Epigenetics found in Single-Cell Archaea, not just Eukaryotes

By Maria Groussis

In a study by the University of Nebraska-Lincoln, epigenetics was found in single-celled archaea, meaning that they are not only present in eukaryotes as previously thought. Evidence of epigenetics was found in Sulfolobus solfataricus, a sulfur-eating species that live in the boiling, acidic springs of Yellowstone National Park. Through previous studies where they increased levels of acidity through the years, scientist developed three independent and genetically different strains. These super acid-resistant derived strains were named Crenarchaeota (SARC) and they showed a resistance 178 times greater than that of their Yellowstone ancestors. This heritable acid-resistance trait was believed to be resulted from a mutation, but this later was proven to be a false assumption. By sequencing the genomes of the three strains of SARC (SARC-C, SARC-O, and SARC-I) and comparing it to the parental genome the mutations were found. SARC-C had 5 mutations and SARC-O had 29, while SARC-I had none. This implies SARC-I must have a different non-mutation mechanism. The scientists then disrupted proteins that are thought to control the expression of resistant-relevant genes and left no change in the DNA. This immediately stopped the resistance in future generations. Therefore, it can be concluded that SARC-I has an epigenetic-like mechanism.

This new evidence of Archaea having epigenetics indicates that it is not as relatively ‘new’ thing to the Earth. It also raises the question whether the shared common ancestor of Archaea and Eukaryotes had this mechanism, or did each evolve epigenetics independently through coevolution. This also raises the question if epigenetics is the reason why no known archaea cause disease or are antibiotic like bacteria. This finding could accelerate the study of epigenetics in Humans. The differentiation of eukaryotic cells and the occurrences of cancer makes it difficult to study in eukaryotes, but the simplicity of archaea and the structural similarity to eukaryotes make it easier to study. Using archaea to study epigenetics is also faster and cheaper. This may finally help scientists determine how to reverse epigenetics and learn how to switch it on and off.

https://www.eurekalert.org/pub_releases/2018-12/uon-nit113018.php

https://news.unl.edu/newsrooms/today/article/not-in-the-dna-evolution-sans-mutation-discovered-in-single-celled-archaea/

http://www.pnas.org/content/115/48/12271.full

According to an article titled "Coffee or Tea? The Answer Might Be In Your Genes" written by Nicola Davis, a genetic predisposition to perceiving the bitterness of particular substances is key in our selection of beverages. This study involves two sets of data. The first study shows that particular genetic variants are linked to the strength of perception of different tastes: one specific variant was associated with slightly higher ratings of bitterness for caffeine and another to great bitterness for quinine and a third to greater bitterness for a drug known as propylthiouracil, or prop. The team found people with a greater genetic predisposition to perceiving the bitterness of caffeine drank a little more coffee but an increase perception of the bitterness of quinine and prop were linked to a small reduction in coffee drinking. The team also found that greater perception of the bitterness of prop was linked to a lower chance of being a heavy drinker of alcohol. Their findings also lead to the conclusion that people who prefer to drink tea, drink it as it contains a lower concentration of bitter substances meaning that it might prove more acceptable than coffee to those with a heightened perception of bitterness. It has also been reported that the preference towards tea can be seen as a consequence of abstaining from coffee because our genes might have made coffee a little bitter for our palates to handle.

Nana Evison

First Genome-Wide Significant Loci Associated with ADHD Identified

this article published by the Guardian on Monday the 26th states that a major breakthrough has been made in regards to the genetic variants that increase the risk of ADHD. The original study The study the first genome-wide significant risk loci and indicates an important role for common variants in the polygenic architecture of ADHD. Future work is going to be needed to find the strong source of association in each loci, but this is a breakthrough nonetheless. In the past it was hard to really pinpoint any source of ADHD because many of the genes thought to be involved increased the risk by a small degree. This is the first time that genome wide significant loci associated with ADHD has been identified. Some of the revelations of the study were already predicted such as the association with ADHD and other neurological conditions such as insomnia to schizophrenia. So in a GWAS meta-analysis of over 55,000 individuals over 12 study cohorts they were able to identify 12 locus that could be deemed significant risk loci. The results of this study not only hope to shed light on the biological factors associated with ADHD and hopefully be able to develop new drugs for ADHD (which is largely trial and error) and to encourage a dimensional view of ADHD and some argue that this could help destigmatize it too.



Seeran Enayet

Did humans domesticate themselves?

This article presents new genetic evidence from a study showing that humans probably self-domesticated themselves to select for pro-social traits. The original journal article compared the genomes of anatomically modern humans to genomes of other domesticated species (i.e. cows and dogs) and their wild types (i.e. wolves and Neanderthals). It claims that AMH and domesticated species do share overlapping genes that are associated with domestication traits. Such domestication traits are associated with docile phenotypes and behaviors. There was also no significant overlapping between AMH and Neanderthals. In case of random overlapping, researchers made sure to also compare human and domesticated species genomes to greater apes and found that this wasn't the case, which is positive evidence for self-domestication. They also looked at nearly fixed ancestral or derived SNPs in archaic lineages that have variants in AMH that would represent "under-domesticated" traits. Using other literature sources, they found that there's an ancestral mutation related to symptoms of aggressiveness and developmental delays in certain AMH diseases. Lastly, they noticed there were changes in genes associated with neural crest development in AMH from Neanderthals/Denisovans that were the same changes seen in neural development of self-domesticated species. This study can improve our understanding of why social cooperation so clearly defines modern human cognition.

Paulette Ma

Early Human Dispersals within the Americas

A new study entitled, “Early Human Dispersals within the Americas” was published in Science on November 8^th by researchers from the University of Copenhagen and University of California schools summarized in Science Daily.  The researchers sequenced the genome of 15 ancient humans found in North America (ranging from Alaska to Patagonia), including some that had not been analyzed previously and compared them to genomes from nearly 400 contemporary humans as well as to SNP panels of nearly 200,000 SNPs. They found that Native Americans did not migrate out of Beringia until about 12,000 years ago and once they did engaged in a rapid expansion and split into many different populations. They also found that these early Native Americans first reached South America about 11,700 years ago and found they mixed with an Australasian population around this time. In the middle to late Holocene another wave of migration came from Mesoamerica into South America. Finally, they were able to discern that two samples from Lagao Santa and Spirit Cave that were initially labelled to be “paleoamericans” that predated the presence of Native Americans in the Americas due to their unusual cranial morphology were, in fact, Native Americans that likely had unusual skulls as a result of population isolation.

Ancient DNA and Migratory Patterns

Original Article: https://www.cell.com/cell/fulltext/S0092-8674(18)31380-1
News Article: https://www.eurekalert.org/pub_releases/2018-11/cp-ade110118.php


New genome-wide ancient DNA data is being utilized to revise the history of the peopling of Central and South America. This history of migratory patterns in the Americas has long been the focus of archeogeneticists, geneticists, and biologists of many different fields.  The history is constantly being revised as new date presents itself. Now, new genome-wide ancient DNA data has being utilized by an international research team to revise the history of the peopling of Central and South America.

Many recent studies have come to the same conclusion as this particular study, which involves co-senior author David Reich.  The researchers involved used DNA from 49 individuals from Central and Southern America.  Their DNA suggests that within the ancestral lineage of migrants that originally populated these areas there are two previously unknown migrant lineages.  One of these migrants waves was displaced by a new wave of migrants 9 kya.  The descendants of these new migrants are very closely related to peoples in modern who are located in the same region.

Additionally, the study found that certain groups of individuals in Central and South America were closely related to the Clovis peoples who were mainly located in North America.  Prior to this, it was not known that Clovis peoples had succeeded in spreading beyond North America.

Hannah Jacobson

Civil War POW study finds a father's stress can alter a son's genetics

A new study of the offspring of Union soldiers adds to a growing body of evidence that suggests traumatic events experienced by one generation can have profound effects on the next. This all concerns the growing field of epigenetics, the ability for our DNA to be affected by and interact with the environment. The study, based on an analysis of National Archives records of Civil War prisoners of war and their families, turned up stories of surviving captivity in the notorious Andersonville prison in Georgia, where crowding, starvation, and poor sanitation were rampant. To see how these conditions affected or did not affect POWs and their offspring, click here.

For the full study, click here.

Variation In The Shape of the Human Birth Canal

The common understanding has been that the shape of a human mother's birth canal has been fashioned by the evolutionary forces that it needs to be wide enough to allow large brained babies to pass through but narrow enough for women to walk efficiently. This evolutionary compromise is known as the obstetrical dilemma. Research by biological anthropologist, Lia Betti, and evolutionary ecologist, Andrea Manica, challenge the obstetrical dilemma. The obstetrical dilemma would suggest that birth canal shape around the world would be relatively standardized but the findings of these researches did not support this. Betti and Manica measured the pelvises of 348 female human skeletons from 24 different parts of the world. They found women from sub-Saharan Africa and some Asian populations has pelvises that were narrow from side to side and deep from front to back. They found that Native American women had wider canals and that Native Americans and Europeans had the most oval-shaped upper canals. They saw that there was less variability in shape in populations farther from Africa.  Their analysis proposed that the variable shapes were due to neutral evolution through genetic drift and migration.  They hypothesized that climate could have contributed to different shapes however they found little evidence for it and suggest further research into other ecological factors.  Betti and Manica said their research could be important for modern obstetric practice in multi-ethnic societies as modern medical understanding is developed mainly on studies of European women.

https://www.sciencemag.org/news/2018/10/birth-canals-are-different-all-over-world-countering-long-held-evolutionary-theory
http://rspb.royalsocietypublishing.org/content/285/1889/20181807

Maeve Curran

Neanderthal and Modern Human Hybridization

Two researchers, one from the University of Arizona and one from Stanford University, recently published an article in which they analyzed segments of Neanderthal ancestry in the modern human genome related to virus resistance. They ultimately found 152 introgressed gene fragments. They then tested these fragments to try to address their “poison-antidote” hypothesis. Their hypothesis was that as the two species exposed each other to new viruses, they also exchanged virus-interaction proteins (VIPs), which allowed them to have some resistance to these viruses without developing these proteins through natural mutations. These VIPs interact with a variety of RNA viruses such as modern-day HIV, influenza A, and hepatitis C. The specific RNA virus-based VIPs are seen in higher proportions in European than East Asian populations. Most of these introgressed segments in modern humans originated from the second major interbreeding event. This type of analysis of introgressed segments can also be used to detect ancient epidemics. This study can have profound impacts on ancient genetic epidemiology and understanding how these introgressed segments impact the human genome as discussed in recent news articles such as this one.

Joshua Porter

Domestication of the Red Fox

This red fox experiment has been in the works for almost 60 years. The foxes are bred in captivity and then put into one of three groups for genotyping. These groups are the Tame, conventional, and aggressive populations. The foxes have the same window of DNA genotyped, while researchers look for the presence of a "friendliness" gene. Then once the fox's genes have been assessed, a physical test is made to back up the results. What is noted is that the domesticated fox isn't like a dog, they are anxious and curious and they are not like dogs at all. 

https://www.nature.com/articles/s41559-018-0611-6#MOESM4

https://www.theverge.com/2018/9/11/17842410/pet-tame-foxes-domestication-dogs-genetics

Mouse pups with same-sex parents born in China using stem cells and gene editing

Researchers from the Chinese Academy of Science were able to use haploid ESCs to create healthy viable mice that has DNA from two mothers; however, mice from male parents survived in utero but only lived for 48 hours outside the womb. The process of creating mice from same-sex parents had been done before, but when the mice from two females were born the first time it was tried with out the use of haploid ESCs they were stunted in growth and did not live very long. The mice created from two males did not even survive birth the over grew in utero and didn't survive birth. This discovery does not mean that haploid ESCs to create same sex offspring can be used in all species of mammals that cannot same sex reproduce because each species has different imprinting sites that have to be recognized and deleted to produce viable offspring, but it is a step in identifying all the possibilities of gene editing and stem cells.

original paper:
https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30441-7
Science Daily report:
https://www.sciencedaily.com/releases/2018/10/181011143115.htm

Post by Sophia Sanchez

According to an article titled, "The Epigenetics of Being Black and Feeling Blue: Understanding African American Vulnerability to Disease", written by Dr. Darron Smith African American are suffering from various mental health serious due to racial discrimination, which remains a societal norm and a routine a part of their everyday lives. It influences human biology and physiology at the cellular level, leaving the poor, the impoverished, and the targeted more vulnerable to chronic disease. The result is epigenetic tags with harmful gene expressions. 

Nana Evison 

FDA Lifts Clinical Hold; Green-Lights Vertex and CRISPR’s Sickle Cell Gene Therapy Trial

According to this article published in BioSpace last week (as well as this article from Globe News Wire), in May of this year the FDA placed a clinical hold on an experimental trial for a treatment for sickle cell and other such diseases. The treatment was being co-developed by CRISPR Therapeutics and Vertex Pharmaceuticals, and was put on hold due to "concerns" from the FDA that needed to be reviewed before proceeding in experimental trials. The gene-editing treatment is known as CTX001, and is an ex vivo therapy for people who have inherited disorders involving hemoglobin, like sickle cell anemia or beta-thalassemia. CTX001 edits the genes through CRISPR technology to increase production of fetal hemoglobin in a patient's red blood cells. Fetal hemoglobin naturally exists in newborn babies, but sometimes carries over into adulthood, where it can provide protection for people with blood diseases. CTX001 appears to be safe because it affects only cells at the targeted site (via). The FDA did not say the specific "concerns" that they had, though it is speculated that they are being cautious about human trials because "it's a permanent alteration of a person's genetic code" (Brian Skorney). However, since CTX001 is CRISPR's "most advanced program," it seems that the FDA would rather be safe than sorry with regards to gene-editing treatments, considering potential dangers brought up regarding CRISPR technology in the past.

Ezra Lowe

Reproductive Revolution: how our skins cells might be turned into sperm and eggs

Scientists have recently discovered a way to make somatic cells into sperm and egg cells in vitro in mice (iPSC cells). They do this by injecting somatic cells with a cocktail of genes that generate transcription factors that then tricks the cell to into thinking it is a different type. To turn the cells into gametes, the iPSCs receive chemical signals from the tissues in the ovaries or sperm cells. Once the cells are induced they can then be planted back into the mouse to mature to their full development. This study has not been conducted on humans yet, however, this great of leap in science could lead to genetically modifying human offspring. It would also allow same sex partners to have a genetically related child, and even a single parent to create a child from 100% of their cells.

https://www.theguardian.com/science/2018/oct/14/scientists-create-sperm-eggs-using-skin-cells-fertility-ethical-questions?CMP=share_btn_link

Giraffes Inherit Their Spots From Their Mothers

Though slightly random due to being about giraffes this article titled Giraffes Inherit Their Spots From Their Mothers in the Science News Journal which referenced this study by the Journal of Life and Environmental Sciences which focuses on the spots of giraffes, how they are passed on from one generation to the next and ultimately how that impacts the survival of the offspring. Through photographic samples, parent-offspring regression statistics and field observation of the sampled giraffes the researchers found that there was an inheritable aspect of the spots for giraffe offspring. Those spots do have an impact on survival rates and though the fathers of these offspring were not included the similarity between offspring and parent indicates a correlation between coat patterns and survival rates of the offspring. The researchers found that circulatory and solidity patterns improved overall offspring survival fir neonates and juveniles. While results indicate high similarity to the mothers' coat patterns there are still many things to discover and expand upon with this research and the question of how the spot patterns relate genetically between offspring and mother as well has how those patterns impact survival.

High-Resolution Comparative Analysis of Great Ape Genomes

     Leading as the feature article in Vol. 360 of Science Magazine, the Great Ape Genome project was a multi-institutional study involving over 40 scientist who generated higher quality assemblages of genomes from the great apes; humans, chimpanzee, gorillas, & orangutans. By using single-molecule, real-time (SMRT) long-read sequencing technology, the humanizing bias in previous ape genomes have been reduced allowing a more unambiguous view of genetic similarities and differences that arise as the hominin lineage diverged from the great apes. From their data, 10 million years ago the apes genome underwent a segmental duplication expansion where these sections of DNA that repeated were more prone to deletion and duplication mutations which influenced the evolutions of the various species. This support the hypothesis of bigger brain size in humans compared to other apes being due to the up-regulation of synaptic neurons in the prefrontal cortex because the gene for this neuron have been duplicate numerous times in the human genome. This article is the first step to truly understanding what makes us uniquely human because only by getting higher quality ape genome data and comprehensively comparing them can we understand our own genome and genetic difference.

-Denzel Walker

Recent Success of In Utero Gene Editing

In a recent Popular Science article, author Kat Eschner explains the content and future impacts of the Nature paper "In utero CRISPR-mediated therapeutic editing of metabolic genes".  For the first time researchers used in utero base editing to treat a genetic disorder. The experiment was restricted to mice and many more successful studies need to be completed before researchers are able to begin human trials, but there were hopeful results. The researchers found that the mice who were treated in utero for their rare liver disease (HT1) with base editing, thrived in comparison to those mice not treated and even those treated after birth with nitisinone. Furthermore, the edited cells persisted through development. They discovered that Pcsk9 targeting decreased cholesterol levels and Hpd targeting resulted in 'rescuing' the deadly phenotype of HT1. The long term goal for this research is for base editing to be utilized in humans to prevent life-threatening genetic disorders.

Genome-edited skin epidermal stem cells protect mice from cocaine-seeking behaviour and cocaine overdose

In this article gene therapy using CRISPR is used to modify the gene that produces the BChE protein. This protein hydrolyzes cocaine in the bloodstream; the unmodified protein is slow and inefficient. Using CRISPR the scientists have modified the gene in stem cells then implanted it back into the body under the skin. It is 4,440 times more efficient at hydrolyzing the drug, cost-efficient, and seems to be a long-term solution to cocaine addiction. The mice with the modified gene no longer craved the drug and were able to survive fatal doses of it. They hope to continue this research by testing on humans and possibly applying the process to other addictions such as alcohol and nicotine.
https://www.nature.com/articles/s41551-018-0293-z.pdf
https://www.theguardian.com/science/2018/sep/17/cure-for-cocaine-addiction-in-reach-say-scientists

How Child Abuse Can Impact Your DNA

https://www.independent.co.uk/news/health/child-abuse-dna-trauma-genetics-molecular-scars-sperm-harvard-university-a8563906.html

"Child abuse leaves molecular 'scars' in DNA of victim's sperm, new study suggests"

A Harvard study consisting of thirty-four men, twenty-two of which had suffered abuse as children, found a significant difference in the amount of methylation present in the DNA of the abused men versus in the non-abused. Twelve locations of DNA were identified as being consistently affected by methylation in the men who had experienced abuse as children. While the newly discovered information proves how trauma has a long term impact on the abused individual, it also suggests that future generations can also be affected, due to the presence of methylation in sperm cells. The impact is still relatively unknown, but studies conducted with mice have shown that methylation in sperm cells has proven to have negative health impacts in offspring. While there hasn't been enough research done, it's possible that methylation markers could be used in the future in a legal setting as a tool to determine the approximate age of the person who has left DNA behind at a crime scene. The correlations between methylation and child abuse could also one day allow scientists to calculate the probability that someone has experienced child abuse. This study has provided a lot of information to potentially progress what we know about DNA methylation, but Dr. Andrea Roberts of Harvard says that study still remains to be replicated by others.

The Dangers of DNA Testing

A recent article posted in the New York Times discusses the results of a study posted in Forensic Science International, exploring the possibility of error in forensic laboratory DNA testing. 108 different crime laboratories were sent the same DNA sample mixtures and asked to identify possible suspects in a crime. While almost all the labs correctly identified the major contributors of the "crime", 74 labs implicated an innocent third suspect. This study exposed high levels of variation among results received from various forensic laboratories, suggesting a possible need to standardize aspects such as training, etc. While these results do not necessarily imply innocent people are being sent to jail, they pose a question of preciseness of results in complex sample mixtures.

Allie Henderson

What Americans Think About Gene Editing for Babies

In an article by Science News, they analyze the Pew Research Center's findings on the attitudes of Americans towards tweaking the genes of unborn babies. 72% of Americans surveyed favored changing an unborn babies' genetic makeup to treat a disease or condition that would be present at birth. On the other hand, Americans are not on board with the idea of "designer babies," with about 80% agreeing that boosting intelligence with gene-editing would be taking medical technology too far. Furthermore, 65% said they did not support gene-editing if it required experimenting on human embryos, however, experiments on embryos are already underway in Europe and China. Only time will tell how the attitude of gene-editing on babies will be in the future.

What 13,000 Patents Involving the DNA of Sea Life Tell Us About the Future

This article published by the New York Times discusses a paper from Science Advances on patents on genes of living organisms that are located in the ocean. The articles begins the discussion by introducing a recent debate in the United Nations about how the genes of many living organisms are being used and the development of a global legal framework for genetic resources. Private companies in Germany, USA, Japan, Norway, Britain, France, Denmark, Canada, Israel, and the Netherlands own 98% of the patents involving marine organisms’ DNA; and this is leaving to a new kind of global inequality. These genetic prospectors are looking for organisms with exceptional traits that provide the missing portion of a product that will hopefully develop a new or alternative treatment. After various examples, the article concludes with the experimentation of growing of Omega-3 fatty acids on land modifying genetic codes of a Canola plant with DNA from marine microorganisms. 

Ana Maria Torres Martinez