tag:blogger.com,1999:blog-61882409856967173582024-03-05T14:56:10.531-08:00Yale Molecular Anthropology LabA collection of links (vaguely) relevant to molecular anthropology, primatology, and bioanth in general. Feel free to post any bits and bobs of potential interest or amusement.Brendahttp://www.blogger.com/profile/12553243724827755891noreply@blogger.comBlogger625125tag:blogger.com,1999:blog-6188240985696717358.post-30858928437324109662014-07-01T10:09:00.000-07:002014-07-01T10:12:02.869-07:00A Gutsy Step Forward for Diabetes<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYXVWTF42-IMnU71UwrPSV0HOWhj21lUsCxtBiAyhMzFQGYWyrFoDcnPmjQ2oXu7Ko03gk1GE4zyAYkvQfT7qn27TgWFnmr2W6Q4a2BCYhc-FNp9K3ZuNFyJG11fHWbrg45wi2njSvxFyX/s1600/intestines+diabetes.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYXVWTF42-IMnU71UwrPSV0HOWhj21lUsCxtBiAyhMzFQGYWyrFoDcnPmjQ2oXu7Ko03gk1GE4zyAYkvQfT7qn27TgWFnmr2W6Q4a2BCYhc-FNp9K3ZuNFyJG11fHWbrg45wi2njSvxFyX/s320/intestines+diabetes.jpg" /></a><br>
Researchers at Columbia University’s Berrie Diabetes center may have found a way to treat people with type 1 diabetes using gastrointestinal (GI) cells. Dr. Accli’s lab has recently replicated a study previously conducted that used diabetic mice treated with genetically engineered GI cells. The study showed by turning off only a single gene, FOX01, GI cells became insulin-producing cells that could almost normalize a diabetic mouse’s glucose levels. The experiment proved successful with humans as well. By turning off FOX01, GI cells proved to be a more feasible option than insulin-producing cells created from embryonic and adult stem cells. This is due to the fact that the converted cells were able to release insulin only as a response to glucose levels. Dr. Accli is hopeful for a drug that can be used to inhibit FOX01 in GI cells to treat diabetics.
<a href="http://www.eurekalert.org/pub_releases/2014-06/cumc-imt062614.php">Article</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-26212788702801208362014-06-26T14:19:00.004-07:002014-06-26T14:19:59.933-07:00Turtle Draft-Genomes Yield Insight into Their Body Development and Evolution<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-m1vwHJ25RVc/U6yNeFPBmGI/AAAAAAAAAAM/hT_uwY4ctuY/s1600/turtle+anatomy.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-m1vwHJ25RVc/U6yNeFPBmGI/AAAAAAAAAAM/hT_uwY4ctuY/s1600/turtle+anatomy.png" height="176" width="400" /></a></div>
<span id="docs-internal-guid-3e59de64-da07-7b96-500c-96b028ff016b"><span style="background-color: white; color: #333333; font-family: Arial; font-size: 15px; vertical-align: baseline; white-space: pre-wrap;">The first genome wide phylogenetic analysis of </span></span><span style="background-color: white; color: #333333; font-family: Arial; font-size: 15px; white-space: pre-wrap;">two turtle species tackles the questions about the origin of the turtle’s unique anatomical features. Turtles have a unique exterior shell and skeletal layout that differs from that of their fellow tetrapods. Their carapace is a transformed vertebrae and ribs, their shoulder blades are ventral rather than dorsal, and their skulls lack temporal fenestra. These characteristics led to an analysis of their genome that found that turtles are closely related to Archosauria and that their morphological evolution was the cause of alterations in their signaling cascade. Investigations into their embryonic gene regulation led to the belief that they are morphologically similar to chickens, but have an hourglass-like divergence that shows where exactly (vertebrate phylotypic period) the structure of the shell begins to form. </span><br />
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<span><span style="background-color: white; color: #333333; font-family: Arial; font-size: 15px; vertical-align: baseline; white-space: pre-wrap;"><a href="http://www.nature.com/ng/journal/v45/n6/full/ng.2615.html">Article</a></span></span>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-81999859470422945942014-06-26T07:48:00.000-07:002014-06-26T07:48:05.331-07:00Research team unravels genetic mechanism underlying common SNP associated with blond hair in Europeans.<a href="http://www.nature.com/ng/journal/v46/n7/full/ng.2991.html">Guenther et al. publish in this week's Nature Genetics on their research</a> demonstrating that a single nucleotide substitution in a transcription factor binding site upstream of the <i>KITLG</i> gene decreases the binding of the LEF1 transcription factor, thereby decreasing expression of the gene by ~20% and contributing to lightened pigmentation of the hair. Many genome wide association studies reveal associations between SNPs and phenotype, but discovering the exact genetic basis of these correlations remains challenging. This study provides a great example of painstaking effort by the research team to identify the causal SNP in a blond-associated haplotype and the necessary experimental validation of its functional impact in human cell lines and transgenic mice. Although this is an impressive achievement, <a href="http://www.nature.com/ng/journal/v46/n7/full/ng.3019.html?WT.ec_id=NG-201407">as Hopi Hoekstra writes in a comment piece</a>, it also demonstrates the challenges facing researchers in identifying and characterizing the impact of cis-reulgatory changes.<br />
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Also particularly notable about this paper is its citation <a href="http://www.ncbi.nlm.nih.gov/pubmed/22917817?dopt=Abstract&holding=npg">of the work</a> of YMAL lab member, Susan Walsh!Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-8280929357499534392014-06-25T13:26:00.001-07:002014-06-25T13:26:27.653-07:00New Data Further Complicates Human Origins<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-IDhdr8Mhk2s/U6saFf4ouBI/AAAAAAAAAAM/TduKlzcgKaU/s1600/20140621_STP001.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-IDhdr8Mhk2s/U6saFf4ouBI/AAAAAAAAAAM/TduKlzcgKaU/s1600/20140621_STP001.jpg" height="180" width="320" /></a></div>
Mitochondrial (mtRNA) testing of 17 individuals from the <i>Sima de los Huesos</i>, or “Bone Pit” archaeological site has further complicated the current understanding of human evolution. Previously, the site in Burgos, Spain has yielded 6,500 pieces of human skeletons, representing at least 28 individuals. These were classified as <i>Homo heidelbergensis</i>, the name given to the first humans who lived in Europe starting about 600,000 years ago. However, mitochondrial DNA testing found that these individuals had more similarities with another group of proto-humans, the Denisovans. The Denisovans and <i>heidelbergensis</i> were thought to have evolved distinct mtDNA prior to migration. Thus finding Denisovan mtRNA in Spain is contradictory, as they were only found in Asia. In the words of the article, these new findings only prove that "building a coherent story out of [human evolution] is a long-winded business.”<div>
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<a href="http://www.economist.com/news/science-and-technology/21604527-another-piece-frustrating-jigsaw-humanitys-fossil-history-probing" style="font-family: Baskerville; font-style: italic;">Article Link</a></div>
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Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-55652271638046816722014-06-16T18:51:00.003-07:002014-06-16T18:55:08.821-07:00Genetic Diversity In Mexico<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-w0sPieJ_YMQ/U5-f7l6JyaI/AAAAAAAAAAM/D4BoG1RdUWY/s1600/Screen+Shot+2014-06-16+at+9.11.00+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-w0sPieJ_YMQ/U5-f7l6JyaI/AAAAAAAAAAM/D4BoG1RdUWY/s1600/Screen+Shot+2014-06-16+at+9.11.00+PM.png" height="245" width="320" /></a></div>
Researchers have shown that there is substantial genetic variation between ethnic groups in Mexico. Generations of geographic separation have fostered differences between populations, and the data have allowed the authors to come to interesting and medically relevant conclusions. First, the variation has made it possible to genetically map historical movements between the populations. Mexican history has, for many Mexican residents, generated a medley of ancestry including indigenous, European and African descent. Second, understanding this variation and its sources allows doctors to know genetic risks for the relevant populations. For example, the researchers identified a gene variant that affects lung function, and there are direct diagnostic implications.<br />
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Links:<br />
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<a href="http://news.sciencemag.org/biology/2014/06/people-mexico-show-stunning-amount-genetic-diversity">Article</a><br />
<a href="http://www.sciencemag.org/content/344/6189/1280.abstract?sid=f39719cb-3ec0-49f6-9df9-34e34d09a2ec">Abstract</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-1497203646745422022014-06-12T19:12:00.001-07:002014-06-16T07:13:14.088-07:00 Genome Sequencing Beats Cancer<div>
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<a href="http://graphics8.nytimes.com/images/2012/06/10/science/video-cancer/video-cancer-articleLarge.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://graphics8.nytimes.com/images/2012/06/10/science/video-cancer/video-cancer-articleLarge.jpg" height="180" width="320" /></a></div>
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The time and costs of genome sequencing are getting smaller every year. Within 5 to 10 years, cancer treatments tailored to individuals may be commonplace.<br />
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Dr. Lukas Wartman, a leukemia doctor, was diagnosed in 2003 with Acute Lymphoblastic Lymphoma. After his second relapse in 2011, the future seemed grim. As a last resort, his colleagues at Washington University in St. Louis decided to sequence his entire genome, exome, and RNA sequence. The university was able to pool its resources, and it took only a few weeks to extract and analysis his genetic information. After determining through RNA analysis that his FLT3 gene was over-expressed in cancer cells, his doctors prescribed Sutent, a drug made by Pfizer. Two weeks after taking this drug, Dr. Wartman's bone marrow biopsy and flow cytometry came back clean. Dr. Wartman then underwent another bone marrow transplant. As of September 2013, the cancer has not returned.<br />
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<a href="http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?_r=2&pagewanted=all&">http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?_r=2&pagewanted=all&</a><br />
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<a href="http://genome.wustl.edu/articles/detail/doctor-survives-cancer-he-studies/">http://genome.wustl.edu/articles/detail/doctor-survives-cancer-he-studies/</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-41239007916848065712014-06-09T13:28:00.004-07:002014-06-09T13:30:41.781-07:00Blind mole rat genome sequenced<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnRHqpi-BpsXhGEqveCV0jyJsWjAcL3v752cEQRucOgDwUH2NYKllASVrwgw5Yg7HQ_7aosdmUeUInQ7vznGuEVoNm456JwI9j9413NrhiY0nN0Skom4Een-_BKZ-cgWAgTxPMnAu0j30/s1600/img-thing.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgnRHqpi-BpsXhGEqveCV0jyJsWjAcL3v752cEQRucOgDwUH2NYKllASVrwgw5Yg7HQ_7aosdmUeUInQ7vznGuEVoNm456JwI9j9413NrhiY0nN0Skom4Een-_BKZ-cgWAgTxPMnAu0j30/s1600/img-thing.jpeg" height="200" width="200" /></a></div>
A new <a href="http://www.nature.com/ncomms/2014/140603/ncomms4966/full/ncomms4966.html" target="_blank">Nature Communications</a> paper examines the comparative genomics of the blind mole rat. Blind mole rats show unusual resistance to cancer, and this study identified some specific protein changes (at gene p53) that might underlie this medically-relevant trait. Even more interesting -- the study found genomic signatures of adaptations to living underground. For example, changes to circadian rhythm genes (<i>CLOCK</i>) show interesting patterns of convergent evolution with the distantly-related naked mole rat.B.Bradleyhttp://www.blogger.com/profile/18440131304537532317noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-39439686118049176482014-06-04T15:52:00.001-07:002014-06-12T05:47:13.469-07:00Toiletries to aid your microbiome!From the New York Times Magazine: <a href="http://www.nytimes.com/2014/05/25/magazine/my-no-soap-no-shampoo-bacteria-rich-hygiene-experiment.html" target="_blank">"My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment"</a><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrao49SqToM3MpLunBHM0OX9HysO5KqkL2c0jYqf1mSWrlhQXUdlAcCv_8bwvl5WgJxIbT-XgmDFXpx29vRui0zwppbOd60t7WK5o6SYbOw7JWYrgGRz9OOBRUw-s_WgclLZYW7ByTZWU/s1600/mag-25Bacteria-t_CA0-master675.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrao49SqToM3MpLunBHM0OX9HysO5KqkL2c0jYqf1mSWrlhQXUdlAcCv_8bwvl5WgJxIbT-XgmDFXpx29vRui0zwppbOd60t7WK5o6SYbOw7JWYrgGRz9OOBRUw-s_WgclLZYW7ByTZWU/s1600/mag-25Bacteria-t_CA0-master675.jpg" height="213" width="320" /></a></div>
The thousands of bacterial species that make up our microbiome provide a "second genome" with an important role in maintaining and promoting human health. Soaps that kill bacteria on our skin might in fact be more damaging than hygienic. Arguing that adding specific microbes can promote hygiene and treat skin ailments, a new start-up company, AOBiome, is marketing a body spray (<a href="https://www.aobiome.com/bacteria-new-black" target="_blank">AO+ <span style="background-color: white; color: #333333; font-family: georgia, 'times new roman', times, serif; font-size: 16px; line-height: 23px;">Refreshing Cosmetic Mist</span></a>) with ammonia-oxidizing bacteria. Journalist Julia Scott tried it for a month... and seems unconvinced. B.Bradleyhttp://www.blogger.com/profile/18440131304537532317noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-33897384105721314132014-04-16T11:40:00.001-07:002014-04-16T11:40:20.703-07:00Aotus monogamyObservations suggest that Azara's Owl Monkey is monogamous, which is rare in the animal kingdom. they are the first primate to be documented as being monogamous. <br />
**Note: I saw this blurb in the NY Times Science Times a few weeks back and forgot to post it--sorry for the delay! The NY times blurb and the original paper are linked here:<br />
<a href="http://www.nytimes.com/2014/03/25/science/no-monkeying-around-for-these-partners.html?_r=0">http://www.nytimes.com/2014/03/25/science/no-monkeying-around-for-these-partners.html?_r=0</a><br />
<a href="http://rspb.royalsocietypublishing.org/content/281/1782/20140195">http://rspb.royalsocietypublishing.org/content/281/1782/20140195</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-12183056164998203202014-04-15T08:33:00.001-07:002014-04-15T08:33:17.321-07:00Correlated evolution of sensory structures and sensory genes in mammalsAn <a href="http://rspb.royalsocietypublishing.org/content/281/1783/20132828.short">article by Garrett & Steiper</a> just published in Proceedings of the Royal Society B looked at anatomical correlates of main olfactory system (ethmoid) and vemoronasal system (vemoronasal organ, VNO) across mammals as well as the size of the related gene families (<i>OR, </i><i>V1R, </i>and <i>V2R</i>)<i> </i>in mammalian genomes. They found that absolute ethmoid area is correlated with the proportion of functional <i>OR</i>s and that the relative size and complexity of the VNO is correlated with proportion of functional <i>V1R </i>genes in mammalian genomes. These results show nice concordance between anatomical and molecular evolution and may indicate a role for natural selection in the evolution of these genes families.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-31614174294375894222014-04-14T06:58:00.001-07:002014-04-14T06:58:25.319-07:00Genome wide association of methylation with BMI A recent issue of The Lancet featured an epigenome wide association <a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)62674-4/abstract">study</a> (EWAS) of methylated CpGs associated with BMI. Sites were identified in an initial cohort of 479 Europeans and, after filtering data for false positives, inspected in a replication cohort of 339 people. Sites still significant were tested in a larger second replication cohort of 1789 individuals. Five sites were identified as significantly associated with BMI, three of which fall within the first intron of the gene <i>HIF3A, </i>which encodes a subunit of the Hypoxia Inducible Transcription Factor (HIF)<i>. </i>Chromatin state at this intron indicates regulatory activity. For all these cases, increasing methylation is linearly correlated with increasing BMI. Notably, the association is tissue specific, manifesting in blood and adipose tissues, but not skin.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-40602876604366343842014-04-13T18:44:00.005-07:002014-04-13T18:44:46.738-07:00Alu elements found to function similarly to enhancers<div dir="ltr" style="text-align: left;" trbidi="on">
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In a recent issue of <i style="mso-bidi-font-style: normal;">Cell</i>
authors <a href="http://www.cell.com/cell-reports/abstract/S2211-1247%2814%2900189-2">Su <i style="mso-bidi-font-style: normal;">et al.</i></a> carried out
genome-wide analyses of genomic distribution, evolutionary conservation,
histone positioning and epigenetic profiles to examine the characteristics of
Alu elements. They found that Alu elements in multiple tissues and cell-lines
resemble those of putative transcription enhancers. They also find that Alus
show long-range interactions with gene promoters, and their similarity to
enhancers becomes more prominent with their age in the human genome. The authors
conclude that some Alu elements can function as enhancers, and, further, that
many more Alus may be proto-enhancers that serve as a repertoire for the de
novo birth of enhancers.<o:p></o:p></div>
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-89783760355875960152014-04-13T18:16:00.001-07:002014-04-13T18:23:39.905-07:00A critical period discovered in development of the olfactory bulb<div dir="ltr" style="text-align: left;" trbidi="on">
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Authors <a href="http://www.sciencemag.org/content/344/6180/197.abstract">Tsai and Barnea</a> report in the most recent issue of <i style="mso-bidi-font-style: normal;">Science</i> that a critical period exists during which an olfactory “sensory map” becomes established. Previous findings
show that the olfactory system exhibits enhanced plasticity that is maintained
throughout life due to continuous neurogenesis of sensory neurons in the nose
and olfactory bulb. However, the authors found evidence in mice that there is
less plasticity than originally thought and that a sensory map is created
during a developmental critical period. Specifically, the authors were able to
test the neural pathways of transgenic mice, finding that perinatal expression
of the transgenic odorant receptor (i.e. before the sensory map is established)
led to activation of new axons. In contrast, expression of the transgenic
receptor after the sensory map was established did not activate new axons.<o:p></o:p></div>
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-30478976938663245432014-04-06T16:49:00.000-07:002014-04-06T16:50:04.664-07:00A review of methods for DNA methylation analysis<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="http://www.nature.com/nrg/journal/v11/n3/abs/nrg2732.html">Peter Laird</a>, in a 2010 issue of <i style="mso-bidi-font-style: normal;">Nat. Rev. Genet.</i>, reviews the technology of genome-wide DNA
methylation analysis. The review gives the pros and cons of each methodology,
as well as the principle behind the analyses. Additionally, he provides information
on statistical issues and a list of bioinformatics resources for DNA
methylation analysis.<o:p></o:p></div>
</div>
Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-38739513559419418602014-04-06T16:31:00.003-07:002014-04-06T16:31:37.376-07:00Positive selection of hair, skin and eye pigmentation in Europeans over the last 5000 years<div dir="ltr" style="text-align: left;" trbidi="on">
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In the current issue of <i style="mso-bidi-font-style: normal;">PNAS</i>
<a href="http://www.pnas.org/content/111/13/4832.full">Wilde et al.</a> find evidence for positive selection of skin, hair and eye
pigmentation in Europeans during the last 5000 years. They looked at selection acting
on three polymorphic sites that been previously identified in GWAS and
fine-mapping SNP association as related to pigmentation in Europeans. They used
ancient DNA and computer simulations to estimate the strength of selection on
these genes. Their results and analyses indicate that positive selection on
pigmentation variants associated with depigmented hair, skin and eyes has been
operating within western Eurasia for the past 5000 years. The authors propose two hypotheses for the selection on hair and eye color, in particular. They hypothesize that changes in hair and eye pigment may be byproducts of a
selection on skin pigment, or they propose that selection for depigmented eyes and hair may be driven by mate preference.<o:p></o:p></div>
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-57615718817581321672014-04-05T23:34:00.001-07:002014-04-05T23:34:10.897-07:00An In-depth look at gene expression in the developing brainMiller et al. published a <u><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13185.html?WT.ec_id=NATURE-20140403">paper</a></u> in this week's Nature describing the group's study of gene expression in the brain across tissue types during gestational weeks 15-21. RNAs were analyzed from over 300 anatomical regions and in situ hybridization was used to localize expression of elements of interest. Several genes show differential patterns of expression in humans compared with the mouse. Genes nearby human-accelerated noncoding regions show high differential expression among different regions of the neocortex. Notably, <i>FOXP2 </i>expression is enriched in putative language areas. More about the paper's many analyses and findings can be heard on the Nature <a href="http://www.nature.com/nature/podcast/">podcast.</a>Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-46187575237768577382014-03-31T10:00:00.000-07:002014-03-31T10:00:05.691-07:00Multigenerational Effects of Stress in a Rat ModelA recent p<a href="http://www.sciencedirect.com/science/article/pii/S0018506X14000464#">aper</a> in Hormones and Behavior describes a rat model of social stress and its intergenerational effects. The study investigated the effects of stress (exposure to intruding males) on lactating rat mothers on their offspring and offspring's offspring. These stressed mothers groomed and fed their infants less often, and were more aggressive. Upon reaching adulthood and breeding, offspring females (F1) showed a deficit in maternal care, as well as decreased oxytocin, vasopressin, and prolactin gene expression. Their own offspring (F2) demonstrated decreased social activity as juveniles and adults, as well as depressed plasma corticosterone.The authors propose that this system offers a useful model for human anxiety and depression.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-19464901661663577402014-03-30T16:15:00.001-07:002014-03-30T16:18:23.955-07:00Crosstalk between genetic and epigenetic regulation in a model of stem cell regeneration<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="http://www.pnas.org/content/111/10/E880.full.pdf+html?sid=fca8c957-508b-484a-b5fa-83c065d4a0df">An article</a> from <i style="mso-bidi-font-style: normal;">PNAS</i>
earlier this year examines how adult stem cells regulate differentiation,
proliferation and apoptosis through crosstalk between genetic and epigenetic
regulation. <span style="mso-spacerun: yes;"> </span>These three processes are
important in organs and tissues to maintain cell populations that undergo
stochastic fluctuations and genetic mutations over the course of a lifetime.
The authors take a mathematical approach, without considering molecular details,
to show how control strategies of these three processes during cell division
may be chosen to maximize expected performance. Their model incorporates the
performance functions of stem cells at two time scales: the time of one cell
cycle and the lifetime of the tissue. Their model includes a feedback
regulation that controls proliferation through both the cell population and
heterogenous dependence on the epigenetic states, which is different than the
typical feedback model that only depends on the size of the cell population.
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on apoptosis at each cell cycle. The authors suggest that this apoptosis maximizes the efficiency of stem
cell regulation and demonstrates the cross-talk between DNA variants and
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-1373434370734428072014-03-30T15:49:00.002-07:002014-04-06T07:22:23.860-07:00A review of breast cancer genetics and personalized cancer care<div dir="ltr" style="text-align: left;" trbidi="on">
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The most recent issue of <i style="mso-bidi-font-style: normal;">Science</i>
was partly dedicated to articles on breast cancer research. <a href="http://www.sciencemag.org/content/343/6178/1466.full.pdf">One article</a> by
authors Couch, Nathanson & Offit reviewed how genetic testing in breast
cancer has developed over the past twenty years. They discuss the clinical advancements
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biomarkers, as well as targeted therapy for breast cancers over-expressing the
HER2/neu receptor. The evolution of clinical treatment for breast cancer is an
example of how genetic testing is a burgeoning field and will allow for more
personalized care in the future. <o:p></o:p></div>
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-285630445967647992014-03-30T09:37:00.002-07:002014-03-30T09:37:58.113-07:00FANTOM project announces mammalian transcriptional "atlas"In a recent <a href="http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html">Nature article</a>, the FANTOM (Functional Annotation of the Mammalian Genome) project announced the release of data from a large effort to produce an "atlas" of promotors across cell types in human and mouse. The group performed cap analysis of gene expression (CAGE) via single molecule sequencing across 573 normal human and 128 normal mouse cell samples, as well as human cancer cell lines, human post-mortem cells, and mouse cell types at various developmental stages. This sequencing approach results in sequences of full cDNAs for transcribed mRNAs within cells, including the 5' transcription start site, allowing for the comparison of transcription start sites (TSS) across cell types. The study strongly indicates that gene expression and promotor function is highly cell-type specific, with only 6% of identified genes' expression patterns characterized as "housekeeping," defined as expressed within a 10-fold range in >50% of cell types. This ubiquitously- and uniformly-expressed gene set was enriched for genes involved in RNA processing. Comparison with mouse TSS suggests differing evolutionary patterns for cell-specific v. broadly functioning TSS, with more restricted TSS showing more evolutionary change.<br />
<br />
A <a href="http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html">companion paper</a> published in the same issue looks at enhancer activity across cell types. Data from the project is available <a href="http://fantom.gsc.riken.jp/5/">online</a>.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-27518569911962695922014-03-29T12:11:00.004-07:002014-03-29T12:11:57.476-07:0040th Anniversary Issue of CellThis <a href="http://www.sciencedirect.com/science/journal/00928674/157/1">week's issue of Cell</a> celebrates the journal's 40th birthday with a series of insight reviews. These reviews cover a range of great topics on the cutting edge of biology including <a href="http://www.sciencedirect.com/science/article/pii/S0092867414003389">non-coding RNA</a>, <a href="http://www.sciencedirect.com/science/article/pii/S0092867414002864">epigenetic inheritance</a>, <a href="http://www.sciencedirect.com/science/article/pii/S0092867414003456">microbiomes and the immune system</a>, <a href="http://www.sciencedirect.com/science/article/pii/S009286741301605X">human molecular evolution</a>, and many, many more. Check them out!Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-32127796385732422712014-03-28T10:11:00.001-07:002014-03-28T10:11:28.291-07:00Medieval Biological Time CapsulesAn analysis of ancient human dental calculus from medieval skeletons published in <a href="http://www.nature.com/ng/journal/v46/n4/full/ng.2906.html">Nature Genetics</a> allowed a taxonomic survey of dental microbes, as well as dietary components. Notably, the study identified "antibiotic resistance genes" within these dental microbiomes, providing additional evidence for the antiquity of such genes. You can also read a <a href="http://www.nature.com/ng/journal/v46/n4/full/ng.2930.html?WT.ec_id=NG-201404">news piece</a> on the research.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-6093587082144058352014-03-23T18:30:00.000-07:002014-03-23T18:31:42.714-07:00The epigenetic basis of complex traits in plants<div dir="ltr" style="text-align: left;" trbidi="on">
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In the March 7<sup>th</sup> issue of <i style="mso-bidi-font-style: normal;">Science</i> <a href="http://www.sciencemag.org/content/343/6175/1145.full">Cortijo et al.</a> are able to quantify the impact of heritable
epigenetic variation on traits in the model plant <i style="mso-bidi-font-style: normal;">Arabidopsis</i>. They used inbred plant lines that share identical DNA, yet have differentially methylated regions (DMRs). They showed that DMRs can be stably
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root length. The detected epigenetic QTL have all the necessary phenotypic
properties to become targets of natural or artificial selection. The authors
suggest their findings are a component of the so-called “missing heritability.”<o:p></o:p></div>
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-15784588689996102202014-03-23T17:51:00.002-07:002014-03-23T17:55:22.681-07:00New finding that humans can detect over 1 trillion different olfactory stimuli<div dir="ltr" style="text-align: left;" trbidi="on">
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In the current issue of <i style="mso-bidi-font-style: normal;">Science</i>
<a href="http://www.sciencemag.org/content/343/6177/1370.full">Bushdid et al.</a> find that humans are able to discriminate at least 1 trillion
olfactory stimuli. This finding far exceeds the previous estimates that humans can
detect only 10,000 different odors. The authors used combinations of 128
odorous molecules to determine how many unique stimuli exist. They performed
tests with human subjects to determine the discriminability of mixtures that
varied in the percentage of odor components and from there applied a
theoretical framework to determine the number of unique olfactory stimuli. They
found a large discrepancy between the abilities of subjects to discriminate
different mixtures, and they believe their estimate of 1 trillion
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Anonymoushttp://www.blogger.com/profile/12109438552025065623noreply@blogger.com0tag:blogger.com,1999:blog-6188240985696717358.post-9167990314990683602014-03-05T11:46:00.001-08:002014-03-05T11:46:19.842-08:00Craig Venter launches Human Longevity, Inc. to combat age-related diseasesYesterday, March 4th, Craig Venter and entrepreneur colleagues announced the launch of their new company, Human Longevity, Inc. (HLI). The company plans to sequence massive numbers of full human genomes, as well as the DNA of human-associated microbes and pathogens, to discover the bases of aging and degenerative diseases. HLI's goal is to sequence 40,000 human genomes in the first year and the first disease to be targeted is cancer. This announcement was featured in many popular new sources, including <a href="http://www.nytimes.com/2014/03/05/business/in-pursuit-of-longevity-a-plan-to-harness-dna-sequencing.html?_r=0">The New York Times. </a>Unknownnoreply@blogger.com0