Wednesday, July 30, 2014

Research Project Progress Report

Besides mucking about with the straw business, I've been quite busy with the actual working parts of the latest feeding trial. Last Sunday, I collected about 10 g of fresh excreta from each pen. On Monday, we sacrificed one chicken from each pen. We collected the digesta from the lower part of their small intestines. This involved removing the GI tract from the esophagus to the cloaca, including the liver, pancreas, gall bladder, and spleen, which are pretty much integrated with the intestines, weighing the whole mess then pulling it all apart and cutting out the lower part. I then squeezed the contents of the lower part into plastic vials, sort of like gently squeezing stuff out of a long, cooked ziti pasta. We want to look at the digesta and the excreta because we want to know if the enzyme we are adding is helping the chickens digest the whole flaxseed better. That is, we want to know how much of their diet is just passing through and how much of it are they actually incorporating. If the enzyme is helping them digest the flaxseed, we should see that reflected in their digesta and excreta, and we should expect to see an increase in beneficial fatty acids in their tissues at the end of the trial.

Collecting the excreta turned out to be no big deal. Chickens fed these kinds of special diets don't have poop that looks like what the blue jay shat onto your car windshield two days ago. These broiler chickens poop out sticky turd-shaped poops. It doesn't smell all that bad either. Sure, if they keep shitting on the same litter for months and months, the ammonia smell will increase but remember that broilers are sacrificed at 6 weeks of age. Plus, after years of owning dogs, I'm not terribly wound up about poop. Well, that's not true. I'm rather interested in it but I'm not afraid of it or squicked out by it.

Then on Tuesday, we mixed the second-stage diets, 100 lbs each of four diets. That basically involves me weighing each 100 lbs out in 3-pound-scoop increments. Good for toning the arms. We make the diets ourselves by mixing calculated amounts of ground corn, wheat middlings, soybean meal, canola oil, flaxseed, and extra vitamins and things such as salt, calcium, amino acids. We have to weigh the remnants of the first-stage diet, emptying all the feeders, then refill them with a weighed amount of the new diet. Lots of scooping and weighing and hauling buckets from one end of the barn to the other. It's hot, dusty, physical work. By the end of feed mixing days, I am covered from head to toe in a fine, pale dust. It takes two wash cycles to get my clothes clean.

Today, I started analyzing the digesta samples. The dry matter determination involves weighing the samples out then drying them in an oven. Oddly, they smelled kind of sweet, a lot like the whole grain bread that I eat. I'll do the same procedures on the excreta tomorrow. I am afraid to even speculate what chicken poop will smell like when it is drying in the oven! I don't think it will smell like whole grain bread. Those gut bacteria have had their way with things once the food is turned into excreta. 

I'm pretty pleased with my advisor's management style. She prints up protocols for sample collection and analysis procedures, shows me how to do lab procedures once all the way through then simply turns me loose to sort it out myself. I have made some mistakes but none that are costly in terms of data or equipment. Two weeks ago, I had a bunch of unexpected and unwanted null results. After thinking about it for a day, I devised a set of three sensitivity tests to figure out what I was doing wrong. Using those tests, I isolated the problem and I expect to be back on track with those analyses quickly. I'm glad that she is letting me flail around a bit--she's busy and can't micromanage me but I don't think that's her style anyway. It is working out well between us.

On top of all of this excitement, I have set a goal that I must read at least two papers every day, summarize them, and get the information into my thesis draft. I plan to have the literature review/introduction done by the end of the summer. So far, so good. The thesis draft is 32 pages long (1.5-line spacing with section headings but otherwise unformatted) and I've read and incorporated half of the more than 100 references I've collected to date. I keep having to dig up new references though, especially when I need to get a primary source (in that case, those are actually the older papers). "John said that Mary said that this is so" doesn't work when writing a thesis (or dissertation). You need to try to get Mary's original paper to find out what she said. I add two or three new papers for every half dozen that I read. But I know from experience that this will slow down as I start to hone in on the most important concepts. 

Friday, July 25, 2014

Doing Science

This morning, I went into the lab next door to get some distilled water (the still is set up in that lab; you can buy lab-grade distilled water but most labs that don't need an extreme level of purity simply make it). The department I am in is called Animal and Rangeland Sciences, and the lab next door is being used by some of the rangeland folks. They study all aspects of rangeland: development, ecology, flora/fauna, hydrology, grazing, etc. One of the faculty has a grad student or post-doc, I'm not entirely sure of his status, visiting for the summer. I walked in to find this visiting researcher filling a 10-gallon aquarium with dirt and water. Um, I asked him, are you making a tank of mud? Yep, he said. I said, why are you doing that? He told me they wanted to test a set of subsurface temperature sensors that will be installed in a muddy area--he was replicating the field setup in the lab. With a tank of dirt and water. I laughed and said, that's pretty neat, and I'm glad I don't have to clean that up!

Then again, on Sunday, I have to collect 10 g of clean excreta (that is, chicken poop) from each of our 16 pens. The samples can't be contaminated with anything like litter or feathers. Imagine a poop lying there: I have to scoop off the top part that isn't touching anything. And I have to find enough fresh piles to make 10 g from each pen, which isn't much in terms of actual volume (a paperclip weighs about a gram), but I will have to hunt around each pen to find the freshest, cleanest poops.

Science is fun!

Azza and HellBeast

This is how my bed normally looks:

This is how it looks after a couple of minutes of the Azza and HellBeast variety show:

They would have stripped the bed down to the fitted sheet in just a couple more minutes!

HellBeast was on a roll today. He found the treat bag that I wear when I walk the dogs. I usually put it in a cabinet as soon as we get back but this morning I got distracted by other things and left it on a shelf by the front door. While I was in the shower, he knocked it to the floor where the dogs got it. I found it in the bedroom, almost certainly taken there by Azza--she likes to take toys and used kleenex and such in there to chew on in private. There wasn't a crumb left in the bag. I suspect Mimi ate most of the treats (just their usual kibble) since she is wise to the ways of the cat and she's queen bee.

Enriching the Broiler Chicken: Update

The straw seems to be just the thing. They are scratching around in it, pulling the flakes apart. They climb on top of the flakes, flap their little wings madly, and jump off. I watched one chick use the extra height to launch itself into the feeder rim this morning--that was pretty funny. Broilers commonly develop metabolic disorders that are caused by the rapid increase in muscle tissue and the inability of the skeletal and cardiovascular systems to keep up. The extra exercise they will get from climbing around the straw will be very good for them.

Wednesday, July 23, 2014

Vet School Application: Supplemental Applications

I was told by the admissions officer at the OSU vet school that, every year, at least one person tries to apply to every vet school. Each DVM admissions office gets a report from VMCAS which shows, for applicants to their school, the other schools those applicant also applied to. I of course believed her--she had seen the report showing that someone who applied to OSU also applied to all of the other US schools (there are 29 in the US). But now as I am working on the supplemental applications for the measly six schools I am applying to, I am not sure I believe that those crazy people really and truly applied to 29 schools. Sure, perhaps they paid the fee to send their VMCAS application to each one but it would take something inhuman to complete all of the supplemental apps too!

I am getting bogged down in prerequisites for two schools in particular. Some schools base their review on all of the course info you enter into VMCAS and the transcripts that VMCAS verifies, but others want you to fill out more or less the same information about specific courses using their forms and their terminology. I suspect a weedout mechanism. For example, for one school, if the title of your prerequisite course was not "Introductory Biology," you need to send the school a "prerequisite evaluation request" form, a copy of the course description, a letter from the instructor or program chair if the course description doesn't mesh well with theirs, unofficial transcripts, a cover letter (not explicitly required but sort of obvious), and so on. It has taken me several days to compile this kind of information for two schools in particular (I won't name them; I'm writing about the process, not trying to single any one school out). Then I mail out enormous envelopes and sit back and wait. I can't finish their supplemental applications until I get a response, and in fact, if my prerequisites don't meet their approval, I can't apply to those schools at all. That would make me sad but that's why I have a short list. I still have one school that I can add to the list if any of my first selections don't work out.

The supplemental applications all have essay questions. One school had a really great one about the role of the veterinarian in global health issues, using MERS as the discussion point (MERS may have camel origins). Some are more generic: describe a challenge and how you overcame it, that sort of thing. So in addition to the VMCAS personal statement, you must craft a bunch of other essays, some long, some as short as 200 words (but there were six of those). 

I feel like I am in the home stretch now. Rather than send a nagging email to my referees, I sent them all a nearly final draft of my personal statement, using that opportunity to nudge them along. One of them submitted his letter today. I'm pleased he was so prompt because that is an important trigger. VMCAS won't begin to evaluate your application until all transcripts and at least one reference letter are in their hands--those basic elements are now in place. I haven't formally submitted my part of it yet (see: prerequisite comments above) but I at least know that when I click on that final "pay now" button, the VMCAS process will continue to roll along.

So far, I've been working on the vet school applications for about five weeks. This doesn't include the work I did in advance, like collecting emails and other things I've written that could be used in the personal statement, gathering transcripts, preparing for and taking the GRE. My goal to finish by the end of July was probably too optimistic. But I've still got a week!

Enriching The Broiler Chicken

One of the big buzzwords in animal science these days is "enrichment." This is sort of ironic because our feeding trials are attempts to enrich poultry meat with health-positive omega-3 fatty acids, but we are talking about two different kinds of enrichment.

It's no longer sufficient to provide research animals (or zoo animals, for that matter) with clean bedding, water, and food. The researcher is also required to provide additional items in the animal's environment that will stimulate it physically or mentally. Even so, enrichment can't of course interfere with any particular experimental goals.

There is a slight disconnect since enrichment is not used in commercial production settings. If your experiment is supposed to mimic that commercial setting, you probably shouldn't provide enrichment. But wouldn't it be better if we turned that argument around? Why not provide enrichment in commercial facilities? I think this could be an interesting area of research. 

Broiler chickens are typically kept in buildings that house hundreds of thousands of birds and there is an accepted mortality rate of 2 to 5 %. If you could show that enrichment could reduce the average mortality by even 1%, it might be possible to convince commercial producers to give it a try. Of course, whatever enrichment you put in place must have a total cost of implementation and management that is less than the profit that a producer would get from that additional 1 % of birds that survive. 

All universities and companies who do animal research and who receive federal research dollars to do so are subject to intensive, repeated reviews and site visits by IACUC, Institutional Animal Care and Use Committees. The IACUC-specific paperwork associated with live animal experiments is thorough and time-consuming to complete.

Currently, the OSU IACUC has a bee in their bonnet about enrichment. I decided to give it a try. Our second feeding trial began 17 days ago. About one week in, I added stalks of celery to the pens. The chicks weren't too interested. Last weekend, a large tree branch from my neighbor's tree fell into my yard. I cut it up and hauled leafy branches to the barn, enough for each pen. The chicks didn't seem too interested. Keep in mind that modern broilers have been genetically selected for many generations to be eating, breast-meat-growing machines. Plus we keep them on a 23/1 light cycle: 23 hours of light, one hour of dark. Chickens don't eat when it is dark. So whenever they wake up from a nap, they start eating again.

My next enrichment experiment was straw. This morning, I divided a bale of straw into the 16 pens. According to the farm manager, "IACUC loves straw!" I won't really know how well the straw works until tomorrow or Friday.

A flake of straw, the dried out leafy branch, the wilted celery stalk. Enrichment. The chicks are more interested in the fresh water I gave them. They will be using the line watering system by the weekend.

We will be switching the chicks over to different diets next week. Once they settle into those, I'll put whole carrots in their pens. And I have a final enrichment experiment: shiny balls which I will make from aluminum foil. Apparently the farm manager has heard that ping pong balls can be used but I don't have any of those. I do have some foil in the cabinet.

The straw may be the only effective enrichment feature because they can climb on it, nest in it, and move it about by scratching in it (they can do this with their litter too but the straw is a different texture and composition). I at least have given enrichment for broiler chickens a try.

Tuesday, July 15, 2014

It is a Riddle Wrapped in a Mystery Inside an Enigma

I am continuing to analyze the samples from the first trial. Chicken parts ground up in chloroform have a distinctive odor that is a mixture of meat and chloroform, but chicken parts ground up in acid (perchloric acid, to be precise) smell like vomited-up, partially digested chicken. Yum, yum. 

Our second feeding trial started last week. I keep a daily log, doing head counts, checking water and feed levels, room temperature, litter quality. Today, day 9 of the trial, there was a surprise waiting for me.

I really hope that our newest batch of chicks have not developed some mad telekinetic skills. It seems that we had an escapee in the 24 hours since I was last in the barn. One pen had only six chicks in it this morning--it's supposed to have seven! I counted again and again. I counted the chicks on the other side of the partition. Maybe they developed the ability to levitate? Nope, the proper number of chicks was on the other side. I started sifting through the litter drifts--maybe it was dead and the others buried it? (If chickens are developing burial rituals, well, we've got bigger issues than a missing chick.) I found nothing, smelled nothing (dead chicks quickly get pretty stinky since their pens are kept between 80 and 82 degrees).

There are other workers at the farm. I thought that perhaps one of them found a dead chick in that pen but failed to record it. That's sloppy record-keeping but easily corrected. There is usually a 2 to 5 % mortality rate in the first 10 days or so so a chick death isn't unexpected. We've already had one chick die (it was really small, just failed to thrive). There is no internet access out there so I decided to complete my morning rounds and email the farm manager when I got to campus.

Directly across the hall is another room with two more pens on the same diet. In the pen by the door there was EIGHT chicks! I couldn't believe my eyes! I counted them over and over to be sure. I randomly grabbed one and put it in the other pen.

Was one of the student workers yanking my chain? Did a chick slip out of a room before I closed the door yesterday and I didn't notice it? Believe it or not, this is one of the things I check for before I leave every day.

The farm manager has since confirmed that rarely a smaller chick might squeeze under a door but never in her years at the farm has she known one to squeeze under twice.

So basically we are back to telekinesis. We are doomed.

(link to source of post title)

Sunday, July 13, 2014

Surrounded by Lavender

This weekend is the annual Lavender Festival in Oregon. Some of the farms are open year-round but on this weekend, all of them open their gates to the public. The festival website was fun to explore--it included useful map tools since the farms are scattered across the central part of the state. A friend and I did a little bit of planning and yesterday we visited three small farms that were relatively close to us.

This field was vibrating with thousands of bees.

I came home saturated with lavender. Depending on the farm, you might find essential lavender oil, lavender soap, lavender lotion, lavender-infused honey, mint tea with lavender buds, fruit and lavender jams, lavender chocolates, lavender lemonade (you can even get that in most coffee shops this time of year), lavender-infused herbs and salt, dried and fresh and potted and U-cut lavender, make-your-own lavender wreaths, lavender-themed artwork...and some of the larger farms had additional vendors, food, even music.

My friend and I had a good time looking over the lavender bounty. We hung around the distillation demonstrations--for the aromatherapy! I thought that the oil was in the leaves but it is in the buds. They have to be picked before they flower. When you distill, you start with an enormous pile of cut lavender, including stems, and a lot of water, and end up with a few liters of essential oil, a mash of plant material, and many gallons of lavender-infused water, a sort of weak tea. Some farms filter this water and sell it as a body mist; I thought that recycling was pretty clever.

I bought three plants--two are an unusual white-flowering variety developed at one of the farms. Even though HellBeast consumes everything organic that I leave out in the house (and some inorganic things, like flip flops), I also bought a bunch of cut lavender. HB seems to have met his match--he gave it a very thorough examination but the taste test did him in and he won't go near it now!

We sampled homemade lavender chocolates. The cilantro-lavender was a surprise but the white chocolate infused with lemon-geranium-lavender was outstanding.

This farm had landscaped gardens, fountains, and gazebos of various sorts in and around their lavender fields.
For my dinner that evening, I combined lavender honey, soy sauce, white wine, and crushed mint leaves that I cut right outside my front door and used this to pan-glaze a pork chop. I tossed a yam and green onions in the pan to soak up the extra juice. Mmm! You could really taste the lavender. It was fabulous.

Wednesday, July 09, 2014

Vet School Application: Personal Statement

I just got back home from my appointment at the Writing Center at the university library. This is a free service available to all students. The woman that I met with told me she'd been working there for more than two years, that she's evaluated hundreds of writing projects in that time, and that my personal statement was some of the best writing she's ever seen. She was effusive.

I actually blushed and stammered. Yeah, I know.

I suppose it's because I've invested, no, the better word is risked, so much to get to this point. I wasn't prepared for praise.

After a few preliminaries, she had me read my essay out loud. This is a very nice technique--it never would have occurred to me to do this on my own.

She made some excellent suggestions to clarify a couple of muddy points. I knew those bits were weak but couldn't see my way to anything better. She suggested moving one paragraph. I wrote chronologically, nothing wrong with that, of course, but she encouraged me to see that I could recast the entire essay in a problem-solution-action format with that one move. The paragraph didn't even need to be modified all that much. Composition and rhetoric are not particularly useful when writing a scientific report. The organization of those is rigid and unchanging: abstract, introduction, methods, results. The personal statement needs to address the assigned questions and at the same time it needs to sparkle. It needs to set me apart from the other applicants and accomplish that in less than 5,000 characters.

Overall, it was time very well spent.

(No, I won't be posting the statement here. Plagiarism is practiced widely and casually by far too many students.)

Thursday, July 03, 2014

Vet School Application: Almost There!

One of the last unfinished components of my application is the personal statement. Schools may weight this essay anywhere from five to twenty percent of your application. Here are the instructions:

Discuss briefly the development of your interest in veterinary medicine. Discuss those activities and unique experiences that have contributed to your preparation for a professional program. Discuss your understanding of the veterinary medical profession, and discuss your career goals and objectives.

You are allotted a total of 5000 characters in which to cover these topics. Characters, not words. My current draft has 4894 characters, 865 words. It's not quite where I want it to be, but it might be close. I've made an appointment next week with someone at the Writing Center at the library on campus to review it (free service, why not use it). I need some other eyeballs too--if any of you want to be of help, email me at lilspotteddog at gmail. I could use critiques of both grammar and organization of thoughts and of how well the essay addresses the questions.

Entering in all of the college courses I have ever taken took quite a bit of time. But one of the other time-consuming sections of the application is the experience section. Fortunately, I heeded the warnings of other students about this and I had already collected a lot of the relevant information in a version of my CV, which I refer to as the "animal" CV.

You have to list at least one activity under each of these categories: Vet, Animal, Research, Employment, Honors and Awards, and Community Activities. It would not look good to click the box that says "I do not have any X experience." For each particular entry, you have a maximum of 480 characters to describe what you did. That was probably the hardest part, condensing each one of my activities down.

Employment, that was easy. Research, thankfully I could fill that section out with a great master's project in poultry nutrition. Animal, well, I can draw on a decade of animal-assisted therapy, flyball, agility, and conformation, and of course four years of classes that I taught while in Saudi Arabia. Honors and Awards, this stumped me for a bit. I briefly considered firing up an old PC I have stored in a back closet and dredging up an old CV that lists all the awards I got when I was an undergrad the first time around. Coming to my senses, I decided that was obsessive and annoying. I limited it to one award from that era, one from grad school the first time around, and the ones I've earned while I've been at OSU. I suppose I am taking it for granted that I have Honors and Awards to even go on about, but I'm in competition here. I am applying as an out-of-state candidate to all six of my short-list schools. I need to make sure I stand out in every single category, not just one or two. 

Community Activities really stopped me for a couple of days. The instructions allow you to include hobbies and sports. But all my hobbies and sports were covered under the Animal category. I ended up going with French. I calculated that I took around 200 hours of French while I was in Saudi, plus another three terms here at OSU. I plan to complete three more terms (the third year) by next April even though not one of those credits will count towards my master's degree. French seems to be as close to a hobby as anything else I do.

When I arrived here in April of last year, I knew that the hardest task ahead of me was gaining enough vet-supervised experience to use on the application, and doing it in just a year or two. I have been pretty focused on that goal. And now, upon reviewing the list, I have to say it doesn't look too bad. I am a bit thin on large animal experience, but the poultry research helps me in this regard. Chickens aren't large animal but they most certainly aren't classified as companion animals!

Even when all the parts are done, I won't hit "submit" until the end of July. I will review everything once or twice and give it time to settle. In the meantime, I'll start working on the supplemental applications for each school.

Tuesday, July 01, 2014

Vet School Application: Fees and More Fees

I just spent $162 to send my GRE scores to my short list of six vet schools. You might be thinking, well, that's not too bad.

But wait, there's more.

We also need to factor in the cost of the GRE itself (around $200), plus the study guide and the extra online practice exams that I purchased (combined cost $70). I also had to pay a $50 fee when I changed the date of my exam.

It will cost me around $200 per school to send them my VMCAS application when it is completed. So there's $1200.

All six of my short list schools have additional supplemental applications on their own websites that have to be completed, and of course, those have to be submitted with fees as well. Can't have VMCAS or ETS raking in all the money on fees, can we? These are usually around $50-75 per school, so that will be around $400.

I also have to pay UT Austin to send official transcripts to VMCAS ($10). OSU will send them for free.

These are just the fees that I know about. I'm sure that more will come up between now and the end of the summer!

Thankfully, the master's degree will not cost me very much. My tuition is paid, I get a small scholarship each quarter, and I'm employed as a graduate research assistant for the entire period, even summer, so I receive a small monthly paycheck. These aren't enough to fully cover my living expenses but I'm just happy that the tuition is taken care of!

Despite the annoying money leakage caused by these creeping fees, I'm keeping my eye on the end game...