Category Archives: Stem Cells

Introducing Aba-seq for Enzyme Based High-Res Mapping of Mammalian Hydroxymethylomes

Posted on February 22, 2013 by Nicole Kelesoglu

New England Biolabs is well known for its extensive in house research programs – churning out numerous publications every year. The role of hydroxymethylation as a possible cancer biomarker is a topic of keen interest for all Epigenetics researchers. So, NEB researchers are especially enthused about their recent publication in Cell, along with their collaborators from Emory University School of Medicine. Sun, Z. et al. High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells. (2013) Cell Reports 3, 567-576. describes the Aba-seq method, an AbaSI enzyme based high-resolution hydroxymethylome mapping. (Open access.) In nature, AbaSI is a weapon in the arms race between bacteria and bacteriophages. Wildtype bacteriophages such as T4, are resistant to most restriction enzymes due … Continue reading →

Posted in Applications, Biomarkers, DNA Methylation, Enzymology, Genomewide Methylation Profiling, Hydroxymethylation, Methylation Sensitive Restriction Enzymes, New Lab Methods, Oncology, Stem Cells | Tagged , , , , , | Leave a comment

A Better Way to Discriminate iPSCs vs ESCs

Posted on October 17, 2012 by Nicole Kelesoglu

First of all, a hearty congratulations to Dr. Shinya Yamanaka and Dr. John Gurdon for winning this year’s Nobel prize for Medicine, for their discoveries that adult cells could be transformed back to embryonic-like states. Recently, Dr. Yamanaka has publicly warned of dangerous “stem cell therapies” currently offered in various countries, without any pre-clinical testing in animals. This was an important message considering possible tragedies, both for any patients desperate for a cure, who end up sick or dead…and for the public, who might lose their trust in potential future stem cell therapies developed safely under strict scientific methods. Induced pluripotent stem cells (iPSCs) can be transformed from somatic cells, through the expression of only four transcription factors, using Kyoto … Continue reading →

Posted in Cellular Biology, DNA Methylation, Reduced representation bisulfite sequencing, Regenerative Medicine, Stem Cells | Tagged , , , | Leave a comment

Dosage Makes All the Difference! Zahnow & Baylin Labs Show Epigenetic Reprogramming of Cancer

Posted on April 3, 2012 by Nicole Kelesoglu

Many of you are probably attending AACR this week. Cancer research into Epi-drugs is certainly a big theme. Along those lines, there is good news from the Cynthia Zahnow and Sephen Baylin teams at John Hopkins University in this paper, Hsing-Chen Tsai et al. Transient Low Doses of DNA-Demethylating Agents Exert Durable Antitumor Effets on Hematological and Epithelial Tumor Cells.(March 2012) Cancer Cell 21, 430–446 . I’ll highlight the best bits. Obviously, the paper is awesome, and you need to read the details! The authors explain one of the most “striking effects” they observed is their accumulated evidence that this low dosage epigenetic chemotherapy can broadly reprogram stem-like cancer cells in solid cancers. Now, the exact molecular mechanisms of these … Continue reading →

Posted in Biomarkers, DNA Methylation, Flow Cytometry, Genomewide Methylation Profiling, Leukemia, Methylated DNA Capture, Oncology, Pharmacology / Toxicology, Stem Cells, Translational Research | Tagged , , , , , , , | Leave a comment

The Clock that Ticks Methylations & the Epigenetics of Aging

Posted on February 28, 2012 by Chris Womack

To my mild shame, I watched a little of the Oscars the other night. We’re all familiar with many of these folks, but we don’t see them very often, so it’s especially striking as they age from svelte starlet to grand dame, or what have you. The stages seem to come in rapid succession. Ol’ Nick Nolte just turned 72! He was way more spry — but equally gruff — 30 years ago, in the 1982 hit 48 Hours. And how he’s changed since those hijinks of only 10 years ago. (See, it’s not always for the worse.) So what’s different about Nick Nolte’s epigenome now, versus when he played opposite wise-cracking trickster Eddie Murphy? Could you guess his age … Continue reading →

Posted in Biomarkers, DNA Methylation, Gene Regulation, Genomewide Methylation Profiling, Methyltransferases, Stem Cells, microRNA | Tagged , , , , , | Leave a comment

The Big Picture : 5-hmC Content is Differentiation Dependent in Adult Tissues

Posted on September 16, 2011 by Nicole Kelesoglu

They say beauty is in the eye of the beholder. For me, well done immunolocalization images demonstrate scientific artistry. Last week I was pleased to find this paper, Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers Oncotarget Sept. 2, 2011 (Haffner et al), posted on the Dr. Denise O’Keefe lab blog (E3 member). This research showed that fully differentiated adult tissues had the highest levels of 5-hmC, while stem cells had very low levels. There was uniform loss of 5hmC in cancer tissues, matched to normal adult tissues. Reductions in 5-hmC can occur independently of 5mC in solid tumors. Global loss of 5-hmC could be an early event of carcinogenesis. The work came … Continue reading →

Posted in DNA Methylation, Flow Cytometry, Imaging, Immunofluorescence, Immunohistochemistry, Methyl-specific Antibodies, New Lab Methods, Oncology, Pathology, Stem Cells | Tagged , | Leave a comment

Regenerative Medicine: Using Adult Stem Cells to Regenerate Human Organs

Posted on June 24, 2011 by Nicole Kelesoglu

Recently, I visited the Chihuly glass art exhibit at the Boston Museum of Fine Arts. Seeing Dale Chihuly’s work for the first time, is like the first time you see the Grand Canyon. It’s breathtaking!  You have to see one of his towers in person, made up of hundreds of boldly colored glass spikes, to fully appreciate them. Interestingly, the tower I saw was reassembled for the new exhibit location, without instructions for identical structure. Each glass spike is NOT numbered for placement. Rather, the assemblers work to approximate the intended shape, gaging the spikes for size, color and direction, ultimately creating the intended overall pattern, albeit uniquely expressed. The process reminded me a bit of how stem cells can … Continue reading →

Posted in Animal Models, Cell Culture Models, Cellular Biology, Immunology, Stem Cells | Tagged , , | Leave a comment

Epigenetics, Eh! to Promote Canadian Collaboration

Posted on April 30, 2011 by Nicole Kelesoglu

Late registration is still available online for Epigenetics Eh!, the Canadian Conference on Epigenetics, which is taking place in London, Ontario from May 4 to May 7th, 2011. Part of the stated mission for this conference is to promote a Canadian Epigenetics Research Network (EPIGENETICS CANADA). The epigenetic research areas of the speakers for this conference include, but are not limited to the following. Diabetes Early detection of cancer Leukemia Pluripotency in ES cells Proteomics to study protein import into the nucleus Genomic CNV and epigenetic changes in Neurobehavioral disorders Chromatin factors in brain development Molecular mechanisms underlying cell fate specification, proliferation, and differentiation of neural stem cells Genomic imprinting X chromosome inactivation Dicer expression and/or microRNA function. ING family … Continue reading →

Posted in Applications, Bioinformatics, Biomarkers, Cellular Biology, Chromatin Structure, DNA Methylation, Developmental Biology, Divergent Transcription, Evolutionary Epigenetics, Gene Regulation, Gene Silencing, Genetics, Hematology, Histone Modifications, Leukemia, Neuroscience, Non-coding RNA, Plant Epigenetics, Reproductive Biology, Stem Cells, Translational Research, chIP, siRNA | 2 Comments