Thursday, January 04, 2007


'Silent mutations' may not always be silent...

A press release from the National Cancer Institute:

A genetic mutation that does not cause a change in the amino acid sequence of the resulting protein can still alter the protein's expected function, according to a new study conducted at the National Cancer Institute (NCI), part of the National Institutes of Health (NIH). The study shows that mutations involving only single chemical bases in a gene known as the multidrug resistance gene (MDR1) that do not affect the protein sequence of the MDR1 gene product can still alter the protein's ability to bind certain drugs. Changes in drug binding may ultimately affect the response to treatment with many types of drugs, including those used in chemotherapy. The results of this study appear online in Science Express on December 21, 2006.

The genetic mutations examined in this research are known as single nucleotide polymorphisms (SNPs) and are very common. Some SNPs do not change the DNA's coding sequence, so these types of so-called 'silent' mutations were not thought to change the function of the resulting proteins.

"This study provides an exception to the silent SNP paradigm by showing that some minor mutations can profoundly affect normal cell activity," said NCI Director John E. Niederhuber, M.D. "These results may not only change our thinking about mechanisms of drug resistance, but may also cause us to reassess our whole understanding of SNPs in general, and what role they play in disease."

Despite success in treating some cancers with chemotherapy, many tumors are naturally resistant to anticancer drugs or become resistant to chemotherapy after many rounds of treatment. Researchers at NCI and elsewhere have discovered one way that cancer cells become resistant to anticancer drugs: they expel drug molecules using pumps embedded in the cellular membrane. One of these pumps, called P-glycoprotein (P-gp), is the protein product of the MDR1 gene and contributes to drug resistance in about 50 percent of human cancers. P-gp prevents the accumulation of powerful anticancer drugs, such as etoposide and Taxol, in tumor cells. The same pump is also involved in determining how many different drugs, including anticancer drugs, are taken up or expelled from the cell.

In this study, researchers led by Michael M. Gottesman, M.D., head of the Laboratory of Cell Biology within NCI's Center for Cancer Research, demonstrated that SNPs in the MDR1 gene result in a pump with an altered ability to interact with certain drugs and pump inhibitor molecules. In order to show that SNPs can actually affect pump activity, the researchers genetically engineered cells in the laboratory to contain either normal MDR1 or a copy of the MDR1 gene that contains one or more SNPs. Then, they used fluorescent dyes to track pump function based on the accumulation of dye in the cell or the export of dye out of the cell with and without various inhibitors of P-gp. This showed that although the SNPs did not change the expected P-gp protein sequence, the presence of one particular SNP, when in combination with one or two other SNPs that frequently occur with it, resulted in less effective pump activity for some drugs than normal P-gp without the SNP.

The P-gp protein sequences and production levels were normal in both the cells that received the normal MDR1 gene and those that received the mutant versions. Therefore, in order to determine how the SNPs affected pump function, Chava Kimchi-Sarfaty, Ph.D., lead author of the study, and co-workers used an antibody that could distinguish between different P-gp structural conformations. They found significant differences in antibody binding consistent with the existence of different protein conformations in the products of MDR1 genes with or without the SNPs. These results indicate that the shape of a protein is determined by more than its amino acid - or primary - sequence.

Like all proteins, P-gp is comprised of amino acid building blocks. While making P-gp, the cell's protein synthesizing machinery knows exactly which amino acids to put together and in which order by reading a copy of the MDR1 gene coding sequence. DNA consists of a sequence of chemical bases, and the code for individual amino acids is represented by specific sets of three adjacent DNA bases called codons. The SNP that Gottesman and his colleagues studied had only one changed base in one codon of the MDR1 gene. Since several different codons can contain the code for the same amino acid, this SNP only altered the gene by converting one common codon to a rare one, but did not change the amino acid for which it coded.

"We think that this SNP affected protein function because it forced the cell to read a different DNA codon than it usually does," said Gottesman. "While the same exact protein sequence eventually got made, this slight change might slow the folding rhythm, resulting in an altered protein conformation, which in turn affects function."

Since silent SNPs are frequently found in nature, their biological role has largely been overlooked. However, this study raises the possibility that even 'silent' mutations could contribute to the development of cancer and many other diseases.

Original press release "Researchers Find That a 'Silent' Gene Mutation Can Change the Function of an Anticancer Drug Pump" (Posted: 12/21/2006) available via this link


Related paper from the journal Science:

A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity

Chava Kimchi-Sarfaty, Jung Mi Oh, In-Wha Kim, Zuben E. Sauna, Anna Maria Calcagno, Suresh V. Ambudkar, Michael M. Gottesman


Synonymous Single Nucleotide Polymorphisms (SNPs) do not change the coding sequences, and, therefore, are not expected to change the function of the protein in which they occur. Here, we report that a synonymous SNP in the Multidrug Resistance 1 (MDR1) gene, part of a haplotype previously linked to altered function of the MDR1 gene product, P-glycoprotein (P-gp), nonetheless results in P-gp with altered drug and inhibitor interactions. Similar mRNA levels and protein, but altered conformations were found for wild-type and polymorphic P-gp. We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of co-translational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.


General info from Mutations: The start of the evolutionary process:

"Silent mutations are a type of substitution mutations in which a base substitution in the DNA template results no change in the amino acid. This is because the substitution simply resluts in another codon for the same amino acid. Thus these mutations are silent, since you cannot detect them by looking at the protein's sequence of amino acids."

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Monday, January 01, 2007


Talking Fish: Wide Variety of Sounds Discovered

There are more than 25,000 species of living fishes. That's more different kinds of fish than any other animal with a spine in the whole history of our planet. Today, we know of more than 1,000 species that make sounds. Scientists who study fish noises have discovered many things over the past 20 years about how and why they make sounds.

How do seahorses make noise? Not through their mouths and voiceboxes and breaths like people. Seahorses actually have bones in their heads that click!

Over 100 years ago, scientists noticed that seahorses make a clicking sound. At first they thought that when the seahorse lifted its head, it made small gas bubbles explode. But using new video techniques, scientists noticed that a sound came out as the top of the seahorses' heads moved in a funny way that rubbed two bones near the top of the seahorse's head and "mane." The bones would pop up and down to make the sound, much like snapping two tiddlywinks together. This way, the sea horse could click to mates, strangers, and also during feeding.

A lot of fish have an air pocket inside their bodies known as a "swim bladder." Minnows, eels, anchovies and goldfish all have swim bladders that they use to keep themselves from sinking in the water. Some kinds of fish use this bladder for more than just staying in place. Some fishes make muscles in their bladders move back and forth very quickly, twitching in the same way the muscles in your jaw twitch when your teeth chatter.

However, scientists have recently discovered one fish has a swim bladder to make sound, but it doesn’t have fast, jittery muscles controlling it. The pearlfish has a much slower muscle in its swim bladder, and it uses the bladder to make sound. The pearlfish doesn’t live like other fish, swimming around in the ocean or lake. It lives inside a live starfish or a tube-shaped animal called a sea cucumber. So, how do these fish talk to each other from inside their houses? That slow muscle inside the swim bladder pulls back, then it releases the front of the swim bladder like a snapped rubber band against a drum. This makes a very strong, low sound that the other pearlfish can hear, even if they are outside the starfish.

One particular fish scientist, Art Myrberg Jr. [1], spent his whole life thinking about questions like these. Fish sound scientists gathered together last month at a scientific meeting to hear about some things Myrberg discovered about fish noises. Here are some things Myrberg found out about noisy fish.

Fish make sounds for different reasons. They may try to find food, look for mates, or see who's a stranger and who's a friend, using sound. Myrberg studied several species of fish called damselfish. That sounds like it might be a sweet young fish who'd take you home for a cup of tea, but really the damselfish is aggressive, yelling at and chasing strangers.

A male damselfish can chirp and make lots of other sounds. He chirps when he is trying to attract a female to his nest, and he makes chirps and pops when warning strangers away from his area. The damselfish listens for the time between noises to find out if the noise comes from the same or another kind of damselfish. If that other fish is a damselfish, but not a friend, the damselfish gets aggressive and makes a "keep out!" sound. It's a code of communication between damselfish, like talking in humans.

Source: The American Institute of Physics' Inside Science News Service - see the following entry under Archive: 'Fish Stories' (2006) by Timothy Tricas*

[1] See "Fish say the darndest things - fish communication"


*Timothy Tricas co-contributed 3 papers on Wednesday, 29th November 2006 to a meeeting of The Acoustical Society of America:

2:40pm Sound production and hearing ability in the Hawaiian sergeant fish.

3:25pm Sound communication by the forceps fish, Forcipiger

3:40pm Acoustico-lateralis communication in coral reef butterflyfishes


Info from Timothy Tricas' homepage:

"Our research is focused on the evolution of sensory systems in relation to the natural behavior and ecology of coral reef fishes. The coral reefs of Hawaii and other Pacific regions afford excellent opportunities to study the sensory biology and behavior of marine fishes. One important group is the butterflyfishes (family Chaetodontidae), which occur on nearly all coral reef systems. Some of our current projects include the evolution of a specialized hearing mechanism in butterflyfishes (the laterophysic connection), sound production, neuropeptides as modulators of hearing and lateral line sensory systems, and the evolution of social behavior."


A recently published paper:

Acoustic communication in territorial butterflyfish: test of the sound production hypothesis

Timothy C. Tricas, Stephen M. Kajiura and Randall K. Kosaki

The Journal of Experimental Biology 209, 4994-5004
Published by The Company of Biologists 2006


Butterflyfishes are conspicuous members of coral reefs and well known for their visual displays during social interactions. Members of the genus Chaetodon have a unique peripheral arrangement of the anterior swim bladder that connects with the lateral line (the laterophysic connection) and in many species projects towards the inner ear. This morphology has lead to the proposal that the laterophysic connection and swim bladder system may be a specialized structure for the detection of sound. However, the relevant stimuli, receiver mechanisms and functions for these putative hearing structures were unknown because butterflyfishes were previously not recognized to produce sounds during natural behavior. We performed field experiments to test the hypothesis that Chaetodon produces sounds in natural social contexts. Acoustic and motor behaviors of the monogamous multiband butterflyfish, C. multicinctus, were evoked and recorded by placement of bottled fish into feeding territories of conspecific pairs. We demonstrate that territory defense includes the production of agonistic sounds and hydrodynamic stimuli that are associated with tail slap, jump, pelvic fin flick and dorsal-anal fin erection behaviors. In addition, grunt pulse trains were produced by bottled intruders and are tentatively interpreted to function as an alert call among pair mates. Acoustic behaviors include low frequency hydrodynamic pulses: less than 100 Hz, sounds with peak energy from 100 Hz to 500 Hz, and a broadband high frequency click (peak frequency=3.6 kHz), which is produced only during the tail slap behavior. These results provide a biological framework for future studies to interpret the proximate function of the acoustico-lateralis sensory system, the evolution of the laterophysic mechanism and their relevance to butterflyfish social behavior.


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Sunday, December 31, 2006


Evolution Of Influenza A Virus (PR + Paper)

A PLoS Pathogens press release:

An understanding of the evolutionary dynamics of the influenza virus determines scientists' ability to survey and control the virus. In a new study, published online in the open-access journal PLoS Pathogens, Dr. Eddie C. Holmes* of the Department of Biology at Pennsylvania State University and colleagues at the National Institutes of Health, the Wordsworth Center and the Institute for Genomic Research used genomic analysis to investigate the evolutionary properties of the H3N2 subtype of human influenza A virus.

The authors, in the first population-based study of its kind, collected a sample group of 413 complete influenza genomes from across New York State. Comparative analysis of the samples revealed genetically distinct viral strains circulate across the state within any one season and occasionally exchange genes through reassortment.

These results indicate that adaptive evolution occurs only sporadically in influenza virus, and that influenza virus diversity and evolution is strongly affected by chance events, such as reassortment between strains coinfecting a host or the introduction of a particular variant from elsewhere. These factors make predicting future patterns of influenza virus evolution more difficult, as vaccine strain selection then becomes dependent upon intensive surveillance, whole-genome sequencing, and phenotypic analysis.


Based on the paper:

Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus

Citation: Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, et al. (2006) Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus. PLoS Pathog 2(12): e125 DOI: 10.1371/journal.ppat.0020125


A comparative analysis of 413 complete genomes of the H3N2 subtype of human influenza A virus sampled from New York State, United States, the largest and first population-based study of its kind, reveals that viral evolution within epidemic seasons is dominated by the random importation of genetically different viral strains from other geographic areas, rather than by natural selection favoring local strains able to escape the human immune response. Multiple clades of genetically distinct viral strains cocirculate across the entire state within any season and occasionally exchange genes through reassortment. Both genetic diversity and geographic viral "traffic" are extensive within epidemics. Therefore, the evolution of influenza A virus is strongly shaped by random migration and reassortment and is far harder to predict than previously realized. Consequently, intensive sampling and whole-genome sequencing are essential for selecting viral strains for future vaccine production.


Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.


A 2003 Letter to Nature:

Ecological and immunological determinants of influenza evolution

Neil M. Ferguson, Alison P. Galvani and Robin M. Bush

Nature 422, 428-433 (27 March 2003) | doi:10.1038/nature01509; Received 18 November 2002; Accepted 21 February 2003

Opening Paragraph

In pandemic and epidemic forms, influenza causes substantial, sometimes catastrophic, morbidity and mortality. Intense selection from the host immune system drives antigenic change in influenza A and B, resulting in continuous replacement of circulating strains with new variants able to re-infect hosts immune to earlier types. This 'antigenic drift'1 often requires a new vaccine to be formulated before each annual epidemic. However, given the high transmissibility and mutation rate of influenza, the constancy of genetic diversity within lineages over time is paradoxical. Another enigma is the replacement of existing strains during a global pandemic caused by 'antigenic shift' - the introduction of a new avian influenza A subtype into the human population1. Here we explore ecological and immunological factors underlying these patterns using a mathematical model capturing both realistic epidemiological dynamics and viral evolution at the sequence level. By matching model output to phylogenetic patterns seen in sequence data collected through global surveillance2, we find that short-lived strain-transcending immunity is essential to restrict viral diversity in the host population and thus to explain key aspects of drift and shift dynamics.


*Info on Eddie C. Holmes (abridged):

"My research integrates ideas from a number of different fields, most notably evolutionary genetics, virology and the ecology of infectious disease. I am currently concentrating on three main areas, using RNA virus study systems: Evolutionary genetics, Comparative genomics and Molecular epidemiology"

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Dinosaur gastroliths: stones did not help with digestion

A University of Bonn Press Release: Sauropods did not have a 'gastric mill'. How they processed their food without molars remains unclear.

The giant dinosaurs had a problem. Many of them had narrow, pointed teeth, which were more suited to tearing off plants rather than chewing them. But how did they then grind their food? Until recently many researchers have assumed that they were helped by stones which they swallowed. In their muscular stomach these then acted as a kind of 'gastric mill'. But this assumption does not seem to be correct, as scientists at the universities of Bonn and Tubingen have now proved. Their research findings can be found in the current issue of the journal Proceedings of the Royal Society.

What do you do if you do not have good teeth, and food is hard to digest? Some herbivorous birds which have a toothless beak, such as ostriches, solve the problem with what is known as a gastric mill. Their muscular stomach is equipped with a layer of horn and contains stones which help to break up, crush and thereby also to digest food.

Giant dinosaurs from the Jurassic and Cretaceous period (200 million to 65 million years ago) such as Seismosaurus and Cedarosaurus must have had similar digestive problems. The animals, some of which weighed more than 30 tonnes, were the largest herbivores which have ever existed. Many of them had a very small head, in relation to the size of their body, and narrow, pointed teeth, which were more suited to tearing off plants rather than chewing them. At the same time, they had to digest enormous amounts of food for their rapid growth and the metabolism of their gigantic bodies. Smoothly polished stones, which were found in several cases at excavations involving skeletons of sauropods, are also interpreted as gastric stones.

However, Dr. Oliver Wings* from the Institute of Earth Sciences at the University of Tubingen, and Dr. Martin Sander from the University of Bonn have shown that this cannot at least be a gastric mill such as birds, today's relatives of the dinosaurs possess. Among these the ostrich is the largest herbivore. For their investigations, the scientists therefore offered stones such as limestone, rose quartz and granite as food to ostriches on a German ostrich farm.

After the ostriches had been slaughtered, the scientists investigated the gastric stones. It became clear that they wore out quickly in the muscular stomach and were not polished. On the contrary, the surface of the stones, which had been partly smooth, became rough in the stomachs during the experiments. The mass of the stones then corresponded on average to one per cent of the body mass of the birds.

"Whereas occasionally stones were found together with sauropod skeletons, we don't think they are remains of a gastric mill such as occurs in birds," Dr. Sander comments. In that kind of gastric mill the stones would have been very worn and would not have a smoothly polished surface. Apart from that, gastric stones are not discovered regularly at sauropod sites. When present, their mass is, in relation to the body size, much less than with birds. "In comparing these we extrapolate over four orders of magnitude, from an ostrich weighing 89 kilograms to a sauropod weighing 50,000 kilograms. This may seem a bit daring. However, within birds the range of body weight and corresponding masses of gastric stones also spans four orders of magnitude, from the 17 gram robin to the ostrich," says Oliver Wings, who moved from Bonn University to Tubingen only recently.

Yet what else were the dinosaurs' gastric stones used for? The researchers presume that they were accidentally eaten with their food or could have been swallowed on purpose to improve the intake of minerals. But if the stones did not help to crush vegetable food, the sauropods' digestive system must have used other methods, since the decomposition of large amounts of material which is difficult to digest requires the assistance of bacteria in the digestive system. The smaller the pieces are, the better they can break down the food. Possibly, the scientists conclude, the intestines of the sauropods were formed in such a way that the food was retained there for a very long time, in order to improve the digestive process.

There is another group of dinosaurs, however, whose remains of gastric stones can be linked up with a birdlike gastric mill, according to Oliver Wings' research. From these dinosaurs known as theropods today's birds developed. The gastric mill could therefore have developed in the ancestral line of birds.

Original press release ("Dinosaurs - stones did not help with digestion" December 2006) available via this page


Based on the paper:

No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches

Oliver Wings and P. Martin Sander


Polished pebbles occasionally found within skeletons of giant herbivorous sauropod dinosaurs are very likely to be gastroliths (stomach stones). Here, we show that based on feeding experiments with ostriches and comparative data for relative gastrolith mass in birds, sauropod gastroliths do not represent the remains of an avian-style gastric mill. Feeding experiments with farm ostriches showed that bird gastroliths experience fast abrasion in the gizzard and do not develop a polish. Relative gastrolith mass in sauropods (gastrolith mass much less than 0.1% of body mass) is at least an order of magnitude less than that in ostriches and other herbivorous birds (gastrolith mass approximates 1% of body mass), also arguing against the presence of a gastric mill in sauropods. Sauropod dinosaurs possibly compensated for their limited oral processing and gastric trituration capabilities by greatly increasing food retention time in the digestive system. Gastrolith clusters of some derived theropod dinosaurs (oviraptorosaurs and ornithomimosaurs) compare well with those of birds, suggesting that the gastric mill evolved in the avian stem lineage.


*From Oliver Wings' personal website:

"Gastroliths are stones and other hard objects which have formed in the stomach or which were swallowed and reside in the digestive tract. I am especially interested in swallowed stones which do occur commonly in fossil and living archosaurs (dinosaurs, crocodilians, and birds), and some other vertebrate groups such as tangasaurids, plesiosaurs, or pinnipeds. Today, herbivorous birds regularly use gastroliths (grit) to triturate foodstuff in their gizzard, the so called "gastric mill". Grit intake is commonly known from chicken, songbirds, and ratites. In dinosaurs, gastroliths have been reported in a number of taxa. To reveal the function of dinosaur gastroliths, I have conducted experiments with ostriches (Struthio camelus), the largest living bird species.

Gastroliths can help answering paleobiological questions such as composition of diet or reconstruction of migrational routes. In my PhD., I have focused on the function and distribution of gastroliths in sauropod dinosaurs. Currently, I am working on several gastrolith research projects, such as the identification of gastroliths (important because of finds of isolated pebbles which may have been used as gastroliths) or the function of gastroliths in aquatic vertebrates.

I am very interested in collaborations in gastrolith research. There are still so many open questions regarding stomach stones and there are just a few people worldwide working seriously on that topic. As far as I know, I am the only one who has spent several years entirely on this subject."


Recent posts which reference gastroliths:

Tarbosaurus: Rare dinosaur fossil unearthed by Korea-led team

Volcanic Blast Likely Killed Preserved Antarctic Fossil Plesiosaur

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