Biotechnology

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

2008-11-12T20:01:00.001+05:30

Background

Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3' targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133.

Results

We show that at the gene expression level, the Exon Array performs comparably with the two 3' targeted platforms. However, correlation of the results is slightly lower than between the two 3' arrays. We show that some of the discrepancies stem from the RNA amplification protocols, e.g. the Exon Array is able to detect expression of non-polyadenylated transcripts. We also show that many other differences are the result of the ability of the Exon Array to monitor the more exact isoform-level changes: we show several examples where the changes detected by the 3' platforms are actually isoform variations, and that the nature of these variations can be resolved using Exon Array data. Finally, we show how the Exon Array can be used to detect alternative isoform differences, such as alternative splicing, transcript termination, and alternative promoter usage. We discuss the possible pitfalls and false positives resulting from isoform-level analysis.

Conclusions

The Exon Array is a valuable tool which can be used to profile gene expression, but also provides valuable additional information regarding the types of gene isoforms that are expressed and variable. However, analysis of alternative splicing requires much more hands on effort and visualization of results in order to correctly interpret the data, and generally results in considerably higher false positive rates than expression analysis. One of the main sources of error in the MAQC dataset is variation in amplification efficiency across transcript, which is not adequately corrected using existing statistical methods. We outline approaches to reduce such errors by filtering out potentially problematic data.

Differential solubility of curcuminoids in serum and albumin solutions: implications for analytical and therapeutic applications

2008-11-12T20:00:00.001+05:30

Background

Commercially available curcumin preparations contain a mixture of related polyphenols, collectively referred to as curcuminoids. These encompass the primary component curcumin along with its co-purified derivatives demethoxycurcumin and bisdemethoxycurcumin. Curcuminoids have numerous biological activities, including inhibition of cancer related cell proliferation and reduction of amyloid plaque formation associated with Alzheimer disease. Unfortunately, the solubility of curcuminoids in aqueous solutions is exceedingly low. This restricts their systemic availability in orally administered formulations and limits their therapeutic potential.

Results

Methods are described that achieve high concentrations of soluble curcuminoids in serum. Solid curcuminoids were either mixed directly with serum, or they were predissolved in dimethyl sulfoxide and added as aliquots to serum. Both methods resulted in high levels of curcuminoid-solubility in mammalian sera from different species. However, adding aliquots of dimethyl sulfoxide-dissolved curcuminoids to serum proved to be more efficient, producing soluble curcuminoid concentrations of at least 3 mM in human serum. The methods also resulted in the differential solubility of individual curcuminoids in serum. The addition of dimethyl sulfoxide-dissolved curcuminoids to serum preferentially solubilized curcumin, whereas adding solid curcuminoids predominantly solubilized bisdemethoxycurcumin. Either method of solubilization was equally effective in inhibiting dose-dependent HeLa cell proliferation in culture. The maximum concentration of curcuminoids achieved in serum was at least 100-fold higher than that required for inhibiting cell proliferation in culture and 1000-fold higher than the concentration that has been reported to prevent amyloid plaque formation associated with Alzheimer disease. Curcuminoids were also highly soluble in solutions of purified albumin, a major component of serum.

Conclusions

These results suggest the possibility of alternative therapeutic approaches by injection or infusion of relatively small amounts of curcuminoid-enriched serum. They also provide tools to reproducibly solubilize curcuminoids for analysis in cell culture applications. The differential solubility of curcuminoids achieved by different methods of solubilization offers convenient alternatives to assess the diverse biological effects contributed by curcumin and its derivatives.

Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic

2008-11-06T16:11:00.000+05:30

Background
Due to the global occurrence of multi-drug-resistant malarial parasites (Plasmodium falciparum), the anti-malarial drug most effective against malaria is artemisinin, a natural product (sesquiterpene lactone endoperoxide) extracted from sweet wormwood (Artemisia annua). However, artemisinin is in short supply and unaffordable to most malaria patients. Artemisinin can be semi-synthesized from its precursor artemisinic acid, which can be synthesized from simple sugars using microorganisms genetically engineered with genes from A. annua. In order to develop an industrially competent yeast strain, detailed analyses of microbial physiology and development of gene expression strategies are required.

Results
Three plant genes coding for amorphadiene synthase, amorphadiene oxidase (AMO or CYP71AV1), and cytochrome P450 reductase, which in concert divert carbon flux from farnesyl diphosphate to artemisinic acid, were expressed from a single plasmid. The artemisinic acid production in the engineered yeast reached 250 ug mL-1 in shake-flask cultures and 1 g L-1 in bio-reactors with the use of Leu2d selection marker and appropriate medium formulation. When plasmid stability was measured, the yeast strain synthesizing amorphadiene alone maintained the plasmid in 84% of the cells, whereas the yeast strain synthesizing artemisinic acid showed poor plasmid stability. Inactivation of AMO by a point-mutation restored the high plasmid stability, indicating that the low plasmid stability is not caused by production of the AMO protein but by artemisinic acid synthesis or accumulation. Semi-quantitative reverse-transcriptase (RT)-PCR and quantitative real time-PCR consistently showed that pleiotropic drug resistance (PDR) genes, belonging to the family of ATP-Binding Cassette (ABC) transporter, were massively induced in the yeast strain producing artemisinic acid, relative to the yeast strain producing the hydrocarbon amorphadiene alone. Global transcriptional analysis by yeast microarray further demonstrated that the induction of drug-resistant genes such as ABC transporters and major facilitator superfamily (MSF) genes is the primary cellular stress-response; in addition, oxidative and osmotic stress responses were observed in the engineered yeast.

Conclusion
The data presented here suggest that the engineered yeast producing artemisinic acid suffers oxidative and drug-associated stresses. The use of plant-derived transporters and optimizing AMO activity may improve the yield of artemisinic acid production in the engineered yeast.

Recombinant amyloid beta-peptide production by coexpression with an affibody ligand

2008-11-06T16:08:00.001+05:30

Background
Oligomeric and fibrillar aggregates of the amyloid beta-peptide (Abeta) have been implicated in the pathogenesis of Alzheimer's disease (AD). The characterization of Abeta assemblies is essential for the elucidation of the mechanisms of Abeta neurotoxicity, but requires large quantities of pure peptide. Here we describe a novel approach to the recombinant production of Abeta. The method is based on the coexpression of the affibody protein ZAbeta3, a selected affinity ligand derived from the Z domain three-helix bundle scaffold. ZAbeta3 binds to the amyloidogenic central and C-terminal part of Abeta with nanomolar affinity and consequently inhibits aggregation.

Results
Coexpression of ZAbeta3 affords the overexpression of both major Abeta isoforms, Abeta(1-40) and Abeta(1-42), yielding 4 or 3 mg, respectively, of pure 15N-labeled peptide per liter of culture. The method does not rely on a protein fusion or tag and thus does not require a cleavage reaction. The purified peptides were characterized by NMR, circular dichroism, SDS-PAGE and size exclusion chromatography, and their aggregation propensities were assessed by thioflavin T fluorescence and electron microscopy. The data coincide with those reported previously for monomeric, largely unstructured Abeta. ZAbeta3 coexpression moreover permits the recombinant production of Abeta(1-42) carrying the Arctic (E22G) mutation, which causes early onset familial AD. Abeta(1-42)E22G is obtained in predominantly monomeric form and suitable, e.g., for NMR studies.

Conclusions
The coexpression of an engineered aggregation-inhibiting binding protein offers a novel route to the recombinant production of amyloidogenic Abeta peptides that can be advantageously employed to study the molecular basis of AD. The presented expression system is the first for which expression and purification of the aggregation-prone Arctic variant (E22G) of Abeta(1-42) is reported.

Fast Algorithms for Computing Sequence Distances by Exhaustive Substring Composition

2008-10-29T12:55:00.000+05:30

The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are hardly fulfilled by the more traditional measures of sequence similarity and distance, like string edit and gene rearrangement, due to a mixture of epistemological and computational problems. Alternative measures, based on the subword composition of sequences, have emerged in recent years and proved to be both fast and effective in a variety of tested cases. The common denominator of such measures is an underlying information theoretic notion of relative compressibility. Their viability depends critically on computational cost. The present paper describes as a paradigm the extension and efficient implementation of one of the methods in this class. The method is based on the comparison of the frequencies of all subwords in the two input sequences, where frequencies are suitably adjusted to take into account the statistical background.

Top 10 Common Biotech Terms You Should Know

2008-10-22T12:28:00.001+05:30

1. What are Enzymes?
Enzymes are proteins that catalyze specific biochemical reactions in cells. They are important tools in biotechnology for the industrial production of bioproducts, and for other processes related to cleaning (e.g. degreasing, remediation), digestion (e.g. cellulases, deinking, bleaching in the pulp and paper industry) and more.
Genetic modifications to enzymes through protein engineering techniques such as site-directed mutagenesis and DNA shuffling have allowed scientists to enhance the catalytic properties of certain enzymes under specific industrial conditions such as extremes of temperature or pH, or the presence of harsh chemicals.

2. What Does GMO Stand For?
GMO stands for genetically modified organism. This refers to bacteria or other microorganisms, or multicellular organisms such as plants and animals, whose genetic makeup has been altered by scientists.
Often, GMOs are produced using gene cloning methods as a means of introducing a non-native gene into a new organism. An example of this is introduction of genes for natural pesticides into non-native crop plants, to enhance insect resistance and reduce the need for chemical pesticides.
There are numerous applications for GMOs in the biotech industry. However, they are often viewed as suspect by many and public controversy surrounds their use in food, drug and other commercial products.

3. What is Cloning?
In biotechnology, one meaning of the term "clone" is any living organism (or the production of such an organism) with genetic material that is identical to that of the parent organism from which it was created.
A second meaning refers to cloning DNA, or the act of creating copies of an individual gene, for expression in a foreign host, which leads to generation of exact replica macromolecules (e.g. DNA, RNA, proteins).

4. How do Buffers Work?
Buffers are solutions that have the capacity withstand the addition of small amounts of protons and/or hydroxide ions, or undergo dilution, without a dramatic change in pH. They are comprised of a mixture of a weak acid and its conjugate base, or a weak base and its conjugate acid. The buffering action is a result of the equilibrium between the acid-base pair.
Optimum buffering capacity occurs when the components of the acid-base pair are present at nearly the same concentrations. When they are present in equal amounts, the buffer will resist pH changes in the range of its pKa (acid dissociation constant).

5. How Long Does it Take to Get a Patent?
Getting a patent is the best way to protect your IP. The length of time from filing at patent to getting approval varies depending on where the application is filed. In the US, the process generally takes about 2 1/2 years. The processing time depends on whether or not the examiner rejects the claim based on prior patents, and whether the new patent application has to undergo amendments.
Of course, the overall time required to get a patent also depends upon the time required for research and development, prior to filing, and, in the case of new drugs, clinical studies, all of which can take 10+ years.

6. Why Are New Drugs So Expensive?
The entire process of bringing a new drug to market involves years of laboratory research and development, animal trials, toxicity testing and, finally, clinical trials. Typically, this process plus the patent filing, takes over 10 years, so it is a long time before the pharmaceutical company can start earning any payback for its investment which can amount to hundreds of millions of dollars. Obviously the company needs to earn back some of that investment, so the costs are passed on to consumers.

7. How Are Biochemical Solutions Sterilized?
In the mid-1800's, the process of pasteurization was described by Louis Pasteur, who discovered that heating solutions to moderate temperatures would reduce the numbers of contaminating live microorganisms. This research laid the groundwork for the development of today's autoclaves: Instruments in which solutions and dry materials are heated under pressure, for sterilization. Materials are heated rapidly, typically to about 121 degrees Celsius, under a pressure of about 15 psi. The high pressure prevents liquids from boiling over, thus allowing such high temperatures to virtually eliminate most live microorganisms.

8. What is Bioremediation?
Remediation is the restoration of contaminated land, air or water from a contaminated state. Bioremediation is the process of utilizing live organisms (typically bacteria, but sometimes plants) to accumulate, transform or (usually) degrade chemical contaminants.
When plants are used, the process is referred to as phytoremediation. Phytoextraction is a technique whereby plants are used to bioaccumulate non-degradable materials, typically metals, which are thus removed from soil, and then removed from the environment during harvesting.

9. Where do Stem Cells Come From?
The most widely known source of stem cells is human/animal embryos, prompting controversy over stem cell research based on bioethics and the view that life begins at conception. It is now known that stem cells can also be obtained from placenta and amniotic fluids, and pluripotent cells can be derived from adult cells of the skin, blood and other tissues. Research on the use of stem cells from non-embryonic sources has received more attention in recent years as scientists in some countries, particularly the US, are forced to search for publicly accepted, ethical alternatives.

10. Where Do Pharmaceutical Companies Get Subjects for Drug Trials?
Clinical trials on human subjects are an important step in the development of new drugs and help assess both their safety and efficacy. For many new drug trials, healthy volunteer subjects are needed and are usually paid, up to $10,000 for their participation, depending on the risks. Individuals interested in becoming a test subject can access lists of upcoming drug trials online, or can investigate the research programs at individual universities and teaching hospitals.

Search and Discovery Strategies for Biotechnology: The Paradigm Shift

2008-09-27T10:37:00.001+05:30

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnologytargets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnologypenetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

The Blind Shall See

2008-09-20T09:41:00.004+05:30

Since losing his vision some 36 years ago, "Jerry" has been in a world of darkness. In a stunning course of events, researchers at the Dobelle Institute announced that through the use of an innovative device, Jerry can "see."

Jerry doesn't "see" in the conventional sense but with the device he is able to make out shapes. He can discern objects based on white dots on a black background similar in many respects to a photo negative.

A pair of sunglasses with a built-in distance measuring device in one lens and a pinhole camera in the other.

A "wearable" computer attached to the glasses worn on the user's belt that receives and processes information from the devices in the glasses.

A second computer that sends signals to electrodes directly on the brain's surface.

Wiring connections from the computer to the surface of the brain.

Electrodes are attached to the surface of the brain.
In a previous demonstration of the device, Jerry has been able to place a black hat (hanging on a white wall) on the head of a mannequin.

A total of six patients have been tested with the device.

Interestingly enough, the applications of this technology are not confined to helping the blind to see. Since the techniques used involve nerve stimulation, the researchers have used the underlying technology in a variety of situations.

The researchers hope to have an improved version of the device for commercial use later in the year.

What do you think? How long do you think it will take before we have the technology to simulate full sight? Do you think that ultimately the technology will be affordable so that we won't have haves and have-nots?

Human clones: New U.N. analysis lays out world's choices

2008-09-07T10:54:00.004+05:30

The world community quickly needs to reach a compromise that outlaws reproductive cloning or prepare to protect the rights of cloned individuals from potential abuse, prejudice and discrimination, according to authors of a new policy analysis by the United Nations University’s Institute of Advanced Studies (http://www.ias.unu.edu/).

A legally-binding global ban on work to create a human clone, coupled with freedom for nations to permit strictly controlled therapeutic research, has the greatest political viability of options available to the international community, says the report: Is Human Reproductive Cloning Inevitable: Future Options for UN Governance, released Nov. 12 by A.H. Zakri, Director of UNU-IAS, based in Yokohama, Japan.

Virtually every nation opposes human cloning and more than 50 have legislated bans on such efforts. However, negotiation of an international accord foundered at the UN in 2005 due to disagreement over research cloning (also called therapeutic cloning).

"Human reproductive cloning could profoundly impact humanity," says UN Under-Secretary-General Konrad Osterwalder, Rector of UNU. "This report offers a plain language analysis of the opportunities, challenges and options before us – a firm and thoughtful base from which the international community can revisit the issue before science overtakes policy."

Without an international prohibition, human reproductive cloning accomplished in certain countries could be judged perfectly legal by the International Court of Justice, warn UNU-IAS co-authors Brendan Tobin, Chamundeeswari Kuppuswamy, Darryl Macer, Mihaela Serbulea.
“Failure to outlaw reproductive cloning means it is just a matter of time until cloned individuals share the planet,” says barrister Mr. Tobin of the Irish Center for Human Rights, National University of Ireland, Galway. “If failure to compromise continues, the world community must accept responsibility and ensure that any cloned individual receives full human rights protection. It will also need to embark on an extensive awareness building and sensitivity program to ensure that the wider society treats clones with respect and ensure they are protected against prejudice, abuse or discrimination.”

There is almost universal international consensus on the desirability of banning reproductive cloning based in part on religious and moral grounds, but mostly on concerns about underdeveloped technologies producing clones with serious deformities or degenerative diseases, Mr. Tobin adds. As technologies advance and possibilities of success increase, the current consensus is likely to erode and with it the possibility of securing a ban on reproductive cloning.

According to the UNU report, the widest international consensus would be achieved around an agreement that prevents progress towards full reproductive cloning but authorizes strictly controlled therapeutic cloning to prevent the uncontrolled production and destruction of embryos.
Failure to deal with the cloning issue reflects on "the credibility of the UN institution itself and its capacity to respond to society’s need for competent leadership," says the report.

“Whichever path the international community chooses it will need to act soon – either to prevent reproductive cloning or to defend the human rights of cloned individuals,” says Dr. Zakri.
The report calls the prospect of human cloning “one of the most emotive and divisive issues to face UN negotiators and the international community in recent years.”

Efforts in 2005 to negotiate an international convention fell through over so-called research or therapeutic cloning.

Whereas reproductive cloning is meant to duplicate a person or animal, research cloning is meant to produce tissues that genetically match those of the person or animal whose cells are cloned.

Proponents of research cloning for regenerative medicine say it offers great hope of producing replacement tissue without the fear of immunological rejection, that it offers a potential cure for millions of people suffering common diseases of the industrialized world – diabetes, stroke, spinal injury, and neurodegenerative diseases such as Alzheimer’s or Parkinson’s.
Opponents view research cloning as the unethical production and destruction of living embryos to produce stem cells upon which such therapies are based. The clash of positions led to a compromise non-binding UN Declaration on Cloning.

There have been no substantiated claims of cloned human embryos grown into fetal stages and beyond but such an historic event is not far off, most experts agree.

Clones have been achieved with mice, sheep, pigs, cows and dogs and U.S. researchers last summer accomplished the first cloning of a primate – a rhesus monkey embryo cloned from adult cells and then grown to generate stem cells.

National efforts to outlaw reproductive cloning of humans are easily skirted if researchers can simply move to other jurisdictions. Disgraced South Korean medical researcher Woo Sook Hwang, whose human clone claims were unsubstantiated, reportedly continues his work in Thailand.
The report explores in depth the difficult ethical considerations behind the issue.

“It is frequently argued, for instance, that reproduction should occur by chance and through natural selection. This argument may be based upon religious lines, which defer to a supernatural or higher power for choice, or to natural selection and the importance of ensuring continued human diversity.

“More convincing for some are arguments against the commoditisation of life. Fears exist that allowing reproductive cloning will lead to a spare parts market for harvesting human organs from cloned “brain-less bodies” for the rich as they seek to extend their lifespan, a result which many see as a contravention of individual and collective human dignity.

“These are not issues which can be lightly dismissed; however, it is clear that any debate on human dignity needs to separate the various elements of the debate in order to consider whether opposition to cloning stems from concern for human dignity or respect for divine dignity. As well as to determine whether it is designed to protect the individual that may be cloned or the society whose sense of personal and collective identity might be challenged by the concept of sharing the world with cloned individuals.”

The Real Fountain of Youth

2008-09-03T21:58:00.005+05:30

Wow, first cloning and now immortality? Okay, we're jumping the gun a bit. But seriously, scientists announced that they have succeeded in producing cells that divide many times over their normal limit. In normal cells, division takes place a certain number of times and then the cell stops dividing. Likewise, cells in vitro usually divide about 50 times or so before they cease dividing. Scientists succeeded in producing cells that divided over 90 times with no signs of slowing down! But how?

In the nucleus of a cell, each chromosome contains the genetic information, aka DNA, for the individual. When cells divide, DNA is replicated. On the end of chromosomes is a protective "cap" of sorts, called a telomere. As cells divide, the telomere becomes shorter and shorter until the cell ages and stops dividing. Scientists have known that telomere shortening is associated with the aging process, but it wasn't known whether shortening is an exact cause or a byproduct of aging.

Last week, scientists at Geron Corporation and the University of Texas Southwestern Medical Center added an enzyme called telomerase to the cell's chromosomes. Telomerase caused the telomeres to grow longer, thus circumventing the normal shortening process. From this experiment, scientists were able to conclude that telomeres do act as a biological clock in the aging process.

This could have interesting implications. Theoretically, scientists would be able to treat a variety of genetic defects and/or diseases by removing a group of cells from a person, rejuvenating them, and returning them.
There are several unanswered questions. Because cancerous cells have telomeres that do not shorten, there is some debate whether or not the natural shortening of telomeres is an evolutionary adaptation to ward off cancer. By circumventing this natural process, we may in fact be destroying a natural defense mechanism of the body. As additional experiments and investigations are performed, we will be better able to see if this process is indeed an "immortality" breakthrough.

What do you think? Will we achieve cell immortality? What are the implications for future generations?

The Biological Computer

2008-09-03T21:53:00.005+05:30

Imagine a computer the size of cellular components that could interact with the cellular apparatus. In response to predetermined events, the tiny computer could synthesize RNA that would direct the production of proteins. Imagine no more! Israeli scientists recently took the first steps toward developing a rudimentary prototype.

The prototype is based on the Turing machine, a computing device developed in the 1930s. Before the prototype, an actual Turing machine had not been built.

Researchers hope to one day synthesize a subcellular computer that would interact with cellular components. A wide variety of applications, such as synthesizing drugs inside of cells, would then be possible.

They further hope that with the advent of improved molecular synthesizing techniques, the computer could be built from actual biomolecules. Its size would then be greatly reduced from the prototype.

Since the goal is to ultimately produce the device from these molecules, all of the programmatic instructions are derived from current cellular processes such as polymer elongation and ligation. Like ribosomes, programming rules determine a specific "step." For ribosomes, transfer RNA serves to specify a translation "step." Like a ribosome, the device can operate on two polymers at the same time.

Such a device could have wide ranging effects on a cell. The device could respond to a cellular state, such as a certain concentration of various molecules, and produce an effect based on that cellular state. This would allow doctors to have a potential in vivo (within the living organism) cellular aid.

Ribosomes are crucial to the cellular apparatus. They translate the "message" from messenger RNA into a protein. Messenger RNA is transcribed from DNA, so, in effect, ribosomes ultimately translate the DNA code into an actual protein.

What do you think? Does nanotechnology hold promise for the future of biology?

Implantable Insulin Pumps

2008-08-26T22:49:00.002+05:30

Researchers at the University of Delaware recently announced that "smart" implantable insulin pumps may one day provide relief for people with Type I diabetes. Approximately 16 million people suffer from markedly fluctuating glucose levels because of their body's inability to produce insulin. Insulin helps the body process sugar. Sugar levels must be controlled within a specific range as high levels have been linked to blindness and a host of other medical problems.

The basis of the proposed technique is a sophisticated algorithm for controlling sugar levels. Scientists believe that all of the technology components are now in place--from the mathematical model used to the computer chip necessary to house the instructions. Once the instructions are encoded onto a chip, the result becomes compatible with standard insulin pumps.

If successful, implants will provide much relief to diabetics who now must either prick themselves several times a day to measure blood sugar levels or deal with bulky monitoring systems. Implants will allow people to lead more active lives.

While existing implantable pumps deliver a specific dosage at a specific interval, the goal is for the implants to more closely simulate the normal function of the pancreas by using glucose sensors and the predictive mathematical models. The sensors would assess the level of glucose in the blood and pass the information to the "algorithm." Based on the data, the algorithm would cause the appropriate action by the pump.

Interestingly enough, the algorithms predict based on the past behavior of the insulin-glucose system in the body. This past behavior allows the algorithms to accurately assess and predict for future events.

Scientists are assembling the needed parts into a comprehensive system. They estimate that it will be three to five years before such devices are readily available.

What do you think? Could this implant technology provide relief from other chronic diseases?

Heart-to-Heart Tool

2008-08-26T22:29:00.002+05:30

We all know the statistics: millions suffer from heart disease, and many suffer heart attacks. Even more alarming is the fact that by some estimates more than 350,000 people die from so-called "sudden death" after a heart attack. Researchers have been baffled by the exact nature and cause of these deaths. Last week, scientists at the University of North Carolina Chapel Hill unveiled a promising new modeling procedure which may shed some light on the mechanisms associated with heart attacks and sudden death.

This new system involved cultured heart cells. In a heart attack, some cells become deprived of oxygen while others continue to receive sufficient oxygen. The region between these two types of cells, called the border zone, is simulated in the cultured model. Since the culture focuses on the interactions in the border zone, it could be very helpful in studying arrhythmias. Arrhythmias are irregularities in the heartbeat usually associated with decreased blood flow in the coronary arteries.

The complex interactions within a particular organism and the size of the actual zone have made animal models particularly difficult in studying the border zone. Likewise, single cells don't display the border irregularities. By using a culture of cells, the research team was able to overcome both limitations. The border zone can be produced and the interactions are essentially isolated for practical purposes.

The cultures appear to be stable for a couple of hours, thus allowing the team to do basic time-based studies.

Since the causes and mechanisms associated with sudden death are so poorly understood, researchers are optimistic that this new modeling system will shed some light on sudden death. By focusing on the internal changes associated with cells and the resulting interactions, the team believes that the culture model will be successful.

What do you think? Might this new technique be helpful in reducing the instances of sudden death? What other therapies and/or procedures might be used to produce a synergistic effect?

Brain Power

2008-08-25T16:14:00.001+05:30

Researchers at Duke University and MCP Hahnemann University have developed a technique for using brain signals to control a robotic arm. This feat was accomplished by recording signals from electrodes that were implanted in the brains of rats. It is believed that this new method may some day offer hope to those suffering from spinal cord injuries who have prosthetic limbs. Theoretically, the electrodes could be implanted into the brain to allow the person to have control over limb movement, much as they would an actual limb.

In the experiment, rats were taught to operate a robotic arm by pressing a lever. Pressing the lever resulted in the rats receiving a reward. Researchers recorded the neuronal activity responsible for muscle movement using implanted electrode arrays. Once the specific groups of neurons that were used for muscle movement when pressing the lever were identified, researchers changed the control of the robotic arm from the lever to the electrode implants.

The rats promptly learned that they could move the robotic arm to receive a reward without having to press the lever. All they had to do was to activate the particular neurons in the brain that they had previously used when physically pressing the lever.

This ground-breaking study established the first tangible evidence that neuron signals can be used to control external devises. Prior to this study, scientists suspected that neuronal control of external devices was possible but there was no demonstrable proof.

Researchers speculate that the knowledge gained from this study could be used to develop new techniques to treat those suffering from a variety of disabilities including spinal cord injuries, cerebral palsy, and locked-in syndrome. Since those with locked-in syndrome may have intact thinking skills but no ability to interact with their environment, external control of devices through neurons may be particularly helpful.

The researchers also strongly emphasize that there are still significant technical obstacles that must be overcome before any attempts at human clinical trials can begin. They do however believe that these obstacles are not impossible to overcome.

New Skin

2008-08-25T16:08:00.002+05:30

Sometimes we take the simple things for granted: a gentle touch or a hug from a loved one. For some, such small gestures can have dire consequences. For people suffering from a set of rare genetic disorders, the skin may blister from the smallest touch. For years, people suffering from epidermolysis bullosa had little hope for relief from the disease.

Scientists at the University of Miami recently announced a new technique for bioengineering skin that offers hope to those suffering from the severe forms of the disease. An eight-week-old baby became a recipient of this bioengineered skin, known as Apligraf. Approximately 45% of her body has been covered with the new bioengineered skin. The skin is simply placed on her body and held in place by gauze and petroleum based products, similar to Vaseline. The baby's hands and feet are wrapped to make sure that she doesn't injure herself while the skin takes hold. Doctors hope to prolong her life with the replaced skin, although they don't believe that a full cure is imminent.

The baby has a particularly severe form of epidermolysis bullosa called Dowling Meara disease. Her cells lack the necessary cellular components that make skin "stick" together. As a result, the slightest contact can cause a tear in the skin. Likewise, persons with this disease are particularly susceptible to infections.

Apligraf was developed by a company called Organogenesis and was recently approved by the Food and Drug Administration. It is a combination of a baby's foreskin and bovine collagen. A small piece of foreskin can produce enormous amounts of new skin. The foreskin is usually obtained after babies have been circumcised.

Apligraf has been used to heal both long-term and open venous wounds. In each case, the wounds did not heal on their own before the application of Apligraf. Organogenesis notes that the procedure has been reported by recipients to be thoroughly less painful than other procedures.
The doctors hope to continue their work with the use of Apligraf in regenerative medicine. They hope that the bioengineered skin will shorten patient stays in the hospital and allow them to effectively treat a host of skin problems.

Animal Testing Without Animals

2008-08-25T16:03:00.002+05:30

Two researchers at the Rensselaer Polytechnic Institute have developed an Electric Cell-substrate Impedance Sensing (ECIS) device that uses electricity to study complex cell behavior. The device offers researchers a way of testing cell interactions through non-invasive means.
The ECIS device is an "electronic eavesdropper" on cells and can measure the activity of cells over time. Because it is connected via software to a computer, all data acquisition and analysis can be automated. Data about a cell's response can be taken as frequently as every quarter second.

The device works by electrically "culturing" live cells in a set of trays which sit in bays that are supplied with a low-level alternating current from an electrode. When electricity is present, cells will expand over the electrode, allowing changes to be measured.

This electrical sensor allows a new level of detail for the results. Instead of the traditional petri dish for cultures and examination by a microscope, the entire procedure is now automated.
Many people question the use of animals in research, particularly in nonessential testing. Others maintain that animal modeling is a necessary prerequisite for the discovery of new treatments. One target is the cosmetics industry. This device could markedly reduce or even eliminate the need to use live animals to test and measure the toxicity levels of chemicals.

The device is also cost effective. Data can be taken in real time essentially 24 hours a day with minimal human interaction. The device is manufactured by Applied BioPhysics and retails for approximately $40,000. Several large universities and biotechnology companies in Japan, Taiwan, and the United States are currently using the machine.

Should scientists create new life?

2008-08-12T13:01:00.000+05:30

Should scientists try to create a new life form?

That profound question was put on the nation’s agenda when two of the world’s premier geneticists, Craig Venter and Hamilton Smith, announced Thursday that they had received millions of dollars in federal funding to attempt such a project.

IN A NUTSHELL, what Venter and Smith propose to do is create a very simple microbe. Some viruses have only 400 or 500 genes. Venter and Smith are going to remove the genes from one such tiny bug, synthesize a new set of genes, drop them into the bug and see if the new instructions will bring the microbe to life. If they do and if the genes are a blueprint that has never existed before in nature then these two scientists can say that they have created the world’s first artificial microbe.

Aside from the glory involved there are some very good reasons to build artificial viruses and bacteria. It would be of enormous importance to know what sequences of DNA put in the right order can make something come “alive”. Such knowledge could one day enable us to make microbes that we could use to prevent pollution, kill other bugs that cause us much misery such as those involved in gonorrhea, malaria, tuberculosis and AIDS, and to make tiny microbes that could provide some immunity against disease.

But there are some reasons to think hard about the wisdom of trying to create new life. Some will worry that it is not our place in the cosmos to create living things. Only god should do that. Others may fear that the creation of new microbes holds the potential for having something escape from the lab that could cause havoc out in the real world. Still others correctly note that this kind of synthetic genomics could be used to make nasty critters that terrorists or evil nations could use against us.

It might be noted, too, that those who can build a bug can also claim ownership over it making it possible that someone might actually try to patent “life” itself!

I don’t think we should fear the creation of new life forms. After all, we have essentially been doing that for many centuries through systematic breeding of animals and plants.

As far as I can determine, no major religion is opposed to the creation of life forms as an act that defies god’s will or places humanity in a role that is inappropriate. Playing god is a common criticism of what scientists do but if you create a life form that can cure disease or feed the world then you won’t find many religious leaders objecting.

And yes, nasty microbes may escape and bad guys could synthesize some pretty nasty critters but what we need here are adequate safeguards and controls. Perhaps not every bit of information about how to make a microbe belongs on the Internet or in a publicly available journal. And if we don’t want anyone to own new life forms then it is well within our power to pass legislation that would prohibit them from doing so.

So, amazing as the idea is of generating new life from scratch I think there is merit in pushing ahead. But if this ship is going to sail we have to get busy making the rules and the safeguards as well as the genes.

Mad cow probe offers little reassurance

2008-08-12T12:59:00.000+05:30

The Bush administration announced earlier this week that it was calling off the search for cattle that might have mad cow disease. Is this really a good idea? Probably. But is the government doing enough to insure that mad cow does not imperil the lives of Americans and at the same time destroy a crucial part of our economy? Hardly.

The hunt for animals that might be infected with mad cow began seven weeks ago when the first case of mad cow in the United States was discovered at a dairy farm in Washington state. Soon after, investigators from the U.S. Department of Agriculture set out to determine whether there were any other infected cows.

During the investigation, officials found that the Washington cow was one of at least 80 other possibly infected cows that had entered this country from the Canadian province of Alberta. But finding these animals proved to be as difficult an assignment as searching for a competent singer on American Idol.

In their hunt for the animals, the investigators visited scores of farms in three states and sifted through the records of roughly 75,000 cows. No wonder the USDA, after finding just 29 of the suspect cows, cashed in its chips. The paper trails on cows born more than three years ago in other countries are non-existent, and the ear tags that are put on cows' ears to help identify them don’t stay on for all that long.

The USDA's wild-goose chase makes it clear that trying to track down herds that might be infected with mad cow disease after the fact is never going to work. The systems are just not in place to facilitate such an extensive search. But if adequate tracking systems are not going to be set up, the government must instead institute a tough policy to test cattle for mad cow.
Each year there are about 35 million cows slaughtered in the United States. Last year only 20,000 cattle were randomly tested for mad cow, while this year the government expects to test 40,000.

This situation is nuts. All it would take is one death attributed to an infected cow that ended up in a cheeseburger to bring the entire U.S. economy to a halt. If anyone doubts this assessment, they need only look at what happened to the British beef industry in the years after the outbreak there.

If it is hard to look back to pinpoint the source of an infection, then it is prudent to look forward and aggressively screen for mad cow disease. Screening less than one in every 20,000 animals that you and I eat is not nearly enough.