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Biotech / Biomedical
In a letter released today by Nature, scientists from Harvard University demonstrate what they describe as "charitable" behavior among cultures of bacteria with antibiotic resistance. The development of antibiotic resistance in pathogenic microorganisms is a growing medical problem. Researchers are scrambling to understand how resistance develops and is passed between organisms, in order to fight the proliferation of "Superbugs": Bacteria with multi-drug resistance. The authors of the Nature paper (Lee et al., 2010) have found that individual microorganisms, within a culture of drug-resistant E. coli, vary widely in terms of differences in their ability to survive. The biochemical indole, produced by microorganisms, triggers drug efflux pumps and oxidative stress responses, helping them resist the effects of antibiotics. The authors found that, within the culture, weaker strains survive an onslought of pharmaceuticals because the stronger isolates sacrifice their own robustness to produce indole for the entire culture. After sequencing the entire genome, the researchers concluded that indole production was unrelated to mutations for drug resistance, but that the small number of resistant organisms can provide protection to others in the population, in the presence of antibiotics.
Why E. coli is Used in Research
Biotech "Firsts" - Including the First Whole Genome Sequenced...
New Findings in "Superbug" Research originally appeared on About.com Biotech / Biomedical on Thursday, September 2nd, 2010 at 18:59:41.
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A new study was published online this weekend that may lend support to the argument against using bisphenol A (BPA) in plastics. BPA is a chemical used in water bottles and packaging for consumer products that helps to make the plastic rigid. Over the past few years, concerns have arisen over the amount of BPA that leaches into our food and beverages, and what effects ingestion of those concentrations have on our bodies. BPA is known to be an endocrine disruptor, meaning it interferes with normal hormone activities in our bodies.
A research team from Washington State University used a mouse model to study the effects of BPA on the reproductive system of developing embryos, in exposed mothers. The paper is presented in the journal Biology of Reproduction. The team began by validating their genomic array protocol for studying the expression of genes involved in meosis. They then used their array method on normal mice and knockouts, to demonstrate that doses of BPA considered equivalent to what humans are exposed to, can result in down-regulation of genes involved in cell division, in the ovaries of mouse embryos. This means that, while the offspring of the exposed mice may seem unaffected, THEIR offspring could suffer mutational or epigenetic consequences.
Source:
Lawson, S. et al. 2010. Exposure to low doses of BPA alters gene expression in the fetal mouse ovary. Biology of Reproduction, published online August 25, 2010. doi:10.1095/biolreprod.110.084814.
Prenatal BPA Exposure and Meotic Disturbances in Mice originally appeared on About.com Biotech / Biomedical on Monday, August 30th, 2010 at 20:19:54.
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Cyclodextrins (CDs) are circular chains of sugars used in the food and pharmaceutical industries for a variety of purposes. CDs typically consist of 6 to 9 D-(+) glucopyranose units attached by alpha-(1, 4) glucosidic bonds. They form a 3-dimensional structure with a lipophilic inner layer and are hydrophilic on the outside, which makes them ideal for encapsulating or solubilizing other molecules. These biomolecules are a product of fermentation and have many uses in the biotechnology industry. Just about every processed food you eat probably contains some cyclodextrins in one form or another, to help stabilize flavors and prevent contamination. Pharmaceutical uses include production of different types of nanoparticles for drug delivery, particularly for proteins and genes, due to their effects on drug solubility and stability.
The physicochemical properties of CDs are dependant on a number of factors including degree, and positions of, subsituents on the sugar molecules, and number of links in the oligomer chain. Research is ongoing, to identify new CDs with special properties that make them better for various food or drug applications. Recently, Cheirslip et al. (2010) reported kinetic studies on beta-CD production by a newly isolated strain of Bacillus bacteria, with the objective of optimizing enzyme processes for industrial production of CD from starch.
Examples of Food Biotechnology
Early Biotechnological Practices
Sources:
Challa, R. et al. 2005. Cyclodextrins in drug delivery: An updated review. AAPS Pharma. Sci. Tech. 6(2):E329-E357. DOI:10.1208/pt060243
Cheirslip, B. et al. 2010. Kinetic characteristics of beta-cyclodextrin production by cyclodextrin glycosyltransferase from newly isolated Bacillus sp. C26. Electronic Journal of Biotechnology 13(4). July 15, 2010. DOI: 10.2225/vol13-issue4-fulltext-6
New Bacterial Enzyme for Cyclodextrin Production originally appeared on About.com Biotech / Biomedical on Wednesday, August 25th, 2010 at 20:34:32.
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If you have a garden, you probably have, in your front or back yard, the treatment for a number of different types of cancer. The Yew is a popular ornamental bush for gardens around the world. It has soft, evergreen needles, is a hardy plant and stays an attractive green year round, even in harsh northern climates. But did you know that the Yew produces a compound that has already been approved for treatment of breast, ovary and certain lung cancers? The compound is called paclitaxel, sold under the tradename TaxolTM by Bristol-Myers Squibb. Although Taxol is generally now synthesized, the initial process of extracting it from plants is an ideal example of agricultural biotechnology.
According to Natural Resources Canada, Taxol was first extracted from the bark of the Pacific yew (Taxus brevifolia) in the 1960's, as part of screening program for detecting natural remedies, by the National Cancer Institute (NCI). However, although the anti-tumor properties were reported by chemist Monroe Wall, the NCI apparently did not take notice until his findings were confirmed in the late 1970's. Clinical trials were performed throughout the 1980's and research is ongoing, but don't get any ideas about eating Yew branches or leaves, or even making tea out of them, since paclitaxel's ability to inhibit cell division also makes it extremely toxic!
To this day, research continues on alternative medicinal uses for Taxol, for fighting a variety of diseases, and on manufacturing Taxol analogues with less side effects, greater efficacy, or that are easier to synthesize. Some studies also focus on overcoming patient resistance to Taxol. Check out Luo et al. (2010) for a paper on using green tea extract (-)-epigallocatechin gallate (EGCG) to sensitize breast carcinoma to Taxol treatments.
Early Biotechnological Practices
George Washington Carver and Agricultural Biotech
Sources:
Luo, T. et al. 2010. (-)-Epigallocatechin gallate sensitizes breast cancer cells to paclitaxel in a murine model of breast carcinoma. Breast Cancer Research 12(1): R8 (open access online). doi:10.1186/bcr2473
The taxol story - An overview. Natural Resources Canada. http://cfs.nrcan.gc.ca/subsite/yew/taxol.
Medicinal Properties of a Common Garden Bush originally appeared on About.com Biotech / Biomedical on Monday, August 23rd, 2010 at 20:46:14.
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SUMO (small ubiquitin-related modifier) is a small polypeptide that binds reversibly to proteins and influences their structure and activity. It is a post-translational protein modifier, acting in a similar fashion to other processes you may have heard about like acetylation or phosphorylation, that are found in cell signalling cascades. The process of protein modification with SUMO is called SUMOylation.
SUMO is widely distributed in nature, from yeast to human cells, and has many different roles, controlling the expression of certain enzymes, manipulating protein relocation and influencing stability. Links have been reported between the cellular functions of SUMO and various human diseases (Andreou and Tavernarakis, 2009)
The widely used assay for detecting SUMOylation uses GFP bound to SUMO, for visualization. Until recently, this method required preparation of a number of recombinant proteins and was fairly time consuming. This month, a research team from Japan has reported a simplified version of the assay in which GFP-SUMO-1, in a crude extract of transgenic E. coli cells, is combined with ATP and used to detect SUMOylation in HeLa cells (Muramatsu et al., 2010). They also demonstrated how the assay could be used to measure the efficacy of biochemical agents or pharmaceuticals that inhibit SUMOylation and propose this assay as a useful screening tool for the development of new drugs.
Essentials for Cloning and Studying Genes
Sources:
Andreou, A. and Tavernarakis, N. 2009. SUMOylation and cell signalling. Biotechnology Journal 4:1740-1752. doi:10.1002/biot.200900219.
Muramatsu, M. et al. 2010. A simple in-situ cell-based SUMOylation assay with potential application to drug screening. Bioscience, Biotechnology and Biochemistry 74(7):1473-1475. doi:10.1271/bbb.100081.
A Simplified SUMOylation Assay for Drug Screening originally appeared on About.com Biotech / Biomedical on Friday, August 20th, 2010 at 06:55:13.
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S-Adenosyl Methionine (SAMe) is a biomolecule that our bodies produce naturally, for a multitude of purposes. It is essential to our well-being and is one of the most active donors of methyl groups in our cells. From my recent blogs, you probably now have an idea of the importance of DNA methylation in epigenetics. Gene expression is highly controlled by epigenetic modifications, and too much or too little methylation can be a major factor in the development of cancer or other genetic diseases. SAMe levels appear to decline as we age, and can be correlated with other disorders besides cancer, including depression and central nervous system (CNS) disorders. For this reason, Detchanamurthy et al. (2010) have embarked on a mission to produce transgenic E. coli strains that overproduce SAMe in fermentation units, for therapeutic purposes. Their paper, in the July 15 issue of Electronic Journal of Biotechnology, describes overexpression of the gene S-Adenosyl Methionine Synthetase in E. coli, and production of SAMe in 6 litre, fed-batch fermentation units.
Why is E. coli used in Genetic Research?
Cell-Free versus Whole Cells: Making the Choice for Bioprocessing
Source:
Detchanamurthy, S. et al. 2010. Cloning and expression of S-Adenosyl Methionine Synthetase gene in recombinant E. coli strain for large scale production of SAMe. Electronic Journal of Biotechnology. 13(4). July 15, 2010. DOI: 10.2225/vol13-issue4-fulltext-2
Overexpression of Methyl Donor, SAMe, in E. coli originally appeared on About.com Biotech / Biomedical on Thursday, August 19th, 2010 at 21:11:02.
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I had one more blog to do, on pharmaco-epigenetic research, when I saw that intriguing Discovery Channel documentary over the weekend, but am now back on topic to close off what I've learned in the past two weeks about how epigenetic research is being used to study cancer and other diseases, and discover new biomarkers for disease. The process of determining DNA alterations that don't include the actual nucleotide sequence, is known as epigenetic mapping. At present, this is a complicated process, since histone and chromatin structure are poorly preserved during sample preparation in the laboratory. DNA methylation is a covalent modification that is better preserved, therefore a more reliable means of epigenetic mapping. There are three potential applications for epigenetic markers in a therapeutic setting:
Complementary diagnostic tools: Sensitive variations of PCR methodology can be used to detect CpG islands and other patterns in DNA methylation, using non-invasive sources such as blood, urine and stool samples.
Prognosis: As relationships are established between methylation (or other DNA modification) patterns and types of cancers, it might be possible to predict the progression of the disease, chances of survival and best course of action.
Predicting treatment response: Choice of treatment might be based on known epigenetic patterns and established responses to the various treatment options.
Applications for Epigenetic Biomarkers in Cancer Management originally appeared on About.com Biotech / Biomedical on Wednesday, August 18th, 2010 at 20:41:29.
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Are you curious about cascades and information networks in cells? Have you wondered if there are patterns to protein interactions? Are you interested in computational biology? This is a little out of my realm, but yesterday I watched a documentary on Discovery called "Six Degrees of Separation" that attempts to explain how cellular networks operate, in layman's terms. Everyone has heard of the "Six Degrees" theory. This show talks about it in terms of social networks AND natural processes. I had a hard time following but if this sort of thing is your forte, check out the documentary, or papers like the one by Royer et al. (2008) where software called Power Graphs was used to study protein-protein interaction networks and to show clustering of transcription factors and target genes. Using the algorithms produced by Power Graph analyses, and applying them to proteomic research, the authors proposed that networks of protein interactions can be simplified, visualized and better understood.
Source:
Royer et al. 2008. Unraveling Protein Networks with Power Graph Analysis. PLoS Computational Biology, July 2008.
Power Graphs Analysis of "Six Degrees" in Protein Interactions originally appeared on About.com Biotech / Biomedical on Sunday, August 15th, 2010 at 12:13:04.
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The use of pharmaco-epigenomics has already lead to the approval of several drugs for treatment of different types of cancer. These drugs work by reversing epigenetic changes that have lead to development of the disease. According to Claes et al. (2010), two gene families have received the bulk of attention in recent years, as targets for pharmaco-epigenomic therapy, the HDAC (histone deacetylase) and DNMT (DNA methyltransferase) families. These inhibitors seem to be most effective for treating hemaologic malignancies (e.g. the DNMT inhibitor decitabine), and are not as useful for solid tumors, but there is a lot of potential for use of compounds like these in synergism with more conventional cancer therapies. For example, synergistic treatments might allow reduced doses of more traditional chemotherapeutic drugs to be used. Also, as was observed for some HDAC inhibitors, reduced DNA repair efficiency may enhance radiation treatments by increasing cellular radiosensitivity.
Although epigenetic treatments are not without risks, clinical data suggests they are reasonably safe. It appears that activation or silencing of transcription is not necessarily a global effect. DNMT inhibitors, for example, appear to act only on dividing cells, and abnormally silenced genes seem to be the preferred targets of epigenetic drugs. Approaches to improving the safety of these drugs include use of promoter-specific transcription factors like the one artificially produced by Beltran et al. (2007), to reactivate the methylated promoter of the tumor-suppressor gene MASPIN.
Dendreon Corporation: ACIs for Cancer Treatment
deCODE Genetics: DNA-Based Diagnostics
Source:
Claes, B. et al. 2010. Pharmaco-Epigenomics: Discovering Therapeutic Approaches and Biomarkers for Cancer Therapy. Heredity, 105:152-160.
Epigenetic Therapies are Synergistic with Conventional Treatments originally appeared on About.com Biotech / Biomedical on Friday, August 13th, 2010 at 07:00:27.
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The new field of Pharmaco-Epigenomics is being applied for diagnosis, prognosis and treatment of leukemia, according to research to be published this month in the journal Epigenetics. Tong et al. (2010) have used genome-wide DNA methylation profiling to study epigenetic markers and chronic lymphocytic leukemia (CLL). Prior research has linked excessive DNA methylation with reduced transcription of tumor suppressor genes, and revealed that specific methylation patterns in acute lymphoblastic leukemia (ALL) can be used to predict a patient's prognosis. Likewise, DNA methylation in patients with CLL shows distinct patterns. Tong et al. found bias towards certain chromosomes and when they investigated genes on chromosomes 17 and 11, they found those alterations appeared linked to poor prognosis. Aberrant DNA methylation is of interest to biomedical researchers because it can be reversed by drugs that reduced the specific activity of enzyme DNA methyltransferase, which is responsible for methylating DNA.
Pharmacokinetics: The Fate of Drugs
Source:
Tong, W. et al. 2010. Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact. Epigenetics August 16, 2010, obtained online prior to printing.
Epigenomics in Leukemia Research originally appeared on About.com Biotech / Biomedical on Monday, August 9th, 2010 at 08:55:27.
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