Ever since the genomics revolution took off, scientists have been busily deciphering vast numbers of genomes. Cataloging. Analyzing. Comparing. Public databases hold 239 complete bacterial genomes alone.
But scientists at The Institute for Genomic Research (TIGR) have come to a startling conclusion. Armed with the powerful tools of comparative genomics and mathematics, TIGR scientists have concluded that researchers might never fully describe some bacteria and viruses–because their genomes are infinite. Sequence one strain of the species, and scientists will find significant new genes. Sequence another strain, and they will find more. And so on, infinitely.
“Many scientists study multiple strains of an organism,” says TIGR President Claire Fraser. “But at TIGR, we’re now going a step further, to actually quantify how many genes are associated with a given species. How many genomes do you need to fully describe a bacterial species?”
[…]
Analyzing the eight GBS [Streptococcus agalactiae] genomes, the researchers discovered a surprisingly continual stream of diversity. Each GBS strain contained an average of 1806 genes present in every strain (thus constituting the GBS core genome) plus 439 genes absent in one or more strains. Moreover, mathematical modeling showed that unique genes will continue to emerge, even after thousands of genomes are sequenced. The GBS pan-genome is expected to grow by an average of 33 new genes every time a new strain is sequenced.

More on these elusive little buggers!

The chimpanzee genome has been sequenced, joining that of the cat, dog, horse, cow, mouse, elephant and others. Unfortunately, they’re all written in Klingon.

But when researchers announced the latest addition to the genome list last week, it made national headlines, thanks to the nature of the beast – our closest living relative, the chimpanzee. The $25 million chimp project was part of a federal program to sequence animal genomes that costs taxpayers $130 million a year.
Some enthusiasts claimed that data from the project proved Darwin’s theory of evolution beyond a reasonable doubt. Others said the information could eventually make it easier to develop treatments for diseases such as Alzheimer’s and Parkinson’s.
But some scientists are now questioning whether the expensive and complex sequencing of so many animal genomes is worth the effort. They argue that science needs more research on the anatomy and physiology of the animals themselves – and less into genetic heritage.
“We’ve sequenced all these animals, but it really doesn’t help much yet because we don’t know the functions of so many human genes, or their counterpart genes in other animals,” said Bernard Wood, an anthropology professor and an expert on apes and evolution at George Washington
University.
“You could say that the technology has advanced beyond our ability to make good use of the information.”
Wood’s review of the anatomical differences between chimpanzees and humans, published a few years ago in Proceedings of the National Academy of Sciences, found that of 1,700 anatomical structures in humans, there are only 200 counterpart structures that match up in chimps.
“We still don’t know enough about chimpanzees,” he said.
Genome sequencing is the process of identifying the order of the billions of pairs of genetic code that dictate an organism’s functions and characteristics. To sequence a genome, researchers extract DNA from a blood or tissue sample and use sophisticated machines to identify the arrangements of the long chains of chemicals, known as “base pairs,” that together form different genes.
But the genetic code is written in an unfamiliar language, so sequencing a genome of any plant or animal doesn’t immediately lay open its genetic secrets.

Not only is it written in an “unfamiliar language”, that language can be “reinterpreted” differently from individual to individual, by the action of genes at other loci or environmental influences once thought unlikely – such as prenatal diet. For all the hoopla, it’s unlikely that gene therapy is going to have much more than very limited applications for the forseeable future.
From the Baltimore Sun.

Those damned Koreans are at it again;

Like Dolly and other predecessors, Snuppy was created using a method called somatic cell nuclear transfer, or SCNT.
Scientists transfer genetic material from the nucleus of a donor adult cell to an egg whose nucleus – with its genetic material – has been removed. The reconstructed egg holding the DNA from the donor cell is treated with chemicals or electric current to stimulate cell division.
Once the cloned embryo reaches a suitable stage, it is transferred to the uterus of a surrogate where it continues to develop until birth.
Dog eggs are problematic because they are released from the ovary earlier than in other mammals. This time, the researchers waited and collected more mature unfertilized eggs from the donors’ fallopian tubes.
They used DNA from skin cells taken from the ear of a 3-year-old male Afghan hound to replace the nucleus of the eggs. Of the three pregnancies that resulted, there was one miscarried fetus and one puppy that died of pneumonia 22 days after birth.
That left Snuppy as the sole survivor. He was delivered by Caesarean section from his surrogate mother, a yellow Labrador retriever.
Researchers determined that both of the puppies that initially survived were genetically identical to the donor dog.
Schatten said the Afghan hound’s genetic profile is relatively pure and easy to distinguish compared to dogs with more muddled backgrounds. But dog experts said the researchers’ choice of breed choice was disquieting.
“The Afghan hound is not a particularly intelligent dog, but it is beautiful,” said psychologist Stanley Coren, author of the best-selling manual “The Intelligence of Dogs.” He ranked the Afghan hound last among 119 breeds in temperament and trainability.
“Many people who opt for the cloning technique are more interested in fashionable looks,” he said. “Whenever we breed dogs for looks and ignore behavior, we have suffered.”

(Dog breeder’s aside; Why does the reporter inject this meaningless prattle from faux-expert Stanley Coren (who is to the world of canine science what Oprah Winfrey is to the study of subatomic particles) into this story? His ignorance is underscored by the very quotes they provide.)

More evidence of a genetic basis for autism;

Using DNA samples from 120 families likely to possess a genetic risk factor on chromosome 17, the team found 19 different SERT mutations ( or variants ) in families with multiple affected males, consistent with the well-known sex-bias seen in autism incidence.
Four of these variants were in ‘coding’ regions, or parts of the gene that get translated into protein. The other 15 variants were in ‘noncoding’ regions, which are edited out of the final protein product but may have important regulatory roles in the expression of the gene. “These coding mutations tracked with an increased severity of rigid- compulsive behaviors,” Sutcliffe explained. These types of behaviors are a common characteristic of autism and related disorders like obsessive-compulsive disorders.
The findings underscore the relationship between autism and disorders like OCD and may explain why SSRIs are effective in treating these conditions, he said.
[…]
Based on these findings, Blakely and Sutcliffe predict that there will one day be a way to test autistic children for these gene variants, similar to the testing done for cystic fibrosis, a disease linked to a single gene but triggered by many different mutations.
“Autism has such a high genetic risk, but these new findings suggest that there may be many variants of individual genes at work,” Blakely said.
With such genetic testing, said Sutcliffe, “you might be able to predict which kids would respond positively to particular SSRI medications.”
“We now have concrete evidence in our families that the SERT gene is a risk factor in autism,” Blakely said. “Perhaps more importantly, we also have new pathways that could have some therapeutic end points, and that, to us, is really good news.”

Wired;

Challenging a scientific law of inheritance that has stood for 150 years, scientists say plants sometimes select better bits of DNA in order to develop normally even when their predecessors carried genetic flaws.
The conclusion by Purdue University molecular biologists contradicts at least some basic rules of plant evolution that were believed to be absolute since the mid-1800s, when Austrian monk Gregor Mendel experimented with peas and saw that traits are passed on from one generation to the next. Mendelian genetics has been the foundation of both crop hybridization and the understanding of basic cell mutations and trait inheritance.
In the Purdue experiment, researchers found that a watercress plant sometimes corrects the genetic code it inherited from its flawed parents and grows normally like its grandparents and other ancestors.
Scientists said the discovery raises questions of whether humans also have the potential for avoiding genetic flaws or even repairing them, although they said the actual proteins responsible for making these fixes probably would be different in plants.
Details of the experiments appear in Thursday’s issue of the journal Nature.
“This means that inheritance can happen more flexibly than we thought,” said Robert Pruitt, the paper’s senior author.
In the experiment, the Purdue researchers found that 10 percent of watercress plants with two copies of a mutant gene called “hothead” didn’t always blossom with deformed flowers like their parents, which carried the mutant genes. Instead, those plants had normal white flowers like their grandparents, which didn’t carry the hothead gene and the deformity appeared only for a single generation.
The normal watercress plants with hothead genes appear to have kept a copy of the genetic coding from the grandparent plants and used it as a template to grow normally.
However, Pruitt’s team didn’t find the template in the plants’ DNA or chromosomes where genetic information is stored and they did not determine whether a particular gene is encoded to carry out the recovery of the normal DNA.
Where the normal genetic template is stored and how it is triggered will take additional research and probably involve more genes, Pruitt said.
Humans and other animals do not carry the hothead gene, so if this process occurs in higher organisms it must use a different trigger, he said.
Other scientists described the results as “spectacular.”
Detlef Weigel and Gerds Jurgen of the Max Planck Institute for Developmental Biology in Germany wrote in an accompanying commentary in Nature that the mechanism for recovering the normal DNA in the watercress plants might be lurking in the plant’s RNA, which carries out genetic orders in cells.

Meeting your wife at the family reunion ain’t a phenomenon peculiar to Tennessee[1].

It began as the kind of childhood crush that often becomes family lore shared at reunions years later.
Eventually, first cousins Donald W. Andrews Sr. and Eleanore Amrhein realized they had a deeper love and wanted to wed. It couldn’t happen in their state of Pennsylvania, though, or 23 other states that prohibit first cousins from marrying each other.
Instead, they tied the knot in Maryland last month.
”This is a decision me and my husband have made on our own,” said Eleanor Andrews, 37. ”We didn’t want the publicity. We wanted the rights like anybody had the rights.”
Advocates say the issue is misunderstood. Such marriages are common in the Middle East, Asia and Africa and are legal in Europe and Canada.

Everyone has advocates these days!

Robin Bennett, associate director of the medical genetics clinic at the University of Washington, said laws prohibiting cousins from marrying are ”a form of genetic discrimination.”
Close cousins face a risk of birth defects that is 1.7 percent to 2.8 percent higher than for unrelated couples, according to a study, funded by the National Society of Genetic Counselors, and the U.S. Health and Human Services Department.

That part is accurate. The actual risk of producing an offspring affected with a serious recessive inherited defect is relatively small – certainly lower than the existing frequency in the population of dominant gene defects that predispose us to cancer, diabetes, autoimmune diseases.
For example, this new finding may explain why prostate cancer is more prevalent in African American populations. 70% carry an anti-malaria gene that “reduces production of a chemical used by malarial parasites to infect red blood cells but also may play a role in inhibiting the growth of new blood vessels the tumors need to grow”.
Genetics is complicated.
For all the raised eyebrows the topic draws, the primary risk in consanguous marriages is the complications they raise for relationships in the extended family. When you have a fight and both go home to mother, it’s probably best that they not be the same woman.
Footnote:
[1] Don’t even think of sending me hate mail.

Genetic Savings And Clone* announces plans for world’s first 1,200 lb turkey.

I recieved this via an email list. The only links I could come up with were behind a subscriber wall, so I”m reposting it here in its entirety. There is more in the extended entry – fascinating stuff for both the dog breeder and medically oriented. For dog breeders who have been following discussions raging around genetic diversity over the past few years (an offshoot of the environmental and animal rights cults), the findings about the frequency of new mutations undermines some old mythology that physical extremes in dog breeds are due to inbreeding.

Old tricks make new dogs
Dozens of new dog breeds have taught Dallas scientists one of evolution’s very old tricks. The researchers have uncovered a previously unappreciated genetic mechanism that, over millions of years, may have helped sculpt the many different shapes of the world’s animals.
The findings based on a gene that helps give dog breeds their distinctive head shapes may also explain how massive St. Bernards, tiny Chihuahuas and everything in between descended from the wolf in just a few thousand years.
Understanding this genetic process could also give scientists new clues to the development of the human form and brain, as well as the rampant growth of cancers.
“We’re just beginning to scratch the surface of all the gadgets and tools that nature has come up with,” said John “Trey” Fondon, one of the biologists from the University of Texas Southwestern Medical Center at Dallas who performed the new research. “This is just one of them. But what
it says is that we don’t know nearly what we think we know about how evolution works.”
Original Research Article here (pdf), courtesy of John Fondon.
The report describing the research, released Monday [12-13-04], appears online in the Proceedings of the National Academy of Sciences.
Several years ago, Dr. Fondon and UT Southwestern collaborator Harold “Skip” Garner began to study portions of the genetic blueprint that stood out from the rest. The genetic blueprint of all organisms exists in long chains of four DNA chemicals, abbreviated A, T, C and G. Embedded in those chains are series of the same letters, repeated over and over again, such as CAGCAGCAGCAGCAG.
The scientists noticed that many of these repeated series were smack in the middle of genes that instruct cells to make proteins important for sculpting the body’s form during an animal’s development.
Curious about whether different repeated lengths cause different body shapes, Dr. Fondon decided to investigate them in a species that encompasses a vast range of shapes — man’s best friend, the domestic dog.
92 breeds studied
Drs. Fondon and Garner used dogs — including their own pets — representing 92 breeds to obtain DNA from blood samples. The scientists then used a laser 3-D scanner to create computer models of dog skulls from the same breeds, loaned from museums in Alaska, Washington, D.C., Los
Angeles and Switzerland. Finally, they analyzed the repeated sequences in several genes and tried to make correlations between the length of the repeats (which varies among breeds) and the shapes of the dogs’ skulls.
The UT Southwestern scientists found that the number of repeats in a gene called Runx-2 correlates with the angle and length of a breed’s nose. For instance, bull terriers dogs with long, downturned snouts, typified by former Budweiser mascot Spuds McKenzie, had 13 repeats in a row. But the boxer, with a short and upturned nose, had 16 repeats.
The scientists concluded that the lengths of genetic repeats in all the dogs studied had to be a result of domestication and breeding because dogs had repeat lengths well outside the range in their ancestor, the wolf. That fits with the fact that the dog noses can be much shorter or much longer than wolf noses.
The findings also mean that established dog breeds continue to change — and new ones continue to appear — because breeders are creating new genetic material as they select dogs with the highly prized, more extreme physical traits.
Dr. Fondon suspects that along with head shape, many aspects of a breed’s appearance, including leg length, girth, tail type and overall size, may be due to variation in repeats found in key genes.
Conventional wisdom says all the traits seen in modern dogs were presentbut simply hidden in wolves, Dr. Fondon said.
“Our data shows that dogs are creating new variation all the time,” he said.

Continue reading →

Pete at Gull Chased Ship;

This has got to be the strangest story yet. They haven’t even found a “gay gene”, nor will they ever, and yet they’re trying to bring in legislation to prevent someone from aborting gay children. You’re allowed to be pro-choice, but you’re only allowed to abort straight babies.

And male ones.
update – Jonah Goldberg delves into the matter. I suspect that Maine State Rep. Brian Duprey may be one shrewd operator – legislation like this holds the promise of spontanious head explosions for the left.
On a related topic, I stumbled on this post from last December by John C. A. Bambenek, on the cover-up of child sex abuse cases by Planned Parenthood.

A truth the bears telling is that the dirty little secret in town is that it looks like Planned Parenthood covers up for child rape. Yes, you read that right. Here’s the scoop.
[…]
Using a combination of public records of abortions on minors (age 12 to 15), Planned Parenthood’s own research, and comparing the number of abuse reports made be medical professionals, the following is an estimate of the number of sex abuse cases per state that abortion providers covered up in the year 2000. (Not all states are represented because data was not complete for all 50):
State Number of child sex abuse cases unreported
Arizona 4054
California 25359
Florida 11364
Georgia 9240
Illinois 9792
Indiana 5961
Kansas 2958
Michigan 9432
Missouri 6888
New York 16106
North Carolina 7406
Ohio 10392
Pennsylvania 12989
Tennessee 5534
Texas 18077
Virginia 4911

The things that hide “in plain sight”.
Hat tip – North Western Winds.

As gay activists mobilize to defend the sexual orientation equality rights of zoo penguins (put a group of male inmates together, and you know… what happens, happens…) – gene therapy is curing guinea pigs that still won’t come when they’re called.
Something tells me there’s going to be hell to pay.

Ants’ ‘genetic engineering’ leads to species interdependency

Findings reported this week reveal how an evolutionary innovation involving the sharing of genes between two ant species has given rise to a deep-seated dependency between them for the survival of both species populations. The new work illustrates how genetic exchange through interbreeding between two species can give rise to a system of interdependence at a high level of biological organization–in this case, the production of worker ants for both species.
Millions of years before the first modern humans evolved, ants were practicing many of the social innovations we consider to be our own: division of labor, agriculture, and even slavery. Indeed, these traits have been taken to their extreme in many ant species, such as the case of slavemaker ants, which have become so specialized for raiding food from the colonies of other ants that they can no longer feed themselves or raise their younger siblings. Recent work on ants suggests that we may need to add genetic engineering to the list of innovations ants have evolved to employ. In two species of harvester ants, populations have been discovered in which queens mate with males of another species to produce genetically novel hybrid workers. In a new study, Dr. Sara Helms Cahan and colleagues demonstrate that both of the species involved have effectively given up the ability to produce pure-species workers in favor of the hybrids, thereby becoming completely dependent on one another for survival.
Female ants are generally found in two forms: reproductive queens and sterile workers. The role, or caste, of an individual is determined for life at a certain stage in her development. In virtually all ant species, it is the environment in which a female is raised, rather than a genetic predisposition, that determines which caste she will adopt. However, in two harvester ant populations in southern New Mexico, queens and workers from the same colonies are genetically very different; in both species at the site, only the queens are genetically derived from a pure species-specific lineage, whereas all the workers are hybrids that possess a combination of genes from the two species in a single individual. It is not currently known whether the ants benefit from having hybrids do the work, but, as is evident from the researchers’ own attempts at selective breeding and genetic engineering, combining genomes is an easy way to produce novel characteristics that may be highly advantageous for growth, environmental tolerance, or disease resistance. Regardless of the specific advantages, however, it is clear that these ants have committed themselves to the hybrid workforce strategy. When the researchers prevented queens from mating with males of the other species, very few succeeded in making any workers at all, a handicap that would lead to certain population failure in the field. The new findings suggest that specialization involving reliance on interspecific hybrid workers has left these species unable to survive independently of one another.

A little like Paul Martin’s minority government…

Over the past year or so, debate has waxed and waned about issues of political interference in the field of human genetics – stem cell research, bans on cloning. I covered it in March with these thoughts prompted by criticism of Bush appointments to the President’s Council on Bioethics.
A William Saletin column from Friday, in Slate, provides sobering evidence that there may be a very real need for checks and balances, if this commentary is representative of some of the mindsets in the research community.

Eric Juengst, a jovial bioethicist with a puffy white beard, takes the stage after lunch. He looks like Santa Claus and sounds like an elf. But the gift he brings isn’t for children. It’s a caustic wit aimed at anti-biotech hysteria. Juengst says human nature has been changing all along and will keep changing. He calls up a picture of an imaginary creature, half human and half cheetah. “Cheetah Man,” he jokes�or as the creature’s track-meet competitors might call him, “Cheater Man.” Next comes a drawing of a half-ape humanoid designed to fight wars, followed by a Weekly Standard article warning that the cloning of pigs to grow organs for humans will lead to “pig-men.” Juengst reads from the article in the hammed-up voice of a guy narrating a horror-movie trailer. The whole audience laughs.
Well, almost the whole audience. After Juengst finishes, Richard Hayes, the director of the Center for Genetics and Society, rebukes his “mocking, sarcastic” dismissal of people’s fears. Juengst replies that the pig-man article is funny. Hayes says it isn’t. The next questioner, biotech enthusiast Lee Silver of Princeton University, agrees with Juengst that humanity is always evolving. He asks whether popular belief in the sanctity of our species is religious and irrational. He cites the argument of his Princeton colleague, Peter Singer, that humans aren’t much more valuable than chimps.

Read it all.

Finally, I can get a good nights sleep. It’s not my fault, after all.
It was all because of those Cro-Magnan SUV’s.

A Christmas gift idea for the white supremacist who has everything.

Customers recieve a CDROM with their raw genetic data, a bar graph showing the percentages of each group and a specialized representation of their data called a triangle plot, along with a users manual. Ancestry cannot be determined by any genetics test in a black/white litmus test fashion. Instead, the results are reported as statistical estimates, and are qualified with confidence intervals. From over 6,000 tests so far performed, and extensive mathematical simulation, we know that the test is accurate to from 4-8% and sensitive enough to detect, for many customers, a single (100%) African or European great great grandparent, or a single (100%) Native American or East Asian great grandparent. Most customers use the test in an attempt to confirm recent admixture events such as this – where the family tree is primarily European for instance but one or more recent ancestors are of other ancestry, such as Native American.
[…]
High levels of admixture are highly characteristic of recent admixture events and various populations show systematic types of admixtures. The average African American shows 20% European admixture, and Carribean Hispanics tend to show significant European, Native American and African admixture. Non-African Hispanics tend to show relatively even European/Native American admixture with some showing more (even all) European, and others more (even all) Native American.
Lower levels of admixture, particularly in Europeans, require a bit of detective work to interpret. This is because the test does not only report recent admixture events, but we believe, ancient events as well. Because our genetic history is very complex, and interactions between separated populations occurred many times before recorded history, individuals of certain ethnic groups tend to show specific admixture results. Examples include Russians, Scandanavians and Eastern Europeans showing low levels of East Asian admixture (even without a Chinese great grandparent), which possibly arose from widespread interaction between Europeans and Asians during and before the Hun invasions and subsequent ethnic amalgamation. Greeks, Italians, Middle Easterners and Jews reliably and systematically show low levels of Native American admixture (even without an American Indian great grandparent) for anthropological and genetic reasons that are not yet well understood.

Test kits start at $219 US. Cool.

A photo essay– by the Seattle Times on Brenna Johnston, who was born with a rare genetic condition called Crouzon Syndrome . I’m not sure what purpose the article serves, but this is one brave little kid.

Scientists seek to create ‘three-parent’ babies
What on Earth for, you may ask?

The aim is ultimately to prevent children from inheriting genetic diseases caused by mutations in DNA housed by their mitochondria – components of cells which produce energy.

In other words, because they can.

The procedure would involve fertilising a woman’s egg by in-vitro fertilisation outside the body and transplanting the fertilised nucleus to an egg from another woman which has had its nucleus removed.
Any child born following implantation of such an embryo would have cells containing a nucleus with genes from both parents, and mitochondria from a woman other than their mother.
Normally, mitochondria are inherited from the mother via the egg. Mitochondrial mutations are more prevalent in older women, so using a young woman as the egg cytoplasm donor would reduce the risk of inheriting mitochondrial diseases.

A reproductive technology that humanity desperately needs.

Women have superior colour sense
PhysOrg.com: