Roberta May Fisher

Of Mini-Pigs and Men?

It’s not just mice and rats that are used for metabolic research at CBMR. Research Assistant Ann Normann Hansen from the Barrès Group has been working with a different kind of animal to help her understand how diet can change the epigenetic marks that are passed onto offspring through sperm – the mini-pig!

First of all, what even is a mini-pig?

The miniature pig (generally referred to as a ‘mini-pig’) is an animal model that has been developed for biomedical research. The first attempt to develop miniature pigs goes back to the 1940s in the United States where scientists started to use pigs more frequently in biomedical research, and therefore the need for a smaller and more manageable version of the domesticated pig arose.

Compared to the 150-400kg body weight of an adult domestic pig, a mini-pig only weighs around 35-45kg. Besides the smaller size, which makes them more easy to handle, other advantages of small pigs are that they require less food and space, as well as the pharmacological products and anesthetics needed. And they are quite cute.

And what are you using them for?

We are using the mini-pigs as an animal model to investigate effects of chronic nutritional stress on the epigenetic landscape of spermatozoa. This is one project out of many within the GECKO international research consortium whose main research goal is to understand how a father’s diet before conception influences the metabolic health and predisposition to obesity in future offspring.

We think that specific paternal diets can modify the epigenetic information carried in the spermatozoa, which is then transferred to the oocyte at the point of fertilization. This contributes to an altered offspring phenotype through differential programming of the developing embryo.

The GECKO consortium is also particularly interested in finding out whether these epigenetic modifications represent a biological response that is evolutionary conserved across different species. In other words, do all animals respond in the same way at the epigenetic level to nutritional challenges, or does each species have a specific response? This is one reason why we have chosen to work with mini-pigs, as they will represent a species within our comparative analysis of vertebrate sperm epigenomes.

What exactly are you feeding them?

We are feeding the mini-pigs a “Western diet”, i.e. a diet rich in saturated fat, fructose and cholesterol over a period of three months to induce the nutritional overload/stress in the animals. We are collecting sperm samples at different time points throughout this dietary intervention, and will perform different epigenetic analyses – mainly DNA methylation, small RNA profiling and chromatin accessibility – to identify gene families/ or regions in the genome that are changing in response to the diet.

Why are they useful for the kind of research you are doing? Why not mice?

Mini-pigs are pretty useful because they share a similar anatomy, physiology and metabolic profile with humans. Sadly, mini-pigs are – like humans – also very prone to obesity and upon extended high fat-sugar dietary intake, they develop a phenotype similar to the metabolic syndrome, including visceral adiposity, dyslipidemia, glucose intolerance, insulin resistance and high blood pressure. Therefore, they are a very good model for the human obese condition – although interestingly, pigs rarely become diabetic!

What do you hope to find out?

I hope this project will help us to better understand the molecular effects of a chronic high-caloric intake/nutritional overload on the epigenetic information carried in spermatozoa – of fathers to be – what genomic regions/genes are affected, and how this potentially translates to a differential programming and phenotype in a future developing offspring.

How has COVID-19 affected the mini-pigs project?

We are conducting the study in collaboration with a private biomedical research facility, BIONEA LAB, which is located in the South of France. The animals are housed in their facility and they are responsible for the daily care and many of the experimental procedures, such as sperm collection. Due to the COVID-19 outbreak, I have only been able to visit the mini-pigs once, but I really hope to be able to go again in the near future and follow the last part of the study in person.

Despite the many challenges, I think we have been quite lucky that we were able to initiate and continue the study at BIONEA LAB during the lockdown in France. This was not the case for many other research projects across Europe and the rest of the world.

You’ve told us a bit about sperm collection. I’m a little nervous to ask, but how exactly does this work?

A particularly important reason why mini-pigs are useful is that we can train them to deliver a natural ejaculate, thereby getting only the mature sperm cells, which mimics the human situation. A bonus here is also that the ejaculate volume in mini-pigs is very large – up to more than 100ml – so you can get plenty of sample material to work with!

But collecting semen from a mini-pig is not an easy task and requires a lot of training – just until the mini-pigs figure out what it’s all about! Normally, you train the mini-pigs to mount a dummy sow. The first step is to expose them to the dummy sow several times with daily intervals to make them acquainted with the dummy. After this, they should learn to deliver an ejaculate each time they are mounting the dummy. Sometimes, this doesn’t occur, typically because of distraction, so you need to establish an environment that facilitates the willingness and mating behavior of the mini-pigs.

For example, the room needs to be quiet – no talking! – with no food hoppers and waterers around. Moreover, it’s important that the semen collection from one mini-pig is made immediately after the collection from another trained mini-pig, as the pheromones and odor from the first can ‘trick’ the second to be excited.

At BIONEA, the technicians collect the semen in the same room as where all the mini-pigs are housed, precisely because the pheromones produced by the animals stimulate the others. When the mini-pigs are trained, the semen collection is easy and takes at most five minutes each. Now the mini-pigs even run to the dummy themselves when they are let out of their box!

A virtual R course with Leo

Many of us find ourselves with the opportunity to learn a new skill while we are working from home. Bioinformatics is central to much of the research at CBMR, and is a specialist skill that takes many years of training and experience – so much so that many lab scientists don’t get the chance to train in bioinformatics (and vice versa).

A photo of a laptop with the caption, Learning a new skill from the home office. — *Learning a new skill from the home office*

Leonidas Lundell and Lars Ingerslev, who are both bioinformaticians in the Barrès Group, decided to share their programming expertise and teach the basics of programming in R (a popular and useful programming platform) with three other members of the group. Unusually, they have a background as bench scientists, and so understand how challenging it can be when starting out.

They thought it would be a good idea to teach researchers to solve some common problems they face when processing their data – to take some of the workload off the bioinformaticians! For example, they taught the basics of plotting so that researchers can modify figures themselves and the basics of processing microarray data. Of course, the main goal was to pass on programming skills to researchers who might otherwise not have the chance to learn them.

Ann Normann Hansen, who participated in the course, says: “We are learning things that are potentially very relevant for molecular biologists to use, such as visualizing data in different ways, sub-setting and converting data into different formats, and creating nice and consistent looking plots. Seen from a group-perspective it is also a win-win (hopefully!), as teaching us non-bioinformaticians some basic R programming skills could help relieve some of the very common tasks for the bioinformaticians. As we all know, they are very popular and busy guys!”

A screenshot of the program microsoft teams through which Leo is teaching the programming language R.

Learning to program in R on Microsoft Teams

During the course, Leo was surprised that the virtual format actually had a key strength over traditional classroom teaching. People can individually share their screens if they have a problem, and the other students get to follow the problem-solving process. This is in contrast with traditional classroom-settings, where individual troubleshooting is rarely shared amongst the class.

Ann echoed this advantage: “A good thing about learning to code ‘virtually’ is that we are a small group of people, which makes it a lot easier to ask questions. I wouldn’t have necessarily had this opportunity if I was sitting in a big class with lots of people, and it also feels more comfortable. The small-format ‘meetings’ also allow us to easily share our screens and codes with each other, for example when Leo and Lars are going over new topics, when we discuss specific exercises, or if we are stuck on a question. Also, by learning to code this way, we have a good opportunity for seeing and discussing different ways of solving the same question.”

As well as this initiative from the Barrès group, there are lots of ways researchers can learn new things during the lockdown. There are a number of online seminar series, for example @EcoEvoSeminars, whichare open to researchers from all disciplines, giving people the chance to step out of their comfort zone and hear from experts. Leo also suggests ‘The Science of Well Being’ course, hosted by Yale University – if you fancy something a little different! Ann sums up how the lockdown has impacted her thinking: “Looking at all of this in a positive way: instead of being busy with many of the weekly tasks we would normally do if we were in the lab, we have more time and opportunity to learn new things – both individually and together, such as having our little R course”.

A day in the life: Platform Manager Mie Mechta

As everyone settles into daily life working from home, I spoke to Mie Mechta about how she is juggling managing the Single Cell Omics Platform and parenting two young boys. Here’s a normal day in Mie’s life, alongside her husband and kids.

5:30 – The kids wake up between 5:30 and 6:00. As myself and my husband are both working full-time, we try to stick to a schedule throughout the day where we alternate work and childcare shifts of around two hours. I am a morning person, so I take the first shift and let my husband sleep in for another hour or so.

Mie’s workspace at home

7:00 – My husband takes over so I can start my work day. I start by making a to-do list and by preparing for any meetings I have that day. This is also the time I can go through my emails and reply to anything urgent.

8:00 – Back on kid duty, we do an activity together. Yesterday we colored Easter eggs, which kept them occupied for a while!

Painting easter eggs

9:00 – I attend a virtual lab meeting with the Barrès group for a couple hours. Normally, I try to attend lab meetings from several groups, since this is a good way to be updated and hear about new projects and protocols. This morning, we talked through what we completed last week and the tasks we are hoping to get done this week. It’s nice to hear from colleagues and get updates on the different projects.

11:00 – An early lunch with the kids.

12:00 – We go outside for a short bike ride, to get fresh air and stretch our legs. This is especially important with two small boys who are full of energy!

The view from our bike ride

14:00 – I meet with Mette and Helle, who are the lab technicians on the platform, to talk through their tasks. As the labs are closed due to the lockdown, we have been focusing on setting up Labguru, a digital lab book for the Center. I also fit in some work on the platform’s webpage, which we launched a few months ago. I am building some price examples for different services we offer and writing a short explanation of how to acknowledge the platform in publications.

17:30 – Early dinner with the family.

19:00 – The kids go to bed and I am able to get a couple more hours of work in. Last night I worked on producing a sequencing calendar for the platform in Labguru. When I work in the evenings, I try to focus on easy tasks as I am usually pretty tired! Then, I go to bed and start all over again the next morning…

Productivity starts with positivity

Cells have been frozen, flights have been canceled, data quickly stored on shared drives, and lab meetings have become virtual. With the lockdown set to continue for another two weeks, here’s how CBMR’s Barrès Group has been coping with our new reality.

The lockdown is forcing us, and many others, to be creative how we communicate and support each other as scientists. Social media and virtual platforms like Microsoft Teams, Zoom and Skype – so often seen as secondary to ‘being there in person’ – are proving their value and providing crucial human contact and inspiration in this unprecedented situation.

We still hold a lab meeting once a week, only we now use Microsoft Teams, which allows us to meet virtually with video, chat, share screens and present Powerpoint presentations. Other than a few teething problems, we are so far finding the platform to be quite effective, particularly the instant chat and creation of ‘channels’ for distinct projects.

My role as Research Coordinator has actually not changed a huge amount despite working from home, as I spend a lot of my time communicating with our collaborators is Sydney and Chicago via email and Skype. Keeping in touch with them has also given me an insight into their experiences of how the US and Australia are responding to the COVID-19 pandemic. However, one of the resources that I have found particularly useful in this transition is the infographic below by Dr. Zoe Ayres, which shows different ways in which we can use this time at home and help maintain focus.

For me, connecting with colleagues and letting go of guilt are two of the most important tips I try to remember. Chatting on Teams and making sure I take time to have a coffee, do a home workout, or listen to a podcast has helped me stay sane and happy over the past few weeks. There has been a huge focus on maintaining productivity – but you can’t be productive if you don’t have a positive outlook.

Many of the PhD students in our group have adopted some of these strategies, most notably the importance of sticking to a schedule. It has been no great surprise to hear that they have struggled to maintain focus while working at home – I can definitely relate to that! This is especially true for those members of the lab who have children and other family members to care for.

PhD student Eleonora Manita shares her experiences:

“Sitting in front of the computer all day is not easy. Going into the lab kind of gives you a routine and also a break, since it’s more manual. Doing experiments takes time and attention but some parts of it are also very automatic. So I would say that the biggest challenge has been being focused. Also, because of the situation we are facing, it is easy to get distracted by the news, which makes the whole experience a bit different than just a week where you work from home. I’ve been trying to keep a normal schedule as if I were at work, working and taking breaks when I usually do, but there is space for improvement!”

But for some, at least, the lockdown has created an unexpected silver lining – PhD student Emil Andersen is finally getting a chance to write his thesis!

A day in the life: Jessie Preston

The University of Copenhagen has now been shut down for almost two weeks, so how are CBMR staff getting on at home? PhD student Jessie Preston shares her daily routine, which involves baking, starting early, but waiting until mid-afternoon to get ready for the day – why not?

7:15 – For the most part I wake up at about the same time as I did when I was going into the office, however, it does differ each day because, well, I can! I immediately pop a loaf of bread in the oven that has been proofing overnight. Is it just me who has gotten incessantly into baking during the quarantine? There is currently a cake, some brownies, blueberry muffins, and two types of bread on the countertop. It is safe to say the quarantine is not great for my waistline.

I am not held back by the great danish yeast shortage of 2020!

7:30 – I have realised that my brain is sharpest first thing in the morning so I have been attempting to complete mentally-strenuous tasks first. This morning I proceed to finish pulling the data from literature for a power calculation, do some calculations for a future animal experiment, and go through my emails for the day.

My morning workspace including several Ikea impulse-buys after realising that I would be working from home for several weeks and did not own a desk.

9:15 – One of our group members has arranged to use this time to teach an R tutorial. It is great to finally have the time to dedicate to learning a new skill that has been on the to-do list for a while. I attend a two-hour video conference via Microsoft Teams with four other members of the Barrès lab.

This is what our R course looks like, setup and organised by Leo in Microsoft Teams.

11:00 – I go through and respond to a few messages from colleagues. Our team has mostly been engaging in “chats” using Microsoft Teams. Although not the same as having casual encounters with them in the office, it is a meaningful replacement.

11:15 – After several hours of using my brain, it is feeling a bit foggy. I decide now is a good time to get in some exercise while the sun is shining and go for a run in the park.

Attempting to find less crowded running routes while the parks miraculously seem to be far more crowded than usual.

12:30 – The CBMR Labguru Working Group has set up a Labguru Training webinar via GoToMeeting, which I sit in on. It seems most online meetings I have attended use different platforms to the point where I have now downloaded 4 new softwares for video conferencing. They all work relatively well.

This afternoon’s work space. See pictured, on left, a muffin – I am not letting quarantine get in the way of CBMR’s tradition for afternoon cakes!

14:00 – After the 90-minute seminar, my concentration is waning. I chat on the phone with a friend in a different time zone. A definite plus of working from home is the ability to take calls with friends and family in different parts of the world with a lot more ease of scheduling.

14:30 – I take a shower and get dressed for the day. Better late than never.

15:30 – I find that I have a lull in my concentration in the afternoon, so I have basically stopped attempting to do work during this time as I know I will get nothing done. Instead I run some errands: go to the store, do my laundry, and finish some housework.

17:00 – Most evenings I get a second wind where I can complete the bulk of my lengthy but more mundane tasks. Tonight, I spend two hours going through literature that I have flagged to read for the study I am planning, and another two hours making some edits to a document that a colleague has recently proofread. I complete these while sitting in on a virtual “party” that my flatmate is throwing for her parent’s wedding anniversary over Zoom (yes, another video conferencing software). It is inspiring to see all of the alternative ways that we are able to connect during these weird times. I can definitely cheers to that!

My evening workspace. My flatmates and I set up a proper at-home office when we realized that we may have to be prepared for the long-haul.

21:00 – I finish the day by going through my to-do list, marking off what has been complete, the tasks I hope to accomplish tomorrow, and adding any new assignments to the load. There is definitely plenty to be done even when working from home, the trouble seems to be actually doing it. But by giving myself space and forgiveness for having different expectations while in lockdown, I seem to have found a way to work that works for me.