About.com Biotech / Biomedical

Nematode was the First Sequenced Genome

Mon, 23 Nov 2009 07:30:38 +0000

The fruit fly, (Drosophila), has been used as a genetic research tool for a very long time, because of it's easily observable phenotypic differences, and adherence of many of these traits to the basic rules of Mendelian inheritance. Because of this, I always assumed, or thought I'd heard somewhere, that it was the first multicelled organism for which the entire DNA sequence was determined. This is wrong, however, and, according to the NCBI Nematode Genome Resources webpage, the nematode was the first multicellular eukaryote to have it's genome completely sequenced.

This information was bought to my attention during a presentation at the SETAC conference I am attending, on the use of genomics and DNA microarray techniques to study nanoparticle toxicity using silver nanoparticles (Ag NP). The soil nematode is a popular test organism for toxicity studies. The Ag NP were found to severely downregulate several genes in this organism, by affecting transcription. This paper provided further support for the use of the nematode as a bioindicator organism for environmental contamination, using proteomic and genomic techniques.

_{Source: Roh, JY. et al. 2009. Ecotoxicity of silver nanoparticles on the soil nematode Caenorhabditis elegans using functional ecotoxicogenomics. Environmental Science and Technology 43:3933-3940.}

Nematode was the First Sequenced Genome originally appeared on About.com Biotech / Biomedical on Monday, November 23rd, 2009 at 07:30:38.

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Nanotoxicity Data Accumulating

Sun, 22 Nov 2009 22:19:34 +0000

While the industrial biotechnology sector is rushing full steam ahead to develop and commercialize new nanotechnology products, scientists working in areas of human and ecological toxicity are scrambling to keep up. Nanoparticle toxicity is a prominent topic at this year's SETAC NA conference, with several dedicated platform and poster sessions. The society is primarily concerned with environmental toxicology, rather than human, but the number of papers, and the variety of different types of nanoparticles and target organisms being investigated, is reassuring. I'm glad to see the potential dangers of nanoparticle toxicity are being taken seriously by industry and regulators alike. Here are some of the presentations I came across:

Kovacs, T. et al. Ensuring the Environmental Compatibility of Manufactured Nanocrystalline Cellulose (NCC). NCC is being developed for the pulp and paper industry. Four aquatic species were tested to determine possible adverse effects of an accidental release. Both acute and subacute endpoints were measured and conclusions were that NCC is of low risk to the aquatic environment.
Ahamed, M. et al. Silver Nanoparticles-Induced Heat Shock Protein 70, Oxidative Stress and Apoptosis in Drosophila melanogaster. Silver nanoparticles (Ag NP) are already in commercial use in many different forms. There were a number of presentations on their uptake, accumulation and toxicity. This paper reported the induction of a number of enzymes involved in apoptosis, DNA repair, reactive oxygen species scavenging and a number of other response mechanisms to cellular stressors. In another presentation (Shoults-Wilson, W. et al. The Influence of Particle Size, Concentration and Surface Functionalization on Bioavailability of Ag Nanoparticles in the Earthworm Eisenia fetida), earthworms were found to avoid soil containing Ag NP. Bioaccumulation of Ag NP was observed, and exposure resulted in a dose-dependant reduction in reproduction.
Roh, J.Y. et al. Toxicological Investigation of Multi-Well Carbon Nanotubes in Caenorhabditis elegans Using Genomics and Proteomics Approach. The soil nematode was exposed to multi-well carbon nanotubes (MW-CNT) and toxicity investigated using endpoints such as mortality, growth and reproduction, in addition to whole genome microarray and proteomics methods. Although mortality was not significantly affected, reproductive potential was reduced after exposure to the MW-CNT. A number of genes were differentially expressed including those for heat-shock proteins, suggesting the organisms were under stress. Work from the same research team also reported for Ag NP, for which toxicity was measured using this organism and an ecotoxicogenomic approach (Park, YJ and Choi, J. A Toxicity Assay Using Stress Responsive Caenorhabditis elegans Mutant Strains).
Kim, J. et al. Ultraviolet B Light Enhances Toxicity of CdSe/ZnSe Quantum Dots in Daphnia magna. The results of this study suggest that phototoxicity is mediated by both release of Cd from the quantum dot (QD), and production of reactive oxygen species on the QD surface.

Nanotoxicity Data Accumulating originally appeared on About.com Biotech / Biomedical on Sunday, November 22nd, 2009 at 22:19:34.

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Proteomics Used to Study PAH Exposure in Dolphins

Sun, 22 Nov 2009 00:05:52 +0000

Developments in proteomics and genomics make it possible to study the impacts of environmental contaminants on the expression of hundreds, even thousands, of genes. 2-Dimensional Gel Electrophoresis is a protein separation method used in proteomics, for partitioning proteins from a mixture according to two criteria, instead of just one. Traditional gel electrophoresis, usually applied to the separation of DNA, works in just one direction.

In a presentation today, at the SETAC North America conference (New Orleans, LA), Jennifer Cole, of Texas Tech University, described using proteomics to study the effects of benzo(a)pyrene (B(a)P), a potent carcinogen, on protein expression in the blubber of the Bottlenose Dolphin. The work is the first of its kind on a marine mammal. Skin and blubber cultures from freshly stranded dolphins, were treated with B(a)P which is a known contaminant in marine environments. Proteins were extracted, desalted and separated on a 2-D gel. The gels were run in one direction to separate the proteins based on isoelectric point (the pH at which the sum of charges of the amino acids is zero), and in a second direction to separate based on molecular weight. Using the gels, the team could also apply protein purification methods to isolate and identify specific enzymes and determine which ones were up regulated and which were down regulated, as a result of exposure to the PAH compound

Proteomics Used to Study PAH Exposure in Dolphins originally appeared on About.com Biotech / Biomedical on Sunday, November 22nd, 2009 at 00:05:52.

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Biomarkers in Environmental Toxicology

Sat, 21 Nov 2009 21:55:07 +0000

Biomarkers are an important tool used by toxicologists and environmental scientists, to study environmental exposures of plants and animals to potentially toxic compounds. Many of the methods for studying gene expression and enzyme activity, attributed to biotech and biomedical research, are also applicable to environmental studies. I am privileged to be able to attend the SETAC North America conference in New Orleans (LA) this week. While on the lookout for new information on ecological risk assessments, I've also come across a number of examples of how genetic methods are being applied to bioindicator discovery.

In one example, quantitative reverse-transcriptase (RT) PCR was used to study Vitellogenin (Vg) gene expression in male fathead minnows exposed to estrogenic substances. Vg is an egg-yolk precursor protein usually only expressed in female fish. The gene is dormant in males, but is expressed when they have been exposed to estrogenic compounds (chemicals that mimic the effects of the hormone estrogen). Reddy et al., of the US EPA, purified total RNA from the minnows and subjected the samples to reverse transcription using a retrovirus reverse transcriptase enzyme, producing cDNA, which was then quantified by PCR. Vg gene expression was altered at concentrations below routine laboratory detection limits, for three of the four compounds tested. Therefore, measurements of Vg might provide a good biomarker of exposure to estrogenic compounds, where chemical analysis is not sensitive enough.

_{Source: Reddy, TV et al. Induction of vitellogenin gene expression in adult male fathead minnows for select estrogens in 48-hr continuous addition and daily renewal exposures. Presented at SETAC NA, New Orleans, Nov. 2009.}

Biomarkers in Environmental Toxicology originally appeared on About.com Biotech / Biomedical on Saturday, November 21st, 2009 at 21:55:07.

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Breakthroughs in Tissue Engineering

Tue, 17 Nov 2009 06:22:53 +0000

A tissue is an aggregate of cells, growing and thriving in an environment where they adhere and interact with one another. Tissue Engineering is the use of bioengineering methods to create, improve, develop and grow tissues, which then may be used for grafting, cartilage repair or, ultimately, regenerative medical procedures. The study of tissues is aimed at determining the answers to fundamental questions such as how cells react and interact in a specific matrix, and may involve the use of proteomics to study gene expression and protein production in complex environments. This form of systems biology might look at cellular functions such as excretion of intercellular signaling substances, and epigenetic factors that determine physical features such as size and shape of organs.

One of the goals of tissue engineers is to reverse the effects of injury or aging of cartilage, nerve damage or scarring from burns and other trauma. Another major achievement would be the ability to grow entire organs using stem cells taken from the organ recipient, replacing the need for a suitable donor and eliminating the risk and waiting time required for finding said donor, or the potential complications of xenotransplantation.

One breakthrough in tissue engineering announced in 2009 was the development of a biodegradable resin, by a group at University of Twente, that could be used as a scaffold in situ, for human organ generation. Another significant development, announced by scientists at Stanford and NY University School of Medicine, was the ability to grow tissues in an environment of well-vascularized cells. Using laboratory animals, they demonstrated that fatty tissue from the groin area of rats containing blood vessels, fat and skin, could be used as a scaffold for stem cells. They called the scaffolds "explanted microcirculatory beds" (EMBs). Once the cells are well embedded in the tissue they can be transplanted back into the animal, where they are not rejected. Both of these discoveries hold enormous promise for therapeutic cloning and organ transplant research.

_Sources:

InSciences Organisation. Breakthrough in Twente: Biodegradable synthetic resin replaces vital body parts. 13 June 2009.

Chang et al. 2009. Tissue engineering using autologous microcirculatory beds as vascularized bioscaffolds. FASEB Journal, March 2009. doi:10.1096/fj.08-114868.

Breakthroughs in Tissue Engineering originally appeared on About.com Biotech / Biomedical on Tuesday, November 17th, 2009 at 06:22:53.

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Challenges Remain for Stem Cell Therapies

Mon, 16 Nov 2009 21:20:29 +0000

There are many challenges to making stem cell therapies such as regenerative medicine actually work in a therapeutic setting. We might be able to harvest stem cells, from either blastocysts or by creating pluripotent cells from already differentiated tissues, but that's really only the beginning of a medically viable process. Once a cell line is cultured in a maintainable way, the following questions remain:

How to direct differentiation into the desired tissue type
Optimizing growth conditions and the physical environment for cell cultures or for growing organs for transplant
How to inject and transport stem cells to the target location in the body

Challenges Remain for Stem Cell Therapies originally appeared on About.com Biotech / Biomedical on Monday, November 16th, 2009 at 21:20:29.

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Imagine H1N1 in 1850

Thu, 12 Nov 2009 06:33:05 +0000

It's the year 1847, at a hospital in Vienna. The theory of spontaneous generation is still prevalent in medical circles and story of biotechnology has not yet begun. Hungarian doctor, Ignaz Semmelweis, noting high incidence of post-partum deaths from puerpural fever (caused by Streptococcus organisms), in a wing where medical students are trained, postulates that the students were spreading diseased particles to the new mothers after having handled infected cadavers. He begins a program wherein the students wash their hands with chlorinated water before making rounds, and the death rate drops dramatically.

Although Dr. Semmelweis was not quite on the mark about the cause of childbed fever, he had pinpointed a key fact that we take for granted today: Hand washing prevents the spread of germs. A key strategy for fighting H1N1 (Swine Flu) around the world today, is public education on the importance of washing our hands especially after sneezing, blowing noses or contact with other potentially infected individuals. Dr. Semmelweis was ridiculed by the medical profession and lost his job. Imagine where we would be today, in the fight against Swine Flu, if the germ theory had never caught on? If only he was around today to see how significant his observations were!

The Semmelweis Society International is a website named in honor of the shamed doctor, with the intent to address bioethics issues and assist physicians and other medical professionals who are falsely accused of misconduct or subjected to biased peer review.

_{Source: Biotech Chronicles: www.accessexcellence.org}

Imagine H1N1 in 1850 originally appeared on About.com Biotech / Biomedical on Thursday, November 12th, 2009 at 06:33:05.

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Biotech Discoveries and the World War II Connection

Wed, 11 Nov 2009 08:27:11 +0000

It's Veteran's Day in the USA, Remembrance Day in Canada and England, and, while it may be called something different in other countries of the world, a day to remember the sacrifices of those who defend our freedom. Did you know there's a connection between World War II and one of the greatest discoveries in biotechnology? In the late 1920's Alexander Fleming made a chance discovery, that Penicillum mold, while non-toxic to humans, secreted an antibacterial substance. In 1929, his paper on the topic did not garner much interest, but during WWII, two chemists at Oxford, Howard Florey and Ernst Chain, isolated the substance, called penicillin, and discovered it kept it's antibacterial properties when dehydrated and stored as a powder.

Development of this substance into a drug was expedited by the need for an antibiotic to treat soldiers injured in the war. Thus, penicillin saved the lives of many veterans, and, as the first antibiotic, is one of the most significant achievements in the history of biotechnology.

Scientists would later discover restriction enzymes while investigating bacterial defenses against antibiotics. Antibiotics and restriction enzymes are two very important tools that made it possible to develop techniques for cloning and studying genes.

Biotech Discoveries and the World War II Connection originally appeared on About.com Biotech / Biomedical on Wednesday, November 11th, 2009 at 08:27:11.

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PCR and Synthetic Biology

Mon, 09 Nov 2009 07:33:47 +0000

When asked about the origins of synthetic biology, the most primitive, and first commercially expoited, example that comes to my mind is the construction of oligonucleotides for PCR. Oligo means short or small, and short-chains of nucleotides (DNA or RNA fragments) have become important tools in biotechnology and genetic research, ever since our ability to sequence DNA. In PCR, small pieces of DNA, usually about 15-20 base pairs long, are needed as primers. Oligonucleotides are also used for gene probing, a process for detecting certain specific sequences, and for enzyme optimization techniques like DNA shuffling and site-directed mutagenesis. We now have the ability to make much longer oligonucleotides, and technology is improving to make the process faster. According to a summary paper prepared by BIO for the 2008 World Congress, one of the most significant synthetic biotechnology breakthroughs this decade has been the in vitro construction of an entire chromosome, called PhiX174, in just 14 days. This achievement was reported in the journal PNAS by the J. Craig Venter Institute (JCVI) and team of scientists lead by Drs. Smith, Hutchinson and Venter, in 2003.

PCR and Synthetic Biology originally appeared on About.com Biotech / Biomedical on Monday, November 9th, 2009 at 07:33:47.

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H1N1: What are the Real Risks?

Sun, 08 Nov 2009 17:10:27 +0000

Travelling during a global pandemic is a risky business! I just got back from a trip to another province of Canada, a four hour flight away. While Ontario is handing out Swine Flu vaccine to the "priority groups" - small children, seniors and health-care workers, BC is facing a shortage and Alberta is dealing with bioethics issues arising from the public outcry over vaccination of the Calgary Flames, and a debate over whether firefighters are a high-risk group. One of the participants of a meeting I attended refused to shake anyone's hand for fear of getting sick, and last week I heard from a friend that children in her neighborhood of Toronto were not allowed to go Trick-or-Treating, because of influenza fears.

During my flight home I wasn't feeling the greatest and my colleague said, a little too loud, "I hope you aren't getting sick". I quickly told her not to say that too loud and looked around for the lynch mob that might throw me off the airplane at 10,000 feet. Every year there is a percentage of people getting the flu who die from it. In the USA, approximately 36,000 people die every year from the flu, although many of those are cases complicated by additional infections such as Pneumonia and Staphylococcus. This year, the US Centers for Disease Control and Prevention (CDC) has developed a new PCR-based diagnostic kit for detection of H1N1, which will not only help diagnosis but will aid in collection of more accurate statistics. In many past cases, flu patients also had known risk factors that compromised their immune system, but many don't, including roughly half of the pediatric cases. The CDC estimates mortalities due to H1N1 at somewhere over 1000, 114 of which were children, as of the end of October. Initial reports were that this strain had actually turned out to be fairly mild, so while people weigh the risks of taking the new vaccine against risks of getting, or even dying from H1N1, confusion abounds and we are experiencing the same sort of panic that prevailed in Toronto during the SARs epidemic.

H1N1: What are the Real Risks? originally appeared on About.com Biotech / Biomedical on Sunday, November 8th, 2009 at 17:10:27.

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