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https://www.readbyqxmd.com/read/30315621/insight-into-the-evolution-and-functional-characteristics-of-the-pan-genome-assembly-from-sesame-landraces-and-modern-cultivars
#1
Jingyin Yu, Agnieszka A Golicz, Kun Lu, Komivi Dossa, Yanxin Zhang, Jinfeng Chen, Linhai Wang, Jun You, Dingding Fan, David Edwards, Xiurong Zhang
Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties...
October 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30315521/transcriptome-profiling-of-rubber-tree-hevea-brasiliensis-discovers-candidate-regulators-of-the-cold-stress-response
#2
Xiao-Xiao Gong, Bing-Yu Yan, Jin Hu, Cui-Ping Yang, Yi-Jian Li, Jin-Ping Liu, Wen-Bin Liao
Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling...
November 2018: Genes & Genomics
https://www.readbyqxmd.com/read/30314797/identification-of-avian-influenza-virus-subtype-h9n2-in-chicken-farms-in-indonesia
#3
Melina Jonas, Aprilla Sahesti, Theresia Murwijati, Christina Lilis Lestariningsih, Ine Irine, Clara Sinta Ayesda, Wahyu Prihartini, Gusti Ngurah Mahardika
Avian influenza virus subtype H9N2 (AIV-H9N2) has become established in domestic poultry in Asia and Africa. AIV-H9N2 has not been reported previously in Indonesia. Here we describe the presence of AIV-H9N2 in chicken farms in Indonesia. Ninety-nine cases were observed in various provinces in Indonesia. Clinical signs, pathologic lesions and egg production were recorded. Confirmation was made using virus isolation, reverse transcriptase PCR (RT-PCR), and sequencing. To construct hemaglutinin (HA) phylogeny, the secondary data of Eurasian lineages were downloaded from GenBank...
November 1, 2018: Preventive Veterinary Medicine
https://www.readbyqxmd.com/read/30314482/cgmp-interacts-with-tropomyosin-and-downregulates-actin-tropomyosin-myosin-complex-interaction
#4
Lihui Zou, Junhua Zhang, Jingli Han, Wenqing Li, Fei Su, Xiaomao Xu, Zhenguo Zhai, Fei Xiao
BACKGROUND: The nitric oxide-soluble guanylate cyclase-cyclic guanosine monophosphate (NO-sGC-cGMP) signaling pathway, plays a critical role in the pathogenesis of pulmonary arterial hypertension (PAH); however, its exact molecular mechanism remains undefined. METHODS: Biotin-cGMP pull-down assay was performed to search for proteins regulated by cGMP. The interaction between cGMP and tropomyosin was analyzed with antibody dependent pull-down in vivo. Tropomyosin fragments were constructed to explore the tropomyosin-cGMP binding sites...
October 12, 2018: Respiratory Research
https://www.readbyqxmd.com/read/30314355/characterization-of-critical-functions-of-long-non-coding-rnas-and-mrnas-in-rhabdomyosarcoma-cells-and-mouse-skeletal-muscle-infected-by-enterovirus-71-using-rna-seq
#5
Ying Li, Chao Zhang, Luwei Qin, Dong Li, Guangyuan Zhou, Dejian Dang, Shuaiyin Chen, Tiantian Sun, Rongguang Zhang, Weidong Wu, Yuanlin Xi, Yuefei Jin, Guangcai Duan
Enterovirus 71 (EV71) is the main pathogen of severe hand-foot-mouth disease (HFMD). Long non-coding RNAs (lncRNAs) are recognized as pivotal factors during the pathogenesis of viral infection. However, the critical functions of lncRNAs in EV71⁻host interactions have not been characterized. Here, for the first time, we performed global transcriptome analysis of lncRNA and mRNA expression profiles in EV71-infected human rhabdomyosarcoma (RD) cells and skeletal muscle of mice using second-generation sequencing...
October 11, 2018: Viruses
https://www.readbyqxmd.com/read/30314286/plp1-mutations-in-patients-with-multiple-sclerosis-identification-of-a-new-mutation-and-potential-pathogenicity-of-the-mutations
#6
Nancy C Cloake, Jun Yan, Atefeh Aminian, Michael P Pender, Judith M Greer
PLP1 is located on the X-chromosome and encodes myelin proteolipid protein (PLP), the most abundant protein in central nervous system myelin. Generally, point mutations in PLP1 result in X-linked dysmyelinating disorders, such as Pelizaeus-Merzbacher disease (PMD) or spastic paraplegia type 2 (SPG2). However, several case studies have identified patients with missense point mutations in PLP1 and clinical symptoms and signs compatible with a diagnosis of multiple sclerosis (MS). To investigate if PLP1 mutations occur relatively frequently in MS, we sequenced the coding regions of PLP1 in 22 female MS patients who had developed disease after the age of 40 and in 42 healthy women, and identified a missense mutation in exon 2 of PLP1 resulting in a Leu30Val mutation in the protein in one of the MS patients...
October 11, 2018: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/30313540/a-new-species-of-microhyla-tschudi-1838-anura-microhylidae-from-west-coast-of-india-an-integrative-taxonomic-approach
#7
Kumar K Vineeth, U K Radhakrishna, R D Godwin, Saha Anwesha, K Patil Rajashekhar, N A Aravind
A new species of microhylid frog Microhyla kodial sp. nov. from the west coast of India is described in this paper. It is distinct from all described species of Microhyla occurring in South and Southeast Asia as revealed by a combination of morphological, molecular and acoustic characters. The new species is characterized by absence of lateral body stripe, tuberculated dorsal skin surface, absence of webbing between fingers, presence of basal webbing between toes and absence of dorsal marginal groove on finger and toe disc...
May 16, 2018: Zootaxa
https://www.readbyqxmd.com/read/30312913/co-expression-network-analysis-of-peripheral-blood-transcriptome-identifies-dysregulated-protein-processing-in-endoplasmic-reticulum-and-immune-response-in-recurrent-mdd-in-older-adults
#8
Liliana G Ciobanu, Perminder S Sachdev, Julian N Trollor, Simone Reppermund, Anbupalam Thalamuthu, Karen A Mather, Sarah Cohen-Woods, David Stacey, Catherine Toben, K Oliver Schubert, Bernhard T Baune
The molecular factors involved in the pathophysiology of major depressive disorder (MDD) remain poorly understood. One approach to examine the molecular basis of MDD is co-expression network analysis, which facilitates the examination of complex interactions between expression levels of individual genes and how they influence biological pathways affected in MDD. Here, we applied an unsupervised gene-network based approach to a prospective experimental design using microarray genome-wide gene expression from the peripheral whole blood of older adults...
October 1, 2018: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/30311857/effect-of-the-bmp-2-doses-on-the-osteogenic-potential-of-hmscs-containing-te-constructs
#9
Adeline Decambron, Nausikaa Devriendt, Nathanael Larochette, Mathieu Manassero, Marianne Bourguignon, Hanane El-Hafci, Hervé Petite, Véronique Viateau, Delphine Logeart-Avramoglou
The addition of bone morphogenetic protein-2 (BMP-2) with multipotent stromal cells (MSC) is an attractive strategy to enhance the bone-forming potential of MSC-based tissue engineering (TE) constructs. However, the effective dosage of BMP-2 remains to be determined. In this study, we evaluated the effects of human MSCs co-delivered with BMP-2 at either low or high dosage on the bone-forming potential of constructs in a mice ectopic model. Our results showed that the addition of only low dose of BMP-2 was beneficial to enhance the bone-forming potential of MSCs, whereas high dose of BMP-2 overcame the advantage of combining this growth factor with MSCs...
October 12, 2018: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/30311630/lentiviral-based-reporter-constructs-for-profiling-chondrogenic-activity-in-primary-equine-cell-populations
#10
A Martin-Pena, R M Porter, G Plumton, T M McCarrel, A J Morton, M V Guijarro, S C Ghivizzani, B Sharma, G D Palmer
Successful clinical translation of mesenchymal stem cell (MSC)-based therapies for cartilage repair will likely require the implementation of standardised protocols and broadly applicable tools to facilitate the comparisons among cell types and chondroinduction methods. The present study investigated the utility of recombinant lentiviral reporter vectors as reliable tools for comparing chondrogenic potential among primary cell populations and distinguishing cellular-level variations of chondrogenic activity in widely used three-dimensional (3D) culture systems...
October 12, 2018: European Cells & Materials
https://www.readbyqxmd.com/read/30311379/clingen-advancing-genomic-data-sharing-standards-as-a-ga4gh-driver-project
#11
Lena Dolman, Angela Page, Lawrence Babb, Robert R Freimuth, Harindra Arachchi, Chris Bizon, Matthew Brush, Marc Fiume, Melissa Haendel, David P Hansen, Aleksandar Milosavljevic, Ronak Y Patel, Piotr Pawliczek, Andrew D Yates, Heidi L Rehm
The Clinical Genome Resource (ClinGen)'s work to develop a knowledge base to support the understanding of genes and variants for use in precision medicine and research depends on robust, broadly applicable, and adaptable technical standards for sharing data and information. To forward this goal, ClinGen has joined with the Global Alliance for Genomics and Health (GA4GH) to support the development of open, freely-available technical standards and regulatory frameworks for secure and responsible sharing of genomic and health-related data...
November 2018: Human Mutation
https://www.readbyqxmd.com/read/30311353/construction-of-an-efficient-genomic-editing-system-with-crispr-cas9-in-the-vector-mosquito-aedes-albopictus
#12
Tong Liu, Wen-Qiang Yang, Yu-Gu Xie, Pei-Wen Liu, Li-Hua Xie, Feng Lin, Chen-Ying Li, Jin-Bao Gu, Kun Wu, Gui-Yun Yan, Xiao-Guang Chen
Aedes (Stegomyia) albopictus, also known as the Asian tiger mosquito, is a mosquito that originated in Asia. In recent years, it has become increasingly rampant throughout the world. This mosquito can transmit several arboviruses, including dengue, Zika and chikungunya viruses, and is considered a public health threat. Despite the urgent need of genome-engineering to analyse specific gene functions, progress in genetical manipulation of Ae. albopictus has been slow due a lack of efficient methods and genetic markers...
October 11, 2018: Insect Science
https://www.readbyqxmd.com/read/30311263/identification-of-key-genes-in-prostate-cancer-gene-expression-profile-by-bioinformatics
#13
Wenzong Lu, Zhe Ding
The aim of this study was to identify key candidate genes in prostate cancer. The gene expression profiles of GSE32448, GSE45016, GSE46602 and GSE104749 were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between prostate cancer and normal samples were identified by R language. The gene ontology functional and pathway enrichment analyses of DEGs were performed by the Database for Annotation, Visualization and Integrated Discovery software followed by the construction of protein-protein interaction network...
October 11, 2018: Andrologia
https://www.readbyqxmd.com/read/30310931/lncrna-meg3-impacts-proliferation-invasion-and-migration-of-ovarian-cancer-cells-through-regulating-pten
#14
Juelan Wang, Wenqian Xu, Yangke He, Qi Xia, Siwei Liu
OBJECTIVE AND DESIGN: We investigated the expressions of lncRNA MEG3 and PTEN in ovarian cancer tissues and their effects on cell proliferation, cycle and apoptosis of ovarian cancer. METHODS: Expression levels of MEG3 in ovarian cancer cell lines and normal ovarian cell lines were detected by qRT-PCR. Cell viability was detected by MTT assay. Cell apoptosis and cell cycle distribution were measured by flow cytometry. Cell invasion capability was tested by transwell assay...
October 11, 2018: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/30310500/a-mirna-combination-as-promising-biomarker-for-hepatocellular-carcinoma-diagnosis-a-study-based-on-bioinformatics-analysis
#15
Jia Ji, Hao Chen, Xiao-Ping Liu, Yu-Hui Wang, Chang-Liang Luo, Wu-Wen Zhang, Wen Xie, Fu-Bing Wang
Background: miRNAs dysregulate in hepatocellular carcinoma (HCC), showing promise for diagnostic biomarkers which may be found through exploration of differentially expressed miRNAs when comparing HCC and normal liver tissues. Materials and Methods: In the present research, candidate miRNAs were selected and verified using screening dataset GSE12717 and training dataset GSE10694, respectively. A miRNA combination was constructed using stepwise logistic regression analysis and validated using two datasets GSE74618 and TCGA...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/30309818/hoxa9-pcdh17-pou4f2-and-onecut2-as-a-urinary-biomarker-combination-for-the-detection-of-bladder-cancer-in-chinese-patients-with-hematuria
#16
Yishuo Wu, Guangliang Jiang, Ning Zhang, Shenghua Liu, Xiaoling Lin, Chelsea Perschon, S Lilly Zheng, Qiang Ding, Xiang Wang, Rong Na, Jishan Sun, Jianfeng Xu
BACKGROUND: DNA methylation biomarkers for bladder cancer (BCa) have not been evaluated extensively in the Chinese population. OBJECTIVE: To develop and validate a urinary biomarker combination of methylation assays in a group of Chinese patients with hematuria. DESIGN, SETTING, AND PARTICIPANTS: A total of 192 urine samples were collected and evaluated from patients with microscopic or gross hematuria, including 97 BCa patients and 95 controls with benign diseases...
October 8, 2018: European Urology Focus
https://www.readbyqxmd.com/read/30308829/changes-of-the-denitrifying-communities-in-a-multi-stage-free-water-surface-constructed-wetland
#17
Jing Li, Jun-Tao Wang, Hang-Wei Hu, Zhang-Jie Cai, Yin-Ru Lei, Wei Li, Man-Yin Zhang, Zong-Ming Li, Yi-Nuo Zhu, Li-Juan Cui
Microorganisms play crucial roles in the nitrogen removal processes of wetlands. However, the key functional genes and microbes related to the nitrogen removal remain largely unknown in the free water surface constructed wetland (FWS CW). Here we studied the abundances of denitrifiers by targeting the key functional genes (nirS, nirK and nosZ) and investigated the community compositions of denitrifiers and their correlations with the abiotic variables in a FWS CW. The increase of nosZ/(nirS + nirK) and nirS/nirK ratios in the outlet indicated a shift of denitrifiers' communities which tended to release less nitrous oxide at the genetic potential level...
February 10, 2019: Science of the Total Environment
https://www.readbyqxmd.com/read/30308595/transgenic-overexpression-of-glutathione-s-transferase-%C3%AE-type-1-reduces-hypertension-and-oxidative-stress-in-the-stroke-prone-spontaneously-hypertensive-rat
#18
Erin Olson, Michal Pravenec, Vladimir Landa, H H Caline Koh-Tan, Anna F Dominiczak, Martin W McBride, Delyth Graham
BACKGROUND: Combined congenic breeding and microarray gene expression profiling previously identified glutathione S-transferase μ-type 1 (Gstm1) as a positional and functional candidate gene for blood pressure (BP) regulation in the stroke-prone spontaneously hypertensive (SHRSP) rat. Renal Gstm1 expression in SHRSP rats is significantly reduced when compared with normotensive Wistar Kyoto (WKY) rats. As Gstm1 plays an important role in the secondary defence against oxidative stress, significantly lower expression levels may be functionally relevant in the development of hypertension...
October 10, 2018: Journal of Hypertension
https://www.readbyqxmd.com/read/30308493/high-glucose-promotes-epithelial-mesenchymal-transition-of-uterus-endometrial-cancer-cells-by-increasing-er-glut4-mediated-vegf-secretion
#19
Chun-Jie Gu, Feng Xie, Bing Zhang, Hui-Li Yang, Jiao Cheng, Yin-Yan He, Xiao-Yong Zhu, Da-Jin Li, Ming-Qing Li
BACKGROUND/AIMS: Uterus endometrial cancer (UEC) is the common malignancy among gynecologic cancers, and most of them are type I estrogen-dependent UEC. Diabetes is well-known risk factor for the development of UEC. However, the underlying link between high glucose (HG) and the estrogen receptor in UEC remains unclear. Epithelial-mesenchymal transition (EMT) has also been shown to occur during the initiation of metastasis in cancer progression. The aim of this study was to determine the relationships and roles of HG, estrogen receptor and EMT in the growth and migration of UEC...
October 11, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/30308489/mir-136-5p-regulates-the-inflammatory-response-by-targeting-the-ikk%C3%AE-nf-%C3%AE%C2%BAb-a20-pathway-after-spinal-cord-injury
#20
Guiying Deng, Yunbing Gao, Zhongxi Cen, Jichen He, Baichuan Cao, Gaofeng Zeng, Shaohui Zong
BACKGROUND/AIMS: miR-136-5p participates in recovery after spinal cord injury (SCI) via an unknown mechanism. We investigated the mechanism underlying the involvement of miR-136-5p in the inflammatory response in a rat model of SCI. METHODS: Sprague-Dawley rat astrocytes were cultured in vitro to construct a reporter plasmid. Luciferase assays were used to detect the ability of miR-136-5p to target the IKKβ and A20 genes. Next, recombinant lentiviral vectors were constructed, which either overexpressed miR-136-5p or inhibited its expression...
October 11, 2018: Cellular Physiology and Biochemistry
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