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Xue-Dong Liu, Xiao Liu, Xiu-Fen Guo, Jian-Min Luo, Ying-Hua Li
OBJECTIVE: To investigate the relationship of DNA methyltransferase 1 ( DNMT1 ) with hematopoietic cell phosphatase (SHP-1) gene expression and promoter 2 methylation status in cell line K562. METHODS: The promoter sequence of SHP-1 gene promoter 2 in NCBI database was analyzed, the K562 cells were transfected with the lentiviral plasmids-the specified retroviral vector psiHIV-mU6-shDNMT1 and psiHIV-mU6-mcherryFP-control. The methylation status of SHP-1 gene promoter 2 in K562 cells was detected by methylation-specific polymerase chain reaction (MSP) and bisulfite-modified sequencing (BSP)...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
Beatriz Baselga-Cervera, Julia Romero-López, Camino García-Balboa, Eduardo Costas, Victoria López-Rodas
The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h-1 ) and contaminated with metals, mainly U (from 25 to 48 mg L-1 ) and zinc (from 17 to 87 mg L-1 )...
2018: Frontiers in Microbiology
Ning Su, Litao Qin, Hongdan Wang, Hai Xiao, Qiannan Guo, Tao Li, Shixiu Liao
OBJECTIVE: To detect potential mutation in a Chinese pedigree affected with familial exudative vitreoretinopathy (FEVR). METHODS: Clinical data of the pedigree was collected. Coding regions of candidate genes were amplified by PCR and subjected to next generation sequencing (NGS). Suspected mutations were verified by Sanger sequencing and segregation analysis. RESULTS: Two novel heterozygous mutations (c.1695dupC and c.552-563del) were respectively detected in the LRP5 and ZNF408 genes in the proband...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
K L McCarthy, A M Wailan, A V Jennison, T J Kidd, D L Paterson
We have recently characterised the epidemiology of P. aeruginosa blood stream infection (BSI) in a large retrospective multicentre cohort study [1]. Utilising corresponding patient BSI isolates we aimed to characterise the genotypic virulence profile of the P. aeruginosa isolates that were associated with rapid death in the non-neutropenic host. Five P. aeruginosa BSI episodes were identified from a larger cohort of P. aeruginosa BSI episodes previously described by McCarthy et al. [1]. The genotypic profile of another 5 isolates from this cohort in whom the non-neutropenic host had survived one year post the BSI was also analysed for comparison...
April 2, 2018: Microbial Pathogenesis
Damian Miles Bailey, Benjamin S Stacey, Mark Gumbleton
OBJECTIVE: While physiological responses during acute ascent to terrestrial high altitude (HA) have the potential to alter the pharmacokinetics (PKs) that define absorption and disposition of medicinal drugs, there have been no systematic reviews and meta-analyses performed to date. METHODS: We conducted a systematic literature search in June 2017 using NCBI PubMed, EMBASE, Web of Science, and Ovid MEDLINE databases to identify relevant observational studies. Studies were deemed eligible based on the following criteria: (1) participants: healthy, nonacclimatized male or female lowlanders (born and bred at sea level) and (2) environment: exposure to low altitude (LA, ≤600 m), followed by terrestrial high altitude (HA, ≤24 hours to ≥2500 m), the time course specifically selected to avoid interpretive complications associated with erythrocytosis...
April 5, 2018: High Altitude Medicine & Biology
Wei Liu, Li Li, Hua Ye, Huan Tao, Huaqin He
Public transcriptome databases provide a valuable resource for genome‑wide co‑expression network analysis and investigation of the molecular mechanisms that underlie pathogenesis. To discover genes that may affect patient survival, a large‑scale analysis of human colorectal cancer (CRC) datasets that were retrieved from the NCBI Gene Expression Omnibus was performed. A gene co‑expression network was constructed using weighted gene co‑expression network analysis (WGCNA). A total of 18 co‑expressed gene modules were identified, of which two genes corresponded to cell migration and the cell cycle, two genes were involved in immune responses, two genes corresponded to mitochondrial function, and one gene corresponded to RNA splicing...
March 23, 2018: Oncology Reports
Stefan Bletz, Sandra Janezic, Dag Harmsen, Maja Rupnik, Alexander Mellmann
Clostridium difficile , recently renamed to Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, a highly discriminatory subtyping is necessary. Today, methods based on whole genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature is missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C...
April 4, 2018: Journal of Clinical Microbiology
Sahira Nsayef Muslim, Israa M S Al-Kadmy, Ibtesam Ghadban Auda, Alaa Naseer Mohammed Ali, Sawsan Sajid Al-Jubori
Background : Lectin was initially called hemagglutinin or agglutinin because of its capacity to agglutinate human as well as human erythrocytes. They are a heterogeneous group of proteins or glycoproteins of nonimmune origin. Because of their chemical properties, they have become a useful tool in several fields such as immunology, cell biology, molecular biology, membrane structure, pharmacology, cancer research, clinical chemistry, and genetic engineering. Objective : The wide applications of lectins users urged the need to isolate lectins from a new strain of bacteria can produce new and high yield of lectin because the current production of lectin from Pseudomonas spp...
April 4, 2018: Journal of AOAC International
Jaehee Jung, Jong Im Kim, Young-Sik Jeong, Gangman Yi
Summary: Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes...
March 29, 2018: Bioinformatics
Amrita Banerjee, Yashi Umbrey, Rohit M Yadav, Somnath Roy
A new isolate (Mg-mungbean-1) of yellow mosaic virus (YMV) was identified and characterized from mungbean growing in mid-hill condition of Meghalaya, India. Full genome of components (DNA A and DNA B; NCBI accessions number KU95030 and KU95031, respectively) of the virus were amplified through rolling circle amplification and sequenced. Both, DNA A and DNA B shared a common region (CR) with 90.4% similarity. The DNA A of Mg-mungbean-1 showed maximum (97.59%) nucleotide identity with mungbean yellow mosaic India virus (MYMIV) isolate (HF922628) reported from West Bengal, India and DNA B showed ~ 96% nucleotide identity with mungbean yellow mosaic virus (MYMV) isolates having variant DNA B...
March 2018: Virusdisease
Voon-Ching Lim, Rosli Ramli, Subha Bhassu, John-James Wilson
Background: Intense landscaping often alters the plant composition in urban areas. Knowing which plant species that pollinators are visiting in urban areas is necessary for understanding how landscaping impacts biodiversity and associated ecosystem services. The cave nectar bat, Eonycteris spelaea , is an important pollinator for many plants and is often recorded in human-dominated habitats. Previous studies of the diet of E. spelaea relied on morphological identification of pollen grains found in faeces and on the body of bats and by necessity disregarded other forms of digested plant material present in the faeces (i...
2018: PeerJ
Wenzhao Wang, Yihui Zhou, Yingling Wu, Xinlong Dai, YaJun Liu, Yumei Qian, Mingzhuo Li, Xiaolan Jiang, Yunsheng Wang, Liping Gao, Tao Xia
Tea is an important economic crop with a 3.02-Gb genome. It accumulates various bioactive compounds, especially catechins, which are closely associated with tea flavor and quality. Catechins are biosynthesized through the phenylpropanoid and flavonoid pathways, with twelve structural genes being involved in their synthesis. However, we found that in Camellia sinensis, the understanding of the basic profile of catechins biosynthesis is still unclear. The gene structure, locus, transcript number, transcriptional variation and function of multigene families have not yet been clarified...
April 1, 2018: Journal of Agricultural and Food Chemistry
Khanchuila Shingnaisui, Tapan Dey, Prasenjit Manna, Jatin Kalita
ETHNOPHARMACOLOGICAL RELEVANCE: Houttuynia cordata Thunb. (Family: Saururaceae) is an herbaceous perennial plant that grows in moist and shady places. The plant is well known among the people of diverse cultures across Japan, Korea, China and North-East India for its medicinal properties. Traditionally the plant is used for its various beneficial properties against inflammation, pneumonia, severe acute respiratory syndrome, muscular sprain, stomach ulcer etc. Oxidative stress and inflammation were found to be linked with most of the diseases in recent times...
March 29, 2018: Journal of Ethnopharmacology
Marcella A Teixeira, Noa Sela, Hagop S Atamian, Ergude Bao, Ritu Chaudhary, Jacob MacWilliams, Jiangman He, Sophie Mantelin, Thomas Girke, Isgouhi Kaloshian
The potato aphid, Macrosiphum euphorbiae, is an important agricultural pest that causes economic losses to potato and tomato production. To establish the transcriptome for this aphid, RNA-Seq libraries constructed from aphids maintained on tomato plants were used in Illumina sequencing generating 52.6 million 75-105 bp paired-end reads. The reads were assembled using Velvet/Oases software with SEED preprocessing resulting in 22,137 contigs with an N50 value of 2,003bp. After removal of contigs from tomato host origin, 20,254 contigs were annotated using BLASTx searches against the non-redundant protein database from the National Center for Biotechnology Information (NCBI) as well as IntereProScan...
2018: PloS One
Maciej Janiak, Kamila Caraballo Cortés, Karol Perlejewski, Dorota Kubicka-Russel, Piotr Grabarczyk, Urszula Demkow, Marek Radkowski
The infection with more than one hepatitis C virus (HCV) genotype especially in subjects with a high risk of multiple HCV exposures has been demonstrated. The role of HCV mixed-genotype infection in viral persistence and treatment effect is not fully understood. The prevalence of such infection varies greatly depending on the technique used for genotype determination and studied population. Next-generation sequencing (NGS) which is suitable for extensive analysis of complex viral populations is a method of choice for studying mixed infections...
March 29, 2018: Advances in Experimental Medicine and Biology
Ezazul Haque, Urmila Banik, Tahmina Monwar, Leela Anthony, Arun Kumar Adhikary
Human adenovirus type 3 (HAdV-3) respiratory infections occurs worldwide in both children and adults, leading to severe morbidity and mortality, particularly in the paediatric age group and especially in neonates. During HAdV infection, neutralizing antibodies are formed against the epitopes located in the hyper variable regions (HVRs) of the hexon protein. These neutralizing antibodies provide protection against reinfection by viruses of the same type. Therefore it is reasonable to speculate that variations of HAdV-3 in the HVRs could impair the immunity acquired by previous infection with a different strain with variation in its HVRs...
2018: PloS One
Erin E Gill, Luisa S Chan, Geoffrey L Winsor, Neil Dobson, Raymond Lo, Shannan J Ho Sui, Bhavjinder K Dhillon, Patrick K Taylor, Raunak Shrestha, Cory Spencer, Robert E W Hancock, Peter J Unrau, Fiona S L Brinkman
BACKGROUND: Understanding the RNA processing of an organism's transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5'-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions...
March 27, 2018: BMC Genomics
Reaz Uddin, Faiza Jamil
Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core proteomic analysis and Protein-Protein Interactions (PPIs) studies. The non-redundant reference proteome of 68 strains having complete genome and latest assembly version of P. aeruginosa were downloaded from ftp NCBI RefSeq server in October 2016...
March 8, 2018: Computational Biology and Chemistry
Vidya Vasudevan, K Veena Gayathri, Mary Elizabeth Gnanambal Krishnan
Dibenz(a,h)Anthracene (DBahA), classified as a probable human carcinogen (B2) is the first Poly Aromatic Hydrocarbons (PAH) to be chemically purified and used for cancer-based studies. Till date, only 30 papers focus on the bioremediation aspects of DBahA out of more than 200 research publications for each of the other 15 priority PAHs. Thus, the review raises an alarm and calls for efficient bioremediation strategies for considerable elimination of this compound from the environment. This article reviews and segregates the available papers on DBahA bioremoval from the beginning till date into bacteria, fungi and plant-mediated remediation and offers suggestions for the most competent and cost-effective modes to bioremove DBahA from the environment...
March 15, 2018: Chemosphere
Tehmina Bharucha, Onanong Sengvilaipaseuth, Manivanh Vongsouvath, Malavanh Vongsouvath, Viengmon Davong, Phonepasith Panyanouvong, Géraldine Piorkowski, Jeremy A Garson, Paul N Newton, Xavier de Lamballerie, Audrey Dubot-Pérès
BACKGROUND: Japanese encephalitis virus (JEV) is a major cause of encephalitis in Asia, and the commonest cause of mosquito-borne encephalitis worldwide. Detection of JEV RNA remains challenging due to the characteristic brief and low viraemia, with 0-25% of patients positive, and the mainstay of diagnosis remains detection of anti-JEV IgM antibody. METHODS: We performed a systematic review of published RT-PCR protocols, and evaluated them in silico and in vitro alongside new primers and probes designed using a multiple genome alignment of all JEV strains >9,000nt from GenBank, downloaded from the NCBI website (November 2016)...
2018: PloS One
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