Summer Fieldwork During A Biology Internship

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. A recent Edge Hill graduate, Heather Wickson, and I 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, and will soon be sequencing them ready for fragment analysis. After sequencing, I hope to help Elizabeth with the analysis and perhaps present a poster on the findings at the upcoming Annual Biology/Geography Postgraduate Research Forum!

Summer Biology Internship

As I mentioned a few weeks ago, 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. This year, 6 lecturers offered internships, in disciplines such as genetics, ecology, microbiology, covering organisms including plants, invertebrates and humans. I was lucky enough to receive a place on Paul Ashton’s internship, after applying for two of them (you can apply for two internships maximum) with a CV and cover letter. Being abroad at the time of application, I participated in a Skype interview – a strange experience!

The subject area of my internship is titled, “Does meadow restoration conserve genetic variation?”, although 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). Right now I’ve been assisting in the final steps of DNA extraction, cleaning up the extracted DNA to try and get rid of any impurities in the samples. This 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.

A Visit From Home and A Paper In The Works

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.

Board-Games and Field-Work

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. Lately, I’ve come to realise that I enjoy these kinds of events much more than going out to a crowded club or bar, something that I certainly enjoyed during the previous two years at university. Maybe it’s the fact that I’m in a new place with new people that has pushed me to enjoy a more quiet setting over a high energy one.

I enjoyed my first Seder at the start of Passover, 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.

New England Thoughts

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 RStudios 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.

Working in R again got me thinking back to second year, when myself and Heather tackled a small research project during our Research Methods module. Our study was on leaf morphometrics and involved ~80 samples from 6 sites. This, of course, pales in comparison to a full dissertation but was a very useful intro to the world of research. My dissertation next year is still something I need to be thinking about, as are my module choices for third year. Currently, BSc Genetics students only have one optional module in their final years, making this decision particularly difficult – I’m considering at least 4 modules right now.

This slideshow requires JavaScript.

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, which accompanies the Mt Holyoke College Botanical Garden (which has a corpse flower!). 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 LGBT 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.

Life at The Field Museum

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.

Earlier this month was of course 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.

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.

New Year, New Work, New Adventures

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 that show that you’ve gained something from your time in industry.

 

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.

 

Holidays in Chicago/New Field & Lab Work

If it feels like a long time since my last blog, that’s because it has! It has been just over of a month since my last Chicago post, 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 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 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 my 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 still 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.

Soon, I’ll be moving over to The Field Museum to assist my colleague Mira on some more lab work, but not before I take a brief respite in Utah, where I’m visiting a friend!

Erasmus Reflection

Roughly two months ago, I wrote a post about my experience with the ERASMUS+ program at Edge Hill University – both how I go onto the program, and my first week abroad. Since I have now completed my internship at the Swedish University of Agricultural Sciences (SLU) in Umeå, here is a rundown of the main scientific events.

A window trap successfully hung in a forest in Gällivare

For roughly a week, I got to spend time up in Gällivare, a town in the far north of Sweden. The purpose of this was to set up a whole load of window traps, used to collect insects over the spring, thus gaining an idea of the ecosystem and biodiversity of the area. Since Spring came late this year, there was plenty of snow still on the ground, especially in the forested areas we were trekking through.

As well as the far-flung Gällivare, there were some sites closer to Umeå that I got to explore. They helped me get an idea of the kind of places where ecological work takes place, and also helped me visualise some of the specific work that SLU are undertaking. Two sites were to do with the “fish people” of SLU, a river a the coast, where fish were captured, tagged, and released. Another example was a plantation forest where some of the work required it to be partially cleared in a specific way. From one of these sites, we collected beetles.

The beetles, ah the beetles. The last month of my internship was spent almost exclusively with the phratora. The beetles were used to test whether a certain species of wild plant would “smell” different to its genetically modified counterpart, and the beetles collected are known to graze on that species of plant. This was a great look into real ecological work, from collecting and caring for the species to running and collecting data from an actual experiment.

Another experiment I helped out on was part of a global study. This study set out to test how fast logs would decompose around the world. I assisted in collecting the logs from the mosquito-ridden site where they were being kept, and then regularly checking the weight of the logs over a number of weeks whilst they were being dried. Unfortunately, the logs had not finished drying by the time my internship was up, so I didn’t get to carry out any further tests on the logs.

Biosciences Cyprus Residential

About 8 weeks into my first year at university, then studying straight biology and not genetics, the year-group attended a week long residential in Cyprus. This was part of the module ‘Biology In Practice’ and included two assessed oral presentations. Although first year didn’t count towards my final degree mark, it was a vital time to adjust to university life and the type of work and assessments that we would face in the years to come.

We stayed in the village of Kritou Terra, in the Paphos province, and actually visited Paphos (which has been named one of the European Capitals of Culture 2017) during one of the days – we had free reign to explore the ruins, seafront, restaurants and shops. I also took this time to flex my novice photography muscles.

This slideshow requires JavaScript.

We explored various aspects of the island’s ecology during the trip, primarily the variation between Cistus plants; as well as fire ecology – how forest fires influence the species composition of forests during years after a burn; invertebrate diversity (and how to use a key to identify them); and reptiles – particularly their thermoregulatory behaviour. The work we completed in assigned groups at Akamas Peninsula National Park on the Cistus genus was the topic of our first presentation and was our first rough look at what a scientific report should be composed of (we’d get a more detailed look later on in the module back home). The specific aspect of Cistus variation was also assigned to us.

After experiencing these topics, we then had the opportunity to choose our own groups and work on whichever topic we wished. This would be the subject of our second presentation, to be presented at the end of the trip. The group I was part of chose to head back to the mountainous slopes of Akamas Peninsula National Park and test the variation of Cistus some more.

Spending a week abroad, so soon after moving to uni and with a whole host of new people, was certainly daunting. But it was incredible. Not only did the experience give me insight into the years ahead, but what I think was more valuable was getting to know my coursemates (and lecturers). Working with them really helped cement friendships and put everyone at ease in the lab back in the UK. Overall, it was a wonderful trip; there was plenty of partying working, but that didn’t stop us having a great time.

(End note: Do not go out to social the night before the trip. You’re gonna have a bad time on the flight.)