date. This study investigated …             Simultaneous MR imaging for tissue engineering in a rat model of stroke ▶     Francesca J. Nicholls, Wen Ling, Giuseppe Ferrauto et al.     In situ tissue engineering within a stroke cavity is gradually emerging as a novel therapeutic paradigm. Considering the varied lesion topology within each subject, the placement …             Hypothalamic overexpression of mutant huntingtin causes dysregulation of brown adipose tissue ▶     Rana Soylu-Kucharz, Natalie Adlesic, Barbara Baldo et al.     Expression of mutant huntingtin (htt) protein has been shown to cause metabolic imbalance in animal models of Huntington disease (HD). The pathways involved are not fully …             Evidence of a dissociation pattern in default mode subnetwork functional connectivity in schizophrenia ▶     Huaning Wang, Ling-Li Zeng, Yunchun Chen et al.     The default mode network (DMN) is suggested to play a pivotal role in schizophrenia; however, the dissociation pattern of functional connectivity of DMN subsystems remains …             Seed priming with polyethylene glycol regulating the physiological and molecular mechanism in rice (Oryza sativa L.) under nano-ZnO stress ▶     Sheteiwy Mohamed Salah, Guan Yajing, Cao Dongdong et al.     The present study was designed to highlight the impact of seed priming with polyethylene glycol on physiological and molecular mechanism of two cultivars of Oryza sativa L. under …             Infants born large-for-gestational-age display slower growth in early infancy, but no epigenetic changes at birth ▶     Valentina Chiavaroli, Wayne S. Cutfield, José G. B. Derraik et al.     We evaluated the growth patterns of infants born large-for-gestational-age (LGA) from birth to age 1 year compared to those born appropriate-for-gestational-age (AGA). In …             Anthelmintic activity of trans-cinnamaldehyde and A- and B-type proanthocyanidins derived from cinnamon (Cinnamomum verum) ▶     Andrew R. Williams, Aina Ramsay, Tina V. A. Hansen et al.     Cinnamon (Cinnamomum verum) has been shown to have anti-inflammatory and antimicrobial properties, but effects on parasitic worms of the intestine have not been investigated. …             Antigen exposure in the late light period induces severe symptoms of food allergy in an OVA-allergic mouse model ▶     Kana Tanabe, Eri Kitagawa, Misaki Wada et al.     The mammalian circadian clock controls many physiological processes that include immune responses and allergic reactions. Several studies have investigated the circadian …             Protocatechuic acid ameliorates neurocognitive functions impairment induced by chronic intermittent hypoxia ▶     Xue Yin, Xiuli Zhang, Changjun Lv et al.     Chronic intermittent hypoxia (CIH) is a serious consequence of obstructive sleep apnoea (OSA) and has deleterious effects on central neurons and neurocognitive functions. This …             Doxorubicin-poly (ethylene glycol)-alendronate self-assembled micelles for targeted therapy of bone metastatic cancer ▶     Wei-liang Ye, Yi-pu Zhao, Huai-qiu Li et al.     In order to increase the therapeutic effect of doxorubicin (DOX) on bone metastases, a multifunctional micelle was developed by combining pH-sensitive characteristics with bone …             Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance ▶     Meenu Kesarwani, Erika Huber, Zachary Kincaid et al.     Emergence of genetic resistance against kinase inhibitors poses a great challenge for durable therapeutic response. Here, we report a novel mechanism of JAK2 kinase inhibition by …             Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature ▶     Youhuang Bai, Sen Wang, Hong Zhong et al.     To investigate the changes in transcript and relative protein levels in response to temperature, complementary transcriptomic and proteomic analyses were used to identify changes …             Brain extracellular matrix retains connectivity in neuronal networks ▶     Arthur Bikbaev, Renato Frischknecht, Martin Heine     The formation and maintenance of connectivity are critically important for the processing and storage of information in neuronal networks. The brain extracellular matrix (ECM) …             Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity ▶     Tom J. J. Schirris, Tina Ritschel, G. Herma Renkema et al.     Cannabinoid receptor 1 (CB1R) antagonists appear to be promising drugs for the treatment of obesity, however, serious side effects have hampered their clinical application. …             Preimplantation death of xenomitochondrial mouse embryo harbouring bovine mitochondria ▶     Manabu Kawahara, Shiori Koyama, Satomi Iimura et al.     Mitochondria, cellular organelles playing essential roles in eukaryotic cell metabolism, are thought to have evolved from bacteria. The organization of mtDNA is remarkably …             Response of plant nutrient stoichiometry to fertilization varied with plant tissues in a tropical forest ▶     Qifeng Mo, Bi Zou, Yingwen Li et al.     Plant N:P ratios are widely used as indices of nutrient limitation in terrestrial ecosystems, but the response of these metrics in different plant tissues to altered N and P …             Melanin production through novel processing of proopiomelanocortin in the extracellular compartment of the auricular skin of C57BL/6 mice after UV-irradiation ▶     Hiroyuki Yamamoto, Tomohiro Yamane, Kazuaki Iguchi et al.     The production of melanin is regulated by α-melanocyte-stimulating hormone (α-MSH), which is produced from proopiomelanocortin (POMC). Keratinocytes release POMC along with lower …             Global change feed-back inhibits cyanobacterial photosynthesis ▶     E. Walter Helbling, Anastazia T. Banaszak, Virginia E. Villafañe     Cyanobacteria are an important component of aquatic ecosystems, with a proliferation of massive cyanobacterial blooms predicted worldwide under increasing warming conditions. In …             Hepatitis C-like viruses are produced in cells from rabbit and hare DNA ▶     Eliane Silva, Hugo Osório, Gertrude Thompson     Hepatitis C virus (HCV), a major causative agent of acute and chronic liver disease, belongs to the Flaviviridæ family and contains a single-strand positive-sense RNA genome, …             Full-color structured illumination optical sectioning microscopy ▶     Jia Qian, Ming Lei, Dan Dan et al.     In merits of super-resolved resolution and fast speed of three-dimensional (3D) optical sectioning capability, structured illumination microscopy (SIM) has found variety of …             The body fades away: investigating the effects of transparency of an embodied virtual body on pain threshold and body ownership ▶     Matteo Martini, Konstantina Kilteni, Antonella Maselli et al.     The feeling of “ownership” over an external dummy/virtual body (or body part) has been proven to have both physiological and behavioural consequences. For instance, the vision of …             The shadow of the future promotes cooperation in a repeated prisoner’s dilemma for children ▶     Peter R. Blake, David G. Rand, Dustin Tingley et al.     Cooperation among genetically unrelated individuals can be supported by direct reciprocity. Theoretical models and experiments with adults show that the possibility of future …             Development of ‘Redox Arrays’ for identifying novel glutathionylated proteins in the secretome ▶     Lisa Mullen, Miles Seavill, Raneem Hammouz et al.     Proteomics techniques for analysing the redox status of individual proteins in complex mixtures tend to identify the same proteins due to their high abundance. We describe here …             A streamlined search technology for identification of synergistic drug combinations ▶     Andrea Weiss, Robert H. Berndsen, Xianting Ding et al.     A major key to improvement of cancer therapy is the combination of drugs. Mixing drugs that already exist on the market may offer an attractive alternative. Here we report on a …             Local bacteria affect the efficacy of chemotherapeutic drugs ▶     Panos Lehouritis, Joanne Cummins, Michael Stanton et al.     In this study, the potential effects of bacteria on the efficacy of frequently used chemotherapies was examined. Bacteria and cancer cell lines were examined in vitro and in vivo …             Increased epigenetic alterations at the promoters of transcriptional regulators following inadequate maternal gestational weight gain ▶     Tomoko Kawai, Takahiro Yamada, Kosei Abe et al.     Epigenetic modifications are thought to serve as a memory of exposure to in utero environments. However, few human studies have investigated the associations between maternal …             Inhibition of the Rho/Rho kinase pathway prevents lipopolysaccharide-induced hyperalgesia and the release of TNF-α and IL-1β in the mouse spinal cord ▶     Cunjin Wang, Siyuan Song, Yang Zhang et al.     Administration of lipopolysaccharide (LPS) by various routes produces profound inflammatory pain hypersensitivity. However, the molecular events that induce this response remain …             Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren ▶     Arko Sen, Nicole Heredia, Marie-Claude Senut et al.     We report that the DNA methylation profile of a child’s neonatal whole blood can be significantly influenced by his or her mother’s neonatal blood lead levels (BLL). We recruited …             Identification of an iridium(III) complex with anti-bacterial and anti-cancer activity ▶     Lihua Lu, Li-Juan Liu, Wei-chieh Chao et al.     Group 9 transition metal complexes have been widely explored as therapeutic agents due to their unique geometry, their propensity to undergo ligand exchanges with biomolecules …             Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom ▶     Xiaoming Song, Weike Duan, Zhinan Huang et al.     In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few …             A 3D map of the islet routes throughout the healthy human pancreas ▶     Constantin Ionescu-Tirgoviste, Paul A. Gagniuc, Elvira Gubceac et al.     Islets of Langerhans are fundamental in understanding diabetes. A healthy human pancreas from a donor has been used to asses various islet parameters and their three-dimensional …             Synergy of multi-scale toughening and protective mechanisms at hierarchical branch-stem interfaces ▶     Ulrich Müller, Wolfgang Gindl-Altmutter, Johannes Konnerth et al.     Biological materials possess a variety of artful interfaces whose size and properties are adapted to their hierarchical levels and functional requirements. Bone, nacre, and wood …             Differential Plasma-cell evolution is linked with Dermatophagoides pteronyssinus immunotherapy response ▶     Tahia D. Fernández, Enrique Gómez, Inmaculada Doña et al.     Allergic rhinitis is highly prevalent worldwide. Immunotherapy has been shown to control its symptoms, however, up to 30% of patients may not respond. Previous studies of the …             Downregulating p22phox ameliorates inflammatory response in Angiotensin II-induced oxidative stress by regulating MAPK and NF-κB pathways in ARPE-19 cells ▶     Yiguo Qiu, Lifei Tao, Chunyan Lei et al.     Oxidative stress and inflammation are two interrelated biological events implicated in the pathogenesis of many diseases. Reactive oxygen species (ROS) produced under oxidative …             PTBP1 and PTBP2 impaired autoregulation of SRSF3 in cancer cells ▶     Jihua Guo, Jun Jia, Rong Jia     Splicing factors are key players in the regulation of alternative splicing of pre-mRNAs. Overexpression of splicing factors, including SRSF3, has been strongly linked with …                 npj Systems Biology and Applications - first articles published Publishing the finest research on systems biology and its approaches, npj Systems Biology and Applications has now published its first content. 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