theshortread5
Welcome to The Short Read, our weekly peek behind the curtain at the people who make this amazing community tick. Make sure to check back every Tuesday for the latest installment.

Kazuharu Arakawa

Kazuharu Arakawa, Associate Professor, Institute for Advanced Biosciences, Keio University

Kazuharu Arakawa is devoted to comprehensive and quantitative understanding of extremophiles such as tardigrades, and high performance materials of biomaterials like spider silk.

As an Associate Professor at Institute for Advanced Biosciences at Keio University, Japan, his team is currently working on collecting and sequencing 1000 spider genomes from across the world using the Nanopore MinION to decode the mechanical properties of their silk. He is also a visiting fellow at Japan-based Spiber Inc., which is looking at using spider silks for materials in clothing, cars and renewable plastics.

 

What are you working on right now?

I’m focused on decoding spider genomes to understand what properties the specific genes actually translate into: marrying the phenotype to the genotype. We’re currently sequencing 1000 spider genomes, of which my team is around the 900 mark. 

Spiber was founded by my students, and although I’m not directly involved in their development, we’re teaming up with them based on this research to understand different mechanical properties of spider silk.

Spiders produce seven types of silk and Spiber has already made several composite materials from these. The silk can be produced synthetically by inserting the spider genes into microbes and then mass producing the silk via fermentation.

You don’t have to make the spider proteins into fibres though, you can also make gels and sheets and “rubbery” like materials which can have shock absorbent properties. Another idea is to produce renewable plastic based on this composites.  

These flexible bio-based materials, from car seats to clothing, have secured Spiber partnerships in other industries, such as with Toyota at the Paris Motor Show and The North Face fashion brand.

 

What’s the biggest challenge you face in your work at the moment?

I suppose working on the high-volume strands. Spider genomes are very long and repetitive, which was a challenge when using other sequencing instruments to get the full >10Kb reads.

We tried using several traditional NGS sequencers, such as the Illumina platform and PacBio sequencer, but neither of these could not span the entire spider gene when sequencing (limited to around 10kb), or assemble all the repeats.

It was only with the MinION sequencer we could finally span out to 30Kb or 50Kb reads which contain the complete spider genes.

 

Name one big development that you would like to see in your field the next 18 months.

We’re finding the repeated motifs, but we cannot find the complete sequence of the spider genes using conventional sequencers. So we’re looking to use more MinIONs to get the actual full-length genes for all of the spiders we’re sequencing.

With our team of around 15 people it shouldn’t be too difficult to do in that time frame.

The Short Read

Kazuhara and his team at Keio University / Bioinformatician.org

 

What are you most proud of in your career?

I’m really interested in how the dynamics of life arise from matter, and last year a paper of ours was published in Nature Communications disproving a long-standing theory in tardigrade genomics.

I’m now describing a new species of Macrobiotus tardigrade found local to our campus area in Japan. I isolated the species from there and we’re now sequencing this species genome.

So I suppose I’m most proud of being a comprehensive all-round researcher into tardigrades, from finding news species to creating the culturing protocols.

 

Which scientists, living, dead, or fictional, would you invite to dinner, and why?

Francis Crick, of course. I’d also love to Schrödinger, for well, what does life mean? Ha.

 

What advice do you wish someone had given you at the start of your career?

One of my mentors on the course always said: “stick to the question”. For example, when many researchers are good at genome sequencing, they stick to that method even if the question you want to answer is not possible that way.

So you must change the protocol and method every time in order to focus on the question, and not get too caught up with secondary findings in the technology itself.


Why not check out The Short Read archives? 

George Church 
“Follow Your Dreams, not the Drove”

George Church, Professor of Genetics, Harvard Medical School

Amalio Telenti 
Defying the “Exome-Centric” View

Amalio Telenti

Anna Middleton 
“It’s OK to Be a Bit Creative and Entrepreneurial”

Nan Doyle
“Get Clear on What Matters to You”  

Nan Doyle

David Smith 
The “Real Keys to Scientific Success”

Hannes Smárason 
The Importance of Grit

Hannes Smárason

Eric Topol 
“Always Question; Never Accept Dogma”

Kristen Sund
“You Don’t Change Culture Overnight, it Happens in Baby Steps”

Kristen Sund

Manuel Corpas 
“Don’t Rely on the Future to Make Your Choices Now”

Manuel Corpas

Brendan Gallagher 
“Let Your Work’s Ripple Effects Help Sort the Future Out”

Hayley Robinson
When Technology Outpaces Policy

Hayley Robinson - MGH

Valentina Nardi 
“Like a Detective Solving a Puzzle”

Valentina Nardi

Stephen Kingsmore 
“Don’t Forget to Breathe!”

Stephen Kingsmore

Judith Benkendorf 
“Do Not be Afraid to Look For Mentors” 

Judith Benkendorf

David Flannery
“If Only We Could Predict the Future” 

David Flannery ACMG

Sarah Teichmann
Exploring the Vast Variety 

Sarah Teichmann

T. Patrick Hill
“Never Forget That Humility is the Mark of Greatness” 

Never forget that humility is the mark of greatness

Liz Harley 
“Give Yourself Permission to be Challenged” 

Liz Harley

Nick Lench
“Strive to Work With the Best”  

Nick Lench

Carlos Bustamante
“We’re All Adding Our Stone to the Pile” 

Dr. Carlos Bustamante

Paula Goldenberg
“Genetics is a Rapidly Changing Field” 

Paula Goldenberg

Said Ismail
“Making WGS Affordable to Labs and Individuals in Lower Income Countries” 

Said Ismail

James Christensen 
“Research is a Marathon, Not a Sprint” 

James Christensen

Enrique Velazquez
“Innovative Technologies are Potential Game Changers” 

enrique velazquez

Damien Tully 
“Once You Get the Bug for Science, It’s Infectious” 

Damien Tully

Nazneen Rahman
“Sciences is Surprisingly Fashion Driven” 

Nazneen Rahman

 


Who would you like to see interviewed for The Short Read? Let us know via contact@frontlinegenomics.com


Opinions and views expressed in The Short Read are the interviewee’s and not those of the home institution

More on these topics