Experimental design for microbiome research in space.

Thanks to Project MERCCURI, I’ve been fortunate to develop a relationship with Sharmila Bhattacharya, a researcher at NASA Ames who is doing Drosophila research on the ISS. Her group is developing a “Fruit Fly Lab” for any researcher to run experiments on the ISS. She’s sending up her own experiments on several upcoming SpaceX flights, and when possible, she is providing me with samples of fly carcasses, dissected fly guts, and/or fly feces obtained from swabbing the interior of the enclosures. She is interested in (among other things) the affect of spaceflight on immune function. Dovetails nicely with my interest in microbiome research, right!?

So, the first experiment (HEARTFLIES) I got two groups of fly dissected guts, enclosure fecal swabs, and fly carcasses. I did 16S rDNA PCR sequencing from them and found a HUGE difference between the flies that went to the ISS and the flies that stayed on the ground. That was pretty exciting until I realized that the space fly gut microbiomes looked basically like regular old fly gut microbiomes and the ground fly microbiomes contained something like 99% of a single OTU of Lactobacillus.

As it turns out, the media for the ground flies dried up. The flies were very dehydrated (which affected their heart assays as well.) “Never fear,” they told me, “we are going to re-do those ground controls.” Huh? It’s been more than a month since the space flies were sent into space. A new batch of flies cannot be used asa control for those space flies. It doesn’t matter that they are the same genotype, maintained in the same conditions. They are a totally different population now with respect to their gut microbiomes.

For these ISS experiments, they always use this type of “asynchronous control.” Why? Because they cannot synchronously mimic on the ground the conditions that the flies are experiencing in space. Why not? Because ambient conditions on the ISS fluctuate and they don’t learn about those fluctuations on the ground until well after they’ve already occurred. Makes sense. So, in subsequent experiments, they have been running “best guess” synchronous ground controls in addition to their asynchronous controls.

Tomorrow, I’m finally going to get to tour her lab at NASA Ames. We’re going to chat about these kinds of issues. For one thing, flies can swap microbiomes, but not genotypes. Do their experimental enclosures separate the genotypes? I have no idea. We’ll see tomorrow. I wonder if anyone who has piggybacked on experiments in animals like this has any wisdom to share?

Fly Hunt: College Station to Las Vegas (Part One)

This was a pretty long, but relatively uneventful leg that I made in two days.

Day One: I stopped in West for Kolaches. Then, I took hwy 6 across West Texas. I’ve traveled due west from the DFW area many times, but I’m not sure I ever took this route. Maybe I always feared it would be too slow and I just wanted to get out of the state already, but I’m glad I took it this time. The speed limit was usually 65 or 70, not too much small town slow down, and it was actually quite pretty. I kept forgetting that I was in West Texas. I passed through a lot of quaint little towns (frequently encouraging me to drink Dr. Pepper on a regular basis,) and beautiful, green, ever so slightly rolling hills and farm country. I stopped on the side of the road many times to kick the rotting prickly pear cactus, hoping that flies would come swarming out. (Not one.) This majestic Brahman bull/cow/whatever watched me and laughed (I know s/he was laughing!!) Anyway, beautiful creature, really. When you drive by, you have to do a double-take because it feel like you just drove past some very large, silver exotic animal.

I tried to make it to Roswell. I’ve been there before, but I thought it might be a different sort of experience to camp there. But, I got out of College Station a bit later than I’d planned, and once again, I’d taken the scenic route, so I didn’t really get close to Roswell before I had to stop. I stayed at a very cheap, but comfortable and clean motel. I think this photo of the towels in the bathroom sorta captures the spirit of the place. Obviously, they wash these towels frequently, and they care enough to fold them as best they can, however, they can’t afford to get new ones when they fall apart. Or, maybe it’s just not wort it. I paid $27 cash for the room, including a $5 key deposit that I got back the next morning. I slept on top of the bedding, wrapped in my own sheet. Those who know me well know that these are extreme measures for me.

I discovered that the flies that Spencer and I collected were all dead. I’m not sure if they didn’t wake up from the CO2 or if it got too hot (but, I was very careful about regulating the temperature – by now I’d learned my lesson!) I still tried to dissect some of them because I knew I had a mushroom feeder that was really different from the other mushroom feeders I’d found, but it was pointless. They all went into the ethanol, whole.

It was after 3am, and I was completely exhausted, but I decided to put the hookah together. I had a nice smoke and watched Blind Date or something – telling myself that I could sleep as long as I wanted in the morning and I’d just get to Vegas when I got to Vegas.

Fly Hunt: Mansfield to College Station

I hung out in Mansfield with my folks for a couple of days. While I was dissecting the flies that I’d caught in Fayetteville, I realized that the light on my scope was getting dim and I’d left the charger at the JGI. Fortunately, I was able to have someone (thanks, Jen!) overnight it to me. But, for a wile there, mom and I were joking that I’d have to do the dissections with her reading glasses (which I tried to do.) Actually, I realized that for some of the flies, I could do the dissections without any magnification at all. I’m such a pro now. (Plus these were a pretty large species, plus their guts are dark purple.)

Jen Lin, this picture’s for you!

A little culinary diversion here. While I was home, we went to Joe T Garcia’s, probably my favorite restaurant in the world. That’s right, move over Michael Mina, Joe T is in la casa. I’m having to stop myself from writing a full restaurant review, but let me just say that if you are in the Ft. Worth area AND you have at least 4 people in your party AND you have a couple of hours to kill, then go there. You will probably have to stand in line outside of the restaurant to get in, almost no matter what time you go, but the experience it is worth the wait. AND, while you’re waiting, walk up to the patio bar and order a pitcher of margaritas and some plastic cups to bring back out to the line with you.

With a happy belly and no hangover (watch out for those margs!) I left my parents’ house the next afternoon and headed south for College Station, stopping in West for some sausage and Kolaches! Yum. I stopped at the Village Bakery on my way there and at the Czech Stop on my way back, and let me tell you, there was no contest in my mind. The Village Bakery was definitely the winner. I’m still kicking myself for straying. I used to go to West every year to hear Brave Combo play at West Fest. I highly recommend this experience to anyone in the area (Holly, are you out there?)

So, I got to College Station and it was raining pretty hard. Spencer took me out to Lick Creek Park to put out some traps. It was wet and muddy. Spencer is a “true gentleman” as he would say of someone he admires, and I had a great time listening to him. I was most fascinated by this insect called Strepsiptera which are very strange and mysterious. The males and females look nothing alike, and you’re almost guaranteed to never see them together. That’s a male on the left and a female on the right, both adults. (Sorry, I can’t remember from where I swiped these images, and I can’t seem to find them again!) The females live their entire lives inside a host insect. They decrease the nutrient intake of the host and cause them to be sterile, but if I remember correctly, they actually extend the lifespan of the host! The female hangs out with the tips of her body projected through the exoskeleton of the host and waits for a male to come along and fertilize her. The males, after emerging from their host insects (literally, on the fly!) have about 5 hours to fly around and find a female to inseminate. Crazy! It’s also interesting how the Strepsipterans hijack their host’s own tissue to create a barrier so that they aren’t recognized as a foreign object. And, there’s more. If you’re as intrigued as I was, which you’re probably not, google them. There’s lots more great stuff. Or, I think that Carl Zimmer might talk about them in his book. I haven’t even read it yet and I have no problem calling it a must-read! It’s at the top of my “reading for nerdy pleasure” list.

So, the next morning, Spencer and I went to the traps. A couple of them were flooded, but a couple of them yielded a pretty good haul. And, we found some more mushroom-feeders. So exiting! I also saw a larva wiggling around in some sap flowing out of a tree. A slime flux, I think it’s called. Collecting with Spencer was so much fun! I’m pretty sure he would have stayed out there poking around in the forest with me all day, but I had to get on the road again, so we went back to the lab to sort flies. This was my best species identification learning experience. By now, I had a little more confidence, thanks to what I’d learned from others along the way, and Spencer had plenty of time to sit with me and help. He had the Patterson and Stone book handy, so we could look in the scope and then flip through it, back and forth. When we were finished sorting the flies, he showed me how he uses the flow cell sorter to estimate genome sizes in flies (and other things, I guess,) but I didn’t have time to stick around for the whole demo.

Oh, I almost forgot! We went to the George Bush Presidential Library and Museum. It was pretty cool. This sculpture has pieces of the Berlin Wall in in, and these horses are supposed to represent freedom or something. I’m no arteest, and while I remember the wall coming down, I think I’m too young (and socially ignorant) to really appreciate what the wall stood for. But the horses were beautiful, and it was cool to see chunks of the wall.

Fly Hunt: Fayetteville to Mansfield

I was prepared to fall in love again with Arkansas as I drove south along hwy 71. I drove from New Orleans to Fayetteville years ago, and found that I loved the Ozarks. Also, I found Fayetteville to be a lovely town full of hippies and jam bands.

This trip was something else. Here was my first hint that I ain’t in college-town nomore. Yep, squirrel puppies. Do you think they’re breeders? Did they forget to spay their squirrel bitch?

Then, I drove past a revival tent. And, it wasn’t like a “Come to the REVIVAL this Saturday night!!” You know, the kind that draws people from 6 counties like a State Fair, so the five year old can stare wide-eyed at her grandma getting tapped on the head and falling, convulsing to the ground, to the soundtrack of a ridiculously talented gospel choir, while at a nearby table Josie sells her wood-carved squirrel puppy nativity scene, next to the enthusiastic purveyor of fossils that somehow prove that the age of the Earth is less that 10,000 years old. No, not like that. It was more like a used car lot. “Come on down to the tent, folks, every Thursday, we got ‘yer best deals on salvation right here. Holy Ghost early bird special from 6-7pm, but you’ll want to stick around for the miraculous miracle hour beginning at 9pm. Our head to toe salvation package comes with a first through tenth commandment, six-day warranty.” Thank goodness it was not a Thursday, or I would have been SO tempted to stick around. As it was I was hungry, and I stopped at this little restaurant called “Grandpa’s catfish” or something like that. Maybe it was “Jack’s” Anyway, I figured that I needed to eat some local catfish, and grandpa’s recipe was probably great. It was a quaint little converted house. What I really loved about the experience was when I ordered the catfish dinner and the waitress (probably Jack’s great-granddaughter) asked me if I wanted “salad or service with that.” I said, what’s “service?” She said, “pinto beans, cole slaw, hush puppies, dressing (tartar sauce,) and green chiles.” Are you kidding me? Who wants SALAD??? Maybe I should have asked her what “salad” was. Anyway, the catfish was overcooked and flavorless and the cornmeal coating was kinda chewy. The service was awesome. There are very few restaurants to which I would return solely based on the service, but this is one for sure!

OK, so I was feeling like the Arkansans were sorta strange, very religious, and somewhat charming, but then I saw this. I had a very strong, very negative reaction to this sign. Click on it and look at it up close. I found it to be vile and disturbing and asinine and somehow insulting. I felt insulted for Jesus. It made me want to leave Arkansas immediately. I spent a lot of time wondering, who ARE these people? Who, after waking up from his Budweiser-induced hangover, still thought that his idea was good enough to make into a giant (10ftX10ft) roadside sign? Who approved it? Who was the artist? Maybe I just don’t get it. I wondered if it would have been funny if it were educated yet stoned Berkeley hippies making up cheesy slogans about the Buddha. I don’t know. I didn’t want to know. I just wanted to get to Texas, the land of the erudite Coors Light drinkers!

Fly Hunt: Athens to Fayetteville

I’m learning that I need to post stuff right away or I’ll lose interest in posting it all together. I’m doing this just for the sake of completeness at this time. I think it’s kinda like research in that it’s really cool and fun while you’re doing it and it’s fun immediately after when you’re analyzing the data, but when you’re finished and it’s time to write it up, it’s boring.

Anyway, Daniel had given me a couple of Roadfood books, so I was looking to hit at least one recommended restaurant along the way. I ended up at Edna’s in Chatsworth, Georgia. I had a great meal of fried chicken, green beans, mashed potatoes and gravy, and cornbread for $5.37! Yum!

Growing up in the southeast, I figured that any day now, the Kudzu was going to completely take over the highways, but I was surprised at how little of it I saw in the Carolinas. I did see a lot in Georgia, though.

Western Tennessee is beautiful. I felt like I was driving through a Grateful Dead song.

I spent the night in Lawrenceburg, TN. I dissected flies until 4am, then hit the road again at 8am. The drive to Fayetteville was uneventful, but pretty. I was in a hurry to get to Bill Etges’ house at a reasonable hour. I arrived at around 7pm. He’d already put several traps out in his back yard, which was a forest, so we chatted over a beer. It’s funny the things you end up talking about. In addition to learning some really cool stuff about cactus-feeding drosophila, I got some good gossip about other biologists! Bill is a super-nice guy, as is his wife. I really enjoyed spending time with them. The next morning, we caught a ton of flies at the traps and took them back to the lab to sort them. This is how it’s supposed to work! By 11am, I was on the road again.

Fly Hunt: Chapel Hill to Athens

It was really rewarding to find the mushroom-feeding drosophila actually feeding on mushrooms! I felt a sense of discovery that I didn’t feel so much when collecting at the baits. After looking at these flies under the scope, I realized that (not surprisingly) there were a bunch of flies that I’d not seen before. They all looked the same at first glance, but after staring at them for hours, I realized that I probably had 3 different species. Corbin wasn’t too familiar with these (and he was super-busy!) so I did my best to key them out, but after about 5 hours, I gave up. I was supposed to be on the road to Athens by noon, and it was after 3pm when I decided to just keep a voucher specimen for each of the groups I’d made and dissect the rest. My plan is to use PCR to amplify some marker gene in the fly gut tissue to confirm which species of fly the gut came from anyway. So, hopefully that works out.

Anyway, the point of all that is that I didn’t get on the road to Athens (6 hours away) until about 6pm on Thursday! My next host, Daniel Promislow was kind enough to let me show up at his house late (2am!) Since we should have been putting out traps while I was on the road, I just decided to be a day behind schedule. So, on Friday, Daniel and I picked up some over-ripe fruit at the Food Bank, put out some traps at the botanical gardens, and then went to meet his friend for a drink at the local wine bar. That was fun. We each got the same flight of reds and did that thing that oenophiles do, with the “I smell…” and “it tastes like…” and “the finish is…” and “do you get?…” Later, we went to a bar/club called the Melting Pot where they were showing a Charlie Chaplin film with a live band doing the score. More fun! Then, we stuck around for the Dromedary Quartet until about midnight. I loved this group! I was totally exhausted after getting about 4 hours of sleep the night before and 2 hours of sleep the night before that, but I kept thinking, “OK, one more song, then we’ll go.” But, I stayed for the whole show!

I should interject here, that the morning after I arrived in Athens, I went out to my car to get my purse and realized that it was not there. I last remember having my purse when I left the bar, Tyler’s Taproom, – fun place, by the way! – on my last night in Durham but I thought that I’d left it in my car, and I’d been assuming all day that it was somewhere in my car. But, it wasn’t. Fortunately, my cell phone, my ATM card, my digital camera, and $200 in cash were all in my pockets! The cable that connects my camera to my computer was in my purse, though, so I won’t be posting any more pictures until I get a new one. Probably tomorrow…

ANYWAY, Daniel and I set out to collect early Saturday morning – first we went to Roots Farm where we found a decent number/variety of flies. Then, we went back to the botanical gardens to collect our traps. Then, we went back to the lab where Daniel helped me sort the flies. By this time, I was out of vials of sterile, colored food, so Daniel gave me vials and “agar” and everything else I needed to make new vials. We sorted the flies into empty vials so that later, once my sterile food vials had solidified, I could transfer them. Then, I hit the road.

Fly Hunt: Chapel Hill

Corbin Jones, at UNC was ridiculously generous with his scarce free time while I was in town. He took me and Shelah on a hike through the forest near his house. It was a very cool place. We walked a couple of miles (maybe?) on this loop through the forest, setting out bait along the way. Early the next morning, Corbin and I went back through to collect the traps. Unfortunately, it had rained quite hard the night before, so most of the traps were flooded and useless. Fortunately, it had rained quite hard the night before, so I was witness to a lovely thunderstorm. For those who don’t know, the San Francisco Bay Area does not have thunderstorms. I see a streak of lightning about once a year here, and I’m not sure that I’ve ever heard thunder. I took a video of the storm with my camera. I love how the thunder goes on forever. I turned out all of the lights, opened my doors, and enjoyed the storm with my hookah.


Anyway, Corbin and I collected the traps and we also found a ton of drosophila feeding on some mushrooms. I’m posting a bunch of pictures of them here, so that someone will tell me what kind of mushrooms these are. The little black insect on the underside are some kind of wasp, but the red-eyed buggers on top are my Drosophila.

I also couldn’t get over the poison ivy in this forest. I grew up around poison ivy, but I’ve never seen anything like this. Apparently, it grows like a giant, red, hairy vine all over these trees. Dead vines were everywhere!

I also saw a lot of really cool insects here, as well as a lizard with a blue tail and a copperhead snake! (I know that’s not an insect there on the right, by the way.)

There were two insects that were really bizarre. One of them is this black freaky thing on the ground (below left) and one was this cryptic little bug that I saw getting attacked by a spider when I was trying to take a close-up picture of the hairy poison ivy. The spider kept running at him and he kept waving his front legs around in the air at the spider. His legs looked like medieval weapons, like maces. Anybody know what these are?