All posts by Carl Lewis

Synthetic Yeast Chromosome Manipulation

Tom Drake

Singer Instruments, Roadwater, Somerset, TA23 0RE, UK.
 
 

Introduction

Saccharomyces cerevisiae has long been utilised as a model organism due to the replicable nature of eukaryotic processes. Recent advances in genome editing, with tools such as CRISPR becoming more efficient and controlled, have enabled further advances into the manipulation of S. cerevisiae including modifications to the karyotype. Recent publications in Nature from Shao et al.1 and Luo et al.2 have done just this and opened the door to further research in chromosome biology and the evolutionary nature of chromosome development and function.

 

 

S. cerevisiae

Wild type S. cerevisiae contains 16 chromosomes, each with a distinct set of genes, a centromere and a telomere at each end. How this species came to have 16 chromosomes is a question not fully understood. For example, we know some of our closest ancestors in primates have 24 pairs of chromosomes, yet we only have 23 pairs. This is due to an ancestral fusion in what we now know as Chromosome 23. The number of chromosomes that a species has is unlikely to be chance, and more likely to be a product of an evolutionary advantage, but what happens if a species had less chromosomes?

Two groups simultaneously investigated what would happen to S. cerevisiae if they reduced the number of chromosomes, without removing any essential genes.

The two groups; from Institute for Systems Genetics, NYU Langone Health, USA, and Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, China both published their results in Nature on August 1st 2018. Both groups simultaneously worked on reducing the number of chromosomes whilst maintaining the genome of S. cerevisiae. Utilising CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), which is one of the most aggressive engineering strategies, Luo et al. removed telomeres and one centromere at a time to reduce the number of chromosomes from n=16 stepwise to n=2. This process produced a variety of strains with varying chromosomal numbers which are beneficial for further genotype and phenotype research.

Fusing yeast chromosomes

Shao et al. created a single linear chromosome containing each of the 16 chromosomes, through successive end-to-end fusions and centromere removal. Interestingly, Luo et al. were unable to produce a stable yeast with only one chromosome, yet Shao et al. were. This is potentially due to the differing techniques used to edit the genome, or something as simple as the order of the fusions contributing to the success of the strain. Further research into this would prove interesting as this may suggest why one method was more successful.
 

Great, now we have n=1 and n=2, so what?

Now the strains had been engineered to only contain one, or two, chromosomes, the question was to investigate what difference this made compared to the wild type (n=16). As the role that chromosomes can play in the regulation of genes is not yet fully understood, they were careful to investigate gene expression in their new strains. Surprisingly, there was very little difference identified in the transcriptome or phenome of the n=1 strain and n=16. The other group, with n=2, reported modest transcriptomic changes although growth was shown with no major defects. This research suggests that a reduction in karyotype may have much less of an impact than first thought.
 

What if they mate?

S. cerevisiae grows as a haploid, meaning it only has one copy of each chromosome – humans are diploid, in that we have two copies of each chromosome. Haploid yeast can grow asexually, and continue to be clonal, or they can mate sexually and form diploid yeast before sporulating into haploid spores. This process transfers genomic material through genetic recombination. What happens if two strains with differentiating numbers of chromosomes mate sexually?

Luo et al. investigated this, and with varying results, showed that as the number of chromosomes drops below 16, the viability of spores decreases. When n=12, the viability of spores was less than 10%. When the wild type crossed with n=8, the viability of spores was less than 1%. Conversely, these strains could mate with others with the same number of chromosomes and produce viable tetrads and spores. This suggests that eight chromosome fusion events isolate these strains from reproducing and therefore enable isolated genetic evolution potentially leading to new species.

 

What have we learnt?

From the genetic engineering of S. cerevisiae chromosomes, reducing the total number from 16 to 1, we’ve seen that there are no major reductions in transcriptomes or phenomes. The reduction in chromosome number has also been investigated in terms of mating ability, with spore viability decreasing as the difference in chromosome number increases. Although, each strain could still mate with an identical chromosome number, and produce viable spores.

This research has created the basis for further investigation into the function, structure and purpose of chromosomes and the role that they play in a variety of essential processes in the cell. Alongside paving the way for the study of chromosome evolution and the significance of chromosome number within S. cerevisiae.

 
Jef Boeke and his laboratory at the Institute for Systems Genetics, NYU Langone Health, New York, USA, utilise an MSM tetrad dissection microscope to dissect spores, and have more recently added a SporePlay+ tetrad dissection microscope, a ROTOR HDA colony manipulation robot and a PhenoBooth colony counter to their laboratory.
 
Jef Boeke - Singer Instruments MSM 400 Tetrad Dissection ScopeJef Boeke - Singer Instruments MSM 400 Tetrad Dissection Scope

 

References

1. Yangyang Shao, Ning Lu, Zhenfang Wu, Chen Cai, Shanshan Wang, Ling-Li Zhang, Fan Zhou, Shijun Xiao, Lin Liu, Xiaofei Zeng, Huajun Zheng, Chen Yang, Zhihu Zhao, Guoping Zhao, Jin-Qiu Zhou, Xiaoli Xue & Zhongjun Qin. Creating a functional single-chromosome yeast. Nature (2018)
2. Jingchuan Luo, Xiaoji Sun, Brendan P. Cormack & Jef D. Boeke. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature (2018).
3. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA. Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proc Natl Acad Sci U S A. (1991);88(20):9051-5.

PhD PIPS Lab Automation Placement

Singer Instruments internship

Suzy Hocking
PIPS Student
London School of Hygiene and Tropical Medicine

 

“I had a fantastic three months and made lots of friends – I was very sad to leave!”

 

When I first applied for my PhD, the PIPs internship was a great talking point in the interview, but in reality, wasn’t something I was that thrilled about. As I entered my second year, and pressure to get my PIPs sorted increased, I had a half-hearted look around – fully expecting to find some run-of-the-mill internship, where I would be wearing a suit, making coffee, and staring at a computer screen all day.

 
The internship at Singer Instruments was advertised by our careers advisor. I read the job posting, researched the company a bit and, even though robotics had never really been an interest of mine, decided to bite the bullet and apply. What really set Singers apart, even this early in the application process, was the clear emphasis on community at the company and it seemed from the website that it was a pretty fun and interesting place to work.
 
I was interviewed, and soon after offered the place!
 
It was a bit of a lifestyle change for me – from the smoggy, concrete jungle of London to the green fields of Somerset; where buses after 6pm are a myth, cider with dinner is (mostly) compulsory, and there are probably more cows than people.
 
I got in on my first day to find that everything had been set up for me and spent day one learning, and quickly forgetting, everyone’s names. I settled in quickly, and was soon given various projects to work on.
 
From day one I was treated as an important member of the team – not necessarily how an intern expects to feel. My day was split between the office, doing market research for new product development; the lab – where I was working on the scientific testing of Singers’ latest product – the PIXL; and R&D – hanging around with the engineers and software developers – usually so they could fix something for me, but often being helpful as well! The people that I worked with were wonderful, and I was never left to muddle through something on my own, they were all too happy to help!
 
It was easy to see how the work I did on my PIPs benefited the company, and the skills I’ve taken away will be invaluable (it was also a very nice 3-month break from the daily grind of PhD life!). Singer Instruments was worlds away from the academic environment of my PhD and I loved being able to learn about so many new things and I have a newfound appreciation for just how many specialists it takes to develop, build, and launch a product.
 
On top of the work, there was lots of cake and cups of tea, sushi, pub visits (complete with some questionable cider), and one very enjoyable christmas party. I had a fantastic three months and made lots of friends – I was very sad to leave!

I first met the guys from Singer at a conference. I’ve always had a keen interest in robotics as a hobbyist, not to mention red decals and profanity. From the off, I knew that they were different, I distinctly remember Hawaiian shirts and offering out shots of vodka in SBS format dishes. Having struggled for a while to think of somewhere to do an internship, 3 months that were a requirement for my Ph.D., suddenly it clicked. I fired off an email, confessing my love for robots, somewhat naive, yet I was surprised to get an email back within the hour.

 
By the time the week was out, I’d had an interview and was all set. After a Christmas break, me and my ramshackle Peugeot 206 trekked down to Somerset from my home in the Midlands (a place only known to northerners… in the south it’s simply called ‘the north’). Having a high tech engineering facility, nestled in the sleepy village of Roadwater was one of the greatest juxtapositions I had ever seen! I love small towns and villages, so having the chance to work in one, while still being at the state of the art was really exciting.
 
The joy of working with an SME like Singer, is you really have to fill any role required, and you gain an enormous amount of experience. The company really values the opinion of each of its members, and it was amazing to see that as an intern I was contributing to real change within the company. For the most part, I spent my time working as an interface between the R&D team and the Sales team.
 
On the R&D side this included prepping samples for testing the ROTOR HDA, as well as the PhenoBooth that was undergoing the last stages of testing. During my work in the lab I had gained a keen eye for detail, but you really get a different approach working in a team. You learn not only to see what’s going wrong and why, but also how to communicate this in a cross-disciplinary manner, allowing recreation and adequate troubleshooting. The Singer team is second to none, and while everyone is working flat out to do the best job they can, they are all friendly and engaging.
 
Like all good places to spend time, work wasn’t everything. I spent a lot of time exploring the local area, being on the doorstep of the Exmoor National Park. I met new friends in new pubs, trained with a baseball team, and discovered a love of farmhouse cider!
 
The lure of Singer Instruments was too much to resist. Upon completion of my Ph.D. I was given the opportunity to return, managing the in-house scientific research, and UK sales portfolio. Jumping at the chance, I now live and work in Somerset! What was a diverse and rewarding internship, has become an ideal beggining to my career. I have found a role where my specialist learning makes a direct impact on the UK bioeconomy, at the end of each day seeing the changes that I’ve made and influenced, and… I spend most of my days playing with robots.
 
Interested in doing your PIPS Placement with Singer Instruments?


Singer Instruments internship

Ollie Severn
PIPS Student
University of Nottingham

 

“By the end of the internship, I was surprised by how many skills I had gained.”

 

Grow Your Own GFP Xmas Tree

Is it Christmas yet? The Singer lab has certainly been getting into the festive spirit. The flasks are full of sherry and the turkey’s in the incubator! All that’s left to sort out is the Christmas tree. But, if like us, you’re sick of untangling the tree lights and cleaning up the constant shower of pine needles, we have the ultimate solution: grow a GFP Christmas tree!
 


 


To create your own GFP Christmas tree you will need:

 

Ready? Let Christmas commence!

 
1. Load the Stinger file into the ROTOR.
 
2. Follow the on-screen instructions for loading your 384-density, GFP source plate and the target plate, then hit go!
 
3. Drink some sherry and be merry while the Stinger does its thing.
 
4. Use the PhenoBooth to watch the GFP tree glow and come to life.
 

Download our Stinger template file and get pinning!
We’d love to see how yours turn out. Share your fluorescent colonies on our Facebook / Twitter pages using the hashtag: #gfpxmas
 

Merry Christmas to all and to all a good science.


Competition: Change the chest of science!

Singer Instruments Science T-shirt Competition 2016

Win custom lab coats for your whole lab!

Want to see thousands of scientists worldwide wearing your lab coat or t-shirt design? Enter your ideas below for scientific stardom!

Simply upload an idea using the form below. Don’t worry if your drawing looks like something out of your undergrad lab book! Our graphic designers will turn it into a work of art. Still not convinced? Just enter a description of your idea and we’ll do the rest!

Become your lab’s hero!

RULE 1: Celebrate science!
RULE 2: Be awesome!




Fill out my online form.

Agar Plate Pourer (Competition)

Currently the Serial Filler is unavailable. We have received a lot of fantastic feedback and improvement suggestions from existing Serial Filler customers. Rather than investing in the next large Serial Filler production run, Singer Instruments are in the process of considering an improved model.

…And after much (a couple of years) tribulation, we are proud to announce that the winner is Dan Smethurst from the Campbell Gourlay lab, in the Kent Fungal Group at the University of Kent!

Watch the moment we ‘surprised’ Dan Smethurst with his fabulous new Automatic Agar Plate Pourer – the Serial Filler:

Deep question: What’s my role in the World? What will be my scientific legacy? What is the answer that I am devoting my entire academic life and therefore soul into finding?

Maybe its curing cancer, explaining prion protein misfolding, or preventing death?! Maybe its understanding the role BCL2 plays in ear colour or some other hypothesis so niche that three years later you begin to doubt whether you can even buy a can of ravioli from the corner shop without sweating profusely and mumbling inanely about stop codons.

You’ve spent years producing network diagrams, learning how to spell Aduncuperistomatus or trying to understand why the hell you need to comb DNA. The bottom line is that you are bloody clever! And with this being true, you should be spending your high functioning brainpower doing bloody clever things! As such we reached one vehemently emphatic conclusion:

Pouring plates… what a f**king waste of time!

Solution: We have made a kick-ass plate pourer.

But with Slime Mold marginally edging the intelligence scale when pitted against our Product Development team, we realised that coming up with a name ourselves again (like we did with the spectacularly creative MSM 100, 200, 300 and then 400 microscopes) was probably not the greatest idea.

But wait! Fear thee not! We know scientists! And scientists are clever! Three months of blood, sweat and coffee later, and triumphantly our team devised an intrepid plan:

Microbiologist + Competition = Good name for plate pourer

Singer Instruments’ scientific advisory team stepped in and highlighted a chemical imbalance, and made one small alteration:

Microbiologist + Competition = Good name for automatic plate pourer + Free plate pourer for winner

Here are but a handful of the wonderful entries that we received:

Thanks very much to everybody who took part! You are all legends!