Tuesday, May 6, 2008

Samurai Crab

Submitted by Nasir Sadeghi.


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Heikegani crabs of Japan have markings on their carapace that resemble a human face, the face of a medieval samurai to be exact. It is locally believed that these crabs are reincarnations of the spirits of the Heike warriors defeated at the Battle of Dan-no-ura as told in the >Heike Monogatari ("The Tale of the Heike"). It is believed that when caught, these crabs are not eaten, but are thrown back into the water because if they're resemblance to a human face. This raises a question: how could the face of a samurai end up on the carapace of a Japanese crab?


It is thought that from the first crab that had a carapace shaped remotely like a human face, it was thrown back into the water, and thus humans were applying artificial selection on the crabs. Fishermen were probably reluctant to eat a crab with a human face, and because of this, these crabs were selected for, and thus this phenotype was passed down the hereditary line. Over the generation of interaction between humans and these crabs, the crabs with patterns resembling the samurai face preferentially survived. None of this involves the crab making a conscious decision about its carapace pattern (Lamarkian Evolution), but it is the artificial selection being imposed on the crabs from the outside that is responsible for this phenomena.



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Monday, May 5, 2008

Framing Global Warming @ Café Scientifique tonight

Just a quick reminder that tonight we have another meeting of the Central Valley Café Scientifique:


How the News Media Frame Global Warming: A Harbinger of Human Extinction or Endless Summer Fun?


Dr. Andrew Jones, Assistant Professor, Department of Sociology, CSU-Fresno


Monday, May 5, 2008, 6:30-8:30 PM @ Lucy’s Lair.


Read more about it on the cafe website, and please join us for another fun evening!



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On Sloths

Heidi Rivera contributed this post


I did my term paper on sloths and I thought that I would share some interesting information that I learned while completing the paper starting with this short video.



As you can see from the video, current extant, tree-dwelling sloths that are put on land are very slow moving. Its hind limbs provide almost no help in propelling it forward and its long claws get in the way. On land, sloths have to dig their claws into the ground and drag their bodies with their stronger front limbs to move. They can move more easily on the ground if they have leaves, roots or branches to grasp. Although sloths have great difficulty moving on land, they are very efficient swimmers.


Habitat


Sloths inhabit the lowland tropical forests of Central and South America. Bradypus variegates can be found in Central and South America from Honduras to northern Argentina. Bradypus tridactylus is found in South American, and Bradypus torquatus is confined to a small Atlantic forest of southeastern Brazil (National Geographic 1996). There current extant sloths can be found in the tropical canopies sunbathing, eating or resting. Their bodies are built for life in the treetops. They spend most of their time hanging from tree branches and are able to do so because of their long sharp claws and very strong grip. This grip is so powerful that dead sloths have been known to retain their grip and remain suspended from a branch. Sloths also sleep in trees and are known to sleep for 15 to 20 hours a day. In general, sloths are nocturnal, and when they are awake at night, they eat. They go down to the ground only once a week to urinate and defecate (Britton, 1941)


Appearance


The two species of two-toed sloths are distinguished by the color of the fur on their throat. Choloepus didactylus has a dark colored throat whereas the Choloepus hoffmanni sloths have a pale gray to white colored throat (Crawford 1934). The four species of the genus Bradypus can also be distinguished from one another. B. variegates has brown fur on its throat and B. torquatus has dark fur on its throat. In comparison, B. tridactylus has pale fur on its throat. B. pygmaeus is distinguishable from others because it is significantly smaller in size. Both genera of sloths have long, thick hair that allows them to be camouflaged in their surroundings so that predators, such as jaguars and eagles have difficulty finding them. During the rainy season, some species of sloths develop an incrustation of symbiotic cyanobacteria on the surface of their hair. This offers the hosting sloth additional camouflage with its surrounding area, providing even more protection from predators (Muizon 2004).


Two-toed sloths are a little bigger than three-toed sloths. The two-toed adults are approximately 24 to 27 inches long, and can weigh about 17.6 pounds (National Geographic 1996). In comparison, the three-toed adults are approximately 23 inches long and on average weigh only 8.8 pounds (National Geographic 1996). Both species of sloths have a flat, short, rounded heads, large round eyes, a snub nose and highly reduced ears. The three-toed sloths have a short, stumpy tail whereas the two-toed sloth’s tail is absent or vestigial (Gaudin 2004).


Sloths are characterized by the number of long claws that they have on each front foot. The three-toed sloths have three long, curved sharp claws on all four limbs, while the two-toed sloth has two long claws on its front limbs and three claws on each of its hind limbs. Sloths have very long limbs, the front limbs being longer than the hind limbs. These long limbs are useful for suspending from tree branches, which they do for the majority of the day. Sloths are mostly nocturnal; however, they can be active in the day as well. They only spend about ten percent of their time moving, making them the world’s slowest mammal (Crawford 1934). Their lack of movement helps them to stay camouflaged with their surroundings and helps them to avoid any potential predators.


Another difference between two-toed sloths and three-toed sloths is the number of vertebrae they have. Most mammals have seven neck vertebrae but two-toed sloths have only six or seven (depending on the species) and three-toed sloths have eight or nine (depending on the species). Having eight or nine vertebrae allows these sloths to turn their head through a 2700 arc (National Geographic 1996). The benefit of their specialization is not fully understood.


I hope you guys enjoyed learning a little bit about one of my favorite animals!


References:


Britton, W. S. 1941. Form and Function in the Sloth (Concluded). The Quarterly Review of Biology. The University of Chicago Press. Vol. 16:190-207


Crawford, C. S. 1934. The Habits and Characteristics of Nocturnal Animals. The Quarterly Review of Biology. The University of Chicago Press. Vol. 9: 201-214


Gaudin, T. J. 2004. Phylogenetic Relationships Among Sloths (Mammalia, Xenarthra, Tardigrada): The Craniodental Evidence. Zoological Journal of the Linnean Society. Vol. 140: 255-305


Muizon, D. C., H. G. McDonald, R. Salas, and M. Urbina, 2004. The Youngest Species of the Aquatic Sloth Thalassocnus and a Reassessment of the Relationships of the Nothrothere Sloths (Mammalia: Xenarthra) Journal of Vertebrate Paleontology. Vol. 24: 387-397


National Geographic. 1996. Sloths.




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Evolution of drug resistance in TB

Student post submitted by Pritha Singh


ResearchBlogging.orgIn the article “Evolution of Drug Resistance in Mycobacterium tuberculosis: Clinical and Molecular Perspective”, the author Stephen Gillespie describes the clinical circumstances and the molecular mechanisms that are involved in the emergence of drug resistance in tuberculosis (TB). Even after so many years of introduction of very effective drug therapy for TB, the number of people infected worldwide is still increasing due to the development of drug resistance. The basic tool that the medical community has used to control this deadly disease is the combination therapy that uses antibiotics like isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), ethambutol (EMB) and streptomycin (SM).


The author first describes the clinical circumstances for the resistance development in Mycobacterium tuberculosis. He states that the reason why drug therapy for tuberculosis is different than the most bacterial infections is due to the long generation time and ability of dormancy in M. tuberculosis. Apart from this, it has a very slow metabolic rate which makes it difficult to target. There are many different populations of the bacterium present within the host. M. tuberculosis may be found in the pulmonary cavities, empyema pus and solid caseous material. The location of the bacterium makes it very difficult for the antibiotics to penetrate or the low pH conditions interfere with the activity of the anti-TB drugs. Thus each of the anti-TB drugs has a unique role in dealing with these different populations of mycobacterium. For example, INH is a drug that is active only against aerobically growing organisms and so it plays a major role very early in the drug therapy against bacteria growing in pulmonary cavities. On the other hand, PZA is a drug only active in low pH conditions thus is used for killing bacilli residing inside the caseous necrotic foci. RIF is most effective in killing the mycobacterium that are metabolizing slowly. Hence, due to the specific roles of these drugs, poor adherence to the drug therapy can result in resistant strains in mycobacterium.


Gillespie goes on to explain the molecular mechanism for the emergence of drug resistance. The way the researchers have started to understand the molecular mechanism of resistance in M. tuberculosis is from the action of these anti-TB drugs. The resistance in this bacterium occurs through single step mutations at the chromosomal level. He states that rate at which resistance emerges is different for all the anti-TB drugs which could be calculated by using the mutation rate. Mutation rate rather than mutation frequency is used to calculate the rate of resistance because calculating frequency has a risk of recording mutation per cell division. However, mutation rate is more apt as it records the proportion of the mutant cells. The author provides an equation and hypothetical calculations for resistance rate in the mycobacterium which suggests that even a small deviation from the standard drug regimen may lead to the emergence of resistance in a TB patient.


To describe the development of drug resistance in M. tuberculosis, the author talks about two anti-TB drugs: streptomycin (SM) and rifampin (RIF). A point mutation in rpsL gene results in high level of resistance to SM which can be categorized into restrictive and nonrestrictive mutations. Restrictive mutations are associated with an attenuation of virulence, whereas nonrestrictive mutations are not. He lists various clinical studies that show that resistant strains were equally divided between restrictive and non-restrictive mutations. However, the author does not explain how SM works on the bacterium or how the mutation in a specific gene leads to resistant strains which could have helped in better understanding of this section. Moreover, he does not mention an additional mutation that takes place in rrs operon which could also lead to drug-resistance.


The mycobacterium strains that are resistant to RIF have a mutation on the beta subunit of rpoB gene encodes for DNA-dependent RNA polymerase. Experimental studies have shown that more than 70% of the RIF’s mutations are restricted to the rpoB gene. He also mentions the study conducted by using the model of guinea pigs that were infected with M. tuberculosis in which katG gene was inactivated. These studies showed that the virulence of the strains was far less than the parent strain. However, the virulence was restored when katG gene was reintegrated in the genome. The author does a fair job in stating the clinical studies, however does not mention anything about the drug mechanism. KatG gene encodes for enzymes that are involved in mycolic acid biosynthesis but there was no mention of how mutation in katG gene is what leads to the INH resistance.


Lastly, the author mentions about human studies of resistance emergence. He mentions a report in which a brother and a sister suffered multiple drug resistance due to non adherence to the drug therapy. This case provides the evidence that variation in biological fitness has an affect on outcome of the therapy. In this study, the bacterium in one case showed multiple-drug resistance (MDR) whereas in the other case, it was completely susceptible which suggested that fitness deficit was directly related to the difference in susceptibility. However, Gillespie also mentions that multidrug-resistant M. tuberculosis strains with identical susceptibilities have different in vitro fitnesses. He provides data of a study conducted on an infected human female that suggests that changes occur on passage in humans. Since initially resistant strains have a fitness deficit, transmission of the organism in a group of immunocomprised people may allow the bacterium to adapt and be transmitted while adapting. This also agrees with previous studies that show MDR numbers have increased in immunocomprised patients.


The author ends his articles by stating that these molecular and clinical studies have shown that resistant organisms over time can become fully virulent. Thus to prevent the multi drug resistance tuberculosis, steps must be taken that patients are effectively treated. Drug-resistance is a major threat to human population and to stop these numbers from rising, it is important to understand the mechanisms of resistance development in this organism. Treatment with internationally approved regimens is very effective in preventing the resistance development. This is due to the fact that combination of drugs involved in the therapy makes it very unlikely for spontaneous mutations to occur to all the antibiotics involved. Inadequate treatment of tuberculosis or treatment with only one type of drug can lead to resistant strains. When these strains that are resistant to single agents are exposed to the combination drug therapy, the effectiveness of the drug therapy is depleted which further leads to multiple-drug resistance.


The author of this article Stephen H. Gillespie is a Professor of Medical Microbiology at University College London. He has done a lot of research in the treatment and diagnosis of tuberculosis and other respiratory infections. The author provides plenty of reference articles and studies to refer for further clarification for the reader. He backs up his statements with evidence collected from various research studies. However, the author’s use and interpretation of the evidence was unclear to me in many sections. To wrap up, my opinion of this article is that it was very difficult to follow at times and the author should have included some basic information about the drug action on the mycobacterium before talking about the gene mutations that lead to the drug resistance.


Reference:


Gillespie, S.H. (2002). Evolution of Drug Resistance in Mycobacterium tuberculosis: Clinical and Molecular Perspective. Antimicrobial Agents and Chemotherapy, 46(2), 267-274.


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Sunday, May 4, 2008

Pheasant Sexual Selection





Kara ward shares this video follow-up to the recent classroom discussions of sexual selection.



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Impressions from the Central California Research Symposium

Kara Ward shares her experience attending the 29th Annual Central California Research Symposium held recently on campus.


Overall Impression:


The 29th annual CCRS symposium, held at Cal State-Fresno, was without doubt an experience to remember. Although I cannot say that it was my preferred activity for the afternoon, I can definitely say that when I left the symposium I had acquired a greater knowledge of how many undergraduate and graduate science talks and public presentations progress. I myself have not attended many of the weekly Friday Biology seminars they have here at Fresno State so it was definitely a treat to attend this symposium and I was actually very interested in seeing work produced by my peers.


Out of the six presentations that were actually presented to us, it was apparent that each presenter had a different angle and strategy in the planning and preparation of his or her presentation. Of the six presentations, a few presenters actually did an excellent job in presenting their topic thoroughly in the sparse time allotted to them. These few presenters stood out because of their ability to utilize all of their skills to present a complete presentation. Others, however, failed in many areas such as utilizing their allotted time efficiently, in using the correct grammar and speech necessary to give a public presentation, and most importantly, in presenting the material and data in a manner that we the audience could understand. It is my opinion that these presenters would defiantly [sic] benefit from more practice and possible lessons in how to give public presentations. I can definitely understand that they had to present a lot of information and data in a very short time, but more practice on the presentation itself may have produced much smoother delivery and pace. It was apparent that many of the presenters were nervous and a public speaking course could and would serve them well. Overall my assessment of this symposium is fair, and based on my experience attending this symposium, I would positively attend next year should I be afforded the opportunity and recommend that all science majors do the same.


Critique 1: The Identification of Brachyuran Megalopae of the San Francisco Bay Estuary


Presented by: Vanessa Gonzales


I chose this presentation to critique because I had heard a few things about the Chinese mitten crab in prior classes; however I had never actually been presented with such detailed facts about the crab’s lifecycle and I was extremely intrigued by it. I liked the flow of the presentation and appreciated how she began her talk explaining the problem before going into the details of the experiment. I thought Gonzales did and great job of explaining how the presence of the crabs negatively affected the habitat by competition with and predation of some of the native species; however, I would have liked her to speak a little more about some of the native species which were affected. I also thought that the presenter did an excellent job of providing graphs, charts and tables which illustrated the facts and stressed the points that she was trying to make. As I stated earlier, I feel that the presenter did a great job of going through all of the important stages in the life cycle of the crab. This background information would be vital to know prior to being able to understand the full extent of the problem at hand as well as understanding how the experiment was set up and I feel that she was wise to include it. As the presentation continued and Gonzales entered the research portion of the presentation, I felt that she entered into somewhat of a read and speak mode. By read and speak mode I mean that it almost seemed like she was just reading lines from her note cards and it was apparent that she may have gotten lost in her notes, because between every sentence she would say phrases akin to “um” and “like”. Aside from these minor areas, I felt that the presenter did a good job of presenting the information in an organized manor. The presentation flowed and each section was explained well by Gonzales who utilized her time well.


Critique 2: Potential Impacts of Selenium on California Red-Legged Frog (Rana draytonii)


Presented by: Foung Vang


I chose this presentation to critique because I had never heard of the primary organism of this study, the Red-Legged Frog, and just the name was enough to warrant my interest. After reading the abstract, provided by the presenter, my initial thoughts went to the Zebrafish experiment we conducted in our Developmental Biology lab in which we treated the fish with varying amounts of ethanol. Based on my experiences with the Zebrafish lab, I knew that most experiments monitoring early development are quite interesting and could really go either way so I was definitely interested in seeing the outcome of this experiment. Overall I felt that there were some strong areas of the presentation as well as some weak areas. The weak areas in the presentation for me, was the lack of background information on the frogs as well as the lack of graphics and illustrations. Where the presenter did a great job of providing us with a background of selenium and the issues presented by selenium in the environment, he hardly spoke at all about the history and life cycle of the frogs. It almost seemed as if the presenter was too eager to begin the discussion of the hypothesis and results section of the experiment, but in doing so, the presentation came off as being unbalanced and dry. Although this lecture presented a lot of facts and data, I still felt as if something was lacking in the overall presentation. Perhaps the problem for this presenter was merely a time management issue, trying to put too much information in a twelve minute presentation; however, this should not be an excuse. My overall assessment of this talk was that it was very informative and the presenter was well spoken, however, I still would have preferred a little more background information on the target organism as well as a little more visual stimulation.



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Permission to act like a monkey!

Nasir Sadeghi shares this video with the class.



here is a video for some laughs. this person uses obscene and irrational arguments to rationalize intelligent design, and thus blaming everything on SATAN. He decides to mock evolution by comparing it to "the evolution of a knife into a fork". this is a prime example of taking things out of context, and later using them in a matter to one's own advantage (in this case, it didn't really work, but it does give people all over the world something to point and laugh at). either way, hope you all enjoy this as much as i did!


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Thursday, May 1, 2008

The real reason Republicans oppose stem cell research

...and the Democrats are unable to do anything about it:

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Did chimpanzees learn tool use from humans, or did humans learn from chimpanzees?

Amanda Scott has a different take on the tool using Chimpanzee story written about by Scott Brown, and seen in this video

ResearchBlogging.orgToday we know that chimpanzees use tools such as modified sticks and rocks to assist in their feeding. Rocks are used to crack open shells of nuts or seeds. Today fossil remains in Tai National Park have been identified as chimpanzee tools. Physical characteristics that distinguish them as being products of thrusting or percussion separate them from the other rocks in the area. Furthermore, starch found stuck to some rocks are said to prove that the rocks were used in feeding. These fossils predate known human inhabitants in the Tai National Park.


These geofacts found date back 4,300 years. Since humans did not inhabit the area before then, we are left wondering how chimpanzees learned their stone-age technology. This evidence suggests that either chimpanzee stone-age and humans stone-age took place at approximately the same time, or that chimpanzees evolved their tool using abilities independently (without watching or learning from) humans.


The study classified the area the artifacts were found in as “muddy sands” by an Ingram – Wentworth model that shows “pebble, cobble, and boulder sized rock fragments would be naturally lacking” (Mercader). Examiners proved their ability to distinguish between geofacts and other rocks by analysis of rocks collected from Canadian glacier sites mixed amongst rocks from a proven behavioral site. Scientist examiners were in 90% agreement at to which stones were geofacts. Additionally starch residues found on the geofacts are said to be remnants of the food the chimpanzees consumed.


This interesting study based its hypothesis, results, and conclusions on what we know today. Today chimpanzees are observed to use mostly granitoid as well as laterite, diorite, feldspar, and quartz. This information was used to show that the choice of stone in the mid- Holocene atones mirrored modern day choices in the Tai forest.


Additionally the authors admit that the starch residue could be from root growth or anything that came into contact with the stones in the last few thousand years, however they included “all nut and tuber species relevant to modern hominid starch use plus other species present in the study area” for analysis by examiners. 37% of the residues on the rocks matched one of these plant materials. All three examiners only agreed on classification for the starch grains 48% of the time.


Blind testing showed examiner’s ability to distinguish the rocks used for thrusting or percussion, from any other rock, to have accuracy values of 65%, 75%, and 90%. Examiners distinguished between different rocks by logical reduction patterns such as radial cores vs. systematic flaking. “Because chimpanzees have not yet been observed to flake stone intentionally it is unquestionable that human lithic reduction is present…the possibility that humans could be the sole culprit of our stone collections must be carefully examined.” Basically the authors argue that the large sizes of some stones are more comparable in size to the hand of a chimpanzee and therefore some must be from chimpanzee origins.


From reading this article I can conclude that the authors have much more work to do and that this paper is based on one hypothesis. I don’t disagree with their overall conclusions, however their assumptions based on current plants and rocks as well as the marginal agreement between examiners is not entirely convincing.


Reference:


Mercader, J., Barton, H., Gillespie, J., Harris, J., Kuhn, S., Tyler, R., Boesch, C. (2007). 4,300-Year-old chimpanzee sites and the origins of percussive stone technology. Proceedings of the National Academy of Sciences, 104(9), 3043-3048. DOI: 10.1073/pnas.0607909104


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Predicting insecticide resistance

Student post submitted by Philip Lockton

ResearchBlogging.orgThis article is a good example of the effects of evolution on current day pests and parasites. In regards to pest management, pesticides and insecticides have been developed in the last century to deter the effects of parasitic damage. In agriculture, insecticide use is critical in managing and controlling both crop and livestock production. The development of chemical insecticides has allowed humans to produce more reliable agricultural goods with greater quality and quantity. However, with the increased use of insecticides arises another problem, which is ‘insecticide resistance.’ The article talks about insecticide use on sheep, which is intended to control ectoparasites. With persistent use of chemical agents, resistance can evolve in an organism. This article addresses the concept of predicting such resistance mechanisms.


Many strategies have arisen to manage resistance to particular insecticides. Although, as the article notes, management strategies to resistance of a particular insecticide are typically devised after the resistance has already evolved. The goal is to be able to predict and correct possible resistance problems before they ever occur. This would allow us to manage susceptibility in various organisms.


In sheep, a common ectoparasite is the Australian sheep blowfly, Lucilia cuprina. Sheep are used in agriculture for their wool primarily. Lucilia cuprina agitate the dermis of the sheep causing the fur (wool) to fall out or become discolored or damaged causing quality to drop. Management of this problem has been done by the use of insecticides. Using Lucilia cuprina in lab, blowflies were introduced to insecticides such as dieldrin, diazinon and malathion. These were then compared to previously evolved flies (resistant) from a natural population in order to predict resistance capacity. Using this approach with known capacities, it was used to predict possible mechanisms for resistance of another insecticide, cyromazine. Cyromazine has been used as an effective insecticide against L. cuprina for over almost twenty years. Using the laboratory-generated resistant variants, these researchers found that they showed low levels of resistance. According to adjusting insecticide concentration, resistance occurred at different rates.


Resistance is a major problem in our modern day society. Insecticide resistance is a good example of such a problem. Other types of resistance occur such as herbicide resistance and antibiotic resistance. Resistance is one of the best examples of evolution in action. The purpose of this experiment is to try to predict possible resistance problems before they happen, rather than trying to assess the damage after. The goal is to be able predict resistance for the control purposes and to ‘minimize evolution of resistance.’ Current methods of resistance control include increased concentration and strength of such things as pesticides and antibiotics, however, these methods only further contribute to the evolution of increased resistance. We need to come up with more effective ways of fighting resistances, rather than just increasing it in the long run. Being able to predict resistance is a wonderful concept, and may soon help us better control for various types of ‘unwanted’ resistances’ before they have a chance to evolve, or at least slow it down.


Reference:


McKenzie, J.A., Batterham, P. (1998). Predicting insecticide resistance: mutagenesis, selection and response. Philosophical Transactions of the Royal Society B: Biological Sciences, 353(1376), 1729-1734. DOI: 10.1098/rstb.1998.0325


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