Freebies for freshies!

This idea is truly risky, but if students don’t agree with the results, the hospital doors are always open. They will be given a sample they can keep; they can ask for another testing from other professional persons. Plus, it has been four years since this article was posted, meaning the professors and specialists already spent more than four years preparing for this mass genetic testing program. They must be very ready by now, and I guess students are, too, for this year’s batch will be the first to be analyzed. I hope it will be a success for Berkeley, considering all the negative assumptions of people from different universities and hospitals.

College Bound, DNA Swab in Hand
By TAMAR LEWIN
Published: May 18, 2010

Instead of the usual required summer-reading book, this year’s incoming freshmen at the University of California, Berkeley, will get something quite different: a cotton swab on which they can, if they choose, send in a DNA sample.

Winfried Rothermel/Associated Press
The university said it would analyze the samples, from inside students’ cheeks, for three genes that help regulate the ability to metabolize alcohol, lactose and folates.

Those genes were chosen not because they indicate serious health risks but because students with certain genetic markers may be able to lead healthier lives by drinking less, avoiding dairy products or eating more leafy green vegetables.

Berkeley’s program for the class of 2014 is the first mass genetic testing by a university. Jasper Rine, the professor of genetics who is leading the project, said it was designed to help students learn about personalized medicine and identify their own vulnerabilities.

“The history of medical genetics has been the history of finding bad things,” he said. “But in the future, I think nutritional genomics is probably going to be the sweet spot.”

The testing will be voluntary and confidential, with no one at Berkeley knowing which sample comes from which student.

Each freshman will get two bar code labels, one to put on the sample and one to keep. After the genotyping is complete, the results will be posted on a Web site using the bar code identification, so only the person who provided the DNA sample will know whose it is.

“In the decade ahead, the new genetics is going to penetrate everyday medical practice,” said Mark Schlissel, dean of biology at Berkeley. “We wanted to give students a sense of what’s coming, through genes that can provide them with useful information. I think it’s one of the best things we’ve done in years.”

But some bioethicists say the whole idea of genetic testing outside a medical setting is troubling.

“It’s a bad precedent to set up mass testing without some sort of counseling support,” said Arthur Caplan, director of the Center for Bioethics at the University of Pennsylvania. “I’d rather people get their results in a medical setting, where they can ask questions about the error rate or the chances of passing it on to their children, and not just see it posted on some Web site.”

Dr. Schlissel said that he understood the concern about counseling but that he believed it applied mostly to testing for genetic diseases, not necessarily the relatively innocuous gene variants that Berkeley is looking for.

Berkeley, like many colleges, has for several years tried to create a common intellectual experience for new students by assigning a summer reading book. Last year, freshmen and transfer students in its College of Letters and Sciences received “The Omnivore’s Dilemma,” By Michael Pollan.

But for the class of 2014, the program will be especially ambitious. After the genetic testing, the university will offer a campuswide lecture by Mr. Rine about the three genetic markers, along with other lectures and panels with philosophers, ethicists, biologists and statisticians exploring the benefits and risks of personal genomics.

There will also be a contest in which students who submit creative entries on the theme will have a chance to win further genetic testing from 23andMe, a private company that offers DNA profiling.

Berkeley has not yet chosen a company to analyze the DNA samples, but Dr. Schlissel said it was unlikely to be 23andMe. Estimates are $35,000 to $40,000 per 1,000 samples.

While the Berkeley professors see the gene testing as relatively harmless, others say that all genetic knowledge carries risks.

“They may think these are noncontroversial genes, but there’s nothing noncontroversial about alcohol on campus,” said George Annas, a bioethicist at the Boston University School of Public Health. “What if someone tests negative, and they don’t have the marker, so they think that means they can drink more? Like all genetic information, it’s potentially harmful.”

Reference:
http://www.nytimes.com

Not everything comes naturally now, does it Selena?

The first thought that came into my mind as I read the title was, “like cloning?” Brain said yes as I read the words synthetic biology. I’m not sure if I am misconceiving the whole article because of what I initially thought of. If these procedures are for purposes alike cloning, then I am certainly out.

Recreating the stripe patterns found in animals by engineering synthetic gene networks

Date: September 23, 2014
Source: Center for Genomic Regulation

Pattern formation is essential in the development of animals and plants. The central problem in pattern formation is how can genetic information be translated in a reliable manner to give specific spatial patterns of cellular differentiation.

The French-flag model of stripe formation is a classic paradigm in developmental biology. Cell differentiation, represented by the different colours of the French flag, is caused by a gradient of a signalling molecule (morphogen); i.e. at high, middle or low concentrations of the morphogen a “blue,” “white” or “red” gene stripe is activated, respectively. How cellular gene regulatory networks (GRNs) respond to the morphogen, in a concentration-dependent manner, is a pivotal question in developmental biology. Synthetic biology is a promising new tool to study the function and properties of gene regulatory networks (GRNs) by building them from first principles. This study developed synthetic biology methods to build some of the fundamental mechanisms behind stripe formation.

“We have performed a very innovative and ambitious study: we applied a three-step approach for the effective exploration and creation of successful synthetic gene circuits. We created a theoretical framework to study the GRNs exhaustively” — 100,000 versions of over 2800 networks were simulated on the computer. We then successfully developed a synthetic network engineering system and, finally, we confirmed all the new experimental data by fitting it to a single mathematical model” explains the corresponding author James Sharpe.

First, Andreea Munteanu, co-author of the study, performed a theoretical screen for finding all design classes that produce the desired behaviour (stripe formation in a morphogen gradient). During this step she discovered four fundamentally-different mechanisms for forming a stripe. Next, Yolanda Schaerli, first author of the study, successfully demonstrated that the four networks are functional by building them in the bacteria E. coli using the tools of synthetic biology. The third step was to verify the distinct mechanisms by fitting all the experimental data to a mathematical model.

The success of this procedure allowed the researchers to go one step further to find a deeper design principle of stripe formation. They identified a simpler 2-node network — where the stripe gene is directly controlled by both activation and repression from the morphogen sensor gene- that replicates the stripe-forming ability in its simplest form. They were successful in building this archetype of stripe forming networks and ultimately discovered that it can even display an “anti-stripe” phenotype (fig. 2).

“Combining exhaustive computational modeling with synthetic biology is more efficient and powerful than building networks one-by-one” says the corresponding author Mark Isalan. “Our approach provides a new and efficient recipe for synthetic biology — a new scientific discipline which aims to engineer all kinds of useful biological systems.”

Reference:

          http://www.sciencedaily.com/releases/2014/09/140923110750.htm

         

Not everything is shared

This article is so interesting I would like to make further researches on other scientists’ explanations. I bet they themselves had amplified enthusiasms the moment they heard about this case. I also want to know why this happened, how come it was possible, and at what percentage do they think it could happen to other identical twins. This case is truly mystifying.

Identical twins, one case of Down syndrome: a genetic mystery
April 16, 2014 | By Melissa Healy

A rare occurrence in the earliest days of a pregnancy produces an unusual and mystifying outcome: Identical twin fetuses are conceived of the same meeting of egg and sperm. And despite their shared DNA, one of the twins has Down syndrome (the most common genetic cause of intellectual impairment), but the other does not.

For those who labor to understand how 3 billion base pairs of DNA result in the complexity of a single human, it’s difficult to discern what effect an extra chromosome has on gene expression across the genome: from individual to individual, there’s just too much natural variation for comparisons between two people to reveal truths that apply to all.

But these aborted identical twins — one with an extra copy of chromosome 21 and the other without — offered scientists a remarkable opportunity: given the twin fetuses’ otherwise exact DNA match, how would this one difference translate across the genome?

Continue reading