Sunday, August 31, 2008

Labor Day

I listened to someone speak today about Labor Day, and he subsequently got into the area of how it is typical for Americans to want more from their jobs than to merely provide money for food, shelter and clothing. A lot of us at least partly define ourselves by our work, and we want to be seen as doing work that has some purpose.

He mentioned how even people who do repetitive jobs tend to seek ways to improve the job they do, or some component of the process. And finally, many of us wish to grow in our jobs; we want to be doing a job where we can learn new things.

Then again, our "work" may not involve our job. I have heard of people staying in dead-end jobs because of the health care benefits, and wonder if those people have other outlets.

As for me, I like my job. I also see my work as involving things outside my job. Of course being mom to the fabulous Mr W is right up there, as well as being a good partner to CB, and being a good friend, family member, neighbor, and member of my community. I also do things for my own pleasure, like knitting, that mostly count as, I don't know, 'self therapy'?

I posted earlier that I would try to get an answer to the question "what do you do for a living?" after CB's co-workers asked me and I felt I gave them a mediocre answer.

I work in a lab whose purpose is to study the Ecology and Entomology of mosquitoes that are disease vectors. So much of what is known about mosquito taxonomy is based on morphology alone, that we do a lot of work with DNA-based molecular markers (you know, bands on a gel) to help determine species' distribution, and also information about particular species at the population level

These are different levels of organization. With the taxonomy, the species is the basic level, so we use markers that show differences among species. With the population-level stuff, we look at markers that are more variable, and thus let us characterize the amount of diversity within and between populations.

Who cares? Well, the population-level analyses let us see how two closely-related subspecies grade into one another across a hybrid zone, and also to characterize the degree of hybridization. For example, it looks like, at least in the lab, some hybrids are capable of exhibiting heterosis, where the hybrids show a more extreme version of a trait (like vector competence) than either parental species.

So my job involves both finding markers that we can use to characterize species at the level of populations, and analyzing samples of mosquito populations from wherever. Still doesn't quite roll off the tongue, though.

I use DNA markers to examine differences between species of disease-carrying mosquitoes.


Friday, August 29, 2008

As we age...

I was at the eye doctor yesterday for an eye exam. My glasses are three years old and I now have eye insurance, so it was definitely time. They do a lot of different things, test color vision, peripheral vision, the annoying puff-of-air glaucoma test, etc. I had the option of either getting my eyes dilated for them to look at my retinas, or I could pay $20 and have them take a digital picture of it. No contest, take the picture.

My retinas are fine, thank you, and I was impressed that they could tell things like diabetes-related issues and high blood pressure from pictures of one's retinas.

Back in the room after all the tests, the doctor comes in and we're going over how my eyes have changed since the last exam. He starts out explaining how the lens of the eye gets less responsive "as we age" blah blah.

It took me a minute, but I realized that he was preparing me for needing bifocals. I stopped him and said, "I already have bifocals, so you don't have to soften the blow." He laughed, looked again and said, "oh yeah, you do" and then just said I needed a slightly stronger magnification.

That's OK, I can still get my no-line bifocals. It doesn't actually bother me, because the improvement is so noticeable. I spend enough time reading and/or in front of the computer that I need them.

What frames? It seems all but the frameless ones look weird, but CB's coming in next week and he'll help me pick out something.

Tuesday, August 26, 2008

Shiny and New

Perhaps because it corresponds with the beginning of school for other folks around here, I'm feeling a bit renewed because I have a brand new lab notebook. Can you picture it? There I am, walking down the hallway, clutching my new lab notebook to my chest as I eagerly make my way to the lab.

Around here, we have nice lab notebooks, Sort of a hard-back cardboard cover, black, with the words "LABORATORY NOTEBOOK," as well as the division where I work, written on the front in silver. Said notebooks are not just laying around for the taking, oh no. They are kept by the secretary of the branch I work for, and one must ask Vickie for one. She always gives them out when asked, but this strikes me as a little odd. Sort of like making sure we don't take more than our share.

Although I don't think anyone else has ever looked at my lab notebook, I like to think I keep good enough notes so that if someone had to replicate what I do (yes, I'm working on that post) they could do so. It's not particularly neat, but it has lots of information and references back to important pages and that kind of thing, so I'm pretty proud of it.

This is my fourth lab notebook since I started this job. I think they're getting more interesting as time goes on.

Saturday, August 23, 2008

Glamour! Excitement! Flat Tires! Delays!

I just got back from a visit with CB. Part of the visit was spent at his company's annual business meeting. It was great to have the opportunity to meet his colleagues, and everyone was very nice and obviously passionate about what they do. The company organizes bird watching tours all over the world. They go to fabulously exotic places, see amazing wildlife, plants, geologic features and cultural attractions.

When CB and I first started dating, I had sort of a preconceived notion of what it would be like to be a tour leader. Travel (for free) to all these great places, be paid to birdwatch, what's not to like? The reality is that it is still a job. These folks work very hard to ensure that ALL the clients, some of whom are easy keepers and some who are not, have a good time and feel like they've gotten their money's worth.

And things happen, like the group that went to Alaska after CB's tour and got stuck in Nome for 4 or 5 days because of weather. They really do fix lots of flat tires too, or end up waiting for repairs.

But still, it made my lab job seem boring and routine by comparison. The funny thing was, I found myself having to think back, "now, why was it that I didn't end up being a field biologist?" And there is a reason. At the time I was going back for my Ph.D., I was wanting to have a kid. Sure, there are plenty of people who go out and do fieldwork and have families. But I had an interest in doing population genetics, and also saw a straight job as making the most sense when planning on getting pregnant.

This remembering of why I'm a lab monkey is related to another thing that happened. Lots of people asked me what I did for a living. In retrospect, I failed to get across the gist of why I do what I do, and this has made me want to get a better description that I can reel off when asked, "so, what is it you do?"

When I was in school, I remember a professor saying, "if you can't say what you do in a sentence, then you don't know enough about what you do." This is true to some extent, especially when one is around colleagues. However, this past trip has made me think maybe a two sentence one is more helpful. Or maybe I just need to rework my sentence.

That will be in the next post.

Wednesday, August 20, 2008

Pooch Plunge 2008

The City of Fort Collins has an annual Pooch Plunge at the end of every pool season.  For two evenings, after the pool is closed to human swimmers, they open the pool to dogs and their owners.  This was our second PP, and I think Sally really enjoyed herself.  There were some reluctant pooches, but no one had to tell Sally twice that the water was there for her enjoyment.  

She didn't want to get out to the deeper water and swim with the Labs, but was happy to play fetch with a tennis ball in the shallower water.  So much so that when the ball developed holes and sank when I threw it, she put her whole head under water and find the ball.  

At $8 a pooch, the City made some money on the event and it's a great PR gesture for them as well.  Colorado in general is very dog-friendly (and bike friendly too), but I think that this is an especially cool event.

And, she was very clean, if not a little chlorine-smelling.

Tuesday, August 19, 2008

Finally, a use for rutabagas

Yes, I'm afraid I don't care for rutabagas.  My sister used to put them in her stew and in my humble opinion, altered the taste of the whole thing (ewww!)

Well, at Michigan State, researchers are turning to rutabagas as a potential source of biofuel.  They are genetically modifying the rutabaga genome by inserting a modified version of a gene (the article doesn't say from what organism) that increases the plant's ability to turn carbohydrates into lipids.

The thinking is that if the plants can be modified to store lipids in their roots (which I think are actually tubers - modified stem tissue as opposed to actual roots) they can be grown for biofuel in places like Michigan, that can use all the new agribusiness it can get.

Ha! Here's a site devoted to rutabaga enthusiasts.  I didn't know that they're in the Brassicaceae, or Mustard family.  Last month was National Rutabaga Month, by the way.

Sunday, August 17, 2008

on a lighter note...

Seen on PostSecrets this morning:

Rest in Peace, Leroy

When my sister was diagnosed with colon cancer in November 2006, I searched around the Internet for information. The NPR (National Public Radio) website has several blogs and one of them is called My Cancer, which up until a couple of days ago was written by Leroy Sievers, a former journalist who told his story through a series of blog posts for the two and half years he had the disease. This is a link to the blog. This is a link to NPR's remembrances of him.

Leroy died in his sleep Friday night. He and his partner, Laurie, were planning on transferring him to hospice soon, so I assume he died in his sleep in his own home.

I just visited the blog and became the 596th person to leave a comment there. Talk about having an impact. You wouldn't think this would be a new thing, to blog about cancer, but he just seemed to have a way of talking about the disease and how it affected so many aspects of his life. And, more importantly, he strove to be defined not soley by his cancer, but by other things he had done and believed in.

And the treatments. His cancer was in several places: spine, ribs, brain, lungs. And they would systematically treat each one and Leroy got more time out of it. He had many procedures besides chemo, and it was a lesson for me in what possible treatment options are available these days. He never went down the "alternative medicine" route, though, and I respect him for that.

He said that the blog was his greatest accomplishment. This from a person who was an embedded journalist in the Iraq war in 2003, and reported on crises from all over the world.

I hope that his partner Laurie will agree to carry on and blog about the grieving process. I know that when my sister died, there was a tendency for people to assume things had returned to normal before they really had.

*sigh* I'll miss you Leroy. It's like losing a friend.

Wednesday, August 13, 2008

Sure, I can do that

Way back when I was in graduate school, my advisor was co-author of a grant proposal that entailed developing microsatellite markers to obtain population genetic data for the species of interest. I remember her showing me the protocol and saying something like, "wow, this is a ton of work!"

Somehow, that has stuck with me and ever since, and I have assumed that I'd be unable to undertake developing the markers from scratch. For the work I've done so far at my current job, I'm using markers I found in the literature.

Well, I've been thinking about what I want to do next at work, seeing as I'm at a point where this question makes sense, and I thought, "I'd like to have the experience of developing microsats, maybe I should look into that."

And you know what? I can do it. We'll have to buy a few supplies, but it basically involves digesting genomic DNA with restriction enzymes, fishing for the markers you want with probes, and cloning and sequencing the pieces. Of course there's lots of steps, but none of the parts made me think I couldn't do it.

I've been doing a lot of cloning and sequencing lately, so I think maybe that part of it isn't nearly as daunting as it used to be. Perhaps the processes have become more forgiving, both cloning (follow the steps in the booklet), and sequencing (our great tech has the reagents already mixed and all we have to do is one more PCR and he takes it from there).

Funny how that worked. I only considered doing this project in the first place because I was a bit exasperated with the manuscript that never seems to end and was looking around for what I wanted to do (so there!).

Maybe I could be a Turbo Tech when I grow up.

Tuesday, August 12, 2008

Wolbachia - arthropod mind control

I'm working on developing additional markers for my mosquito projects. We have several microsatellite markers that work well, but in some places the extent of hybridization between taxa is so extensive that it would be nice to have a maternally inherited marker, to get more information as to what subspecies was originally the mother.

Enter Wolbachia. What's Wolbachia, you ask? The link goes to a nice Wikipedia article about it, but it's an endosymbiotic bacteria that is present in many arthropod species. Saying it's an endosymbiont is being kind of generous, though. It's more of a parasite, because it's able to control the reproductive efforts of the species it inhabits.

It was first discovered in a species that I work with, Culex pipiens, so it's full name is Wolbachia pipientis. Ha, it's kind of like Madonna, so famous that it doesn't need a last name!

One of the most striking effects of a Wolbachia infection is CI, or cytoplasmic incompatibility. This happens when infected males mate with unifected females, and the eggs die. CI can also happen if two individuals are infected with different strains of Wolbachia.

Other things that can happen as a result of Wolbachia infection include the killing of males due to infection, the feminization of males into sterile pseudo-females, and parthogenesis, where females can produce fertile eggs without fertilization from a male.

As you might imagine, this scenario sets the stage for some very interesting evolutionary biology. Patterns observed may not make sense unless one views them in light of possible Wolbachia infection. The rate of infection is high in Culex mosquitoes, but work is still being done to quantify all the strains.

My interest in Wolbachia at this point is that new maternally-inherited marker. A paper came out recently that detailed a protocol to amplify, with the same primer set, two different sized (and therefore subspecies-diagnostic) fragments from a gene for a surface protein. It is interesting because it's not mosquito DNA that I'm using for a mosquito marker; it's the Wolbachia. I have followed the protocol, but alas get results opposite of the paper. P is supposed to have the smaller fragment and Q the larger, but they are switched.

So I'm working on cloning and sequencing the fragment to figure out what's going on. If I can duplicate the results of the paper, it would be a useful marker, but if I can't, I'd like to know what's being amplified.

UPDATE: 8-13-08 It looks like this marker is not going to be as great as I thought. I ran the same set of samples with a known marker and again with this Wolbachia marker and got lots of drop out. That's when there's just no amplification. My known marker amplified in every individual, so I know the DNA's OK, but the Wolbachia one isn't going to cut it. Too bad, and the search for a maternally interited marker continues.

Sunday, August 10, 2008

A PostSecret gem

On Postsecrets this morning...

Weekend activity

I'm not sure of the mental and/or emotional components that must be in place, but lately I've been going through my stuff, gearing up for either a big Goodwill donation or garage sale with my neighbor. I don't have enough stuff to justify my own sale, but enough that it's becoming a presence in my basement, and I really don't use the stuff anymore.

Likewise, I FINALLY (I have no idea what held me back, really) got rid of two large cardboard boxes, one filled with the biodegradable packing peanuts, that had been living in my garage for almost three years. The cardboard got flattened and we dropped it at the recycling center on our way down to Denver yesterday.

I also:
1. Washed my carmats (eww, how can they get so gross?)

2. Weed wacked the edges of my yard (at least the bindweed gives the illusion of a green yard)

3. Washed spider webs off the side of the house

4. Washed off a few large rocks that Mr W will paint to decorate the new mulched treelawn (the soil is finally dry enough to work this morning, so - yippee!)

5. Beat back the pumpkin vine, which is threatening to take over the entire alley

It seems this sort of productivity comes in bursts for me, but I'm glad that stuff got done.

image from here

Saturday, August 9, 2008

Catching up with friends

I went over to a friend's house for dinner last night. We share an academic history; she was my advisor when I started my Ph.D. program. She, in my version of history anyway, took a chance on a non-traditional student who had expressed an interest in plant genetics and had never actually studied either beyond a couple of undergraduate courses.

I'd like to think it paid off. I did finish, got a couple of publications out of it, and have employment doing what I learned in school, even if it's with a different kingdom of organisms. Hey, DNA is DNA, whether it comes from a mosquito or a plant.

She ended up taking a different path, and leaving academia. She now works as a safety officer for one of the several government agencies in town. In the end, it was the rate of publishing required of a junior faculty member that made her realize she didn't want to continue.

I am hearing this sentiment loud and clear lately, as the manuscript I submitted was returned by the journal I submitted it to because they thought it wasn't as good of a fit as I did. I spent most of the last week reformatting it, and earning a bit of scorn from my boss, who seems to think I made things less clear in my attempts to streamline my thoughts.

I have come to the conclusion that boss and I have different writing styles, and there's not much that can be done besides acquiesce to his opinion in order to get it out the door. Case in point, I lifted a sentence from the manuscript and send it to friend La Guera, who is my source for things grammatical because she teaches Spanish. Yes, indeed this sentence, which boss marked in red, "not a sentence" was indeed a sentence, albeit one with a little different sentence structure.

I like to believe I'm in the process of learning how to do this, and that it will take a few more papers until the process is smooth, and that it will get easier. Sometimes it doesn't seem that way, but if I want a career doing research, it has to be.

As to my friend/former advisor, she is happy, leading a full life, and.... back in school! Yes, in order for her to turn her term position into a FTE, she needs to get a MS in something safety related, which her employer is willing to pay her for. So it looks like that will work out.

Me, I'm not ready to change careers quite yet.

Wednesday, August 6, 2008

How does my garden grow

The mulch project drags on. If you've not been privy to this saga, I have a tree lawn that is hard to water and cut, so I wanted to cover it with something to make it look nicer. I stopped watering it some time last summer , and it has looked like hell for weeks (but the weeds were doing well).

Tom (or Saint Tom, as I will refer to the gardening services guy because he worked a miracle with his rototiller) turned up the soil on the tree lawn first thing Monday morning. Then on Tuesday the nice people from the landscape supply company unloaded the three cubic yards of mulch in the street in front of my house.

Come Tuesday afternoon, I'm ready to start raking dirt into its final formation, and moving mulch. Then the rain came. I know it's just a coincidence, but for the two days we've had torrential downpours in the afternoon. Wow, lots of rain.

So my mulch pile waits. I'm happy it didn't wash away with the rain, but now it will be a few days before I can work on this. It's just so funny how this project has taken a lot of mental energy, and then, once everything's in place, I have to wait on rain.

It's OK, though, it will look nice. In other news, get a load of my Black Eyed Susans! If you garden, get yerself some of these babies, because they look like this for weeks. It's the most amazing thing; they don't seem to be dying off. That's them in the picture above. You can also see the mulch pile, drying out from the first rain.

I'll post more pictures soon, when the light is better. I'm happy with my garden this year. One of the things I really like about gardening is how it changes over time. Sure, the garden seems to peak in terms of how much stuff is flowering, but stuff comes and goes and I love investigating to see how things are doing. I put in a bunch of perennials, but am leaving space for annuals that catch my interest.

And the pumpkin. I think it's cool how bees will sleep (that's what it looks like, anyway) in the flowers, which are probably 6"x6" (plenty of room). We've got one fruit that's really taking off, and Mr W and I look at it in the morning before we get in the car. The thing is growing 1/2" in diameter a day, it seems. For all the photosynthesis going on in that monster of a plant, I guess it's not too much of a surprise.

Saturday, August 2, 2008

Plant Rarity - Plant of the Week (month? summer?) #2 Hybridization

I wanted to write about a few aspects of my research from school, specifically hybridization/polyploidy and population genetics . Here's a start on the hybridization stuff.

A couple of papers came out in the early 1990's by Norman Ellstrand, telling a cautionary tale that it was possible that rare plants could be hybridized out of existence by a process called "genetic swamping". Swamping occurs when the rare plant is outnumbered by a nearby closely related plant, and the volume of heterospecific pollen results in fewer and fewer pure offspring of the rare species. One of the best known cases of swamping is in the Catalina Island Mahogany (that CB and I got at least sort of close to when we went whale watching), Cercocarpus traskiae. It occurs on a specific soil type (on an island, no less), and the current population estimate is that there are 7 mature individuals and 20-50 immatures. Another species of Cercocarpus, C. betuloides var. blancheae, is also present on the island and studies have shown the two species hybridize. So much so that the original work by Rieseberg et al. (1989) suggested that there were only two pure C. traskiae individuals and what they thought were five more were actually hybrids.

This is a recent status report that has more details, but the short version is that C. traskiae is in a holding pattern after workers removed the more common species and fenced off the area against herbivores.
I looked at two species of Physaria, both endemic to Colorado. The rarer of the two is P. bellii, which occurs in three counties, and the more common is P. vitulifera, which occurs in six. That's a P. bellii photo up at the top, notice the rounded leaves. The ranges of the two overlap a little, and reports of purported hybrids in that area got me interested in the project in the first place.

But wait, there's more. This is a wierd thing about Physaria, but one species can have populations that are different ploidy levels. The genus is sort of wacky to begin with because of their generally low numbers of chromosomes. For example, in some populations of P. vitulifera, all members are diploid, with 8 chromosomes. Other populations are tetraploid, and have 16 chromosomes. They are all P. vitulifera, but the tetraploid ones have an extra set of chromosomes. It isn't known how the offspring do when a diploid individual crosses with a tetraploid, thereby making a triploid individual with 12 chromosomes. Generally, though, triploidy isn't a good thing, because it leaves some chromosomes without partners when it's time for meiosis. Below is a shot of P. bellii root tip cells, with 8 chromosomes.

So one of the things I investigated was the ploidy levels of a sample of P. vitulifera populations that were near P. bellii populations. The hypothesis was that if nearby populations of P. vitulifera were tetraploid, they wouldn't be a threat to P. bellii, which is always diploid and has 8 chromosomes. I was extremely lucky that there were so few chromosomes to work with, because I still did hundreds of squashes to get enough data to make some generalizations. The populations of P. vitulifera near P. bellii were generally tetraploid, except those that occurred close to the hybrid population, suggesting that hybridization between the species would likely be confined to known sites, and therefore P. bellii wasn't threatened by genetic swamping.

Above is P. vitulifera in the rocky soil that it's found in. Notice the leaves that are kind of violin shaped.
OK, enough for one post. I'll cover the population genetics stuff next time.

C. traskiae pic from here.

Ellstrand, NC. (1992) Gene flow by pollen: Implications for plant conservation genetics. Oikos 63: 77-86.

Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implications for plant conservation. Annu Rev Ecol Syst 24: 217-242.