Undergrad Final Year: Part Two – Genetics and Genomics 🧬

When the winter holidays are said and done, semester two comes along to have some fun. The two modules that I had lined up for the second half of the year were Applications of Genetics and Genomics & Bioinformatics.

Applications of Genetics could largely be divided into two sections, one that focused on the different kinds of PCR, sequencing and gene-editing; the other on expression studies, linkage mapping, and cloning. An ethics session was also included for good measure as well as some practical work – qPCR, from RNA extraction to quantification of cDNA. Another essay was due for this module, but this one came with a twist – it was to be a layperson’s essay. Our task was to take a paper (from a given list) and write a piece that could communicate the information to a non-scientist. All in 800 words. The paper I chose was titled “Meganuclease-assisted generation of stable transgenics in the sea anemone Nematostella vectensis”, by Eduard Renfer and Ulrich Technau, 2017. I then wrote an essay titled, “Genetically Modified Sea Anemones Allow Research Into The Evolution Of Symmetry In Complex Life” – not a catchy title, but hopefully a more understandable one… To summarise, by creating a lineage of genetically modified sea anemone, researchers were able to understand more about how bilateral symmetry (which is along one plane like in people, fish, worms, etc.) evolved from radial symmetry (like in jellyfish, starfish, flowers, etc.). I scored 85% in this one so was very pleased to see I could accurately synthesise and communicate a complex topic!

I carried out an equally niche research dive in my other module of the semester, Genomics and Bioinformatics. The bulk of the module was a group project – a group paper, specifically – on microbes from the Red Sea. Group projects can be troublesome and sometimes painful to work through, but I was very lucky to have an outstanding group to work with (shout out to “Dream Team Genomics” 😉)! The paper’s focus was on comparing two species through the use of genomics – studying the genome of an organism; comparing two Red Sea brines through metagenomics – studying the collective genomes gathered directly from an environment; and highlighting osmotic stress adaptations – how an organism deals with high salinity. We primarily used the databases and systems available through RAST and MG-RAST for analysis, drawing knowledge from the wider literature to draw context and understand both what to look for and what we were discovering. It was fascinating to piece together the biological mechanisms used by these tiny creatures. On top of that, learning more about the taxonomy of archaea and the debate over the number of domains was another interesting highlight.

After first reading about the Lokiarchaeota a couple of months ago whilst researching archaea for an assignment, I've been fascinated over the two vs three domain debate! https://t.co/8onXSLcvAr

— Ashley Tuffin (@TuffinAshley) May 15, 2019

Genomics and Bioinformatics featured probably the most literal take on a data retrieval exam that there is – the exam focussed on retrieving information from online genomic databases like NCBI (National Center for Biotechnology Information). I felt quite prepared for this as this kind of data retrieval work was the primary focus of the coursework from this module as well as the coursework from second year’s Molecular Genetics. In first year, I scored my lowest exam grade from a data retrieval – barely passing. In my very last exam, the Genomics and Bioinformatics data retrieval exam, I scored my highest exam grade. Not only that, but this module was my highest overall across my entire degree. Cyclic narrative AND finishing on a high!

So that’s my final year! It’s been just over a month since I graduated with a First, and a couple of months longer than that since I started my first proper job as a Research Assistant in Molecular Biology. My next post will either be about the first few months of my job or my experience completing my dissertation on large-leaved lime trees in the South Downs – we’ll see!

Feature image: RAST annotations of the Halorhabdus tiamatea genome centred on glutamine synthetase, with highly similar sequences in related organisms compared.

Undergraduate Final Year: Semester One! 🌳

Over the past 9 months, I’ve been completing my third (fourth, if you count the placement year) and final year of my undergraduate genetics degree. The year consisted of five modules, one of them being the dissertation module, which for me began before I even had my first lecture of the year – it was an arid summer and I needed to sample some healthy leaves for my thesis! But my dissertation is a topic best left for a separate post. Being what it is, a project that forms a module that’s weighted twice as much as normal and lasts twice as long, there’s quite a lot to say!

Day 3 in Pembroke, doing a whole host of things here on my first 3rd year module, Biodiversity and Conservation! pic.twitter.com/uquZLV1Juj

— Ashley Tuffin (@TuffinAshley) September 5, 2018

A few weeks after my summer internship (and my dissertation sampling), my first module – Biodiversity and Conservation – began. This was a field-based module located in Pembrokeshire, Wales. I was in a new peer group for my final year, having taken a year out of the regular university schedule, and a week-long module forcing people to spend time with you is probably one of the best ways to get acquainted with new people! Since it wasn’t the whole year group, it wasn’t too overwhelming and was definitely a great way for me to settle back into uni life. In terms of actual content: we (humanely) trapped and released small mammals on site; performed a bioblitz on Skomer island; photographed badgers, foxes and a cat on a night vision camera trap; and did some good ol’ invert identification from pitfall traps in various forest stands. I unleashed my inner mountain goat (other comparisons included deer and frog!) exploring the rocky shore of a beach and had an evening at the pub and also by the campfire with the group. On one day I even stumbled across a very clean fox skull – a nice souvenir!

“There’s a unique feeling that accompanies these residential field trips… The travel, the communal living, the long hours in the field and lab… They are the highlights of my university experience”

There’s a unique feeling that accompanies these residential field trips, with the Cyprus trip and the Marine Biology module. The travel, the communal living, the long hours in the field and lab. Reminiscing is always clouded with nostalgia – if I think hard enough, I can recall the exhaustion – but all three of these trips succeeded in bringing me closer to my peers and lecturers and are some of the highlights of my university experience. I hope my career, or at least my personal life, allows me to relive that feeling.

We've come full circle! In first year, we dissected many, many lime seeds to assess fertility and on Monday, as a third year, we collected the seeds for new students! pic.twitter.com/0gRULWEyQp

— Ashley Tuffin (@TuffinAshley) October 3, 2018

Despite being thrown directly into the mix during BioCon, it was still tricky to adjust to being back at Edge Hill. The first hurdle being only knowing a few people, either from a year or two below or others that took a year off/were completing a masters; the second hurdle being settling back into classes and not a 9-5. This shift really started with Ecological Genetics, my first typical module of final year, and my only typical module in semester one. Ecological Genetics can be defined broadly as the junction of ecology, evolution, and genetics; the study of genetics within and between species in natural populations. The particular topics we covered were as follows: hybridisation, ecotypes, reproductive isolating mechanisms, cladistics, the species concept, and conservation genetics. Personally, the novelty of hybridisation; the structure of cladistics; the importance of conservation genetics; and the overall scale of the whole subject took my fancy. This is a topic that fascinates me for many reasons yet one I find difficult to wrap my head around. Everywhere you look there’s more to study – the past, present and future of all living species is concerned with the discipline!

Although I found settling into lectures and a new social circle tough, my real challenge was completing coursework. Both BioCon and EcoGen were assess via essays, both on a species (or taxon) and the nature of the module. As with Biogeography in my second year, many hours were spent researching the topic of my assignment and I largely enjoyed the experience. It was challenging (partially my own fault – I didn’t exactly start these essays early) but also deeply rewarding to learn, as best I could, the full depth of a single topic. The titles of my assignments for BioCon and EcoGen ended up being: “Uplands in Britain and Ireland and Management Implications for the Hen Harrier (Circus cyaneus)” for the former and “Evolutionary History Of Quercus” for the latter. Earning around 69% each, I was happy with my first two assignment grades of the year. Nice.

That about wrapped up semester one – it ended up being a good junction back into uni life. Working as a Campus Communicator for the Campus Life team at Edge Hill alongside the semester also gave me a great way to meet some people and keep me from getting too relaxed! The modules, “Applications of Genetics” and “Genomics and Bioinformatics” were semester two’s modules and wow were they something – I hope you enjoy hearing about my experience with them when I have time to post the next update!

Feature image: Bosherston Lakes and Stackpole Court. Taken during Biodiversity and Conservation module, September 2018.

Fieldwork with Wildlife Trust

As part of the summer internship at Edge Hill University, I’ve recently gotten out to do some sampling! Related to the topic of the internship, “Does meadow restoration conserve genetic variation”, this sampling trip was a test run for a larger project. Myself and a recent Edge Hill graduate, Heather Wickson, took a trip over to Wigan and met the Lancashire Wildlife Trust at this branch. They’ve an Edge Hill friend and graduate, Mark Champion, working there and also a current student on a work placement. The team over at the Wigan office, as well as Heather and I, were to help Elizabeth Sullivan on this test run. If we could get the kinks ironed out and prove that this method can work, then she hopes the project can be rolled out over a wider area, having people from other areas collected specimens for genetic analysis.

Setting off for sites such as Wigan Flashes Local Nature Reserve (LNR) and Low Hall LNR to sample Plantago lanceolata (ribwort plantain) and Lotus corniculatus (bird’s-foot trefoil). These areas were teeming with life, plenty of butterflies, damselflies and dragonflies in the air, no doubt a result of the extreme heat we’ve been experiencing for the past few weeks. I managed to get a few good snaps of some butterflies around the area – particularly the common blue. Although I didn’t manage to grab a picture of the dragonflies out that day, I did snap a good one on the first year biology residential field trip to Cyprus.

Since collecting these samples from meadows in the Wigan area, Heather and I have been in the lab, processing samples she and another recent Edge Hill graduate, Katherine Judson, collected a few weeks ago. These samples were of Rhinanthus minor (yellow rattle) and were collected from roadside verges down in Worcestershire. These roadside collections help build up the bigger picture, filling in the gaps of connectivity in meadows as part of Elizabeth’s work.

Currently, Heather and I are extracting DNA from these yellow rattle samples, amplifying them with fluorescently tagged microsatellite markers, sequencing them – ready for fragment analysis. After sequencing, I hope to help Elizabeth with the analysis and present a poster on the findings at the upcoming Annual Biology/Geography Postgraduate Research Forum!

An Internship Closer to Home

It’s been over 12 months since I’ve been properly on campus – with an ERASMUS+ internship in Sweden and a placement year in the USA, it’s weird to be back! However, there’s no rest for the wicked so I’m back on another internship, this time a lot closer to home. The biosciences department offer a number of summer internships aimed at second years who are progressing into third year. Being abroad at the time of application, I participated in a Skype interview – a strange experience! In the end, I was lucky enough to receive a place on Paul Ashton’s internship titled, “Does meadow restoration conserve genetic variation?”

However, I haven’t actually got to that part of the work yet! Before I start on that project (being worked on by a Graduate Teaching Assistant (GTA) and PhD student, Elizabeth Sullivan), I’m assisting on a different project to do with lime trees. This project is Carl Baker’s (a Postdoc Researcher). Recently, I’ve been assisting in the final steps of DNA extraction, cleaning up the extracted DNA and ridding any impurities from the DNA product. One part of this “CTAB extraction” process involves inverting and emptying a tube of liquid whilst keeping a pellet of DNA precariously stuck to the bottom – quite nerve-wracking to see your sample hanging by a thread!

Another unexpected aspect of this internship was setting up and running a session for the 2018 Edge Hill Biology Olympiad. The Olympiad is a series of challenges completed by teams from various sixth forms and colleges that come to Edge Hill University for the day. Each activity is graded and the scores released in a ceremony at the end of the day. I didn’t expect to be doing this kind of work but thoroughly embraced it – it was a great opportunity to push myself and see what it felt like to run a teaching exercise of sorts.

Back at Edge Hill on a summer internship and running the 2018 Biology Olympiad species identification activity! #biologyolympiad

— Ashley Tuffin (@TuffinAsh) June 21, 2018

I’m looking forward to getting more involved in the research here and hopefully preparing myself for my dissertation on large-leaved lime trees!

More to come, soon!

TCJ – 12: Final Days in the USA

The Chicagoland Journals

I realise that Altree has been a bit quiet lately! That’s because 1 month ago, on May 10th, I officially finished my placement at The Morton Arboretum. During the “grace period” of my visa, I continued collaborating with some people at the arboretum on a project, as well as volunteering in the prairie one last time. It was nice to see the prairie coming into bloom, particularly since it was the Spring ephemerals that were blossoming – plants that I missed flowering last year since I arrived in late Autumn. Here is Phlox pilosa (downy phlox or prairie phlox)[left] and Dodecatheon meadia (shooting star or prairie shooting star)[right]:

In the latter half of May, I was lucky enough to spend a long weekend in Washington DC and New York City. Washington DC has many galleries and museums that are part of The Smithsonian Institution – nineteen total, plus the National Zoo. I managed to visit six of these over two days: National Museum of Natural History, Portrait Gallery, Hirshhorn, Freer Gallery Of Art, Sackler Gallery, and Renwick Gallery.

The National History Museum was the first museum on the agenda. Instead of being greeted by the fossil of a beloved Tyrannosaurus rex, as I am at The Field Museum in Chicago, an African elephant stands guard at the entrance. Named the Fénykövi elephant, it was the largest land mammal on display in a museum at the time of its unveiling in 1959. This history museum is not without bones, however. There is a whole hall dedicated to bones and osteology and even has an augmented reality app that fleshes out and brings to life the specimens. After the museum, the Portrait Gallery was next, mainly to see Former-President Barack Obama’s portrait. Sadly, Michelle Obama’s portrait had been moved so wasn’t easily found. On the same day, I also visited the Hirshhorn, Freer Gallery Of Art, and Sackler Gallery. At the Freer-Sackler Gallery, I was particularly fond of the Peacock Room and Monkeys Grasp for the Moon.

Neon “Silence = Death” slogan developed for the ACT UP campaign as part of the “Art and Commodity in the 1980s” exhibit.

The following day, a day far hotter and drier than the previous one, I explored the National Mall – a large strip of land that features monuments and memorials. I particularly enjoyed the Martin Luther King Jr. Memorial, it’s large like the Lincoln Memorial but more empowering than it is imposing. Before that, however, I checked out the Burning Man exhibit at the Renwick Gallery. Burning Man is known for its large burning effigy, but what I didn’t know is that many artists exhibit other works, such as sculptures, at the event. The Renwick exhibit, known as “No Spectators”, houses sculptures that draw inspiration from Burning Man as well as pieces by artists who have previously showcased their work at the event. I particularly liked the giant sculptures of crows, Untitled by Jack Champion. They just look cool!

The day after checking out the National Mall and the Burning Man sculptures (exhibit named “No Spectators”), Diana, who was accompanying me on this whirlwind tour of DC and NYC, took me around Georgetown, a really pretty neighbourhood next to the Potomac River that also features a historic canal that is currently being restored. Since there had been a lot of rain before my visit, the Potomac was almost bursting its banks with rapids having formed along its length. From one of the bridges that crossed a sidestream, I was able to see rocks with tiny patches of vegetation hanging on for dear life – even a tiny tree struggling to stand its ground! One person was even kayaking in the main river, not for the fainthearted!

The next day we got a train to New York. Unfortunately, it was raining when we arrived and I, lacking a raincoat, got to ‘jellyfish up’ in a lovely yellow rain mac. The rain let off by the time we had eaten lunch, allowing us to see Times Square without being drenched. If you’ve ever been to London, think Piccadilly Circus but bigger – like most things in the US!

On the following day, we explored many squares in NYC, as well as some parks and Lady Liberty from a distance. NYC has some lovely areas to see, although it’s very compact and pretty busy too. I ate a traditional New York bagel (again, huge) with some vegan garlic and herb cream cheese, which was pretty damn good. Later on, we saw the 9/11 memorial fountains which were quite a sight to see. After seeing the sights, it was time for the flight back to Chicago and catching an Uber to the airport was an absolute nightmare!

To make the most of the sunny weather in Chicago, Diana and I took a trip up to the Chicago Botanic Gardens (CBG), I was particularly interested in seeing the bonsai trees. It’s a huge garden so there was no way for us to see all of it in the time we had, plus, it was far too hot to stay for long. On another sunny day, we visited the beach and I got to play some volleyball – a sport I’ve missed playing a bunch whilst in the states.

In the final few weeks before I left the US, I got to spend some time with some of the wonderful people I met whilst living in Chicago. We played games, went to the Lincoln Park zoo, had a boozy brunch, took an architectural boat tour, even went out to a club for a drag show. I’m very sad to leave them and my life in Chicago behind, but of course am excited for what the future holds back in the UK, including a summer internship with the Biology department at Edge Hill!

TCJ – 11: Games & Visit

The Chicagoland Journals

Towards the start of April, I went to not one, but two board game parties – both for the birthdays of some Chicagoans. Sarah from the Arboretum and Katie who is Arb-adjacent, the housemate of someone who works at the Morton. I finally got to play Settlers of Catan, a game I’ve wanted to play for about a year but never found the opportunity to – although simple in its basic rules, a lot of strategy can be implemented.

This year, I enjoyed my first Passover Seder, complete with vegan Matzah ball soup and many cups of wine. There was a condensed reading which was very informational and interactive – a piece of Matzah, the afikoman, was hidden before the service and since there were no children present to look for it, we did. Also, being the youngest at this dinner meant that I read a specific part of the text.

Over the at the Field Museum, I used the Bioanalyzer for the first time, which was slightly daunting if only for the fact that each individual chip costs around $60. I also attended another talk, this one by Nathan Lord on jewel beetles, their incandescence, and how and what they see. Fascinating stuff, stretching over a broad range of disciplines from biochemistry to taxonomy. Another Super Speaker, Meg Staton, was at the Morton Arboretum in early April also, presenting on a citizen science app, TreeSnap, which aims to help affiliated scientists gather data on specific trees such as the American Chestnut or Ash trees.

Back in the field, I was put to work outside as the prairie restoration project is coming alive again after Winter. The prairie needed to be burnt to rid the site of last year’s dead growth, and I assisted Mary-Claire in readying the plots so that they were in the best condition for ignition. Sadly, I missed the actual fire, as the conditions were so good that the burn team completed their work in a flash.

Around mid-April, I was visited by a friend from home – Hollie, who went to the same sixth form as I. Fortunately enough, I had a few days off to show Hollie around the city and make the most of their time over here. Having come over in early Spring, Hollie got to experience Midwestern weather at its most capricious – with the weather nice enough for shorts bookended by light snow and heavy rain. Whilst the sun blessed us with heat, we trekked around the city, visiting The Bean and shopping in some indie “thrift” stores that didn’t seem to be entirely secondhand. I also took another trip to the Neo-Futurists to see The Infinite Wrench. As per the nature of the show, in the time between my two viewings, the individual plays had changed entirely. Although I preferred the shows during my first viewing, I did get to go up on stage this time, which makes two for two on ‘member of my party being directly involved in the show’!

On the rainy days of Hollie’s stay, we still braved the cold outdoors to visit the Shedd Aquarium and Adler Planetarium. Honestly, a highlight of the day we went to the planetarium was Pokemon Go Community Day – we both caught some gems including our first shinies of the game and the North American regional exclusive Tauros. On the last full day, I showed Hollie some of the best and worst that Chicago has to offer – the Impossible Burger and Malort – one being a delicious vegan meal, the other a harsh drink that has a lasting bitter flavour.

During my days back at the Arboretum, I’ve been making progress on the work that’s going into the upcoming paper I’m working on with Lane and Andrew. I’ve already managed to create a few nice boxplots and we’re starting to see some interesting results from our analyses – time to get it written up into a suitable format! Working inside at the arboretum whilst it’s sunny and fairly warm outside makes a change from last Autumn when I was working in the prairie. Over at the Museum, I’ve assisted on the bait capture stage of the experiment, a stage that is similar to using the Bioanalyzer in that although it’s a simple procedure, the pressure is on with timing and expensive reagents.

TCJ – 10: City Excursions and Super Talks

The Chicagoland Journals

Shortly after returning from Boston, I took a trip to Garfield Park Conservatory. The conservatory hosts a number of rooms, each with a different theme – the front room is home to palms, the centre room to ferns, and another to aroids. The showroom at the time of my visit was featuring the Spring Flower Show, “Hashtag No Filter”. Next up on the list is the Chicago Botanic Garden, hopefully, I’ll make it up there in time for their orchid show.

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Also towards the end of February, I saw a reading for a play written by a new friend, Hannah Verdon, called Eleanor Absolute, which is based on true events and tells the story of a journalist, Lorena Hickok, and her romantic relationship with Eleanor Roosevelt – whilst questioning who gets to decide on a person’s legacy.  I went to another show in March, this one with Molly, who drove up for the weekend. This show was called The Infinite Wrench and was by a group called the Neo-Futurists. The show is an hour long and the aim is to perform 30 short plays, with interrupting “wrenches” that add a new dimension or obstruction to the performance. Some plays were silly and short, others were longer and heartfelt, Molly was even chosen to dance in one of the shows. It was worth enduring the cold for as we queue to get in (we arrived far too early).

The following day, Diana and I made it down to Maggie Daley Park on the final day of ice-skating on their rink. Having not skated in years, and never being proficient at it anyway, I think I faired fairly well by simply not falling over. Diana pointed out that it was easier to skate with speed and, although far more nerve-wracking, she was right – we picked up a decent pace as we made a few loops around the ribbon. Our time on the rink was cut short by the Zamboni, but it was a nice day out and the park was nice to walk around.

Whilst I spend most of my time in the city now, since I work in the Pritzker Lab at the Field Museum labs instead of at the Arboretum, I do work at the Arb on Thursdays. During this time I’ve been analysing the data gathered from biomass and vegetation indices in R, working on a potential paper. I’m quite proud of the various graphs I’ve made, utilising the “ggplot” package. Since this is a group effort, we’ve taken to using GitHub to streamline our workflow. Although I’ve used GitHub to access other people’s data before, I’ve never used it to upload my own data and collaborate on others’. The process has been largely straightforward and we’re making good use of the system.

I made an exception to my usual schedule the other week when I worked at the arboretum on Monday. This was because there wasn’t just any Tree Talk happening, there was a Super Tree Talk. Presented by Nathan Swenson from the University of Maryland, this talk was on the structure and dynamics of tree assemblages, from traits and phylogenies to transcriptomes and functional phylogenomics. Back at the Field Museum, I’ve recently also attended talks on indigenous archaeology and the root microbiome.

Just down the road from the Field Museum is Adler Planetarium. I’d never been to a planetarium before until a few weeks ago when I went to “Adler After Dark” with Diana. As you might suspect, the event was in the evening, at a time when the planetarium would usually be closed. Although there was a theme (game-night), we’d never been to the standard exhibits or shows, so those were the priorities of the evening. The two shows we saw were on the “Cosmic Wonders” of the observable universe and of the sky as seen from Chicago on that night. The first showed the many deep sky objects humanity has observed, including the incredible photo of 5,550 galaxies from Hubble’s eXtreme Deep Field, featuring galaxies formed just 450 million years after the big bang, and a photo of gravitational lensing on a galactic scale. The second pointed out the many asterisms and constellations visible in the night sky. We also were given a tour of the telescope and got to turn the roof – very fun. That night also marked the second time I’ve held a piece of the moon and Mars!

TCJ – 09: Field Museum, Data, and New England

The Chicagoland Journals

One perk of working at The Morton Arboretum are the Monday lunchtime Tree Talks – short lectures presented either by a member of staff or a visiting scientist. Although I spend most of my time at The Field Museum now, it’s nice that the perk has seemingly carried over. Although not on a regular schedule, there have been numerous interesting talks over the past few weeks. From Dr. Tyrone Lavery and the “Tree-Dwelling, Coconut-Cracking Giant Rat” to Dr. John Novembre’s work on the human genetics mirroring geography. Another great talk was presented by Dr. Corine Vriesendorp’s, for the Women in Science’s February meeting, on the creation of a new national park in Peru – Yaguas National Park – which took 15 years to be recognised! Dr. Robert Hart also spoke on the topic of ethnobotany and the value of local knowledge when assessing change in biodiversity. Yet another perk – the dollar-beer happy hour on Fridays isn’t bad either!

The Field Museum’s mascot, SUE the T. rex, has now been dismantled and is being moved out of public display until Spring 2019. Taking up their mantle is a titanosaur, Patagotitan mayorum, which, according to The Field Museum’s website, is “25 Danny DeVitos in length.” Whilst I’ll miss walking past SUE at work, their twitter account, @SUEtheTrex (Specimen FMNH PR 2081), will keep their legacy alive hopefully for years to come – even whilst they’re out of the public eye.

One big event last month was the Super Bowl. Despite having seen half a game of American football last year, I still didn’t really understand the rules – Molly and I were mainly there for the halftime show – but now, after watching most of the Super Bowl, I have a better idea. We had a little beer tasting whilst the game was on, with one beer from the Lagunitas Brewery, which I actually visited towards the end of January! It was pretty huge – although it is the only brewery I’ve had a tour of, so maybe I don’t have a good standard of measurement.

My house at the arboretum, surrounded by snow.

Also, after six months in the US, I’ve finally had my first repeat Uber driver, a zoology-major who remembered me as “The Botanist” which I can only assume means that I’ve made it as a plant scientist, coupled with the fact that I used “carex” in a game of Words With Friends the other week.

Although I’m working at the Field Museum most days, I still work at the arboretum on Thursdays. The main purpose of this is for the individual and group lab meetings, but it’s also a good time for me to focus on analysing the data from the prairie restoration project, this includes the biomass data I collected in autumn, as well as NDVI and soil data collected previously by Lane and other researchers. Towards the start of the month, Andrew and I sat down and worked through the data, analysing the NDVI readings from one section of the experiment, with particularly deep soil, to their replicates in other sections. Later in February, I cleaned up the code and set aside what worked, making use of RStudio notebooks that use markdown – I’m finding them very handy. Next up is checking to see if the results observed from the NDVI data are reflected in the biomass data.

 

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In the middle of February, I took a trip over to New England, specifically Mount Holyoke College, to visit some friends. Although I didn’t get to see much of Boston, Massachusetts seems like a beautiful state and reminded me more of home than anywhere else in the US so far. Mt Holyoke College is also remarkable, being a fairly old women’s college that features grand brick buildings and a variety of trees, such that they form the Talcott arboretum. It was nice to hear that they’re also a progressive women’s college, accepting trans and non-binary students, perhaps unsurprising considering the college’s gay history. The nearby town of Northampton (or ‘Noho’) even features a rainbow zebra crossing. Everyone I met was friendly and welcoming, letting me join them in some interesting lectures and also indoor rock climbing – something I’ve missed doing whilst being over here.

 

TCJ – 08: Holidays and Beyond

The Chicagoland Journals

If it feels like a long time since my last blog, that’s because it is! It has been just over a month, and with Christmas and New Year’s sitting right in the middle, that’s only made it seem like longer. I’ve had a variety of tasks at work as the prairie project has been finishing up for the winter, and my other duties have just started taking off.

My celebrations over the fieldwork being done were slightly premature, as I still had bags of biomass that needed to be distributed back to various plots in the prairie (and still do have remaining bags). This was back on December 20th-21st, when the Illinois landscape didn’t resemble an arctic tundra. Although cold, it was still possible to get the biomass dumped – unlike now, where snow has covered the tags indicating the ID number of the plots! A one-off task I assisted in was sonic tomography. Marvin needed a little help one day so I got some experience knocking on wood. To measure the density of trees in a fairly non-invasive way, sensors are hooked up to some permanent nail fixtures in the trees, then are tapped with a hammer. The sensors record the vibrations around the ring and calculate the internal structure.

On the eve of Christmas Eve, I volunteered for Illumination again, this time as a fire pit monitor! Counter to my initial thoughts, this was colder than the Illu-medallion distribution, as that was in a heated marquee and this was obviously out in the cold. Christmas away from home was a strange and new experience, however, it was nice to see some family over a video call after their Christmas dinner (and just after I woke up). I spent the actual holiday with two friends from work, we went to the cinema, got a meal, and had some drinks, so a good day was had.

In the strange not-quite-holiday days between Christmas and New Year’s, I made an attempt at dumping the final portion of biomass, but the plot numbers were completely disguised underneath snow and soil. Without the map, which was back at the office, it wasn’t productive. Instead, I worked that week on DNA quantification, using a Qubit fluorometer – this was a good exercise into getting back into the lab practice.

With the coming of the new year came the beginning of my time at The Field Museum. Although I haven’t got started on the core of the work yet, I have started lab work there. Mira and I performed some DNA dilutions in preparation for the next generation sequencing (NGS), specifically HybSeq, that will give us the results of this project. As well as the dilutions, I performed some more DNA quantification – I’m certainly getting a lot of practice with Qubit.

During my time not in the prairie, or at the Field Museum, I’ve been working on a project with another research assistant, Lane, comparing data from the prairie that she collected with her drone’s multispectral imaging camera with the biomass data I collected last semester. Processing both datasets and importing them into “R”, the software we use for analysis, was quite challenging, but in the end, we succeeded. The results seem promising so far but more analysis is needed, although it’s no groundbreaking research it’s very exciting! I even got to fly the drone the other day, something I’ve never done before. They’re amazing pieces of technology, although hearing one up close (it sounds like a swarm of bees), I can understand why some people might be wary of them.

Despite being all the way over in the United States, I’m still technically on four modules at Edge Hill University, placement modules. These modules cover personal reflections and activities, as well as two assignments on the placement organisation – specifically an issue with the organisation, and the solution to this issue. Although I would’ve much rather just carried on with the work at the arboretum and museum, they’re important assessments to show something has been gained by the time spent working in indsutry.

Halfway through the month of January, I took a trip over to Utah to visit a friend, Avery. We had originally planned to drive down to California, visiting more friends in Los Angeles but unfortunately that plan fell through. Instead, we’ve been based around central Utah, a couple hours south of Salt Lake City. So far we’ve watched many films, including The Last Jedi and Mary and The Witch’s Flower in the cinema; driven around the local mountains, specifically the Skyline Drive near the Manti-LaSal National Forest; and visited the Loveland Living Planet Aquarium and Natural History Museum of Utah. Although it was sunny and almost warm when I arrived, snow has now hit along with sub-zero temperatures. Seems like I brought the Chicagoan winter with me! It’s been a nice break from work, but I must say that I miss Chicago – the city must’ve really grown on me in the past few months.

TCJ – 07: Biomass? Weighed.

The Chicagoland Journals

In my last blog post, I was excited to have all the biomass collected and waiting to be dried – hopefully before the end of December. Well, that was certainly a low bar, since all the biomass was weighed by the 13th December! My house is now empty of plant matter – and looking slightly empty for it. Looking back, it’s almost unfathomable how many bags I ended up weighing, I’m incredibly grateful to Lindsey and the volunteers for helping out in the field, collecting just wouldn’t have been possible without them. Now all that’s left to do is empty the remaining weighed bags of biomass back onto their original plots.

It may not be visible, but it was snowing when this photo was taken.

In addition to collecting all the biomass from the prairie, it has also been winterized – the hoses, sprinklers and electric fence removed, as well as data from the weather station downloaded. It certainly feels like winter has arrived, to me at least, with light snow every other week, temperatures regularly dropping below freezing, and winds that often cause my phone to flash a “Weather Warning” alert at me, however, I get the impression that the worst is yet to come! I’ve received numerous sets of thermals from family as presents for my birthday, however, so I feel suitably prepared.

The past few weeks have seen Thanksgiving – which I spent with my supervisor, Andrew Hipp, and his family – and my 21st birthday, which I spent with my dad, doing various touristy things over the weekend, such as visiting the Art Institute of Chicago, Field Museum, Shedd aquarium and Skydeck. For my birthday (observed) the following weekend, I went out for drinks and a meal with many of the other research assistants (RAs) at the Arboretum, since I am now legally allowed to drink (odd since I have been able to drink since 18 back in the UK). Since it was also the third night of Chanukah, menorahs were lit and dreidels were spun.

 

I also got to see Molly again, as she visited to see Illumination (which I have started volunteering for). Finally, after my last attempt was left incomplete by the threat of the setting sun, we took the trip over to Big Rock – it was conquered. We also baked pie and visited a mall, where I saw my first Hot Topic – an unexpected American Bucket List item.

During Molly’s visit, I was disappointed by a store-bought vegan pizza. Thankfully, my faith in fake cheese was restored the following weekend when I visited the city with Diana, one of the RAs. We saw some local theatre and a drag show – I think the first I have been to. Both shows were great, but Lizzie, the punk, feminist, musical preceding the drag show, blew me away. Described as “American mythology set to a blistering rock score with rage, sex, betrayal and bloody murder” by the theatre, it was like nothing I’d ever seen.

Aside from the prairie work and social activities, I’ve got a university assignment to focus on, which is proving harder than I thought! Identifying problems at the Arboretum that can be discussed and solutions proposed is challenging when the place is pretty shipshape!