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Epigenetics via ChIP-Seq (Chromatin Immunoprecipitation Sequencing)

 

As technology progresses, so does the curiosity of scientific minds around the globe. As more and more scientists shift from traditional DNA sequencing methods to massively parallel DNA sequencing, the new discoveries are increasing at an exponential rate. Such discoveries come with the popularization of chromatin immunoprecipitation sequencing or ChIP-Seq. ChIP sequencing is able to take scientists who were once excited to decipher the genomic code and stimulate new discoveries by determining how those genes are expressed. Laboratories, such as MR DNA, are assisting researchers from universities around the world to pinpoint how DNA and/or RNA are interacting with certain proteins by employing the ChIP-Seq protocol on a routine basis. Contact the highly experienced team at MR DNA in order to take advantage of their affordable cost and rapid turnaround time for your next epigenetic study.

 

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We provide services for high-throughput next-generation sequencing using the … (ChIP–SEQ), RNA discovery and Multiplex sequencing … Pricing forHiSeq 2500 sequencing is based on ……..sequencing run,  …

 

 

 

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Services. Transcriptomics. mRNA-Seq: Stranded and non-stranded, high levels of multiplexing … ChIP–Seq. Transcription factor analysis; Histone modifications

 

21. Genome Med. 2016 Jul 1;8(1):72. doi: 10.1186/s13073-016-0327-7.

 

Capturing the diversity of the human gut microbiota through culture-enriched

molecular profiling.

 

Lau JT(1), Whelan FJ(1), Herath I(1), Lee CH(2,)(3), Collins SM(4), Bercik P(4),

Surette MG(5,)(6).

 

Author information:

(1)Department of Biochemistry and Biomedical Sciences, McMaster University,

Hamilton, ON, L8S 4K1, Canada. (2)Department of Medicine, Division of Infectious

Diseases, McMaster University, Hamilton, ON, L8S 4K1, Canada. (3)Hamilton

Regional Laboratory Medicine Program, Hamilton, ON, L8N 4A6, Canada.

(4)Department of Medicine, Farncombe Family Digestive Health Research Institute,

McMaster University, 1280 Main St W, HSC 3N-9, Hamilton, ON, L8S 4K1, Canada.

(5)Department of Biochemistry and Biomedical Sciences, McMaster University,

Hamilton, ON, L8S 4K1, Canada. surette@mcmaster.ca. (6)Department of Medicine,

Farncombe Family Digestive Health Research Institute, McMaster University, 1280

Main St W, HSC 3N-9, Hamilton, ON, L8S 4K1, Canada. surette@mcmaster.ca.

 

BACKGROUND: The human gut microbiota has been implicated in most aspects of

health and disease; however, most of the bacteria in this community are

considered unculturable, so studies have relied on molecular-based methods. These

methods generally do not permit the isolation of organisms, which is required to

fully explore the functional roles of bacteria for definitive association with

host phenotypes. Using a combination of culture and 16S rRNA gene sequencing,

referred to as culture-enriched molecular profiling, we show that the majority of

the bacteria identified by 16S sequencing of the human gut microbiota can be

cultured.

METHODS: Five fresh, anaerobic fecal samples were cultured using 33 media and

incubation of plates anaerobically and aerobically resulted in 66 culture

conditions for culture-enriched molecular profiling. The cultivable portion of

the fecal microbiota was determined by comparing the operational taxonomic units

(OTUs) recovered by 16S sequencing of the culture plates to OTUs from

culture-independent sequencing of the fecal sample. Targeted isolation of

Lachnospiraceae strains using conditions defined by culture-enriched molecular

profiling was carried out on two fresh stool samples.

RESULTS: We show that culture-enriched molecular profiling, utilizing 66 culture

conditions combined with 16S rRNA gene sequencing, allowed for the culturing of

an average of 95 % of the OTUs present at greater than 0.1 % abundance in fecal

samples. Uncultured OTUs were low abundance in stool. Importantly, comparing

culture-enrichment to culture-independent sequencing revealed that the majority

of OTUs were detected only by culture, highlighting the advantage of culture for

studying the diversity of the gut microbiota. Applying culture-enriched molecular

profiling to target Lachnospiraceae strains resulted in the recovery of 79

isolates, 12 of which are on the Human Microbiome Project's "Most Wanted" list.

CONCLUSIONS: We show that, through culture-enriched molecular profiling, the

majority of the bacteria in the human gut microbiota can be cultured and this

method revealed greater bacterial diversity compared to culture-independent

sequencing. Additionally, this method could be applied for the targeted recovery

of a specific bacterial group. This approach allows for the isolation of bacteria

of interest from the gut microbiota, providing new opportunities to explore

mechanisms of microbiota-host interactions and the diversity of the human

microbiota.

 

DOI: 10.1186/s13073-016-0327-7

PMCID: PMC4929786

PMID: 27363992  [PubMed - in process]

 

 

22. World J Gastroenterol. 2015 Jan 21;21(3):803-14. doi: 10.3748/wjg.v21.i3.803.

 

Application of metagenomics in the human gut microbiome.

 

Wang WL(1), Xu SY(1), Ren ZG(1), Tao L(1), Jiang JW(1), Zheng SS(1).

 

Author information:

(1)Wei-Lin Wang, Shao-Yan Xu, Zhi-Gang Ren, Liang Tao, Jian-Wen Jiang, Shu-Sen

Zheng, Department of Hepatobiliary and Pancreatic Surgery, First Affiliated

Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang

Province, China.

 

There are more than 1000 microbial species living in the complex human intestine.

The gut microbial community plays an important role in protecting the host

against pathogenic microbes, modulating immunity, regulating metabolic processes,

and is even regarded as an endocrine organ. However, traditional culture methods

are very limited for identifying microbes. With the application of molecular

biologic technology in the field of the intestinal microbiome, especially

metagenomic sequencing of the next-generation sequencing technology, progress has

been made in the study of the human intestinal microbiome. Metagenomics can be

used to study intestinal microbiome diversity and dysbiosis, as well as its

relationship to health and disease. Moreover, functional metagenomics can

identify novel functional genes, microbial pathways, antibiotic resistance genes,

functional dysbiosis of the intestinal microbiome, and determine interactions and

co-evolution between microbiota and host, though there are still some

limitations. Metatranscriptomics, metaproteomics and metabolomics represent

enormous complements to the understanding of the human gut microbiome. This

review aims to demonstrate that metagenomics can be a powerful tool in studying

the human gut microbiome with encouraging prospects. The limitations of

metagenomics to be overcome are also discussed. Metatranscriptomics,

metaproteomics and metabolomics in relation to the study of the human gut

microbiome are also briefly discussed.

 

DOI: 10.3748/wjg.v21.i3.803

PMCID: PMC4299332

PMID: 25624713  [PubMed - indexed for MEDLINE]

 

 

23. Environ Health Perspect. 2015 Jul;123(7):679-88. doi: 10.1289/ehp.1409055. Epub

2015 Mar 13.

 

Persistent Organic Pollutants Modify Gut Microbiota-Host Metabolic Homeostasis in

Mice Through Aryl Hydrocarbon Receptor Activation.

 

Zhang L(1), Nichols RG, Correll J, Murray IA, Tanaka N, Smith PB, Hubbard TD,

Sebastian A, Albert I, Hatzakis E, Gonzalez FJ, Perdew GH, Patterson AD.

 

Author information:

(1)Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary

and Biomedical Sciences, The Pennsylvania State University, University Park,

Pennsylvania, USA.

 

Comment in

    Environ Health Perspect. 2015 Jul;123(7):A187.

 

BACKGROUND: Alteration of the gut microbiota through diet and environmental

contaminants may disturb physiological homeostasis, leading to various diseases

including obesity and type 2 diabetes. Because most exposure to environmentally

persistent organic pollutants (POPs) occurs through the diet, the host

gastrointestinal tract and commensal gut microbiota are likely to be exposed to

POPs.

OBJECTIVES: We examined the effect of 2,3,7,8-tetrachlorodibenzofuran (TCDF), a

persistent environmental contaminant, on gut microbiota and host metabolism, and

we examined correlations between gut microbiota composition and signaling

pathways.

METHODS: Six-week-old male wild-type and Ahr-/- mice on the C57BL/6J background

were treated with 24 μg/kg TCDF in the diet for 5 days. We used 16S rRNA gene

sequencing, 1H nuclear magnetic resonance (NMR) metabolomics, targeted

ultra-performance liquid chromatography coupled with triplequadrupole mass

spectrometry, and biochemical assays to determine the microbiota compositions and

the physiological and metabolic effects of TCDF.

RESULTS: Dietary TCDF altered the gut microbiota by shifting the ratio of

Firmicutes to Bacteroidetes. TCDF-treated mouse cecal contents were enriched with

Butyrivibrio spp. but depleted in Oscillobacter spp. compared with

vehicle-treated mice. These changes in the gut microbiota were associated with

altered bile acid metabolism. Further, dietary TCDF inhibited the farnesoid X

receptor (FXR) signaling pathway, triggered significant inflammation and host

metabolic disorders as a result of activation of bacterial fermentation, and

altered hepatic lipogenesis, gluconeogenesis, and glycogenolysis in an

AHR-dependent manner.

CONCLUSION: These findings provide new insights into the biochemical consequences

of TCDF exposure involving the alteration of the gut microbiota, modulation of

nuclear receptor signaling, and disruption of host metabolism.

 

DOI: 10.1289/ehp.1409055

PMCID: PMC4492271

PMID: 25768209  [PubMed - indexed for MEDLINE]

 

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