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Monday, 24 November 2008

Genetics gone wild

In today's edition:

  1. Bio Lab in Galveston Raises Concerns
  2. Scientists clone from frozen mice
  3. African, Asian join the library of genomics
  4. Australia leads world first global effort to improve diagnosis of genetic disorders

Bio Lab in Galveston Raises Concerns

October 28, 2008

GALVESTON, Tex. — Much of the University of Texas medical school on this island suffered flood damage during Hurricane Ike, except for one gleaming new building, a national biological defense laboratory that will soon house some of the most deadly diseases in the world.

How a laboratory where scientists plan to study viruses like Ebola and Marburg ended up on a barrier island where hurricanes regularly wreak havoc puzzles some environmentalists and community leaders.

Officials at the laboratory and at the National Institutes of Health, which along with the university is helping to pay for the $174 million building, say it can withstand any storm the Atlantic hurls at it.Получер

Built atop concrete pylons driven 120 feet into the ground, the seven-floor laboratory was designed to stand up to 140-mile-an-hour winds. Its backup generators and high-security laboratories are 30 feet above sea level.

The project enjoyed the strong support of three influential Texas Republicans: President Bush, a former Texas governor; Senator Kay Bailey Hutchison; and the former House majority leader, Tom DeLay, whose district includes part of Galveston County. Officials at the National Institutes of Health, however, say the decision to put the lab here was based purely on the merits. It is to open Nov. 11.

Dr. LeDuc acknowledged that hurricanes would disrupt research. Each time a hurricane approaches the island, scientists will have to stop their experiments and exterminate many of the viruses and bacteria they are studying.

And Hurricane Ike did not provide the worst-case test the laboratory will someday face, some critics say. Ike’s 100-m.p.h. winds were on the low side for a hurricane, yet it still flooded most of the island’s buildings. The university’s teaching hospital, on the same campus as the lab, has been shut down for more than a month.

“The University of Texas should consider locating its biohazards lab away from Galveston Island and out of harm’s way,” Ken Kramer, director of the Lone Star Chapter of the Sierra Club, said. “As destructive as it was, Hurricane Ike was only a Category 2 storm. A more powerful storm would pose an even greater threat of a biohazards release.”

The laboratory is one of two the Bush administration pushed after the Sept. 11, 2001, terrorist attacks. The second is being built at Boston University Medical Center, where it met stiff community resistance.

Not so in Texas, where there was hardly a whimper of protest. For starters, the University of Texas Medical Branch is one of the largest employers on the island of 57,000 people.

In addition, the leaders of the medical school skillfully sold community leaders and politicians on the high-tech safety measures at the lab and on the economic boon to Galveston, an impoverished town in need of the 300 jobs the laboratory would bring.

University leaders met twice a month with community leaders for several years to dispel fears of pathogens escaping. Then they created a permanent advisory committee of residents that included some of their critics. The campaign to win over residents was effective.

Nonetheless, some community members remain skeptical about the safety measures.

“It is not a geographically good location, and the safety measures are only as good as the people who work there,” said Jackie Cole, a former City Council member who now serves on a citizen’s advisory board for the laboratory.

Dr. LeDuc and other scientists at the laboratory say it is almost impossible for diseases to escape. The air pressure in the laboratories is kept lower than in surrounding hallways. Even if the double doors into the laboratories are opened accidentally, air rushes in, carrying pathogens up and away through vents to special filters, which are periodically sterilized with formaldehyde and then incinerated.

All the laboratory tables have hoods that suck contaminated air through the vents to the filters, as do the rooms themselves. Liquid waste, feces and urine go to tanks on the first floor, where it is heated to a temperature at which nothing can survive before being put into the sewage system.

Other waste — carcasses of laboratory animals and disposable lab equipment — is sterilized in autoclaves, giant steam-pressure cookers, before being incinerated off site, Dr. LeDuc said.

When hurricanes threaten the island, researchers will shut down their experiments at least 24 hours before landfall, decontaminate the labs and then move the stocks of deadly pathogens into freezers on upper floors, where they are kept at 70 below zero, Dr. Joan Nichols, an associate director of research, said.

Even if the emergency power system were to fail, the freezers can keep the samples of killer diseases dormant for about four days, she said.

The precautions are necessary. The laboratory will do research into some of the nastiest diseases on the planet, among them Ebola, anthrax, tularemia, West Nile virus, drug-resistant tuberculosis, bubonic plague, avian influenza and typhus.

In the top-level secure laboratories, where deadly filoviruses like Ebola are studied, the scientists work in pressurized spacesuits inside rooms with airtight steel doors. Before leaving the secured area, they take a chemical shower for eight minutes in their suits, then a conventional shower, Dr. LeDuc said.source

My comment: Very nice. Almost like in a movie. Although the security measures seem to be very tight, nothing is impossible, especially when playful humans are involved. What I like the most is, however, how the scientists bought the locals. It's an example of good manipulation of the public opinion. I'm not saying the building isn't safe, it sounds very safe. But if you account for the viruses they work with, I'd prefer that building to be on Moon. And even that's not safe enough.

Scientists clone from frozen mice

Japanese scientists have managed to create clones from the bodies of mice which have been frozen for 16 years.

Cloning has largely been done using just live donor cells, transferring their DNA to recipient eggs.

Using previously frozen cells runs the risk of ice damage to the DNA unless carefully handled.

The scientists said they created their mice from the brain cells of rodents that had been kept in laboratory conditions at -20C.

The scientists in Kobe, Japan, said their technique raised the possibility of recreating extinct creatures, such as mammoth, from their frozen remains.

Many of the successful clones since Dolly the sheep was born in 1996 have been created by a method where the nucleus of a cell has been removed, placed in an empty egg and kick-started into replicating by chemicals or electricity.

It is not the only cloning technique, and Australian researchers reported cloning a pig in 2001 from cells that had been frozen for two years. The Adelaide-based team said its cloning method differed from the Dolly approach in important respects.

Professor John Armitage is director of tissue banking at the Bristol Eye Hospital, UK.

He commented: "Mitochondrial and some nuclear DNA fragments have previously been isolated from mammoths frozen in permafrost, but the key question is whether sufficiently intact nuclei could be extracted from mammoth cells, which will have been frozen for at least 10,000 years at relatively high sub-zero temperatures.

Professor Armitage added: "-20C, the temperature at which the mice used in these experiments were stored, is insufficient to stop physical and chemical reactions of biological significance - even food in a domestic freezer has a limited storage time based on changing texture and taste.

"To achieve long-term storage of viable cells, including embryos, requires far lower temperatures of at least -140C in the presence of cryoprotectants."

Viable eggs, sperm and embryos are already retrieved from the frozen state for use in in vitro fertilisation (IVF). source
My comment: Nice! The mammoths part at least. Anyway, I like to trace those steps, because each and every new technology in genetics improves our knowledge and presents new opportunities.

Researchers Could Grow Replacement Tissue to Patch Broken Hearts

Researchers have built a honeycomb-like scaffold that resembles natural heart tissue, and found that when they seeded the artificial structure with heart cells from young rats the cells grew and joined together in an approximation of normal heart muscle. The cells had also formed electrical connections with one another, allowing them to contract in coordination – and when an electric field was applied along the long axis of the honeycomb, the cells indeed contracted. “You could see the cells ‘beating’ on the scaffold,” says [study coauthor] George Engelmayr [New Scientist].

Other researchers have constructed biodegradable scaffolding on which to grow different types of tissue, but heart tissue poses particular technical challenges. Heart tissue must be flexible enough to change shape as the heart contracts, but also strong enough to withstand the intense forces generated by these contractions. So, the researchers used a polymer. [Technology Review].

In the study, published in Nature Materials, researchers found that an accordion-like polymer structure caused the cells to contract in one direction, while remaining rigid in the other direction. In the short term, researchers say the heart simulacrum would be useful for testing heart drugs in the lab. If the system is approved for human use, the technology could eventually be used for “patches” to mend the hearts of patients who have had damaged tissue removed after a heart attack, or for children with congenital heart defects.

Farther still down the line, scientists want to grow different components of the heart – such as valves and cardiac muscle patches – which may within a decade or so be combined together before being transplanted into a patient. [The Independent]. source

My comment: Nice, right? I know I don't need to comment this, since everyone gets the benefits-hearts are probably the mostly transplanted organ after skin, but it's so hard to get it and when you do, it either won't work or it will give you a new personality or something in this lines. Whatever.

African, Asian join the library of genomics

Laboratories have for the first time sequenced the full genetic code of an African and an Asian in what amounts to a major step towards the goal of a tailor-made profile of one's DNA.

Until now, the genomes of only two individuals -- James Watson, who co-determined DNA's double-helix structure, and maverick biotech entrepreneur Craig Venter -- have been unravelled.

Both men are of European descent, which leaves gaps in knowledge about how people of different ethnic backgrounds could be susceptible, or alternatively immune, to inherited diseases or respond to medicine.

Two studies, released on Wednesday by the British-based journal Nature, aim to fill in some of those blanks, with the genomes of a Han Chinese male and a man from the Yoruba ethnic group in West Africa.

The two teams describe the methods they used to expose the three billion base pairs of code in the anonymous individuals' DNA.

Later work, analysing the genomes of the four men, will compare and contrast changes in the code that could be linked to disease.

The two new genomes were compiled using sequencers made by Illumina Inc., a San Diego, California, biotech firm, which with rival firms 454 Life Sciences and Applied Biosystems has been credited with slashing the cost of genomics.

An international consortium called the 1,000 Genomes Project seeks to build the current library of four individual genomes to at least 1,000 people from around the world, in order to get the broadest possible view of the genetic mosaic.

© 2008 AFP source
My comment: Lol, double victory after Obama. Haha. Well, it's great to expand the knowledge of human genom, no doubts in that. I'm just more curious over the next research, that would examine the differences in the different types. I guess that they won't be big, but still, I'm curious.

Australia leads world first global effort to improve diagnosis of genetic disorders

An Australian-led global initiative to improve the diagnosis of genetic disorders and reduce errors in the reporting of genetic variations has been published today in the prestigious scientific journal Science.

"There is a staggering error rate of up to 40 percent in some reporting of genetic variations," said Professor Richard Cotton, lead author of the paper, Convenor of the Human Variome Project and honorary researcher at the University of Melbourne. "This means clinicians and specialists cannot solely rely on the research literature to inform the life and death decisions of diagnosis and prognosis of genetic disorders."

Over 60 percent of people worldwide will be affected by a genetic change at some point in their lives that can result in a range of diseases such as cystic fibrosis, epilepsy and cancer.

"In a world first, we aim to collect information on every fault in every gene worldwide."

"Ultimately the project will provide the first global standardization of the reporting of genetic mutations and their effect on human health so clinicians can reliably diagnose, treat and inform patients," he said.

The Australian-led global project combines the talents of University of Melbourne researchers and colleagues within the Florey Neuroscience Institutes, the Department of Medicine at the Royal Melbourne Hospital and the Epilepsy Research Centre, as well as international colleagues from around the globe.

The project has the support of World Health Organization, UNESCO and OECD countries.

The completion of the Human Genome Project in early 2000 empowered researchers with the genomic mapping of the human body. But out of the 20,000 human genes mapped, only 3,000 have any information available on their variations.

"In the next few years it is expected that the number of genes in which disease-causing variations are recognized will increase dramatically," Professor Cotton said.

"Currently there is no standardized way to capture this information and make it of use to clinicians."

The Human Variome Project will produce standards for the storage, transmission and use of genetic variation information which for many will reduce the enormously time consuming task of seeking data to assist in providing patients with information.

The Science paper details the establishment of a range of pilot projects being organised around the world that will examine how to systematically collect genetic, clinical and biochemical information in either a country specific or gene specific manner.

Countries already signed on to these pilots include Australia, China, Japan and Kuwait.

"Once these pilot projects are complete, we will be able to roll out suitable systems around the globe and improve the health of billions of people," he said.

Source: University of Melbourne source
My comment:
This project will improve our knowledge on human genome without a doubt. However, I question its practical benefits.

People still believe that one genetic mutation is responsible for a disease. So, let's guess that we monitor all the pregnancies. What happens if a baby has a mutation that could lead to any type of cancer? What are we doing with that baby? To leave the "ethical" problems aside, I simply doubt this is a workable solution for prevention of diseases and I find it very unlikely that there is a baby born with perfect genes.

But then, if the project succeed, we'll have enough data and my guess is that it will show that genetic predisposition doesn't equal disease and that there's more to life than this. After all look at the viruses-they are a genetic laboratory and with all their imperfectnesses, they are the most brutally surviving species around.

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