An interesting, frightening and and at the same time, potentially hopeful, paper has just appeared in the latest issue of Proceedings of the Royal Society B.
Co-authored by a previously highlighted Conservation Scholar Georgina Mace, the paper by Boakes and colleagues entitled Extreme contagion in global habitat clearance is probably one of the strongest bits of [...]... Read more »
I have just read a Nature paper reporting some experimental work studying the pattern of decay in two soft-bodied species, Lampetra and Branchiostoma, which are thought to be the best proxies of the early chordates (chordates are the group of animals that includes the vertebrates and those invertebrates that are their closest relatives). The authors, Sansom et al. (2010), note that our understanding of the early evolution of the chordates is very sparse, in large part because the early chordates were entirely soft-bodied and are only rarely preserved, and in part because the interpretation of those soft-bodied fossils we do have is complex. It is especially hard to distinguish the earliest true chordates from their close, non-chordate relatives (called the "stem chordates"). They suggest that this might be rectified by better understanding of the sequence in which features of early chordates decay. In particular, we need to know whether the characteristics which characterise the true chordates decay relatively fast upon the death of their bearer, as if this is true, the partially-decayed true chordates will be misinterpreted as stem chordates, which they now resemble (Sansom et al. 2010).And, indeed, this is exactly what Sansom et al. found was the case. In their experiments, which tracked the order in which features of the two species decayed, those which were lost first were those which were most informative about the relationships between early chordates. As a result, the relative abundance of stem chordates in comparison with true chordates in the fossil record may be the result of the incomplete preservation of the crucial characteristics which would enable researchers to identify their real relationships.I think this paper is fascinating. At the same time, though, if it is true that the characteristics which are most informative about early chordate evolution are those which decay first, it is difficult to see how we will every sort the true chordates from their stem chordate relatives, barring finds of even more exceptionally preserved fossils than we already have from the relevant period. Despite this, knowing more about taphonomy (the processes of decay and destruction that affect dead organisms) can only inform our reconstructions of the evolutionary history of life, even if some parts of that history can never be fully resolved.ReferencesSansom, R., Gabbott, S., & Purnell, M. (2010). Non-random decay of chordate characters causes bias in fossil interpretation Nature, 463 (7282), 797-800 DOI: 10.1038/nature08745... Read more »
Sansom, R., Gabbott, S., & Purnell, M. (2010) Non-random decay of chordate characters causes bias in fossil interpretation. Nature, 463(7282), 797-800. DOI: 10.1038/nature08745
The brain is essentially an electric organ. Other than slow chemical signals that pass between neurons, information is carried around the brain by electrical impulses, creating a noisy storm that represents our senses, commands and thoughts. Experimentally, scientists can make some sense of this electric din by lowering an electrode into the brain and recording [...]... Read more »
Saleh, M., Reimer, J., Penn, R., Ojakangas, C., & Hatsopoulos, N. (2010) Fast and Slow Oscillations in Human Primary Motor Cortex Predict Oncoming Behaviorally Relevant Cues. Neuron, 65(4), 461-471. DOI: 10.1016/j.neuron.2010.02.001
Utah’s Dinosaur National Monument is best known for the exquisite collection of Jurassic-age fossils that have been discovered there since the beginning of the 20th century, but what is less well known is that more recent Cretaceous critters can be found there, too. When I visited the national park last summer I dropped by a [...]... Read more »
Chure, D., Britt, B., Whitlock, J., & Wilson, J. (2010) First complete sauropod dinosaur skull from the Cretaceous of the Americas and the evolution of sauropod dentition. Naturwissenschaften. DOI: 10.1007/s00114-010-0650-6
Over at Thoughtomics, Lucas has a post up about the evolution of mitochondrial import systems. He starts by going back in time two billion years:"Life was well underway at the time, with proto-bacteria already populating the oceans for over hundreds of millions of years. One of the cells alive at the time, swallowed an alpha-proteobacterium. Something remarkable happened: the alpha-proteobacterium did not die but survived in the host cell. Over time, the host and symbiont became to be dependent on each other." That symbiont became a mitochondria.He gets massive brownie point for writing 'proto-bacteria' rather than bacteria, and it is a very remarkable event to have happened. However from the point of view of a plant, it's only half the story, because plants carry two endosymbionts within them: the mitochondria and the chloroplast. Their stories are remarkably similar. After becoming engulfed by the surrounding cell, two major things happened to them: First (and it had to be first otherwise major problems would have arisen!) a protein import mechanism arose, creating more communication between the symbiont and the host and allowing things to pass between them. Second, the symbiont lost bits of its genome, transferring them into the nucleus of the surrounding cell to create the cooperative arrangement seen today:Picture above from the amazing science illustration gallery by California state University. Nucleus is purple, chloroplasts are green, and the mitochondria are orange. Lucas's post covered the evolution of the import mechanism for the mitochondria. I'm going to write about the same thing, but for chloroplasts. After all, the plants already have mitochondria so they can't use exactly the same import process, they have to be able to differentiate between the two.Like mitochondria, the chloroplasts are surrounded by two membranes, and outer membrane and an inner membrane. Two transporters are therefore required to get proteins across. In the mitochondria these are called TOM and TIM (Transport of Outer, and Inner Membrane respectively) and in the chloroplasts they are called TOC and TIC, just to keep things simple (Transport of Outer and Inner Chloroplast membrane). They look fairly similar to TIM and TOM, but recognise different sequences attached to the proteins. While the mitochondrial transport machines recognise sequences that contain a lot of the amino acid arginine and form a specific helical shape, the chloroplast machines (TOC and TIC) recognise sequences rich in serine and proline:TOC and TIC. The proteins of the TOC machine are coloured green, and the TIC machine proteins are all the rest. Diagram from here.One of the questions that Lucas asks in his post is: where did all of these proteins come from? After all, before you have an endosymbiont, you don't need any kind of apparatus to transport proteins into them. Once you start looking closer at the transport machinery it starts looking suspiciously like a rather rushed and last minute job. Different proteins with different functions have been cobbled together, and while there's still a bit of a debate as to whether these proteins came from the surrounding cell or the endosymbiont I suspect that it may be a bit of both. The cell needs to communicate with the little alien inside it, and once the endosymbiont started loosing genes, it needed a way to keep resources coming in.So how do you make a protein importer? What do you assemble it from? Plants had a slightly easier task with the chloroplasts as they already had a perfectly serviceable TIM/TOM transporter present. Looking at the TIC complex, the first two components to come in contact with the imported protein (TIC22 and 20, shown in the diagram above in dark purple and orange) show homology to components of the TIM machinery; TIM23 and 17 for anyone interested in the detail. However TIC22 also has far stronger homologues in cyanobacteria, which means it is likely to be a protein owned by the chloroplast, similar to the proteins owned by the mitochondria that got roped in to help with protein import.The TOC proteins (all green in the diagram above) all appear to have no other function in modern plants other than protein transport. Toc 34 is the GTPase, and as there are many GTPases in cells (used to provide energy) it could have arisen from any one of them. The other TOC proteins are involved in membrane and may have arisen from ancestral membrane receptor proteins, while some components, (including TOC64, not shown above) appear to be rather redundant, as the machinery works perfectly well without them.The research on this is a little sketchy, there are no good solid biochemical means as yet to discover what might of happened somewhere around two billion years ago in order to create a transport mechanism between the cell and it's organelles. There are plenty of different views out there as well, about where the different subunits might have come from. The only thing that seems clear is that like the mitochondrial import system, this was clearly pulled together from bits of old machinery lying around. It had two billion years to get better after all, and reach the efficiency of the modern-day protein import machines.---... Read more »
Gross J, & Bhattacharya D. (2009) Revaluating the evolution of the Toc and Tic protein translocons. Trends in plant science, 14(1), 13-20. PMID: 19042148
Insect control in Apiaries is really difficult. Your product is an insect which pollinates crops, and it’s very valuable. Strawberries, blueberries, peppers, broccoli…you name a food and it’s probably pollinated by honeybees. They’re valuable. Really valuable. Like you and I would be dead without them valuable. Using pesticides around your bee colonies is a really [...]... Read more »
J. D. Ellis, S. Spiewok, K. S. Delaplane, S. Buchholz, P. Neumann, and W. L. Tedders. (2010) Susceptibility of Aethina tumida (Coleoptera: Nitidulidae) Larvae and Pupae to Entomopathogenic Nematodes. The Journal of Economic Entomology. info:/
A recent article by Roger Byard in the Journal of Forensic Science about the potential forensic significance of herbal medicines (1) caught my attention. I was curious about the phrase “potential forensic significance”; what does that mean exactly? It became clearer to me when I read Byard’s recommendation that “the role of herbal medicines in forensic [...]... Read more »
Roger W. Byard. (2010) A review of potential forensic significance of traditional herbal medicines. Journal of Forensic Sciences, 55(1), 89-92. info:/10.1111/j.1556-4029.2009.01252.x
Not all species are equally important in the eyes of scientific research. As a new paper in the journal Conservation Biology shows, some types of species are much more commonly studied than others.... Read more »
Small farms may be better for tropical forests than intensive agriculture
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Perfecto, I., & J. Vandermeer. (2010) The agroecological matrix as alternative to the land-sparing/agriculture intensification model. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.0905455107
In 1997, a lineage of H5N1 bird flu was transmitted to a child in Hong Kong who died of respiratory problems. This was the first of a number of recorded cases of transmission of this virus from poultry to humans.
Since then, the world follows the circulation of this virus with concern. Although we associate it [...]... Read more »
Beigel JH, Farrar J, Han AM, Hayden FG, Hyer R, de Jong MD, Lochindarat S, Nguyen TK, Nguyen TH, Tran TH.... (2005) Avian influenza A (H5N1) infection in humans. The New England journal of medicine, 353(13), 1374-85. PMID: 16192482
Chen, H. (2006) Establishment of multiple sublineages of H5N1 influenza virus in Asia: Implications for pandemic control. Proceedings of the National Academy of Sciences, 103(8), 2845-2850. DOI: 10.1073/pnas.0511120103
Nutrient pollution could boost risk of some diseases
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Johnson, P.T.J. et al. (2010) Linking environmental nutrient enrichment and disease emergence in humans and wildlife. Ecological Applications, 20(1), 16-29. DOI: 10.1890/08-0633.1
“Give us this day our daily sunlight”, plants might pray, if they were Christian. Light is, after all, their main source of energy, captured by photosynthesis. But the machinery of photosynthesis isn’t always the best tool to detect light, and plants have an array of molecular sensors to detect small amounts of light in different [...]... Read more »
Land conservation not to blame for Silicon Valley housing prices
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Denning, C., Mcdonald, R., & Christensen, J. (2010) Did land protection in Silicon Valley reduce the housing stock?. Biological Conservation. DOI: 10.1016/j.biocon.2010.01.025
My wife is from a very large family. Inevitably at in-law gatherings, I find myself whispering into my wife’s ear, “How are you related to that person?” Unfortunately, my wife has never provided me a nice family tree so I can see how these dozens of people fit together. Much is the same for the [...]... Read more »
Miya, M., Pietsch, T., Orr, J., Arnold, R., Satoh, T., Shedlock, A., Ho, H., Shimazaki, M., Yabe, M., & Nishida, M. (2010) Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective. BMC Evolutionary Biology, 10(1), 58. DOI: 10.1186/1471-2148-10-58
It's almost a given that, during any discussion about male infidelity, someone will throw out some variation of "men are biologically programmed to spread their seed."Why is there this theory that men are more driven to cheat? Part of it has to do with the size of their gametes. If bigger is better, then men are pathetic, for their little sperm are 1/100th the size of a woman's egg. Because women have such a greater investment in each offspring right from the get-go, the assumption is that women are pickier when it comes to who they allow to fertilize their eggs. Men, since it doesn't cost them much anyway, are better off getting as many women to agree to let them fertilize. In mammals (like us), this difference in investment is further exacerbated by long, internal pregnancies and lactation, which place even more of the burden on the mother. It just makes so much sense - it's clear, simple, and like most biological explanations that are clear and simple, it's nowhere near the whole story.Even still, we've internalized this supposed biological explanation so much so that it's almost an excuse. In an article about why men cheat, for example, it's carefully explained that "The biological urge to mate with many different partners is stronger in men than it is in women" and that "males mate with multiple females to ensure the survival of the species." Well, I guess if it's to ensure the survival of the species... Perhaps, then, my female readers will appreciate a new study published in Current Biology which suggests that it's the women whose infidelity is important in ensuring species survival. Indeed, as they explain, females having multiple male partners may be vital in preventing extinction!Ever since the "spreading the seed" explanation for why males are so sexually liberal was proposed, there have been a few issues with it. The most glaring one was that in many animals, women, too, have multiple partners. Some species seem to have the roles reversed, where women are dominant and have harems of male suitors. Even in species that seemed monogomous, it turned out the women were cheating - in many species of monogomous birds, for example, females actively seek "extra-pair copulations" (ornithologist speak for affairs), and up to 75% of the chicks were being raised by males that were not their dad!Biologists began to realize that women, too, can benefit from sneaking around. In monogamous species, a female is stuck with whatever guy she gets to raise her young, even if isn't the biggest or the brightest. It's a shame, to her, that she can't have better babies, for surely her lackluster hubby's offspring will be less than ideal. Cheating, it was believed, gave a woman the best of both worlds. She gets to have a dedicated, loyal sub-par male take care of her young, but the young are born from better stock that she secured on the side. The problem is, nothing explained polyandry - a mating system where women have multiple "husbands" or partners. Considering that there is a higher biological cost to the female to mate, why would she ever want to have a permanent array of suitors demanding her attention? It seemed like there was something missing. Biologists Tom Price, Greg Hurst, and Nina Wedell believed there was more to the story.It turns out that the bigger picture may be genetic. Mutations in chromosomes can lead to what is called sex ratio distortion. There are certain alterations that, for whatever reason, cause the sperm containing either the X (female) or Y (male) chromosome to fail to fertilize. They are termed Sex-Ratio Distorter Genes or Chromosomes (SR genes or chromosomes) because they alter the balance of males to females in a population. Because mutations are constantly occurring, there is always a risk that all-male or all-female broods will be born, the result of which is potential extinction of a population or a species, if the altered gene becomes widespread. The team hypothesized that female promiscuity may help protect against SR chromosomes that develop in males. They tested their hypothesis using a known SR chromosome in the the fruitfly Drosophila pseudoobscura. This particular mutation, when carried by a male, causes all of his sperm that carry a Y chromosome to die before they can fertilize, though it has no clear effect on eggs when carried by females. Because it doesn't detriment female gametes, this kind of mutation can persist and spread until, eventually, not enough males are being produced to maintain a population. They created populations of fruitflies where 30% of the flies carried the SR mutation. They then had one population breed freely, where females mated with a number of males, while in the other, females were restricted to a male apiece. They bred these populations for several generations to see if there were any differences between the two.In just fifteen generations, almost half of the monogamous populations became extinct because there weren't enough men around. Meanwhile, none of the populations with the promiscuous girls died out. In the monogamous populations that survived, the SR chromosome was far more prevalent than in the polyandrous ones.Why did those populations fare so much better? It's likely the effect of sperm competition. When a female mates with many males, each of their sperm is vying to fertilize her eggs. Since the SR males produce half the sperm that normal males do, they've got an instant disadvantage in a system where they have to compete, meaning the damaging chromosome is less likely to spread.This study is the first to suggest that a polyandrous mating system could have evolved as a means to protect against sex-ratio distortion-induced extinction. Of course, extrapolating these results to other species is more difficult, so it's impossible to say that this study has any grand relevance to humans. It does, however, plant the seed of possibility that female promiscuity is a healthy and vital in a population. So boys, next time I hear you say that men are dogs because it's 'biological', expect to hear a lecture about how girls can sleep with whomever they want because it will save the species. Jus' sayin'.Price, T., Hurst, G., & Wedell, N. (2010). Polyandry Prevents Extinction Current Biology DOI: 10.1016/j.cub.2010.01.050
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The current issue of PNAS carries an interesting paper on the evolution of human limb proportions. The authors, Young et al. (2010), propose that one key change in the evolution of humanlike limb adaptations is a reduction in the strength of the developmental links between fore- and hindlimbs, and moreover, that this change actually occurred in a non-hominin ancestor we shared with other great apes.The quadrupedal primates, like most vertebrates, have strong serial homologies between their limbs. Each limb is composed of three units, specifically the thigh/arm, the leg/forearm and the foot/hand, which are, in most species, tightly coupled such that changes in the relative proportions of the parts of the hindlimb will bring about corresponding changes in the forelimb and vice versa (Young et al. 2010). Humans, in contrast, have differently proprtioned fore- and hindlimbs, with the patterns linked to their different functions in fine manipulation and bipedal locomotion respectively. In addition, the fossil record of human evolution suggests that the changes from the ancestral pattern occurred in an evolutionary mosaic, with fore- and hindlimbs changing independently and at different times, in response to separate selective pressures (Young et al. 2010).For me, the most interesting part of this article is not the proposal that the move towards weaker coupling of fore- and hindlimbs was important to human evolution (as this seems fairly straightforward, although interesting), but Young et al.'s suggestion that the change actually happened in a human-ape common ancestor rather than within the hominin clade. Many great apes do have functionally differentiated and differently proportioned fore- and hindlimbs, likely as the result of a reduction in the number of pleiotropic genes. Pleiotropic genes are those which influence more than one anatomical structure. This, to me, suggests we are justified in spending more time developing our understanding of the locomotor anatomy of the great apes.ReferencesYOUNG, N., WAGNER, G., & HALLGRIMSSON, B. (2010). Development and the evolvability of human limbs Proceedings of the National Academy of Sciences, 107 (8), 3400-3405 DOI: 10.1073/pnas.0911856107... Read more »
We've all experienced the agonising wait for feedback, whether it's for exam grades, news from a job interview, or results from a grant application. These verdicts can have a massive influence in our lives but they can often take weeks or even months to arrive. And that's a big problem, according to Keri Kettle and Gerald Häubl from the University of Alberta.
They have found evidence that we do better at tasks the sooner we expect news about our performance. If we think we'll be evaluated quickly, the threat of a negative appraisal looms ever larger. And this greater sense of danger motivates us to work harder.
Kettle and Haubl asked 271 students to give a four-minute presentation as part of a university course. Their performance would be judged by their peers and it would count towards their final grade. The students were told about the date of their presentation and when they would hear about the results, with waiting times ranging from a few hours to 17 days later.
The duo found that students who anticipated the quickest feedback achieved the higher grades. On average, those who knew they would hear back later on in the day scored within the top 40% of the group. Those who thought they would hear back 17 days later received scores that skirted the bottom 40%. It seems that even the anticipation of quicker feedback can boost performance.
To make sure that other events going on at the time weren't affecting the scores, Kettle and Haubl also asked some students to give presentations on the same day as their previous group, but without any advance warning about their results date (they're the "nonparticipants" in the graph). Without this knowledge, all the students scored equally well regardless of when they received their feedback.
However, neither set of recruits had any idea about the advantage of faster feedback. In fact, those who were prepared to find out their scores within the day grossly underestimated their scores, while those who settled in for a longer wait thought they would do much better than in reality. As Kettle and Haubl say, "People do best precisely when their predictions about their own performance are least optimistic!" The duo think that these poor predictions are a way of bracing ourselves for disappointment.
Kettle and Haubl's work certainly supports their hypothesis, but there's probably a bit more work to do here. For a start, the duo only did a single experiment; it would be good to see if the promise of swifter feedback improved performance under a variety of settings. Likewise, we often expect feedback to come at a certain point because of our experience, even if we aren't given any specific dates. Do these predictions affect our performance too?
There are a lot of questions to answer, but for the moment, it seems that seemingly trivial details as the date of a person's feedback could make a big difference to how well they perform at a task. Kettle and Haubl also point out that their results are directly relevant to people "who are responsible for mentoring and for evaluating the performance of others." If such performance is associated with snappy feedback, then managers and mentors might think harder about providing comments and criticisms to their staff more promptly.
Reference:Kettle, K., & Haubl, G. (2010). Motivation by Anticipation: Expecting Rapid Feedback Enhances Performance Psychological Science DOI: 10.1177/0956797610363541 If this link isn't working, read why here
More psychological goodies:
Clean smells promote generosity and fair play; dark rooms and sunglasses promote deceit and selfishness
Becoming better mind-readers - to work out how other people see you, use the right lens
People who think they are more restrained are more likely to succumb to temptation
The bigger the ego, the harder the fall - how self-awareness buffers against social rejection
The peril of positive thinking - why positive messages hurt people with low self-esteem
tweetmeme_style = 'compact';
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Kettle, K., & Haubl, G. (2010) Motivation by Anticipation: Expecting Rapid Feedback Enhances Performance. Psychological Science. DOI: 10.1177/0956797610363541
This is the fifth and last post in the CAPRI series, summarizing the presentations of Xiaoqin Zou and Ora Schueler-Furman (Saving the best for last..), as provided by the speakers. I hope the CAPRI series was able to give a snapshot of the state of computational protein-protein docking and its community. I want to thank again to everyone that took part in the meeting and helped me with this series.
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London N, Movshovitz-Attias D, & Schueler-Furman O. (2010) The Structural Basis of Peptide-Protein Binding Strategies. Structure (London, England : 1993), 18(2), 188-199. PMID: 20159464
Measuring scientific productivity is a concern at many different levels especially in terms for promotions and the competition brought on by limited funding sources. The area of life sciences is no exception to this; the National Institutes of Health (NIH) saw a flat budget between 2003-08. And even though the NIH will enjoy a temporary budget increase thanks to the Recovery Act and with President Barack Obama's 2011 budget request, there are no guarantees for what the future holds. The most common method for assessing the performance of researchers is by looking at a researcher's publication record and the journal impact factor of those the publications. A more recent development in quantifying research output is the h-index by Jorge Hirsch in 2005 that looks at scientific output also as a measure of publication citations. Bornmann and Daniel outline the methodology of the h-index and various concerns about using the metric in their 2008 publication. For those curious about their own h-index value, here is an h-index calculator built using Google Scholar. But what else do researchers do that could be seen as "scientific output" and how could these activities be measured? As a computational biologist, I have a specific interest in online databases, which often serve as the main sources of data for projects in my field, and ways that researchers could be encouraged to contribute to them. Jesse Schell, a Carnegie Mellon professor who teaches Game Design, recently gave a presentation at the Design Innovate Communicate Entertain (DICE) 2010 summit where he speaks about recent successes in game design in which games break into reality, drawing on ones' real social networks or achievement metrics that transcend individual games. Towards the end of the presentation, he imagines a world where one day we might earn bonus points simply by brushing our teeth or high-fiving friends. The video clip below shows the relevant segment and the full video can be found at G4TV. So what about the life sciences? Where are the scientific bonus points? One idea proposed by Martijn Van Iersel, a developer for Pathvisio and WikiPathways, as a Google Summer of Code project is the development of a Scientific Karma website. The proposal calls for some standardized and automated way for contributions to various online communities to be scored. The website would display a list of wikis and communities that researchers have contributed to and a contributor's score for that site. Active contribution to online databases is important as it enhances all of our understandings and access to larger datasets helps research projects draw better conclusions about increasingly complex biological systems. Bornmann, L., & Daniel, H. (2008). The state of h index research. Is the h index the ideal way to measure research performance? EMBO reports, 10 (1), 2-6 DOI: 10.1038/embor.2008.233... Read more »
Bornmann, L., & Daniel, H. (2008) The state of h index research. Is the h index the ideal way to measure research performance?. EMBO reports, 10(1), 2-6. DOI: 10.1038/embor.2008.233
This is a story about an event that took place 2 billion years ago. With the benefit of hindsight and a great deal of human bias, we could argue that it was one of the pivotal moments in the evolution of life on earth. What happened? Life was well underway at the time, [...]... Read more »
Clements, A., Bursac, D., Gatsos, X., Perry, A., Civciristov, S., Celik, N., Likic, V., Poggio, S., Jacobs-Wagner, C., Strugnell, R.... (2009) The reducible complexity of a mitochondrial molecular machine. Proceedings of the National Academy of Sciences, 106(37), 15791-15795. DOI: 10.1073/pnas.0908264106
Dolezal, P. (2006) Evolution of the Molecular Machines for Protein Import into Mitochondria. Science, 313(5785), 314-318. DOI: 10.1126/science.1127895
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