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Dian-Yun Hou, Lin-Chun Shi, Meng-Meng Yang, Jiong Li, Shuang Zhou, Hong-Xiao Zhang, Hua-Wei Xu
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization...
2018: PloS One
Xiaofan Xu, Mingming Pan, Alexis E Gasiewicz, Rongzi Li, Shiu-Ming Kuo
MDCK cells are widely used to study the differential targeting of membrane transporters to apical and basolateral membrane but its canine origin limited the commercial tools available for the analysis of protein trafficking machinery. Because apical and basolateral membranes are only found in differentiated epithelial cells, genes critical for differential targeting may be specifically up-regulated upon MDCK cell differentiation. To search for these genes, a cross-species screening strategy was used. We first analyzed the human microarray data for protein trafficking-related genes that were up-regulated in colon carcinoma Caco2 cells upon differentiation...
June 2017: Biochimie Open
Fatma Gomaa, Maxim Gersh, Colleen Cavanaugh
Diverse species of Legionella and Legionella-like amoebal pathogens (LLAPs) have been identified as intracellular bacteria in many amoeboid protists. There are, however, other amoeboid groups such as testate amoeba for which we know little about their potential to host such bacteria. In this study we assessed the occurrence and diversity of Legionella spp. in cultures and environmental isolates of freshwater arcellinid testate amoebae species, Arcella hemispherica, Arcella intermedia, and Arcella vulgaris, via 16S rRNA gene sequence analyses and fluorescent in situ hybridization (FISH)...
February 14, 2018: Journal of Eukaryotic Microbiology
Gaofeng Deng, Jian Yang, Qing Zhang, Zhi-Xiong Xiao, Haoyang Cai
BACKGROUND: The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools...
February 13, 2018: BMC Genomics
Justin Sybrandt, Michael Shtutman, Ilya Safro
Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts. Typically, these systems operate on domain-specific fractions of public medical data. MOLIERE, in contrast, utilizes information from over 24.5 million documents. At the heart of our approach lies a multi-modal and multi-relational network of biomedical objects extracted from several heterogeneous datasets from the National Center for Biotechnology Information (NCBI)...
August 2017: KDD: Proceedings
Smail Ait Bahadou, Abderrahmane Ouijja, Abdelkarim Karfach, Abdessalem Tahiri, Rachid Lahlali
The effectiveness of antagonistic bacteria to control Erwinia amylovora was evaluated under in vitro and field conditions. Among 61 bacteria isolated from soil and flowers of fire blight host plants of different Moroccan areas, 20 bacterial isolates showed higher antagonistic activity against the pathogen during agar-diffusion-test, attached blossoms assay and in a bioassay on immature pear fruits. Effective isolates were identified by using biochemical tests and 16 S rRNA genes sequencing. These isolates were grouped into the following genera: Alcaligenes (ACBC1), Bacillus (CPa12, CPa2, HF6, JB2, LMR2, SF14, SF16, SP10, SP13, and SP18) Brevibacterium (SF3, SF4, SF7, and SF15), Pantoea (ACBC2, ACBP1, and ACBP2), Pseudomonas (SP9), and Serratia (HC4)...
February 8, 2018: Microbial Pathogenesis
Mohammad Ahmadi Jebelli, Afshin Maleki, Mohammad Ali Amoozegar, Enayatollah Kalantar, Fardin Gharibi, Neda Darvish, Hamidreza Tashayoe
Health of millions of people is threatened by the risk of drinking arsenic-contaminated water worldwide. Arsenic naturally conflicts with the concept of life, but recent studies showed that some microorganisms use toxic minerals as the source of energy. Hence, the researchers should consider the development of cost-effective and highly productive procedures to remove arsenic. The current study was conducted on a native bacterial population of Seyed-Jalaleddin Spring Kurdistan, Iran. Accordingly, the arsenic amount in water samples was measured >500 μg/L by the two field and in vitro methods...
February 7, 2018: Journal of Environmental Management
Alok Kumar Mishra, Asit Ranjan Ghosh
Gut microbiota remains a prominent source for a diverse range of potential probiotics. In this context, the current study explored the rectal region of experimental Wistar rat for the isolation of potent probiotic. Sixteen lactic acid bacteria (LAB), from rectal swab of Wistar rats, were subjected to evaluation of probiotic properties. Among all, AG5 was found unique with consistent probiotic properties and was further identified as Enterococcus faecalis AG5 (NCBI accession number KT248537) using 16S rDNA sequencing, followed by BLAST analysis...
February 9, 2018: Probiotics and Antimicrobial Proteins
Xuelin Wang, Feng Cheng, Dekai Rohlsen, Changwei Bi, Chunyan Wang, Yiqing Xu, Suyun Wei, Qiaolin Ye, Tongming Yin, Ning Ye
Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants...
2018: Horticulture Research
Yandong Guo, Jing Xiong, Jing Wang, Jing Wen, Fachao Zhi
The prevalence of inflammatory bowel disease (IBD) has increased worldwide and IBD has been demonstrated to promote the development of colorectal cancer. The Rac family of proteins are involved in key mitogenic pathways. However, to the best of our knowledge, no prior studies have investigated the expression and role of Rac on colitis and colitis-associated cancer (CAC). In the current study, Rac expression in patients with colitis was analyzed according to the expression value from NCBI GEO database (GDS3268)...
2018: American Journal of Cancer Research
Yu-Chen Cheng, Wen-Chiuan Tsai, Yu-Chi Sung, Hsin-Han Chang, Ying Chen
BACKGROUND/AIMS: Glioblastoma (GBM) is a malignant brain tumor with a poor prognosis. Proteasome subunit beta type-4 (PSMB4) is an essential subunit that contributes to the assembly of the 20S proteasome complex. However, the role of PSMB4 in glioblastomas remains to be clarified. The aim of this study was to investigate the role of PSMB4 in GBM tumor progression. METHODS: We first analyzed the PSMB4 protein and mRNA expression in 80 clinical brain specimens and 77 datasets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database...
January 31, 2018: Cellular Physiology and Biochemistry
Xiaole Yin, Xiao-Tao Jiang, Benli Chai, Liguan Li, Ying Yang, James R Cole, James M Tiedje, Tong Zhang
Motivation: Much global attention has been paid to antibiotic resistance in monitoring its emergence, accumulation and dissemination. For rapid characterization and quantification of antibiotic resistance genes (ARGs) in metagenomic datasets, an online analysis pipeline, ARGs-OAP has been developed consisting of a database termed Structured Antibiotic Resistance Genes (the SARG) with a hierarchical structure (ARGs type-subtype-reference sequence). Results: The new release of the database, termed SARG version 2...
February 2, 2018: Bioinformatics
Reema Nath, Reeta Bora, Biswajyoti Borkakoty, Lahari Saikia, Pratap Parida
In this retrospective study from 2012 to 2015, 333 clinical isolates of yeasts were identified using Vitek 2 Compact System YST ID card (Biomerieux, France) and internal transcribed spacer (ITS) sequencing. Eighteen species were identified by ITS sequencing. Candida albicans was the most common species (46.5%), followed by Candida tropicalis (27%). The total species supported by Vitek System was 11 (61.11%). The sensitivity of the system in identifying these 11 species was 66.66%-100%; specificity 98.37%-100%; positive predictive value 70%-100%, negative predictive value 96...
October 2017: Indian Journal of Medical Microbiology
Erik Anderson, Bhakti Shah, Anne Davidson, Richard Furie
OBJECTIVE: In the present review, four new cases of bone marrow failure are presented and the potential contribution of systemic lupus erythematosus (SLE) is discussed. Furthermore, a comprehensive literature review of cases of autoimmune myelofibrosis (AIMF), aplastic anemia (AA), and paroxysmal nocturnal hemoglobinuria (PNH) with concurrent SLE aims to allow their direct comparison. Based on a clearer characterization of reported cases and our own experience, diagnostic and therapeutic strategies of these disorders in SLE are proposed based on lessons learned from the present and previous cases...
December 8, 2017: Seminars in Arthritis and Rheumatism
Piyanat Teinlek, Kannika Siripattarapravat, Chanin Tirawattanawanich
Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH) and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates so to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the 4 Thai indigenous chicken varieties were obtained by Sanger direct sequencing of PCR amplicons of 1231-1232 base pair in size...
January 26, 2018: Asian-Australasian Journal of Animal Sciences
Shibao He, Yaru Yin, Xi Zheng, Dongdong Guo, Jia Xin, Yong Zhu
The head of the silkworm is a nerve center and a sense organ, contains antennaes and sensory hair, feels the outside signal, and responds to the external signal delivered to the brain. Juvenile hormone is mainly synthesized and secreted by corpora allata, and it needs to be played with the aid of the hormone binding protein, because the juvenile hormone binding protein is the carrier of juvenile hormone transport and plays a functional in vivo, they have an extremely important function in insects. The objective of this study is to screened and identify a novel BmTOL proteins that it has a conserved structure of the juvenile hormone binding protein family by SilkDB and NCBI database...
January 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Qilin Li, Md Asif Ahsan, Hongjun Chen, Jitong Xue, Ming Chen
Most of non-coding RNAs are considered to express at low levels and have a limited phylogenetic distribution in the cytoplasm, meaning that they may be only involved in specific biological processes. However, recent studies showed the protein-coding potential of ncRNAs, indicating that they might be source of some special proteins. Although there are increasing non-coding RNAs identified to be able to code proteins, it is challenging to distinguish coding RNAs from previously annotated ncRNAs, and to detect the proteins from their translation...
January 27, 2018: ACS Synthetic Biology
Igor Kissin
The different stages of the life cycle of a drug - 'prenatal' stage, birth of a drug, rapid growth, maturity and stability, decline, and status before 'death' - are reflected in the three following databases: journal articles (; patents (US Patent Office-; and approved drugs (FDA - These databases are huge, from authoritative sources, correctly classified, and they properly link different datasets...
January 18, 2018: Trends in Pharmacological Sciences
Noor Zafirah Ismail, Hasni Arsad, Mohammed Razip Samian, Mohammad Razak Hamdan, Ahmad Sofiman Othman
This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C...
January 2018: 3 Biotech
Qing Yu, Fengcheng Sun
A population of cyst nematode with terminal protuberance was found in soil samples associated with and on the roots of Polygonum aviculare L. at N45°23.480', W75°40.463' in South Ottawa, Ontario. Both J2 and cysts were found. It was subsequently confirmed with morphological and molecular methods as Cactodera estonica Krall and Krall, 1978 (Krall and Krall, 1978). The cysts are dark brown, elongated with length/breadth ratio more than 2, and vulval fenestra circumfenestrate 33 ± 4.1 (20-48) µm in diameter...
December 2017: Journal of Nematology
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