Science stuff

On the value of peer review

2008-07-04T06:34:00.001-07:00

Just thought I'd post this comment that I excerpted from a message board. It discusses the value and limitations of the peer review process.

I don't think its the peer review that is the problem, but rather our perception of what it means.

Peer review is just a way of vetting an article to make sure it's not whacked out. The reviewers don't repeat experiments, recalculate all the data, etc.

Being published in a peer reviewed journal simple means that the author has made a respectable argument. Kinda of like a indictment.

The actual court case doesn't happen until after it's been published. When others may dispute the results, repeat the experiment, etc.

But the simple fact that the article has been published in a peer review journal does not make it inherently correct, just like being indicted for crime doesn't mean you are actually guilty.

Tobacco mosaic

2008-06-15T11:41:00.000-07:00

Adapted from the book, Scientists and Discoveries:

In 1892, Dmitry Ovanovsky, a Russian botanist, investigated the sap from tobacco plants affected by mosaic disease. This is a condition that stunts the growth of tobacco plants and mottles their leaves in a characteristic mosaic pattern (hence the name). He passed the sap through filters so fine that they would trap all known bacteria. The sap retained its ability to produce the disease in new plants. Ovanovsky thought there was some flaw in his experiment, not realizing that viruses (which had not yet been discovered) were at work.

Bull snake

2008-05-30T20:03:00.000-07:00

I captured a bull snake recently -- twice, in fact. It was a pet snake that had escaped, and I found it in my closet three days later. I placed it in a temporary travelling cage so that I could show him to some children, but after I brought him home, he managed to pop the lid off the cage overnight.

That does it. Next time, I'm placing him directly in his permanent cage. Ugh.

Inaccurate assay description

2008-05-28T20:40:00.001-07:00

I just discovered that this site says, "ELISpot assays employ the sandwich enzyme-linked immunosorbent assay (ELISA) technique." That is not very accurate. To be sure, there are some undeniable similarities between the ELISPOT method and the ELISA assay technique, but it's a bit of a misrepresentation to say that the former uses the latter. I would certainly be extremely uncomfortable making such a claim.

Yeargh.

Originator of chaos theory dies

2008-04-17T11:03:00.000-07:00

Edward Lorenz, the man who created the field of chaos theory, died on Wednesday at the age of 90. His name will be unfamiliar to most of the world, even among the well-educated, yet those of us who have studied his work will surely mourn.

As the cited article says, "His discovery of 'deterministic chaos' brought about 'one of the most dramatic changes in mankind's view of nature since Sir Isaac Newton,' said the committee that awarded Lorenz the 1991 Kyoto Prize for basic sciences. It was one of many scientific awards that Lorenz won."

Cytometers

2008-04-15T07:31:00.000-07:00

Cytometers are used for counting cells. Biotech applications that involve various cell types use cytometers to keep track of the types and quantities of cells. For example, a hemocytometer is used in biotech applications that involve blood cells.

Traditionally, cytometry was performed using microscopes and special cytometry slides. This made it a tedious and laborious process. Even a skilled scientist can only count about 200 cells per minute.

Nowadays, much of cytometry is more thoroughly automated. For example, a flow cytometer employs monochromatic light (typically a laser beam) to enumerate, sort, and identify cells within a laminar flow of liquid.

Dysthymia

2008-04-05T08:10:00.000-07:00

Dysthymia is basically low-grade depression, being less severe and pervasive than major depression.According to the APA, two or more of six possible symptoms must be present for a diagnosis of dysthymia. Symptoms can include the following:

Poor appetite or overeating
Insomnia or hypersomnia
Low energy or fatigue
Low self-esteem
Poor concentration
Difficulty in making decisions
Feelings of hopelessness.

For a proper clinical diagnosis, an individual must experience symptoms for at least two years and should have no longer than a two-month period without symptoms being present. These symptoms must result in clinically significant distress or impairment in social, occupational, academic, or other major areas of functioning (APA, 2000).

Microplate readers

2008-03-21T15:19:00.000-07:00

The following has been excerpted from Biotechnology 101 by Brian Robert Shmaefsky. Some grammatical issues have been corrected. Also, please note that the description provided in this excerpt is a bit simplistic. It's accurate when it comes to ELISA assays, but not for assays in which specific structures are generated, such as FluoroSpot and ELISpot assays or colony counting applications.

"The microplate reader works by shining a particular type of light at each of the samples in [a] microwell plate. It can be adjusted to[sic] in various ways. It can read a few to all [of] the samples in a particular sequence or it can read several samples at a time. A particular type of light is selected based on the type of analysis being done. Some chemicals absorb a particular color of light. Their presence or quantity can be determined by measuring how much of the light is absorbed by the sample. This is called absorbance detection. Hence, a scientist looking for the production of a particular chemical made by a cell would notice more and more light being absorbed by the reader as the chemical is produced. Some chemicals glow when exposed to a particular light. This is called fluorescence detection. The amount of chemical is measured by the intensity of glowing. Microplate readers feed the absorbance or fluorescence measures into a computer program that analyses the particular information being collected."

BTW, this guy could have used a better editor.

Groups of animals

2008-02-26T20:17:00.000-08:00

I came across teh follwoing list of unusual names for animal groupings. Thought I'd post it here.

A convocation of eagles
A prickle of porcupines
A charm of finches
An unkindness of ravens
A skulk of foxes
A shiver of sharks
A troubling of goldfish
A pod of whales
A smack of jellyfish
A descent of woodpeckers
A mob of kangaroos
A zeal of zebras
A shrewdness of apes
An exaltation of larks
A battery of barracudas
A troop of monkeys
A kaleidoscope of butterflies
A parliament of owls
A quiver of cobras
An ostentation of peacocks
A murder of crows
A rookery of penguins

ELISA spot in a flash animation

2007-06-17T20:31:00.000-07:00

I love using visual aids to educate myself. I wish that I had more of them available when I was growing up. Heck, I wish that I could use them more extensively in my current self-education.

That's why I like this little animated clip. It depicts a biological assay that's used to capture the secretory footprints of blood cells. Certain B cells will secrete certain antibodies, for example. Additionally, different T cells will secrete different types of cytokines. That's the kind of assay that's depicted here. It shows how many T cells responded with a given cytokine to a particular type of stimulus.

Smallpox

2007-04-26T20:39:00.000-07:00

The National Institutes of Health (NIH) is attempting to develop a new, safer vaccine against smallpox. This is part of an ongoing attempt to protect the nation against the threat of bioterrorism and bioweaponry--that is, the use of weaponized pathogens. Similar research is being conducted to protect the populace against other diseases, such as the plague.

Various species of monkeys have been used to test the efficacy of the proposed vaccine (modified vaccinia Ankara, or MVA). Monkeys are inoculated with MVA, then exposed to the monkeypox virus, which closely resembles smallpox. The researchers then determine if the vaccine provides any protection against the virus. Unfortunately, this does result in the monkeys' deaths.

It would clearly be unethical to test the vaccine on humans in the same fashion. (I have a hard enough time thinking about these poor simians.) Fortunately, the ELISPOT technique allows immune response monitoring to be performed ex vivo; that is, without injecting any pathogens into a human host.

SciWeb

2007-04-18T20:47:00.000-07:00

Nothing earthshaking, folks. I just wanted to plug the SciWeb website. It's pretty neat and a pretty good informational resource for life science research, equipment and so forth.

I especially like the SciJobs section. Oh, I'm not looking for a job, mind you. However, I wish I had known about this resource four years ago, when I was searching for employment. The company directory and press releases sections are also quite nice. So is the product announcements section, although some of the announcements appear to be kinda trivial.

I would kinda like to advertise this job opening that my employer has; however, I don't think we want to spend any money on these job ads.

Manipulator grasp classifications

2007-04-17T08:24:00.000-07:00

Gripper and fixture grasps can fall under different categories. The two most important grasp classifications are known as form closure and force closure grasps. These terms were first used by Reuleaux in his studies of machine design, and were later applied to robotic grasping by Salisbury. However, recent inconsistent use of these terms has confused their meanings.

A fixed set of contacts on a rigid object is said to exhibit form closure if the object's equilibrium is maintained despite any possible externally applied wrench (i.e. a force, a torque, or a combination thereof). In other words, the geometries and relative poses of the object and the contacting body--a gripper or fixture, for example--suffice to hold the object in place with complete kinematic constraint. Form closure is therefore more preferable to force closure, in which the applied manipulator force is further required as a consideration.

In developing a gripper or fixture, one should therefore strive for form closure. In certain important instances, however, this would be is impossible. For example, any part which is axisymmetric (such as a sphere) cannot be kinematically constrained in form closure. Under such circumstances, a robotic manipulation strategy should strive for frictional form closure (a type of force closure) instead. Under frictional form closure, friction contributes to immobilize a grasped part which is otherwise not fully kinematically constrained by a gripper.

Multiple sclerosis

2007-04-14T05:52:00.000-07:00

Disseminated sclerosis is a chronic, inflammatory disease that affects the central nervous system. It is more commonly known as multiple sclerosis. Its symptoms include changes in sensation, visual problems, muscle weakness, cognitive impairment, dysfunctions in balance, speech and muscular coordination, severe fatigue, depression, overheating, and pain.

Multiple sclerosis is believed to be an autoimmune disease in which some unknown trigger initiates an immune response against brain proteins. This is known as an autoaggressive response, and according to this hypothesis, it causes the breakdown of the myelin sheaths that protect nerve axons. This leads to impaired nerve conduction and subsequent neurodegeneration, both of which are characteristic of MS.

Epitope mapping has applications in understanding multiple sclerosis. This mapping can be performed using ELISPOT assays.

Revisiting ELISA Spot assays

2007-01-15T21:29:00.000-08:00

ELISA spot assays are used for the quantitative determination of single cells secreting a specific cytokine. They are known as ELISA spot assays due to their similarities to the ELISA method, but nowadays, they are more commonly referred to as ELISPOT assays.

Kits are available which contain the basic components and protocols required to perform colorimetric assays wherein one spot marks one cell to be identified.

Blood, plasma and serum

2006-10-12T07:48:00.000-07:00

Well all know what blood is, of course. It's that red stuff that circulates through your body. More specifically though, blood is composed of plasma and blood cells suspended in plasma, a clear, yellowish fluid that makes up more than half the volume of blood.

Blood cells can be categorized as erythrocytes (red blood cells), leukocytes (white blood cells), and thrombocytes (platelets). These are suspended in the plasma with other particulate matter.

Serum is the clear, cell-free fluid that is left over when the cells and clotting factors are removed.

Leonardo and science

2005-12-04T04:32:00.000-08:00

Leonardo da Vinci is often applauded as a great scientist, in addition to being a great artist. He was a Renaissance man in every sense of the word.

But a scientist? Not in a strict sense. He dabbled, but he generally (if ever) did not draw firm conclusions, as a true scientist would. His methodology was more observational than anything else.

Oh, and please don't call him "da Vinci." That's not his name. "Da Vinci" is Italian for "from Vinci," and simply denoted where he was from. Check out any encyclopedia and you'll see that they refer to him as "Leonardo." So do art historians. Anyone who calls him "da Vinci" is simply speaking out of ignorance.

Curse you, Dan Brown, for perpetuating that bit of misinformation (along with the many other falsehoods recorded in your book)!

Cytokine production by different blood cell types

2005-07-27T08:36:00.000-07:00

Spot size and morphology frequently allow researchers to distinguish cytokine production by different cell types within mixed cell populations. For example, when IL-10 production by human peripheral blood mononuclear cells (PBMC) is measured in ELISPOT assays, most of the “antigen-induced” spots are not T cell derived (as would be expected), but are produced by macrophages in response to LPS contamination of the antigen. Such macrophage-derived IL-10 spots are considerably smaller than the IL-10 spots generated by antigen-specific T cells. While the LPS-induced macrophage-derived spots provide no information on specific immunity, the antigen-induced T-cell-derived IL-10 spots do, since they indicate the presence of T regulatory cells. In order to measure the latter, the former need to be excluded from the counting results by setting appropriate size thresholds. ELISPOT image analysis must therefore be capable of distinguishing different spot sizes and morphologies to provide information relevant for T cell diagnostics.

The antigen dose affects the cytokine secretion rate of T cells. Stimulation of a T cell clone with a high dose of the nominal antigenic peptide induces stronger cytokine production in the individual T-lymphocytes (that is, it triggers larger and/or denser spots) than does the stimulation of the same clone with low dose peptide. Therefore, when stimulated with a single antigen dose, as is frequently the case in ELIPSOT assays, high-avidity T-lymphocytes within the PBMC produce larger spots than low-avidity clones. Confirming this notion, increased T cell costimulation was shown to result in increased per cell productivity. In diseases such as HIV, the per cell cytokine productivity can be reduced, resulting in smaller spots. One advantage of ELISPOT assays is their ability to determine whether decreased net cytokine production in disease states is caused by a decreased number of cytokine-secreting T cells or from reduced per cell productivity by unchanged frequencies of T cells. In order to compensate for physiological and pathological variations in per cell productivity, ELISPOT image analysis tools must therefore be versatile, with the ability to permit fine-tuning of the image processing parameters.

More about the limitations of science

2004-12-30T06:13:00.000-08:00

Continuing the previous discussion about the limitations of science...

I mentioned that some people insist that the scientific method is the only way through which truth can be discerned. I also mentioned that when they say that, I ask "so what scientific methodology did you use to determine that to be true?"

Unfortunately, that doesn't stop some people from insisting on that claim. Instead of re-examining that belief, some of them say "But it's true! It's obvious!" or words to that effect. The thing is, unless one can demonstrate it to be true [em]using the scientific method[/em], that claim remains unsubstantiated.

Indeed, how would one even begin to test this claim? I ask people that sometimes. Some of the more hard-headed ones say, "Well, you design an experiment to test this belief, and then you conduct the experiment. That's how science works!" However, this answer completely glosses over the question of HOW someone would design such an experiment -- or even if such an experiment is possible.

Some go a bit further, and say "Well, you take all the possible methods of learning knowledge, and then you test every single one of them. That will prove that science is the only means to knowledge." This answer is a bit more complete, but still unsatisfactory. For one thing, it ignores the question of HOW one would identify all the possible paths to knowledge. And second, it dodges the question of how one would test all these methods.

Indeed, how would one know that one has identified all paths to knowledge? For that matter, how would one know that ANYTHING is a means of discerning truth? If the claim is true, then one must first conduct a scientific experiment to establish these things to be true.

What's more, if someone is to claim that science is the ONLY way through which knowledge can be truly obtained, then one must test ALL possible methods under ALL possible circumstances. For if there is even a single situation in which one of these methods can work, then the scientific method is not the sole means to truth.

This is why I'm severely disappointed when people claim that only science holds the keys to truth. It's a statement that sounds neat, but which people often don't examine closely. It has no basis in reality.

The limitations of science

2004-12-28T08:40:00.000-08:00

Every now and then, I hear people claim, "The scientific method is the only way that truth can be known!" The problem is that this is a self-refuting claim. It also betrays great naivete about the nature of science.

Self-refuting, you say? Yes indeed. Consider this: If the scientific method is the only way by which truth can be known, then what scientific methodology would one employ to arrive at that truth? The people who make this claim clearly have not performed any such experiment, and so their claim remains unproven. What's more, it CANNOT be demonstrated to be true, since one would have to identify all possible alternatives to science and then demonstrate that none of them are ever valid.

"But it's obvious!" some exclaim. Well, if you claim that it's true by virtue of being obvious, then you're not using the scientific method. Rather, you are claiming that something is self-evident. Ergo, you have implicitly demonstrated that science is not the only means by which truth can be discerned.

I know one guy who says, "The methodology that I use is observation. It's science!" Um, no. Observation is merely the first step in applying the scientific method. It is not an example of scientific methodology. Without the subsequent phases of hypothesis-forming and experimentation, one does not have a scientific method.

Indeed, there are things that science implicitly assumes, and thus, cannot prove. It assumes that the laws of logic and mathematics are valid, for example. As such, attempting to prove these tenets using science would amount to circular reasoning. Now, I'm not about to deny that the laws of math and logic are valid; however, my point is that one cannot use science to prove their validity. That would be begging the question, pure and simple.

Ohm's Law

2004-12-03T22:09:00.000-08:00

Ohm's law states that the voltage drop between the ends of a conductor (or resistor) is directly proportional to the current flowing through it, provided the temperature doesn't change. This is commonly stated as V=IR, where V is the voltage drop, I is the current and R is the proportionality constant (or "resistance").

Ohm's Law is not truly a law. There is a popular misconception among many less knowledgeable engineers that Ohm's Law always holds true; however, most substances do not display the proportionality described. In such cases, the voltage and current have a more complex relationship, which is described as a transconductance curve.

Indeed, no real-world device obeys this "law" perfectly. However, Ohm's Law is an adequate approximation for the behavior of many objects, such as strips of metal.

Granzymes

2004-11-21T21:31:00.000-08:00

Granzymes are exogenous serine proteases that are released by the cytoplasmic granules within cytotoxic T cells and natural killer cells. Cytotoxic T cells and natural killer cells release a pore-forming protein (perforin) which attacks the target cells. Granzymes can enter through these pores, inducing apoptosis.

Agile manufacturing

2004-11-08T07:42:00.000-08:00

The term "agile manufacturing" can have different definitions, depending on how the term is used. As a result, it can be confused with similar and related terms such as "flexible manufacturing" and "just-in-time (JIT) manufacturing." The most useful definition, however, describes it as the ability to achieve rapid changeover between the manufacture of different assemblies. This is extremely helpful in modern contexts, wherein product changeover is frequent.

Agile manufacturing is more of engineering than science; however, we shall mention it here because its effective use ideally requires the application of diverse intelligent disciplines -- computer vision and object recognition, intelligent robotic manipulation, intelligent object sensing and so forth. As such, it can straddle the boundary between science and engineering.

This philosophy also requires tight mechatronic integration, interlinking mechanical, electronic and software design in a synergistic manner.

Histocompatibility

2004-10-25T19:03:00.000-07:00

Histocompatibilty is the condition in which the body allows the grafting of tissue or the transfusion of blood without rejection. Ultimately, this means that there is anabsence of interference from the body's immune system.

Histocompatibility is governed by Major Histocompatibility Complex (MHC) molecules. Crudely stated, their purpose is to distinguish "self" from "non-self". More specifically, their primary immunological function is to bind and present antigenic peptides on the surfaces of cells for recognition by antigen-specific T cell receptors.

Controlling and inducing histocompatibility is central to ensuring the success of organ transplants. This field is known as transplantation immunology.

Buoyancy question

2004-10-24T20:51:00.000-07:00

Here's a question for people to ponder.

Say you have a boat floating in a swimming pool. Suppose that there's a rock sitting in the boat. Now suppose that someone takes the rock and drops it into the pool.

Does the water level rise or fall? Think about it.

Spot counting and "Zytokinen"

2004-10-20T22:30:00.000-07:00

Durch automatische Auszählung mittels Software kann so bestimmt werden, welche spezielle Aktivität die Immunzellen besitzen, was für die Forschung und Diagnostik von Autoimmunerkrankungen, Transplantationsrisiken, Allergien und Infektionskrankheiten nützlich ist, ebenso wie für die Impfstoffforschung.

Cytokines

2004-10-20T09:01:00.000-07:00

Cytokines are regulatory proteins that are released by cells of the immune system. These act as intercellular mediators in the generation of an immune response. They can have stimulating or suppressing effects on lymphocyte cells and immune responses.

Well-known examples include the interleukins, interferons and tumor necrosis factors. Cytokine production can be detected using certain laboratory techniques that have been discussed previously.

ELISA illustration

2004-10-17T02:00:00.000-07:00

Today, I just wanted to post this link to an animated illustration of the ELISA process. They say that a picture paints a thousand words, and in this case, an animated (and interactive) picture says a whole lot more.

Scientific illiteracy

2004-10-16T10:08:00.000-07:00

Scientific illiteracy is a tremendous problem in this country. I'd like to quote the following statements by George Dvorsky (as reproduced in this web essay).

Most of those who live in the West, particularly North Americans, are guilty of an anti-intellectual bias. Scientists are supposed to be nerds, right? And who wants to be a nerd? This sentiment, combined with a general suspicion of science and the predominance of aggressive theological and pseudoscientific memes, has resulted in much of the scientific illiteracy that now pervades our society.

It doesn't help that the educational system is in shambles and without focus, and that fatuous postmodernism and its insistence that nothing can truly be known now dominates many disciplines at most universities. Consequently, too many people wear their ignorance like a badge of honor, as if being clueless about science is something to be proud of.

Memory cells

2004-10-15T20:30:00.000-07:00

Memory cells allow the body to remember previous infections and quickly mobilize defenses against them. This is the mechanism by which the human body remembers that someone contracted chicken pox, for example, and which prevents future infections of that type from occuring.

Time is short, so instead of discussing this at greater detail, I'll post a (slightly paraphrased, for brevity) excerpt from a technical paper on this subject.

Single-Cytokine-Producing CD4 Memory Cells Predominate in Type 1 and Type 2 Immunity

The patterns of Ag-induced cytokine coexpression in normal, in vivo-primed CD4 memory T cells has remained controversial because the low frequency at which these cells occur has effectively prevented direct ex vivo measurements. We have overcome this limitation by using two-color cytokine ELISPOT assays and computer-assisted image analysis. We found CD4 memory cells that simultaneously expressed IL-2, IL-3, IL-4, IL-5, and IFN--y to be rare (0-10%). This cytokine segregation was seen in adjuvant-induced type 1, type 2, and mixed immunity to OVA, in Leishmania infection regardless of the Ag dose used or how long after immunization the assay was performed. The data suggest that type 1 and type 2 immunity in vivo is not mediated by classic Thl or Th2 cells but by single-cytokine-producing memory cells.

Alexey Y. Karulin, Maike D. Hesse, Magdalena Tary-Lehmann, and Paul V. Lehmann, The Journal of Immunology, 2000, 164: 1862-1872.

Lymphocytes

2004-10-14T08:11:00.000-07:00

Lymphocytes are a category of white blood cell, or leukocyte. The main categories of lymphocytes are B cells and T cells. B cells are responsible for manufacturing antibodies, whereas T cells have more complex roles. Depending on the category of the T cell, it may be responsible for destroying invading cells, for secreting cytokines in response to an antigen, or for activating macrophages and NK-cells. These processes shall be discussed at a later date.

Flow cytometry was previously mentioned, and one application of this technique is in counting specific lymphocyte population. The ELISPOT method was mentioned as well; this technique is used for counting the number of B cells that secrete a specific antibody, or the number of T cells that produce a given cytokine or granzyme.

Cytokines

2004-10-12T19:37:00.000-07:00

Cytokines are regulatory proteins that are released by cells of the immune system. They are the means by which cells communicate in the generation of an immune response. Well-known cytokines include prostaglandin, the interleukins, the interferons and the lymphokines.

Cytokines trigger responses by binding to cell-specific receptors located in the cell membrane. This allows a distinct signal cascade to start in the cell, eventually generating biochemical and phenotypical changes in the target cell.

Production of a specific cytokine can be detected using the aforementioned ELISPOT assays, which can also determine the percentage of cells that produce the cytokine in question.

Robotic grasp theory

2004-10-09T10:28:00.000-07:00

Robotic grasp theory is a magnificent marriage of science and engineering. The human hand is a magnificent piece of design -- flexible and adaptable beyond belief. It's no surprise that many robotic efforts have attempted to duplicate its capabilities.

Sadly, these efforts often go too far in either extreme. Some attempt to duplicate the human hand too closely. The result? Anthropomorphic robot hands that require hopelessly complex control algorithms, and which lack the fine sensing capabilities of a human hand. These devices are cumbersome, and often impractical to use. Others use primitive parallel jaw grippers, which are decidedly more restricted in their capabilities. Since most parts require some custom tooling in order to be held securely, this greatly limits the range of workpieces that a parallel jaw gripper can hold.

(Other variants exist, such as three-fingered end-effectors. The end results is similar, though -- limited grasp capabilities.)

Velasco et al. offered a compromise in which rapid prototyping technology was used to develop gripper tooling based on CAD models of the parts to be grasped. The CAD capabilities allowed the tooling to be developed rapidly, and with due consideration to part clearances and manufacturing variability. This gave parallel jaw grippers a great deal more versatility than could be achieved using rudimentary tooling, without requiring the complex mechanisms or ocntrol algorithms required of anthropomorphic robot hands.

Vaccine development

2004-10-08T07:21:00.000-07:00

The first vaccine was developed by Edward Jenner in an abhorrently crude fashion. Jenner noticed that milkmaids were not readily susceptible to smallpox infections, which had been ravaging the populace. He theorized that they had somehow gained immuniity through regularly exposure to cowpox lesions. In a bold move, Jenner inoculated an eight-year-old boy with scrapings from cowpox lesions, thus proving his theory.

Such an experiment would never be allowed nowadays, due to medical ethics. To Jenner's credit though, it worked, and this paved the way toward stamping out smallpox across the world.

Nowadays, more sophisticated techniques are available for vaccine development. In an earlier write-up, we discussed the ELISPOT technique in brief. Suffice to say that this methodology allows the monitoring of immunological responses to antigen invasion at the cellular level. This eliminates the need for crude experiments with human subjects under coarse conditions.

Asthma and immunology

2004-10-05T11:05:00.000-07:00

I suffered a mild asthma attack while cycling to work today, thanks to the influx of cold air into my lungs. So, I decided to write a little about asthma.

Asthma is an immunological disorder in which the patient suffers respiratory difficulty. In this disease, the bronchioles in the lungs are narrowed by inflammation, thus requiring treatment with bronchodilators. The symptoms include wheezing and shortness of breath, which can prevent the afflicted person from engaging in prolonged exercise.

There are several theories which purport to explain the rising incidence of asthma. One places the blame on air pollution. Another purports that the hygenic conditions in the First World cause reduced bacterial exposure, causing inadequate stimulation of the immune system during early childhood. Yet another suggests that the problem is due to non-exposure to parasites such as tapeworms, since the cells which combat these parasites are the same ones which trigger the asthmatic reaction.

T cell clone avidity

2004-10-03T02:51:00.000-07:00

Tonight I decided to cite the abstract of a published paper that I got my hands on. It's about memory cells, which are used to retain a record of previously encountered antigens. These cells allow the immune system to respond more rapidly to subsequent invasions.

The patterns of Ag-induced cytokine coexpression in normal, in vivo-primed CD4 memory T cells has remained controversial because the low frequency at which these cells occur has effectively prevented direct ex vivo measurements. We have overcome this limitation by using two-color cytokine enzyme-linked immunospot assays and computer-assisted image analysis. We found CD4 memory cells that simultaneously expressed IL-2, IL-3, IL-4, IL-5, and IFN--y to be rare (0-10%). This cytokine segregation was seen in adjuvant-induced type 1, type 2, and mixed immunity to OVA, in Leishmania infection regardless of the Ag dose used or how long after immunization the assay was performed. The data suggest that type 1 and type 2 immunity in vivo is not mediated by classic Thl or Th2 cells but by single-cytokine-producing memory cells.

(Maike D. Hesse, Alexey Y. Karulin, Bernhard O. Boehm, Paul V. Lehmann, and Magdalena Tary-Lehmann. The Journal of Immunology, 2001, 167: 1353-1361.)

Biotech

2004-10-02T13:47:00.000-07:00

Biotechnology is the marriage of engineering and technology principles to the biological sciences. Common applications include the development of new microorganisms or biological substances for industrial applications. These can include hormone production, waste cleanup, bioconversion of organic wastes, genetic engineering of new organisms, drug manufacturing and so forth.

Biotechnology does not necessarily use living organisms. For example, it can focus on DNA chips in genetic research, or radioactive medical tracers. It can even use active cells from living organisms -- but not the organism itself -- such as when human lymphocytes are used in vaccine development.

Among the most exciting of biotech fields is the engineering of new microorganisms, with the goal of producing insulin or antibiotics cheaply and efficiently. Other applications include the development of transgenic plants and animals, in which foreign genes are introduced externally, so as to produce enhanced organisms (e.g. cows that produce extraordinary quantities of milk).

Viral plaques

2004-10-01T22:56:00.000-07:00

Viral plaque assays are a simple yet ingenious way of enumerating the number of viruses within a sample. This technique requires introducing the viruses into a nutrient medium (typically agar) in which a culture of bacteria or other cells has been grown.

In this approach, the viruses spread through the cell culture, invading and destroying the cells in question. The viruses thus generate zones of cell destruction, which we call plaques. These plaques can be detected visually, but they may not necessarily be visible to the naked eye. Sometimes, they can only be seen through the assistance of other techniques such as staining, microscopy, hemadsorption or immunofluorescence.

Naturally, this technique is not foolproof, since plaques can overlap and even occlude one another. Statistical methods must then be used to estimate the actual number of viruses introduced into the sample.

Flow cytometry

2004-09-29T14:42:00.000-07:00

Flow cytometry is a technique for examining, sorting and enumerating microscopic particles suspended in a stream of fluid. IT is frequently used in counting biological cells, especially blood cells.

In this technique, a beam of monochromatic light (typically a laser beam) is directed onto a narrow stream of fluid containing the particles in question. The particles are then counted and characterized based on their fluorescent or light-scattering properties.

Spot formation

2004-09-27T23:10:00.000-07:00

In the aforementioned ELISPOT assays, colored spots are formed within microtiter plate wells. The coloration of these spots depends on the chromogenic substrate used, and their morphology depends on the assay conditions and the type of secretion. These spots can be counted manually or using automated systems (of which I'll say more at a later date).

ELISPOT assays

2004-09-25T09:32:00.000-07:00

Previously, I briefly discussed ELISA assays. Out of the ELISA method came the more sophisticated ELISPOT technique, which is a versatile tool for analyzing the substances secreted by peripheral blood and lymphoid cell populations. It is also extremely sensitive, capable of achieving single-cell resolution if properly applied. The ELISPOT technique allows researchers to measure the frequencies (i.e. the relative concentrations) of individual cytokine-, antibody- or granzyme-secreting cells within cultured cell populations.

Here we see how an ELISPOT assay is performed. That link also provides information on reagents for performing a Granzyme B assay.

ELISA assays

2004-09-22T07:33:00.000-07:00

The ELISA (Enzyme-Linked Immuno-Sorbent) assay is a biochemical laboratory technique for determining if a certain substance is present in a sample. This is done using antibodies specific to the substance in question. These antibodies are linked to an enzyme which produces a signal.

The sample is first applied to a substrate within an ELISA plate. (This is a type of microtiter plate, designed to work specifically with ELISA assays.) Enzyme-linked antibodies are applied, such that some of them bind to the substance. The unlinked antibodies are then washed away.

Next, a chemical is applied--one which is activated by the enzyme, such that it generates a fluorescent signal. Thus, if the well fluoresces, then the sample is known to contain the substance in question. The intensity of the fluorescences indicates the concentration of this substance.

Immunology

2004-08-24T09:33:00.000-07:00

Immunology is the branch of biomedicine that is concerned with the structure and function of the immune system. Subtopics include innate and acquired immunity, histocompatibility, the various cells of the immune system and the interaction of antigens with specific antibodies.

There has been exponential growth in the development, refinement and implementation of various laboratory techniques in immunology research. Early methods used tehcniques such as viral plaque assays, but more recent and advanced techniques include ELISA and ELISPOT assays. This is a meaty subject matter though, better suited for a more thorough discussion at a later date.

Arachnid pedipalps

2004-08-12T18:31:00.000-07:00

Upon viewing some of the larger spiders (e.g. tarantulas, wolf spiders), many people are surprised to find that they appear to have ten legs, rather than eight. That's because apart from their legs, they also have two arm-like limbs calld pedipalps. These are used for seizing their prey, and in the case of males, they also use them for mating purposes. They dip the pedipalp tips in their own sperm webs, this infusing them with live sperm cells.

Chaos theory

2004-08-06T19:59:00.000-07:00

Chaos theory deals with the behaviour of certain nonlinear dynamical systems that, under the proper conditions, exhibit chaotic behavior -- that is, behavior which is characterised by long-term sensitivity to initial conditions. This means that the final outcome will vary tremendously, based on minor variations in the initial conditions. This has been observed in mathematics, economics, fluid dynamics, plate tectonics and a wide variety of other systems.

This is NOT the same as noise or modeling uncertainty. In a non-chaotic system ( e.g. a linear system), the variability in the outcome (if any) will depend on the degree of noise present. As a result, establishing bounds on the amount of noise in the initial conditions will likewise establish bounds on the final outcome variability. In a chaotic system, however, even the tiniest variation will be amplified to essentially unpredictable results. (See: Butterfly effect.)

One consequence of chaotic behavior is that even the most precise measuring instruments cannot be used to predict the final outcome with any degree of precision. Even with a perfect model of the system, finite measurement precision and computational round-off errors will combine to produce uncertain results.

A. geniculata

2004-07-28T19:25:00.000-07:00

One of the most stunning of arachnids is the Acanthoscurria geniculata, aka the giant white knee tarantula. This is a massive species with spectacular coloration and a voracious appetite. They are bulky and strong, yet only moderately aggressive. Unlike most of the larger terrestrial tarantulas (e.g. Theraphosa blondi, Lasiodora parahybana), it is actually quite colorful, as indicated by the bright white stripes on its leg joints.

The hairs of this species have been known to be quite irritating, although personal experience varies considerably. I have held one of these creatures before, with ho adverse effects; however, since they are known to be semi-aggressive, I have refrained from holding them in recent years. I would rather not break my record of never having been bitten, ever.

This species is native to Brazil, just as Lasiodora parahybana is. It was an immediate hit with tarantula hobbyists, due to its combination of size and attractiveness. It is not recommended for beginning tarantula wranglers, though.

Diabetes research

2004-07-26T21:39:00.000-07:00

The detection of islet autoreactive T cells has been a key componnet in research work on the immunology of diabetes. Cytokine assays are used to determine how T cells respond in such circumstances. Indeed, such assays play a key role in immunology research in general, and are frequently used in the development of vaccines for diseases such as SARS, HIV infection, and the West Nile virus.

Subsequent entries will focus on various assay types, such as the ELISA and ELISPOT assays. In addition, there will be some discussion of the various instruments and technologies which are used to conduct these assays, to automate the procedures involved, and to reduce or remove subjectivity from the evaluation of their results.

Arachnology

2004-07-24T09:23:00.000-07:00

The study of arachnids is fascinating. Tarantulas are especially fascinating, due to their humongous size and wide range of dispositions. Theraphosa blondi, for example, is gargantuan in size, with a nasty temperament. Others are unbelievably gentle, such as the classic Grammastola rosea.

Someday soon, I'd like to say something about Grammastola aureostriatum, which is one of my favorite species of all time.

Trivia: What do you call the fore and aft body segments of a spider? They are commonly referred to as the cephalothorax (head+thorax) and the abdomen, respectively; however, that's not strictly accurate. The thorax is supposed to house various organs which are actually present in the aft body segment of a spider. The more scientifically accurate terms are prosoma and opisthosoma.