genomics

Good article about some contemporary genomics research

Bravely Default ask meme.
  • 1. Favorite Character
  • 2. Least Favorite Character
  • 3. Favorite Warrior of Light
  • 4. Favorite Asterisk Holder
  • 5. Favorite NPC (not including previous two questions)
  • 6. Favorite Ship
  • 7. Favorite Nation
  • 8. Favorite Crystal Boss
  • 9. Favorite Asterisk
  • 10. Least Favorite Asterisk
  • 11. Favorite Command and Support Command Combo
  • 12. Favorite Voice Actor
  • 13. Favorite Weapon
  • 14. Favorite Weapon Class
  • 15. Favorite Spell
  • 16. Favorite Ability
  • 17. Favorite Bonus Outfit
  • 18. Favorite Conversation
  • 19. Favorite Song
  • 20. Favorite Ending
  • 21. Favorite Part
  • 22. Favorite Nemesis
  • 23. Favorite Dungeon
  • 24. Least Favorite Dungeon
  • 25. Favorite Special
  • 26. Favorite Subquest
  • 27. Favorite Enemy Monster
  • 28. Favorite Genome
  • 29. Favorite Support Ability
  • 30. Favorite Loop

Why the fuck do all these white-hating black people try to say that all these weird things are our fault? And I’m not talking about police brutality or American slavery or racism, no, I’ve seen these morons say:

  • Whites invented bestiality and are the only ones who rape animals
  • Whites are the reason homosexuality exists/whites are gay more often and that makes them bad (plus: Why are so many black people homophobic? Seriously?)
  • White people are pedophiles because we’re not black (???????)
  • White people are albino versions of black people and because of that we’re genetically inferior and somehow not even human because scientists discovered distant traces of neanderthal DNA in our genome (?????????????????)
Like, black people, you guys have sexual deviants and immoral assholes too. White people didn’t invent these things and they’re certainly not exclusive to our race, like…??? What?? And that guy who argued we’re albino neanderthal black people, what are you smoking? That’s not how science works.

First comprehensive atlas of human gene activity released

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

“Now, for the first time, we are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles,” said Winston Hide, associate professor of bioinformatics and computational biology at Harvard School of Public Health (HSPH) and one of the core authors of the main paper in Nature. “This is a major advance that will greatly increase our ability to understand the causes of disease across the body.”

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches”—called “promoters” and “enhancers”—are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

“We now have the ability to narrow down the genes involved in particular diseases based on the tissue cell or organ in which they work,” said Hide. “This new atlas points us to the exact locations to look for the key genetic variants that might map to a disease.”

Above: A resolved Tree of Life with eukaryotes colored red, archaea green and bacteria blue

Defining the tap roots to the tree of life

It was way back in 1977 that American microbiologist Carl Woese applied phylogenetic taxonomy 16s ribosomal RNA to discover the third Domain of Life, the Archaea, depicted in green in the phylogenetic tree above. Phylogenetics based on the comparison of the slow-evolving ribosomal genes thus replaced those solely based on the subjectivity of organism morphology. Prior to Woese, all prokaryotes were lumped together. Ever since Woese, there has been increasing acceptance of the three-domain tree of life with taps roots of the Bacteria, the Archaea and the Eukarya. Moreover, it has been increasingly accepted that the Eukarya are descended from the Archaea, and not Bacteria. Next Generation Sequencing (NGS, also called deep sequencing) is now enabling science to apply ever more rigorous tests of the three-domain hypothesis; no small feat given that events in question likely occurred well more than a billion years ago. Technological advances have brought the cost of sequencing down to less than $1000/per full genome.

In the 6 May issue of Nature, Sprang et al. present research using NGS with impressive bioinformatics to define a new group of Archaea named Lokiarchaeota, and present strong evidence that places it as the closest known prokaryotic relative of the eukaryotes. Moreover, Lokiarchaeota’s genetic machinery are consistent with requirements for carrying out endocytosis or phagocytosis, as would have been required for a prokaryote to engulf a cyanobacterium as prescribed in the theory of endosymbiosis, leading to the mitochondrial powerhouses of eukaryote cells. This work portends that technology has reached a stage that many hypotheses about evolution in deep geologic time well be tested in the years ahead.

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If you haven’t heard by now - their ‘Real Vegan Cheese’ Indiegogo campaign is nearly fully funded - a team of Biohackers from Oakland, CA are currently developing cruelty-free vegan cheese by studying animal genomes to source natural milk-protein genetic sequences, which are then optimized for yeast to produce a yeast milk protein, synthesize, then, once placed in yeast cells, real milk-protein is produced from the DNA “blueprint” procured by the team.

Why do this? From the campaign site:

Indiegogo || Facebook || Twitter || Wiki || YouTube || Website

Read the article over at Motherboard to learn more, because this is as cool as it sounds.

Support this!

DNA: Celebrate the unknowns | Philip Ball

On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level, suggests Philip Ball.

This week’s diamond jubilee of the discovery of DNA’s molecular structure rightly celebrates how Francis Crick, James Watson and their collaborators launched the ‘genomic age’ by revealing how hereditary information is encoded in the double helix. Yet the conventional narrative — in which their 1953 Nature paper led inexorably to the Human Genome Project and the dawn of personalized medicine — is as misleading as the popular narrative of gene function itself, in which the DNA sequence is translated into proteins and ultimately into an organism’s observable characteristics, or phenotype.

Sixty years on, the very definition of 'gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level.

That sounds to me like an extraordinarily exciting state of affairs, comparable perhaps to the disruptive discovery in cosmology in 1998 that the expansion of the Universe is accelerating rather than decelerating, as astronomers had believed since the late 1920s. Yet, while specialists debate what the latest findings mean, the rhetoric of popular discussions of DNA, genomics and evolution remains largely unchanged, and the public continues to be fed assurances that DNA is as solipsistic a blueprint as ever.

[Read more]

Schizophrenia not a single disease but multiple genetically distinct disorders

New research shows that schizophrenia isn’t a single disease but a group of eight genetically distinct disorders, each with its own set of symptoms. The finding could be a first step toward improved diagnosis and treatment for the debilitating psychiatric illness.

The research at Washington University School of Medicine in St. Louis is reported online Sept. 15 in The American Journal of Psychiatry.

About 80 percent of the risk for schizophrenia is known to be inherited, but scientists have struggled to identify specific genes for the condition. Now, in a novel approach analyzing genetic influences on more than 4,000 people with schizophrenia, the research team has identified distinct gene clusters that contribute to eight different classes of schizophrenia.

“Genes don’t operate by themselves,” said C. Robert Cloninger, MD, PhD, one of the study’s senior investigators. “They function in concert much like an orchestra, and to understand how they’re working, you have to know not just who the members of the orchestra are but how they interact.”

Cloninger, the Wallace Renard Professor of Psychiatry and Genetics, and his colleagues matched precise DNA variations in people with and without schizophrenia to symptoms in individual patients. In all, the researchers analyzed nearly 700,000 sites within the genome where a single unit of DNA is changed, often referred to as a single nucleotide polymorphism (SNP). They looked at SNPs in 4,200 people with schizophrenia and 3,800 healthy controls, learning how individual genetic variations interacted with each other to produce the illness.

In some patients with hallucinations or delusions, for example, the researchers matched distinct genetic features to patients’ symptoms, demonstrating that specific genetic variations interacted to create a 95 percent certainty of schizophrenia. In another group, they found that disorganized speech and behavior were specifically associated with a set of DNA variations that carried a 100 percent risk of schizophrenia.

“What we’ve done here, after a decade of frustration in the field of psychiatric genetics, is identify the way genes interact with each other, how the ‘orchestra’ is either harmonious and leads to health, or disorganized in ways that lead to distinct classes of schizophrenia,” Cloninger said. 

Although individual genes have only weak and inconsistent associations with schizophrenia, groups of interacting gene clusters create an extremely high and consistent risk of illness, on the order of 70 to 100 percent. That makes it almost impossible for people with those genetic variations to avoid the condition. In all, the researchers identified 42 clusters of genetic variations that dramatically increased the risk of schizophrenia.

“In the past, scientists had been looking for associations between individual genes and schizophrenia,” explained Dragan Svrakic, PhD, MD, a co-investigator and a professor of psychiatry at Washington University. “When one study would identify an association, no one else could replicate it. What was missing was the idea that these genes don’t act independently. They work in concert to disrupt the brain’s structure and function, and that results in the illness.”

Svrakic said it was only when the research team was able to organize the genetic variations and the patients’ symptoms into groups that they could see that particular clusters of DNA variations acted together to cause specific types of symptoms.

Then they divided patients according to the type and severity of their symptoms, such as different types of hallucinations or delusions, and other symptoms, such as lack of initiative, problems organizing thoughts or a lack of connection between emotions and thoughts. The results indicated that those symptom profiles describe eight qualitatively distinct disorders based on underlying genetic conditions.

The investigators also replicated their findings in two additional DNA databases of people with schizophrenia, an indicator that identifying the gene variations that are working together is a valid avenue to explore for improving diagnosis and treatment.

By identifying groups of genetic variations and matching them to symptoms in individual patients, it soon may be possible to target treatments to specific pathways that cause problems, according to co-investigator Igor Zwir, PhD, research associate in psychiatry at Washington University and associate professor in the Department of Computer Science and Artificial Intelligence at the University of Granada, Spain.

And Cloninger added it may be possible to use the same approach to better understand how genes work together to cause other common but complex disorders.

“People have been looking at genes to get a better handle on heart disease, hypertension and diabetes, and it’s been a real disappointment,” he said. “Most of the variability in the severity of disease has not been explained, but we were able to find that different sets of genetic variations were leading to distinct clinical syndromes. So I think this really could change the way people approach understanding the causes of complex diseases.”

New Reprogramming Method Makes Better Stem Cells

A team of researchers from the University of California, San Diego School of Medicine, Oregon Health & Science University (OHSU) and Salk Institute for Biological Studies has shown for the first time that stem cells created using different methods produce differing cells. The findings, published in the July 2, 2014 online issue of Nature, provide new insights into the basic biology of stem cells and could ultimately lead to improved stem cell therapies.

Capable of developing into any cell type, pluripotent stem cells offer great promise as the basis for emerging cell transplantation therapies that address a wide array of diseases and conditions, from diabetes and Alzheimer’s disease to cancer and spinal cord injuries. In theory, stem cells could be created and programmed to replace ailing or absent cells for every organ in the human body.

The gold standard is human embryonic stem cells (ES cells) cultured from discarded embryos generated by in vitro fertilization, but their use has long been limited by ethical and logistical considerations. Scientists have instead turned to two other methods to create stem cells: Somatic cell nuclear transfer (SCNT), in which genetic material from an adult cell is transferred into an empty egg cell, and induced pluripotent stem cells (iPS cells), in which adult cells are reverted back to a stem cell state by artificially turning on targeted genes.

Until now, no one had directly and closely compared the stem cells acquired using these two methods. The scientists found they produced measurably different results. “The nuclear transfer ES cells are much more similar to real ES cells than the iPS cells,” said co-senior author Louise Laurent, PhD, assistant professor in the Department of Reproductive Medicine at UC San Diego. “They are more completely reprogrammed and have fewer alterations in gene expression and DNA methylation levels that are attributable to the reprogramming process itself.”

Read more here

Pictured: Scanning electron micrograph of cultured human neuron from induced pluripotent stem cell. Image courtesy of Mark Ellisman and Thomas Deerinck, National Center for Microscopy and Imaging Research, UC San Diego

CRISPR could protect genetic intellectual property by self-destructing synthetic sequences:

“A lot of efforts have been made around creating [biological] kill switches. We’re building on that, so that [a bacterium] wouldn’t just kill itself, but delete its synthetic DNA before doing that.” It’s like the biological version of hitting CTRL-Z.”

Wondering if it’s working with DNA Storage.

Comparative circular visualization of the organization of homologous chromosomes in collared flycatcher and zebra finch. Collared flycatcher is shown to the left, zebra finch to the right. Scale is indicated on the zebra finch side of plots, in Mb.

Kawakami, T., Smeds, L., Backström, N., Husby, A., Qvarnström, A., Mugal, C., Olason, P., & Ellegren, H. (2014). A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution Molecular Ecology, 23 (16), 4035-4058 DOI: 10.1111/mec.12810

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Leave me your DNA … and I’ll 3D-print your face | The Guardian

Your DNA is as personal as you can get. It has information about you, your family and your future. Now, imagine it is used – without your consent – to create a mask of your face. Working with the DNA bits left behind by strangers, a Brooklyn artist makes us think about issues of privacy and genetic surveillance.

Heather Dewey-Hagborg, a 30-year-old PhD student studying electronic arts at Rensselaer Polytechnic Institute has the weird habit of gathering the DNA people leave behind, from cigarette butts and fingernails to used coffee cups and chewing gum. She goes to Genspace (New York City’s Community Biolab) to extract DNA from the detritus she collects and sequence specific genomic regions from her samples. The data are then fed into a computer program, which churns out a facial model of the person who left the hair, fingernail, cigarette or gum behind. Using a 3D printer, she creates life-sized masks – some of which are coming to a gallery wall near you.

[Read more]

3D Sculpture pictured is by: Sophie Kahn

Would you make your DNA and health data public if it may help cure disease?

The 39-year-old Toronto professional is the brave or, perhaps, foolhardy Canadian volunteer who will be first to go public this week in a project that will reveal the coded secrets hidden in her genome, the six billion chemical units of her DNA.

They may include not only her susceptibility to diseases such as cancer but the levels of her propensities to alcoholism, depression or obesity, or even personality traits such as risk-taking. She will also provide the personal context required to make sense of the biological data – her age, height, weight; medical records; details about how she lives, works and plays; and even her photo if she’s game.

This information – everything but her name and address – will be placed on an online database that will be open and available to anyone in the world. Even in this digital age of perpetual show and tell, exposing oneself so completely amounts to a molecular full monty: Even without a name attached, any participant might be identifiable.

Ms. Davies is making a leap of faith that at least 100,000 of her fellow citizens are also being asked to take – even though Canadian law has no strict guidelines on how this confidential knowledge might be used or misused by any insurance company, employer, police force or identity thief.

Read more

Detecting Fetal Chromosomal Defects Without Risk
Noninvasive sequencing is faster, cheaper and safer for mother and fetus, say researchers

Chromosomal abnormalities that result in birth defects and genetic disorders like Down syndrome remain a significant health burden in the United States and throughout the world, with some current prenatal screening procedures invasive and a potential risk to mother and unborn child.

In a paper published online this week in the Early Edition of PNAS, a team of scientists at the University of California, San Diego School of Medicine and in China describe a new benchtop semiconductor sequencing procedure and newly developed bioinformatics software tools that are fast, accurate, portable, less expensive and can be completed without harm to mother or fetus.  

“We believe this approach could become the standard of care for screening of prenatal chromosomal abnormalities,” said Kang Zhang, MD, PhD, professor of ophthalmology, founding director of the Institute for Genomic Medicine at UC San Diego and a staff physician at the San Diego VA Healthcare System.

The incidence of chromosomal abnormalities – in numbers or structure – is one in 160 live births in the United States, higher in other countries. In China, for example, the rate is one in 60 live births. The effects of these abnormalities, known as aneuploidies, can be severe, from developmental delays and neurological disorders to infertility and death. The incidence rate rises with maternal age, most notably after age 35.

Current diagnoses of fetal aneuploidies often rely upon invasive tests that sample amniotic fluid or placental tissues for fetal DNA that can then be analyzed using a variety of complex and expensive methods, including full karyotyping in which the entire set of chromosomes is viewed microscopically. While highly reliable, these invasive tests may cause infections in the pregnant woman and pose as much as a 1 percent risk of miscarriage and fetal loss. Results are not available for one to two weeks, extending anxiety for families waiting for information.

The new method relies upon massively parallel sequencing of cell-free fetal DNA using a benchtop semiconductor sequencing platform (SSP) called an Ion Torrent sequencer developed by Life Technologies. Cell-free fetal DNA is genetic material from the fetus that circulates naturally and freely in the mother’s bloodstream. It can be obtained through an ordinary blood draw, with SSP analysis achieved in less than four days.

To assess the SSP method, researchers tested 2,275 pregnant women. More than 500 participated in a retrospective analysis, undergoing full karyotyping to establish known chromosomal abnormalities followed by SSP testing. The remainder participated in a prospective study without prior karyotyping, and SSP testing results were then compared to karyotyping results. The sequencing and automated bioinformatics analyses were performed at iGenomics in Guangzhou, China.

“We used the retrospective study to establish the method and the prospective study to validate it,” said Zhang.

In the retrospective study, the researchers found that SSP detected multiple types of chromosomal abnormality with virtually 100 percent sensitivity and specificity compared to full karyotyping.

“To our knowledge, this is the first large-scale clinical study to systematically identify chromosomal aneuploidies based on cell-free fetal DNA using SSP,” said Zhang. “It provides an effective strategy for large-scale, noninvasive screenings in a clinical setting. It can be done in hospitals and outpatient clinics, more quickly and cheaply.”

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A Mitogenomic Phylogeny of Living Primates

  • by Knut Finstermeier, Dietmar Zinner, Markus Brameier, Matthias Meyer, Eva Kreuz, Michael Hofreiter and Christian Roos

“Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels” (read more/open access).

(Open access sourcePLoS ONE 8(7): e69504, 2013; top image: Petter and Desbordes. 2013. Primates of the World: and Illustrated Guide. Princeton University Press)