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https://www.readbyqxmd.com/read/29050437/development-and-validation-of-a-novel-snp-panel-for-the-genetic-characterization-of-italian-chicken-breeds-by-next-generation-sequencing-discovery-and-array-genotyping
#1
E Viale, E Zanetti, D Özdemir, C Broccanello, A Dalmasso, M De Marchi, M Cassandro
The aim of this study was to compare the intra and inter genetic variability and population structure of 7 indigenous chicken breeds of the Veneto region, through a novel panel of 64 SNP, each located in an exonic region and mostly on different chromosomes. A total of 753 blood samples from 7 local chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo, Polverara, Pepòi, Robusta Lionata, Robusta Maculata, and Padovana) was collected and analyzed. Two strains of Polverara (Nera and Bianca) and Padovana (Dorata and Camosciata) were included in the study...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050429/isolation-and-genetic-characterization-of-a-novel-adeno-associated-virus-from-muscovy-ducks-in-china
#2
X N Su, J J Liu, Q F Zhou, X H Zhang, L C Zhao, Q M Xie, W G Chen, F Chen
Adeno-associated virus (AAV; genus Dependoparvovirus, family Parvoviridae) was first discovered in 1965 as a contaminant in adenovirus preparations. The AAVs are generally considered non-pathogenic, and they have the ability to attenuate the replication of other more pathogenic viruses, which makes them attractive as potential therapeutics or preventative measures. This study characterized a novel AAV isolated from Muscovy ducks in China. The novel virus (MHH-05-2015) was isolated after propagating a field isolate of the DAdV-3 virus (a type 3 duck adenovirus) in duck embryo fibroblasts...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050424/a-functional-single-nucleotide-polymorphism-in-the-tyrosinase-gene-promoter-affects-skin-color-and-transcription-activity-in-the-black-boned-chicken
#3
S Yu, J Liao, M Tang, Y Wang, X Wei, L Mao, C Zeng, G Wang
The tyrosinase (TYR) gene is the major melanogenesis-related gene for skin (fur) or plumage color in mammals and birds. Genetic variation in the promoter region of a gene may affect gene expression and phenotypes. This study compared the TYR promoter region between pooled DNA (n = 8) of chickens (Gallus gallus) with black and white skin using direct sequencing. The single nucleotide polymorphism (SNP) c.-2228A>T was found to have the opposite allele distribution in the two groups. The results of genotyping in a larger population (n = 188) revealed that SNP c...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050418/impact-of-egg-disinfection-of-hatching-eggs-on-the-eggshell-microbiome-and-bacterial-load
#4
R Olsen, E Kudirkiene, I Thøfner, S Pors, P Karlskov-Mortensen, L Li, S Papasolomontos, C Angastiniotou, J Christensen
Disinfection of hatching eggs is essential to ensure high quality production of broilers. Different protocols are followed in different hatcheries; however, only limited scientific evidence on how the disinfection procedures impact the microbiome is available. The aim of the present study was to characterize the microbiome and aerobic bacterial load of hatching eggs before disinfection and during the subsequent disinfection steps. The study included a group of visibly clean and a group of visibly dirty eggs...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050390/involvement-of-fast-spiking-cells-in-ictal-sequences-during-spontaneous-seizures-in-rats-with-chronic-temporal-lobe-epilepsy
#5
Adam R Neumann, Robrecht Raedt, Hendrik W Steenland, Mathieu Sprengers, Katarzyna Bzymek, Zaneta Navratilova, Lilia Mesina, Jeanne Xie, Valerie Lapointe, Fabian Kloosterman, Kristl Vonck, Paul A J M Boon, Ivan Soltesz, Bruce L McNaughton, Artur Luczak
See Lenck-Santini (doi:10.1093/awx205) for a scientific commentary on this article. Epileptic seizures represent altered neuronal network dynamics, but the temporal evolution and cellular substrates of the neuronal activity patterns associated with spontaneous seizures are not fully understood. We used simultaneous recordings from multiple neurons in the hippocampus and neocortex of rats with chronic temporal lobe epilepsy to demonstrate that subsets of cells discharge in a highly stereotypical sequential pattern during ictal events, and that these stereotypical patterns were reproducible across consecutive seizures...
September 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29050374/taxonomic-structure-and-functional-association-of-foxtail-millet-root-microbiome
#6
Tao Jin, Yayu Wang, Yueying Huang, Jin Xu, Pengfan Zhang, Nian Wang, Xin Liu, Haiyan Chu, Guang Liu, Honggang Jiang, Yuzhen Li, Jing Xu, Karsten Kristiansen, Liang Xiao, Yunzeng Zhang, Gengyun Zhang, Guohua Du, Houbao Zhang, Hongfeng Zou, Haifeng Zhang, Zhuye Jie, Suisha Liang, Huijue Jia, Jingwang Wan, Dechun Lin, Jinying Li, Guangyi Fan, Huanming Yang, Jian Wang, Yang Bai, Xun Xu
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#7
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050359/next-generation-sequencing-in-chronic-lymphocytic-leukemia-recent-findings-and-new-horizons
#8
REVIEW
Ana E Rodríguez-Vicente, Vasilis Bikos, María Hernández-Sánchez, Jitka Malcikova, Jesús-María Hernández-Rivas, Sarka Pospisilova
The rapid progress in next-generation sequencing technologies has significantly contributed to our knowledge of the genetic events associated with the development, progression and treatment resistance of chronic lymphocytic leukemia patients. Together with the discovery of new driver mutations, next-generation sequencing has revealed an immense degree of both intra- and inter-tumor heterogeneity and enabled us to describe marked clonal evolution. Advances in immunogenetics may be implemented to detect minimal residual disease more sensitively and to track clonal B cell populations, their dynamics and molecular characteristics...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050326/different-effection-of-p-1125val-ala-and-rs11954856-in-apc-on-wnt-signaling-pathway
#9
Fei-Feng Li, Zhi-Xun Zhao, Peng Yan, Song Wang, Zheng Liu, Qiong Zhang, Xiao-Ning Zhang, Chang-Hao Sun, Xi-Shan Wang, Gui-Yu Wang, Shu-Lin Liu
Colorectal cancer (CRC) is among the most common and fatal forms of solid tumors worldwide and more than two thirds of CRC and adenomas patients have APC gene mutations. APC is a key regulator in the Wnt/β-catenin signaling pathway but its roles in CRC remains to be elucidated. In this study, we compared APC genes between CRC patients and controls to determine possible associations of nucleotide changes in the APC gene with the pathways involved in CRC pathogenesis. All participants received physical and enteroscopic examinations...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050316/pharmacokinetics-and-drug-drug-interaction-between-enalapril-enalaprilat-and-felodipine-extended-release-er-in-healthy-subjects
#10
Dai Li, Sumei Xu, Yulu Wang, Dan Li, Xiaomin Li, Jing Pan, Pingsheng Xu
Since angiotensin-converting enzyme (ACE) inhibitors and calcium antagonists have complimentary mechanisms of action, enalapril, an ACE inhibitor, is used in combination with felodipine, a vascular selective dihydropyridine calcium antagonist, for the treatment of hypertension. The present study was designed to investigate the possible drug-drug interaction between these two agents in Chinese healthy subjects. A randomized, open-label, multiple-dose, 3-treatment, 3-period, 6-sequence cross-over study enrolling 12 healthy subjects (six male and six female subjects) was performed...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050284/mutational-analysis-of-a-chinese-family-with-oculocutaneous-albinism-type-2
#11
Xiong Wang, Yaowu Zhu, Na Shen, Jing Peng, Chunyu Wang, Haiyi Liu, Yanjun Lu
Oculocutaneous albinism (OCA) is an autosomal recessive disorder characterized by hypopigmentation of the skin, hair, and eyes accompanied with ophthalmologic abnormalities. Molecular genetic test can confirm the diagnosis of the four subtypes of OCA (OCA1-4). Herein, we report a Chinese family with two patients affected by OCA. Mutations of TYR, OCA2, TYRP1, and SLC45A2 were examined by using PCR-sequencing. Large deletions or duplications of TYR and OCA2 were examined by Multiplex Ligation-dependent Probe Amplification (MLPA) assay...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050264/the-microrna-expression-signature-of-pancreatic-ductal-adenocarcinoma-by-rna-sequencing-anti-tumour-functions-of-the-microrna-216-cluster
#12
Keiichi Yonemori, Naohiko Seki, Tetsuya Idichi, Hiroshi Kurahara, Yusaku Osako, Keiichi Koshizuka, Takayuki Arai, Atsushi Okato, Yoshiaki Kita, Takaaki Arigami, Yuko Mataki, Yuko Kijima, Kosei Maemura, Shoji Natsugoe
We analysed the RNA sequence-based microRNA (miRNA) signature of pancreatic ductal adenocarcinoma (PDAC). Aberrantly expressed miRNAs were successfully identified in this signature. Using the PDAC signature, we focused on 4 clustered miRNAs, miR-216a-5p, miR-216a-3p, miR-216b-5p and miR-216b-3p on human chromosome 2p16.1. All members of the miR-216 cluster were significantly reduced in PDAC specimens. Ectopic expression of these miRNAs suppressed cancer cell aggressiveness, suggesting miR-216 cluster as anti-tumour miRNAs in PDAC cells...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050263/the-prognostic-value-of-osteopontin-in-limited-stage-small-cell-lung-cancer-patients-and-its-mechanism
#13
Fanglei Liu, Chunxue Bai, Zhongliang Guo
Osteopontin (OPN) is known to be overexpressed in numerous carcinomas. Although abundant OPN has been reported to be correlated with poor survival in non-small cell lung cancer (NSCLC) but their clinical and prognostic significance in SCLC remains unknown. In this study, RNA-sequencing was used to obtain gene expression data in SCLC tissue samples and OPN expression levels were then investigated using qPCR, immunohistochemical and Western blot. We found OPN was one of the most upregulated genes. Besides, the correlation of OPN with tumor clinicopathological characteristics was evaluated and we found OPN was associated with advanced tumor stages...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050258/the-diagnostic-prognostic-potential-and-molecular-functions-of-long-non-coding-rnas-in-the-exosomes-derived-from-the-bile-of-human-cholangiocarcinoma
#14
Xianxiu Ge, Youli Wang, Junjie Nie, Quanpeng Li, Lingyu Tang, Xueting Deng, Fei Wang, Boming Xu, Xiaochao Wu, Xiuhua Zhang, Qiang You, Lin Miao
Cholangiocarcinoma (CCA) is an aggressive malignancy associated with unfavorable prognosis, and it's difficult to diagnose and no effective treatments are available. Long non-coding RNAs (lncRNAs) play important roles in tumorigenesis and metastasis. Intact lncRNAs from exosomes have sparked much interest as potential biomarker for the non-invasive analysis of disease. Here, via exosome sequencing on lncRNAs, GO analysis, KEGG pathway and co-expression analysis, receiver operating characteristic curve and survival analyses, we found that, compared with control group, lncRNAs of ENST00000588480...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050247/rnai-mediated-knockdown-of-parp1-does-not-improve-the-development-of-female-cloned-mouse-embryos
#15
Guang-Yu Bai, Si-Hang Song, Rui-Zhen Sun, Zi-Hui Zhang, Jingyu Li, Zhen-Dong Wang, Zhong-Hua Liu, Lei Lei
Somatic cell nuclear transfer is an important technique for life science research, but its efficiency is still extremely low, and most genes that are important during early development, such as X chromosome-linked genes, are not appropriately expressed during this process. Poly (ADP-ribose) polymerase (PARP) is an enzyme that transfers ADP ribose clusters to target proteins. PARP family members such as PARP1 participate in cellular signalling pathways through poly (ADP-ribosylation) (PARylation), which ultimately promotes changes in chromatin structure, gene expression, and the localization and activity of proteins that mediate signalling responses...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#16
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050228/mutation-landscape-and-intra-tumor-heterogeneity-of-two-manecs-of-the-esophagus-revealed-by-multi-region-sequencing
#17
Wenqing Yuan, Zhen Liu, Wanjun Lei, Li Sun, Haijun Yang, Yu Wang, Shweta Ramdas, Xiao Dong, Ruiping Xu, Hong Cai, Jun Z Li, Yang Ke
Mixed adenoneuroendocrine carcinoma (MANEC) in the esophagus is an infrequent but highly malignant cancer with few known genomic alterations. We conducted whole-exome sequencing and whole-genome SNP genotyping for 4-6 tumor subregions and 5-6 adjacent normal tissue sites and 1-3 lymph node metastases in two esophageal MANECs to detect somatic mutations and copy number alterations, and to explore their spatial heterogeneity and underlying clonal structure. TP53 mutation, RB1 deletion or LOH, and PIK3CA, PTEN, KRAS, SOX2, DVL3, TP63 amplification appeared in all regions in both tumors...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050160/-value-of-mdixon-quant-sequence-diffusion-weighted-imaging-in-quantitatively-diagnosing-the-sacroiliitis-stages
#18
Y Y An, H X Li, Y Zhan, X W Lei
Objective: To evaluate the value of mDIXON-Quant sequence, diffusion-weighted imaging (DWI) in quantitative diagnosing of the sacroiliitis stages in patients with ankylosing spondylitis (AS). Methods: Based on the Bath Ankylosing Spondylitis Activity Index (BASDAI) and laboratory parameters, a total of 51 patients were diagnosed with AS. They were divided into two groups as early active group (n=20) and chronic active group (n=31), and at the same time, 25 healthy people from Tianjin were included as control group...
October 10, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29049985/insight-into-the-structure-function-relationships-of-deep-eutectic-solvents-during-rice-straw-pretreatment
#19
Xue-Dan Hou, Ao-Lin Li, Kai-Peng Lin, Yuan-Yuan Wang, Zhi-Yin Kuang, Shi-Lin Cao
Rice straw pretreatment mediated by choline chloride (ChCl) or lactic acid (Lac) sequences deep eutectic solvents (DESs) was investigated in this work. Hydrogen bond acceptors (HBAs) and hydrogen bond donors (HBDs) proved to be both important for DESs pretreatment efficiency. DESs containing lots of hydroxyl or amino groups with a high intermolecular hydrogen-bond (H-bond) strength exhibited weak biomass deconstruction abilities. The presence of strong electron-withdrawing groups in DESs was benefit for xylan removal, thus furnishing higher cellulose digestibility...
October 7, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29049982/characterization-of-soluble-microbial-products-in-a-partial-nitrification-sequencing-batch-biofilm-reactor-treating-high-ammonia-nitrogen-wastewater
#20
Jibin Li, Jinglin Wei, Huu Hao Ngo, Wenshan Guo, Haibao Liu, Bin Du, Qin Wei, Dong Wei
In present study, the characterization of soluble microbial products (SMP) was evaluated in a partial nitrification sequencing batch biofilm reactor (SBBR). During the stable operation of SBBR, the NH4(+)-N removal efficiency and nitrite accumulation ratio were 96.70±0.41% and 93.77±1.04%, respectively. According to excitation-emission matrix (EEM), the intensities of protein-like substances were reduced under anoxic and aerobic phases, whereas humic-like substances had little change during the whole cycle...
October 6, 2017: Bioresource Technology
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