Thursday, August 21, 2008

The DNA Network

The DNA Network

BRCA1 mutation among Yorubans [Yann Klimentidis' Weblog]

Posted: 21 Aug 2008 06:56 PM CDT

They seem to have found the second of 2 known BRCA1 founder mutations in individuals of African descent. Four out of 365 breast cancer patients have this BRCA1 Y101X mutation. Although BRCA1 mutations probably account for a small proportion of breast cancer cases, these mutations are highly penetrant and therefore strong predictors of breast cancer. They discuss how the identification of these population-specific mutations can be used for genetic screening strategies for breast cancer.

Evidence for an ancient BRCA1 mutation in breast cancer patients of yoruban ancestry.
Zhang B, Fackenthal JD, Niu Q, Huo D, Sveen WE, Demarco T, Adebamowo CA, Ogundiran T, Olopade OI
Familial Cancer
Abstract: Background BRCA1 recurrent mutations have rarely been assessed in non-founder populations. Still, identifying such mutations could be important for designing genetic testing strategies for high-risk breast/ovarian cancer families in non-founder populations. Objective To determine whether the recurrent BRCA1 Y101X mutation identified in Yoruban breast cancer patients represents a single historical mutation event, and determine the prevalence of this mutation in a hospital based cohort. Methods 365 breast cancer patients and 177 controls of Yoruban ancestry from Nigeria, unselected for age of onset or family history were screened for the BRCA1 Y101X mutation. The haplotypes on which the Y101X mutation occurred were characterized using microsatellite markers and single-nucleotide polymorphisms (SNPs). Phase ambiguity was resolved using allele-specific PCR. Results The BRCA1 Y101X mutation was detected in four Yoruban patients with no documented family history of breast cancer among a cohort of 365 (1.1, 95% C.I. = 0.43-2.78%) unrelated Yoruban breast cancer patients. This study reveals the four Y101X mutations occur on a single, rare haplotype. Further characterization in a patient of European ancestry with a strong family history of breast/ovarian cancer revealed the same Y101X mutation on the same haplotype as those in the Yoruban carriers. These observations suggest the Y101X mutations identified in the Yoruban patients may have originated from a single mutation event. Conclusions BRCA1 Y101X is the first reported recurrent mutation occurring in patients of African ancestry for which prevalence has been determined. Identification of this mutation in a woman of European ancestry with strong family history of breast/ovarian suggests further that this mutation occurred once, probably many generations ago.

Redefining “Natural” in Agriculture: A review of Tomorrow’s Table in PLoS Biology [Tomorrow's Table]

Posted: 21 Aug 2008 04:04 PM CDT

Check out the latest review of "Tomorrow's Table" published in PLoS Biology.

Here is a response to one of the points raised in the review as to what is "natural" or appropriate for agriculture.

Because plants are rich in sugars, proteins, vitamins and minerals, they make obvious and tempting treats for various predators. Plants cannot run away, so instead they have evolved a set of defenses to protect themselves. Celery is seemingly benign, yet it produces toxic compounds called psoralens to discourage predators and avoid being a snack too early in its life cycle. Sometimes humans are the accidental victims of psoralen poisoning.

Breeders have selected celery with relatively high amounts of psoralens because farmers prefer to grow insect resistant plants and consumers prefer to buy undamaged produce. Unfortunately, workers who harvest such celery sometimes develop a severe skin rash (NAS 2004), an unintended consequence of this conventional breeding.
Raoul, who is an organic farmer discovered that green potatoes make pretty good rodent poison. One day he went into the certified organic hoophouse to find three dead mice near some freshly eaten green potatoes. Potatoes produce glycoalkaloid solanine, a toxic compound, although most varieties have amounts so small that they are considered nonhazardous to animals. Some potato varieties, however, have higher levels than others and certain conditions such as light can cause hazardous levels of the toxin to be produced.

So far, compounds that are toxic to animals have only cropped up in foods developed through conventional breeding approaches. There have not been any adverse health or environmental effects resulting from commercialized GE crops. This may be because foods produced by GE undergo additional scrutiny, or it may be that there simply are not yet many GE crops on the market. Whatever the reason, this important fact is sometimes lost in the debates on GE food.

Many people view genetic engineering of crops as "unnatural" and see it as an inappropriate tool to use in crop breeding.

What sort of criteria, then, can we use to assess its benefits? An appropriate technology, as asserted by the economist Schumacher in his book Small is Beautiful, should promote values such as health, beauty, and permanence (Schumacher 1973). Low cost and low maintenance requirements are also of prime importance in Schumacher's definition. Considering both Schumacher's observations and our goals for ecological farming, it is apparent that GE will sometimes be appropriate for food modification and sometimes not. This is because GE is simply a tool that can be applied to a multitude of uses, depending on the decisions of policy makers, farmers, and consumers.

Still, as we attempt to show in our book, GE comprises many of the properties advocated by Schumacher. It is a relatively simple technology that scientists in most countries, including many developing countries, have perfected. The product of GE technology, a seed, requires no extra maintenance or additional farming skills. Its arrangement of genes can be passed down from generation to generation and improved along the way. It is therefore clear that humans will likely reap many significant and life-saving benefits from GE. This is because even incremental increases in the nutritional content, disease resistance, yield, or stress tolerance of crops can go a long way to enhancing the health and well-being of farmers and their families. There is also potential for applications of GE to reduce the adverse environmental effects of farming and enable farmers to produce and sell more food locally. Indeed, the use of GE has already drastically reduced the amount of pesticides sprayed worldwide, saved the U.S. papaya industry, and provided new tools to save the lives of impoverished children.

Trewavas, T. (2008). Redefining “Natural” in Agriculture. PLoS Biology, 6(8), e199. DOI: 10.1371/journal.pbio.0060199

Scientific Stereotype [Sciencebase Science Blog]

Posted: 21 Aug 2008 04:00 PM CDT

Scientific stereotype

The wacky characters that introduce kids to science may be doing more harm than good. Reinforcing the white-man-in-a-lab-coat or mad-scientist stereotype could diminish not only children’s interest in science, but also the diversity of future scientific workplaces.

The Web is littered with “Ask a Scientist” sites aimed at getting children “into” science. Some of these sites do provide useful resources for youngsters curious about things such as “Why is the sky blue?”, “Why do
have nipples?
Why do men have nipples?“, and “How can I best extrapolate a Hurter-Driffield curve in my experiments on photographic material transmission densities?”

OK, I made that last one up. But the critical feature of many of these sites is the personification of the so-called expert with names like Ask a Boffin, “Find Out Why with Dr. Calculus,” Ask a Mad Scientist, or some such. Almost invariably, a cartoon character will be a stumpy guy in a white coat, with wild gray hair, waving a test tube around or wielding a clipboard. And, on the whole, he will be white. I was personally involved in one such “expert questions” site several years ago, and to my chagrin, the editor called the site “Ask the Egghead” - and created just such a character in the form of Professor Hypothesis.

What does this say about the common adult perception of how children perceive scientists? Well, for a start, it reinforces the classic stereotype
of scientists as absent-minded
it reinforces the classic stereotype of scientists as absent-minded professor cliche, generally messing around with chemicals or constantly scribbling notes in lab books and, almost certainly, white and male.

While grandiose efforts to promote high-quality science education abound, and public understanding of science (PUS) initiatives are high on the agendas of learned societies everywhere, these could be doomed from the outset by ingrained views we gain as children about what scientists do, what they look like, and who they are.

A fairly formal assay of children’s views of scientists was undertaken recently by a team at Leicester University in England and Australia’s Curtin University of Technology. Although the results have not yet been published, based on preliminary analysis the main conclusion from the research is that children think of scientists as boring white men with glasses, beards, and strange hair. According to lead researcher Tina Jarvis, director of Leicester’s School of Education, many children say they do not want to be a scientist because scientists never have fun!

Jarvis and colleagues, along with Lionie Rennie of Curtin, studied the responses of more than 4,000 children in Britain and Australia over the last eight years and concluded that the stereotypes persist, at least among six- to eight-year-olds. Worryingly, children of Asian and African-Caribbean descent generally held the same opinion as their white peers. Most children’s sketches of scientists endowed them with a white, male face and the usual eccentric hair. Boys, Jarvis says, never drew women, and girls did so only very occasionally. While there may well be a minority of scientists who fit the category, it indicates a very narrow view of scientists, one that is so very often reinforced through TV programs and cartoons, comic books, and comments from nonscientist parents and other adults. We then wonder why so many girls and non-white children find it very difficult to envision themselves as future scientists.

Elizabeth Moss, a Cambridge, England mother of two young children, believes there is a simple explanation for these results: “From age 2 or 3 to 5, children have such vivid imaginationschildren have such vivid imaginations, but then they go to school and are made to feel that they should think and act like everyone else and they seem to lose their individual imaginations, and draw what is expected of them.”

Alan Gray is 13 and in eighth grade in Ontario, Canada. “Recently, in our science class, we were asked to draw a picture of a scientist,” he reports. “When we handed it in, our teacher got what she expected: mostly all of us had drawn men with white lab coats and tubes with liquids in them.” He does not think the class was pandering to a greater stereotype, though. “If you asked us to draw popular kids, we’d draw them with makeup and nice clothes and big houses. If you asked us to draw farmers, we’d draw men with overalls, baseball caps, and straw in their mouths.”

Marilyn Fleer, associate professor of education at the University of Canberra in Australia, notes, “Although there are still stereotypical responses given when children are asked to draw a scientist, if you interview them they will qualify their work by saying they had to draw it that way, so that you know what it is.”

“This is an interesting area,” says Christine Khwaja, who teaches primary school teachers at Middlesex University in London. But she also asks whether children draw scientists as boffins because that is what they think scientists are really like, or because that is what they think they are expected to draw? “There seems to be very little in the national curriculum on the nature of science, who does it, and why,” she adds. She suggests, “A discussion around these areas might make children think more widely about who is a scientist and what scientists actually do.” She even suggests that there are many jobs, from hairdresser to zookeeper, in which science is important and that children’s image of scientists might be helped by raising awareness of these.

West Coast scientist and teacher Monique DeRuggiero says she much prefers jeans to lab coats, although she still keeps a well-decorated lab coat for messy labs and is not concerned by revelations of children perceiving scientists as stereotypes. “I do not see a problem with children drawing pictures of scientists as men in white coats; we do need to know what children’s perceptions
are before
we can change them
we do need to know what children’s perceptions are before we can change them.” She emphasizes the point that once you know what children expect, you can then teach them the reality by exposing them to examples of real scientists, showing them pictures, movies, stories of all types of scientists in all types of work. Getting real scientists to visit the school or taking a class trip to a lab can also help eradicate misconceptions.

Jupadhye Upadhye, a computer programmer with an Indian software company based in Singapore, blames comic books with characters like Inspector Gadget and stories that are littered with scientist stereotypes: Professor Calculus, Captain Nemo, Frankenstein, “Doc” Brown in the movie Back to the Future - even legendary quirky scientists such as Newton, and especially Einstein. “All of these add to the image,” she says. “Moreover, everyone likes to build myths and interesting characteristics around scientific personalities, to set them aside as somehow different from the rest of us.”

“It is important to challenge children in their thinking, and the adults who work with them,” believes Kate Banfield, who manages a preschool daycare center in West Yorkshire. If the children are portraying scientists as white middle-aged men in lab coatschildren are portraying scientists as white middle-aged men in lab coats, she says, you need to offer them an alternative experience. Invite non-white or female scientists from local labs to talk about their work; find books and stories about scientists who are women or ethnic minorities. However, the most important strategy for breaking down stereotypes is to raise children’s awareness of what they are and how they are perpetuated. Encourage them to question assumptions and confront stereotypes.

The SCICentre (National Centre for Initial Teacher Training in Primary School Science) at Leicester University, of which Jarvis is director, produces materials to educate parents and educators about science, scientists, and technology. The latest booklet, entitled Helping Primary Children Understand Science and Technology, seeks to improve children’s ideas of scientists by getting them involved in activities such as role playing, discussions, and reading and writing about science. The booklet is illustrated with photographs of a diverse range of scientists at work with the aim of broadening views, presumably of both children and educators.

But Martin Counihan of the University of Southampton worries that children don’t think very much about scientists at allchildren don’t think very much about scientists at all these days, compared with a couple of decades ago. “What image do children have of other rare breeds such as, say, theologians? Or historians?” he asks. “And insofar as children do think about scientists, their image is probably colored much more by the biosciences than previously.”

With the focus in school curricula on numeracy and literacy, especially in the U.K., there is little room for science. Yet Jarvis believes there is no reason why science cannot be incorporated into these two key areas and indeed enhance them. She believes that if children do not learn to love science before they are eleven, then the scientific part of their secondary education is essentially lost on them.

Fleer has looked into how technology education for young children has changed through the years. There’s been an increase in resource development to support technology teaching in schools, she says, but only a limited amount of research has been done in the three-to-eight-year-old age group to assess the effects. Although most parents are familiar with the seemingly innate scientific curiosity of their offspring, Fleer’s pilot study revealed that children as young as three years can engage in oral and visual planning as part of the process of making things, such as model giraffes and butterflies, from different materials.

Greg Degeyter is a meteorologist from Mississippi State University who has made several school appearances. “The students seemed genuinely interested in what was being said. Any well-presented information seems to strike their imagination and make them interested in the subject,” he says. He does not feel that the children expected someone in a white lab coatchildren expected someone in a white lab coat, but then accedes that most of their experiences with a meteorologist includes someone in a dress coat and tie, and suggests that is what they expect. “In general,” he adds, “I do think that children are intimidated by science. Perhaps not the younger ones but as they get older.” As for stereotypes seen by younger children, “It probably is true for scientists in general,” he suggests, “Most children seem to think of a doctor as someone who studies science, and he is in white garb.” He asks whether it is a bad thing. “Children think of scientists as smart, albeit a bit weird (as shown by the hair), and dedicated to the profession. If anything should be done it is to have more interaction between the scientific community and the public.”

Toby Bankson, a ninth grader in Mountlake Terrace, Washington, believes the stereotype may actually have some benefits. “It may be one of the things that turns a young child’s eyes toward science in the first place,” she says. “In a video show at school, for instance, would kids watch a ‘normal’ scientist for even 15 minutes?” she asks. Which is why shows like Bill Nye: The Science Guy and Beakman’s World are so popularScience Guy and Beakman’s World are so popular and get children to pay attention willingly to information about science. “With everything else a kid could watch these days, that’s a small miracle!” adds Bankson.

Stereotypes persist in all walks of life, but in the realm of science, where public trust has become frazzled by the seeming autocracy of those guys with crazy hair wearing lab coats and wielding chemicals, perhaps it’s time to say goodbye to Professor Hypothesis and his cronies, and introduce children to some real scientists.

This feature article originally appeared under the title, Uncool boffins, all - children’s stereotypes of scientists - in my Adapt or Die column in the sunk HMSBeagle on the scuppered BioMedNet, it was reprinted here 2001-05-21 but hopefully its sentiments are worthy of repeating today if only to nudge the Null Physics item down to #2 ;-)


Scientific Stereotype

That didn’t take long []

Posted: 21 Aug 2008 02:22 PM CDT

See? All I have to do is wave my magic wand and the world conforms to my wishes. Scary!

Ach, if only that were true…

California gets its act together: OK's Navigenics and 23andMe []

Posted: 21 Aug 2008 11:23 AM CDT

In unusual fits of intelligence and rapid action, the California Department of Public Health has decided that personal genomics companies 23andMe and Navigenics will be granted a license to perform their testing in the state. The state originally sent the companies cease and desist letters back in June ( [word doc warning]) when they dared offer consumers a service without the blessing of bureaucrats. New York took a similar action back in April. It's nice to see California change their...

Read more and join the community...

Where is the outrage about the genetic engineering of humans? [Mary Meets Dolly]

Posted: 21 Aug 2008 11:06 AM CDT

This story highlights the anger and frustration many of us feel about what appears to us as an out of control biotech industry. Unfortunately, violence is never the answer to "big biotech" but some people just don't get it. In 2001, the Earth Liberation Front set fire to a University of Washington facility where they believed engentically engineered trees were being produced. From the
Seattle Times:

A Spokane woman who helped set the a 2001 fire that destroyed the University of Washington Center for Urban Horticulture has been sentenced to three years in prison. Lacey Phillabaum, 33, was one of five members of the Earth Liberation Front arrested in connection with the attack.

The Earth Liberation Front had targeted the UW office of Toby Bradshaw, whom arsonists mistakenly believed was involved in genetically engineering poplar trees that would pollute natural forests. The center was severely damaged, and later was rebuilt at a cost of about $7 million.

According to federal pre-sentencing paperwork, Phillabaum helped draft a letter rationalizing the arson as a way to "stop genetic engineering."

While the outrage at genetically engineering plants that maybe harmful to existing forests may have been appropriate, the action clearly was not. Arson is no way to "stop genetic engineering."

But this story has me thinking, where is the outrage at the genetic engineering of humans that is already occuring? Where is the outrage at human embryos being created with somatic cell nuclear transfer, better known as cloning? Where is the outrage at human embryos being cloned using cow and rabbit eggs? I am outraged. Are you?

My inspiration [Mary Meets Dolly]

Posted: 21 Aug 2008 10:38 AM CDT

With four kids, a husband with diabetes and a crazy puppy, I need all the inspiration I can get to keep blogging about the biotech arena. My mom sent me this and I try to remember it everyday:

Live your life in such a way that when your feet hit the
floor in the morning, Satan shudders & says...
'Oh sh**...she's awake!!

A gene by many other names and thoughts on teaching bioinformatics [Discovering Biology in a Digital World]

Posted: 21 Aug 2008 08:05 AM CDT

One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.

One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been collecting 3 dimensional structures of the enzymes and annotating polymorphic amino acids. That part is very straightforward. The complicated part of the project is figuring out how the structures correspond to the genes, genetic data, and association studies with diverse polymorphisms.

Read the rest of this post... | Read the comments on this post...

Kudos on the placozoan genome! [Genomicron]

Posted: 21 Aug 2008 07:16 AM CDT

Trichoplax adhaerens is a bizarre little animal with a decidedly simple morphology. (You can see some here). There has been some question as to the relationship between this critter and other animal groups, but mitochondrial sequences (Dellaporta et al. 2006) and, as of this week, a complete nuclear genome sequence (Srivastava et al. 2008), suggest that it is a modern representative of the earliest branch to split from the rest of the animal lineages (for more detail, check out John Timmer's discussion). The term "basal" is usually applied to lineages like this, often with the assumption that basal means primitive. Sometimes genome sequencing articles exhibit misunderstanding of what "early branching" actually means, but I must give kudos to Srivastava et al. (2008) for their refreshingly apt conclusions:

Trichoplax's apparent genomic primitiveness, however, is separate from the question of whether placozoan morphology or life history is a relict of the eumetazoan ancestor. For example, the flat form and gutless feeding could be a 'primitive' ancestral feature, with the cnidarian–bilaterian gut arising secondarily by the invention of a developmental process for producing an internal body cavity (as in Bütschli's 'plakula' theory), or it could be a 'derived', uniquely placozoan feature that resulted from the loss of an ancestral eumetazoan gut. Unfortunately, the genome sequence alone cannot answer these questions, but it does provide a platform for further studies.

New research suggests diabetes transmitted from parents to children [Think Gene]

Posted: 21 Aug 2008 01:58 AM CDT

Josh: We must remember that not all inherited diseases are genetic in origin. Not only does the “genetic code”, the sequence of A, G, C, and T, matter but so do other modifications to that code. Examples are DNA methylation and histone modification.

A new study in the September issue of the Journal of Lipid Research suggests an unusual form of inheritance may have a role in the rising rate of diabetes, especially in children and young adults, in the United States.

DNA is the primary mechanism of inheritance; kids get half their genes from mom and half from dad. However, scientists are just starting to understand additional kinds of inheritance like metabolic programming, which occurs when an insult during a critical period of development, either in the womb or soon after birth, triggers permanent changes in metabolism.

In this study, the researchers looked at the effects of a diet high in saturated fat on mice and their offspring. As expected, they found that a high-fat diet induced type 2 diabetes in the adult mice and that this effect was reversed by stopping the diet.

However, if female mice continued a high-fat diet during pregnancy and/or suckling, their offspring also had a greater frequency of diabetes development, even though the offspring were given a moderate-fat diet. These mice were then mated with healthy mice, and the next generation offspring (grandchildren of the original high-fat fed generation) could develop diabetes as well.

In effect, exposing a fetal mouse to high levels of saturated fats can cause it and its offspring to acquire diabetes, even if the mouse goes off the high-fat diet and its young are never directly exposed.

The study used mice so it’s not time to warn women to eat differently during pregnancy and breastfeeding but earlier research has shown that this kind of inheritance is at work in humans. For example, there is an increased risk of hypertension and cardiovascular disease in children born of malnourished mothers.

Source: American Society for Biochemistry and Molecular Biology

“Effects of High Fat Diet Exposure During Fetal Life on Type 2 Diabetes Development in the Progeny”. Donatella Gniuli, Alessandra Calcagno, Maria Emiliana Caristo, Alessandra Mancuso, Veronica Macchi, Geltrude Mingrone, and Roberto Vettor. Journal of Lipid Research, Vol. 49, 1936-1945, September 2008

Wikifying Peer Review [business|bytes|genes|molecules]

Posted: 21 Aug 2008 12:14 AM CDT

Nature is experimenting again. Take a look at this wiki accompanying Lincoln Stein’s article for Nature Review Genetics

The wiki is a dynamic companion to the paper and is meant to be a resource for the community. It’s an idea that I love. I’d argue that something like this should accompany other types of papers. Too often people publish papers with incremental improvements. Perhaps they could avoid doing that and update a companion wiki or something along those lines.

I do have one question though. Is this best done by a publisher, or the author? I can see both models having pluses and minuses. After all the information belongs to the author and if they self host, it could become the norm. On the other hand, the publisher hosting it does provide reduce some friction.

Reblog this post [with Zemanta]

Complexity of Breast Cancer []

Posted: 19 Aug 2008 04:31 PM CDT

This is an exciting time in the study of hereditary factors involved in breast cancer susceptibility. Breast cancer for a long time was classified according histology. Now genetics play a significant role and better knowledge ensures better management and treatment.

Hereditary breast cancer (HBC) accounts for as much as 10% of the total BC burden. Only about 30 percent of these cases will be found to be due to a germline mutations in well known BRCA1 and/or BRCA2 genes, but the rest won’t have these mutations. Less than 10 percent of remaining HBC will fall into other rare conditions - and here we can see breast cancer as heterogeneous disease (ref.):

Cowden, Li-Fraumeni syndromes, heterozygosity for Ataxia telangiectasia-mutated gene (ATM) or for CHEK2 1100delC or other rare conditions Nijmegen breakage syndrome (NBS1), familial diffuse gastric cancer (CDH1), Peutz-Jeghers syndrome (STK11), Fanconi anemia (BRIP1, PALB2), Bloom syndrome (BLM)) contribute sligthly - there is consensus for ten most important genes involved in HBC (ref.)

An estimated additional 15–20% of those affected with BC will have one or more first- and ⁄ or second-degree relatives with BC (familial or polygenic breast cancer). Therefore, when these numbers are combined, familial BC risk accounts for approximately 20–25% of the total BC burden (see figure).

Here we’re talking about so called low-penetrance susceptibility genes and variants (SNPs), like rs2981582 in FGFR2, rs889312 in MAP3K1, rs3803662 in TNRC9, rs1801270 in CASP8 and many more, most of which were hot topics in the recent years. Particular alleles (particular “letter” variants of these digitalized “rs” SNPs) only increase risk slightly (twice or so) and are intense study object now, but they sooner or later will enter clinical practice.

No comments: