genomics

Gene Variants Identified as Having a Role in Macular Degeneration 

Age-related macular degeneration can start with blurry or fuzzy vision, or with the weird sense that straight edges—like doorframes or windowsills—actually curve. Eventually, it can lead to a total loss of sharp, central vision, leaving those affected legally blind.

The disease is a leading cause of blindness among the elderly worldwide, affecting more that 15 percent of people aged 65 and older, approximately 150 million people globally. More than 10 million Americans have AMD, more than those who suffer from cataracts and glaucoma combined, according to the American Macular Degeneration Foundation. While some treatments exist, there is currently no way to cure or prevent the disease.

Now, a study has identified 52 common and rare genetic variants distributed across 34 genomic regions—including 13 previously unknown—that play a role in AMD. The findings, published online in Nature Genetics, offer clues to the onset and progression of the disease that may eventually lead to better treatments or a cure.

“We think of these variants as potential targets for new drug development, or biomarkers that could identify people who are at very high risk, so we could potentially intervene early, even before the disease becomes apparent,” says Lindsay A. Farrer, chief of the biomedical genetics section at Boston University School of Medicine (MED). “That’s the hope.”

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Funding: The study was funded by the National Institutes of Health (NIH) and the Edward N. and Della L. Thome Memorial Foundation.

Raise your voice in support of expanding federal funding for life-saving medical research by joining the AAMC’s advocacy community.

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Don't freak out, but scientists think octopuses 'might be aliens' after DNA study
Not to send you into a meltdown or anything but octopuses are basically ‘aliens’ – according to scientists.

Researchers have found a new map of the octopus genetic code that is so strange that it could be actually be an “alien”.

The first whole cephalopod genome sequence shows a striking level of complexity with 33,000 protein-coding genes identified – more than in a human…

Octopus Genome Sequenced For the First Time

You probably have seen all the headlines going viral in the last few days… “Octopuses ‘are aliens’, scientists decide after DNA study”, “Don’t freak out, but scientists think octopuses 'might be aliens’ after DNA study” or “Octopus genetic code is so strange it could be an ALIEN”…. That news is going viral.

Sadly, all these very sensational headlines don’t quite reflect the true science behind. Let’s just start with this: no, octopuses are not aliens.

(Source)

The original discovery was published in Nature, where scientists have found that octopuses possess an unusually large genome. 

If you do not know by now, octopuses are extremely intelligent and highly intuitive creatures. From their ability to mimic other creatures to their irrefutable displays of intelligence, they are truly complex animals. Here, researchers wanted to understand how the cephalopods, a class of free-floating molluscs, produced an animal that is clever enough to navigate highly complex mazes and open jars filled with yummy crabs and other treats.

What this study found is that the octopus genome turned out to be almost as large as a human’s, and to contain a greater number of protein-coding genes — some 33,000, compared with fewer than 25,000 in Homo sapiens.

Originally posted by gifheaven

This study shows  octopuses to have the second-largest gene family yet discovered, with 18,000 genes coding for versions of the zinc finger transcription factors — this is second only to elephants, with over 20,000 genes in the olfactory receptor family.

So moral of the story, don’t believe all the headlines you are going to see, and focus on the actual article published in Nature. Most of these crazy, trending articles imply that octopuses have a different evolutionary history than the rest of the species found on Earth, and basically suggest that these creatures really are aliens from outer space. And of course, they are not.

This new discovery still remains groundbreaking, as it is the first whole genome analysis of an octopus, and it shows that the evolution of the octopus genome was probably driven by the expansion of a few specific gene families, systemic genome shuffling, and the appearance of novel genes. All this could help scientists learn not only how the octopus walked this remarkable evolutionary path, but perhaps more importantly, why.

Originally posted by rorschachx

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Could this be the most powerful scientific tool?

Described as “the biggest biotech discovery of the century” by the scientific community, CRISPR-Cas has been all the rage in labs around the world for its exceptional ease and accuracy in editing the gene of almost any organism.

In 2012, UC Berkeley’s world-renowned RNA expert and biochemist Jennifer Doudna was part of a research team that discovered that you could use the CRISPR system as a programmable tool: scientists can precisely target a gene sequence, cutting and changing the DNA at that exact point. 

CRISPR, which stands for “clustered regularly interspaced short palindromic repeats” are repeated DNA sequences that are an essential component of a bacteria’s defense system against viruses.

And what started out as a study to understand the bacterial immune system unwittingly resulted in a powerful technology that has the potential to cure genetic diseases, create more sustainable crops, and even render animal organs fit for human transplants.

We’ve had gene-editing technology for decades, but now, “we’re basically able to have a molecular scalpel for genomes,” says Doudna.

“All the technologies in the past were sort of like sledgehammers.”

GIF source: Business Insider

vimeo

CRISPR in a nutshell

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.”

Darwin’s… Tanagers?

DYK? Darwin’s finches aren’t finches at all – they are more closely related to tanagers! In 2002, Field Museum ornithologist Shannon Hackett and her coauthors used Field specimens and collections in order to generate a genetic tree of life for songbirds. Darwin’s Finch DNA sequences were pulled from the public database GenBank, and when compared to the DNA songbird tree of life, these scientists discovered the ‘Finches’ are actually nestled into the tree among the tanagers. Just another way in which museum collections, paired with new technologies, enhance our understanding of biodiversity.

Happy Darwin Day

Burns, K. J., S. J. Hackett, and N. K. Klein. 2002. “Phylogenetic relationships and morphological diversity in Darwin’s Finches and their relatives.” Evolution 56: 1240-1252.

Read more on Darwin and Museum Collections!

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.”

Storing 1 Zettabyte In 10 Grams w/ DNA assembly tech

A team of scientist at France’s Institut Charles Sadron & Aix-Marseille Universite have built binary data into the strand of a synthetic polymer. It can store 1 zettabyte of information in 10 grams of matter. More information from DNAforce:

The method is similar to how information is stored in DNA which is also a polymer. However, unlike DNA which has four letters: G, A, T and C organized in pairs, the polymer stores data in binary format. DNA never evolved to become the best possible molecular information storage system. In fact, in living organism, redundancy and duplication is required for DNA to maintaining the genetic integrity of living organism over millions of years in an environment with pollutants and ultraviolet radiation from the Sun. Also DNA is able to easily unfold itself which simplifies copying and reproduction. For a data storage system in a controlled environment, the duplication can be removed, leaving only the highly optimized and efficient information storing features.

The team decided to create an artificial polymer from the ground up for the sole purpose of storing information. The results outdo DNA. The system is also spectacular at copying information. In fact, George Church professor at Harvard, used this method to produce 70 million copies of his book. All copies were held in a drop of liquid.The current limiting feature of the technology is the encoding time. It takes a few days to encode 10 MB of data. The data can be read relatively quickly using full genome DNA testing technologies.

[read more] [paper] [DNA Storage]

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.”

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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!

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So uh

Last night I 

Kind of got a little drunk

And made this

Oops… 

Interested in the Human Genome?

A few years ago, the US Department of Energy’s Genomic Science Program produced a poster highlighting the loci (gene location) of hundreds of genetic conditions.

Unfortunately they had a very small supply, and this was quite a few years ago, so it has long since been out of stock. However, their website for the poster is still up, and they offer a high quality PDF file of the poster for download. I highly recommend checking it out.

They also have individual image files of each chromosome for easier legibility, which look something like this:

I only remembered this porter tonight when replying to a post about another science poster, but it occurred to me that the science side of tumblr might find it as neat as I do.


Source/credit: U.S. Department of Energy Genomic Science program’s  Biological and Environmental Research Information System (BERIS). Their website states that permission to use these images is not needed however credit is requested.  Website: http://genomicscience.energy.gov.


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

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DNA Laser Printing: Hacking Life’s Code and Creating New Organisms with 3-D Printed DNA

There’s a new emerging technology (or just another buzzword) in town: DNA Laser Printing. Austen Heinz, founder of Cambrian Genomics, was part of the glowing plant kickstarter (2013).

“To think that we can’t make organisms that aren’t more efficient than existing, I don’t think is correct,” says Austen Heinz, founder of the biotech startup Cambrian Genomics. “Because nature doesn’t have DNA laser printers, and we do.”

Reason TV’s Zach Weissmueller sat down with Heinz to discuss the ramifications of a technology that dramatically brings down the cost of sequencing and assembling DNA, suddenly making the ability for consumers to create their own organisms an economic reality. Heinz partnered with a company to crowdfund a “glowing plant,” which led to a subsequent ban on GMO-related projects on Kickstarter, and he expresses concern with the lagging regulatory structure governing biotech development. But Heinz is undeterred by regulatory and cultural obstacles and foresees a future where consumers can affordably leverage his technology to fix errors in their own DNA or even design their own creatures in the same way that 3-D printing companies like MakerBot allow for custom models.

“[With] MakerBot, you would print out, say, a plastic dinosaur. With Cambrian, the idea is that eventually you’ll be able to print out your own little dinosaur that actually walks across the table,” says Heinz. “Everything around us is just code. Wouldn’t it be great if we could just snap our fingers and just re-imagine the world around us, where everything is programmable, everthing is re-writeable?”

[Cambrian Genomics]

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.

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