Research Blogging - Biology - English

Nutrition and protein: training, performance and long-term health.

2012-05-25T20:18:03Z

These are interwoven issues. The aim of training is improve the body’s ability to perform certain tasks (and in the case of CrossFit it is to achieve a high degree of effectiveness and competence in a wide range of skills and efforts). The goal of nutrition in training is to help the body (the entire thing) adapt and remodel, or at least maintain what you have and can do. Bodies like efficiency. Your body will see no point in maintaining bone or muscle that does not look like it’s going to be used any time soon and will let it go. That’s why people who have been ill and disabled for a long time become so frail. When challenged your body (which means here not only muscle and bone, but brain, nerves, biochemical pathways and efficiency, cell proliferation and organelle numbers and function, and neurotransmitters) changes to meet that particular challenge. Protein is important here for repair, strengthen and reinforcement of stressed tissue. Strength-oriented athletes have traditionally made efforts to increase protein intake and there is some evidence that this is effective in increasing muscle mass. There is also evidence that increasing protein intake can reduce the rate of loss of muscle mass seen in aged people. Not all of the protein you can consume will be used to increase mass. Your body will use what it needs, or what it anticipates needing in the near future (in case you persist in doing all those squats, jerks, kettle bell swings and pushups.) Consuming a lot of protein will probably not hurt you. Not consuming enough will slow repair and limit your ability to adapt to physiological and mechanical stress. Endurance athletes have long been encouraged to eat plenty of carbohydrates since availability of carbs can be a limiting factor in performance. This is why consuming dilute fruit juice (or sugar water) can delay exhaustion and allow an athlete to continue to run, bike or whatever longer than they would if they had been drinking plain water. However if you are always running on carbohydrates you may not adapt biochemically speaking. Normally, if you are low on carbohydrates (or glycogen) your body will attempt to increase the rate at which is uses its own fat stores for energy. Being habitually low on carbs will increase your ability to generate energy by other means. You will probably be uncomfortable for at least a while, but you should improve at this the longer you train. So . . . while training, remember that you are training more than muscles. A lot of people involved with CrossFit advocate some interesting dietary approaches. It probably won't hurt you, and for a lot of people it will be better than what they were eating before. Keeping with the program helps people bond and gives them a sense of control. That can be very good, as long as it doesn't get too rigid or ridiculous. There are really too many unknowns floating around at present to know exactly what is best. What is best probably varies by individual, situation, stage of life, and training goals. New information becomes available. We'll see how things fall out. Churchward - Venne, T., Burd, N., Phillips, S., & Research Group, E. (2012). Nutritional regulation of muscle protein synthesis with resistance exercise: strategies to enhance anabolism Nutrition & Metabolism, 9 (1) DOI: 10.1186/1743-7075-9-40 Logan-Sprenger, H., Heigenhauser, G., Killian, K., & Spriet, L. (2012). The effects of dehydration during cycling on skeletal muscle metabolism in females Medicine & Science in Sports & Exercise DOI: 10.1249/MSS.0b013e31825abc7c Symonsi, T., Sheffield-Moore, M., Mamerow, M., Wolfe, R., & Paddon-Jones, D. (2010). The anabolic response to resistance exercise and a protein-rich meal is not diminished by age The journal of nutrition, health & aging, 15 (5), 376-381 DOI: 10.1007/s12603-010-0319-z...

Churchward - Venne, T., Burd, N., Phillips, S., & Research Group, E. (2012) Nutritional regulation of muscle protein synthesis with resistance exercise: strategies to enhance anabolism. Nutrition , 9(1), 40. DOI: 10.1186/1743-7075-9-40

Logan-Sprenger, H., Heigenhauser, G., Killian, K., & Spriet, L. (2012) The effects of dehydration during cycling on skeletal muscle metabolism in females. Medicine , 1. DOI: 10.1249/MSS.0b013e31825abc7c

Symonsi, T., Sheffield-Moore, M., Mamerow, M., Wolfe, R., & Paddon-Jones, D. (2010) The anabolic response to resistance exercise and a protein-rich meal is not diminished by age. The journal of nutrition, health , 15(5), 376-381. DOI: 10.1007/s12603-010-0319-z

Neuroscientists should study Zombie Ants

2012-05-25T15:32:00Z

Zombie ant controlled by fungus (source)The fungus-controlled zombie ant is one of natures' greatest wonders. A fungus (e.g. O. Unilateralis) is inhaled by an ant (e.g. Camponotus Leonardi), and begins to grow inside its body. Eventually the fungus infests the brain of the ant, causing it to drunkenly wander, periodically convulse, climb up a leaf and clamp down on its ridge. Once the ant is securely in place, the fungus devours the brain and innards of the ant and grows out the back of its head often (but not always) releasing its spores onto the ground below. Un-freaking-believable, right?As if this wasn't amazing enough, it's not like it is only one fungus species that infects only one ant species. There are many of these fungi and they infect many different kinds of insect, but somehow maintain a species specificity. In other words, fungus#1 can infect SpeciesX, but not SpeciesY, and Fungus#2 infects SpeciesY, but not SpeciesQ, and so forth. So WHY does this happen? and HOW has no one looked at the brain cells of these ants? Though no one has looked at the brains of these ants, Last year a paper painstakingly characterized their behavior under 'fungi control'. The most interesting characteristics are:The ants display a 'drunkard's walk' (the author's words)The ants periodically spasm and fall down (if they are above ground level)The ants clamp down on the underside main vein of a leaf (never the side of the leaf, never the top) Interestingly they all bite down on the leaf around solar noon.Figure 1, Hughes et al., 2011This figure shows the behavior of several ants. Each ant was observed during the time of the horizontal blue bar. The black vertical lines and 'spasms' which caused the ants to fall down (gray stars), and the red triangles are when the ant bit down on the leaf ridge. Because we have no idea how the fungus is manipulating the ant, let's wildly speculate.1. The Drunken Walk:Why: The reason for this is not clear. The ant doesn't go far, so the non-directional walking could be to keep it close to more ants.How: The mechanism is also not clear, but usually an ants directional walking could be following a pheromone trail. The fungus could presumably cause random walking by confusing the ants ability to sense pheromones. It could possibly even cause 'hallucinatory' pheromone sensing.2. The Periodic Spasms: Why: The authors speculate that the purpose of these spasms is to keep the ant near the ground. The infect ants spend much more time on the ground level than the uninfected ants, and the spasms are often followed by a fall.How:A fungus could essentially cause a seizure in the ants brain by manipulating potassium or calcium channels. On the other hand, I suppose the fungus could be acting directly on the muscles, causing them to twitch in an uncontrolled way. 3. The Clamping: Why: This has an obvious function, to root the ant for ultimate fungal growth and dispersion. How: First of all, biting and even walking on leaves is not something these ants normally do. So the fungus isn't just hijacking a behavior that the ant already has, it's basically creating a new one. The correlation with solar noon indicates that a light or heat signal could contribute to the trigger, but basically nothing else is known about it. Interestingly, the clamping does not always have to be one single event either. A few of the ants clamped down on the leaf vein more than once. The authors of this paper spend time discussing fungi's direct effect on the mandible muscles of the ant.Figure 3 Hughes et al., 2011They show that the mandible muscles of the normal ant are fat and healthy (B), but the muscles of the infected ant are separated and reduced in size (C). Though this image is of an ant at the moment of biting, the authors suggests that the deterioration of the mandible muscle might be to prevent re-opening of the clamp. They do not speculate on how the clamp is initiated in the first place, or why it occurs at noon. So please, fellow neuroscientists, somebody stain these brains! It's just too fascinating to resist exploration. What proteins are altered? What is the receptor composition of behaviorally-specific neurons? Are the dendrites differently shaped? And who knows what sort of great advances might be hidden in these brain-controlling fungi. The magic of optogenetics comes from lowly light-sensitive bacteria, just think of the possibilities hidden in brain-controlling fungus. To be fair, some neuroscience has been done on parasitic brain control, but it is very limited. In fact it is limited to basically one histological study about parasitic worms who infest crickets and cause them to drown themselves (the subject of a future blog post). However, suicide-crickets are no zombie-ants and the exact mechanisms of the interaction © TheCellularScaleHughes DP, Andersen SB, Hywel-Jones NL, Himaman W, Billen J, & Boomsma JJ (2011). Behavioral mechanisms and morphological symptoms of zombie ants dying from fungal infection. BMC ecology, 11 (1) PMID: 21554670...

Hughes DP, Andersen SB, Hywel-Jones NL, Himaman W, Billen J, & Boomsma JJ. (2011) Behavioral mechanisms and morphological symptoms of zombie ants dying from fungal infection. BMC ecology, 11(1), 13. PMID: 21554670

Octopuses Host a Masterclass on Hiding

2012-05-25T11:02:02Z

When you're surrounded by an ocean full of potential predators, the best way to avoid seeing the inside of one's stomach is to make sure none of them see you in the first place. Octopuses and some other cephalopods are experts at camouflage, manipulating the colors and textures of their skin to hide in plain sight. But their strategy, it turns out, has nothing to do with disappearing into the background. To learn the camouflaging secrets of the masters, researchers led by Noam Josef at Ben-Gurion University of the Negev in Israel went scuba diving. On reefs in the Red Sea and Tyrrhenian Sea, they snapped pictures of two octopus species (Octopus cyanea and O. vulgaris) whenever they saw an individual hiding—crouched low and motionless for a minute or longer. For the pictures to work in the team's digital image analysis, they had to be sunlit just so and taken from directly above. Over three years, they captured just 11 photos that fit their criteria. "These images are a bit hard to get," Josef said in an email. Not to mention the challenge of finding a camouflaged octopus in the first place. Hint: Look for the coral with tentacles. Each bird's-eye, or rather shark's-eye, photo was converted to a grayscale image. Researchers selected a rectangle showing the pattern on the octopus's mantle (the part that's not tentacles). Then a software algorithm compared the mantle sample to rectangles from everywhere else in the photo, shifting the frame one pixel at a time and searching for a match. The best matches to the octopuses' camouflage patterns were not to be found in the gravely ground beneath them. Instead, 10 out of the 11 octopuses had clearly mimicked a specific object nearby. They played coral, rock, weird sand blob, or algae patch. View this picture larger and you'll see that one coral has eyes on top. A camouflaged animal's best strategy depends on the viewpoint of its predators. Many fish have light-colored bellies that blend in with the sky when seen from below. Certain pygmy sharks take this trick a step further and emit a blue glow from their undersides. When viewed from above, fishes' darker-colored backs vanish into the background of the ocean. An octopus sitting on a reef has to worry about big fish hunting from above, as well as moray eels and other predators that creep up from the sides. Since these enemies approaching from different angles will see the octopus framed against different backdrops, maybe it makes sense for the octopus to forgo blending in altogether. It's stuck being obvious, so it may as well pose as an obvious object that's less edible. "Sometimes octopuses make an honest mistake and simply become conspicuous" by camouflaging, Josef says. "However, in a complex environment like the coral reef, acquiring key features of an object may serve the octopus better than just matching the general look of the reef." You can see a few of those convincing key details in the photos above, where octopuses have contorted themselves into the knobby branches of a coral or a shell's striped ridges. Scientists have discovered some of the specialized cells in octopus skin that help them pull off their elaborate imitations—pigment holders, reflectors, light scatterers. But Josef says there are still more questions than answers: "What visual cues are used by these animals? How do octopuses match their colors even though they're colorblind?" (Yes. Colorblind.) "What information is transmitted from the eye to the brain? And what does an octopus really see?" We're still "far from understanding" the camouflaging act of the octopus, Josef says. We'll have to keep hunting for scraps of information the cunning cephalopods let slip. That is, assuming we can find them first. Josef, N., Amodio, P., Fiorito, G., & Shashar, N. (2012). Camouflaging in a Complex Environment—Octopuses Use Specific Features of Their Surroundings for Background Matching PLoS ONE, 7 (5) DOI: 10.1371/journal.pone.0037579 Images: Top, Ms. Keren Levy. Middle and bottom, Mr. Zvika (Ziggy) Livnat....

Josef, N., Amodio, P., Fiorito, G., & Shashar, N. (2012) Camouflaging in a Complex Environment—Octopuses Use Specific Features of Their Surroundings for Background Matching. PLoS ONE, 7(5). DOI: 10.1371/journal.pone.0037579

DNA vaccines: a work in progress

2012-05-25T09:13:00Z

You are all familiar with the idea behind vaccines: an attenuated form of the pathogen stimulates the immune system to produce T-cells and antibodies specific to that particular antigen. These immune responses then become part of our T- and B-memory cells, cells that have previously encountered a certain antigen and have already specialized to recognize it. The challenge behind a vaccine is to use a form of antigen that's weak enough so not to cause the actual disease, but strong enough so to prompt the appropriate immune response. An efficient immune response has to be broad (it has to recognize all possible strains of the antigen) and strong (enough T-cells and antibodies have to be produced in order to clear the infection). First generation vaccines use the whole organism as an antigen. Unfortunately, weakened forms may still induce full infection in immunocompromised people. Second generation vaccines use portions of the organism. For example, in HIV, one protein that's been used a lot in vaccine trials is env, the envelope protein: this is the outer shell of the virus, and the part most visible to the immune system. The so called "DNA vaccines" are the third generation vaccines. The idea is to inject a circular molecule of DNA (plasmid) that encodes for the specific antigen proteins. DNA is rapidly absorbed by cells and, once inside, it can use the cell machinery to assemble the proteins it encodes for. Just like in a viral infection, these proteins are then displayed on the cell's surface and presented for recognition by the immune system. The advantage of a DNA vaccine is obvious: there is no risk that the DNA itself will trigger the actual disease. Furthermore, studies have so far shown that no anti-DNA antibodies are produced. Some DNA vaccines are already in use in veterinary medicine. In humans, though safe and well tolerated, they seem to have lower immunogenicity than other vaccines, and hence their potential hasn't been fully exploited yet. While the reason for this is still unknown, several studies have attempted to use other genes and proteins in combination with the vaccine to improve immunogenicity, in particular, genes and proteins that are involved in immune recognition pathways and cell-signaling pathways. "Advancements in antigen design, improved formulations, inclusion of molecular adjuvants, and physical methods of delivery have greatly enhanced the immunogenicity of DNA vaccines [1]." In [1] Ferraro et al. review the current studies in this field specifically for vaccines targeting influenza, human papilloma virus (HPV), and HIV. In the case of influenza, the appeal of a DNA vaccine is that it would considerably shorten the preparation time. In terms of immune responses, DNA vaccines have not been able to trigger good antibody responses, but, on the other hand, tend to perform well in triggering cellular responses (recruiting natural killer cells, T-cells, and phagocytes). In HIV in particular, both antibodies and T-cell responses are needed, both broad enough to cover the variability of the virus. Therefore, it is feasible and promising to combine a DNA vaccine with a protein one. "Combining a DNA prime and viral boost creates a synergistic enhancement in the magnitude of antigen-specific CD81 T-cell responses. A phase I trial that combined a multi-clade DNA vaccine prime with an Ad5 boost demonstrated that this strategy was capable of eliciting humoral responses in addition to cellular responses." [1] Ferraro, B., Morrow, M., Hutnick, N., Shin, T., Lucke, C., & Weiner, D. (2011). Clinical Applications of DNA Vaccines: Current Progress Clinical Infectious Diseases, 53 (3), 296-302 DOI: 10.1093/cid/cir334...

Ferraro, B., Morrow, M., Hutnick, N., Shin, T., Lucke, C., & Weiner, D. (2011) Clinical Applications of DNA Vaccines: Current Progress. Clinical Infectious Diseases, 53(3), 296-302. DOI: 10.1093/cid/cir334

When introductions go bad

2012-05-25T09:09:00Z

My first sighting of the red squirrel was in Camperdown Park in Dundee in 2003. I remember that scene vividly. I had since tried desperately to see this elusive animal again but to no avail, save a brief sighting, again in Camperdown Park, in Autumn 2010. This is because although red squirrel, which is native to UK and is protected in Europe, is outnumbered by its foreign relative, the grey squirrel that was introduced to the UK from America. Grey squirrel has several competitive advantages including its resistance to squirrel parapox virus which is fatal to the red (grey squirrels are vectors), increased fecundity, and greater ability to digest a wider variety of food. In fact, the future of the red squirrel in the British Isles is rather precarious. The Forestry Commission estimates that there there are only 140,000 red squirrels compared to over 2.5 million greys. Recently during a holiday near Lake Geneva, Switzerland, I encountered 2 red squirrels and 1 black squirrel (resembled the red squirrel with respect to the ear tufts, but with a black/grey rather than red coat). You can see a video here in Youtube: http://www.youtube.com/watch?v=g4SqcK9CME8 There is a lot of debate on how the introduction of alien species can affect the native species and tilt ecosystems, but studies indicate that certain ecosytems could be more vulnerable that others. As early as 1958, Charles Elton claimed that ecosystems with higher species diversity were less subject to invasive species as there are fewer available niches. A recent paper by Eisenhauer et al shows that species diversity could stabilise communities during invasions. It appears as if biodiversity of ecosystems provides increased resilience against onslaughts including that by foreign invaders. Caution should be exercised when foreign species are introduced. In light of these observations, a proposed law in Brazil is of importance. A recent correspondence in Nature by Vitule et al (May 2012) warns of the repecussions of a new law that, if approved, would allow farming of foreign fish species in cages. The fishes that are being considered for introduction are tilapia and carp. The authors warn that the indigenious aquatic ecosystem would be disrupted if these introduced species were to escape and would jeopardise the aquatic biodiversity which is already fragile due to human activities such as pollution and construction.References:Vitule JR (2012). Ecology: Preserve Brazil's aquatic biodiversity. Nature, 485 (7398) PMID: 22596145Eisenhauer N, Scheu S, & Jousset A (2012). Bacterial diversity stabilizes community productivity. PloS one, 7 (3) PMID: 22470577http://www.europeansquirrelinitiative.org/the_threat.htmlRed Squirrel image source: Sarah Stephen...

Vitule JR. (2012) Ecology: Preserve Brazil's aquatic biodiversity. Nature, 485(7398), 309. PMID: 22596145

Eisenhauer N, Scheu S, & Jousset A. (2012) Bacterial diversity stabilizes community productivity. PloS one, 7(3). PMID: 22470577

An Aboriginal Australian genome reveals separate human dispersals into Asia

2012-05-25T03:04:32Z

This blog section concerns a trendy debate in science, the human population history, which has extensions into daily life, as it can constitutes a topic of general public curiosity. Therefore, let’s see what is contribution described herein.BackgroundModern human populations seems to be derived from a single African ancestral population, under the well supported “out of Africa” hypothesis (1). Particularly, for eastern Asian colonization a “single-dispersal” model have been hypothesized (2), which suggest the aboriginal australians are a lineage diversified recently within the Asian cluster. This hypothesis could be summarized in a topological representation, as drawn in figure 1A of the article (Africans,(Europeans,(Asians,Australians))). Recent studies dated the split between Europeans and Asians around 17K-43K years before the present (ybp). In addition, archaeological evidence supports modern humans in Australia back to ~50K ybp. Those inferences are incompatible with the above mentioned hypothesis, at least in a time framework. A second scenario could be hypothesized, with an early branching process and occupation of Australia, and probable later genetic exchange between Asians and Australians, described as (Africans, (Australians,(Asians, Europeans)). This possibility has been non tested so far. Using an ancient, free of current admixtures, aboriginal australian genome, and SNPs data from different human populations, as well as, a background in molecular evolution and population genetic theories, this paper aims to distinguish between competing hypotheses to tackle the human population relatedness and migrations history of ancient australian populations.The facts in briefA 100-year-old lock of hair from an aboriginal Australian male (from Museum of Archaeology and Ethnology, UK)31 Institutions implied in a worldwide scale58 Authors, with same geographical extentAn ancient genome sequenced by Illumina technology and SNP-chip on other human populationsComputational analyses (PCA, clustering methods, ABBA/BABA expectations)A Science podcast interview (http://www.sciencemag.org/content/334/6052/94/suppl/DC2)Discussion We found the paper quite convincing in testing the two possible scenarios for human colonization in the Australian area. Next paragraphs will describe and discuss the evidence and test they used.1. Testing the genetic clustering of Aboriginal Australian genome.The principal component analysis illustrated in figure 1B shows the clustering pattern from 1220 individuals SNP chip data (449k SNPs), covering 79 human populations. This figure revealed a close relationship between the Australian genome, Highland Papua New Guinea (PNG), Bougainville and Aeta samples, all of them from the australo-melanesian region. That pattern could exclude any European contamination of the sample, which is highly probable by his long handling by Europeans. We noted the geographical tendency of a “continuous” colonization for human populations outside of Africa. I quoted continuous to clarify we are not referring to a single wave of colonization, but to a geographical ordination of the populations. A confusing point was expressed for the PCA inset, which looks like a 3D-box, but it already corresponds just to a zoom-in on the same PCA graph. A further review of the next PCA axes on supplementary material evidenced a very clear differentiation of the australo-melanesian sequences in the axis4.We speculated about the amount of data explained in the first two PCA axes, which is not described. Contrary to our expectations, from experiences in other types of characters (as morphology and climatic variables), the proportion of variance explained on this plot seems to be very low, as usual for genomic studies. Then, we discussed a bit the idea of a checklist of requirements when a publication is being prepared: if you are planning to present an analysis, take at hand i, ii, iii and please do not forget to include them.2. Testing admixture between Aboriginal Australian genome and other populationsThe figure 1C describes the ancestry proportions of all individuals SNPs set, obtained by a maximum likelihood estimation in Admixture software. This clustering analysis resembles the Structure k-categories approach, in which each line in the plot correspond to an individual and the colors represent the ancestral populations identities. The number of k-categories is assigned a-priori, and can modify the ancestry proportions of certain individuals revealing admixture processes between populations. At first, using a k=5, the aboriginal australian sample appears belonging to the same ancestral population than PNG and a higher proportion of the Bougainville individuals. Interestingly, south Asian population seems to share a small proportion of the SNPs with the ancestral aboriginal australian category. Once we moved in deep k-values, as far as k=20, the aboriginal australian genome appears more mixed with PNG, Bougainville, Aetas and South Asian populations.We debated the accuracy of use an individual genome to represent the admixture in the ancestral aboriginal australian population, and the unknown variability of the population at the ancient time, which is not being considered here. We formulated how could be affected the admixture patterns if this aboriginal Australian genome represents the most or the least mixed individual in the ancestral population? We wondered why there are not other recent Australian samples? Even if current aborigines inhabit in Australia. At this point in the discussion, we moved into more socio-political issues about the use of samples and information, as I stated at the beginning, this topic could be of general concern and discussion for several reasons.The evidence presented so far and an additional test below can help to distinguish between single vs. multiple dispersals “out of Africa” and likely the proportion of admixture between the first established populations and the second wave of migration. Furthermore, questions about how or why the second migration replaced almost in a complete way the first one, from my point of view, constitute statements largely "historical" and therefore difficult to draw and test from the evidence available. I consider is very difficult to go beyond of the patterns and processes we are able to model and test.3. D-test and ABBA/BABA hypothesis We tried to identify the goal and configuration of this test to discriminate between the competing hypotheses. Complete information of the test could be found in references 3 and 4. I will try to summarize it in a nutshell. The D-test is a four-taxon configuration (see figure) in which only biallelic sites are considered (A and B variants), two out of four taxa have fixed states, commonly on the outgroup sequence (here the Africans, but also the Europeans), and the other two sites differ between groups (here Aboriginals and Asians). This configuration produces either BABA or ABBA patterns. The next step is to count the number of sites supporting one or other patterns. The D test = ∑ (sites ABBA - sites BABA) / ∑ total sites. Usually, the test was defined to identify admixture between populations (with AB/BA sites), with the expectation of an equal number of the two types of sites. D test can be considered more robust to sequencing errors because it compares nucleotides in more than one sequence, which is less probable that have been taken place twice by error. The authors explicitly said the test do not allow to distinguish neither between the two models of origin, nor gene flow between Asians and Australian populations, however I consider the D-test performed here can support the multiple dispersal model, due to a statistically significant excess of sites grouping Africans and Australian Aboriginal genomes (sites with pattern 2 in figure). Expected vs. observed values of the D-test can facilitate the hypotheses discrimination (as they tried on the Table 2), however the expected values reported here for single and multiple dispersal models are so closer each other (~50%), with no credible intervals, that does difficult to support one or other hypothesis with the observed patterns. Finally, it is worthy of attention in the implementation of the D-test, consider that the patterns on current populations given the hypothetical past events, may have been altered by many other evolutionary processes as secondary gene flow, structure in the ancient population, incomplete lineage sorting, among others.Figure 1. Grouping site patterns 1 and 2 used in D-test. Note that African and European populations have fixed states, whereas that Aboriginal Australian and Asian populations vary. This figure is a modification of the figure 3 in reference 5. Even though it is not clear the ABBA/BABA patters, the different grouping patterns are based on the article text describing the two models of early dispersal hypotheses used to perform the test....

Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T.... (2011) An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science, 334(6052), 94-98. DOI: 10.1126/science.1211177

Discovering underneath a “MudPit”

2012-05-24T12:17:36Z

What is referred to as “MudPit” here is not “a pit of mud” but a technique in the mass spectrometry field which stands for “multi-dimensional protein identification technology”, a very powerful approach that has been widely used since the … Continue reading →...

Washburn, M., Wolters, D., & Yates, J. (2001) Large-scale analysis of the yeast proteome via multidimensional protein identification technology. Nature Biotechnology, 19(3), 242-247. DOI: 10.1038/85686

Yang, F., Shen, Y., Camp, D., & Smith, R. (2012) High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Review of Proteomics, 9(2), 129-134. DOI: 10.1586/epr.12.15

Tran, J., Zamdborg, L., Ahlf, D., Lee, J., Catherman, A., Durbin, K., Tipton, J., Vellaichamy, A., Kellie, J., Li, M.... (2011) Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature, 480(7376), 254-258. DOI: 10.1038/nature10575

A Device that Sorts Single Molecules of Methylated DNA – Q&A with Cornell’s Harold Craighead

2012-05-24T12:00:00Z

Sure, single-cell sorting devices are cool and useful and all, but Harold Craighead’s lab at the Cornell University Department of Biomedical Engineering is developing a microfluidic device that can separate individual methylated DNA fragments from a single cell’s total genetic content. In a lab test reported in their recent open-access paper (pdf) in Proceedings of the National Academy of Sciences, the team used the device to separate methylated plasmids from among 11 femtograms of mixed DNA, hitting a 5.6 percent false-positive rate and 3.5-fold enrichment. That level of enrichment is typical of immunoprecipitation methods that need about 1,000 times as much input DNA....

Cipriany, B., Murphy, P., Hagarman, J., Cerf, A., Latulippe, D., Levy, S., Benitez, J., Tan, C., Topolancik, J., Soloway, P.... (2012) Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1117549109

Clockworks: The Story of Drugs — Part 1

2012-05-24T11:15:00Z

In this installment, I will discuss why it is difficult to discover, design and develop a drug, in view of our current knowledge of physiology.With numerous, intertwined reactions happening, our body is a complex clockwork of biomachinery gears. What do you do, then, if some gears fail—that is, if you got sick? On one hand, it is a consolation that many gears are what biologists call 'redundant', which means that it's alright that a certain gear fails, because there are other gears that can take over its function. On the other hand, due to the intricacy of the gears, it is hard to pinpoint which gear is the problem, let alone fixing it. And the sheer number of gears: ICD-10 classifies tens of thousands diagnoses — tens of thousands ways the gears can fail — and those are only the ones we know; how about those we don't? Granted, some are not caused by our own gears failing, but by interferences of other, pesky gear systems: viruses, bacteria, misfolded proteins, errant microbiome, etc.; but the sense of magnitude is there.So we take drugs. In the past, the way we administer drugs is the equivalent of throwing various types of wrenches to the clockwork and then observe whether the gears are working again. Today we know more about the gears and the various shapes and teeth so that we are able to design a more sophisticated and targeted wrench, but we still don’t know enough.Our current thinking is that the machinery gears, mostly proteins, are of distinct shapes, or perhaps more fittingly, different tooth shapes. A drug has gotta fit into these various shapes. We think that if we can find 'keys' that fit to these 'locks' we can modulate that particular gear's activity: turn it up or down, switch it on or off. The key would fit into the lock, the lock would be induced to change shape / dissociate / do other curious stuff; which triggers happenings in the next gear in line. Like the dominoes falling off in line. Only that ‘the curious stuff’ may be more than a domino keeling over or a gear turning, but something that is more wackily messy, something like a Rube Goldberg contraption than a precise-looking clockwork, in this respect.How should we shape the serrated key? The first problem is scale. These gears are small — not microscopically, but nanoscopically so: To design the keys, we need the moulds, and so these very gears are the moulds. Structural biology to the rescue — X-rays crystallography/multidimensional NMR/cryo-electron microscopy can characterise the gears with varying resolutions.However, structural determination techniques face a big challenge: the interconnectedness of the system. You can't take out a gear out of context of the surrounding gears, examine it, hoping that your examinations will be valid and/or useful. Well, you sort of can. Sure, systems biology is important to gain a bird's-eye view of the whole shebang, but structural biologists routinely single out a gear and determine its structure to make it crystal-clear (heh heh) what its possible activation mechanism is, how it interacts with its activator/inhibitor, how it transduces signal to the next gear, and so on.The structural data, then, has to be taken with a grain of sodium chloride because essentially it is performed—in the physics equivalent of—in vacuo. That said, the gleaned information can be incredibly useful. Case in point: enfuvirtide. This anti-HIV-1 drug mimics a region—C-heptad repeats (CHR)—of the viral envelope glycoprotein, gp41, which is a crucial part of viral:cell membrane fusion machinery [1]. CHR is supposed to fold back to NHR like a hairpin (they are connected) and then Stuff happens, with gory details I will spare you from (Oh, fine: a channel is opened between HIV-1 membrane and that of your soon-to-be-infected T-cell; viral particles are pumped through and soon hijack your T-cell to become baby-virus-producing zombie until it bursts releasing said baby virions. Happy?) Now, the 'folding back' part is a mechanism that was uncovered through cleverly-devised experiments founded in structural studies. Thanks to this, we can deduce that if we somehow have a fake CHR, this 'folding back' can be circumvented. And that's exactly what enfuvirtide is: a dummy gear that connects to NHR gear, but not connected to the gears down the road, thus—hip hip hurray—no zombie outbreak.This is kinda cheating though. Enfuvirtide is essentially free-roaming CHR region of gp41 and no rational design work was done. For example, peptidomimetic strategy could have been used to find something similar to enfuvirtide but is able to survive the gut—since a peptidic drugs like enfuvirtide won’t, so they have to be taken intravenously. But of course, HIV-1-infected individuals don’t have the luxury of time to wait for further work on enfuvirtide optimisation.Back to the 3D protein mould model built by structural determination techniques. Ideally, we can start building up the drug à la Lego bricks, fitting the chimaera into the protein-shape mould, right, right? Couldn't be more wrong. Enter multidimensional fitting. You see, a protein ain't like your Mom's muffin pan. Besides topology, there are other dimensions to fit—electrostatic charges, hydrophilicity/hydrophobicity, to name a few. The topology is not necessarily fixedly rigid either — playing with those poppin’ stick-and-ball molecular models may give us the illusion that proteins are rigid, but protein electron clouds are more like wobbly pudding (Mmmm, pudding...); plus, different environments (pH, oxidising level) may give rise to largely different topologies (e.g. due to different protonation states, broken disulphide bridge(s), etc.).One aspect of nanoscopic scale that is somewhat entangled with multiparameter fitting is that at this scale, there is evidence that quantum effects play an important role. Several examples of such systems have been studied like photosystems and birds’ navigation, but of more interest to a medicinal chemist would be tunnelling effect in certain enzymatic reactions. Who knows if quantum effects are more routinely utilised? Our view of physiology is biasedly mechanical—even my clockwork allegory evokes the mechanistic, so a paradigm shift may well be in order as more is known about the inner workings of such systems. If you blindly design a drug that target such systems, well, you will get an entangled mess—hopefully not the quantum kind. Moving on to pharmacokinetic restrictions: the human body imposes further restrictions from the non-negotiables (e.g. a drug cannot be too insoluble otherwise how can it dissolve in the bloodstream; a drug cannot have side effects outweighing its efficacy), to convenience (e.g. a drug is preferable to be ingested rather than injected). Our own physiology thus severely restricts the chemical space of entities that make up our drug candidate pool. As I mentioned earlier, enfuvirtide is a peptide, so it won’t survive stomach acidity and peptidases in the gut. Even with intravenous administration, it would have a short half-life due to blood proteases. All peptidic drugs—insulin is one—suffer from these problems. And for drugs targeting the central nervous system (CNS), they have to overcome another obstacle, the blood brain barrier.There seems to be some sort of patterns to the drug chemical space. To wit, some have observed that certain chemical scaffolds occur more frequently than others; they are so-called privileged scaffolds (e.g. benzodiazepines) [2] and an experienced medical chemist would be able to take a look at a chemical structure and decide whether it's 'drug-like' (while an inexperienced chemist like me would only know that a drug-like molecule can't be too small and simplistic, possesses some heteroatoms, usually has an aromatic ring or two—that's about it). Problem being, at its current state, drug-likeness is an empirical measure. No one has formulated a set of rules or equations to produce a predictive model. Lipinski's Rule of Five, for example, surveys already-existing drugs and look at the prevalent drug-like characteristics. Useful as rule of thumb; hardly predictive.Next is the issue of specificity. If you choose to take a drug topically, that’s fine and dandy because you can apply the drug locally to the area in need of treatment. But if you take a drug via oral/intravenous/other numerous administration routes, the drug is going to circulate in your bloodstream. How would you ensure that your wrench would reach, and affect only, the faulty gear? You can’t—not with certainty, at least—the wrench is going to wreck another gear, and that’s why you always ha...

Eckert, D., & Kim, P. (2001) Mechanisms of Viral Membrane Fusion and Its Inhibition. Annual Review of Biochemistry, 70(1), 777-810. DOI: 10.1146/annurev.biochem.70.1.777

Welsch, M., Snyder, S., & Stockwell, B. (2010) Privileged scaffolds for library design and drug discovery. Current Opinion in Chemical Biology, 14(3), 347-361. DOI: 10.1016/j.cbpa.2010.02.018

Marusyk A, Almendro V, & Polyak K. (2012) Intra-tumour heterogeneity: a looking glass for cancer?. Nature reviews. Cancer, 12(5), 323-34. PMID: 22513401

Winning at hide and seek in the mesopelagic

2012-05-24T08:34:00Z

A paper published a few months ago in Current Biology serves to highlight just how amazing cephalopods (squid, cuttlefish, octopus and their kin) are. The paper concerns how two species of cephalopods (Japetella heathi an octopus and Onychoteuthis banksii a squid) have evolved to avoid predators in the dynamic light environment of the mesopelagic layer of the open ocean.The mesopelagic layer of the ocean extends from 200 meters to 1000 meters deep. Sunlight in this zone transitions from present, but too dim for photosynthesis at the top, to totally absent at the bottom. This light transition poses a tricky problem for animals living there that want to avoid being eaten.In the shallower parts of the mesopelagic, predators are able to detect the shadows of prey swimming overhead. Here, the best strategy for small animals to reduce the risk of being eaten is for them to be translucent. Tissues that allow light to pass through cast a weaker shadow, which means that predators have to get closer to their prey in order to see them.In the deep dark depths, translucence is not such a good strategy. There's not enough sunlight for predators to hunt for shadows. Some predators, though, bring their own light in the form of light organs near their eyes. In the directed light of bioluminescence small imperfections in light transmission cause the light to be scattered making translucent animals much brighter than the background and easy prey.Where some predators, like the headlight fish (Diaphus effulgens), hunt by producing their own light, it pays to be a colour that absorbs light at the same wavelengths. The vast majority of bioluminescent organisms produce light in the blue wavelengths, which is best absorbed by reds and blacks. Unsurprisingly then, most animals that occur where sunlight is absent are red or black to reduce the risk that predators will find them using biologically produced light.But, some animals, like our two species of cephalopod, range over most of the mesopelagic and encounter a wide variety of light environments. High on the wish list for such animals would be the ability to become translucent in diffuse sunlight and red in directed bioluminescent light. And it turns out that this is exactly what J. heathi and O. banksii can do.Like most cephalopods, J. heathi and O. banksii have pigment containing cells in their epidermis, known as chromatophores. Cephalopods are able to rapidly change colour by expanding the size of the chromatophores. When muscles attached to a chromatophore contract, the pigment containing sac inside stretches out into a flat disc, which increases the visible area of pigment by about 50 times.A diagram showing the structure of a cephalopod chromatophore and the arrangement of the associated muscle and nerve cells (image: Richard Young)Most of the time J. heathi and O. banksii are translucent, but when they are exposed to blue light, like that produced by bioluminescent organs, they rapidly change colour to red. Neither strategy is complete; the chromatophores reduce translucence even when contracted and they are not numerous enough to allow them to become totally red. Thus, I would guess that these cephalopods are at a disadvantage relative to organisms that specialize in being red or translucent. But, in contrast to the these cephalopods, such specialists would be limited in the light environments that they could use.The translucent and red forms of J. heathi (left) and O. banksii (right). Note that neither the translucent nor the red strategy are complete (image constructed from figures in the paper)Interestingly, the images seem to suggest that J. heathi, which has the deeper distribution, is more able to produce the red colouration that is advantageous where predators hunt using bioluminescence. The authors, however, do not test or discuss this possibility. In the article they do briefly mention that older J. heathi are more common at deeper depths and have greater chromatophore coverage. So, the apparent difference in chromatophore coverage between the two species could be a consequence of either age or depth distribution differences, or perhaps both.Zylinski, S., & Johnsen, S. (2011). Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep Current Biology, 21 (22), 1937-1941 DOI: 10.1016/j.cub.2011.10.014...

Zylinski, S., & Johnsen, S. (2011) Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep. Current Biology, 21(22), 1937-1941. DOI: 10.1016/j.cub.2011.10.014