Sunday, December 4, 2011

Wild Dogs in Moscow learn to use the subway

Not exactly related, but we were talking about it so I found the article.  Article from PopSci that describes wild dog packs in Russia.  One specific type, the beggars have adapted their behavior to navigate the subway system in order to beg in more areas.

Wednesday, November 16, 2011

Don't spit on a Brisbane bus!

Bus operators in brisbane are now equipped with DNA kits to identify anyone who violates their strict no-spitting rule!

Sunday, November 13, 2011

What do a bunch of old jews know about living forever?

This is a really cool article about the genetics of longevity from the New York Times.   Its not super sciency but its a pretty good read.  The genetic part of it is that there are genes that prevent major diseases (cardiovascular, cancer, diabetes, and cognitive decline) and there are the telomeres that give you a yardstick for life expectancy.

Monday, November 7, 2011

For those of you asking about Rubber Boy...

Here is some science behind the disease, Osteogenesis imperfecta. OI manifests in a number of symptoms including weak bones, multiple fractures, bowed limbs, short stature, deafness, and short lifespan. An article last week in Molecular Therapy describes the genetic basis of OI - dominant mutations in the type I collagen genes - and a new attempt at treatment through gene therapy.

Or for a more dramatic portrayal of the disease, see Bruce Willis in 'Unbreakable'.

The pursuit of susceptibility genes for Alzheimer's disease: progress and prospects

Because of technological advances, GWAS have begun to make progress in AD genetics. A small proportion of AD patients have an autosomal dominant pattern of inheritance, and genetic studies of these patients can potentially help with patient care. Four genes, APOE, CLU, PICALM, and CR1 have been found to be involved in AD susceptibility. These genes play a role in the pathophysiology of AD, and their discovery "supports ongoing efforts towards intervention in these pathways."

ICHG/ASHG 2011: New research on genetic factors associated with autism, schizophrenia and Parkinson's

The article discussed a recent gathering of scientists in Montreal for the 12th International Congress of Human Genetics (ICHG). The focus of the gathering was to present research on certain diseases and disorders--mostly mental issues--based on genetic research. Although the researchers did not understand the genetic basis for the diseases completely, the researchers were able to get some answers out of their research and were able to make sense of some very complex things. I'm sure that the next conference will have advanced the understanding even more since the research provided great insight into understanding autism, schizophrenia, intellectual disability, epilepsy and Parkinson's diseases. A brief summary of each of the researchers findings can be found at the bottom of the article.


Genetics of Multiple Sclerosis

29 new gene variants have been identified as associated with Multiple Sclerosis, many of which are related to the immune system. This will aid in shedding light on the immuno-pathogenesis associated with the development of the disease.

Sunday, November 6, 2011

Genetic basis of Lupus

This Nature article found a genetic basis for systemic lupus erythematosus.  Using whole genome methylation analysis, it found hypomethylation on the IL10 and IL1R2 promoters was associated with gene  activity, resulting in misregulated activity of T and B-cells.  It also mentions several genes on the HLA region that carry risk factors for the lupus.

Are test-tube babies at an increased risk for imprinting disorders?

Assisted Reproductive Technologies (ART) use has increased exponentially since the first successful report came in 1978. However, it has been suggested that these methods put the babies at higher risk for genomic imprinting disorders. Specifically, Angelman's syndrome and Beckwith-Wiedemann syndrome (imprinting disorder on Ch11)have been the most studied. While these and other imprinting disorders have been shown in some studies to be more prevalent among ART kiddos, in the way of science others have failed to show such results. Global hypomethylation of maternal alleles leads credence to this idea, but small sample sizes and an inability to control for confounding variables muddles up the picture. Ah, we say it again: more science is needed to further elucidate what's really going on. In any case, this brings another moral question to the table. How does everyone feel about ART (from a medical vs. an evolutionary perspective)?

Researchers discover genes involved in colorectal cancer

This study published today in Nature Genetics details the investigation of multiple networks of genes involved in driving colorectal cancer. Researchers profiled a vast number of genes related to the disease using the "Sleeping Beauty transposon system." Since APC mutations are widely believed to play a role in initiating colorectal cancer in humans, Sleeping Beauty was used to perform insertional mutagenesis in mice with Apc mutations. By identifying common insertion sites of Sleeping Beauty from a total of 446 excised tumors, hundreds of genes and 38 genetic networks were implicated as candidates for driving tumorigenesis.

Genome-wide association study identifies susceptibility loci for dengue shock syndrome

The first genome-wide association study for dengue shock syndrome (DSS) identified SNPs at two loci, MICB and PLCE1, associated with this disease. Previous epidemiological studies found that some groups of people are more susceptible to dengue shock syndrome, possibly pointing to a genetic influence. This study compared the genomes of 2,008 pediatric cases of DSS against 2,018 control genomes in Vietnam. Another GWAS study was performed after the first with 1,737 DSS patients against 2,934 controls in order to validate their results. Two loci, MICB and PLCE1, were found to be associated with DSS patients as opposed to the controls, which suggests that dengue susceptibility might be influenced by genetic factors.

Saturday, November 5, 2011

The genetic basis of 130 brain diseases

Like in the cases of Prader-Willi Syndrome and Angelman Syndrome which are both based upon changes in the same locus, it appears that there are many instances of single genes that are implicated in multiple psychological disorders. Last year, the Gene to Cognition project finished their search for proteins involved in the postsynaptic density (the PSD: a molecular machinery involved in synaptic development and function), resulting in a list of 1461 genes, many of which are already associated with psychological disorders. Specifically, 130 diseases are now known to be linked to proteins critical to the PSD, and many of those proteins have been shown to play a role in multiple diseases. With this list of genes and proteins, it will now be possible for scientists to begin designing better therapies for disease, and perhaps creating therapies that may function in multiple diseases with similar genetic bases. It will be interesting to see how many of these disorders seem to be caused by deletions and epigenetic factors like those seen in the readings for this week and how many can be understood by more classical, Mendelian inheritance patterns.

Thursday, November 3, 2011

Genetics and pathogenesis of inflammatory bowel disease

This study looked at the genetics of inflammatory bowel disease (IBD) which arises from an excessive inflammatory response to microbes in the bowel. Healthy food metabolism depends on the co-evolution of the bacteria inhabiting our guts and our immune system; when these two fall out of since, our immune systems attack these helpful bacteria. Using GWAS, 99 different genetic risk loci (28 of which are similar to Crohn's disease) indicating the two arise from problems in the same pathway. The two forms of IBD, childhood-onset and adult-onset, seem to have similar genetic origins, implying other genetic, environmental, and epigenetic contributions to the disease. In addition, there is a weaker association between monozygotic twins having IBD than Crohn's disease (10-15% vs 30-35%). Some of the genes suspected to be involved in both Crohn's disease and IBD are those responsible for barrier function, microbial defense, innate immune regulation, regulation of adaptive immunity, ER stress and metabolism. The frequency of different variants of the disease varies in different populations indicating selective pressures of different environments. This study highlights the proteins involved in the digestive pathway, in addition showing promise for early disease diagnosis and treatment.

Earlier dispersal of modern humans in Europe

Two new studies published yesterday in Nature together suggest that anatomically modern humans may have reached Europe a few thousand years earlier than previously thought. While examples of Aurignacian culture had helped us arrive at a date of approximately 43-42 kyBP for the arrival of AMHs in Europe, physical human evidence dated only to 41 kyBP at the earliest. One study reanalyzed two molars found in Italy in 1964. The molars had long been described as Neanderthal, but have only now been shown to be human through "two independent morphometric methods based on microtomographic data." The molars were dated to 45-43 kyBP. The other study revisited a maxilla, KC4, discovered in a British cave in 1927. Originally underestimated to 36-34 kyBP, researchers dated KC4 to 44.2-41.5 kyBP. The molars and KC4 now represent the oldest evidence of AMHs in all of Europe and in northwestern Europe, respectively. These findings suggest a rapid expansion of humans into Europe before the disappearance of the Neanderthals, adding fuel to the fire of the human-Neanderthal admixture debate.

The "Sixth Nucleotide" and it's epigenetic role in the brain

This is a really interesting article about the "sixth nucleotide" which was discovered about 2 years ago. Related to 5-methylcytosine (5-mc), 5-hydroxymethylcytosine (5-hmc) may have a different function in epigenetics as compared to it's derivative; specifically, it's been implicated in DNA methylation plasticity.

This study, coming out of Emory University, quantified 5-hmc in the brain (it's enriched compared to other tissues - at around 40%) and mapped 5-hmc genome-wide in mouse cerebellum and hippocampus cells from postnatal development through adulthood. 5-hmc seems to be enriched on active genes (in contrast to 5-mc), and regions controlled by 5-hmc revealed both stable and dynamically modified loci during the period of development and aging. The team is now focusing on mapping how 5-hmc changes during development and its relationship to neurological disorders such as Rett syndrome and autism.

You can read the synopsis on Science Daily.

More of the same: getting down with the Denisovans

Researchers from Uppsala University have found evidence for genetic affinity between South East Asians and Denisovans. Instead of comparing whole genomes, they utilized genotype data for many populations and ran a sophisticated model to assess how ascertainment bias (i.e. rare SNPs not being included) could affect signals of archaic admixture. Their study included more than 1,500 samples from geographically disparate regions. Their results indicated genetic admixture among East Asians, and higher genetic affinity between Denisovans and Oceanians (previously known) as well as South East Asians.

Tuesday, November 1, 2011

The role of genetic variation in the causation of mental illness: an evolution-informed framework

This paper is a review of some of the leading hypothesis for why mental disorders are present in high numbers in populations and have not been selected against. Uher focuses specifically on fitness reducing illnesses, such as schizophrenia, autism, anorexia nervosa and biopolar disorder, among others. The persistence of these diseases is a paradox in that fitness reducing genetic variants should be under strong negative selection, however studies have shown that these diseases are highly heritable. Uher concludes that a model of polygenic mutation-selection balance best explains this paradox. Because human mental health and brain function is controlled by a large number of genes and processes, and most mutations that contribute to mental illness are newly arising, environmental factors and the cumulative effects of mildly pleiotropic genes could be responsible. It should be noted that Uher does not entertain any epigenetic contributions to mental disease in this review.

Monday, October 31, 2011

Epigenetic clue to schizophrenia and bipolar disorder

Epigenetic factors have recently been implicated in certain psychological disorders, such as bipolar disorder and schizophrenia. Researchers noticed a difference in the methylation patterns of the gene ST6GALNAC1, which has been previously linked to schizophrenia, GPR24 which has been linked to bipolar disorder, and ZNF694 across 22 pairs of monozygotic twins. Interestingly, over-methylation of ZNF694 was associated with schizophrenia, and under-methylation with bipolar disorder. These new findings provide possible mechanisms of early diagnosis of psychosis, and further twin studies could allow greater resolution into the timing and causation of onset of psychiatric disorders.

A twin approach to unraveling epigenetics

This article from Trends in Genetics explores the significance of monozygotic twin studies in epigenetic research. Because MZ twins are identical in genetics, age, sex, maternal influences, and common environment, they provide a reliable, unbiased source for identifying epigenetic changes associated with complex traits. In particular, MZ twins showing disease discordance can be very helpful for disease research. The authors of this article lay out future direction and implications of twin studies in epigenetics, such as whether assisted reproductive technologies (which include IVF and can result in multiple births) affect epigenetics.

Epigenetics and stress

Professor Eva Jablonka of Tel Aviv University's Cohn Institute for the History and Philosophy of Science and Ideas reviews the current literature on epigenetics and concludes that it is possible to pass on acquired conditions such as stress and environmental damage to offspring.

Stressed dad = depressed children? Investigating the paternal transmission of stress

The article explored a study that explored the link between a father's stress level in his life and the effects that this would have on the children. The study wanted to know whether stress, anxiety, or depression would exist at higher levels if the father of the offspring was stressed. The study determined that the father's stress did play a role. Although environment was most significant factor for the development of stress, epigenetics did play a bit of a role--at least in mice. The next step is to see whether or not the finding will still hold true in humans. In the past, studies have looked at maternal stress levels only. The paternal stress levels had a greater effect on mice who were born naturally; this suggested that behavioral influence was more significant.

Sunday, October 30, 2011

Methylation Mutants = Phenotypic Diversity

Another A. thaliana epigenetics paper published a couple of months ago... and a different conclusion compared to that of Weigel's lab (see Shay's post on Epigenetics and Evolution). Ecker's team looked at epigenetic variation over 30 generations of A. thaliana and found an extremely high amount of epigenetic instability (high mutation rate), but also evidence for epialleles that induced phenotypic changes and were also metastable (heritable). Essentially, they concluded that epigenetic instability could be an important mechanism for generating phenotypic diversity.

Vaccine Cleared Again as Autism Culprit

One example of epigenetics that I think is very well represented in popular media is the vaccines and autism debate.  Many parents, supported by the pseudoscientific study done by Wakefield (described in this article), believe that the MMR vaccine caused autism in their children.  While most reputable science seems to point to the idea that the two are unlinked, the idea of this correlation lives on in the minds of many parents and continues to persist.  Basically the theory is that the vaccine epigenetically changes the expression of genes in the brain.

Great Website

The Learn Genetics website offered through the University of Utah has a bunch of great resources for epigenetics. Relevant to this weeks readings, you can "lick your rat pups" HERE, or watch a video about methylation changes across the lifespan in identical twins HERE.

BPA makes male mice less macho

BPA (bisphenol A) is a chemical found in many plastics that happens to mimic estrogen. Two recent studies have linked early-in-life exposure to BPA with feminized behaviors in adult male mice. In one study, BPA was fed to pregnant deer mice. The offspring were evaluated in terms of spatial and navigational abilities, as well as susceptibility to fear and anxiety. While males typically excel in such tests and females hesitate to explore, the male mice that had been exposed to BPA in the womb were "significantly compromised" in their abilities as compared to males that had not been exposed to the chemical. The female offspring did not appear to be affected by BPA. In the second test, mice were exposed to BPA in adolescence rather than in the womb. The male mice again exhibited feminized behavior, while females displayed abnormally exploratory behavior consistent with males. As one researcher commented, "These novel findings point to the fact that an early environmental exposure can manifest itself later in life...A likely mechanism is epigenetics."

Associations with early-life socio-economic position in adult DNA methylation

Related to Heijmans's paper we read for class, this study investigates ways in which poverty during childhood leads to certain epigenetic markers that might have an influence on adult health and risk for disease. These researchers studied the epigenome of 40 adult males who were involved in the 1958 British Birth Cohort Study, so characteristics of their childhoods and socioeconomic status are well documented among researchers. They used this data to see if there was any correlation between childhood socioeconomic status, and they found that indeed the adult's methylation pattern was more closely related to one's childhood socioeconomic status rather than one's adult socioeconomic status. Many of the regions where these associations occur in the epigenome are seen in "promoters of genes enriched in key cell signalling pathways," calling for more research to see how these altered methylation patterns affect one's adult phenotype and health results.

Saturday, October 29, 2011

Epigenetics and Evolution

I'm going to take you through a couple of steps here, but I promise it ends with empirical research! If you click the title of my post you will be linked to a brief notification regarding a recent study published in Nature by the Weigel Lab at Max Planck. The author seems to think that the only thing worth mentioning is that "epigenetics may not be that big of a deal.....would not have much of an impact on evolution in general". (For a real good time, read the comments). This briefing links you to a real news article summarizing a very interesting paper. The new article can be found HERE, and the PDF of the paper HERE.

Basically, the Weigel lab looked at the mehtylome of Arabidopsis thaliana (mustard weed, the Drosophila of plants) across 30 generations in 10 separate lines. They found that methylation of individual cytosines changed three times more quickly than the rate of DNA mutation. By contrast, wholly methylated regions (for example, at transposable elements), mutated at the same rate as DNA mutation. Additionally, the different lines showed similar methylation patterns.

So what does this mean for evolution? Well, we have to think about methylation that affects functional genes versus methylation that supports architectural integrity. Methylation at transposable elements probably keeps them from jumping, whereas methylation at an individual cytosine might be affecting the functionality of an exonic region. We are still in the infancy of understanding exactly how epigenetic mechanisms impact evolution, but I find the claim that "epigenetics are not important for evolution" to be sadly misinformed. Even when epigenetic marks are not as heritable as DNA marks, they have very important implications for the (non)heritability of traits! And that, my friends, has everything to do with evolution.

Friday, October 28, 2011

Revised Archon Genomics X PRIZE

It's now the the Archon Genomics X PRIZE presented by MEDCO. The competition rules have been revised - "The $10 million prize purse will be given to the first team that accurately sequences the whole genome of 100 subjects within 30 days for $1,000 or less per genome, at an error rate no greater than one per million base pairs." The 100 subjects are centenarians. These changes were implemented in hopes of generating more public appreciation for the project and giving greater medical value to the competition. The judging process will emphasize accuracy and completion in the hope that a "medical grade" genome can be produced, based on the guidelines recently published in Nature Genetics, vol. 43.

The announcement can be found on the Archon X website

Tuesday, October 25, 2011

Epigenetic control of vasopressin expression is maintained by steroid hormones in the adult male rat brain

The authors explored how steroid hormones affect methylation in the adult brain using a rat model. They castrated male rats, effectively removing their endemic source of testosterone. Testosterone exposure is necessary for the synthesis of vasopressin, so castration decreases vasopressin. However, castration also increases estrogen receptor α. They found that castration increased methylation of the vasopressin promoter and decreased the ERα methylation. These results suggest that the methylation of some steroid-responsive genes in the adult brain is maintained by the presence of circulating steroid hormones (in this case, testosterone).

Monday, October 24, 2011

A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations

This article addresses the 20th century debate between the gradualist, incremental and the discontinuous, jerky theories of evolution. With current genome-sequencing technologies, we are able to investigate the patterns of mutation that characterize adaptive change. While there is significant evidence that single loci affect adaptive phenotypes in the wild, researchers still want to answer the question of gradual or jerky evolution. By means of QTL (quantitative trait loci) mapping and population genomics studies, epigeneticists can detect genetic substitutions that over time contribute to adaptive change, a phenomenon termed 'adaptive walk'. Because both quantitative genetic and population genomic studies have their drawbacks, a combination of the two would be ideal. In conclusion, researchers found that, despite Darwin's theories, single mutations can significantly affect phenotype.

Genome duplication encourages rapid adaptation of plants

The study, done by biologist Justin Ramsey who is at the University of Rochester, found that the number of chromosomes in plants can alter adaptability. Ramsey chose a plant that existed in two different climates: one a dry one and the other more moist. He noticed that the plants in the more dry climate had more chromosome sets and tested to see if the plant with less sets would be able to thrive in that environment to the same degree. The results proved that adding sets of chromosomes to the plants that grew in the moist environment allowed for them to survive in the dry climate to a greater degree than plants that were not altered. The study is fascinating because the plants were able to yield the same effects that regular genetic mutation has, which occurs over many years, in such a short amount of time.

Sunday, October 23, 2011

How evolutionary principles improve the understanding of human health and disease

One of the main differences across geography between different groups of people is their immune system and their resistance to disease. These types of differences lead to the question of whether these phenotypic changes between people is allelic or due to natural human plasticity. Epigenetics has confused this question: it now appears that there exist predispositions to certain diseases due to the inheritance of epigenetic markers that were added in very recent history to individuals faced with a certain situation in a certain time. These markers affect how children in very different environments may respond to stimuli despite the fact that these changes are not in the coding region of DNA and therefore will not be found by any SNP chip. Gluckman et al. argues that doctors, in looking to better understand diseases, will have to look at demographics, evolutionary biases, life histories, and family histories to begin to pull together a comprehensive theory of disease.

Population Genetic Analysis of the Uncoupling Proteins Supports a Role for UCP3 in Human Cold Resistance

Published this year, this study provides evidence that genetic variants related to temperature homeostasis in humans are correlated to climate. (It was actually cited in this week's Hancock paper!) By adjusting proton gradients within mitochondria, protein UCP1 helps regulate nonshivering thermogenesis (NST) in humans. This study set out to test whether SNPs associated with increased expression of UCP1 (and homologues UCP2 and UCP3) provide evidence of acclimatization. The SNPs were genotyped in 52 populations around the world, and correlations between allele frequencies and winter climate variables were calculated. The coding regions of the UCP genes were then resequenced in three different populations (Hausa of Cameroon, Han Chinese, and Italians) to clarify signals found in the genotype data. The results of the study suggest that climate adaptation shaped the distribution of UCP1 and UCP3 alleles.

Natural Selection Cuts Broad Swath Through Fruit Fly Genome

This article from a year ago describes an experiment on fruit flies that supports the hypothesis that evolution and adaptation is driven by multiple gene changes. Scientists at the University of California, Irvine, bred fruit flies through 600 generations and chose the ones that hatched first to be the parents of the next generation; such selection led to a 20 percent decrease in the time needed for hatching. After studying the genomes of hundreds of these flies, they concluded that this evolutionary change was driven by a soft sweep (where the trait is affected by many genes) rather than a hard sweep (where a single mutation is spread through the population). Following this view, Jonathan Pritchard of the University of Chicago explained that in human evolution, there seems to be many more soft sweeps than hard sweeps in adapting to new environments. This fruit fly experiment shows that such a mechanism is indeed possible for driving evolution.

Adaptive advantage of obesity gene

I thought the Myles article for this week was so interesting. If something even as ostensibly disadvantageous as obesity was specifically selected for by nature, it emphasizes the enormous role natural selection plays in who we (and all species) are today. Here is a study with rodents, which takes an opposite approach to the study of the origins of the obesity and the potential fitness the genes confer. They took rats, some genetically predisposed to obesity, and subjected them to strenuous exercise and starvation. All the rats under study lost weight, but the effects were much less severe and extreme in the rats with the obese genes, who also survived longer thus proving potential benefits of obese genes. In addition, they also found external influences had an effect on the expression of the obesity genes, particularly in homeostasis: rats that were exposed several times to the harsh, low-food, high-stress situations had a higher rate of survival, but tended to gain much more weight once normal conditions were regained. (Which explains the predicament of yo-yo dieters...) This study confirms the theory that obese genes were originally selected for to help individuals survive less abundant lifestyles than we are accustomed to today. Thus these genes, which are so valuable in environments with food instability, makes individuals in modern society far less fit, underscoring the fact that adaptation (and evolution) always has unfinished business.

Saturday, October 22, 2011

Recent evolution in response to natural selection in a contemporary human population

I just remembered this article I read from the NY Times earlier this month titled "Natural Selection Leaves Fresh Footprints on a Canadian Island". Parish records from the French-Canadian Island of Île aux Coudres have revealed an astonishing decrease in age at first reproduction (AFR, from 26 to 22 years) for women born on the island between the years of 1799 and 1940. Using powerful statistical tests, researchers were able to distinguish between cultural practices and natural selection, two potential drivers of this change. The unique social equality conditions of the island allowed for the detection of a clear genetic and heritable component to AFR. This is one of few studies to show convincing evidence for detection of microevolution over a few generations in a human population.

Climate change: Migration as adaptation

This study was part of the UK Foresight programme report on migration and global climate change. In the next 50 years, there will likely be increased migration of populations due to climate change. We need to give serious thought to our migration policies and consider the possibility that many people may not be able to migrate due to socioeconomic factors. The authors argue that "Migration may be the most effective way to allow people to diversify income and build resilience where environmental change threatens livelihoods. It is therefore necessary to make channels for voluntary migration available." Migration is adaptive in this changing world.

Friday, October 21, 2011

Why Your DNA Isn't Your Destiny

This is a really great TIME article that describes the basics of epigenetics as well as detailing the development of the theory of epigenetics as well as some key experiments in the field.  It especially details Bygren of Stolkholm's paper of the effect of starvation periods on lifespans of an individual's grandchildren.  It also describes a study of the effect of men smoking before puberty on their offspring.

Wednesday, October 19, 2011

Skeletal muscle function and gene regulation

This article describes the changes that skeletal muscle undergoes in response to physiological stimuli. Olson et al. identify the gene sox6 as a regulator of muscle constriction and metabolism. This was likely selected for in order to facilitate skeletal muscle function and dynamics.

Tuesday, October 18, 2011

Convergent adaptation of human lactase persistence in Africa and Europe

(This isn't my regular journal but a good article that I wanted to share, so I hope I'm not stepping on anyone's toes!)

The genes coding for lactose tolerance in Europeans is well known. However, there are populations in Africa that are also able to produce lactase beyond weaning but the genes coding for this have not been explored. Tishkoff and colleagues identify the SNPs associated with lactase persistence in these African populations, and find that it is different from those that code for lactase persistence in Europeans. This represents convergent evolution (and an adaptation) in humans as the result of strong selective pressure after the domestication of mammals.

Monday, October 17, 2011

Near Extinction for Humans

This National Geographic article describes a phenomenon that happened around 150,000 years ago before humans migrated out of Africa.  Because of drought conditions in Africa, the human population dropped to around 2,000 individuals.  These remaining individuals formed two population groups; one in south Africa and the other in east Africa.  These two populations lived in genetic isolation for nearly 100,000 years before recombining and moving out of africa around 40,000 years ago.

Ancient DNA sheds light on the origins of Early European Farmers

This article discusses a project undertaken by Professor Alan Cooper, Director of the Australian Center for Ancient DNA at the University of Adelaide. Cooper and his team analyzed ancient DNA from a neolithic graveyard in Germany, and found that the individuals interred there are genetically similar to Near Eastern populations, rather than European populations. This challenges previous beliefs that early neolithic farmers in Europe were descended from the European hunter gatherers that occupied the area prior to the establishment of agriculture.

Aboriginal Australians: The first explorers

The article discusses the origin and dispersal patterns of aboriginal Australians. After studying a hair from a modern day aboriginal man who lived in the early 1900s. Researchers discovered that the aboriginal Australians have no links to Europe and therefore are direct descendants of the first people who inhabited Australia. The researchers seem fascinated by the fact that these Australians have had ties to a specific region longer than any other group. People were also fascinated by the fact that these people had to be very skilled explorers to be able to get from Africa to Australia at such an early point in history. This study disproved the theory that Australians descended from Asian or European explorers because the aboriginal Australian dates back to about 24,000 years before early Asians and early Europeans differentiated from one another.

A negative perspective on the Genographic Project

This article is a bit older (sorry!), but I felt it warranted review. It is a response to the announcement of the Genographic Project from an indigenous rights attorney. In summary, the article is a classical sociocultural versus biological debate. She is worried that this project is too reminiscent of the Human Genome Diversity Project--a similar project from the '90s that failed to obtain national funding due to bioethical problems. While it is certainly important to protect the rights of indigenous peoples, I believe the author goes a bit too far in her claims that the Genograhic Project will harm these people and the cultures the people are trying to preserve. For example, she says "Despite the speculative nature of genetic research on human histories, the findings of the Genographic Project will carry the weight of science, which could be used to trump indigenous peoples' unique political status and rights".

There are two aspects of this statement that are troubling. The first is the claim that genetic research on human histories is "highly speculative". This shows a misunderstanding of what genetics can tell us. Admittedly, our methods are improving daily and have come a long way since 2005. This doesn't negate that in 2005 we still had quite a solid foundation for the Genographic project (much more solid than in the '90s, to be sure), which is being willfully ignored by the author. The second problem is the notion that big, bad science will come in and "challenge the 'indigenousness' or 'aboriginality' od certain indigenouse populations...". This reads to me like a case of sciencephobia. The notion that an institution like National Geographic will use science to harm indigenous populations is simply ludicrous. It also further reveals her misunderstanding of what kind of "genetic information" is being sought, and what it can tell us. Understanding migration patterns has no bearing on the sociopolitical concept of "indigenousness". In fact, the Genographic Project is directly assisting the preservation of indigenous culture, an example of which is shown HERE.

Sunday, October 16, 2011

Reconstructing the genetic architecture of the "extinct" Taínos

The Taínos were the first Native Americans to meet European explorers in the Caribbean, and as the all too familiar story goes, they were completely wiped out by European disease and violence. Carlos Bustamante from Stanford University has begun to elucidate the genetic structure of this extinct ethnicity from the genomes of modern Puerto Ricans. The inclusion of 70 modern Puerto Rican sequences in the 1000 Genomes project has revealed a mosaic of African, European, and Native American (Taíno) DNA. By estimating the length of African, European, and Native American DNA segments, Bustamante has been able to reconstruct the timing and duration of admixture events. As expected, segments unique to Taínos indicate a short burst of admixture which concurs with historical facts (Taínos were likely extirpated soon after the arrival of Europeans). The African and European segments are quite variable and suggest several waves of migration. The analysis is only in it's preliminary stages, and Bustamante hopes to gain further insight into the ancestral Native American genome.

Mitochondrial Eve vs. Biblical Eve?

Since the days of alchemists, science and religion have always been in conflict, as science always seems to be uncovering information which threatens a literary interpretation of texts like the Bible. However, the tension between science and religion is somewhat relieved in the mitochondrial Eve and the migration from Africa theory. This article describes how the estimated time line for the existence of "Eve", the first female human, is consistent between estimations from the Bible and the evidence from mtDNA. In addition, the amount of genetic variation and higher rates of linkage disequilibrium that exists in the world, assuming constant mutation, is far less that what one would estimate, which supports the idea of The Great Flood followed by subsequent bottle-necking.

Early human migration written in stone tools

This article from Nature discusses the recent discovery of ancient stone tools at Jebel Faya in the United Arab Emirates. Researchers unearthed three collections of broken and unfinished hand-held axes and leaf-like blades, the oldest of which has been dated to 95,000 to 125,000 years old. They believe these tools resemble those of early humans rather than those of our archaic relatives. With genetic evidence suggesting dispersal from Africa at around 60,000 years ago, the discoverers of the Jebel Faya tools incited controversy when they claimed the tools' makers may have actually been modern humans. Many archaeologists maintain that the tools must have been created by our archaic relatives, but as one Jebel Faya team member said, "The idea that they left Africa at 60,000 and ended up at Australia at 50,000--my God, did they ever stop running!"

Yersinia pestis genome sequenced from victims of Black Death

The DNA of Y. pestis, the bacterium responsible for Black Death (BD) that swept across Europe from 1347-1351, was isolated from the dental pulp of several BD victims (exhumed from an established BD burial ground). 30-fold sequence coverage was achieved for the genome, and phylogenetic comparisons with other modern Y. pestis genomes revealed that all strains of Y. pestis originated in medieval times, with the BD strain representing one of the most basal strains. Interestingly, there were no derived substitution positions in the BD strain suggesting that the seemingly increased virulence attributed to this strain's potency was likely due to other factors such as the host's genetic background, climate, social conditions, and vector dynamics.

Continents Influenced Ancient Human Migration, Spread of Technology

Researchers at Brown examined migration patterns across Eurasia and the Americas, trying to determine how population mixing varied between the two. It was known that in Eurasia, people tended to move in an east-west manner, taking advantage of the fact that climates are very similar as they moved laterally. However, the Americas are arranged in a more north-south orientation, spanning many climates from top to bottom. As suspected, this configuration appears to have limited migration and inter-group dynamics, as it was discovered that genes of isolated populations in the Americas varied more than those in Europe. It is thought that migrations occurred less in the Americas because it is more difficult to transverse different climates than to move along a temperature band.

Saturday, October 15, 2011

1920s hair sample reveals Aboriginal Australians' explorer origins

Eske Willerslev led a research team that sequenced the genome of an aboriginal Australian individual from a 90-year old hair sample. Genetic analysis led to the conclusion that "Aboriginal Australians descended from the first human explorers," said Willerslev. This Aboriginal Australian individual was shown to be a descendant of the first human migration out of Africa over 60,000 years ago, since genetic analysis of his genome points to a divergence from other human populations at 60,000 years. Willerslev calls this migratory population the first explorers and that they must have possessed "exceptional survival skills and bravery" to have traversed over such a long distance to reach Australia. Another article on this study (http://www.theaustralian.com.au/news/health-science/genes-map-aborigines-arrival-in-australia/story-e6frg8y6-1226144089835) discusses that the modern Aboriginal Australian population was very excited upon hearing the results of this study, since it validates their strong connection to Australian land by "[establishing] Aboriginal Australians as the population with the longest association with the land on which they still live today."

Wednesday, October 12, 2011

One Man Fathering 150 Children? Why Sperm Banks May Be Unethical

Here's an interesting article that discusses some of the issues we were talking about in class on sperm donations. One sperm donor, who donated anonymously, later found out that he has 74 biological children. He also found a website that helps donor-children find their biological fathers, and used his "donor number" to reach out to people looking for him.

Tuesday, October 11, 2011

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

Contrary to previous studies of genetic diversity in Africa, this study claims that the modern human origins can be traced to Southern Africa. The authors analyzed genome-wide SNPs of hunter gatherers (Hazda, Khoisan, etc.)and 21 other African populations. They found that the best fit model using linkage disequilibrium for location of origin is in southwestern Africa. This is a surprising results, as most other reviews of genetic diversity would place this origin in Eastern Africa.

Monday, October 10, 2011

Personal Genomics in 2011

This article looks at the 'personal genomics landscape' for 2011, and evaluates how the field has progressed since 2010. They raise some very interesting point, especially about the $1000 genome. Specifically, they address the costs of analysis. Sure, you can get a $1000 genome sequence but it will cost "another $100,000" to analyze the data for an individual person. Does this make the personal genome any more accessible for everyday, healthy people? They also address whether the personal genome will stay DTC, and the issues surrounding patents, legislation, and ownership of data. It is a nice starting place for a more updated version of our Gurwitz & Bregman-Eschet reading.

In general this looks like a great site for getting more information about the societal impacts of the genomics revolution (http://www.genomicslawreport.com/).

Disclosure of individual genetic data to research participants: the debate reconsidered

In this article from Trends in Genetics, authors address the ongoing debate of whether or not researchers are morally and ethically bound to release data to participants of genetic studies. The question of disclosure becomes more difficult in genetic studies because the participants are not entering the study with the expectation that they will hear results, which differs from a personally-requested whole-genome sequence or specific gene sequencing from 23andme, for example. Debate currently stands in two fields, restrictive disclosure policy ('no, unless') and qualitative disclosure policy ('yes, if'). Key among this debate is the argument of beneficence, which says that researchers are morally obligated to reveal genetic results to participants if the results will prove valuable to the patient, i.e. life-saving. Authors note that it is interesting how the two extremes of "no disclosure whatsoever" and "full disclosure" are not included in this debate.

How 'personal' is personal genomics?

An editorial in Science this week addresses the 'gaping hole' that still exists in genomics - that is, our lack of knowledge of the biological mechanics behind genetic disease. Greater attention must be turned to systems biology, Chakravarti states, and asks the question: if each individual is genomically unique, then is each individual's biology and disease also unique? Does this lack of understanding of individual biological response to disease causing genetic mutations indicate that personal genomics is not quite as personal as some would hope?

Personal Genomics and Public Health Initiatives

This article reviews a report published by an international panel of experts from a wide variety of fields including medicine, law, bioethics and public health.They investigated the potential for the use of genomic medicine in global public health initiatives. The report concludes that international efforts to utilize personal genomics in medicine are called for, especially with regard to developing countries. They also call for the creation of a public, global database of personal genomic profiles for the purpose of furthering knowledge and investigations into genomic medicine.

6th Annual International Translational Medicine Symposium held at Penn

The article is a glimpse into a conference that is going to take place from October 18-19 at University of Pennsylvania's Medical School. The whole conference is not about personal genomics but a significant portion is--especially towards the beginning of the conference. The specific question that is being posed is: "As access to personal genomic information becomes more widespread, is there more to understanding disease risk and response than simply knowing your genome?" The question is going to be tackled by two different perspectives from across the world. The conference will be streamed online and potentially these speakers will be available for a conference call after their panel. The website to the conference is: http://www.itmat.upenn.edu/symposium.shtml

Gut bacteria affects the brain

Recent studies have suggested that the host's gut microbiota may affect the brain and behavior. A study's results showed that mice fed a broth containing Lactobacillus rhamnosus were less anxious than mice fed sterile broth. The bacteria-fortified mice also possessed a unique GABA receptor distribution profile in the brain as compared to that of sterile broth-fed mice. Interestingly, when they cut the vagus nerve in the mice fed bacteria, they returned to an anxious phenotype similar to that of their sterile broth-fed brethren. The vagus nerve may be an important pathway for inducing behavioral effects caused by gut bacteria.

Sunday, October 9, 2011

Nature - Personal Genomics

Here is a neat article about personal genomics that was published 4 days ago online in Nature. It basically contains statistical data on the opinions of their readers on similar ethical discussion questions to the ones we went over the first day: whether people would be interested in having their genome analyzed (only 15% said no outright), the majority said they would have it done out of curiosity, rather than as a test for a particular disease or concern. I was pretty surprised that 10% had gotten their whole genome sequenced, and 16% had gotten their exome sequenced, but as the article says, many of their readers are scientists themselves so the data is skewed. I was also taken by the author's choice of words in describing the decision to have one's exome sequenced and stored as giving our cells "immortality", because it really hits home the gravity of having our DNA sequenced and having that information exist on a server somewhere out in the world. (And eerie as the company is located in Tucker, Georgia, which reminds me of Tuck Everlasting...)

Ownership of Genes

This article discusses the 2010 court decision to make patents of genes illegal.  The specific court case was over the 'ownership' of the BRCA1 and BRCA2 genes.  Before this case, Myriad had a patent on these two genes which meant that they were the only institution allowed to sell tests for mutations on these genes.  The court decision said that such a monopoly would not be allowed.  However, this decision brought up interesting implications for the patentability of protein-based drugs and antibiotics.

Personal genomics: information can be harmful

This commentary asserts that while personal genomics information can be very helpful, its harmful potential deserves careful examination. The authors state that harms from information are extensive in clinical medicine (e.g. undesirable side effects fostered by "labelling"), and that the "net harm" or "net benefit" of such information must always be taken into consideration. They express concern that the typical careful examination of new biomedical technologies has not been applied to DTC marketing of genomic profiling, and that the assumption that information can only be helpful is far too common and must be corrected as we learn more about personal genomics.

Saturday, October 8, 2011

Faroe Islands' FarGen Project to Sequence Genomes of Entire Population

The Faroe Islands, a territory within Denmark, has plans to sequence the genomes of each of its 50,000 inhabitants in a new project titled FarGen. A pilot program will begin with 100 people, and the entire project is expected to cost $47 million. The project aims to connect each individual's genome with their health records and to make this information available, with certain restrictions, to physicians. This project is especially supported on the Faroe Islands due to the high percentage of genetic disease among their population. The project will also develop a genomics education program throughout the nation to "address the issue of informed consent." Eliasen, of the Faroese Ministry of Health who announced this project, explained "if successful… the Faroe Islands could serve as a global model for implementing whole-genome sequencing into a healthcare system."

Nature Survey on Personal Genomics

A few months ago, Nature opened a survey asking their readers about their attitudes on personal genomics and if they had been involved with personal genomic testing. Of the 1,588 people who took the survey, 18% have had some sort of genome analysis, and 54% of the respondents said that even though they haven't had genome analysis, they would do so if given the opportunity. 50% of those who had genome analysis used the services of 23andMe. Interestingly, intellectual curiosity was one of the highest motivators for genome sequencing, along with medical and general health concerns. More survey results appear on their website.

Britain to launch personalized medicine project

In the United Kingdom, the Cancer Research UK has begun a pilot program for mass genetic screenings of cancer tumors. They plan to take the excess component of biopsies and make a library of genes and mutations in the tumors in the hopes of gaining and understanding of which treatments will be effective on what cancer types. The benefit of a centralized system is that it allows for many researchers to have access to samples but also maintains standards of patient privacy. There also exists the hope that this will provide a model for bringing further personalized medicine into the British healthcare system.

Wednesday, October 5, 2011

Ethical Dilemmas of Genetic Research

At the 4th annual Personal Genomes conference, the ethical dilemmas surrounding genetic information disclosure to subjects involved in genome research was debated. Currently, federal law prohibits research facilities to reveal genetic information to subject unless a certified clinical lab has confirmed the results.

Very much relevant to next week's discussion on personal genomics!

Tuesday, October 4, 2011

Misfolded human tRNA isodecoder binds and neutralizes a 3′ UTR-embedded Alu element

The authors of this article demonstrate how two kinds of RNA, tRNA and Alu RNA, interact. tRNA binds to Alu RNA, causing a rearrangement of 3' UTR. Because of the large number of Alu elements and diversity of tRNAs in humans, they propose that this is a posttranscriptional regulation mechanism that might be unique to primates.

Monday, October 3, 2011

"Outbreak Detectives Embrace the Genome Era"

In Science this week: A team of scientists met in Brussels to discuss the creation of a global database where the genomes of disease-causing mircroorganisms could be shared as soon as they surface. In this way, it is hoped, the centre of disease outbreak can be pinpointed, antiobiotic effectiveness can be determined, and the evolution of microbes monitored.

Shows what the public fear of epidemics (seen 'Contagion' yet?) plus 'literally..more money than God' can achieve.

HGP is 10: the gene therapy challenge

This article addresses the implications of a completed Human Genome Project for gene therapy. It uses the case of cystic fibrosis, the "most common life-threatening single-gene disorder," to illustrate some hurdles to effective gene therapy. The benefits of using a human promoter sequence (rather than that of a virus) in the therapeutic plasmid are discussed, as well as how details down to the plasmid's exact DNA sequence can greatly affect the efficacy of the therapy. Dr. Deborah Gill of the UK Cystic Fibrosis Gene Therapy Consortium says that the HGP has "provided all the tools to make things really easy" and has "revolutionized gene therapy on a support basis." If greater efficiency in gene transfer and a longer response are priorities, how can the information of the HGP be exploited to indeed "revolutionize gene therapy"?

In quest for new therapies, clinician-scientist team unlocks hidden information in human genome

The article talks about how a science researcher and a physician team up in order to study genetic mutations in the human genome to see if these mutations caused diseases. The two, analyzed how the "lock and key" mutation takes place: "the 'lock' – a segment of DNA known as the CArG box – and the 'key' – a protein known as SRF – come together or bind, they unlock the ability of a cell to turn on a gene." The results of their research left unclear which disease the mutations affected although the two were able to link certain mutations to other health issues such as type 2 diabetes. The goal is to find out the issues and solve them at the molecular level so that people with not have to have certain life-threatening diseases.

Sunday, October 2, 2011

1000 Genomes: A World of Variation

The 1000 genomes project is working to sequence the genomes of at least 1000 individuals in the hopes of discovering 95% of the variation that occurs in at least 1% of the population. Already, it has located 15 million SNPs, 1 million short indels and 20,000 large structural variants, for a total of over 16 million variations, half previously unknown. Because many diseases are not the product of one gene, such a widespread database of variation could help researches connect many genes and allelic differences to any given gene. Some researchers also hope that by continuing the project past 1000 genomes and including related individuals could help clarify genetic components to these diseases.

Genomics and Human Disease

Using data from the 1000 human genome project, these researchers are suggesting that recent mutations are more involved in disease protection or susceptibility rather than ancient mutations.  They attempt to present a unified theory of genetic disease that encompasses both common and rare Mendelian, multiple allele, SNP, and copy number variation mutations.  Especially important in their observations is that many diseases are caused by rare alleles, signifying that mutations in the last two generations have a huge impact on disease.
Also, this is a news article that discribes the research as well. http://www.sciencedaily.com/releases/2011/09/110929122751.htm

lincRNAs

Researchers at Stanford University School of Medicine have found that they were able to identify where on the chromatin regulatory RNA’s are acting. They utilized new techniques to elucidate the binding specificity of lincRNAs from fruit fly and two mammalian species. They found that these sites are “focal, numerous and site specific”.

The Human Genome Project, Then and Now

In this article, a researcher analyzed specific quotes from his own article, written in 1986, in which he discussed his optimistic predictions for the human genome project. In general, it seems that all of his goals for the project did come to pass, like a database and determining key genes involved in disease. It's interesting that we have even surpassed some of his predictions. (Although I wonder if they perhaps only chose his points which came to pass?)
http://the-scientist.com/2011/10/01/the-human-genome-project-then-and-now/

Speed-bumps ahead for the genetics of later-life diseases

This article expands on the ideas of Eric S. Lander by investigating further into the genetic makeup of common disease, with a focus on later-life diseases. With age as the dominant risk factor for many diseases, researchers want to know what role genetics play in the aging process. Chance plays a large part in late-onset diseases because of the weakening of natural selection, the complexity of late-life traits, and the fact that aging is largely determined by molecular and cellular damage. While GWAS have revealed a number of genes associated with diseases such as Alzheimer's, researchers suspect that there are many more genes with smaller effects that collectively cause ageing.

Richard Resnick on the Genomic Revolution

Richard Resnick weighs in on moral issues associated with the genomic revolution. A decade has passed since our 2 cornerstone readings for this week were published, and the consequences of the Human Genome Project are unexpected and varied. Resnick goes through some of the reasons why this information has transformed our society (mostly through medicine) for the better. On the flip side he evaluates the realized negative consequences of this information, and predicts imminent problems that we, as citizens of humanity, will soon face. Can you think of anything that he did not cover in this talk that you feel exemplifies either the 'pros' or 'cons' of the genomic revolution?

Mouse genomic variation and its effect on phenotypes and gene regulation

This research team sequenced the genomes of 17 different mouse strains, creating the largest genetic database for any vertebrate organism. 56.6 million SNPs were identified in the mouse genome, and some of these mutations have been related to various disease phenotypes including heart disease and diabetes. Since mice are used in a lot of research for human disease and cancer, it is important to understand their genome and the mutations involved in order to relate this research to human disease. Now, researchers will be able to use a programmed computer mouse, instead of actual mice, to study mutations and particular genetic diseases. One of the researchers, Ian Jackson, said that this study "is transforming our understanding of how DNA sequence variation relates to gene function, and ultimately its association with biology and human health."

Wednesday, September 28, 2011

Bio-molecular signatures associated with psychiatric disorders

This article investigates utilizing methylation profiles at CpG I of the BDNF gene in diagnosing depressive disorders.

Q&A with Leroy E. Hood

This article is a Q&A with Leroy Hood. Hood pioneered the automated DNA sequencer while at Caltech in the 1980s, and more recently has he been a vocal proponent of the Human Genome Project. In this interview, Hood fields questions about the progress in the field of personal genomics, commenting upon the recent wealth of data available to people who wish to sequence themselves and the benefits of potential medical applications of this data.

Monday, September 26, 2011

Genomic parasites responsible for the birth of mammalian pregnancy

I thought this was pretty wild - and it happened right across the street in ESC!

Gunter Wagner (and team) set out to investigate novel phenotypes/cell types - in particular, mammalian pregnancy. How did carrying developing young in the womb evolve?

Wagner and team identified 1500 genes that were unique to the uterus of mammals and involved in placental development. The big kicker? The expression of these genes is under control by transposons. Essentially, large-scale morphological changes (aka - the emergence of mammalian pregnancy) was not due to mutations within key genes, but rather is attributable to the establishment of a novel gene regulatory network (modulated by transposons).

Processed pseudogenes: the 'fossilized footprints' of past gene expression

Though modern technology has allowed the access and sequencing of ancient DNA, evolutionary geneticists would like to access ancient ancestral organisms' transcriptomes in order to investigate more into the evolution of gene expression. Because of the fragility of mRNA and therefore near impossibility of ancient extraction, researchers want to use pseudogenes, which are non-functioning relatives of existing genes that no longer code for proteins. Each expressed gene purportedly has a certain number of "pseudogene offspring", and so researchers believe that these genes can be used as "fossilized footprints" of former gene expression. This process is not wholly accurate, and researchers stress the usefulness of extracting ancient transcriptome information for future studies of evolution.

Ancient DNA extraction techniques in ancient bone

Archaeological research attempting to isolate ancient DNA from skeletal material has met with many difficulties. The issues of preservation, high potential for false negatives, and varied depositional environments have all proved to be confounding factors when attempting to extract genetic material from ancient remains. This study utilizes PCR analysis to measure (mt)DNA quantities in various hard tissues in ancient human and bovid material in order to determine the most promising regions of bone for this type of analysis. They found that using a low speed drill as opposed to high speed drilling or bone pulverization yielded significantly more (mt)DNA. In addition, they found that tooth cementum, as opposed to the more commonly utilized tooth dentin yielded the most (mt)DNA. Finally they found that different types of skeletal material exhibit consistent patterns of exponential fragmentation across varied types of depositional environments.

Evolution's past is modern human's present

In this article it is explained that modern African populations interbred with "archaic" humans. The study, done by Michael Hammer and his team, took the DNA sequence from 3 different African groups and found that part of their genome comes from archaic humans who were biologically compatible to the point of producing fertile offspring. Although fossils have not yet been found to support the findings done by this research, the researchers were able to infer based upon the very thorough simulations that were done. The groups that existed in the past are believed to have come from Central Africa. The article also suggested that interbreeding with archaic humans in Africa lasted much longer than interbreeding in Europe or Southeast Asia.

Cloning of Neanderthals?

Like homo sapiens, the Neanderthals were smart, made tools, and had a complex social system that involved the respectful burial of the dead. And yet, it was our ancestors who survived and not this seemingly equally viable sister species. Sequencing the Neanderthal DNA has allowed scientists to pinpoint their evolutionary relationship to us, answer fascinating questions about their intelligence in relation to ours and whether or not we interbred, and allowed scientists to hazard guesses as to the cause of their downfall, which will inevitably shine light onto our own vulnerabilities. However, along with this insight from a complete genome sequencing of Neanderthal DNA comes the moral question of cloning. Cloning is a complicated process involving the replacement of a nucleus of a stem cell with a nucleus containing the genome of the desired parent. Sequencing the DNA of a deceased organism is already complicated, but that would only be the start (the really tricky part is synthesizing the nucleus, which scientists believe could be accomplished by individually altering the genetic material of a human nucleus, nucleotide by nucleotide). Thus, we are definitely quite a ways away from a cloned Neanderthal, but the idea definitely represents yet another interesting moral dilemma that genome sequencing brings to light. Cloning in general raises moral issues, in the creation of life as "playing God" and in the use of fetal stem cells. However, there is also the issue of bringing back a species whose natural ecosystem has long-since been destroyed, a world in which it can exist only under study in a laboratory. This issue is even more controversial as it is no ordinary extinct species (like the wooly mammoth that scientists at Kyoto University in Japan intend to reserect), but our own sister species, a species that science indicates to have potentially been as sentient and conscious as we are. To clone a Neanderthal would inevitably bring into discussion cloning of one of our own.

Sunday, September 25, 2011

Neanderthal-human Hybrids

Mason and Short propose a solution to the apparent paradox of human-neandertal hybridization: that is, that human mtDNA shows no trace of neandertal lineage and there are few Y-linked neandertal genes in the human genome, yet autosomal DNA shows clear evidence of interbreeding. They suggest that only male neandertals were able to mate with female humans, perhaps due to the larger size and dominance of male neandertals over the human females which would not have existed for female neandertals over male humans. They add that Haldane's Law tells us that heterogametic offspring are often sterile, if even viable, and therefore XY offspring of any interbreeding would not contribute further to the human gene pool. Left would be females with human mtDNA but autosomal components from their paternal neandertal lines.

Ancient Genetic Mixing Seen in Immune System Genes

While it was thought that many of the places in the genome that Neanderthal and Denisovan DNA mixed with modern human's were non-functional, this study shows that this mixing had profound impact on the modern human immune system.  This report looked specifically at HLA genes (coding for HLA proteins).  In European, Asian, and New Guinea populations, more than half the genetic variation in the HLA gene can be attributed to ancient genomic mixing.  The article suggests that this mixing was a way for modern human ancestors to acclimate to new bacteria when moving out of Africa.

Genetic evidence for patrilocal mating behavior among Neandertal groups

This study looked at the mtDNA (HVR 1 and 2) Of a group of Neandertal fossils that were buried at the El Sidrón site in Spain. These individuals are believed to represent a "contemporaneous social group" in that they were buried together as the result of a karst collapse. The mtDNA of the individuals revealed three different maternal lines. They also sexed the fossils (using Y chromosomes) and discovered that the males shared an mtDNA haplogroup while the adult females did not. This led the researchers to conclude that this group of Neandertals was patrilocal.

NCBI Epigenomics

NCBI has launched their epigenomics browser. Think of this as your one-stop shopping for epigenetics information. It compiles all of the studies done in epigenetics, and allows you to search by gene, cell line or organ. This will be a great way to keep track of the explosion of studies and information concerning epigenetics!

http://www.ncbi.nlm.nih.gov/epigenomics

X-linked evidence of a Neandertal genetic contribution to non-africans

This study further confirms the results of the Green et al., (2010) draft of the Neandertal genome. They found an allelic variation of the dystrophin gene that is found exclusively in non-Africans and is shared with Neandertals. This supports the idea that Neandertals contributed to the H. sapiens nuclear genome. Furthermore, it supports a model of contribution that occurred after the first migration from Africa, but before successful colonization of the rest of the globe. The only exception to this finding is that the allele in question was also found in Massai populations. This is explained by a "back-to-Africa" migration hypothesis, but still makes me a bit concerned.

Access the full PDF HERE, and the news briefing HERE.

Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression

Recent highly publicized studies suggest that interbreeding between modern humans and Neanderthals accounts for 1 to 4% of the genome of present-day non-Africans. Using the simulation program SPLATCHE2, Currat and Excoffier modeled differing scenarios of early human expansion in order to investigate the demographic history of early humans and Neanderthals. They found that 2-3% Neanderthal ancestry in non-Africans can be accounted for by interbreeding rates of less than 2%, and suggest that this low rate may be an effect of such gene flow barriers as avoidance of interspecific mating and/or low fitness of hybrids. One scenario with a hybrid success rate of only 5% led to 80% Neanderthal introgression in modern Eurasians, further suggesting that interbreeding was very limited. The authors also suggest that different populations of Neanderthals may have interbred with Europeans and Asians after their division, which could be tested by comparing the specific genomic elements shared between Europeans and Neanderthals versus Asians and Neanderthals.

Saturday, September 24, 2011

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

Reich et al. recently published a new paper on Denisova admixture in Asia and Oceania in The American Journal of Human Genetics. They sampled 33 additional populations to those that were studied in previous papers to describe a more extensive migratory and population model for East and Southeast Asia and Oceania. The research showed that East Asian and western Indonesian populations did not show evidence of Denisovan material, which was present in aboriginal Australians, Polynesians, east Indonesians, and others. Therefore, they conclude that Denisova interbreeding with present-day humans occurred in Southeast Asia and happened before ancestors of present-day East Asians were in Southeast Asia. This challenges the model that the Denisova gene flow occurred in mainland Asia, the supposed geographical limits of the Denisova, and then spread to Southeast Asia; the authors instead suggest that this gene flow happened in Southeast Asia itself. These results broaden the previously-described geographic range of the Denisovans to more areas of Asia, and demonstrate their large "ecological range, from Siberia to tropical Asia."

Friday, September 23, 2011

First Aboriginal genome sequenced

Previous genetic studies on modern Asian and Oceanic populations have suggested a single migration that eventually led to all modern populations in Asia, Australia, and Oceania today. However, sequence analysis of this first aboriginal genome is strongly suggestive of two waves of migration. The first migrants branched off from African humans around 60,000 years ago and constituted the ancestors of modern Papua New Guineans, Australians, and Oceanians. The second wave of migrants were the ancestors of modern mainland Asians.

Further supporting this theory was the discovery that a small portion of the aboriginal genome is derived from Neanderthals and another small chunk is distinctly Denisovan. Papua New Guineans were previously thought to be the only population with Denisovan-derived DNA (until now!). Looks like that first wave of migrants were getting down and dirty, while the second wave kept it clean (to be fair, the Denisovans may have disappeared by the time of the second migration).

Thursday, September 22, 2011

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

This is really cool. The authors studied epigenetic inheritance in a species of plant. The authors conclude that, while many epigenetic changes to last a few generations, over the long-term most are not stable and are reversed.

The Science Daily piece stresses the limited duration of these 'epimutations': "Epigenetic Changes Often Don’t Last, Probably Have Limited Effects On Long-Term Evolution, Research Finds." I tend to feel like they might be missing a bigger point: methylation is a response to short-term (a few generations) information about the environment. Would we expect that a plant would make epigenetic modifications based on current environmental conditions that would affect relatives 10 generations from now? If the environment were stable enough to warrant that duration of change, why wouldn't we expect that to be in the realm of DNA mutation?

Wednesday, September 21, 2011

Antibiotic resistance is ancient

An example of one of the many cool things we can do with ancient DNA!

Question: Is modern clinical antibiotic use responsible for the emergence of antibiotic resistance in bacteria?

Bacterial (ancient) DNA was isolated from 30,000 (!) year-old Beringian permafrost sediments. As with many aDNA studies - there's the problem of contamination. To establish authenticity (I found this part really neat), they amplified 12S rRNA and two chloroplast genes, then BLASTed the amplified fragments to ensure that the sequences matched late Pleistocene (not Holocene - the present geological epoch) flora and fauna. Once authenticity was established, they looked for the presence of resistance-conferring genes in these aDNA bacterial genomes - specifically resistance genes for tetracycline, penicillin, and vanomycin (as a side note, they also looked at genes responsible for "diverse strategies of drug evasion").

The big finding? The ancient bacteria already possessed genes conferring antibiotic resistance - highly similar to the genes we see in modern bacteria. Antibiotic resistance is ANCIENT. And not something that evolved via selection pressures caused by modern clinical antibiotic use.

50 new genes for recessive cognitive disorders

This new study looked at 136 families with autosomal-recessive cognitive disorders and discovered novel mutations in 23 genes that were previously known to be associated with cognitive disorders. Furthermore, they found *probable* disease-causing variants in 50 novel genes. The proteins coding for these 50 novel genes interact directly with previously identified gene products known to be implicated in cognitive disorders. Many of the proteins are integral for the processes responsible for normal brain development and function.

I'm sure these results will rapidly be transformed into a testing option for several personal genome sites...

Monday, September 19, 2011

Hand preferences for coordinated bimanual actions in 777 great apes: Implications for the evolution on handedness in Hominins

Population-level Right handedness is a universal trait of humans. In this article from the Journal of Human Evolution, researchers present an assessment of handedness in four great ape species. After conducting the TUBE test that requires bimanual actions on numerous samples of these different species, results showed that chimpanzees, bonobos, and gorillas all showed population-level right handedness, whereas orangutans showed population-level left handedness. Findings from this experiment were meant to be compared to the results from a similar 2003 experiment by Hopkins et al which used smaller population sizes and therefore produced potentially inaccurate data.

In this experiment, researchers considered many factors such as the influence of age, sex, and human rearing on species' hand preference, concluding age to be the only relevant factor in certain species. Additionally, there seems to be a focus on compiling accurate data for chimpanzees as man's closest nonhuman primate relative. The authors make a note that the lateralization of handedness is linked to language lateralization in humans, which suggests linked evolution. With this in mind, results from this experiment could shed more light on human-primate divergence.

Sex with Denisovans a double-edged sword?

Controversy continues as to whether or not archaic Homo populations contributed to modern human DNA, and if so, whether said DNA is functional. This summer, a large research project led primarily from Stanford suggested that hybridization with archaic populations resulted in the HLA gene repertoire we see today in modern populations, a crucial tool of the immune system used to recognize pathogens.

However there may have been a downside to the Neanderthal flings. High variability in immunity genes may be linked to autoimmune disorders, wherein the immune system turns on itself. In particular, the group are looking at the gene variant HLA-B51, which is thought to have been inherited from Neanderthals, and which has been shown to be linked to the inflammatory disorder Behcet's disease.

Oldest human skeleton offers new clues to evolution

The 2009 article challenges the belief that humans evolved from chimpanzees to support the belief that man and chimps evolved from a common ancestor many years ago. The discovery of this in-between species indicates that humans have been evolving for at least 6 million years. The 1994 discovery was named Ardipithecus ramidus--"Ardi" for short. Ardi's brain was similar to the size of a chimps and Ardi had an opposable toe for grasping branches but Ardi did have some human-like qualities. The fact that Ardi was discovered in Ethiopia is pretty important because this region is believed to be the birthplace of mankind.

Sunday, September 18, 2011

Sequencing the chimpanzee genome: insights into human evolution and disease

This review, published in 2003 amidst growing hype surrounding the Chimpanzee Genome Project, explores the practical implications of chimpanzee-human genome comparison, focusing on biomedical applications. It addresses the use of such comparison to test the "less-is-more" hypothesis, which emphasizes the importance of loss of function mutations in the human lineage, and the hypothesis that phenotypic differences between humans and chimpanzees are caused by changes in gene regulation rather than in the protein repertoire.

RNA editing, DNA recoding and the evolution of human cognition

RNA editing appears to be the major mechanism by which environmental signals overwrite encoded genetic information to modify gene function and regulation, particularly in the brain. We suggest that the predominance of Alu elements in the human genome is the result of their evolutionary co-adaptation as a modular substrate for RNA editing, driven by selection for higher-order cognitive function. We show that RNA editing alters transcripts from loci encoding proteins involved in neural cell identity, maturation and function, as well as in DNA repair, implying a role for RNA editing not only in neural transmission and network plasticity but also in brain development, and suggesting that communication of productive changes back to the genome might constitute the molecular basis of long-term memory and higher-order cognition.

Methylation and gene sequence co-evolve in human-chimp evolutionary divergence

This new study from Cold Spring Harbor shows evidence that methylation has "co-evolved in a kind of molecular slow-dance over the 6 million years since humans and chimps diverged from a common ancestor." The authors explain that "by looking very closely at methylation patterns within individuals and across species, one can begin to piece together previously hidden stories about how species grew apart via evolution." They support the idea that "methylation changes could drive changes in DNA sequence." Since many of the papers we read this week looked strictly at the genetic code, this focus on methylation is an interesting perspective when considering evolutionary changes.

Ancient Human Demography from Individual Genome Sequences

This article estimates when ancient human populations diverged.  It used 6 individual genomes and a bunch of statistics to figure out when population splits between southern africans and the rest of the human population diverged, when eurasian populations diverged from african populations, and when european populations diverged from asian populations.

Increased exonic de nove mutation rate in individuals with schizophrenia

In this new study, scientists used sequencing of individuals with schizophrenia and their parentsin efforts to trace the genetic cause of the disease. They identified 15 de novo mutations associated with the inheritance of the disease. These findings will definitely play a significant role in the diagnosis, prediction, and treatment of the condition, and I expect that it will also play a large role in our society's view of mental illness, in both social settings and judicial systems when deciding on punishment for individuals suffering from the condition. However, as it is a highly complex disease, there are many contributing factors and genes, there is room for further research.

Genetic evidence for archaic admixture in Africa

"Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (≈2%) that introgressed ≈35 kya from an archaic population that split from the ancestors of anatomically modern humans ≈700 kya."

Saturday, September 17, 2011

Whole exome resequencing in non-human primates

This study applied a human-specific whole exome resequencing to non-human primates and had fairly good results. This is a possible new method for detecting genetic variation in non-human primates and may help correct some of the current genome annotation issues for coding regions.

Thursday, September 15, 2011

450k CpG Methylation Microarray NOW AVAILABLE!

This new illumina microarray is capable of analyzing methylation at 450,000 CpG sites in the human genome!!! This is a significant increase from 27,000 sites, the size of their previous 'big' assay. While it will likely be used mostly in cancer research, this could be a very interesting way to characterize methylation diversity across human populations. Do you think we will see more genetic or epigenetic variation?

CLICK HERE for the PDF

Tuesday, September 13, 2011

Personal Genomics is diversifying...

Gastrointestinal woes? MyMicrobiomes is inviting people to have their gut microbiomes sequenced.

Monday, September 12, 2011

Speaking of who the daddy is....

A little fun (click here)

PCR, when you need to find out who the daddy is!

Glowing Kittens Fight Feline AIDS

Scientists have genetically modified cats by infecting their eggs with a virus containing a foreign gene—the first time this method has worked in a carnivore. Experts say the advance could make the cat a valuable new genetic model—and potentially protect it from an HIV-like virus.

Sunday, September 11, 2011

"One Sperm Donor, 150 Offspring"

It's about the large number of children sperm donors in the US are fathering because of the lack of regulation of sperm donation clinics (unlike the US). The article is mainly concerned with the fact that the fathers did not know about the large numbers of children they would be having, and the fact that the children of the sperm donors could have a lot of other half siblings, unbeknownst to them, and risk incestuous relationships.

It did touch on the fact that rare genetic diseases could then be more prevalent in the population because of this preponderance of offspring of a few individuals that could be carriers for a disease. But it also got me thinking, could you even consider this a sort of unnatural population drift? Maybe drift isn't the correct term, but it does seem like a overrepresentation in the gene pool of a few individuals. This has obviously happened before, bringing to mind the famous example of Ghengis Khan. But here we have a different situation where men who are not "actively" involved are fathering a ton of offspring. These men might not have been viable mates outside of the sperm clinic context for any number of reasons as well (or maybe they would be more likely to have many children ...I don't know anything about sociological aspects of sperm donors but I'm sure there's a study out there somewhere).

Friday, September 9, 2011

'Indians and Europeans share a milky past'

A new study from University of Cambridge demonstrates how the shared presence of the lactose tolerance-linked -13910T mutation might shed light on historical migratory events.

Monday, September 5, 2011

More Evidence that Human Evolution Wasn't Linear

New genomic analysis of African hunter-gatherer tribes seems to suggest that genetic mixing happened between ancient Homo species even before they left Africa.

Monday, August 1, 2011

Urban Evolution

NYT article on evolution of white-footed deer mice in NYC - parks are little genetic islands.

Dunbar paper on light and eye size in human

Interesting. They "..demonstrate a significant positive relationship between absolute latitude and human orbital volume"

Guardian recap HERE

so much for the BU longevity study

Quick NPR report HERE

Also raises interesting questions about peer review process...

Race and DNA testing

Good discussion topic for 204:

"Some geneticists, sociologists and bioethicists argue that “black,” “white,” “Asian” and “Hispanic” are antiquated categories that threaten to revive prejudices. Others, however, say that meaningful DNA variations can track racial lines and that ignoring them could deny many benefits of “personalized medicine,” which aims to develop tests and treatments tailored to a person’s genetic makeup."

Wednesday, July 20, 2011

DNA from copulatory plugs can give insights into sexual selection

The authors use copulatory plugs to find out more about pre- and postcopulatory sexual selection in kangaroo rats. This is an interesting study on its own, but methods used might have some applications in primates as well.

Tuesday, July 12, 2011

A novel form of oxytocin in New World monkeys

And we thought we understood the nonapeptides...

The protein sequence and structure of oxytocin is widely thought to be conserved among Eutherian mammals. Curiously, these researchers found a nonsynonymous mutation in a handful of platyrrhines and tree shrews, changing a leucine to proline at position 8 in the signal peptide. Of the noncatarrhines sampled, owl monkeys, capuchins, marmosets, squirrel monkeys and tree shrews had the mutation, while titi monkeys didn't.

I took a quick look at OXT across a handful of mammals after reading this study and found that in that 9 protein sequence, mouse lemurs and tarsiers shared the conserved sequence, suggesting that this was indeed convergent in the platyrrhines and tree shrews. Unfortunately, without sequencing this region in atelines and pitheciines, we don't know if titi's lost the P8 mutation or if it never evolved in that clade.

In a nonprimate note, it seems like elephants have protein changes at positions 3 and 4.

This is an exciting find and it will be very interesting to see what researchers are able to find out about the functional and evolutionary significance of these mutations.

Female bonobos use copulation calls as social signals

Everything you've ever wanted to know about bonobo pillow talk?



To be a bit more serious, it's an interesting study, but I think this might be one of those statistical vs. biological significance issues.

African Genomes

This popular piece takes a look at the unfortunate genomic situation in which we find ourselves: Africa is home to most of the world's genetic diversity as well as heaviest and most diverse disease burdens, yet most genomic sequencing efforts have focused on Europeans and North Americans. Two African-based genomics consortia are discussed - and both seem to be worth following in the future, especially with the idea of genomic sovereignty gaining ground in many parts of the world. This small group of sequencing centers may be where we have to look for any/all African genomic data in the future.

Sunday, April 24, 2011

Frugivory in four sympatric lemurs: implications for the future of Madagascar's forests

"Although some conservationists accept that not all species can be saved, we illustrate the difficulty in deciding which species are dispensable. In this article, we examine the possibility that the integrity of a forest relies on its entire faunal assemblage...Analyses reveal that while lemurs overlap in a number of fruit taxa exploited, 46% (16/35) of families and 56% (29/52) of genera are eaten exclusively by one lemur species. We, therefore, predict local changes in forest composition and structure if certain of these lemur species are eliminated from a forest owing to hunting, disease, or habitat disturbance."

(...plus, my focal animal, Yellow-Blue, made it on the cover!)

Friday, April 22, 2011

Epigenetics and ACE

"Epigenetic regulation of somatic angiotensin-converting enzyme by DNA methylation and histone acetylation." Methylated CpG islands are all up in ACE's grill, messing with somatic ACE expression.

Wednesday, April 6, 2011

Colors of Domestication

Great review article -- lots of useful images and figures

Tuesday, March 29, 2011

Maternal diet and aging alter the epigenetic control of a promoter–enhancer interaction at the Hnf4a gene in rat pancreatic islets

"...we show that the transcription factor Hnf4a, which has been implicated in the etiology of type 2 diabetes (T2D), is epigenetically regulated by maternal diet and aging in rat islets." Epigenetics is very cool.

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

"We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations." Based on data for more than 580,000 SNPs.

Monday, March 21, 2011

Book review: How to get ahead

Gee review of Lieberman's new book The Evolution of the Human Head

Old Female Elephants Make the Best Leaders

cool video

article HERE

Less is more...

particularly re penis spines.
New study from David Kingsley's group on the loss of cis-regulatory elements on the human lineage.
Most notable:
"One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage"

Monday, March 14, 2011

Genomic signatures of diet-related shifts during human origins

nice review from Greg Wray group...

Co-Residence Patterns in Hunter-Gatherer Societies Show Unique Human Social Structure

..and a commentary by Bernard Chapais HERE

Comparative Data Reveal Similar Mortality Patterns Across Primates

"Contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging"

Friday, March 11, 2011

Countershading is related to positional behavior in primates!


Kamilar, J. M. and Bradley, B. J. (2011), Countershading is related to positional behavior in primates. Journal of Zoology, 283: 227–233. doi: 10.1111/j.1469-7998.2010.00765.x

Monday, March 7, 2011

Dividing chimp species / populations

Interesting Katy Gonder PNAS paper on microsats and clustering of chimp populations using e.g. STRUCTURE: pretty clear verus vs everyone else split.

But HERE (Hahn and Worobey -- probably done in connection with Ochman's microbiome stuff) is a recent view of the same issue focused on mtDNA genomes and finds verus + vellerosus vs everyone else split.

Generation of Melanocytes from Neural Crest Cells

PC&M paper: "summarize the current view of how melanocytes are specified from the neural crest "

Save the behavioral ecologists

recent Caro & Sherman review in TREE: Endangered species and a threatened discipline: behavioural ecology

"Behavioural ecologists often see little connection between the current conservation crisis and the future of their discipline. This view is myopic because our abilities to investigate and interpret the adaptive significance and evolutionary histories of behaviours are increasingly being compromised in human-dominated landscapes because of species extinctions, habitat destruction, invasive species, pollution, and climate change."

"Classic Selective Sweeps Were Rare in Recent Human Evolution"

From Molly Przeworski's group:

"Data from the pilot for the 1000 Genomes Project suggest that classic selective sweeps were not the primary mode of evolution of the human genome. Instead, it seems that the majority of human genetic diversity is best explained by purifying selection against deleterious mutations."

Forensic DNA phenotyping

"The Dutch parliament adopted a law in 2003 regulating forensic DNA phenotyping, the use of DNA samples to predict a suspect's ancestry or physical characteristics. But the Netherlands is still the only country to have done so.?

Manfred Kayser: "DNA sleuth"

cool profile of Manfred and forensic DNA profiling in Science

Friends and genotype networks

Maybe I posted this already?

"Framingham Heart Study verifies that DRD2 exhibits significant homophily and that CYP2A6 exhibits significant heterophily."

Pronghorn Genomics and Sexual Selection

Science news tidbit on potentially cool project!:

Byers et al "have over the years collected tissue samples from 835 pronghorns across the generations, and they now plan to genetically profile each animal to determine whether female pronghorns do indeed pick genetic studs."

Microbiome insertion sequencing

Insertion sequencing... involves using mobile DNA elements called transposons to introduce mutations into tens of thousands of bacteria. Before adding the transposons to the bacteria, the researchers tag each transposon with an identifiable DNA “bar code” that allows each mutant bacterium to be tracked—and for the gene disrupted by the transposon to be characterized. With the new sequencing technology, researchers can follow mixed populations of these mutant strains on various growth mediums or in different environments.

Anthropologists Trace Human Origins Back To One Large Goat

'Wait, That Can't Be Right,' Scientists Say

Predicting human cone distribution using pics of Botswana

"only 6% of our cone cells detect blue, and they are mostly located around the edge of our retina. Of the remaining cones, the ratio of red to green cones varies wildly between individuals.

To find out why this is, Tkačik, along with neurobiologist Vijay Balasubramanian of Penn and colleagues, created a database of more than 5000 high-resolution photographs taken at various locations in Botswana, a place near where humans likely evolved and other primates still live. The same scenes were shot at different times of day, with different exposure lengths, apertures, and distances from the camera. Using an algorithm they developed from previous studies of how human cones detect light, the researchers calculated how many photons of different wavelengths the camera had captured and what cone arrangement would pick up the largest number of them."

... and it matched the arrangement of human eyes.

Wine genomics

PNAS paper (by Sean Myles et al) on grape domestication!

New directed gene therapy -- CCR5 disruption in humans

"A gene-therapy method that specifically disrupts a single gene may have had its first success in the clinic, potentially boosting immune-cell counts in a small number of patients with HIV."

Twin studies - new role

Nice review paper on twin studies of epigenetics in recent TIG:

"We describe how large-scale epigenetic studies of twins can improve our understand- ing of how genetic, environmental and stochastic factors impact upon epigenetics, and how such studies can provide a comprehensive understanding of how epige- netic variation affects complex traits."

Friday, February 25, 2011

16th Summer Institute in Statistical Genetics

It's a bit pricey but probably a great workshop for stats and/or genetics geeks. Joe Felsenstein and Sudhir Kumar are among the instructors.

Thursday, February 24, 2011

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

Researchers sort out the mechanism for only methylating hemimethylated CpG sites and therefore avoiding de novo methylation.

The Developmental Role of Agouti in Color Pattern Evolution

Genomic signatures of diet-related shifts during human origins

Review of genomic evidence for dietary shifts in humans

Friday, February 18, 2011

Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

The authors use mitochondrial genomes from fecal DNA to infer an evolutionary history (i.e. divergence dates) of the four subspecies of chimpanzees.

Wednesday, February 9, 2011

Initial impact of the sequencing of the human genome

Nice Lander review article (good for ANTH204)

Janet Rowley on discovery research (aka fishing)

Q. Do you think that the type of career you’ve had would be possible today?

A. No. I was doing observationally driven research. That’s the kiss of death if you’re looking for funding today. We’re so fixated now on hypothesis-driven research that if you do what I did, it would be called a “fishing expedition,” a bad thing.

O.K., we knew about the Philadelphia chromosome, and after banding we had the technology to discover gains and losses among the different chromosomes. But once you knew that, what were the implications of the gains and losses? That’s the “fishing,” because there wasn’t a hypothesis.

Well, if you don’t know anything, you can’t have a sensible hypothesis.

I keep saying that fishing is good. You’re fishing because you want to know what’s there.

Tuesday, February 8, 2011

Wednesday, February 2, 2011

Friendship and shared genes

"...people's friends may not only have similar traits, but actually resemble each other on a genotypic level."

Cool study on relationships between behavior, personality, and genetics in humans.

Correlated genotypes in friendship networks; PNAS 2011

Monday, January 31, 2011

4 NEW ANT GENOMES!!!!!!!!

Ok, so no one probably cares at all about this other than me, but four new ant genomes are hitting the public!

They include one of the fire ants, the Argentine ant and a species of harvester ant. A species of leafcutter ant is on the way next month in PLOS. Including the two already published genomes, this brings the Formicidae total up to 6. Primates currently have nothing on this INTRAFAMILY genomic dataset.

These ants all differ in biology, ecology, etc. But perhaps most interesting is that the various ants also differ in the degree of eusociality. Now we may have an opportunity to look at how epigenetics affect reproduction, colony structure, etc.

Ants!

Sunday, January 30, 2011

Thursday, January 27, 2011

and orang genomic variation

Just to add to Jason's post on the Nature paper -- great that they also have some measure of variation w/i Sumatran and Bornean!

HERE is the New Scientist general summary (thanks Gary)

Wednesday, January 26, 2011

Orangutan Genome

"Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes. . . "
"Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies . . ."

Thursday, January 20, 2011

Complete guide to cat coat/eye colors

This is fabulous. I would think so even if I wasn't a cat person.