keyword
MENU ▼
Read by QxMD icon Read
search

Epigenetics profilling

keyword
https://www.readbyqxmd.com/read/28213885/epigenetic-modifier-induced-enhancement-of-fumiquinazoline-c-production-in-aspergillus-fumigatus-ga-l7-an-endophytic-fungus-from-grewia-asiatica-l
#1
Ankita Magotra, Manjeet Kumar, Manoj Kushwaha, Praveen Awasthi, Chand Raina, Ajai Prakash Gupta, Bhahwal A Shah, Sumit G Gandhi, Asha Chaubey
Present study relates to the effect of valproic acid, an epigenetic modifier on the metabolic profile of Aspergillus fumigatus (GA-L7), an endophytic fungus isolated from Grewia asiatica L. Seven secondary metabolites were isolated from A. fumigatus (GA-L7) which were identified as: pseurotin A, pseurotin D, pseurotin F2, fumagillin, tryprostatin C, gliotoxin and bis(methylthio)gliotoxin. Addition of valproic acid in the growth medium resulted in the alteration of secondary metabolic profile with an enhanced production of a metabolite, fumiquinazoline C by tenfolds...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28209158/gene-regulatory-network-underlying-the-immortalization-of-epithelial-cells
#2
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28203090/exploring-targeted-therapy-of-osteosarcoma-using-proteomics-data
#3
Parunya Chaiyawat, Jongkolnee Settakorn, Apiruk Sangsin, Pimpisa Teeyakasem, Jeerawan Klangjorhor, Aungsumalee Soongkhaw, Dumnoensun Pruksakorn
Despite multimodal therapeutic treatments of osteosarcoma (OS), some patients develop resistance to currently available regimens and eventually end up with recurrent or metastatic outcomes. Many attempts have been made to discover effective drugs for improving outcome; however, due to the heterogeneity of the disease, new therapeutic options have not yet been identified. This study aims to explore potential targeted therapy related to protein profiles of OS. In this review of proteomics studies, we extracted data on differentially expressed proteins (DEPs) from archived literature in PubMed and our in-house repository...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28202904/genome-wide-dna-de-methylation-is-associated-with-noninfectious-bud-failure-exhibition-in-almond-prunus-dulcis-mill-d-a-webb
#4
Jonathan Fresnedo-Ramírez, Helen M Chan, Dan E Parfitt, Carlos H Crisosto, Thomas M Gradziel
Noninfectious bud-failure (BF) remains a major threat to almond production in California, particularly with the recent rapid expansion of acreage and as more intensive cultural practices and modern cultivars are adopted. BF has been shown to be inherited in both vegetative and sexual progeny, with exhibition related to the age and propagation history of scion clonal sources. These characteristics suggest an epigenetic influence, such as the loss of juvenility mediated by DNA-(de)methylation. Various degrees of BF have been reported among cultivars as well as within sources of clonal propagation of the same cultivar...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202316/an-epigenetic-modifier-induces-production-of-10-s-verruculide-b-an-inhibitor-of-protein-tyrosine-phosphatases-by-phoma-sp-nov-lg0217-a-fungal-endophyte-of-parkinsonia-microphylla
#5
Juliana R Gubiani, E M Kithsiri Wijeratne, Taoda Shi, Angela R Araujo, A Elizabeth Arnold, Eli Chapman, A A Leslie Gunatilaka
Incorporation of the histone deacetylase (HDAC) inhibitor, suberoylanilide hydroxamic acid (SAHA), to a culture broth of the endophytic fungus Phoma sp. nov. LG0217 isolated from Parkinsonia microphylla changed its metabolite profile and resulted in the production of (10'S)-verruculide B (1), vermistatin (2) and dihydrovermistatin (3). When cultured in the absence of the epigenetic modifier, it produced a new metabolite, (S,Z)-5-(3',4'-dihydroxybutyldiene)-3-propylfuran-2(5H)-one (4) together with nafuredin (5)...
February 3, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28199194/regulation-of-mitochondrial-gene-expression-the-epigenetic-enigma
#6
Archibold Mposhi, Monique Gp Van der Wijst, Klaas Nico Faber, Marianne G Rots
Epigenetics provides an important layer of information on top of the DNA sequence and is essential for establishing gene expression profiles. Extensive studies have shown that nuclear DNA methylation and histone modifications influence nuclear gene expression. However, it remains unclear whether mitochondrial DNA (mtDNA) undergoes similar epigenetic changes to regulate mitochondrial gene expression. Recently, it has been shown that mtDNA is differentially methylated in various diseases such as diabetes and colorectal cancer...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28196481/nuctools-analysis-of-chromatin-feature-occupancy-profiles-from-high-throughput-sequencing-data
#7
Yevhen Vainshtein, Karsten Rippe, Vladimir B Teif
BACKGROUND: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193886/improved-regulatory-element-prediction-based-on-tissue-specific-local-epigenomic-signatures
#8
Yupeng He, David U Gorkin, Diane E Dickel, Joseph R Nery, Rosa G Castanon, Ah Young Lee, Yin Shen, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker
Accurate enhancer identification is critical for understanding the spatiotemporal transcriptional regulation during development as well as the functional impact of disease-related noncoding genetic variants. Computational methods have been developed to predict the genomic locations of active enhancers based on histone modifications, but the accuracy and resolution of these methods remain limited. Here, we present an algorithm, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), which integrates histone modification and whole-genome cytosine DNA methylation profiles to identify the precise location of enhancers...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192422/identification-of-quiescent-and-spatially-restricted-mammary-stem-cells-that-are-hormone-responsive
#9
Nai Yang Fu, Anne C Rios, Bhupinder Pal, Charity W Law, Paul Jamieson, Ruijie Liu, François Vaillant, Felicity Jackling, Kevin He Liu, Gordon K Smyth, Geoffrey J Lindeman, Matthew E Ritchie, Jane E Visvader
Despite accumulating evidence for a mammary differentiation hierarchy, the basal compartment comprising stem cells remains poorly characterized. Through gene expression profiling of Lgr5(+) basal epithelial cells, we identify a new marker, Tetraspanin8 (Tspan8). Fractionation based on Tspan8 and Lgr5 expression uncovered three distinct mammary stem cell (MaSC) subsets in the adult mammary gland. These exist in a largely quiescent state but differ in their reconstituting ability, spatial localization, and their molecular and epigenetic signatures...
February 13, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28189002/abdominal-aortic-aneurysm-an-independent-disease-to-atherosclerosis
#10
REVIEW
Bradley J Toghill, Athanasios Saratzis, Matthew J Bown
Atherosclerosis and abdominal aortic aneurysms (AAAs) are multifactorial and polygenic diseases with known environmental and genetic risk factors that contribute toward disease development. Atherosclerosis represents an important independent risk factor for AAA, as people with AAA often have atherosclerosis. Studies have shown that comorbidity is usually between ~25% and 55%, but it is still not fully known whether this association is causal or a result of common shared risk profiles. Most recent epidemiological, clinical, and biological evidence suggests that the two pathologies are more distinct than traditionally thought...
January 29, 2017: Cardiovascular Pathology: the Official Journal of the Society for Cardiovascular Pathology
https://www.readbyqxmd.com/read/28187790/retinoic-acid-and-tgf-%C3%AE-signalling-cooperate-to-overcome-mycn-induced-retinoid-resistance
#11
David J Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G Higgins, Walter Kolch
BACKGROUND: Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance...
February 10, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28187703/ihms-a-database-integrating-human-histone-modification-data-across-developmental-stages-and-tissues
#12
Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou
BACKGROUND: Differences in chromatin states are critical to the multiplicity of cell states. Recently genome-wide histone modification maps of diverse human developmental stages and tissues have been charted. DESCRIPTION: To facilitate the investigation of epigenetic dynamics and regulatory mechanisms in cellular differentiation processes, we developed iHMS, an integrated human histone modification database that incorporates massive histone modification maps spanning different developmental stages, lineages and tissues ( http://www...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28184927/downregulation-of-ocln-and-gas1-in-clear-cell-renal-cell-carcinoma
#13
André Luis Giacometti Conceição, Camila Tainah Da Silva, Rodolfo Miglioli Badial, Marina Curado Valsechi, Bruna Stuqui, Jéssica Domingues Gonçalves, Miriam Galvonas Jasiulionis, Marilia De Freitas Calmon, Paula Rahal
Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer. This carcinoma is histologically characterized by the presence of clear and abundant cytoplasm. In the present study, we sought to identify genes differentially expressed in ccRCC and build a molecular profile of this cancer. We selected genes described in the literature related to cellular differentiation and proliferation. We analyzed the gene and protein expression by quantitative PCR (qPCR) and immunohistochemistry, respectively, and examined possible epigenetic mechanisms that regulate their expression in ccRCC samples and cell lines...
March 2017: Oncology Reports
https://www.readbyqxmd.com/read/28179100/nutrition-modulates-fto-and-irx3-gene-transcript-levels-but-does-not-alter-their-dna-methylation-profiles-in-rat-white-adipose-tissues
#14
Joanna Nowacka-Woszuk, Ewa Pruszynska-Oszmalek, Maciej Szydlowski, Izabela Szczerbal
The fat mass and obesity associated (Fto) and iroquois homeobox 3 (Irx3) genes have been recognised as important obesity-related genes. Studies on the expression of these genes in the fat tissue of human and mouse have produced inconsistent results, while similar data on rat are limited. Environmental factors such as diet, should be considered as potential modulators of gene transcript levels through epigenetic mechanisms including DNA methylation. The aim of this study was to evaluate transcription levels and DNA methylation profiles of rat Fto and Irx3 genes in two white adipose tissue depots in response to high-fat and high-protein diets...
February 5, 2017: Gene
https://www.readbyqxmd.com/read/28176655/epigenetics-in-clinical-management-of-children-and-adolescents-with-brain-tumors
#15
Andres Morales La Madrid, Mark W Kieran
Central nervous system (CNS) tumors represent the second most prevalent group of cancers in children and adolescents, yet account for the majority of childhood cancer-related deaths and considerable morbidity among survivors, due to high-intensity non-selective standard therapies delivered to immature nervous system structures undergoing development. These tumors arise at different ages -not infrequently very early in life-, in different locations and cellular contexts, have varied cell types of origin, and have heterogeneous responses to the "classic" current therapeutic approaches...
February 3, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28176652/mechanisms-for-inhibition-of-colon-cancer-cells-by-sulforaphane-through-epigenetic-modulation-of-microrna-21-and-human-telomerase-reverse-transcriptase-htert-down-regulation
#16
Samantha L Martin, Rishabh Kala, Trygve O Tollefsbol
Epigenetic modulations such as histone modifications are becoming increasingly valued for their ability to modify genes without altering the DNA sequence. Many bioactive compounds have been shown to alter genetic and epigenetic profiles in various forms of 6 cancers. Of the many dietary phytochemicals, sulforaphane (SFN), found in cruciferous vegetables such as kale, cabbage and broccoli sprouts, has been present as one of the most potent (histone deacetylase) HDAC inhibitors to date. Recently, it has been 9 identified that HDAC inhibitors may play a vital role in regulating microRNAs (miRNAs) in many human cancers...
February 5, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28176637/personalized-medicine-applied-to-forensic-sciences-new-advances-and-perspectives-for-a-tailored-forensic-approach
#17
Alessandro Santurro, Anna Maria Vullo, Marina Borro, Giovanna Gentile, Raffaele La Russa, Maurizio Simmaco, Paola Frati, Vittorio Fineschi
Personalized medicine (PM), included in P5 medicine (Personalized, Predictive, Preventive, Participative and Precision medicine) is an innovative approach to the patient, emerging from the need to tailor and to fit the profile of each individual. PM promises to dramatically impact also on forensic sciences and justice system in ways we are only beginning to understand. The application of omics (genomic, transcriptomics, epigenetics/imprintomics, proteomic and metabolomics) is ever more fundamental in the so called "molecular autopsy"...
February 7, 2017: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/28175529/365%C3%A2-epigenetic-profiling-reveals-a-unique-histone-code-in-chordoma
#18
Nelson Moussazadeh, Samuel H Berman, Ilya Laufer, Mrinal Gounder, Yupeng Zheng, Joshua Sommer, Mark H Bilsky, Neil L Kelleher, Cameron Brennan
No abstract text is available yet for this article.
August 1, 2016: Neurosurgery
https://www.readbyqxmd.com/read/28174625/sex-and-age-differences-in-the-expression-of-liver-micrornas-during-the-life-span-of-f344-rats
#19
Joshua C Kwekel, Vikrant Vijay, Tao Han, Carrie L Moland, Varsha G Desai, James C Fuscoe
BACKGROUND: Physiological factors such as age and sex have been shown to be risk factors for adverse effects in the liver, including liver diseases and drug-induced liver injury. Previously, we have reported age- and sex-related significant differences in hepatic basal gene expression in rats during the life span that may be related to susceptibility to such adverse effects. However, the underlying mechanisms of the gene expression changes were not fully understood. In recent years, increasing evidence for epigenetic mechanisms of gene regulation has fueled interest in the role of microRNAs (miRNAs) in toxicogenomics and biomarker discovery...
2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28174608/genome-wide-dna-methylation-profile-identified-a-unique-set-of-differentially-methylated-immune-genes-in-oral-squamous-cell-carcinoma-patients-in-india
#20
Baidehi Basu, Joyeeta Chakraborty, Aditi Chandra, Atul Katarkar, Jadav Ritesh Kumar Baldevbhai, Debjit Dhar Chowdhury, Jay Gopal Ray, Keya Chaudhuri, Raghunath Chatterjee
BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples...
2017: Clinical Epigenetics
keyword
keyword
24025
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"