The awesomeness of student researchers (or something like that)

One of the joyful aspects of working in academia is the prospect of having a fresh start every teaching year and the cycle of reflection and potential for improvement that comes with this. As such, autumn is always a time for me to reflect on my achievements and plan where to go next with my work. I am a super harsh self-critic, but I have a pretty good understanding of my strengths and weaknesses. For me, this is an offshoot of my mental health problems. Depression, anxiety and a good dose of neurodiverse thinking mean that I spend a lot of time in my head mulling over my place in the world.

I had my annual work review this week for the first time in a few years and as preparation I read over my achievements from previous reviews, albeit all before COVID. There is something that stands out to me (and likely no-one else) in this record of my achievements. And that is that my most successful academic projects, the ones that have been the most innovative, the ones that I have enjoyed the most and persevered to see their potential being realised, have been in collaboration with our own university students.

My most productive years were the ones where I was awarded students as researchers as part of a university wide research informed teaching scheme. Undergraduates had to apply for roles and were screened and interviewed prior to being employed for 60 hours of research work. I was lucky enough to be allocated five such placements over the years and each time, these students had a positive impact on the direction of my career. I have read many research studies waxing lyrical about the benefit of these projects to students and to the research informed teaching curriculum. But what about the benefit to staff? And what was it that made these placements so beneficial?

Perhaps it was the nature of the projects themselves that were so enjoyable. All of these placements were working on new projects that needed nurture and enthusiasm, ideas and action. And thanks to the fresh, enthusiastic approach of student researchers, they turned into amazingly feasible projects. My favourite part of the process is taking crazy ideas and turning them into a tangible, working project. Does this count as bona fide academic research? Probably not. Does it have outcome and impact? It certainly does. But most importantly, it is an accessible way of generating ideas and innovation in science without the gatekeeping that comes with larger research projects. And honestly, that’s my favourite place in the world, so its where I plan to stay.

Some of my past student as researcher projects that have been far too enjoyable to be considered work (nb it was still work):

Minecraft as a learning tool in science:

Over the years I have had many students working on this project for me. A bona fide reason to have Minecraft on my desktop at work? Yes please! These projects saw students build:

an in-game Minecraft ecology field trip for first year undergraduates as a prep tool prior to a real field trip. I presented this work at the Advance HE STEM conference in 2019 (STEM conference 2019: Using Minecraft in HE as a virtual field trip: One academic’s journey | Advance HE (advance-he.ac.uk)). NB I delivered this presentation in memes…. it was super cool)
a gamified biorefinery that demonstrated the circular economy to KS2 / KS3 aged kids
a MakeCode program that could be deployed in Minecraft and used scoreboard mechanics to keep tabs on your sustainability in the game, such as using non-renewable materials to build and destroying biodiversity.
Here is an in-game snap of one of our field trips:

Campus Biodiversity:

My AMAZING student for this project worked over two placements to design and deploy the Teesside University Campus Bird Count. We had volunteers walk a transect around campus and submit data to study the impact of activity on our birdy friends. We also made bee and bird sheets for general use to highlight the extensive biodiversity we have on campus, and its importance in maintaining a green highway through Middlesbrough.

SciArt in Biosciences:

The student worked with Middlesbrough Institute of Modern Art to investigate the crossover between science and art. This included a number of public engagement events at mima, ran with science students as volunteers, that aimed at engaging families with biodiversity monitoring in Middlesbrough town centre. And it involved knitting of course – we had knitted birds at the mima events:

I feel incredibly lucky to have been gifted with these amazing students and projects. Fingers crossed I might get to work on more of these placements in the future😊.

Any ideas for contributions to the above projects, and science knitting / crochet, are always welcomed!

The Echo Chamber

“Make Mental Health & Well-Being for All a Global Priority”

Monday was world mental health day. I have always tried to be transparent about my own mental health struggles and how these impact my day to day personal and professional life. I’m not a social scientist, so I can’t speak from a place of academic expertise on this subject, but I can talk about lived experience of being an academic with mental health struggles and neurodiverse traits.

I think, interact with people, behave, and generally do lots of things in way that might seem different to others. It’s not that my ways of doing things are wrong… but when you are different, it becomes hard to fit in and that’s exhausting. Most things we do in life are organised around the average person’s brain, and there isn’t much room for compromise (understandably for a lot of things).

As I get older, I am less inclined to worry about fitting in and the impact on my career. Academia is a hub for creativity and generation of ideas and knowledge. If it doesn’t support diversity of thought, it will remain an echo chamber for the average brain, and hence the rest of the world with it. So, I guess the point of this post is to say … solidarity to those who feel they don’t fit; we need you more than ever 😊.

And if you get chance, read this blog post about autism and inclusivity in sport by Josh MacLaren. It’s amazing and important work 🙂 Josh MacLaren – Sports industry, accessibility and digital media blog (tees.ac.uk)

And of course, SOME KNITTING. I’m fatigued from a few big projects and have lots of WIPs at the moment. I am working on things, honest…. just not finishing anything. Here’s a few pics of my current projects:

Photo of four science knitting pieces with no obvious identity for each piece — My latest science crochet / knits (top secret until they are finished)

I have FOUR big science projects underway at the moment. All of these are TOP SECRET until finished and are super exciting. And the picture above does not give away anything 😁.

I also have loads of winter knits on the go, here’s a few latest piccies:

Photo of knitted cream hat with two bobbles — Bobble Hat for Hubby (He needs to pick a bobble, I think the cream one?)

Photo of knitting showing two coloured rows of cream and brown bobbles — Paintbox Yarns Bubble Cardigan in cream and fudge Super Chunky acrylic!

Photo showing a semicircle shaped piece of knitting in cream and red — Just started this two-colour brioche shawl by Andrea Mowry “Cinnabar Shawl” and I am completely in love with the pattern.

Photo of autumn wreath with knitted leaves attached. — A fun one – just finished this crochet autumn wreath decoration. Pattern available for free on the Hobbycraft website.

More updates soon,

Helen x

A stupendous fail 🤷‍♀️

I thought it would be helpful to post about projects I undertake that fail, or those that take a lot of iterations to get to the final product. Below is the pile of earlier versions of the crochet fatty acids from the membrane granny square. It took dozens of attempts to work out a pattern for this piece:

Left: unused earlier pieces of the granny square membrane. Right: final piece.

This week I uploaded a piece of work to the Twitter SciArt Community group as part of SciArtSeptember activity for scientific illustrators to share their work. The work shared by members of this amazingly talented group is phenomenal. And then there’s my contribution….

This piece was rushed, designed and completed in a couple of hours (whilst the kids were still on school hols, so with Roblox and The Simpsons in the background). The prompt for day 1 was the word “Survivor” which immediately made me think of my favourite microbe Deinococcus radiodurans. This bacterium has an amazing ability to withstand radiation and repair itself following exposure, making it a microbe of significant interest in both the biotech and health industries (click here for link to a Nature Micro Reviews article on this bacterium). Hence, I couldn’t resist having a go at making something! Here is the end result (this picture here shows what I was aiming for):

Crochet representation of Deinococcus radiodurans as four neon coloured circles joined together in a tetrad — Final piece – a tetrad of Deinococcus radiodurans cells

Needless to say this was not how I imagined the final piece was going to look. I don’t regret submitting it, it was very different from the other pieces uploaded for that day which perhaps shows a different perspective on the topic. And whilst making the piece, I came up with loads of new ideas for future pieces of work, which I guess was one of the goals of the exercise? So, in some ways it was a success 😜.

PS My 10 year old thinks it looks like butt cheeks….

❄Winter Plasmid Wreath ❄

As promised – here is the winter / frost version of the pUC19 plasmid wreath. I’ve added sparkly crochet stars / snowflakes at the 🧬ori, 🧬AmpR and 🧬lacR binding sites 😃.

Fancy trying your own colour scheme or plasmid map? Tag me into a post on Twitter (@SciKnit) or Instagram (@ilovescienceknittingme) and use the #PlasmidWreath

Autumnal Plasmid Wreath (Crochet)

The idea for the piece…

I’ve had this idea for a while and every time a holiday season comes around, I promise myself that I will write the pattern 😀. Holiday wreaths were traditionally placed as Christmas decorations (having lots of symbolism in the Christian faith) but in recent years have become a main staple house decoration for all seasons and celebrations. Autumn wreaths are very popular in the UK when the beautiful colours of the season arrive and there is plenty of dropped foliage to forage and store.

Within a cell, a plasmid is a piece of DNA that exists in addition to the chromosome and can replicate independently. In older publications plasmids are typically described as small, double stranded circular DNA molecules. More recent publications will allude to other structural confirmations that exist. Nevertheless, the typical image that most science students encounter will be a circular plasmid, drawn in black and white, and labelled with tiny italicised scientific notations. Some links to further reading about plasmids can be found at the bottom of this post.

Some background info…

So both of these worlds need to be joined by the medium of crochet. This pattern will describe how to crochet and construct a plasmid wreath. I have chosen to make the plasmid pUC19 (p = plasmid; UC = University of California where it was created) as it is one of the most well know and commonly used plasmids. And it is one that we would typically use in undergrad teaching and labs. The first stage of the process required me to do some reading around the plasmid itself – its size and which genes it carries. The basic elements of pUC19, and the regions that I wanted to include in the pattern, are as follows:

Region	Approximate Size (nucleotide base pairs)
Whole Plasmid Size	2686
LacZ	400
Multiple Cloning Site	60
Lac operator	20
Lac promoter	30
Origin of replication	600
AmpR	900

Here’s an image of pUC19, courtesy of snapgene pUC19 Details at Snapgene.com

Pattern notes…

For this project, the crochet is a rectangle piece worked flat in single crochet using multiple colours of yarn to give the striped effect. This piece is then wrapped around a wreath and stitched together. I used a polystyrene wreath for this project, but other styles are available (and just using stuffing will suffice). Wreaths can be purchased from many crafting outlets (NB Hobbycraft UK have stopped selling them to reduce their plastic usage).

Measuring up…

In order to ensure your crochet piece fits around your wreath without being too baggy, you will need to measure the dimensions prior to starting as follows:

1. Length of your crochet piece (how many rows you should crochet): first, measure the inner and outer circumference of the wreath. Work out the average of these two pieces and then add on a few centimetres. For my wreath the measurements were:

1. Outer 78 cm
2. Inner 46 cm
3. Average 62 cm
4. Crochet piece to be made to approx. 65 cm

A photo of a polystyrene wreath showing the outer circumference being measured

2. Width of your crochet piece (how many stitches wide your piece needs to be): measure the circumference of the wreath body and using your yarn, crochet a number of chains and test out their fit around the wreath. Take into account your yarn type – how stretchy it is etc. My measurements were:

1. Circumference 17 cm
2. Chosen width 25 chains (which was approx. 14 cm without stretch)

A photo of a polystyrene wreath showing the circumference of the wreath body being measured with a tape measure

So I was crocheting a piece that was 24 stitches wide (plus one turning chain) and 65 cm long. In order to ensure the sizes of the genes were representative, I did some calculations to determine how many centimetres I would crochet for each section of the plasmid. The size of the plasmid is 2868 base pairs to be crocheted over 65 cm piece, so this meant I was crocheting approx. 45 base pairs per cm. Using the table from earlier, I came up with an approximate plasmid wreath map as follows:

Region	Approximate Size (nucleotide base pairs)	Length of crochet piece (see later section for details)	Colour Yarn	Number of rows at 2 rows per cm (see section on Gauge for details)
Whole Plasmid Size	2686	65 cm		130
Plasmid Backbone	approximated here	4 cm	Cream	8
LacZ Gene	400 (split before and after MCS)	6 cm	Burnt Orange	12
Multiple Cloning Site	60	1 cm	Variegated Yarn	2
LacZ Gene	400 (split before and after MCS)	2 cm	Burnt Orange	4
Plasmid Backbone	approximated here	1 cm	Cream	2
Lac Operator	20	1 cm	Yellow	2
Plasmid Backbone	approximated here	1 cm	Cream	2
Lac Promoter	30	1 cm	Brown	2
Plasmid Backbone	approximated here	10 cm	Cream	20
Origin of Replication	600	13 cm	Orange	26
Plasmid Backbone	approximated here	4 cm	Cream	8
AmpR	900	21 cm	Maroon Red	42

I chose autumnal colours for the piece, so here in the UK right now this would be represented by the changing colours of the leaves and foliage from green to browns, reds, oranges and yellows. I used yarn from my stash for this project, where possible choosing what I guessed was double knit weight yarn (seen below, top to bottom these are the colours for MCS, LacZ, AmpR, Lac promoter, Ori, Plasmid Backbone, Lac operator):

A photo of seven small yarn bundles to show the colours used in the project which were yellow, cream, orange, dark brown, maroon, burnt orange and a mixed pink and blue variegated yarn

Working out Gauge…

This is where you work out how many stitches you will need to achieve the correct width and length of your piece. I used a 4 mm hook, with double knit weight yarn. I did a couple of tests (see pictures below) to determine how many rows and stitches I would crochet per cm using my chosen materials.

Earlier I showed how I calculated the width of the piece as being 24 stitches across (with one turning chain at each end – not counted as a stitch) which equalled 14 cm. I crocheted two test pieces, each 24 stitches and one row of crochet, one in single crochet and one in double crochet (these are the US terminologies). The results are shown below. One row of double crochet was 2 cm in height, which I felt was too tall and wouldn’t give me enough definition and density of material. Hence I chose to use single crochet stitches – approx. 2 rows per centimetre of material.

A photo of one row of double crochet next to a tape measure, showing its height of 2 cm — Double crochet stitches with height of 2 cm per row

A photo of one row of single crochet next to a tape measure, showing its height of 1 cm — Single crochet stitches with height of approx. 1 cm per 2 rows

Materials…

4 mm crochet hook

Double knit yarn in seven colours

Yarn needle

Wreath (or toy stuffing)

Tape measure

(You can use any hook size or weight of yarn but will need to take this into account when measuring gauge).

Pattern…

This is a nice, easy crochet pattern that beginners can follow, and I’ve included lots of pictures to help with construction. I hope you enjoy it.

If you create a piece – please tag me in on Twitter (@SciKnit) or Instagram (@ilovescienceknittingme) and use the #PlasmidWreath

Using cream yarn chain 25.
Single crochet into second chain from the hook.
Single crochet into each chain to the end of the row (24 stitches total). At the end of the row, chain one (this is your turning chain).
Turn. One single crochet into each single crochet across the row (24 stitches in total). Chain one.
Repeat step 4 another 6 times (total 8 rows cream)
Step 4 is one row of crochet. Repeat this step for each of the different colour yarns in the following order and for the suggested number of rows:
1. Burnt orange (12 rows)
2. Variegated colour (2 rows)
3. Burnt orange (4 rows)
4. Cream (2 rows)
5. Yellow (2 rows)
6. Cream (2 rows)
7. Brown (2 rows)
8. Cream (20 rows)
9. Orange (26 rows)
10. Cream (8 rows)
11. Maroon red (42 rows)
Measure length as you go along to ensure you are meeting the gauge requirements. When finished, you should have a long piece of striped crochet as below:

A photo showing the final piece of crochet, representing the linearised plasmid, stretched out next to a tape measure showing its final length of 66 centimetres

Finished crochet piece

Constructing the Wreath…

Here, you will need to sew your finished piece around your wreath. Some guidance and pictures below:

I left long yarn ends for each colour and used these to sew up the edges of each piece using mattress stitch and a yarn needle. Once I reached the end of a colour section, I tied the working yarn to the loose end piece of the same colour and left these to tidy up at the end.

A photo showing the flat piece of crochet being wrapped around the wreath and stitched together so that it covers the wreath

Once I had sewed around the edges and sewed each end together I had the loose ends of yarn to tidy up. I used a yarn needle to tuck these into the inside of the piece and cut the loose ends as below:

A photo showing the back of the wreath which is now stitched together but still has loose ends of yarn to be tidied up A photo showing the loose ends of yarn threaded onto a needle and being inserted under the crochet piece to hide them

I then sewed a little piece of yarn onto the top to allow the wreath to hang from a picture hook.

A photo showing that a loop of yarn has been tied to the top of the wreath to allow it to hang from a hook on a wall

And finally…

Its finished!!! What do you think? Essential décor for every lab wall 😍!

A photo of the finished wreath hanging from a picture hook against a cream painted wall

As I said earlier, please send me pics or tag me into posts of you use the pattern. I would LOVE to see some creations of this piece. I have a winter frost plasmid wreath planned already – colour palette below:

A photo of seven small yarn bundles to show the colours that will be used in a future version of the wreath, representing frost and winter, which are white, peach, royal blue, variegated blues & whites. cyan, baby blue and teal

Even better – can you design your own pattern for your favourite plasmid?

Thanks for reading,

Helen x

@SciKnit

Crochet Granny Square Bacterial Cell Membrane

It’s been a while, and I’ve been struggling with serious mental health issues, so apologies for the lack of posts. I’m starting back with an easy post to document the last progress on the bacterial cell membrane!

Gram staining is about the least sexy of all microbial lab experiments, but its my go-to favourite. Lots of visuals, colour and instant results. It’s still the first place I start when identifying unknown bacteria. And I have carried out thousands of them 😫, so it seemed like a good idea for my next science crochet project. I wanted something 3D and tactile rather than the flat images you usually see in text books. So here we have the Granny Square Bacterial Cell Membrane:

Originally the fatty acids were crocheted with 100 % acrylic yarn, but there was too much curling in the final product, so I swapped to cotton yarn which has less curl and a stiffer texture:

Crocheted in 100 % cotton yarn:

Crochet Granny square depicting a cell membrane

And finally, a new addition to the project, some peptidoglycan layering in two colour popcorn stitch!:

Will it be Gram positive or Gram negative 🤔?

I will update with fully labelled images when I’m back at work in mid-August!

Minecraft and me…

Tell me the story behind your tattoo Helen, said no one ever… but here we are (its mostly pictures 😀 )…

I started playing Minecraft in the summer of 2014 during a really difficult period in my life. My beautiful daughter Emma was born in May that year. However, shortly afterwards I developed pretty bad postnatal depression, and struggled to leave the house for a period of time. Every afternoon during Emma’s 1-3 pm post-feed nap, I would play Minecraft on the Xbox, with her sleeping on my knee. See here, its the perfect position:

And this is when the beauty of Minecraft was brought into my life. The soundtrack, gameplay, characters, beautiful scenery, adventure, all helped restore my mental health that summer. Here’s my favourite song from the soundtrack, Haggstrom (still makes me cry):

So the tattoo? In 2020, I designed and knitted a fair isle hat for Emma, based on some of my favourite Minecraft flora. The process of getting from in-game images of the Minecraft flowers (Dandelion, Rose, Cornflower and Pink Tulip) to a complete knitted hat is shown below.

Top & bottom left: final knitted hat; centre: freshly inked tattoo; top & bottom right: images from the Stitchart app

I used the android app Stitchart (built by Caron & Jason Morris) to build prototype designs of the pattern (shown above). The amazing Chez (https://www.instagram.com/chezneychalks.tattoo/) used these images to design and ink the tattoo for me. All healed today and it looks amazing ♥.

Reversible Escherichia coli

Crochet bacterial cell, which can be turned inside out to display the cellular contents.

Biology Week 2016 – Knitting Bomb

Thought I would add some context to this post 😁. In 2016 I organised a biology themed knitting bomb with a group of staff and students at Teesside Uni. The event took place during the Society of Biology “Biology Week 2016”. We had lots of amazing contributions – some pictures below … warning this was prior to my social media days so these are proper old school and not glamorous!! The fab Helen Hodgson (Senior Technician Analytical Chemistry) knitted the brain – my favourite piece.

Some of these pieces are from published patterns as follows:

Blue Tit, Caterpillar and Shell were from the amazing book “75 Birds, Butterflies & Beautiful Beasties to Knit & Crochet” by Lesley Stanfield

Chromosomes, DNA, Agarose Gel are my own designs.

A photo showing Dr Helen Carney standing next to a stand of knitting at the 2016 biology week open day — Me at the event!

A photo showing knitted items on a chair, showing a knitted blue tit, knitted caterpilar, knitted shell, knitted DNA and chromosome, knitted agarose gel — Some of the knits on my horrible office chairs….

A photo of a collection of knitting showing a knitted brain, Noahs ark with animals, knitted bacteria and knitted parrots — Some of the knits on my horrible office chairs….

The stand at the 2016 Biology Week open day knitting bomb

Author: Helen