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.
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.
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.
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.
And we wonder why the US has fallen behind most other industrialized nations in sciences and engineering??
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.
But it feels good. I am ready. I hope I can make it back to Montana.
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.
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 :)
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.
More from the meeting soon.
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?
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.
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.
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.
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).
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.
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.