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https://www.readbyqxmd.com/read/29046457/hiv-1-infection-of-primary-cd4-t-cells-regulates-the-expression-of-specific-herv-k-hml-2-elements
#1
George R Young, Sandra N Terry, Lara Manganaro, Alvaro Cuesta-Dominguez, Gintaras Deikus, Dabeiba Bernal-Rubio, Laura Campisi, Ana Fernandez-Sesma, Robert Sebra, Viviana Simon, Lubbertus C F Mulder
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathologic states, such as viral infections and certain cancers, coincide with ERV expression suggesting transcriptional reawakening is possible...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29038029/expanding-the-spectrum-of-tbl1xr1-deletion-report-of-a-patient-with-brain-and-cardiac-malformations
#2
Ana Carolina Vaqueiro, Claudiner Pereira de Oliveira, Mara Santos Cordoba, Beatriz Ribeiro Versiani, Camila Xavier de Carvalho, Pedro Guilherme Alves Rodrigues, Silviene Fabiana de Oliveira, Juliana Forte Mazzeu, Aline Pic-Taylor
The TBL1XR1 gene product is a nuclear protein ubiquitously produced in most tissues. The protein is a component of SMRT/N-CoR co-repressor complexes and participates in the molecular switch of specific gene transcription. Deletions of the TBL1XR1 gene have been described in two families to date, both presenting intellectual disability and dysmorphisms. Rare recurrent chromosomal microrearrangements, particularly those involving single genes, represent a challenge for clinicians to ensure correlation with phenotype due to the paucity of previously described cases...
October 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#3
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#4
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29019980/radically-truncated-mecp2-rescues-rett-syndrome-like-neurological-defects
#5
Rebekah Tillotson, Jim Selfridge, Martha V Koerner, Kamal K E Gadalla, Jacky Guy, Dina De Sousa, Ralph D Hector, Stuart R Cobb, Adrian Bird
Heterozygous mutations in the X-linked MECP2 gene cause the neurological disorder Rett syndrome. The methyl-CpG-binding protein 2 (MeCP2) protein is an epigenetic reader whose binding to chromatin primarily depends on 5-methylcytosine. Functionally, MeCP2 has been implicated in several cellular processes on the basis of its reported interaction with more than 40 binding partners, including transcriptional co-repressors (for example, the NCoR/SMRT complex), transcriptional activators, RNA, chromatin remodellers, microRNA-processing proteins and splicing factors...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29018412/a-novel-lactobacilli-based-teat-disinfectant-for-improving-bacterial-communities-in-the-milks-of-cow-teats-with-subclinical-mastitis
#6
Jie Yu, Yan Ren, XiaoXia Xi, Weiqiang Huang, Heping Zhang
Teat disinfection pre- and post-milking is important for the overall health and hygiene of dairy cows. The objective of this study was to evaluate the efficacy of a novel probiotic lactobacilli-based teat disinfectant based on changes in somatic cell count (SCC) and profiling of the bacterial community. A total of 69 raw milk samples were obtained from eleven Holstein-Friesian dairy cows over 12 days of teat dipping in China. Single molecule, real-time sequencing technology (SMRT) was employed to profile changes in the bacterial community during the cleaning protocol and to compare the efficacy of probiotic lactic acid bacteria (LAB) and commercial teat disinfectants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29017889/complete-genome-sequence-of-acinetobacter-baumannii-a1296-st1469-with-a-small-plasmid-harboring-the-tet39-tetracycline-resistance-gene
#7
Xiaoting Hua, Chao Pan, Li Zhu, Zhicheng Liu, Qingye Xu, Hengliang Wang, Yunsong Yu
OBJECTIVES: Acinetobacter baumannii is considered an important nosocomial pathogen worldwide due to its increasing antibiotic resistance. This study aimed to determine the complete genome sequence of A. baumannii strain A1296 and comparative analysis among A. baumannii. METHODS: The complete genome sequence of A. baumannii A1296 was sequenced on two SMRT cells using P6C4 chemistry on a Pacific Biosciences Single Molecule, Real-Time RS II instrument. The A1296 genome sequence was annotated via NCBI, and its MLST and resistance genes were analyzed...
October 7, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28986786/dna-methylation-profiling-using-long-read-single-molecule-real-time-bisulfite-sequencing-smrt-bs
#8
Yao Yang, Stuart A Scott
For the past two decades, bisulfite sequencing has been a widely used method for quantitative CpG methylation detection of genomic DNA. Coupled with PCR amplicon cloning, bisulfite Sanger sequencing allows for allele-specific CpG methylation assessment; however, its time-consuming protocol and inability to multiplex has recently been overcome by next-generation bisulfite sequencing techniques. Although high-throughput sequencing platforms have enabled greater accuracy in CpG methylation quantitation as a result of increased bisulfite sequencing depth, most common sequencing platforms generate reads that are similar in length to the typical bisulfite PCR size range (~300-500 bp)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28982984/draft-genome-sequences-of-two-uncultured-armatimonadetes-associated-with-a-microcystis-sp-cyanobacteria-isolate
#9
Jason N Woodhouse, A Katharina Makower, Hans-Peter Grossart, Elke Dittmann
Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.
October 5, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28981454/hybrid-sequencing-of-full-length-cdna-transcripts-of-stems-and-leaves-in-dendrobium-officinale
#10
Liu He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Li, Kin Fai Au, Hui Yao
Dendrobium officinale is an extremely valuable orchid used in traditional Chinese medicine, so sought after that it has a higher market value than gold. Although the expression profiles of some genes involved in the polysaccharide synthesis have previously been investigated, little research has been carried out on their alternatively spliced isoforms in D. officinale. In addition, information regarding the translocation of sugars from leaves to stems in D. officinale also remains limited. We analyzed the polysaccharide content of D...
October 5, 2017: Genes
https://www.readbyqxmd.com/read/28961789/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads
#11
Ergude Bao, Changjin Song, Lingxiao Lan
Motivation: Contigs assembled from the second generation sequencing short reads may contain misassemblies, and thus complicate downstream analysis or even lead to incorrect analysis results. Fortunately, with more and more sequenced species available, it becomes possible to use the reference genome of a closely related species to detect misassemblies. In addition, long reads of the third generation sequencing technology have been more and more widely used, and can also help detect misassemblies...
August 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28957975/comparison-of-the-spectral-temporally-modulated-ripple-test-with-the-arizona-biomedical-institute-sentence-test-in-cochlear-implant-users
#12
Marshall Lawler, Jeffrey Yu, Justin M Aronoff
OBJECTIVES: Although speech perception is the gold standard for measuring cochlear implant (CI) users' performance, speech perception tests often require extensive adaptation to obtain accurate results, particularly after large changes in maps. Spectral ripple tests, which measure spectral resolution, are an alternate measure that has been shown to correlate with speech perception. A modified spectral ripple test, the spectral-temporally modulated ripple test (SMRT) has recently been developed, and the objective of this study was to compare speech perception and performance on the SMRT for a heterogeneous population of unilateral CI users, bilateral CI users, and bimodal users...
September 27, 2017: Ear and Hearing
https://www.readbyqxmd.com/read/28935727/complete-genome-sequences-of-lactobacillus-curvatus-kg6-l-curvatus-mrs6-and-lactobacillus-sakei-fam18311-isolated-from-fermented-meat-products
#13
Christoph Jans, Sandra Lagler, Christophe Lacroix, Leo Meile, Marc J A Stevens
The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28934361/restriction-modification-mediated-barriers-to-exogenous-dna-uptake-and-incorporation-employed-by-prevotella-intermedia
#14
Christopher D Johnston, Chelsey A Skeete, Alexey Fomenkov, Richard J Roberts, Susan R Rittling
Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P...
2017: PloS One
https://www.readbyqxmd.com/read/28929458/backbone-resonance-assignment-of-the-bcl6-btb-poz-domain
#15
Li-Ying Lin, S E Evans, L Fairall, John W R Schwabe, Simon D Wagner, Frederick W Muskett
BCL6 is a transcriptional repressor. Two domains of the protein, the N-terminal BTB-POZ domain and the RD2 domain are responsible for recruitment of co-repressor molecules and histone deacetylases. The BTB-POZ domain is found in a large and diverse range of proteins that play important roles in development, homeostasis and neoplasia. Crystal structures of several BTB-POZ domains, including BCL6 have been determined. The BTB-POZ domain of BCL6 not only mediates dimerisation but is also responsible for recruitment of co-repressors such as SMRT, NCOR and BCOR...
September 19, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28923935/retinoid-x-receptor-suppresses-a-metastasis-promoting-transcriptional-program-in-myeloid-cells-via-a-ligand-insensitive-mechanism
#16
Mate Kiss, Zsolt Czimmerer, Gergely Nagy, Pawel Bieniasz-Krzywiec, Manuel Ehling, Attila Pap, Szilard Poliska, Pal Boto, Petros Tzerpos, Attila Horvath, Zsuzsanna Kolostyak, Bence Daniel, Istvan Szatmari, Massimiliano Mazzone, Laszlo Nagy
Retinoid X receptor (RXR) regulates several key functions in myeloid cells, including inflammatory responses, phagocytosis, chemokine secretion, and proangiogenic activity. Its importance, however, in tumor-associated myeloid cells is unknown. In this study, we demonstrate that deletion of RXR in myeloid cells enhances lung metastasis formation while not affecting primary tumor growth. We show that RXR deficiency leads to transcriptomic changes in the lung myeloid compartment characterized by increased expression of prometastatic genes, including important determinants of premetastatic niche formation...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#17
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28921562/a-novel-approach-using-long-read-sequencing-and-ddpcr-to-investigate-gonadal-mosaicism-and-estimate-recurrence-risk-in-two-families-with-developmental-disorders
#18
Maria Wilbe, Sanna Gudmundsson, Josefin Johansson, Adam Ameur, Eva-Lena Stattin, Göran Annerén, Helena Malmgren, Carina Frykholm, Marie-Louise Bondeson
OBJECTIVE: De novo mutations contribute significantly to severe early-onset genetic disorders. Even if the mutation is apparently de novo there is a recurrence risk due to parental germ line mosaicism, depending on the gonadal generation the mutation occurred. METHODS: We demonstrate the power of using SMRT sequencing and ddPCR to determine parental origin and allele frequencies of de novo mutations in germ cells in two families whom had undergone assisted reproduction...
September 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28915027/structure-and-dynamics-of-membrane-proteins-and-membrane-associated-proteins-with-native-bicelles-from-eukaryotic-tissues
#19
Sean T Smrt, Adrian W Draney, Indira Singaram, Justin L Lorieau
In vitro studies of protein structure, function, and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the extensive and controlled biophysical experiments available in vitro. We present an alternative approach by extracting membranes from eukaryotic tissues to produce native bicelles to capture the rich and complex molecular environment of in vivo studies while retaining the advantages of in vitro experiments...
October 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#20
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 2017: PLoS Genetics
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