when one tugs at a single thing in nature, he finds it is attached to the rest of the world - john muir
U P D A T E S
9.November.17 We have viruses!! VirSorter detected about 34 viruses in the SPAdes scaffolds of the SIMPLE experiment metagenome. Only 2-4 viruses were detected in the gill metagenomes, suggeseting that the phage-enrichment worked! However, I have legitimate control samples to really assess this. Hoping to send those out for sequencing as soon as possible.
8.November.17 Awesome news. I was given the raw reads from three Bathymodiolus gill metagenomes (unfiltered, not phage-enriched) to assemble and compare with the SIMPLE experiment metagenome (phage-enriched-host-depleted). Some pre-processing steps revealed that these gill metagenomes have much more host DNA (53% of reads mapped to host reference sequences) than the SIMPLE experiment metagenomes (0.36% of reads mapped to host reference sequences), suggesting that the host depletion via filtration and density gradient ultracentrifugation worked!!
4.November.17 Increasing memory seemed to be the trick. I finally got the mussel (phage-enriched-host-depleted) sequences to assemble with SPAdes by increasing the memory requested up to 1500Gb. Sure the job was in queue for many days, but I got final.scaffolds!!
18.October.17 Learned about some cool research topics and bioinformatic tools at the first day of the Viromics Workshop at Ohio State.
9.October.17 Still facing some ~phun~ contamination of mussel sequences in my data that's interrupting my life (aka assembly).
2.October.17 Began working at Ohio State. Haven't gotten bullied for my Penn State gear yet.
6.September.17 Completed both of my oral exams in Bioinformatics and Symbiosis. Celebrating the rest of the evening. ;)
4.August.17 Officially committed to completing my master's thesis in the Symbiosis group. I'll be exploring the virome of the Bathymodiolus mussel symbiosis with their sulfur oxidizing bacteria. Most of my project will be carried out at Ohio State University in the Sullivan Lab - which is only a 6 hour drive from home! I'll get to be there for my sister's birthday, Thanksgiving, and Christmas! Very excited about the project and seeing my family and friends. :)
21.July.17 My final official day of work at the DOME. :'( Still didn't see bacteria in the feet or Endozoicomonas in the gills. Wish I could stay longer for when the Endozoicomonas probes in the dye Cy5 or Cy3 arrive so I could see if maaaaybe they're detectable with less interference of autofluorescence. Overall, really, really loved working at the DOME in Vienna. Hope to be back some day!
13.July.17 The FISH worked! But sadly didn't find any bacteria in the feet or Endozoicomonas in the gills. Likely due to the autofluorescence from the fluor dye drowning out any possible signal.
29.June.17 Gah. I cut through my thumbnail using the microtome to section gills for FISH. Thankfully on my non-dominant, right hand. This isn't the first time I cut myself on a microtome.... Putting my blood and tears into this project ;)
20.June.17 Arrived in Vienna and started working at the DOME (Division of Microbial Ecology) with Dr. Jillian Petersen's group. Excited to FISH for any bacteria in the foot of lucinid clams and Endozoicomonas in their gills.
1.May.17 Began my lab rotation in Bionformatics with Antonio Fernandez-Guerra, PhD. I will be determining a suitable clustering method for analyzing networks of biosynthetic gene clusters. Hello, R!
29.April.17 Finished my lab rotation in microsensors. In the end, I cultured bacteria on the surface of the Arctic rhodoliths and measured pH profiles of the rhodoliths exposed to continuous darkness for twenty days. Contrary to previous measurements of rhodoliths exposed to darkness for 24hrs, the surface pH of the rhodolith was lower than the water column after the darkness treatment. Maybe it's microbes at work??
7.March.17 Started my lab rotation in the microsensor group with Laurie Hoffman, PhD. We are going to observe calcification rates and microbial densities of Arctic rhodoliths exposed to darkness for long periods, since they have been measured to calcify in the winter in the wild. What's going on? Also freezing my bum because these samples grow at 32F/4C.
12.December.16 Worked with anaerobic bacteria for the first time! In my practical course, we measured the rate of iron reduction by bacteria with different carbon sources, iron(iii) sources, and electron shuttles.
27.October.16 Just returned from Sylt. What an experience. Dissected some clams, processed push core samples, cultured bacteria associated with particles collected from a plankton trawl, and danced until 2am in the guesthouse kitchen. I hope to return soon... and by that I mean the summer.
17.10.16 Left for a course field trip to the Alfred Wegener Institute in List, Sylt today. Excited to take some samples and get sandy!
4.Oct.16 Now that I'm in Europe, I'm going to start writing the date like them. Today was the first day of classes. I am officially a masters student!
9.18.16 Landed in Hamburg, Germany. Now to wear off the jet lag...
8.8.16 Squeezed in a couple dives at Dutch Springs, PA. So stinkin' cold below 50ft despite the crazy heat PA has been experiencing.
5.13.16 Just accepted my offer for a MSc/PhD position at The International Max Planck Research School for Marine Microbiology. So long Caribbean summer dives, hallo Nordsee!
4.22.16 HAPPY OCEAN (I mean EARTH) DAY! The world is blue and beautiful.
3.13.16 Sadly did not get to dive in Puerto Rico, but had an amazing time snorkeling. Another reason to return some day!
1.27.16 Booked my spring break trip to Puerto Rico! Can't wait to dive there!
1.12.16 My final semester as an undergrad began today. Looking forward to learning the most I can these last few months.
12.18.15 Helped my Invertebrate Zoology professor teach kids from the Friends School about invertebrate animals. My favorite moment of the day: My professor:What's the smartest animal other than humans? A student: Vampires!
12.17.15 Took my last final of my last Fall Semester of undergrad. What a ride!
11.19.15 Tried whole colony PCR on the bacteria I have been culturing and it worked!!
11.9.15 Dove in 50 degree water at Dutch Springs and survived. Officially Nitrox certified!
10.24.15 Returned safely from Cartagena. Such a beautiful city with beautiful reefs. Lots of boulder star coral. Definitely want to return soon.
10.13.15 Left for Cartagena, Colombia with the Medina lab!
10.6.15 Presented my summer research through the Schreyer Honors College series: Scones and Scholarship
9.19.15 Dove for the first time with Nitrox! Loved how I felt after diving.
8.30.15 Went on my first dive with my AAUS Science Diving.course at Jay Street Bridge. Super shallow, but very warm!
8.24.15 Began classes for the semester. Taking an AAUS Science Diving course! Should be a good time!
7.30.15 Presented my project findings at the 42nd Annual Harbor Branch Summer Intern Symposium.
7.23.15 Went diving again with Kyalami charters and saw some huge manta rays!
7.13.15 Just returned from a week-long research cruise aboard the R/V Manta outside of the Flower Garden Banks. Saw some amazing reefs and lots of squirrel fish!
6.28.15 Went diving with Kyalami in Jupiter at the Tunnels and Loggerhead sites. Saw two reef sharks and a lot of sea turtles!
5.26.15 Began my internship at FAU's Harbor Branch Oceanographic Institute in Fort Pierce, FL under Dr. Joshua Voss today. Can't wait to start my project and learn new techniques!
5.4.15 Returned from the cruise safe and sound. What an experience. To learn more about my trip read my latest blog post: https://seagazing.wordpress.com/2015/05/13/nautilus-alive/
4.6.15 Invited to join the Fisher Lab spring research cruise aboard the E/V Nautilus in the Gulf of Mexico! I'll be looking at animals living in the sediment for two weeks!
3.29.15 Went scuba diving in the National Aquarium's Atlantic Caribbean Reef tank with Nittany Divers. The fish were so friendly!
3.28.15 Got to meet Jean-Michel Cousteau at Beneath the Sea this weekend - such an inspiring man!
3.24.15 Was offered and accepted a summer intern position at Florida Atlantic University's Harbor Branch Oceanographic Institute with Dr. Joshua Voss. Is it summer yet??
3.14.15 Returned from Cozumel safely. Saw 2 nurse sharks and like 7 turtles. Definitely want to return some day.
3.3.15 Was appointed to the new position, Social Chair, of Penn State's SCUBA club Nittany Divers. Excited to plan some surface interval activities!
2.14.15 Love the ocean? Check out my blog seagazing.wordpress.com to learn about what's going on in the deep blue! You won't be disappointed.
2.1.15 Booked my ticket to Cozumel for Spring Break! A little over a month to go! Can't wait to dive and see some beautiful reefs!
1.22.15 Classes began last week and I love all of them, for once!
1.6.15 Just returned from the Keys as an Advanced NAUI SCUBA diver. Super excited for dives to come!
12.22.14 Headed to the Florida Keys with my school's diving club after Christmas! Hoping to see some healthy reefs!