Holidays

Well, another year is almost gone. It gets you to thinking about what you've done, not done, and everything in between. I'll focus on what I have done, and what I've been thinking about. The "not dones" are still opportunities.

I've stuck to my plan to get everyone a "gift" of a donation to a cause. I tried to do my best to match people to causes they would appreciate, maybe did better with some than others. I got myself a few things I've been wanting with saved gift cards, and the money I still get from my Dad's insurance- some new pants, a new windblocker fleece that finally went on sale, some slippers. Nothing major. I've always thought that Christmas was over-commercialized and had lost most of its meaning. Donations to charities are down, at the time they need money the most. Hence my plan for donations this year.

Really, we could learn something from our elders- it isn't the stuff you have, it's the people in your life that matter. Spending time with them, doing something special, letting them know you are thinking of them and love them. Getting an expensive gift and mailing it off doesn't show love. The price tag on the present doesn't indicate your value to someone, or your value for someone else. What we should be thankful for and protect is each other and our planet. Life is what matters. How you live it is what matters. How you leave the earth...is it a better place for you having lived? This is what I try to remember and live, everyday.

Peace. Namaste.

Fst

Okay, back to evolution. I know, my other blogs are probably more interesting for most of you, if there are indeed any of you!

But, I have a problem I am trying to think through, and it helps if I write it down. Or in this case, type it out.

There are regions on cocci chromosomes that have low Fst. Fst is a measure of gene flow. Values close to 0 indicate that there is a lot of gene flow- in this case between species. Values close to 1 would indicate no gene flow. Now, what you would expect with 2 different species is values closer to 1 for most of the comparisons- 2 different speices should not be having sex and producing progeny, in sensu stricto.

However, there is good evidence that the 2 species of cocci do indeed have sex, and do produce viable offspring, which can then mate with either parental species (or maybe not, maybe only one, but for this argument let's say it is promiscuous).

Is looking at Fst values a good way to measure this for whole genome analysis? What if the genes are highly variable? What is the effect of repetitive elements in the region? Pseudogenes? I am concerned only because the pattern emerging is highly correlated with genome position, and makes me think something else is going on.

FPS#4

OK, I realize there is one other FP I have seen that didn't happen at Hastings. It was last year, flying home from the east coast. Getting on the plane, I see this guy, with a baseball cap on, looking at the floor, not looking up to meet anyone's eye. Which is suspicious, because usually the ppl in first class are always so happy to gloat at the sad poor people cramming on to the economy section. I look closer. OMG. It is Brett Favre. I am in shock. Anyone who knows me, knows I am a huge Packer fan and definitely a Favre fan. The whole flight I tried think of a way to get his autograph. The stewardess was no help. Now, I am glad I didn't embarrass myself. I was in Milwaukee when I heard that Brett was traded to the Jets. Jerk. No more love for Brett. Sorry. I drowned my sorrow with a PBR. That's allowed, and appropriate. Now I hardly watch football. Last game I went to was the Cat-Griz game. The alumni associations for UM and MSU in Tucson get together and make a big party out of it. It was a lot of fun. And now the Griz are going to the semi finals- or the semi- semifinals. Whatever. Like I said, I don't pay attention to it like I used to. Just doesn't matter as much to me anymore.

FPS #3

So once again, working at Hastings. Only in Missoula now. Video manager. Responsible. Back in school. Finally got my bearings back and direction in my life. Anyway. A woman is in the sale video aisle with her 2 kids. I recognize her but pretend I don't. I smile. She smiles back. I ask her if she needs anything. She is looking for some kids educational videos. Which we don't carry, but I let her know we can order them and they would be in next week. She says fine- so i fill out the order for "Rose Qually." Whose stage name is Andie McDowell. She was still living in Missoula and 9mile. She was still married to a jerk. She seemed very nice and I was glad to hear she found a better man.

FPS #2

Again, working at Hastings. I have to keep this up b/c my bff is competing with me (LOL LD). A co-worker comes back from lunch, and comments that there is a red Porche outside in the parking. OK, if you knew Billings in the 90s- that was something unusual. Anyway, I decided to check it out. I went outside, and it looked like it was actually parked in front of the Subway next door, so I went back and got my wallet so I could get lunch. I went in to Subway, and who was sitting in there eating a friggin Subway sandwich? Tom Cruise and Emilio Estevez. I wanted to ask for autographs so badly. But there is something in me that thinks that is so creepy and weird. So I ordered my sandwich and left. I have often thought "why the hell would Tom Cruise and Emilio Estevez be eating at Subway??" Doesn't it seem a little low-brow?

famous person story

So my friend posted her famous person story. I have some good ones. even living in MT, we see famous ppl. What is funny to me, is that they all happened at Hastings Books Music & Video. In Billings in 1991- incident number one. This really TALL redheaded woman came in. I was working in the stockroom on a Tuesday. Tuesday was the day we got magazines. She was hassling the book person at 10AM, right when we opened, about "where was the new Vanity Fair?" The poor salesperson came back, and lo and behold, we had NOT gotten the new VF in the Tuesday morning shipment. The salesgirl went back out, and this tall redhead FREAKED. I went out and explained to her that we sometimes got only half the shipment of new magazines on Tuesday morning, and got the second shipment on Tuesday afternoon. I would take her number and call her when the new issue came in. She was irate! Said she would go elsewhere. We were IDIOTS. She left. I heard she came back later that day, when the 2nd shipment came in a bought her copy, that as I said came in the afternoon ship. She was on the cover. She is Nicole Kidman. In Montana to film Far and Away. Could have not been a beeyoch. But she was.

my attempt at poetry

the things

i should do

would do

redo

keep me awake in sleep

then dream through the day

sleepwalk

dreamtalk

flying

Its a new day

With a new president. A historic moment yes. My hopes are that Pres Obama listens to his science advisor. That he fully funds science and science education. We can no longer afford to allow ourselves to lag behind other countries in numbers of students pursuing STEM degrees.

Election Day

I think you know where I stand. Regardless, get out and vote! I did early voting, so let's hope my vote actually gets counted. Light a fire people. We have tough times ahead, and only through serious change will we come out on the other side.

Marine Discovery

Been having a great time this week- trying to ignore politics and transformation issues at UA. SO, been enjoying taking my 6th and 8th graders to Marine Discovery. The kids have been loving it. For some, even though their middle school is right across the street, it is the first time they've been on campus. I only hope the memory sticks with them a long time. Peace.

I just can't believe this is an issue

And I am frankly disheartened that Palin and McCain think that "teaching the controversy" is even a reasonable suggestion. To be sure, McCain is less biased here, and has stated he "believes in" evolution. I am even a bit turned off when people say they "believe" in evolution. Folks, it has nothing to do with belief and has everything to do with experimentation, observation and critical thinking. Science, in other words.

And we wonder why the US has fallen behind most other industrialized nations in sciences and engineering??

Eurotiomycetes are my favorite

In 1997 Ericksson and Winka described the class Eurotiomycetes when new ordinal descriptions of the Ascomycota were completed. At the time, only a single order, Eurotiales, was assigned to the class. Over the last ten years, a more complete picture has developed, such that the most recent analysis shows that the class contains at least two subclasses, Eurotiomycetidae and Chaetothyriomycetidae, based on a five gene Bayesian tree (Geiser et al. 2006).
The number of orders contained in the class has also increased. The Eurotiales is still a well-supported order, now placed within the subclass Eurotiomycetidae. In addition, the Onygenales, a previously recognized order in the Plectomycetes (the previous class name) containing many vertebrate pathogens, is a member of the Eurotiomycetidae (Kuraishi et al. 2000). There are an additional 3 orders that will likely be placed in that subclass, the Ascosphearales, Aracnomycetales, and Coryneliales (Gibas et al. 2002, Geiser et al. 2006). The other subclass, Chaetothyriomycetidae, contains three well-supported orders, Chaetothyriales, Verrucariales and Pyrenulales (Tree of Life 2007, Haase et al. 1995). The last order contained in the Eurotiomycetes, the Mycocaliciales, may be a subclass, as it appears to be a sister taxon to the Eurotiomycetidae and Chaetothyriomycetidae, but that observation is based on too few data at this time and thus it is still included within the Chaetothyriomycetidae (Geiser et al. 2006).
The ancestral state of Ascomycota is uncertain and debated (James et al. 2006). The subphylum Taphrinomycotina is the most likely basal group of the Ascomycota (Liu and Hall 2004). This group is highly variable in lifestyle, form and biochemistry. Thus, the ancestral state for the subphylum Pezizomycotina, the group that contains the Eurotiomycetes, is unclear. It has been stated that lichen containing groups must be derived from lichenized ancestors, due to lower rates of gain of lichenized habit than loss (Lutzoni 2001). From that statement, the ancestor to Pezizomycotina must be a lichenized fungus, as this group contains the lineages leading to lichenized fungi. However, due to the high degree of variation in the taxa of the photobionts, and the form and distribution of the lichenized fungi within the group, one could argue that convergent evolution could also explain the pattern observed.
The field of fungal phylogenetics is in the early stages of clarifying relationships among groups. In addition, sampling of these various groups is incomplete. However, recent work on the Eurotiomycete lineage is developing a clearer picture of the organization within that group (Geiser et al. 2006, James et al. 2006). Within the framework of these analyses, patterns of lifestyle can now be added into the analysis to develop hypotheses regarding the likely ancestral state of the Eurotiomycetes.

School starts today

Hard to believe, but this might actually be my last year of school. I've been a professional student for 20 years now, I guess it is time to move on. OK, in actuality, I've had real jobs during that time. I've done the 9 to 5 thing. Didn't really like it. Sure the security is nice. Getting paid vacation. Benefits. Maybe not worrying about affording to go to the doctor. Maybe.

But it feels good. I am ready. I hope I can make it back to Montana.

Update Vol. 2- the scientific part

I attended a Gordon research Conference entitled “Cellular and Molecular Fungal Biology” at the Holderness School in Holderness New Hampshire, June 29th -July 4th, 2008. The stated goal of the conference is to provide a forum for presentation of the latest advances in fungal research with a particular emphasis on filamentous and pathogenic fungi. The meeting brought together leading mycologists from around the world to discuss current research and future directions in fungal biology. A benefit to me was the ability to discuss my research on a less genetically tractable fungus, Coccidioides posadasii, with scientists working on model systems, such as Saccharomyces cerevisiae. The small meeting environment was particularly beneficial for graduate students and postdocs, who often don’t get the opportunity to meet and have in depth discussions with leaders in the field at larger meetings, such as the American Society for Microbiology.

The first session focused on pathogen strategies for overcoming host defenses. A common theme was the similarity in signaling pathways among very distantly related fungi. The next session was concerned with cellular biology of fungi. An important aspect of this session was the unique ways that researchers are using microscopy to visualize cellular processes. The evening session was primarily focused on the interactions between the organism and the environment. Again, signaling plays a major role, and conservation among very distantly related groups shows the utility of model systems to begin to understand how fungi sense and respond to the environment. The next day, the focus was on how there is a fine line between the fungus as a pathogen, and the fungus as a symbiont. Often, the pathways are shared, as even a symbiont must overcome host defenses. The last session of the day was focused on the cell surface interface- the part of the fungus that contains unique molecules that are recognized by the host. The next day was focusing in the biochemistry of fungi- an area I am most unfamiliar with, so it was a great learning experience for me. The evening session was devoted to morphogenesis, an area that I am familiar with. It was interesting to hear that the switch from isotropic to polar growth is often associated with pathogenesis, as it is the opposite in my system. Finally, the last day was devoted to genomics. This was the best session for me, as it directly applied to my research. In addition, I was invited to present my research in the last session of the day, and my talk was well received. I interacted with many scientists over the course of the meeting, and have made permanent connections in the field of mycology.

Meeting Recap vol. 1

So, I promised to do a recap of the meeting, and highlights. This is my first pass. I'll have to do the specifics on the talks from my lab office because I alredy took all my notes to work, and left them on my desk. Part of the problem of having 3 offices...stuff gets lost easily :)

First impressions of the site- New Hampshire is much more rural that I expected! Having been in Woods hole and Cold Springs Harbor, I was expecting fancy multimillion dollar homes. In actuality lots of small places and manufactured homes. Not pretentious at all!

Didn't get to do as much hiking as I'd like- ended up getting involved in dealing with alcohol runs to the local market, as my friend Taylor's postdoc advisor was co-chair of the meeting and the other co-chair was absent because of likelihood of his wife giving birth that week. It was fun though, and got to hang out with Taylor more, and her fellow postdoc Steve. The Madison crew are fun! And will get to see them when I am in Milwaukee in Aug. Beer! Thank goodness for fungi :)

Plans for next month

All in all a good meeting. My talk went well, of course didn't say everything I wanted, in exactly the way I wanted, but I think it was OK. The main points got across. First Gordon conference, and I think I'll try to go next time around, in 2 years, provided I am still in mycology. John Taylor will be a co-chair, so bound to be lots of things I am interested in.

So, this week here in Tucson, getting caught up on some papers, and hopefully getting some work done around the house. Then off to Billings for a week. Really looking forward to it! Will be great to see family, and we're also planning a backpacking trip in the Beartooths.

Then home again for a week, and off to the ESA meeting in Milwaukee. Mainly going for the Fungal ecology workshop, as I got a scholarship to attend the meeting from FESIN.

good summer!

Made it!

Well, I am here in Manchester NH anyway. Still at the airport. An hour away from my final destination. I misread the bus schedule, and turns out I won't be able to catch the bus until 1:30, not 10:30, like I thought (sunday, duh). boohoo. So, at least they are progressive enough to have free wireless at the airport. I am always amazed at the larger airports charging for internet, yet small airports always seem to have it for free. So, I am going to work on my talk for a while. I finished watching a movie, and thought I'd update the blog, just in case anyone is actually paying attention :)

More from the meeting soon.

Meeting time

I'll be heading to a Gordon Conference next week. Specifically, the Cellular & molecular fungal biology conference. I have to give a talk, so will be occupied with that, and not so much blogging. But I'll try to summarize some of the cool work if I can.

Yeast are smarter than people

A recent post on a great site, Panda's Thumb, summarizes a recent article on de novo origination of a gene. What does this mean? de novo is latin for "from new", and its usage is wide, and can mean different things. It can mean "newly arisen function," and might also be referred to as ab initio, or "from the beginning." Anyway, the paper basically shows how brewer's yeast made a brand new gene from a set of nucleotides.

The planet as a petri dish

An interesting, if rather long, article points out that humans may well be over carrying capacity of the planet. I spend a lot of time working with microbes on petri plates, so I have little difficulty in seeing the analogy. It contains a quote from one of my favorite people, R. Buckminster Fuller, "It will be a race to either paradise or oblivion, right to the last moment." Think about how we run our lives as individuals. Rarely do we consider the long term consequences of our actions. Our evolutionary programing tells us to get as much as we can, reproduce as much as possible, and die. We've gotten pretty good at the first 2, and seem very hesitant about the last part. We will hang on as long as possible, the thought of death is frightening.

Believe it or not, I am an optimist. I like to believe better of humanity. I want to think that we are better than this modern world we've created/been born into. I hope the best we can do is yet to come. I don't want to think that it is Walmart, Macdonald's and Wii.

Consider the fact that a gallon of gas will take you, several people, and your gear, 20-30 miles. Do you think you could pay 1 person 4 bucks to do the same job? The reality is we've been able to overshoot our planet's carrying capacity by a lot because we've had "oil slaves" to do the work for 100 years. What will happen when that is gone? Will (can??) we be proactive? Or will it be chaos for many years, until the human population is down to a few million again?

Sex and the Red Queen

There are benefits of sexual reproduction. In 1932, Muller along with Fisher (1930) proposed that sex might purge deleterious mutations, and increase fitness over time. The idea was further expanded upon by Kondrashov (1988). This process has been shown in a homothallic Ascomycete, Aspergillus nidulans, where sexual and asexual lineages have very low level of genetic differences (Bruggeman et al. 2003). Mutations accumulate in both sexual and asexual lineages, but the sexual lineage suffers less fitness decrease over time grown under the same conditions. Another benefit of sex is thought to arise from the evolutionary arms race with competitors, pathogens and predators. This idea was originally proposed by Leigh van Valen (1973) and termed the Red Queen hypothesis, after Lewis Carroll’s "Through the Looking Glass." The Red Queen says to Alice, “it takes all the running you can do to stay in the same place,” meaning in an evolutionary context that for each novel beneficial mutation a species acquires, a competitor or pathogen will acquire a mutation to counter it, and so on, ad infinitum. Sexual reproduction can bring together genetic material from two different sources with unique successful mutations. Recombination potentially leads to novel resistance to a pathogen in a rare individual. Work by Lively, Craddock and Vrijenhoek (1990) demonstrates that populations of Mexican poecillid fish can reproduce sexually and asexually. In pools where there is predominantly asexual reproduction, the fish suffer more infection by parasites. In pools where sexual reproduction is the dominant mode, the population switches between two main genotypes, providing a “moving target” to which the parasite continuously adapts. The sexual population has greater fitness overall, but cannot repopulate pools as rapidly, and hence the maintenance of asexuality. Sex is though to benefit organisms because it increases the rate at which selection can fix beneficial mutations within the population because recombination over time breaks linkage between genes (Maynard Smith 1958, 1993; Fisher 1937). The ability to tolerate or adapt to changing environments, pathogens, predators and competitors is necessary for a species to continue to exist.

Protein-protein networks are robust

The derivation of protein-protein interaction networks of Saccharomyces cerevisiae, C. elegans and Drosophila has recently become a popular method for understanding the biology of these organisms. Network analysis is most advanced in the budding yeast, S. cerevisiae. The network of S. cerevisiae was developed using empirical methods such as yeast two-hybrids (e.g. Ito et al. 2001), expression profiling, identification of proteins in complexes using mass spectrometry, and systematic gene disruptions (Hazbun and Fields 2001). All of these analyses have allowed yeast to be the leading system for the study of protein networks. These networks have been found to be scale-free (Han et al. 2004). Scale-free networks are organized into a system of “hubs” and “spokes” where a few nodes (hubs) have more than five interacting partners, while most nodes (spokes) have five or fewer partners. Disruption of the hubs will cause much greater network perturbation than disruption of a spoke (Han et al. 2004). Therefore, disruption of a random node (protein) is unlikely to cause a serious disruption to function of the overall network (Han et al. 2004). This is one main argument for the ability of organisms to evolve. The protein network is robust, and the organism can still function in spite of mutations.

"we begin life as little scientists"

A really great article in the new yorker, that explains so well how science has affected my life. I came to science "late in life" after dropping out of college, after becoming incredibly disillusioned with life in the modern age. OK, I started reading Kierkegaard in my Norwegian lit class, and it just made me stop and think for about 2 years. That and I realized I didn't really want to be a lawyer, a major in Norwegian wasn't going to get me anywhere, and I was over my head in debt. Amazingly enough, I couldn't work 2 full time jobs, and maintain a 4.0, and live on my own at the same time. The pressure broke me.

Anyway, one morning I was sitting in my apartment in Billings, Montana; pondering what I really loved, what I was passionate about. I loved working in the garden. I loved plants. I loved soil. I loved going for walks, I loved reading and learning about all wonderful creatures on the planet. I realized/remembered/rekindled my love for genetics, ecology and evolution. I decided to move to Missoula that day, and return to school at the University of Montana, where I completed my BA and my MS. Best decision I ever made.

Host resistence to fungal pathogens

The basis of mammalian host resistance to fungal pathogens is relatively under studied. But what is the best model system for studying fungal disease? Many fungi are not host specific, that is, they have the ability to be virulent in many different hosts. Experiments can not be done in vivo in humans, but can they be done on human cell lines. Is a mouse model appropriate for understanding general mammalian immunity? Because mouse studies can be extremely expensive and a regulatory time suck, perhaps other models may be appropriate for understanding virulence in fungi (Casadevall 2005).
Recent work with C. neoformans shows that interactions with other soil organisms can be informative in screening virulence factors (Mylonakis et al. 2002). Further work in this system has revealed a specific gene required for pathogenicity in mice (Tang, et al. 2005). Other systems such as Aspergillus flavus and Candida albicans with the wax moth have also been described and show promise (Brennan et al. 2002; St. Leger et al. 2000). Another tool that is also being used to identify virulence factors in fungi is genome sequencing. Currently, several fungi are sequenced, or in the pipeline. Annotation has proven more difficult than originally thought, so the completeness of the data is limited as of now, and makes searching for "pathogenicity genes" using bioinformatic tools complicated and cumbersome.
The basis of host immunity to fungi is understood at a certain level. When mice without CD4+ lymphocytes are vaccinated with an attenuated Blastomyces dermatitidis and Histoplasma capsulatum vaccine, CD8+ T cells can induce and maintain protective immunity (Wüthrich et al. 2003). Vaccine mediated protection was accompanied by reduced inflammation and fungal burden in the lung. In experiments with mice lacking both CD4+ and CD8+ T lymphocytes, the mice were not able to control the fungal burden very effectively with vaccination, but did show some resistance. Hence, the possibility that antibodies and/or B cells, in addition to other cell types, such as dendritic or NK cells, may play a role in the development of antifungal immunity, and has implications for vaccine development. The main result of this study is that even in the absence of CD4+ T cells, such as in AIDS patients, some immunity to fungal infections was obtained.

the PZ effect

Ha! funny. Never would I get a hit, but because PZ linked my blog, I got 2 comments. 1 nice person, and 1 crazy person.

If ppl want to read about my bits, fits and starts, be my guest. Say hi once in a while, and plz let me know if I say something factually inaccurate.

I love keeping my toes in restoration ecology, because I think that is what hooked me into biology. That and my 7th grade biology teacher who taught me my first Punnett's square. I love genomics, the fusion of computer sciences and biology. I also think the future is in the soil. I used to be a plant ecology/ plant genetics person. But once I got out in the field, I realized the soil is the great unknown in plant ecology.

Now I study fungi. Soil fungi. Ascomycota, generally. Eurotiomycetes, specifically. Well, even more so, Onygenales. And for my PhD primarily Coccidioides. And know you know all there is to know.

random thought for the day

The effects of inbreeding may be mitigated in plant populations by a phenomenon known as purging of genetic load. Over time, inbred plants show decreased fitness followed by a rebound in certain fitness traits, and can exhibit higher fitness than the original population (Crnokrak and Barrett 2002). Darwin first noticed this in his breeding experiments with Ipomoea. This phenomenon is referred to as purging the genetic load, and may be a way in which plants are able to decrease frequency of deleterious alleles in a population. This has been extensively tested under laboratory and greenhouse conditions, however fewer studies have been conducted in the field to determine if this is an important phenomenon in natural populations.

fungal virulence

Virulence or pathogenicity is a microbial trait expressed in a susceptible host and that trait allows the pathogen to cause damage to the host. In general fungi can be divided into two groups, those that are commensal and become an opportunistic infection, and endemics, which are those fungi that are acquired from the environment and have the ability to cause disease (Casadevall et al. 2003; Romani and Howard 1995; Rooney and Klein 2002). Commensal fungi are organisms such as Candida albicans that grow on human skin and do not usually cause any disease, except in rare cases of exposure to extremely virulent strains in hospitals or immune suppression that releases the fungus from host control. Endemic fungi are usually acquired from the environment by inhalation or dermal invasion. Mammals are exposed to fungal spores everyday, but don’t usually get sick. The innate immune system is capable of recognizing and destroying most fungi before any harm is done. Often, sickness results from exposure to toxins, rather than development of a persistent infection. However, when a mammal is exposed to a fungal pathogen such as Coccidioides spp., Histoplasma capsulatum, Cryptococcus neoformans, Paracoccidiodes brasilienses, Aspergillis fumigatus, Penicilium marneffi, Sporothrix schenkii, or Blastomyces dermatiditis, a more severe disease may develop. These fungal pathogens are not restricted to a single class or order; indeed, it appears that fungi have developed virulence in mammalian hosts, independently and multiple times.

To be faculty

I wonder why/how anyone does it?? I feel like I am organized and a smart person, but I have the hardest time publishing. I get the experiments done, figure out the answer, give a talk, and then, I get bored. How can one stay motivated and see it to the finish?? hmmmm. I'd rather go camping.

Plos article

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060124&ct=1&SESSID=6cedc9e903a118743bb7cdc435eabea5

I like to think that the debate is over. I am beginning to realize the threat that science poses to religion. Surrounding myself with others who think as I do, it is often hard to see that most people do not think critically, and indeed view it as a sin to do so.