{"id":35,"date":"2015-02-13T03:40:30","date_gmt":"2015-02-13T10:40:30","guid":{"rendered":"https:\/\/blogs.ubc.ca\/ryanyenn\/?p=35"},"modified":"2015-02-13T03:50:40","modified_gmt":"2015-02-13T10:50:40","slug":"final-project-outline","status":"publish","type":"post","link":"https:\/\/blogs.ubc.ca\/ryanyenn\/final-project\/final-project-outline\/","title":{"rendered":"Final Project Outline"},"content":{"rendered":"

TOPIC CHOSEN:<\/strong><\/h3>\n

Effects of Paternal Alcohol Consumption on Fetal Development<\/p>\n

SPECIFIC QUESTION:<\/strong><\/h3>\n

Are Stfmb2, Snrpn-Ube3a, Dlk-Dio3<\/em> differentially methylated in the sperm DNA of CD1 mice treated with ethanol compared to saline?<\/p>\n

HYPOTHESIS:<\/strong><\/h3>\n

Stfmb2, Snrpn-Ube3a, Dlk-Dio3 <\/em>are differentially methylated in the sperm DNA of CD1 mice treated with ethanol compared to saline.<\/p>\n

EVIDENCE ON WHICH THE HYPOTHESIS IS BASED (INCLUDE REFERENCES):<\/strong><\/h3>\n

It has been observed by Lee et al<\/em>.(2013) that preconception consumption of ethanol by male mice results in skull malformation. Knezovich & Ramsay (2012) found that transgenerational toxic effects are due to epigenetic mutations in sperm DNA caused by alcohol. Laufer et al<\/em>. (2013) found three imprinting control regions (ICRs), Sfmbt2<\/em>, Snrpn-Ube3a<\/em>, Dlk-Dio3<\/em>, that are differentially methylated when the fetus is exposed to alcohol. These three ICRs are related to the development of the brain (Laufer and Singh, 2012).<\/p>\n

PREDICTION(S):<\/strong><\/h3>\n

If these imprinting control regions are differentially methylated, then there would be a possibility that these epigenetic mutations will be passed on to the offspring. This may be a reason why Lee et al.<\/em> (2013) see skull malformations in the fetuses.<\/p>\n

EXPERIMENTAL APPROACH TO TEST PREDICTION (INCLUDE ANY DETAILS THAT YOU HAVE WORKED OUT SO FAR):<\/strong><\/h3>\n

Treat CD1 mice (postnatal day 49) with a 4 g\/kg EtOH with 0.9% saline oral administration once in the morning and once in the evening, for a 7 week period. Control mice would be fed a saline solution. (adapted from Lee et al<\/em>. 2013)<\/p>\n

Mature sperm from the experimental and control group is harvested and DNA is extracted. Using oxidative bisulfite sequencing (OxBS-seq), methylation in the three loci will be analysed. This method is able to distinguish between 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) (Booth et al.,\u00a0<\/em>2013)<\/em>. Knezovich and Ramsay (2012) used a method that could not differentiate between these two bases and proposed that this led to the observation of very little demethylation of the sperm DNA. Look for differential methylation (only 5-mC) in the 3 loci between the control group and the experimental group.<\/p>\n

LIST OF RELEVANT PRIMARY AND REVIEW ARTICLES READ, AND SUMMARY OF RELEVANT INFORMATION FROM EACH<\/strong> (this is the start of an annotated bibliography)<\/em>:<\/strong><\/h3>\n

Laufer et al<\/em>. 2013<\/span> \u2013 found three differentially methylated ICRs when the fetus were treated with alcohol that are related to development of the brain<\/p>\n

Laufer & Singh 2012<\/span> \u2013 more in depth review of Sfmbt2<\/em>, Snrpn-Ube3a<\/em>, and Dlk-Dio3<\/em><\/p>\n

Knezovich & Ramsay 2012<\/span> \u2013 found epigenetic mutations in sperm DNA, will be using an adapted experimental from this paper<\/p>\n

Lee et al<\/em>. 2013<\/span> \u2013 found skull malformations in mice fetuses when the fathers are fed alcohol<\/p>\n

Liu et al<\/em>. 2009<\/span> \u2013 found alcohol to changes the DNA methylation in mouse embryos during early development of neurons<\/p>\n

Booth\u00a0et al.<\/em> 2013<\/span> – paper about oxidative bisulfite sequencing<\/p>\n

HOW DOES THE QUESTION FIT INTO THE BROADER PICTURE, AND WHAT IS ITS IMPACT?<\/strong><\/h3>\n

If we can find a direct link in between how transgenetic toxic effects of alcohol are passed on to offsprings, such as epigenetic mutations in the sperm DNA, it will no longer be just a correlation and people will pay more attention to the consumption of alcohol if they are planning to have offsprings.<\/p>\n

POTENTIAL WAYS TO MAKE YOUR QUESTION KNOWN TO THE PUBLIC AT LARGE (OR TO YOUR NON-BIOLOGIST FAMILY AND FRIENDS):<\/strong><\/h3>\n

Blog posts, posters, word of mouth<\/p>\n

ANY OTHER PARTS OF THE PROJECT COMPLETED SO FAR:<\/strong><\/h3>\n

None yet! Sorry!<\/p>\n

ANYTHING YOU WOULD LIKE SPECIFIC FEEDBACK ON:<\/strong><\/h3>\n

Does the topic need to be more specific? Would “Effect of Paternal Alcohol Consumption on the Epigenome of Sperm” be better?<\/p>\n

Is the length of this experiment adequate? Should I include looking for differentially methylated at these 3 loci in genome of the fetus similar to Knezovich and Ramsay (2012) looked at in the offspring?<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

TOPIC CHOSEN: Effects of Paternal Alcohol Consumption on Fetal Development SPECIFIC QUESTION: Are Stfmb2, Snrpn-Ube3a, Dlk-Dio3 differentially methylated in the sperm DNA of CD1 mice treated with ethanol compared to saline? HYPOTHESIS: Stfmb2, Snrpn-Ube3a, Dlk-Dio3 are differentially methylated in the sperm DNA of CD1 mice treated with ethanol compared to saline. EVIDENCE ON WHICH THE […]<\/p>\n","protected":false},"author":28747,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[12778],"tags":[],"class_list":["post-35","post","type-post","status-publish","format-standard","hentry","category-final-project"],"_links":{"self":[{"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/posts\/35","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/users\/28747"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/comments?post=35"}],"version-history":[{"count":3,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/posts\/35\/revisions"}],"predecessor-version":[{"id":38,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/posts\/35\/revisions\/38"}],"wp:attachment":[{"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/media?parent=35"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/categories?post=35"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ryanyenn\/wp-json\/wp\/v2\/tags?post=35"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}