keyword
MENU ▼
Read by QxMD icon Read
search

Chip sequencing

keyword
https://www.readbyqxmd.com/read/28640909/hiv-tat-regulates-macrophage-gene-expression-in-the-context-of-neuroaids
#1
Loreto Carvallo, Lillie Lopez, Jorge E Fajardo, Matias Jaureguiberry-Bravo, Andras Fiser, Joan W Berman
Despite the success of cART, greater than 50% of HIV infected people develop cognitive and motor deficits termed HIV-associated neurocognitive disorders (HAND). Macrophages are the major cell type infected in the CNS. Unlike for T cells, the virus does not kill macrophages and these long-lived cells may become HIV reservoirs in the brain. They produce cytokines/chemokines and viral proteins that promote inflammation and neuronal damage, playing a key role in HIV neuropathogenesis. HIV Tat is the transactivator of transcription that is essential for replication and transcriptional regulation of the virus and is the first protein to be produced after HIV infection...
2017: PloS One
https://www.readbyqxmd.com/read/28636844/clonal-hematopoiesis-and-risk-of-atherosclerotic-cardiovascular-disease
#2
Siddhartha Jaiswal, Pradeep Natarajan, Alexander J Silver, Christopher J Gibson, Alexander G Bick, Eugenia Shvartz, Marie McConkey, Namrata Gupta, Stacey Gabriel, Diego Ardissino, Usman Baber, Roxana Mehran, Valentin Fuster, John Danesh, Philippe Frossard, Danish Saleheen, Olle Melander, Galina K Sukhova, Donna Neuberg, Peter Libby, Sekar Kathiresan, Benjamin L Ebert
Background Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of an expanded somatic blood-cell clone in persons without other hematologic abnormalities, is common among older persons and is associated with an increased risk of hematologic cancer. We previously found preliminary evidence for an association between CHIP and atherosclerotic cardiovascular disease, but the nature of this association was unclear. Methods We used whole-exome sequencing to detect the presence of CHIP in peripheral-blood cells and associated such presence with coronary heart disease using samples from four case-control studies that together enrolled 4726 participants with coronary heart disease and 3529 controls...
June 21, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28636596/selective-sp-3-c-h-alkylation-via-polarity-match-based-cross-coupling
#3
Chip Le, Yufan Liang, Ryan W Evans, Ximing Li, David W C MacMillan
The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp(3))-C(sp(2)) coupling, there is a growing demand for C-H alkylation reactions, wherein sp(3) C-H bonds are replaced with sp(3) C-alkyl groups...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28634808/mapping-of-genetic-locus-for-leaf-trichome-in-brassica-oleracea
#4
Jiaqin Mei, Jinhua Wang, Yuehua Li, Shuai Tian, Dayong Wei, Chaoguo Shao, Jun Si, Qing Xiong, Jiana Li, Wei Qian
The genetic locus for leaf trichome was identified via marker-based mapping and SNP microarray assay, and a functional marker was developed to facilitate the breeding for hairiness in Brassica oleracea. Plant trichomes are involved in various functions particularly in protecting plants against some biotic and abiotic damages. In the present study, an F2 segregating population was developed from the cross between a glabrous cultivated B. oleracea (CC, 2n = 18) and a hairy wild relative, B. incana (CC, 2n = 18)...
June 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-non-coding-sequences-on-embryonic-brain-development
#5
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28630431/role-of-methionine-adenosyltransferase-2a-in-bovine-preimplantation-development-and-its-associated-genomic-regions
#6
Shuntaro Ikeda, Ryouka Kawahara-Miki, Hisataka Iwata, Miki Sugimoto, Shinichi Kume
Methionine adenosyltransferase (MAT) is involved in folate-mediated one-carbon metabolism, which is essential for preimplantation embryos in terms of both short-term periconceptional development and long-term phenotypic programming beyond the periconceptional period. Here, our immunofluorescence analysis of bovine oocytes and preimplantation embryos revealed the consistent expression of MAT2A (the catalytic subunit of the ubiquitously expressed-type of MAT isozyme) during this period. Addition of the MAT2A inhibitor FIDAS to the culture media of bovine preimplantation embryos reduced their blastocyst development, revealing the particular importance of MAT2A in successful blastocyst development...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28625155/applications-of-optical-dna-mapping-in-microbiology
#7
Diana Bogas, Lena Nyberg, Rui Pacheco, Nuno F Azevedo, Jason P Beech, Margarita Gomila, Jorge Lalucat, Célia M Manaia, Olga C Nunes, Jonas O Tegenfeldt, Fredrik Westerlund
Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28623590/integration-of-genome-wide-tf-binding-and-gene-expression-data-to-characterize-gene-regulatory-networks-in-plant-development
#8
Dijun Chen, Kerstin Kaufmann
Key transcription factors (TFs) controlling the morphogenesis of flowers and leaves have been identified in the model plant Arabidopsis thaliana. Recent genome-wide approaches based on chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) enable systematic identification of genome-wide TF binding sites (TFBSs) of these regulators. Here, we describe a computational pipeline for analyzing ChIP-seq data to identify TFBSs and to characterize gene regulatory networks (GRNs) with applications to the regulatory studies of flower development...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622687/identification-of-a-novel-p53-target-col17a1-that-inhibits-breast-cancer-cell-migration-and-invasion
#9
Varalee Yodsurang, Chizu Tanikawa, Takafumi Miyamoto, Paulisally Hau Yi Lo, Makoto Hirata, Koichi Matsuda
p53 mutation is a marker of poor prognosis in breast cancers. To identify downstream targets of p53, we screened two transcriptome datasets, including cDNA microarrays of MCF10A breast epithelial cells with wild-type p53 or p53-null background, and RNA sequence analysis of breast invasive carcinoma. Here, we unveil ten novel p53 target candidates that are up-regulated after the induction of p53 in wild-type cells. Their expressions are also high in breast invasive carcinoma tissues with wild-type p53. The GO analysis identified epidermis development and ectoderm development, which COL17A1 participates, as significantly up-regulated by wild-type p53...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28620275/genome-wide-target-analyses-of-otx2-homeoprotein-in-postnatal-cortex
#10
Akiko Sakai, Ryuichiro Nakato, Yiwei Ling, Xubin Hou, Norikazu Hara, Tomoya Iijima, Yuchio Yanagawa, Ryozo Kuwano, Shujiro Okuda, Katsuhiko Shirahige, Sayaka Sugiyama
Juvenile brain has a unique time window, or critical period, in which neuronal circuits are remodeled by experience. Mounting evidence indicates the importance of neuronal circuit rewiring in various neurodevelopmental disorders of human cognition. We previously showed that Otx2 homeoprotein, essential for brain formation, is recaptured during postnatal maturation of parvalbumin-positive interneurons (PV cells) to activate the critical period in mouse visual cortex. Cortical Otx2 is the only interneuron-enriched transcription factor known to regulate the critical period, but its downstream targets remain unknown...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28615266/antitumor-effects-of-epidrug-ifnalpha%C3%A2-combination-driven-by-modulated-gene-signatures-in-both-colorectal-cancer-and-dendritic-cells
#11
Alessandra Fragale, Giulia Romagnoli, Valerio Licursi, Maria Buoncervello, Giorgia Del Vecchio, Caterina Giuliani, Stefania Parlato, Celeste Leone, Marta De Angelis, Irene Canini, Elena Toschi, Filippo Belardelli, Rodolfo Negri, Imerio Capone, Carlo Presutti, Lucia Gabriele
Colorectal cancer (CRC) results from progressive accumulation of genetic and epigenetic alterations. IFN signaling defects play an important role in the carcinogenesis process, in which the inability of IFN transcription regulatory factors (IRFs) to access regulatory sequences in IFN-stimulated genes (ISGs) in tumors and in immune cells may be pivotal. We reported that low-dose combination of two FDA-approved epidrugs, azacytidine (A) and romidepsin (R), with IFNa2 (ARI) hampers the aggressiveness of both CRC metastatic and stem cells in vivo and triggers immunogenic cell death signals that stimulate dendritic cell (DC) function...
June 14, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/28615201/the-latency-associated-nuclear-antigen-of-kaposi-s-sarcoma-associated-herpesvirus-inhibits-expression-of-sumo-sentrin-specific-peptidase-6-to-facilitate-latency-establishment
#12
Xiaoxi Lin, Rui Sun, Fang Zhang, Yuan Gao, Lianghua Bin, Ke Lan
Kaposi's sarcoma-associated herpesvirus (KSHV), belonging to γ-herpesviridae, typically displays two different phases in its lifecycle, the latent phase and the lytic phase. Latent-associated nuclear antigen (LANA), the primary viral product during latency, has been reported to bind to a series of cellular gene promoters to modulate gene transcription. To systemically elucidate the cellular genes regulated by LANA, we identified genome-wide LANA binding sites by chromatin immunoprecipitation coupled with sequencing (ChIP-seq)...
June 14, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28615056/oct4-transcriptionally-regulates-the-expression-of-long-non-coding-rnas-neat1-and-malat1-to-promote-lung-cancer-progression
#13
Jayu Jen, Yen-An Tang, Ying-Hung Lu, Che-Chung Lin, Wu-Wei Lai, Yi-Ching Wang
BACKGROUND: Oct4, a key stemness transcription factor, is overexpressed in lung cancer. Here, we reveal a novel transcription regulation of long non-coding RNAs (lncRNAs) by Oct4. LncRNAs have emerged as important players in cancer progression. METHODS: Oct4 chromatin-immunoprecipitation (ChIP)-sequencing and several lncRNA databases with literature annotation were integrated to identify Oct4-regulated lncRNAs. Luciferase activity, qRT-PCR and ChIP-PCR assays were conducted to examine transcription regulation of lncRNAs by Oct4...
June 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28613020/integrated-gene-expression-profiling-and-chromatin-immunoprecipitation-followed-by-sequencing-analysis-of-the-c-terminal-binding-protein-in-breast-cancer
#14
Lu Chen, Yang Yang, Liwei Xu, Rui Liu, Yali Wang
AIM: This study explored the possible mechanisms of the transcriptional regulatory activities of C-terminal binding protein (CtBP) and the role of CtBP in the pathogenesis of breast cancer. METHODS: Microarray data of GSE36529, including three CtBP-knockdown breast cancer MCF-7 cell samples, three control knockdown samples and data of CtBP binding profile in MCF-7 cells, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened between CtBP-knockdown MCF-7 cell samples and controls...
June 14, 2017: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/28611249/a-herpesviral-immediate-early-protein-promotes-transcription-elongation-of-viral-transcripts
#15
Hannah L Fox, Jill A Dembowski, Neal A DeLuca
Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (RNA Pol II). While four viral immediate early proteins (ICP4, ICP0, ICP27, and ICP22) function in some capacity in viral transcription, the mechanism by which ICP22 functions remains unclear. We observed that the FACT complex (comprised of SSRP1 and Spt16) was relocalized in infected cells as a function of ICP22. ICP22 was also required for the association of FACT and the transcription elongation factors SPT5 and SPT6 with viral genomes...
June 13, 2017: MBio
https://www.readbyqxmd.com/read/28609483/histone-posttranslational-modifications-predict-specific-alternative-exon-subtypes-in-mammalian-brain
#16
Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R Grant, Elizabeth A Heller
A compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addition. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is implicated in cocaine exposure in mice...
June 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28607444/identification-of-novel-dysregulated-key-genes-in-breast-cancer-through-high-throughput-chip-seq-data-analysis
#17
Utkarsh Raj, Imlimaong Aier, Rahul Semwal, Pritish Kumar Varadwaj
Breast cancer is the most common cancer in women both in the developed and less developed countries, and it imposes a considerable threat to human health. Therefore, in order to develop effective targeted therapies against Breast cancer, a deep understanding of its underlying molecular mechanisms is required. The application of deep transcriptional sequencing has been found to be reported to provide an efficient genomic assay to delve into the insights of the diseases and may prove to be useful in the study of Breast cancer...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606935/gata6-is-essential-for-endoderm-formation-from-human-pluripotent-stem-cells
#18
J B Fisher, K Pulakanti, S Rao, S A Duncan
Protocols have been established that direct differentiation of human pluripotent stem cells into a variety of cell types including the endoderm and its derivatives. This model of differentiation has been useful for investigating the molecular mechanisms that guide human developmental processes. Using a directed differentiation protocol combined with shRNA depletion we sought to understand the role of GATA6 in regulating the earliest switch from pluripotency to definitive endoderm. We reveal that GATA6-depletion during endoderm formation results in apoptosis of nascent endoderm cells, concomitant with a loss of endoderm gene expression...
June 12, 2017: Biology Open
https://www.readbyqxmd.com/read/28605389/genome-wide-mapping-of-protein-dna-interactions-with-chec-seq-in-saccharomyces-cerevisiae
#19
Sebastian Grünberg, Gabriel E Zentner
Genome-wide mapping of protein-DNA interactions is critical for understanding gene regulation, chromatin remodeling, and other chromatin-resident processes. Formaldehyde crosslinking followed by chromatin immunoprecipitation and high-throughput sequencing (X-ChIP-seq) has been used to gain many valuable insights into genome biology. However, X-ChIP-seq has notable limitations linked to crosslinking and sonication. Native ChIP avoids these drawbacks by omitting crosslinking, but often results in poor recovery of chromatin-bound proteins...
June 3, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28604974/-study-on-the-cfhr1-level-and-its-genetic-polymorphisms-in-type-2-diabetes-mellitus-patients
#20
Jun Wang, Wei Yu, Jiazhang Xu, Liru Feng, Xiaoli Liu
OBJECTIVE: To explore the characteristics in CFHR1 concentration and the frequency of CFHR1 gene polymorphisms of patients with type 2 diabetes mellitus (T2DM) based on the high level of complement factor H (CFH) expression among such patients and the similarity between CFHR1 and CFH in terms of sequence and functions. METHODS: Fifty T2DM patients and 30 healthy controls were selected. The plasma samples were separated by pI with OFFGEL electrophoresis following solution digestion...
June 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
keyword
keyword
103069
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"