bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions
Authors: Silva Joana C. , Cornillot Emmanuel , McCracken Carrie , Usmani-Brown Sahar , Dwivedi Ankit , Ifeonu Olukemi O. , Crabtree Jonathan , Gotia Hanzel T. , Virji Azan Z. , Reynes Christelle , Colinge Jacques , Kumar Vidya , Lawres Lauren , Pazzi Joseph E. , Pablo Jozelyn V. , Hung Chris , Brancato Jana , Kumari Priti , Orvis Joshua , Tretina Kyle , Chibucos Marcus , Ott Sandy , Sadzewicz Lisa , Sengamalay Naomi , Shetty Amol C. , Su Qi , Tallon Luke , Fraser Claire M. , Frutos Roger , Molina Douglas M. , Krause Peter J. , Ben Mamoun Choukri 
Published: October 2016

AbstractBabesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.
Inkjet-Printed Graphene/PEDOT:PSS Temperature Sensors on a Skin-Conformable Polyurethane Substrate
Authors: Vuorinen Tiina , Niittynen Juha , Kankkunen Timo , Kraft Thomas M. , Mäntysalo Matti 
Published: October 2016

AbstractEpidermal electronic systems (EESs) are skin-like electronic systems, which can be used to measure several physiological parameters from the skin. This paper presents materials and a simple, straightforward fabrication process for skin-conformable inkjet-printed temperature sensors. Epidermal temperature sensors are already presented in some studies, but they are mainly fabricated using traditional photolithography processes. These traditional fabrication routes have several processing steps and they create a substantial amount of material waste. Hence utilizing printing processes, the EES may become attractive for disposable systems by decreasing the manufacturing costs and reducing the wasted materials. In this study, the sensors are fabricated with inkjet-printed graphene/PEDOT:PSS ink and the printing is done on top of a skin-conformable polyurethane plaster (adhesive bandage). Sensor characterization was conducted both in inert and ambient atmosphere and the graphene/PEDOT:PSS temperature sensors (thermistors) were able reach higher than 0.06% per degree Celsius sensitivity in an optimal environment exhibiting negative temperature dependence.
Functional diversity exhibits a diverse relationship with area, even a decreasing one
Authors: Karadimou Elpida K. , Kallimanis Athanasios S. , Tsiripidis Ioannis , Dimopoulos Panayotis 
Published: October 2016

AbstractThe relationship between species richness and area is one of the few well-established laws in ecology, and one might expect a similar relationship with functional diversity (FD). However, only a few studies investigate the relationship between trait-based FD and area, the Functional Diversity - Area Relationship (FDAR). To examine FDAR, we constructed the species accumulation curve and the corresponding FD curve. We used plant diversity data from nested plots (1–128 m2), recorded on the Volcanic islands of Santorini Archipelagos, Greece. Six multidimensional FD indices were calculated using 26 traits. We identified a typology of FDARs depending on the facet of FD analyzed: (A) strongly positive for indices quantifying the range of functional traits in the community, (B) negative correlation for indices quantifying the evenness in the distribution of abundance in the trait space, (C) no clear pattern for indices reflecting the functional similarity of species and (D) idiosyncratic patterns with area for functional divergence. As area increases, the range of traits observed in the community increases, but the abundance of traits does not increase proportionally and some traits become dominant, implying a reliance on some functions that may be located in either the center or the periphery of the trait space.
Exogenous glutathione improves high root-zone temperature tolerance by modulating photosynthesis, antioxidant and osmolytes systems in cucumber seedlings
Authors: Ding Xiaotao , Jiang Yuping , He Lizhong , Zhou Qiang , Yu Jizhu , Hui Dafeng , Huang Danfeng 
Published: October 2016

AbstractTo investigate the physiological responses of plants to high root-zone temperature (HT, 35 °C) stress mitigated by exogenous glutathione (GSH), cucumber (Cucumis sativus L.) seedlings were exposed to HT with or without GSH treatment for 4 days and following with 4 days of recovery. Plant physiological variables, growth, and gene expression related to antioxidant enzymes and Calvin cycle were quantified. The results showed that HT significantly decreased GSH content, the ratio of reduced to oxidized glutathione (GSH/GSSG), chlorophyll content, photosynthesis and related gene expression, shoot height, stem diameter, as well as dry weight. The exogenous GSH treatment clearly lessened the HT stress by increasing the above variables. Meanwhile, HT significantly increased soluble protein content, proline and malondialdehyde (MDA) content as well as O2•− production rate, the gene expression and activities of antioxidant enzymes. The GSH treatment remarkably improved soluble protein content, proline content, antioxidant enzymes activities, and antioxidant enzymes related gene expression, and reduced the MDA content and O2•− production rate compared to no GSH treatment in the HT condition. Our results suggest that exogenous GSH enhances cucumber seedling tolerance of HT stress by modulating the photosynthesis, antioxidant and osmolytes systems to improve physiological adaptation.
Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization
Authors: Fahrenkamp Dirk , Li Jinyu , Ernst Sabrina , Schmitz-Van de Leur Hildegard , Chatain Nicolas , Küster Andrea , Koschmieder Steffen , Lüscher Bernhard , Rossetti Giulia , Müller-Newen Gerhard 
Published: October 2016

AbstractSTAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.
Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine
Authors: Kiraly Drew D. , Walker Deena M. , Calipari Erin S. , Labonte Benoit , Issler Orna , Pena Catherine J. , Ribeiro Efrain A. , Russo Scott J. , Nestler Eric J. 
Published: October 2016

AbstractAddiction to cocaine and other psychostimulants represents a major public health crisis. The development and persistence of addictive behaviors comes from a complex interaction of genes and environment - the precise mechanisms of which remain elusive. In recent years a surge of evidence has suggested that the gut microbiome can have tremendous impact on behavioral via the microbiota-gut-brain axis. In this study we characterized the influence of the gut microbiota on cocaine-mediated behaviors. Groups of mice were treated with a prolonged course of non-absorbable antibiotics via the drinking water, which resulted in a substantial reduction of gut bacteria. Animals with reduced gut bacteria showed an enhanced sensitivity to cocaine reward and enhanced sensitivity to the locomotor-sensitizing effects of repeated cocaine administration. These behavioral changes were correlated with adaptations in multiple transcripts encoding important synaptic proteins in the brain’s reward circuitry. This study represents the first evidence that alterations in the gut microbiota affect behavioral response to drugs of abuse.
Induction of Autophagy and Apoptosis via PI3K/AKT/TOR Pathways by Azadirachtin A in Spodoptera litura Cells
Authors: Shao Xuehua , Lai Duo , Zhang Ling , Xu Hanhong 
Published: October 2016

AbstractAzadirachtin is one of the most effective botanical insecticides and has been widely used in pest control. Toxicological reports show that azadirachtin can induce apoptosis in various insect cell lines. However, studies of azadirachtin-induced autophagy in cultured insect cells are lacking. This study reports that azadirachtin A significantly inhibits cell proliferation by inducing autophagic and apoptotic cell death in Spodoptera litura cultured cell line (SL-1 cell). Characteristic autophagolysosome and Atg8-PE (phosphatidylethanolamine) accumulation were observed by electron microscopy and western blotting, indicating that azadirachtin triggered autophagy in SL-1 cell. Furthermore, azadirachtin inhibited survival signaling by blocking the activation of PI3K, AKT and the down-stream target of rapamycin. Similar to the positive control of starvation, azadirachtin induced the activation of insulin receptor (InR) via a cellular feedback mechanism. In addition, the autophagy-related 5 (Atg5), a molecular switch of autophagy and apoptosis, was truncated (tAtg5) to trigger cytochrome c release into the cytoplasm under azadirachtin stress, which indicated that azadirachtin induced apoptosis through autophagy. Our findings suggest that azadirachtin primarily induced autophagy in SL-1 cell by dysregulating InR- and PI3K/AKT/TOR pathways, then stimulated apoptosis by activating tAtg5.
Microbial respiration, but not biomass, responded linearly to increasing light fraction organic matter input: Consequences for carbon sequestration
Authors: Rui Yichao , Murphy Daniel V. , Wang Xiaoli , Hoyle Frances C. 
Published: October 2016

AbstractRebuilding ‘lost’ soil carbon (C) is a priority in mitigating climate change and underpinning key soil functions that support ecosystem services. Microorganisms determine if fresh C input is converted into stable soil organic matter (SOM) or lost as CO2. Here we quantified if microbial biomass and respiration responded positively to addition of light fraction organic matter (LFOM, representing recent inputs of plant residue) in an infertile semi-arid agricultural soil. Field trial soil with different historical plant residue inputs [soil C content: control (tilled) = 9.6 t C ha−1 versus tilled + plant residue treatment (tilled + OM) = 18.0 t C ha−1] were incubated in the laboratory with a gradient of LFOM equivalent to 0 to 3.8 t C ha−1 (0 to 500% LFOM). Microbial biomass C significantly declined under increased rates of LFOM addition while microbial respiration increased linearly, leading to a decrease in the microbial C use efficiency. We hypothesise this was due to insufficient nutrients to form new microbial biomass as LFOM input increased the ratio of C to nitrogen, phosphorus and sulphur of soil. Increased CO2 efflux but constrained microbial growth in response to LFOM input demonstrated the difficulty for C storage in this environment.
Sensitive detection of copper ions via ion-responsive fluorescence quenching of engineered porous silicon nanoparticles
Authors: Hwang Jangsun , Hwang Mintai P. , Choi Moonhyun , Seo Youngmin , Jo Yeonho , Son Jaewoo , Hong Jinkee , Choi Jonghoon 
Published: October 2016

AbstractHeavy metal pollution has been a problem since the advent of modern transportation, which despite efforts to curb emissions, continues to play a critical role in environmental pollution. Copper ions (Cu2+), in particular, are one of the more prevalent metals that have widespread detrimental ramifications. From this perspective, a simple and inexpensive method of detecting Cu2+ at the micromolar level would be highly desirable. In this study, we use porous silicon nanoparticles (NPs), obtained via anodic etching of Si wafers, as a basis for undecylenic acid (UDA)- or acrylic acid (AA)-mediated hydrosilylation. The resulting alkyl-terminated porous silicon nanoparticles (APS NPs) have enhanced fluorescence stability and intensity, and importantly, exhibit [Cu2+]-dependent quenching of fluorescence. After determining various aqueous sensing conditions for Cu2+, we demonstrate the use of APS NPs in two separate applications – a standard well-based paper kit and a portable layer-by-layer stick kit. Collectively, we demonstrate the potential of APS NPs in sensors for the effective detection of Cu2+.
Circular RNA has_circ_0067934 is upregulated in esophageal squamous cell carcinoma and promoted proliferation
Authors: Xia Wenjia , Qiu Mantang , Chen Rui , Wang Siwei , Leng Xuechun , Wang Jie , Xu Youtao , Hu Jingwen , Dong Gaochao , Xu Prof Lin , Yin Rong 
Published: October 2016

AbstractEsophageal squamous cell carcinoma (ESCC) is one of the most prevalent and deadly types of cancer worldwide especially in Eastern Asia and the prognosis of ESCC remain poor. Recent evidence suggests that circular RNAs (circRNAs) play important roles in multiple diseases, including cancer. In this study, we characterized a novel circRNA termed hsa_circ_0067934 in ESCC tumor tissues and cell lines. We analyzed a cohort of 51 patients and found that hsa_circ_0067934 was significantly overexpressed in ESCC tissues compared with paired adjacent normal tissues. The high expression level of hsa_circ_0067934 was associated with poor differentiation (P = 0.025), I-II T stage (P = 0.04), and I-II TNM stage (P = 0.021). The in vitro silence of hsa_circ_0067934 by siRNA inhibited the proliferation and migration of ESCC cells and blocked cell cycle progression. Cell fraction analyses and fluorescence in situ hybridization detected that hsa_circ_0067934 was mostly located in the cytoplasm. Our findings suggest that hsa_circ_0067934 is upregulated in ESCC tumor tissue. Our data suggest that hsa_circ_0067934 represents a novel potential biomarker and therapeutic target of ESCC.
F-O-G Ring Formation in Glycopeptide Antibiotic Biosynthesis is Catalysed by OxyE
Authors: Peschke Madeleine , Brieke Clara , Cryle Max J. 
Published: October 2016

AbstractThe glycopeptide antibiotics are peptide-based natural products with impressive antibiotic function that derives from their unique three-dimensional structure. Biosynthesis of the glycopeptide antibiotics centres of the combination of peptide synthesis, mediated by a non-ribosomal peptide synthetase, and the crosslinking of aromatic side chains of the peptide, mediated by the action of a cascade of Cytochrome P450s. Here, we report the first example of in vitro activity of OxyE, which catalyses the F-O-G ring formation reaction in teicoplanin biosynthesis. OxyE was found to only act after an initial C-O-D crosslink is installed by OxyB and to require an interaction with the unique NRPS domain from glycopeptide antibiotic – the X-domain – in order to display catalytic activity. We could demonstrate that OxyE displays limited stereoselectivity for the peptide, which mirrors the results from OxyB-catalysed turnover and is in sharp contrast to OxyA. Furthermore, we show that activity of a three-enzyme cascade (OxyB/OxyA/OxyE) in generating tricyclic glycopeptide antibiotic peptides depends upon the order of addition of the OxyA and OxyE enzymes to the reaction. This work demonstrates that complex enzymatic cascades from glycopeptide antibiotic biosynthesis can be reconstituted in vitro and provides new insights into the biosynthesis of these important antibiotics.
Neoadjuvant Therapy in Rectal Cancer - Biobanking of Preoperative Tumor Biopsies
Authors: Jo Peter , Nietert Manuel , Gusky Linda , Kitz Julia , Conradi Lena C. , Müller-Dornieden Annegret , Schüler Philipp , Wolff Hendrik A. , Rüschoff Josef , Ströbel Philipp , Grade Marian , Liersch Torsten , Beißbarth Tim , Ghadimi Michael B. , Sax Ulrich , Gaedcke Jochen 
Published: October 2016

AbstractTranslational research relies on high-quality biospecimens. In patients with rectal cancer treated preoperatively with radiochemotherapy tissue based analyses are challenging. To assess quality challenges we analyzed tissue samples taken over the last years in a multicenter setting. We retrospectively evaluated overall 197 patients of the CAO/ARO/AIO-94- and 04-trial with locally advanced rectal cancer that were biopsied preoperatively at the University Medical Center Goettingen as well as in 10 cooperating hospitals in Germany. The cellular content of tumor, mucosa, stroma, necrosis and the amount of isolated DNA and RNA as well as the RNA integrity number (RIN) as quality parameters were evaluated. A high RNA yield (p = 2.75e–07) and the content of tumor (p = 0.004) is significantly associated to high RIN-values, whereas a high content of mucosa (p = 0.07) shows a trend and a high amount of necrosis (p = 0.01) is significantly associated with RNA of poor quality. Correlating biopsies from Goettingen and the cooperating centers showed comparable tumor content results. By taking small sized biopsies we could assess a clear correlation between a good RNA quality and a high amount of RNA and tumor cells. These results also indicate that specimens collected at different centers are of comparable quality.
The B1 Protein Guides the Biosynthesis of a Lasso Peptide
Authors: Zhu Shaozhou , Fage Christopher D. , Hegemann Julian D. , Mielcarek Andreas , Yan Dushan , Linne Uwe , Marahiel Mohamed A. 
Published: October 2016

AbstractLasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique lariat knot-like fold that endows them with extraordinary stability and biologically relevant activity. However, the biosynthetic mechanism of these fascinating molecules remains largely speculative. Generally, two enzymes (B for processing and C for cyclization) are required to assemble the unusual knot-like structure. Several subsets of lasso peptide gene clusters feature a “split” B protein on separate open reading frames (B1 and B2), suggesting distinct functions for the B protein in lasso peptide biosynthesis. Herein, we provide new insights into the role of the RiPP recognition element (RRE) PadeB1, characterizing its capacity to bind the paeninodin leader peptide and deliver its peptide substrate to PadeB2 for processing.
Diversity of antibiotic-resistance genes in Canadian isolates of Aeromonas salmonicida subsp. salmonicida: dominance of pSN254b and discovery of pAsa8
Authors: Trudel Mélanie V. , Vincent Antony T. , Attéré Sabrina A. , Labbé Myriam , Derome Nicolas , Culley Alexander I. , Charette Steve J. 
Published: October 2016

AbstractThe bacterium Aeromonas salmonicida subsp. salmonicida is a common pathogen in fish farms worldwide. Since the antibiotic resistance of this bacterial species is on the increase, it is important to have a broader view on this issue. In the present study, we tested the presence of known plasmids conferring multi-drug resistance as well as antibiotic resistance genes by a PCR approach in 100 Canadian A. salmonicida subsp. salmonicida isolates. Our study highlighted the dominance of the conjugative pSN254b plasmid, which confers multi-drug resistance. We also identified a new multi-drug plasmid named pAsa8, which has been characterized by a combination of sequencing technologies (Illumina and Oxford nanopore). This new plasmid harbors a complex class 1 integron similar to the one of the Salmonella genomic island 1 (SGI1) found in Salmonella enterica and Proteus mirabilis. Consequently, in addition to providing an update on the A. salmonicida subsp. salmonicida isolates that are resistant to antibiotics, our data suggest that this bacterium is potentially an important reservoir of drug resistance genes and should consequently be monitored more extensively. In addition, we describe a screening method that has the potential to become a diagnostic tool that is complementary to other methods currently in use.
Micro-nano structure hard carbon as a high performance anode material for sodium-ion batteries
Authors: Zheng Peng , Liu Ting , Guo Shouwu 
Published: October 2016

AbstractSuperior first-cycle Coulomb efficiency (above 80%) is displayed by filter paper-derived micro-nano structure hard carbon, and it delivers a high reversible capacity of 286 mAh g−1 after 100 cycles as the anode for Na-ion battery at 20 mA g−1. These advantageous performance characteristics are attributed to the unique micro-nano structure, which reduced the first irreversible capacity loss by limiting the contact between the electrode and electrolyte, and enhanced the capacity by accelerating electron and Na-ion transfer through inter-connected nano-particles and nano-pores, respectively. The good electrochemical performance indicates that this low-cost hard carbon could be a promising anode for Na-ion batteries.
Nutritional Predictors of Mortality in Long Term Hemodialysis Patients
Authors: Weng Cheng-Hao , Hu Ching-Chih , Yen Tzung-Hai , Hsu Ching-Wei , Huang Wen-Hung 
Published: October 2016

AbstractSerum albumin had been noted to be a predictor of mortality in hemodialysis (HD) patients. Normalized protein catabolic rate (nPCR) less than 0.8 or greater than 1.4 g/kg/d was also associated with greater mortality. There was no previous study to show the effectiveness of combination of serum albumin and nPCR to predict the mortality in chronic HD patients. Eight hundred and sixty-six patients were divided into 4 groups according to their nPCR and serum albumin levels. Biochemical, and hematological parameters were recorded. The associations between groups, variables mentioned above and mortality were analyzed. Multivariate Cox regression analysis showed that age, diabetes mellitus, fistula as blood access, nPCR <1.2 g/kg/day combined with albumin <4 (Group A), nPCR ≧ 1.2 g/kg/day combined with albumin <4 g/dL (Group B) (nPCR ≧ 1.2 g/kg/day combined with Albumin ≧ 4 g/dL as reference group), non-anuria, hemoglobin, creatinine, and log (high sensitivity C reactive protein) were correlated with 36 months mortality. Group A and group B patients had higher 36 months cardiovascular (CV) and infection related mortality rates as compared with group D patients. In conclusion, Group A and Group B patients had significantly higher rate of all-cause, CV and infection related mortality.