Showing posts with label Biol105. Show all posts
Showing posts with label Biol105. Show all posts

Wednesday, May 27, 2009

A new online collaborative learning space, and a scholarship opportunity

Via email from the Nature Publishing Group I just got word of a new online resource they've developed to help students learn genetics, and perhaps for teachers to teach the subject as well. Scitable is the NPG's new collaborative learning space for science, bringing together a library of scientific overviews with a worldwide community of scientists, researchers, teachers, and students. What's more, Scitable is even (for the moment, I hope forever) free! The first topic area with substantial content now online there is Genetics. Given how much time I spend on population genetics in my Evolution class, this promises to be a good resource for students needing a refresher to keep up with the class. And perhaps my colleagues teaching Genetics will find it useful as well.


And for students checking it out right now, there is also a scholarship being offered:



As a way of introducing students to Scitable, we are running a "Portrait of My DNA" contest that allows students to compete for one of three scholarships. ...



If the first place student is referred by you, your department will receive an additional scholarship of equal value to give to the student of your choice. You can learn more about the contest at http://www.nature.com/scitable/study-center.



So students, if you are still reading this blog even though the semester is over (for you anyway, although I'm still grading!), check the website out, and throw your hat in for the scholarship.



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Tuesday, May 5, 2009

Hmm... you want a study guide for the final exams?

Any questions?


song chart memes


see more Funny Graphs


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Wednesday, December 10, 2008

Why Sex?

Apropos of the recent steamy discussions in class about sex and evolution, Sonica Sangha shares this video she found on the PBS website:



[via Evolution: Library: Why Sex?]


And as a bonus, here's a behind-the-scenes video podcast accompanying the wonderful PBS Nature series "What Females Want and Males Will Do" which aired last spring. Click on the show titles for more fun video clips and information from the PBS Nature website.




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Wednesday, December 3, 2008

Modeling the emergence of multi-drug resistant TB hot zones

ResearchBlogging.orgRebecca Freeman submitted this essay for the Evolution class.



According to the World Health Organization (WHO), a “hot zone” is an area with >5% prevalence (or incidence) of Multi-Drug Resistant Tuberculosis (MDRtb). Sally M Blower and Tom Chou have been using a mathematical method to track the emergence and evolution of multiple strains of drug resistant tuberculosis, but they have now developed a new, more complex mathematical model. Before this model, there was only a two strain model, meaning it was only relevant to individuals that can be infected with a wild type pansensitive strain or a drug resistant strain, but there are many more strains then this. There are a resistant strains only to one drug and some resistant to multiple drugs. This means there is a multitude of strains in these hot zones and there was a need for a better way to track this (Blower and Chou 2004). Blower and Chou realized that a more complex mathematical model is necessary to capture the complexity of the epidemiology of the hot zones, and the evolution of hot zones was very unclear



Understanding drug resistance is important to understanding the, and Blower and Chou explain the evolving of resistance very well. They give three processes that are involved in generating drug resistance: Transmission of drug resistant strains to uninfected individuals, which is transmitted resistance; Conversion of wild pansensitive cases to drug resistant cases, which is acquired resistance; finally, cases where they have drug resistant strains and it becomes resistant to more antibiotics during treatment, which is amplified resistance. What everyone has had to do in the past is just study acquired and transmitted resistance, and now with the new model, they can incorporate amplification resistance. This was a big problem because it has been shown that inadequate treatment of DRtb can result in the amplification of drug resistant strains, which may be an important process of MDR epidemics (Blower and Chou 2004). So this is where Blower and Chou came in. They created a model, the call the amplifier model, that enables the tracking of emergence and evolution of MDR strains, the transmission of these strains and the amplification of these strains during repeated episodes of treatment.


Blower and Chou are really studying the effects of inadequate treatment programs, and how this may lead to a higher prevalence in MDRtb. One problem that this research cannot completely take into account yet is the transmittance ability of MDRtb compared to pansensitive tuberculosis. This is an area that is hazy right now, and so this cannot completely be incorporated into the model. Amazingly, they have measured a general fitness of MDRtb vs. pansensitive tuberculosis, by calculating the treatment fail rates and treatment cure rates of the each category of strains.



The authors were very clear with the purpose of the model. Even though the mathematical model is very complex, the idea and how they explain it is easily understandable. They use R0 to stand for the average number of secondary cases caused by one infectious case in a population where treatments are available. Their model breaks this up into four categories of strains: The wild type pansensitive [R0(1)], which is sensitive to all drugs; Pre-MDR [R0(2)], which is sensitive to one of the main drugs used to treat tuberculosis; MDR [R0(3)], which is resistant to both of the main treatment drugs; and post-MDR [R0(4)], which is resistant to both of the main antibiotics and others as well (Blower and Chou 2004). With the information gathered from over 30 years of date they constructed likely evolutionary trajectories of hot zones, and with this they also took into account low cure rates vs. high amplification probabilities in many areas. They also tried to incorporate which strains are more transmissible, but as I said before this was not really possible with their model and there was a large degree of uncertainty.



The results of their model matched the WHO predictions well, but there were some distinct differences, and I think these differences are what make this research so important. By using all for types (R01-4) they found great variability in incidence and prevalence. When treatments were originally started strains of pre-MDR strains emerged quickly, so incidence and prevalence of pre-MDR strains increased, and this subsequently led to possible amplification of resistance and MDRtb epidemics in certain areas. The question is: Why certain areas and not others? This question is explained by Blower and Chou. Interestingly, areas with bad treatment programs do not necessarily have a really high incidence of MDRtb, it has stayed pretty steady at a 5%-14% (Blower and Chou 2004). This to me seems like an argument that MDRtb is not as easily transmissible, because its rates overall have stayed pretty low, but there was no significant evidence for this. The WHO predictions state that a >5% prevalence OR incidence in MDRtb equals a hot zone. Blower and Chou found the mathematical relationship between MDR prevalence and incidence. MDR prevalence can be three times greater then MDR incidence. They used the results to evaluate the hot zones on prevalence or incidence. If it is by incidence then only 20% of those areas would be considered hot zones and 51% if criterion is prevalence (Blower and Chou 2004). I see this as an argument for the fitness of MDRtb to be very high and transmissible ability to be lower, because there are less new cases, and more cases that have just become more resistant.



When looking at the four strains the hot zones had a much lower R0 for pansensitive strains (median=.82), which suggests that the wild type strain should be slowly eradicated. The R0 for the pansensitive strains in non-hot zones were all above 1 (median=1.39) Looking at the rate of detection of cases and treatment rates in hot zones versus non-hot zones it is 55% to 25% (Blower and Chou 2004). This shows that places where they have control programs were successful at fighting pansensitive strains but ironically it created more MDRtb strains, making it more likely to become a hot zone.



The importance of this research is that they have figured out that the difference between incidence and prevalence rates is significant enough to change the view of an area as being a hot zone or not. Their research looks at many factors that go into the evolution of these hot zones. Out of the many factors they actually saw that case detection and treatment rates were the most important factors. They came to this conclusion because if case detection and treatment rates were low, and the amplification was high, it still did not generate a hot zone. Vise versa, if the case detection and treatment rates were high and the amplification rates were low; it was likely to become a hot zone. The point is that these areas with high case detection and treatment rates should not increase these rates unless high cure rates are achieved first. Blower and Chou have created a model that has multiple dimensions and can help the WHO in the future to prevent hot zones from popping up in high risk regions. The WHO already had a model for this but it was nowhere complex enough to correctly calculate prevalence and incidence of MDRtb, and how their mathematical relationship.


Reference:



Sally M Blower, Tom Chou (2004). Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance Nature Medicine, 10 (10), 1111-1116 DOI: 10.1038/nm1102




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Monday, December 1, 2008

On the Origin of Species - revisited via the ghost of Asa Gray

As you are probably aware, especially if you are a student in my Evolution class, Charles' Darwin's seminal work "On the Origin of Species by Means of Natural Selection" has just passed a significant milestone: its 150th birthday in print! As you may also have noticed, a number of print and online publications and websites have been marking the occasion in various ways; some I have bookmarked for sharing here, but haven't gotten around to as yet!


At the beginning of the semester (as I do every semester), I had asked you students to approach the book through as fresh (even naive) a perspective as you could muster, setting aside any preconceptions and trying to put yourself in the mind of an educated person in 1859 getting your hands on the book for the first time, hot off the presses. That, of course, is easier said than done; especially when in class we are surveying the latest discoveries and insights from evolutionary biology. How can one erase 150 years of scientific progress on the question from one's memory? I'm presuming, of course, that at least some of that accumulated wealth of knowledge from these 150 years has trickled down into your consciousness through your various classes (and despite perhaps your best efforts!). Well, I hope most of you have made it at least most of the way through the wonderful (if tedious to some modern eyes) book. If so, you will appreciate this classic review, reprinted by The Atlantic Monthly where it was first published in 1860 upon the book's maiden voyage across the pond to the American market, and written by Asa Gray, the eminent botanist, contemporary and close correspondent of Darwin himself. Here's a wikipedia excerpt about the two men:

Corresponding with Charles Darwin, Gray was helpful in providing information for the development of Darwin's theory on The Origin of Species. Gray, considered by Darwin to be his friend and "best advocate", also attempted to convince Darwin in these letters that design was inherent in all forms of life, and to return to his faith. Notwithstanding, Gray was a staunch supporter of Darwin in America, and collected together a number of his own writings to produce an influential book, Darwiniana. These essays argued for a conciliation between Darwinian evolution and the tenets of orthodox Protestant Christianity, at a time when many on both sides perceived the two as mutually exclusive.

That should prime you to go read the review, which is pretty sharp and honest, starting on this cautious note:

Novelties are enticing to most people: to us they are simply annoying. We cling to a long-accepted theory, just as we cling to an old suit of clothes. A new theory, like a new pair of breeches, ("The Atlantic" still affects the older type of nether garment,) is sure to have hardfitting places; or even when no particular fault can be found with the article, it oppresses with a sense of general discomfort. New notions and new styles worry us, till we get well used to them, which is only by slow degrees.


Wherefore, in Galileo's time, we might have helped to proscribe, or to burn had he been stubborn enough to warrant cremation-even the great pioneer of inductive research; although, when we had fairly recovered our composure, and had leisurely excogitated the matter, we might have come to conclude that the new doctrine was better than the old one, after all, at least for those who had nothing to unlearn.


Such being our habitual state of mind, it may well be believed that the perusal of the new book "On the Origin of Species by Means of Natural Selection" left an uncomfortable impression, in spite of its plausible and winning ways. We were not wholly unprepared for it, as many of our contemporaries seem to have been. The scientific reading in which we indulge as a relaxation from severer studies had raised dim forebodings. Investigations about the succession of species in time, and their actual geographical distribution over the earth's surface, were leading up from all sides and in various ways to the question of their origin. Now and then we encountered a sentence, like Professor Owen's "axiom of the continuous operation of the ordained becoming of living things," which haunted us like an apparition. For, dim as our conception must needs he as to what such oracular and grandiloquent phrases might really mean, we felt confident that they presaged no good to old beliefs. Foreseeing, yet deprecating, the coming time of trouble, we still hoped, that, with some repairs and make-shifts, the old views might last out our days. Après nous le deluge. Still, not to lag behind the rest of the world, we read the book in which the new theory is promulgated. We took it up, like our neighbors, and, as was natural, in a somewhat captious frame of mind.

and towards the end, warily acknowledges the "uncanny look" as well as the "mischief" of the book:

So the Darwinian theory, once getting a foothold, marches boldly on, follows the supposed near ancestors of our present species farther and yet farther back into the dim past, and ends with an analogical inference which "makes the whole world kin." As we said at the beginning, this upshot discomposes us. Several features of the theory have an uncanny look. They may prove to be innocent: but their first aspect is suspicious, and high authorities pronounce the whole thing to be positively mischievous.

Doesn't that make this your must read essay of the week?


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Friday, November 7, 2008

When a Cutthroat meets a Rainbow

ResearchBlogging.orgSubmitted by Christopher Clapp for the Evolution class.

The introduction of a known species of rainbow trout into a native population of cutthroat trout and the consequences of their contact within their environments is the focus of this study. The interaction of these two species has resulted in their study of subsequent progeny shows hybridization of the two, and thus a decline of the natural populations of cutthroat trout. The implications of this hybridization will show throughout subsequent generations, considering what is known of the native species. Metcalf uses mitochondrial and nuclear markers to determine the levels of crossing of the two species based on the nature of homozygous or heterozygous allele category. These populations of hybridization were evaluated due to the known history of the streams being studied. Trout being separated by natural geographic restrictions such as natural waterfalls or by human chemical treatment conducted in the past forms for a basis of evaluation.

The successful progeny of hybridization between the two locations is evident; however there are differences between the chemically treated streams and the naturally restricted. Interestingly enough, results show that there is a trend of the cutthroat nuclear trout alleles being more prevalent beyond the upstream barrier as expected. The mitochondrial alleles were more prevalent within the hybrid or rainbow species within the areas that direct contact has been introduced within the natural barrier stream. Our study supports the notion that natural waterfall barriers provide a refuge for pure native cutthroat trout genomes across their range (Metcalf et al 2008). In the Cony Creek population, which was subject to chemical treatment in 1984, the nuclear markers were more prevalent within the cutthroat species. This bias toward the pure cutthroat is speculated to be due to the chemical treatment of the streams to eradicate the rainbow trout populations amidst restocking the cutthroat population (Rosenlund et al. 2001). Why is the case? The allele frequency distributions and disequilibrium values suggest that hybridization has been underway for longer in Cony Creek than in Graneros Creek according to Metcalf, et al (2008). I seem to feel that introducing a chemical treatment to an environment that focuses directly on one specific species allows for a re-founding of the native species. However, there findings show the invasiveness nature of the rainbow species. Over time the cutthroat nativity would be eradicated regardless of natural barrier or chemical treatment. This poses two major problems for the environment with regard to the natural species, and the changes of fish populations within streams. The introduction of new fishes for conservation strategies not only directly affect the native population, it affects the ecosystem among other animals within the environment as well. If an aggressive population of trout that is more successful than the native, the impact on resources for the community will also be affected; the environment will be in disequilibrium.


We seem to have two intrusions of the human hand into an environment, one for the introduction of the rainbow, and one to eradicate the rainbow trout species. The study shows that there is greater fitness among the hybrids. The cross between a rainbow trout female and a cutthroat male resulted in a shorter time to hatching and the progeny had a faster growth rate and a greater abundance of yolk at hatch and emergence than the hybrids of the reciprocal cross (Hawkins and Foote, 1998). Nevertheless, the two species form a system of fertility to study the hybrid selection based on natural selection and/or the effects of human based effects in the form of conservation strategies. What is this to say for the natural selection of the hybrid species or the difference between the two, and what are the effects of the introduction on the environment? Historically fishless lakes and streams have been associated with declines in amphibians, changes in invertebrate communities and changes in nutrient cycling (Knapp and Matthews, 2000). However, there is always something to be learned from the development of a new species. The selection and fitness over such a short amount of time is interesting to evaluate within the two species.


It seems to be that the rainbow trout are invading the natural species of cutthroat, and have an effect on the native species. Why are the rainbows so successful at invading this species? What are we to learn of the intrusion of populations by human hands? Either way, I agree with Metcalf in the capacity that the evaluation of the new hybrid species will give insight into long-term conservation strategies. It seems that if we limit the studies and only hold them as individuals there will always be contradiction of the results. Conservation methods and steps may be a bit naĂŻve if you only consider one method to achieve one result. By not considering the whole picture, we are increasing our opportunity cost, and thus the potential for loss.


References:


Denise K. Hawkins, Chris J. Foote (1998). Early survival and development of coastal cutthroat trout (Oncorhynchus clarki clarki), steelhead (Oncorhynchus mykiss), and reciprocal hybrids Canadian Journal of Fisheries and Aquatic Sciences, 55 (9), 2097-2104 DOI: 10.1139/cjfas-55-9-2097


Roland A. Knapp, Kathleen R. Matthews (2000). Non-Native Fish Introductions and the Decline of the Mountain Yellow-Legged Frog from within Protected Areas Conservation Biology, 14 (2), 428-438 DOI: 10.1046/j.1523-1739.2000.99099.x


J. L. Metcalf, M. R. Siegle, A. P. Martin (2008). Hybridization Dynamics between Colorado's Native Cutthroat Trout and Introduced Rainbow Trout Journal of Heredity, 99 (2), 149-156 DOI: 10.1093/jhered/esm118


Rosenlund BD, Kennedy C, Carnowski K. 2001. Fisheries and the Aquatic management of Rocky Mountain National Park. (US Dept. of the Interior).




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