Category Archives: Genome

smithsonian.com April 27, 2017

Researchers from the Dog Genome Project at the National Institutes of Health have released the most detailed canine family tree to date, creating a timeline of when and where dogs from 161 breeds emerged, reports Maggie Fox at NBC News. The researchers compiled the data by sequencing and comparing the genomes of 1,346 individual dogs over 20 years.

The new family tree isnt just a factoid for the kennel club. According to a press release, it has implications for archeology and human health as well. The study, published this week in the journal Cell Reports, suggests thatthe oldest dog breeds are varieties that served a specific function like herding dogs and pointers.

According to the results, herding dogs were bred independently in various parts of Europe with lineages tracing to the United Kingdom, northern Europe and southern Europe. In the past, reports Erin Ross at Nature, researchers had trouble mapping out the lineages of herding dogs, believing they came from a single source. In retrospect, that makes sense, says Elaine Ostrander, an author of the study. What qualities youd want in a dog that herds bison are different from mountain goats, which are different from sheep, and so on.

One of the most interesting finds was that some breeds from Central and South America like the Peruvian Hairless Dog and the Xoloitzcuintle possibly descended from canines that crossed the Bering land bridge with humans thousands of years ago. While there is some archeological evidence that dogs first entered the New World at that time, the study offers potential genetic confirmation. What we noticed is that there are groups of American dogs that separated somewhat from the European breeds, study co-author Heidi Parker of the NIH says in the press release. Weve been looking for some kind of signature of the New World Dog, and these dogs have New World Dogs hidden in their genome.

The study will also give researchers insight into which genes and mutations are associated with human diseases. As Fox reports for NBC, all domesticated dogs are part of the same species, Canis familiaris, and have the same genetic material. There are just a tiny fraction of changes in the genome that separate a Chihuahua from a Great Dane. We have a yellow brick road for figuring out how mutations move around the dog world. We recognize that everything humans get, dogs getepilepsy, cancer, diabetes, heart disease, Ostrander tells Fox. She points out that some diseases are more prevalent in certain breeds, like epilepsy in beagles. We can actually trace diseases as they move around the dog breed population.

The study suggests there were likely two intensive periods of dog breed diversification, writes Ross. The first happened in hunter-gatherer times when dogs were bred for their skills. During the second period, dogs were bred more frequently for their looks. Known as the "Victorian Explosion,"this period was whenmost modern breeds developed.

The canine family tree, however, is not finished. The team has sequenced less than half of the 400 or so recognized dog breeds in the world. The researchers tell Fox they haunt dog shows and Frisbee dog competitions looking for breeds they have not yet sampled. A list of hard-to-find breeds they are currently searching for is on the Dog Genome Project website. It's worth taking a look, perhaps your pup could be one of the missing branches on the canine family tree.

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Dog Genome Project Reveals Secrets of Canine Family Tree - Smithsonian

In regard to point 5) (see the previous post) I agree with Scot that I dont think the later Christian notion of seminal transmission of a sin nature from Adam is a necessary conclusion from what the Bible says. It is the curse that affects the whole human tribe, not Adams sin nature. 6) since all have sinned and lack Gods glory now, it is not necessarily the case that without the historical Adam we dont need the Gospel of salvation, but I would say that Adams sin is the presenting cause which led to the curse which in turn led to fallen human beings.

It is hard for me to doubt that the sorry history of the human race, full of wickedness, bloodshed, hatred, wars etc. is not a profound testimony to sin and fallenness. And besides the Psalmist say in Ps. 51.5- surely I was sinful from the time my mother conceived me. That is hardly a statement about volitional sin after birth. I suspect as well that Pauls language about flesh and his discussion in Rom. 7.14-25 that people can know better, but apart from Christ cannot do the Law, should have some bearing on whether weve all fallen and cant get up without redemption.

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Adam and the Genome Part Eleven - Patheos (blog)

Added Dr. Sandy Macrae, Sangamo's president and CEO: "Edward tirelessly built Sangamo into a leader in the emerging field of genomic therapies. I look to build upon the foundation he established and to realize our shared vision of delivering novel and potentially curative medicines to patients with serious genetic diseases."

Lanphier's career is celebrated for the scientific breakthroughs he enabled at Sangamo and for his public policy and thought leadership in the regenerative medicine and advanced therapies field.

Lanphier founded Sangamo in 1995 as a company focused on regulation of gene expression based upon zinc finger DNA binding protein technology. He fostered scientific innovation within the company, enabling development of methods for highly efficient and specific genome editing. Sangamo's scientists were the first to demonstrate the advantages of this approach in plant and animal species, leading to new methods for the production of novel transgenic animal models and crop modification techniques and laying the foundation for research into human therapeutic uses.

Under Lanphier's leadership, Sangamo scientists were the first to evaluate the safety and efficacy of genome editing techniques in human clinical trials, including the Company's legacy clinical research into cell therapies for HIV. Technologies developed through this program now hold promise as a potential cell therapy approach for cancer and monogenic diseases, including sickle cell disease and beta thalassemia.

Lanphier also championed the development of in vivo genome editing techniques for their potential to cure genetically tractable diseases. Sangamo's zinc finger nuclease (ZFN) technology is the most advanced genome editing technology in development and with its demonstrated efficiency, precision and specificity has earned clearance from the U.S. Food and Drug Administration for in vivo human clinical studies. This year Sangamo is conducting the first ever in vivo genome editing clinical trials evaluating ZFN-mediated therapeutic genome editing approaches for the treatment of hemophilia B, a rare blood disorder, and two rare lysosomal storage disorders, MPS I and MPS II.

A passionate public company CEO, Lanphier developed strong relationships with a broad base of biotechnology investors and industry collaborators and kept Sangamo well financed throughout his tenure, seeking to minimize shareholder dilution and avoiding the use of debt.

Lanphier served as a member of the board of directors of the Alliance for Regenerative Medicine (ARM) from 2012 through 2016 and as chairman from 2014 until 2016. During his term as chairman, ARM grew to include more than 245 members and was recognized as the leading international advocacy organization for gene and cell therapies and the broader regenerative medicine sector. Lanphier heralded the promise of curing diseases through genome editing while also advocating for responsible use of the technology, leading the charge in calling for open debate and discussion of germline genome editing with an editorial published in Nature in March 2015.

"The Alliance for Regenerative Medicine would like to recognize and thank Edward for his extraordinary leadership during his tenure as chair and his commitment to expanding the influence of the organization in the U.S. and Europe.We would also like to acknowledge his significant contributions to the gene therapy and gene editing sectors throughout his 30-plus years in the industry," said Morrie Ruffin, managing director of the Alliance for Regenerative Medicine. "All of us in this field owe Edward appreciation and gratitude for his unwavering belief in the life-saving potential of these technologies."

About Sangamo Therapeutics Sangamo Therapeutics, Inc. is focused on translating ground-breaking science into genomic therapies that transform patients' lives using the company's industry leading platform technologies in genome editing, gene therapy, gene regulation and cell therapy. The Company is advancing Phase 1/2 clinical programs in hemophilia A and hemophilia B, and lysosomal storage disorders MPS I and MPS II. Sangamo has a strategic collaboration with Bioverativ Inc. for hemoglobinopathies, including beta thalassemia and sickle cell disease, and with Shire International GmbH to develop therapeutics for Huntington's disease. In addition, it has established strategic partnerships with companies in non-therapeutic applications of its technology, including Sigma-Aldrich Corporation and Dow AgroSciences. For more information about Sangamo, visit the Company's website at http://www.sangamo.com.

This press release contains forward-looking statements based on Sangamo's current expectations. These forward-looking statements include, without limitation, references relating to the potential of genome editing technology to cure diseases. These statements are not guarantees of future performance and are subject to certain risks, uncertainties and assumptions that are difficult to predict. Factors that could cause actual results to differ include, but are not limited to, the dependence on the success of clinical trials of lead programs, the lengthy and uncertain regulatory approval process, uncertainties related to the timing of initiation and completion of clinical trials, whether clinical trial results will validate and support the safety and efficacy of ZFP Therapeutics, and the ability to establish strategic partnerships. Further, there can be no assurance that the necessary regulatory approvals will be obtained or that Sangamo and its partners will be able to develop commercially viable gene-based therapeutics. Actual results may differ from those projected in forward-looking statements due to risks and uncertainties that exist in Sangamo's operations and business environments. These risks and uncertainties are described more fully in Sangamo's Annual Reports on Form 10-K and Quarterly Reports on Form 10-Q as filed with the Securities and Exchange Commission. Forward-looking statements contained in this announcement are made as of this date, and Sangamo undertakes no duty to update such information except as required under applicable law.

To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/sangamo-announces-the-retirement-of-its-founder-and-genome-editing-pioneer-edward-lanphier-from-the-board-of-directors-300445509.html

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Sangamo Announces The Retirement Of Its Founder And Genome ... - PR Newswire (press release)

A toy xoloitzcuintlel, a dog breed that likely descended from dogs that crossed the Bering Land Bridge with the ancestors of Native Americans.

Penny Inan

At least, parts of its genome have, thanks to the first-ever evolutionary tree for dogs, compiled from genetic sequences gathered from 161 modern breeds and published in the journal Cell Reports.

The gene map, created by a team of scientists led by Heidi Parker of the US National Institutes of Health, was created to tease out the complex relationship between breed development and human migration.

Among a number of surprising findings, the sequencing revealed significant differences between the genomes of certain American dogs notably the Peruvian Hairless and the Xoloitzcuintle and the bulk of familiar breeds developed in Europe and Asia.

Archaeologists long ago established that a type of dog, dubbed New World Dog, arrived in the Americas via the Bering Strait thousands of years ago with the ancestors of Native Americans. However, it was assumed that the breed eventually died out.

Weve been looking for some kind of signature of the New World Dog, and these dogs have New World Dogs hidden in their genome, says Parker.

The new study is not fine-grained enough to sort precisely between New World and European-derived genes in, say, the Peruvian Hairless; doing so remains a target for future research.

The dog family tree also shows perhaps not surprisingly that another cohort of dogs, comprising pointers and gun dogs such as Golden Retrievers, share a very tight genetic grouping. These breeds, largely developed in Victorian England and optimised for use in gun-centred hunting, today display little genetic variation.

The evolutionary tree showing the relationship between dog breeds.

NIH Dog Genome Project

In contrast, genomes from dogs bred for a specific purpose herding harbour considerable differences, indicating the animals were developed independently across a wide range of geographic locations and time periods.

When we were looking at herding breeds, we saw much more diversity, Parker says. There was a particular group of herding breeds that seemed to come out of the United Kingdom, a particular group that came out of northern Europe, and a different group that came out of southern Europe.

This shows herding is not a recent thing. People were using dogs as workers thousands of years ago, not just hundreds of years ago.

The scientists regard the canine family tree very much as a work in progress. About half of the worlds recognised breeds have still to be sampled.

The phylogeny, as it grows, will likely be useful for research in both canine and human health, because dogs and people share a number of diseases and neurological conditions.

Says study co-author Elaine Ostrander: Using all this data, you can follow the migration of disease alleles and predict where they are likely to pop up next, and thats just so empowering for our field because a dog is such a great model for many human diseases.

Every time theres a disease gene found in dogs it turns out to be important in people too.

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Mapping the canine genome reveals origin of dog breeds | Cosmos - Cosmos

For me, where the problem really comes in in Scots presentation is on pp. 107-08 where Scot says that when the adjective historical is attached to Adam and Eve it means ALL of the following things: 1) 2 actual persons named Adam and Eve existed suddenly as a result of Gods creation; 2) those two persons have a biological relationship with all subsequent human beings; 3) their DNA is our DNA; 4)those two died and brought death into the world; 5) those two passed on their sin natures to their descendants 6) without 5) happening and involving all humans, then not all human beings would be in need of salvation; and 7) therefore if one denies the historical Adam one denies the Gospel of salvation.

Now as a historian myself, to use a British metaphor this is way over-egging the pudding. I agree with Scot that too often we have read the Bible through the lens of Augustine and subsequent interpreters of the Bible, to the detriment of getting at the truth of what the Bible actually says. My own view would be yes to no. 1 with a caveat, that we dont fully know how exactly God created Adam and Eve in his image and this last clause is the crucial one. The account we have in Gen. 2 is poetic, but it is also some sort of historical account, more like a primeval saga clothed in ANE garb, than a modern newspaper report.

I do not think Scots no. 2) is a necessary conclusion from any of the statements about Adam in the Bible; 3) may or may not be true, 4) is true in regard to the death of Adam and Eve, and certainly Paul thinks this affected the rest of our kind. The issue is are we talking about physical death or spiritual death or both? I incline to the view that we are talking about spiritual death here, which leads in fact to premature physical death in various cases. We will say more about Scots sevenfold taxonomy of what historical means in the next post.

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Adam and the Genome Part Ten - Patheos (blog)

In celebration of one of the biggest research programs in history, students hosted DNA Day April 25 at the MSC to provide a better understanding of genetics and genomics in healthcare.

Students from a genetics and family health communication course teamed up with genetics graduate students to present A&Ms first DNA Day, which aimed to bring awareness of the importance of genetics and the Human Genome Project, 13-year effort started in 1990 to map and understand human genes. The event featured booths with interactive DNA perspectives and guest speaker Laura Koehly from the National Human Genome Research Institute.

According to the NHGRI, the Human Genome Project allowed researchers to better understand the blueprint of a human being, resulting in more medical advances and better treatment of hereditary diseases. Congress declared April 25 National DNA Day in 2003 to celebrate the Human Genome Project as well as the 1953 discovery of DNAs double helix structure.

In her research at NHGRI, Koehly focuses on how genetic information is translated into family systems. She said she hopes DNA Day will cultivate curiosity in genetics and spark important conversations on family health.

I look at genetics in the context of hereditary cancers, Koehly said. If there is a causative mutation found in a family member, that information needs to flow from family member to family member. My hope is that DNA Day helps those who attend understand the role of genetics and health and hopefully that ripples into family conversations, and gets people discussing what heredity diseases run in their families.

Communication senior Amanda Salerno worked at the forensics booth, which focused on DNA facial recognition, or the use of genes found in DNA to reconstruct what the face may look like. Throughout her semester in genetics and family health communication, Salerno said she was happy with the opportunity to share information about DNA with the public.

We wanted to educate people about why DNA Day is cool and focus on topics such as the Human Genome Project because it is interesting, Salerno said. We want people to see that you dont have to be too interested in science to learn about it.

Assistant communication professor Emily Rauscher teaches the genetics and family health communication class and said she is proud to see how hard the students worked to put on this event.

What I wanted them to get out of this event, was understanding genetics, which is a core component of the class, and also be able to teach it to other people, Rauscher said. They went and got $1,500 in donations by themselves to help with funding the event Ive helped them in terms of giving them deadlines and checking on them but mostly, theyve been really self-sufficient Theyve done a pretty good job.

Communication senior Andrew Bell believes genetic topics are commonly ignored in society today and feels educating people about DNA and how if affects a persons health is useful information for anyone.

It relates to the longevity of your life and the way that you care about your family, Bell said. Weve been given the opportunity to explore those avenues on why it is important to communicate that within the family. Ive had the exposure of learning something that is very important and I think everyone should have the opportunity to learn about.

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DNA Day raises awareness of Human Genome Project - Texas A&M The Battalion

April 24, 2017 Credit: Cancer Research UK

It's been a couple of years since the genome editing tool CRISPR first hit the headlines. And talk of its potential to cure all manner of diseases, create superhumans and bring dinosaurs back from the dead has followed.

But among that speculation, one area of medicine has been quick to pick up the technology and is now leading the way in early clinical trials.

In this second post in our series taking a closer look at CRISPR, we explore its potential for new developments in cancer immunotherapy.

Immunotherapy can take a range of forms. Some experimental approaches use viruses that kill cancer cells and alert the immune system to attack. Others involve giving patients drugs that release the 'brakes' on immune cells to target cancer. And some use specially engineered immune cells that when injected into a patient have the potential to hunt out and kill cancer cells.The aim of immunotherapy treatments is to alert the body's immune system to cancer, so that it's better equipped to recognise and fight the disease.

In each of these cases, scientists need to be able to understand and fine-tune the body's complex immune system. And some are turning to CRISPR for help.

Dr Martin Pule, a clinical senior lecturer in haematology at UCL, says that genome editing techniques such as CRISPR have quickly become part of the tool-kit for researchers like him.

"In the past, many of the technical problems around introducing new genes into cells were worked out, but we didn't have an easy way of efficiently and precisely disrupting existing genes," he says. "New genome editing technologies changed all that."

By using CRISPR, scientists are able to tweak specific genes in viruses or the body's own immune cells, and so make them behave differently.

Researchers have been able to do this before using similar techniques, but the excitement around CRISPR is that this can be done much quicker, cheaper and more precisely than ever before.

Out of the lab, into the patient

Genome editing techniques have been used in people to treat cancer and other diseases before.

There was lots of excitement when news broke in 2015 of a 1 year old girl with acute lymphoblastic leukaemia (ALL) being treated with a similar editing technique known as TALENs, after all other treatments had failed.

She received a transplant of cancer-fighting immune T cells from a donor, which had been tweaked in the lab to give them 2 new characteristics.

Normally, the donated cells would see their new environment as foreign and attack the patient's healthy cells, but genes that control this process were turned off. The T cells would also be susceptible to attack from the anti-cancer drugs that the baby was receiving, and so modifications were made to protect them.

She responded well to the treatment, and another infant received a similar therapy.

Following in the footsteps of its cousin TALENs, CRISPR itself has moved on from the lab to clinical trials. Late last year, a Chinese group became the first to use CRISPR-edited cells in humans.

The team took immune cells from a patient with an aggressive lung cancer and edited them in the lab. This editing deactivates a gene that allows tumours to put the 'brakes' on these immune cells, preventing them from attacking cancer cells.

By switching off the gene, which produces a molecule on the cells' surface called PD-1, the full force of the body's immune system is released, helping it clear the tumour. Drugs that target PD-1 are among the much-lauded immunotherapy treatments already showing promise in advanced melanoma and lung cancers. So there's a lot of hope that CRISPR may provide another step forward here too.

10 patients will be involved in the early-stage Chinese trial, and it will look at whether the treatment is safe, rather than testing effectiveness.

The scientists are also hoping to start clinical trials using CRISPR to treat bladder,prostateandkidney cancers. It's also positive news that both blood cancers and solid tumours appear to be responding to various immunotherapy approaches, as different challenges are faced in treating these diseases.

Kickstart the CAR

One clever immunotherapy trick fuses together 2 components of the immune system with different jobs.

Chimeric antigen receptor (CAR) T cells are a mix of an antibody molecule, which can home in on a specific target on tumour cells, fused to a T cell that provides the knock-out blow to the cancer cell.

We've blogged before about how these engineered cells work, and small trials in 2011 caused lots of excitement. But one of the latest updates is that using CRISPR instead of older genome editing techniques might supercharge these CAR T-cells even further.

The older technology is less precise and can result in the genes mistakenly being inserted at random locations in the cell's DNA. The knock-on effect is that the engineered cells' might be less effective or unintended side-effects could be introduced.

But a US-based group found that CRISPR improved the precision with which the modified gene was inserted into T cells. Their research suggests that the cells were then more potent in their fight against leukaemia in mice because they had more stamina. The researchers are now hoping to test these findings in people.

"Cancer cells are relentless in their attempt to evade treatment, so we need CAR T cells that can match and outlast them," Dr Michel Sadelain, the researcher leading the study at Memorial Sloan Kettering Cancer Center, said at the time.

It's findings like these that will hopefully make engineered immune cell treatments better and kinder in the future, though they aren't yet the Holy Grail.

"In one kind of leukaemia called B-ALL, almost 100% of children who received engineered T cells responded, despite having a disease which had become resistant to all standard treatments," says Pule.

This suggests that, in some circumstances, there may not be an upper limit on who may respond to these treatments. But achieving this in other cancers will take further fine-tuning. In other diseases, such as another kind of blood cancer called DLBCL, the response rates are more like 60%.`

"This reflects the fact that a good CAR T cell product is hard to make, or that there are factors inside the tumour making the T cells less effective," Pule adds.

Lots of the progress using CAR T cells has so far been in blood cancers rather than solid tumours, which have even tougher conditions.

Because CRISPR allows scientists to do lots of small-scale tinkering, this is a rapidly developing field and researchers are trying to find solutions.

"Right now a lot of people are asking why there's this response gap between DLBCL and B-ALL. Can we edit something in the CAR T cell, or put something extra in which will increase the response rates?"

One reason might be that the tumour lives in a hostile environment that stops the engineered T-cells' ability to attack the cancer cells. One way around this is to delete the molecules on T cells that coordinate the stop messages from the microenvironment.

"This strategy looks like it might be quite effective and could increase the number of patients who respond," says Pule.

The other side of immunotherapy

Some of the research that's taken place since CRISPR burst onto the scene has also raised more questions than answers. The immune system is a powerful and complicated machine, and we don't yet understand how to control it.

Not all of these treatments have been as successful as hoped. As well as varying response rates, they can also cause serious side effects, including, in rare cases, death.

There have been recent reports of patients with bladder cancer whose tumours increased in size after immunotherapy treatment, although this has caused some debate among researchers. Side effects including extreme fever or organ damage have also been well documented in clinical trials.

In the US, a total of 5 patients died following treatment with an experimental CAR T cell therapy for ALL. The clinical trial was paused after 3 people died, and then stopped after 2 more deaths.

While this is very rare, it's clear that as well as working to make treatments more effective in more people, researchers also need to look at how they can reduce side effects.

Similar problems were seen in the past in the early days of treatments such as combination chemotherapy, before they were refined.

Pule points to how scientists are already using genome editing to increase safety. For example, in many cases, it isn't possible to engineer a patient's own T cells and so cells from a donor are needed.

But this raises some challenges.

"The donor T cells might attack the recipient causing graft-versus-host disease," says Pule. Graft-versus-host disease is a condition where the donor cells see their new environment as foreign and attack it. "If we remove a specific molecule in the donor T cells using gene-editing technology, we can reduce the chance of this happening."

This is how the two infants with ALL were treated.

Where next?

Like many new technologies, CRISPR was greeted with excited fanfare in some parts, and a more cautious realism is now settling in.

It's clear that CRISPR opens up so many doors for immunotherapy and lets researchers go further, more easily than ever before. But as the technology is understood better, its limitations and challenges also come into focus.

The third part of our CRISPR series will take a look at what the future might hold for CRISPR and cancer research.

Explore further: CAR T cells more powerful when built with CRISPR, researchers find

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CRISPR genome editing and immunotherapy the early adopter - Medical Xpress

THE THEOLOGY CHAPTERS

Scots first chapter deals with four principles with which to read the Bible. As Scot says at the outset Theology which is designed to investigate that nonempirical reality in some ways, can provide a map onto which we can locate science and which can challenge science. (p. 95). Exactly my point. The empirically observable and testable world is not all there is to reality. Scots concern is we will all gain clarity if Christians learn how to speak about Adam and Eve in a context that both affirms conclusions about the genome and challenges some conclusions drawn from the Human Genome Project. (p. 97).

The first of the four principles by which to study the Bible and talk with others about it is respect and respectful discourse for disciplines other than Biblical studies, and in this case science, and particularly genetics. I agree with Scots statement on p. 99 that it is disrespectful to Scripture itself to expect the authors of Gen. 1-11 to be scientists in advance of the scientific era that already understand DNA etc. There is no evidence that they did.

If one takes the related field of cosmology, what we have is the use of phenomenological not scientific language about the relationship of our sun to earth. They talk about the sun rising and setting, which is true from an earthbound observational point of view. Thats how it looks to us. Its not the reality of the situation however. Such observations are not intended to teach us cosmology, merely how things appeared to these ancient people, and indeed, how it appears still today to us. Scot spends considerable time situating Gen. 1-11 in its ANE context in some helpful ways as we shall see. He even recites my favorite dictuma text without a context is just a pretext for whatever you want it to mean.

The second valuable principle is honesty, and again I fully agree. Fundamentalists react to science as if it were a contagious disease, and come up with fear-based theories about both the Bible and science, neither of which are helpful. It results in bad history and bad Bible interpretation and bad science too, the worst of both worlds.

I will certainly never forget the time I hitch-hiked back from the mountains of N.C. in 1969 with two flat landers, who insisted that the moon walk by Neal Armstrong and all those pictures of a beautiful round and revolving earth were a Hollywood stunt. When my friend Doug asked why they thought it was fake the answer was it says in the book of Revelations that the angels will stand on the four corners of the earth. Cant be round if it has four corners. Bless their hearts these folks did not know that apocalyptic literature isnt teaching cosmology, its teaching eschatology, and the whole point was the angels would round up people from all points on the compass, not that the earth was flat! Sometimes invincible ignorance is impossible to dialogue with.

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Adam and Genome Part Eight - Patheos (blog)

April 24, 2017 by Kathleen Phillips The genome of Botryococcus braunii, being studied for its potential for biofuel by Texas A&M AgriLife Research scientists in College Station, has been sequenced. Credit: Texas A&M AgriLife Research photo by Kathleen Phillips

The genome of the fuel-producing green microalga Botryococcus braunii has been sequenced by a team of researchers led by a group at Texas A&M AgriLife Research.

The report, in Genome Announcements, comes after almost seven years of research, according to Dr. Tim Devarenne, AgriLife Research biochemist and principal investigator in College Station. In addition to sequencing the genome, other genetic facts emerged that ultimately could help his team and others studying this green microalga further research toward producing algae and plants as a renewable fuel source.

"This alga is colony-forming, which means that a lot of individual cells grow to form a colony. These cells make lots of hydrocarbons and then export them into an extracellular matrix for storage," Devarenne said. "And these hydrocarbons can be converted into fuels gasoline, kerosene and diesel, for example, the same way that one converts petroleum into these fuels."

Devarenne pointed to previous studies showing that hydrocarbons from B. braunii have long been associated with petroleum deposits, indicating that over geologic time the alga has coincided with and contributed to the formation of petroleum deposits.

"Essentially, if we were to use the hydrocarbon oils from this alga to be a renewable fuel source, there would be no need to change any kind of infrastructure for making the fuel. It could be put right into the existing petroleum processing system and get the same fuels out of it," he said.

Devarenne said his lab wants to understand not so much how to make fuel, but rather how the alga makes these hydrocarbons, what genes and enzymes are involved and how they function.

"Once we understand that, maybe we can manipulate the alga to make more oil or specific types of oil or maybe we can transfer those genes into other photosynthetic organisms to have them make the oil instead of the alga," said Devarenne, whose lab in 2016 announced the discovery of the enzyme used by the algae to produce hydrocarbons.

That's why sequencing the genome was important, he said, because it will help identify all the genes and enzymes in the genome needed for hydrocarbon production and control of this production.

And it isn't easy. Sequencing the genome means isolating all the DNA from the nucleus of the cell, sequencing it into small fragments and then assembling it back together into a complete genome. Think of a 166 million-piece jigsaw puzzle, given that the size of the B. braunii genome is estimated to be about 166 million bases, he said.

Devarenne said that because only portions of the B. braunii genome in this report are "spelled out," so to speak, it is considered a draft genome, or first attempt at assembling all the pieces.

"It's not perfect, but it's still very usable and valuable to the other researchers who are studying this alga," he said. His own lab plans to do a more in-depth analysis and compare it to other known algae and land plant genomes so as to see what's unique and similar.

Along with the sequencing, Devarenne's study found that there are about 18,500 genes in the B. braunii genome and there are portions of genes called untranslated regions that are very long. These regions are not formed into proteins but are rather used for regulatory purposes.

"They can be several thousand base pairs long, whereas in most organisms those regions may be only a couple hundred base pairs long," he said of the untranslated regions. "We don't know what that's about yet."

He said the B. braunii genome has been very challenging to assemble because of lots of repetitive sequences in it.

"Assembling the genome is not a trivial process at all," Devarenne explained. "We send DNA to be sequenced by the Joint Genome Institute, which is part of the U.S. Department of Energy, and they sequence it in lots of very small fragments. These fragments of DNA may be anywhere from 150 to 300 base pairs long. So imagine if we have 166 million bases in our genome, and it is sent back to us in little fragments that have to be assembled back together to arrive at 166 million bases. We used the Texas A&M Supercomputer Center to help."

As more gaps are filled in, he said, a more complete genome will emerge, and that will help researchers dive deeper into the biochemical processes in this alga.That information will then help them understand how and why the organism makes hydrocarbons in very high quantities, how that process is regulated and what the particular biosynthetic pathways are used to make the hydrocarbons.

"Just like the human genome has been sequenced but isn't fully understood, there is still a lot to study. It's really a never-ending process," Devarenne said.

Explore further: Scientists do groundwork for genetic mapping of algae biofuel species

More information: B. M. Carreres et al. Draft Genome Sequence of the Oleaginous Green AlgaUTEX 393, Genome Announcements (2017). DOI: 10.1128/genomeA.01449-16

Researchers from the Wellcome Trust Sanger Institute and their collaborators have shown that receptors in the noses of mice exposed to certain smells during life are different to genetically similar mice that lived without ...

The function of a plant's roots go well beyond simply serving as an anchor in the ground. The roots act as the plant's mouth, absorbing, storing and channeling water and nutrients essential for survival.

Fossils accidentally discovered in South Africa are probably the oldest fungi ever found by a margin of 1.2 billion years, rewriting the evolutionary story of these organisms which are neither flora nor fauna, researchers ...

Banded mongooses target close female relatives when violently ejecting members from their social groups, University of Exeter scientists have found.

The ants of the genus Sericomyrmex - literally translated as 'silky ants' - belong to the fungus-farming ants, a group of ants that have figured out how to farm their own food. The silky ants are the less well-known relatives ...

The bacteria residing in your digestive tract, or your gut microbiota, may play an important role in your ability to respond to chemotherapy drugs in the clinic, according to a new study by scientists at the University of ...

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Correct me if i'm wrong. Yeast has 47 Million base pairs humans have double that. And algae has close to double what humans have? This is genius. It's like our one successful breakthrough to outcast the use of mult-carbons!!! This is cool. This one should go straight to being required. 10 years and it will be a key ingredient in our Construction world. Forget diesel

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Read this article:
Genome sequence of fuel-producing alga announced - Phys.Org

I must admit, I am less willing to critique all the intelligent design folks the way Venema does at the end of his last chapter. I think there is far more to some of their arguments than some would allow. Some of these folks are actual scientists who are also people of faith and are struggling to make sense of both the Bible and evolution. Good for them. We need more, not less efforts to bring the two disciplines together for dialogue, and that does not include and assumption the science and its theories should go unchallenged, and that Bible interpretation should simply adapt to the brave new world of genetic truth.

The third principle Scot mentions is sensitivity to students of science, and again, I totally agree. I do not know if Scots claim on p. 104 that the number 1 reason kids leave the faith is because of questions about science, is true, but certainly some do. In light of the second half of this book, one should be equally concerned about students leaving the faith because someone told them that Adam and Eve did not exist as historical persons. The undercutting of the historical foundations of the Bible can be equally damaging to someones faith.

Scots fourth principle is also a useful one Scot says prima Scriptura is better than sola Scriptura, and I agree if we are talking about knowledge or truth in general. If we are talking salvation, sola Scriptura is closer to the truth.

Read more from the original source:
Adam and the Genome Part Nine - Patheos (blog)