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Aurore Siegfried, Audrey Rousseau, Claude-Alain Maurage, Sarah Pericart, Yvan Nicaise, Frederic Escudie, David Grand, Alix Delrieu, Anne Gomez-Brouchet, Sophie Le Guellec, Camille Franchet, Sergio Boetto, Matthieu Vinchon, Jean-Christophe Sol, Franck-Emmanuel Roux, Valerie Rigau, Anne-Isabelle Bertozzi, David Tw Jones, Dominique Figarella-Branger, Emmanuelle Uro-Coste
We investigated the challenging diagnostic case of a ventricular cystic glioneuronal tumor with papillary features, by RNA sequencing using the Illumina TruSight RNA Fusion panel. We did not retrieve the SLC44A1-PRKCA fusion gene specific for papillary glioneuronal tumor, but an EWSR1-PATZ1 fusion transcript. RT-PCR followed by Sanger sequencing confirmed the EWSR1-PATZ1 fusion. It matched with canonic EWSR1 fusion oncogene, juxtaposing the entire N terminal transcriptional activation domain of EWSR1 gene and the C terminal DNA binding domain of a transcription factor gene, PATZ1...
April 21, 2018: Brain Pathology
Xiaohui Wang, Changdong Wang, Junkang Sui, Zhaoyang Liu, Qian Li, Chao Ji, Xin Song, Yurong Hu, Changqian Wang, Rongbo Sa, Jiamiao Zhang, Jianfeng Du, Xunli Liu
Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger...
April 20, 2018: AMB Express
Chaoling Wei, Hua Yang, Songbo Wang, Jian Zhao, Chun Liu, Liping Gao, Enhua Xia, Ying Lu, Yuling Tai, Guangbiao She, Jun Sun, Haisheng Cao, Wei Tong, Qiang Gao, Yeyun Li, Weiwei Deng, Xiaolan Jiang, Wenzhao Wang, Qi Chen, Shihua Zhang, Haijing Li, Junlan Wu, Ping Wang, Penghui Li, Chengying Shi, Fengya Zheng, Jianbo Jian, Bei Huang, Dai Shan, Mingming Shi, Congbing Fang, Yi Yue, Fangdong Li, Daxiang Li, Shu Wei, Bin Han, Changjun Jiang, Ye Yin, Tao Xia, Zhengzhu Zhang, Jeffrey L Bennetzen, Shancen Zhao, Xiaochun Wan
Tea, one of the world's most important beverage crops, provides numerous secondary metabolites that account for its rich taste and health benefits. Here we present a high-quality sequence of the genome of tea, Camellia sinensis var. sinensis (CSS), using both Illumina and PacBio sequencing technologies. At least 64% of the 3.1-Gb genome assembly consists of repetitive sequences, and the rest yields 33,932 high-confidence predictions of encoded proteins. Divergence between two major lineages, CSS and Camellia sinensis var...
April 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
Qi-Huan Lu, Ya-Qi Wang, Jin-Nan Song, Hong-Bing Yang
Common buckwheat (F. esculentum), annually herbaceous crop, is prevalent in people's daily life with the increasing development of economics. Compared with wheat, it is highly praised with high content of rutin and flavonoid. Common buckwheat is recognized as healthy food with good taste, and the product price of which such as noodles, flour, bread and so on are higher than wheat, and the seeds of which are bigger than that of tartary buckwheat, so if common buckwheat are planted more widely, people will spend less money on this healthy and delicious food...
April 4, 2018: Plant Physiology and Biochemistry: PPB
Simona Granata, Gloria Santoro, Valentina Masola, Paola Tomei, Fabio Sallustio, Paola Pontrelli, Matteo Accetturo, Nadia Antonucci, Pierluigi Carratù, Antonio Lupo, Gianluigi Zaza
The administration of Everolimus (EVE), a mTOR inhibitor used in transplantation and cancer, is often associated with adverse effects including pulmonary fibrosis. Although the underlying mechanism is not fully clarified, this condition could be in part caused by epithelial to mesenchymal transition (EMT) of airway cells. To improve our knowledge, primary bronchial epithelial cells (BE63/3) were treated with EVE (5 and 100 nM) for 24 h. EMT markers (α-SMA, vimentin, fibronectin) were measured by RT-PCR. Transepithelial resistance was measured by Millicell-ERS ohmmeter...
April 20, 2018: International Journal of Molecular Sciences
Bingxing An, Jiangwei Xia, Tianpeng Chang, Xiaoqiao Wang, Jian Miao, Lingyang Xu, Lupei Zhang, Xue Gao, Yan Chen, Junya Li, Huijiang Gao
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight (HW), liver weight (LIW), spleen weight (SW), lung weight (LUW) and kidney weight (KW) in 1217 Simmental cattle...
April 20, 2018: Physiological Genomics
Honglong Chu, Ming Tang, Haihua Wang, Chuyan Wang
AIMS: This study was to investigate pinewood nematode's impacts on root mycoflora of P. tabulaeformis. METHODS AND RESULTS: The biomass, colonization rate, community structure and diversity of root-associated fungi were investigated in pinewood nematode infected and non-infected P. tabulaeformis. The results indicated that the roots of P. tabulaeformis were colonized highly by root-associated fungi, mainly ectomycorrhizal fungi (ECMF) and dark septate endophytes...
April 19, 2018: Journal of Applied Microbiology
Giuseppe Firrao, Emanuela Torelli, Cesare Polano, Patrizia Ferrante, Francesca Ferrini, Marta Martini, Simone Marcelletti, Marco Scortichini, Paolo Ermacora
Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37)...
2018: Frontiers in Microbiology
Sarah Potgieter, Ameet Pinto, Makhosazana Sigudu, Hein du Preez, Esper Ncube, Stephanus Venter
Long-term spatial-temporal investigations of microbial dynamics in full-scale drinking water distribution systems are scarce. These investigations can reveal the process, infrastructure, and environmental factors that influence the microbial community, offering opportunities to re-think microbial management in drinking water systems. Often, these insights are missed or are unreliable in short-term studies, which are impacted by stochastic variabilities inherent to large full-scale systems. In this two-year study, we investigated the spatial and temporal dynamics of the microbial community in a large, full scale South African drinking water distribution system that uses three successive disinfection strategies (i...
March 30, 2018: Water Research
Katherine A Partrick, Benoit Chassaing, Linda Q Beach, Katharine E McCann, Andrew T Gewirtz, Kim L Huhman
Social stress can promote a variety of neuropsychiatric illnesses, many of which have a high co-morbidity with gastrointestinal disorders. Recent data indicate that gastrointestinal microbiota can affect their host's brain and behavior. Syrian hamsters are ideal subjects for social stress research because they are territorial, aggressive, and rapidly form dominant/subordinate relationships. The purpose of this study was to determine if exposure to social stress in hamsters alters gut microbiota in dominants and subordinates after an agonistic encounter and if pre-stress gut microbiota composition is correlated with the outcome of such a conflict...
April 16, 2018: Behavioural Brain Research
G Schiavo, F Bertolini, V J Utzeri, A Ribani, C Geraci, L Santoro, C Óvilo, A I Fernández, M Gallo, L Fontanesi
Casertana is an endangered autochthonous pig breed (raised in south-central Italy) that is considered to be the descendant of the influential Neapolitan pig population that was used to improve British breeds in the 19th century. Casertana pigs are characterized by a typical, almost complete, hairless phenotype, even though a few Casertana pigs are normal haired. In this work, using Illumina PorcineSNP60 BeadChip data, we carried out a genome-wide association study and an FST analysis with this breed by comparing animals showing the classical hairless phenotype (n = 81) versus pigs classified as haired (n = 15)...
April 19, 2018: Animal Genetics
Reiofeli A Salas-Perez, Christopher A Saski, Rooksana E Noorai, Subodh K Srivastava, Amy L Lawton-Rauh, Robert L Nichols, Nilda Roma-Burgos
Amaranthus palmeri (Amaranthaceae) is a noxious weed in several agroecosystems and in some cases seriously threatens the sustainability of crop production in North America. Glyphosate-resistant Amaranthus species are widespread, prompting the use of alternatives to glyphosate such as glufosinate, in conjunction with glufosinate-resistant crop cultivars, to help control glyphosate-resistant weeds. An experiment was conducted to analyze the transcriptome of A. palmeri plants that survived exposure to 0.55 kg ha-1 glufosinate...
2018: PloS One
Zhenxing Wang, XiaoLiang Wu, Yadong Wang
BACKGROUND: DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. RESULTS: Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array...
April 11, 2018: BMC Bioinformatics
Meng Ding, Cheng Wang, Xiaolan Lu, Cuiping Zhang, Zhen Zhou, Xi Chen, Chen-Yu Zhang, Ke Zen, Chunni Zhang
Circulating exosomal microRNAs (miRNAs) are valuable biomarker candidates; however, information on the characterization and mutual agreement of commercial kits for circulating exosomal miRNA profiling is scarce. Here, we analyzed the advantages and weaknesses of four commonly used commercial kits for exosomal miRNA profiling and their application to the sample of serum and/or plasma, respectively. NanoSight and Western blotting were conducted to evaluate the efficiency and purity of the isolated exosomes. In our conditions, the size distribution of the isolated particles was appropriate (40-150 nm), and ExoQuick™ Exosome Precipitation Solution (EXQ) generated a relatively high yield of exosomes...
April 18, 2018: Analytical and Bioanalytical Chemistry
Anahit Nazari-Ghadikolaei, Hassan Mehrabani-Yeganeh, Seyed R Miarei-Aashtiani, Elizabeth A Staiger, Amir Rashidi, Heather J Huson
The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip...
2018: Frontiers in Genetics
Lei Xu, Xi Chen, Yuan Wang, Wen Jiang, Sa Wang, Zongxin Ling, Hui Chen
Dynamic alterations in oral microbiota are closely related to the development of dental caries;however, changes in salivary microbiota during this process have not been extensively studied. In addition, increasing evidence suggests that oral microbiome profiles differ according to dentition stages, but it is unclear whether they change with age during the same dentition, such as deciduous dentition. These two aspects were investigated in a 2-year follow-up study, and caries-free preschool children with complete deciduous dentition were enrolled...
2018: Frontiers in Physiology
James Lee Crainey, Michel Abanto Marín, Túllio Romão Ribeiro da Silva, Jansen Fernandes de Medeiros, Felipe Arley Costa Pessoa, Yago Vinícius Santos, Ana Carolina Paulo Vicente, Sérgio Luiz Bessa Luz
Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite's epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene's barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts...
April 18, 2018: Scientific Reports
Quentin Le Bastard, Tonya Ward, Dimitri Sidiropoulos, Benjamin M Hillmann, Chan Lan Chun, Michael J Sadowsky, Dan Knights, Emmanuel Montassier
Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform...
April 18, 2018: Scientific Reports
Rui Peng, Yuliang Liu, Zhigang Cai, Fujun Shen, Jiasong Chen, Rong Hou, Fangdong Zou
BACKGROUND/AIMS: Giant pandas, an endangered species, are a powerful symbol of species conservation. Giant pandas may suffer from a variety of diseases. Owing to their highly specialized diet of bamboo, giant pandas are thought to have a relatively weak ability to resist diseases. The spleen is the largest organ in the lymphatic system. However, there is little known about giant panda spleen at a molecular level. Thus, clarifying the regulatory mechanisms of spleen could help us further understand the immune system of the giant panda as well as its conservation...
April 13, 2018: Cellular Physiology and Biochemistry
Camila L Chaves, Bernd Degen, Birte Pakull, Malte Mader, Euridice Honorio, Paulo Ruas, Niklas Tysklind, Alexandre M Sebbenn
Deforestation - reinforced by illegal logging - is a serious problem in many tropical regions and causes pervasive environmental and economic damage. Existing laws which intend to reduce illegal logging need efficient, fraud resistant control methods. We developed a genetic reference database for Jatoba (Hymenaea courbaril), an important, high value timber species from the Neotropics. The data set can be used for controls on declarations of wood origin. Samples from 308 Hymenaea trees from 12 locations in Brazil, Bolivia, Peru, and French Guiana have been collected and genotyped on ten nuclear microsatellites (nSSRs), 13 chloroplast SNPs (spSNP), and 1 chloroplast indel marker...
April 16, 2018: Journal of Heredity
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