Category: Biology

A, B, AB, or O?

A blood type (also called a blood group) is a classification of blood based on the presence or absence of inherited antigenic substances on the surface of red blood cells (RBCs). These antigens may be proteins, carbohydrates, glycoproteins, or glycolipids, depending on the blood group system, and some of these antigens are also present on the surface of other types of cells of various tissues. Several of these red blood cell surface antigens, that stem from one allele (or very closely linked genes), collectively form a blood group system.

The ABO system is the most important blood group system in human blood transfusion. The associated anti-A antibodies and anti-B antibodies are usually “Immunoglobulin M”, abbreviated IgM, antibodies. ABO IgM antibodies are produced in the first years of life by sensitization to environmental substances such as food, bacteria and viruses. The “O” in ABO is often called “0” (zero/null) in other languages.

A quite literally vital question when a blood transfusion is required and normally blood type is determined using an antibody and optical examination. However, Austrian researchers at the University of Vienna have developed a novel approach that is much simpler and side-steps expensive antibodies. Their technique is based on the blood-type-specific adsorption of red blood cells (erythrocytes) on a plastic surface “embossed” on the molecular scale.

Production of the analytical chips needed for this method is a simple and inexpensive process: quartz microbalances (tiny piezoelectric quartz crystals) are coated with a wafer-thin film of polyurethane. Erythrocytes of a specific blood type in liquid are placed on a slide and stick to its surface, forming the embossing “stamp”. The polymer is cured to harden it and the cells washed off. The ebmossed plastic surface now contains a large number of tiny impressions with indentations shaped like the antigens on the surface of the blood cells.

If a sample of blood is then placed on the chip, the erythrocytes will preferentially settle into those impressions with a matching shape. The resulting increase in mass is measured with the incredibly sensitive quartz microbalance.

The shape and size of the erythrocytes are the same for all blood types, so how can they be differentiated by these indentations? ‘The outer form is not the deciding factor,’ says team leader Franz Dickert, ‘instead, it is the differences in the surfaces of the different blood types.’ There are sugar-like molecular fragments on the surface of the cells that differentiate the blood types.

‘Despite a noticeable cross-sensitivity for the other blood types, determination of the blood type by the embossed plastic films is unambiguous,’ says Dickert, ‘because the strongest sensor signal comes from the microbalance that carries the impressions corresponding to the blood type of the sample.’

Dickert and colleagues publish details of their technique in Angew Chem, 2006, 45, 2626-2629

Researchers have modified a popular system for protein labelling and modification to reduce the risk of unwanted cross-reactions and so make it more accurate and effective.

With incredible specificity and powerful affinity for each other, the protein streptavidin and its small-molecule target biotin are truly the ‘Dynamic Duo’ of biological research, the researchers explain, and a perennial favourite for use in the design of biochemical experimental techniques. For example, one can easily subject biotin-linked proteins to highly specific labelling with streptavidin-linked fluorophores. Nonetheless, there is an important limitation to the system-streptavidin naturally forms tetramers (assemblies of four protein molecules) that bind up to four molecules of biotin, creating the potential for unexpected cross-linking of biotinylated targets. Efforts to engineer monomeric streptavidin variants have generally resulted in diminished biotin affinity.

Now, Alice Ting and colleagues at Massachusetts Institute of Technology, Cambridge, have developed an alternative approach that involves engineering ‘dead’ streptavidin variants that can bind to each other but not to biotin. By combining the two types of streptavidin monomers in the proper proportions and isolating tetramers that consist of three dead subunits and one active subunit, they obtain streptavidin complexes that are functionally monomeric and bind only one molecule of biotin.

They have demonstrated that the hybrid tetramers retain normal affinity for biotin but induce far less ‘clumping’ of biotinylated targets relative to wild-type streptavidin tetramers. This approach also offers the possibility of building divalent and trivalent tetramers. According to Kai Johnsson of the École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland, “the existing plentitude of applications of the streptavidin-biotin interaction provides an enormous playground for streptavidins with reduced but defined valencies.”

More details can be found in April’s Nature Methods.

Portuguese researchers have developed a technique for classifying genomic-wide metabolic reactions, which they suggest will open up a new approach to diversity analysis of metabolic reactions and comparison of metabolic pathways as well as being generally compatible with the conventional “EC” classification of enzymes.

You can read my complete story on this at spectroscopnow.com

Exposure to environmental poisons is suspected of disturbing the secondary sex ratio, i.e. the difference in numbers of girls and boys born as opposed to the ratio of girls and boys conceived. Indeed, several countries, including Canada, Denmark, England and Wales, Germany, The Netherlands, and the USA, have seen the secondary sex ratio shift during the last hundred years or so that the number of girls among live-births has risen significantly. One of the more significant declines is seen in Mexico, although some countries, Ireland, in particular, have seen the reverse, with more boys.

You can read the complete story in my news story on SpectroscopyNOW.com

A gene associated with disease might vary from a healthy gene in one individual DNA base pair – a so-called point mutation. Investigating point mutations and diagnosing genetic disease would benefit from a simple, cost-effective and rapid sequencing technique.

Now, Japanese researchers have developed a new approach for a miniaturized system that detects small differences in DNA sequences with high sensitivity. In contrast to other methods, this technique works without labeling the bases and exploits a field effect transistor (FET) to detect changes in the charge on DNA molecules.

According to Toshiya Sakata and Yuji Miyahara multiple FETs can feel electrical fields and react to changes by changing the current that flows through their conducting channels. The researchers loaded the surface of an FET with short, single-stranded pieces of DNA. These probes are the exact counterparts to the sequence at the beginning of the DNA segment being investigated. If a sample containing the target DNA comes into contact with the surface, the target DNA binds to the probes. The polymerase chain reaction (PCR) is then used to reconstruct the complete target DNA strand. Cleverly, the team do not use all four DNA building blocks at once but dip the FET into four different solutions, each containing only one of the building blocks, one after the other. After each dip, the electrical characteristics of the FET are measured. If and only if a component has been added to the end of the chain, a change is registered. This occurs because each building block brings with it a negative charge, which changes the electrical field on the surface of the FET. In this way, DNA chains of a length up to about ten components can be precisely sequenced. Missing, extra, or changed nucleotides can be rapidly and unambiguously identified.

You can read more details in Angew Chem Int Edn, 2006, 45, 2225

Mammalian paleobiologists must be a cynical lot. How else to explain their presumably ironic use of the term Lazarus Effect in piecing together the very evidence for evolution that must by its nature preclude much of what is discussed in the same context as Lazarus? Moreover, this particular piece of evidence is one that plugs a gap in the fossil record and helps bring continuity to the theory of evolution, something that is often considered a fatal flaw by those who’d dispossess it. You could say they’ve brought it back to life…

Anyway, a new type of rodent discovered last year in Laos is a survivor of a group believed to
have been extinct for 11 million years, according to a new study published today in Science. Mary Dawson and colleagues compared skeletal remains of the squirrel-like animal with those of a little understood extinct group of Southeast Asian rodents and confirmed that it is actually a living member of this long-gone family. When the new species was discovered in early 2005, it drew wide acclaim because it was thought to be a member of an entirely new family of living mammals. Instead, according to the researchers, the rodent represents a striking example of the ‘Lazarus effect’ in which an organism suddenly reappears after a long gap in its fossil record. That such a phenomenon has only rarely been documented among mammals and other vertebrates shows that Southeast Asia’s prehistoric ‘zoo’ can offer invaluable insights regarding past and present
biodiversity, the researchers write.

The missing piece in the biochemistry of haem (heme) is reported in this week’s spectroscopyNOW. Japanese researchers have used x-ray diffraction to determine the crystal structure of the enzyme human indoleamine 2,3-dioxygenase (IDO). This crucial enzyme splits the pyrrole ring of the amino acid L-tryptophan and incorporates both atoms of a molecule of oxygen, an essential step in dozens of metabolic reactions. The discovery could have implications for other studies involving this enzyme and medical problems with which it is associated.

David Bradley reports in this week’s SpectroscopyNow on how scientists in Israel are using UV-Vis spectroscopy to track the underlying logic of enzyme systems that compute.

The research could lead ultimately to implantable enzyme-based computers that respond to metabolic changes in the body and allow complex drug therapies to be monitored and controlled.

TL:DR – Short news article from 2006 about salamanders. The headline alludes to a lyric from a song by the band Genesis, The Carpet Crawlers.

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Salamanders can transform from an aquatic juvenile form into their terrestrial, adult form only if the stream bed on which they develop is of the right nature. A study published today in the journal BMC Biology reveals that the Oklahoma salamander Eurycea tynerensis metamorphoses into a terrestrial adult form in streambeds composed of fine, tightly packed gravel but stays in the juvenile form in loosely packed streambeds composed of large particles.

The study by Ronald Bonett and Paul Chippindale from the University of Texas at Arlington, Texas, USA, exemplifies how small habitat differences can influence developmental patterns and morphology, they also suggest that such microstructure changes could influence a species’ evolution too.

Bonett and Chippindale explain that large gravel creates porous streambeds with large spaces between particles, where aquatic paedomorphic salamanders can access sub-surface water during dry months. However, if these spaces are filled in by small particles, metamorphosis is the only way they can survive when surface streams dry-up.

Hunger for protein and salt, and a fear of cannibalism, drives the
mass migration of Mormon crickets across western North America, says Stephen Simpson of the University of Sydney, Australia. Mormon cricket swarms, sometimes millions strong covering more than 50 miles in a season. They destroy vegetation in their path and are a severe hazard to drivers.

Locust plagues of Biblical proportions have been with mankind, since, well, Biblical times, at least(!) and usually these creatures swarm in response to a shortage of food. The precise nutritional triggers for the migrations of Mormon crickets though have remained a mystery. Now, field observations by Simpson and his colleagues offer an explanation.

It seems that total starvation is not the driving force, rather migratory crickets preferentially feed at experimental protein-rich and salt rich sources. In the field, crickets were frequently observed feeding on carrion and on each other. When the movement of crickets was experimentally impaired (immobilized by gluing and/or tethering), these insects became targets for cannibalism by neighbouring crickets. These results thus reveal a different model for collective motion, with the crickets’ migration in effect a forced march, the researchers say. The constant threat of cannibalism from the rear appears to push the crickets’ movement as much as the need to find protein and salt pulls it.

Simpson and his colleagues publish further details of their findings today in the online edition of PNAS.