Formerly known as Mas a Tierra and renamed in 1966, this small mountainous island is a remote tropical paradise known mostly for the fact that it’s said to be the inspiration behind Daniel Defoe’s novel Robinson Crusoe, hence the name.
Today, Robinson Crusoe Island is far-flung holiday destination for intrepid travellers, populated by a small island community of around 600. One day, about fifteen years ago, a woman named Pia Villanueva came to the island on holiday for a relaxing break – or, at least, that is until the islanders discovered that she was a speech therapist…
To tell the story, Kat’s joined by Dr Dianne Newbury, senior lecturer and principal investigator in the molecular genetics of speech and language at Oxford Brookes University.
She and her team have been working with the island population, which contains an unusually high number of people with speech and language impairment, to discover what their genes can teach us about speech and language development, and what happens when this goes awry.
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
Welcome to our monthly scamper through the preprints on developmental biology and stem cells (and other related topics). Bumper section this month is the Genes & genomes section
The preprints this month are hosted on bioRxiv, arXiv and preprints.org – use these links to get to the section you want.
Phase transition specified by a binary code patterns the vertebrate eye cup Revathi Balasubramanian, Xuanyu Min, Peter M.J. Quinn, Quentin Lo Giudice, Chenqi Tao, Karina Polanco, Neoklis Makrides, John Peregrin, Michael Bouaziz, Yingyu Mao, Qian Wang, Bruna L Costa, Diego Buenaventura, Fen Wang, Liang Ma, Stephen H Tsang, Pierre J. Fabre, Xin Zhang
A gene regulatory network for neural induction Katherine E. Trevers, Hui-Chun Lu, Youwen Yang, Alexandre Thiery, Anna C. Strobl, Božena Pálinkášová, Nidia M. M. de Oliveira, Irene M. de Almeida, Mohsin A. F. Khan, Natalia Moncaut, Nicholas M. Luscombe, Leslie Dale, Andrea Streit, Claudio D. Stern
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish Damir Baranasic, Matthias Hörtenhuber, Piotr Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio D’Orazio, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Pelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller
Somatic mutation rates scale with lifespan across mammals Alex Cagan, Adrian Baez-Ortega, Natalia Brzozowska, Federico Abascal, Tim H. H. Coorens, Mathijs A. Sanders, Andrew R. J. Lawson, Luke M. R. Harvey, Shriram G. Bhosle, David Jones, Raul E. Alcantara, Timothy M. Butler, Yvette Hooks, Kirsty Roberts, Elizabeth Anderson, Edmund Flach, Simon Spiro, Inez Januszczak, Ethan Wrigglesworth, Matthew W. Perkins, Robert Deaville, Megan Druce, Ruzhica Bogeska, Michael D. Milsom, Björn Neumann, Frank Gorman, Fernando Constantino-Casas, Laura Peachey, Diana Bochynska, Ewan St. John Smith, Moritz Gerstung, Peter J. Campbell, Elizabeth P. Murchison, Michael R. Stratton, Iñigo Martincorena
Kaplow, et al. used a CNN to predict brain OCR ortholog open chromatin status
A 3D transcriptomics atlas of the mouse olfactory mucosa Mayra L. Ruiz Tejada Segura, Eman Abou Moussa, Elisa Garabello, Thiago S. Nakahara, Melanie Makhlouf, Lisa S. Mathew, Filippo Valle, Susie S.Y. Huang, Joel D. Mainland, Michele Caselle, Matteo Osella, Stephan Lorenz, Johannes Reisert, Darren W. Logan, Bettina Malnic, Antonio Scialdone, Luis R. Saraiva
The control of transcriptional memory by stable mitotic bookmarking Maelle Bellec, Jeremy Dufourt, George Hunt, Helene Lenden-Hasse, Antonio Trullo, Amal Zine El Aabidine, Marie Lamarque, Marissa M Gaskill, Heloise Faure-Gautron, Mattias Mannervik, Melissa Harrison, Jean-Christophe Andrau, Cyril Favard, Ovidiu Radulescu, Mounia Lagha
Hematopoiesis at single cell resolution spanning human development and maturation Hojun Li, Jideofor Ezike, Anton Afanassiev, Laura Greenstreet, Stephen Y Zhang, Jennifer Whangbo, Vincent Butty, Enrico Moiso, Guinevere Connelly, Vivian Morris, Dahai Wang, George Q. Daley, Salil Garg, Stella Chou, Aviv Regev, Edroaldo Lummertz da Rocha, Geoffrey Schiebinger, Grant Rowe
Direct reprogramming of human embryonic to trophoblast stem cells Norah M.E. Fogarty, Ahmed Abdelbaki, Afshan McCarthy, Liani Devito, Alice E. Chen, Prabhakaran Munusamy, Paul Blakeley, Kay Elder, Phil Snell, Leila Christie, Paul Serhal, Rabi A. Odia, Mahesh Sangrithi, Kathy K. Niakan
Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta Vashe Chandrakanthan, Prunella Rorimpandey, Fabio Zanini, Diego Chacon, Young Chan Kang, Kathy Knezevic, Yizhou Huang, Qiao Qiao, Rema A. Oliver, Ashwin Unnikrishnan, Daniel R. Carter, Brendan Lee, Chris Brownlee, Carl Power, Simon Mendez-Ferrer, Grigori Enikolopov, William Walsh, Berthold Göttgens, Samir Taoudi, Dominik Beck, John E. Pimanda
Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L Gulzar A. Wani, Hans-Georg Sprenger, Kristiano Ndoci, Srikanth Chandragiri, Richard James Acton, Désirée Schatton, Sandra M.V. Kochan, Vignesh Sakthivelu, Milica Jevtic, Jens M. Seeger, Stefan Müller, Patrick Giavalisco, Elena I. Rugarli, Elisa Motori, Thomas Langer, Matteo Bergami
Clonal dynamics of haematopoiesis across the human lifespan Emily Mitchell, Michael Spencer Chapman, Nicholas Williams, Kevin Dawson, Nicole Mende, Emily F Calderbank, Hyunchul Jung, Thomas Mitchell, Tim Coorens, David Spencer, Heather Machado, Henry Lee-Six, Megan Davies, Daniel Hayler, Margarete Fabre, Krishnaa Mahbubani, Fede Abascal, Alex Cagan, George Vassiliou, Joanna Baxter, Inigo Martincorena, Michael R Stratton, David Kent, Krishna Chatterjee, Kourosh Saeb Parsy, Anthony R Green, Jyoti Nangalia, Elisa Laurenti, Peter J Campbell
Image analysis of an Arabidopisis thaliana ovule using MorphographX 2.0 from Strauss, et al.
MorphoGraphX 2.0: Providing context for biological image analysis with positional information Soeren Strauss, Adam Runions, Brendan Lane, Dennis Eschweiler, Namrata Bajpai, Nicola Trozzi, Anne-Lise Routier-Kierzkowska, Saiko Yoshida, Sylvia Rodrigues da Silveira, Athul Vijayan, Rachele Tofanelli, Mateusz Majda, Emillie Echevin, Constance Le Gloanec, Hana Bertrand-Rakusova, Milad Adibi, Kay Schneitz, George Bassel, Daniel Kierzkowski, Johannes Stegmaier, Miltos Tsiantis, Richard S. Smith
Direct reprogramming of human fibroblasts into insulin-producing cells by transcription factors Marta Fontcuberta-PiSunyer, Ainhoa García-Alamán, Èlia Prades, Noèlia Téllez, Hugo Figueiredo, Rebeca Fernandez-Ruiz, Sara Cervantes, Carlos Enrich, Laura Clua, Javier Ramón-Azcón, Christophe Broca, Anne Wojtusciszyn, Anna Novials, Nuria Montserrat, Josep Vidal, Ramon Gomis, Rosa Gasa
Village in a dish: a model system for population-scale hiPSC studies Drew R. Neavin, Angela M. Steinmann, Han Sheng Chiu, Maciej S. Daniszewski, Cátia Moutinho, Chia-Ling Chan, Mubarika Tyebally, Vikkitharan Gnanasambandapillai, Chuan E. Lam, Uyen Nguyen, Damián Hernández, Grace E. Lidgerwood, Alex W. Hewitt, Alice Pébay, Nathan J. Palpant, Joseph E. Powell
Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A. Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A. Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A. Longacre, John Hickey, Yiing Lin, M. Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J. Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T. Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, Griffin Weber
A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Rafael Dariolli, Sunita L. D’Souza, Arjun S. Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth I. Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen S. Lynch, Katherine C. Michelis, Neelima C. Tangirala, Himali Weerahandi, David C. Thomas, Kristin G. Beaumont, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C. Schürer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar
Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates Lucie A. Bergeron, Søren Besenbacher, Tychele N. Turner, Cyril J. Versoza, Richard Wang, Alivia Lee Price, Ellie Armstrong, Meritxell Riera, Jedidiah Carlson, Hwei-yen Chen, Matthew W. Hahn, Kelley Harris, April Snøfrid Lo Natalie M Kleppe, Elora H. López-Nandam, Priya Moorjani, Susanne P. Pfeifer, George P. Tiley, Anne D. Yoder, Guojie Zhang, Mikkel H. Schierup
MITI Minimum Information guidelines for highly multiplexed tissue images Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Sarah Arena, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe’er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger
In the tenth SciArt profile of the series, we meet Elsa M. Quicazán-Rubio, a science communicator striving to bring the topic of biomimicry to a wider audience
Elsa participating in the Local Plastic Arts Fair (FLAP in Spanish) in Bogotá, 2021 as part of the creative collective Taller Casa Quemada (Photo by Camilo Buitrago)
Where are you originally from, where do you work now, and what do you work on?
I am from Colombia, where I studied my undergrad in Biology and wrote a thesis on biomechanics of hummingbird flight. This subject captivated me, and I completed a Masters degree at the University of California Riverside, USA, and an internship at the Wageningen University and Research, in The Netherlands. I then went back to The Netherlands to do a PhD in fish swimming.
During the pandemic, I was able to give shape to one of my dreams, Bioinspirada, a combination of Art and Science, connected mainly by Biomechanics and Biomimicry. I learnt how to make a website and launched Bioinspirada.com in January 2021. Since then, the ride has been awesome. I currently teach Biomimicry at the Colombian University EAN, collaborate in a team to develop Biomimicry workshops for kids at the Andes University and joined the creative space Taller Casa Quemada. I also participate as a speaker on subjects such as the role of females in science, biomimicry, and science communication.
Who hovers in the air? Hummingbirds. And who hovers in the water? Seahorses. What would the metamorphosis between a hummingbird and a seahorse look like? I was inspired by the work I did years ago on hummingbird flying, and the work on seahorse swimming during my PhD. I did this illustration in ink and colored pencils, using only three colors, 2017 – 2018
Has science always been an important part of your life?
Yes, science has always been an important part of my life. I remember talking to a friend in elementary school when we were about 10 years old, about our dream of becoming scientists. We both became scientists, one in medicine and the other in biology. I wanted to understand how animals work. Looking back at my childhood and youth, I see that the visits to my grandparents farm, and to the university, because of my parents’ jobs, contributed to this curiosity and help me to understand where I could get some of the answers.
As I thought of snails, the question came to mind as to what other purposes could their shell have. What if they flew and the shell was like a balloon? This illustration turned out to be what they call in the cooking recipes a “deconstruction” of a snail in its parts Inks, colored pencils and watercolors, 2020
And what about art – have you always enjoyed being creative?
Since I was little, I have enjoyed painting and creating objects. In one of the kindergarten reports, the teacher refers to my ability to express myself better with drawings than words at the time. I read this just a couple of years ago, and it warmed my heart knowing that drawing has been there even before I can remember. During life I have had the support and guidance from different people. My parents encouraged me and supported me with courses and with their own creative inputs. I took art courses in and out of the University while I studied Biology.
Trees are more active than we generally think. They can communicate with each other. Now, on second thoughts, I think this illustration was inspired by the book “The Secret Life of Trees” by Peter Wohlleben. Color pencils and inks, 2020
What or who are your artistic influences?
Some of my artistic influences are Quino, a Latin American cartoonist with a very clean line. Rien Poortvliet, Alan Lee, and Brian Froud who illustrate natural and fantasy creatures. I especially remember a tales collection called “Cuenta Cuentos” (Salvat ed.) where each story was accompanied by rich visuals and a narrator’s recording. My classes with the Illustrator Esperanza Vallejo and Arts Profesor David Izquierdo had a special influence on my art because they both encouraged me and taught me how to explore and combine techniques, freeing my style.
After a while of moving between countries, cities and houses, I felt the urge to draw my roots. I could see that they travel with me and that they are also of many colors, they are happy, they are deep, and they are even a little strange. Ink and Ecolins (similar to watercolors), 2009 – 2010
How do you make your art?
Usually, I have the idea of illustrating an animal or a feeling and I just let that idea simmer in my subconscious for a while, until a shape comes up in my mind and I draft it. I often look at pictures of the animal that I want to represent and use them as references. Other times, I just have a quick idea and go drafting and finish the drawing over the draft itself. One of the illustrations that represent a feeling is the one with roots. This arose from the need to represent and see my own roots because at that time I was often moving from one country to another.
A fish that can fly using bird wings. I was inspired by the idea of teaching children about flying and swimming in animals. Color pencils and ink, 2019
Does your art influence your science at all, or are they separate worlds?
Up until recently my art and science were mostly separate, although I drew the biomechanics setups, which made them easier to build. But I feel that the freedom that I had while creating the figures of my first first-author paper on fish swimming allowed me to invite my art to dance with my science. I enjoyed the process so much and learnt tips and tricks of what a figure needs to have to be easily scannable, to be enjoyed by people with different color perceptions, and to tell a story by itself. I feel that figures can benefit so much from art and this combination converts them into an invitation for the public to approach our research.
“I feel that figures can benefit so much from art and this combination converts them into an invitation for the public to approach our research.”
Today, I work with art and science creating catchy images that invite conversation about what makes nature a powerful teacher. And I’m starting to collaborate with artists and engineers to enhance the public’s curiosity towards nature.
The Kingfisher, a small bird that hunts fish by diving into the water, is one of the inspirations for one of the fastest trains in the world. And one of the species of this little bird lives in the wetlands of Bogotá, Colombia. That’s how close we are to inspiration. This is a semi-mechanical version of this bird. Watercolors and inks. 2020
What are you thinking of working on next?
Right now, I am developing a course on Biomimetic Illustration which is about learning to illustrate and portray nature’s solutions to human and environmental challenges. One example of this kind of illustration is seen in the Semi-mechanic Kingfisher that I illustrated for a blog post in my webpage Bioinspirada.com. The Kingfisher is the inspiration for the high-speed train redesign because of the shape of its beak and head that allows for a smoother passage between media with different densities. Therefore, in the illustration I represent this beautiful bird with a bionic head and beak.
I also plan to bring illustration to teaching biomechanics and biomimicry to children. Because one of my mid-term goals is to foster a curiosity for nature-inspired design from childhood. This is how I want to contribute to promoting the care and research of nature in future generations.
We’re looking for new people to feature in this series throughout the year – whatever kind of art you do, from sculpture to embroidery to music to drawing, if you want to share it with the community just email thenode@biologists.com (nominations are also welcome!).
With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help your year be a successful one.
The topic of this post is lab life. A lot of the posts of the Node concern lab life and we hope that these give a flavour of doing research in a range of settings.
Look no further than our Day in the life series to find out the day-to-day realities of working with a variety of model organisms. Currently our ‘zoo’ has 42 occupants, but we are keen to add more. We also have a compare and contrast post from Ashrifia Adomako-Ankomah who describes working on sea urchins, zebrafish and chick embryos. Read the post to find out which one comes out as the winner!
If you are interested in the ups and, surprisingly often, downs of doing research, then our Behind the paper stories are the ones for you.
Lastly we would like to focus on collaborations. With the days of single author publications far behind us, it is increasingly infrequent to see single lab publications. Many of these collaborations are interdisciplinary and we have some excellent posts taking you through how these come about and how they work.
We really enjoyed the light-hearted take from the Escudero group on their intra- and interlab collaborations.
If you have model organism you would like to add to our or collection, or a story of lab life you would like to share, please get in touch. You are also welcome post it directly onto the Node. Details of how to register with the Node can be found here. You can contact us at thenode@biologists.com
With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help your year be a successful one.
The topic of this post is dealing with data.
Upstream of analysing data is making a record of your experiment. You can find out The Pros and Cons of having an Electronic Lab Notebook (ELN) here on the Node. The article also includes a link to five popular ELNs, updated in 2020
We have collected below, a series of ‘how to’ guides from Joachim Goedhart, Helena Jambor, Jonas Hartmann and Steph Nowotarski covering organising, visualising and analysing data.
Once you have followed all the tips below, you are ready to present your data to the community. Helena tells us how to make a graphical abstract and how to win a poster prize (or how to make an impactful poster!)
If you have a ‘how to’ guide you would like to share, please get in touch or feel free to post it directly onto the Node. Details of how to register with the Node can be found here. You can contact us at thenode@biologists.com
With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help make your year a successful one.
The first topic we’ll tackle is writing. Whilst you might not currently have a writing project on the go, John Wallingford tells us in his first blog post of the #DevBiolWriteClub why you really should:
“Writing is like a sport. You only get good at it if you practice, with intent, every day.”
You can find John’s series of posts here, including a mention of his spin-off #devbiolgrantclub
We also have Grant writing advice for PhD students and Postdocs from Elisa Genie
For a more focussed look at writing reviews (or an introduction to your thesis), our acting Executive Editor Seema Grewal takes us through the entire process from planning to the finished article. Whilst our Reviews Editor Alex Eve shares what the reviewers of your article are going to be looking for in his post ‘Another look’ at peer review: reviewing review articles
If you are interested in practising your writing skills, we always welcome new authors on the Node. Please get in contact with us at thenode@biologists.com if you would like to discuss your ideas, or to get help with planning or editing. You can also get involved in science communication on our sister sites preLights and FocalPlane. preLights is where ECRs highlight preprints of their choice – you can find out how and why you should get involved here. Whilst FocalPlane is focussed on all things microscopy including ‘How to’ posts and blog series, among many other types of content that you can contribute to. You can find out how to get involved here.
Are you an early career researcher interested in the cell or molecular mechanisms underlying disease? Do you have an outstanding record and an innovative research plan?
The Sir William Dunn School of Pathology at the University of Oxford is looking for outstanding early career researchers seeking a stimulating and supportive environment in which to establish their research group as externally-funded fellows. We are specifically looking for researchers seeking mentoring and sponsorship to apply for career development fellowships (e.g. Wellcome Trust Career Development Award, MRC Career Development Award, CRUK Career Development Fellowship, UKRI Future Leaders, etc). Researchers who succeed in securing a fellowship will then be invited to establish their independent group in the department, benefiting from a generous support package, comprehensive mentorship, career development training and opportunities to recruit Oxford undergraduate and postgraduate students.
Successful candidates will have an outstanding track record in any area of biomedical research, with a particular focus on the fundamental cell and molecular biology underlying disease. The Department celebrates diversity and we welcome applicants from diverse backgrounds that are currently underrepresented at the University of Oxford.
The Dunn School is a dynamic and collaborative department, with 30 research groups and roughly 300 research staff investigating the biology underlying disease, using a wide range of basic and translational approaches. Our interests span many disciplines including cell and molecular biology, microbiology, development, immunology and cancer biology. Our researchers have access to excellent scientific facilities and support services, and the stimulating environment of the South Parks Road science area in particular, and the wider University of Oxford in general.
In the latest episode of Genetics Unzipped we’re taking a trip back in a virtual time machine, soaking in the primordial soup to discover the origins of DNA, find out where genes come from and how some species have stolen theirs from viruses, and explore what’s next for the genetic code.
Experts think that the first step towards life was simply a molecule that was capable of self-replicating. As a geneticist, your mind might jump straight away to the most famous self-replicating molecule of them all, DNA. As we discover, that’s probably the least likely scenario, but what actually happened is still a hot topic of debate among researchers searching for the origins of life.
Moving from DNA to genes, as far as we can tell, all of life on earth evolved from one common ancestor, LUCA, which must have had one set of genes, whatever they looked like. But that leaves the question of how this simple set of genes diversified to encompass the incredible diversity of genes that now exist in trillions of extant and extinct species on earth. We look at where genes come from, and how we’ve managed to steal some from our mortal enemies, viruses.
Finally, you may think you know your A, C, T and G when it comes to DNA, but what about B, P, S and Z? We discover how the genetic code is expanding, thanks to Hachimoji DNA.
If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip
We built an anatomy ontology. You should too – here’s why.
We have an information scale problem. I’m hardly the first to note the exponentiality and rapidity of information growth, as it was a keenly felt sentiment even at the dawn of the Industrial Age: “Knowledge begets knowledge as money bears interest (Conan Doyle, 1885).” Today there are a staggering 32,948,436 papers in the PubMed database (Aug 17th, 20:07 PM CT). Consider this sobering perspective: if a single person wanted to read each and every one of these papers, and, optimistically(!), read 5 papers per day, it would take 6,589,687 days. Or, 18,053 years. Which is the average lifetime of 229 people. And that’s just the papers written about all of the data that was collected.
The information problem in the life sciences in particular is further compounded by the varied types of data in current publications: supplemental figures, spreadsheets, stand-alone databases. With technological advances and increased storage capacity, collecting big data is no longer the bottleneck. New information is cheap. From single cell sequencing to large scale volumetric microscopy imaging, we have more data than we can wrap our heads around. How then do we effectively mine data to generate testable hypotheses with the potential to transmogrify information into new knowledge? Part of the answer lies in creating unified analysis schemes across platforms that are both human and machine readable. One of the ways we are doing this is by using ontologies as frameworks for organizing data.
What is an ontology?
Ontology might be a new word to you, but more than likely you’ve already been using them. Ontologies organize and link data for social media sites and big retailers. Have you ever saved an item to a Pinterest board (Gonçalves et al., 2019)? Used a filter to shop for a specific color, brand, and size of clothing from an online retailer? Run a GO (Gene Ontology) enrichment on a differentially expressed gene set? Used FlyBase or WormBase to browse gene pages? If so, you’ve interacted with an ontology. And you are going to interact with more.
An ontology by definition (Oxford Languages) is:
(1) the branch of metaphysics dealing with the nature of being (not this one!)
(2) a set of concepts and categories in a subject area or domain that shows their properties and the relations between them. (this one!)
If you’re familiar with libraries and the Dewey decimal system, this will all start to sound very familiar. To explain, let’s jump into an example:
“On the Origin of Species” IS A book.
That statement is an ontological axiom. An ontological axiom is a simple sentence that follows a pattern: concept / relationship / concept. In our example, both “On the Origin of Species” and “book” are concepts; IS A is the relationship. Now, let’s take it one step further: the idea of the concept in your head likely has some specific attributes. In ontological terms, those specifics are known as properties.
A set of properties for “On the Origin of Species” could be: Author: Charles Darwin Publication Date: November 24, 1859 ISBNs: 9780521867092, 9780857088475, 9788423918164…
Now we have a concept with properties and the categorical relationships between them. But we don’t have to stop there! We can define other relationships that exist for “On the Origin of Species” and string them together, like this: “On the Origin of Species” IS A scientific non-fiction book; a scientific non-fiction book IS A non-fiction book; and a non-fiction book IS A book. Here’s the super power of ontologies: by adding properties via relationships, we create a clear structure that can be used to run searches of either the properties (return all books where Author = Charles Darwin) or on the relationship (return all non-fiction books), and get resulting sets that include “On the Origin of Species.”
When concepts are visualized with their relations, ontologies are a web of information. Using common rules make ontologies interoperable. This interoperability allows information from different knowledge domains to be connected.
How do we use ontologies in biological sciences?
From how individual genes and what anatomical structures contribute to an organism, to a chemical library of compounds and molecules, to scientific evidence arising from laboratory experiments, ontologies are instrumental for data organization in the biological sciences (Chibucos et al., 2014; Degtyarenko et al., 2008; Haendel et al., 2009; The Gene Ontology Consortium, 2019). Arguably, the Gene Ontology (GO) (http://geneontology.org/), is the most familiar ontology in biology. GO describes how individual genes contribute to the biology of organisms at the organismal, cellular, and molecular levels. Another widely used ontology is the Uber anatomy ontology (Uberon, http://uberon.github.io/) (Haendel et al., 2009), a GO-integrated framework that describes body parts, organs, and tissues across animal species. Uberon unites anatomy ontologies for a growing variety of traditional and emerging research organisms, facilitating comparative evolutionary and developmental studies.
Why build an anatomy ontology?
Everything we study in biology comes down to a process that is happening in a place, in an organism. That single cell data? It came from stem cells sorted from the intestine of a mouse. That volumetric electron microscopy data? It came from mouse intestinal crypts. That in situ data that shows Lgr5 expression in mouse intestinal crypt stem cells… that crypt cell remodeling phenotype… all these disparate data, have the context of anatomy in common. Thus, anatomy is at the root of organizing seemingly disparate datasets and is a de facto way to aggregate data.
Does my research organism have an anatomy ontology?
If you work in an established research organism, great! You likely already have an anatomy ontology to hook your data up to. Check to see if your organism of choice has one at the Ontology Lookup Service. Almost any organism with a “base” (Flybase, WormBase…) already has an ontology and uses it to organize data within the base and as a framework for other tools, like Virtual Fly Brain (Osumi-Sutherland et al., 2014). If you work on an emerging research organism, and you are poised to generate a lot of data, there’s good news here, too. Many research communities are generating anatomy ontologies, notably Ciona and recently, Planarians (Hotta et al., 2020; Nowotarski et al., 2021).
What if my research organism doesn’t have an anatomy ontology?
If your research organism does not have an anatomy ontology, consider starting one! Assemble a squad with an expert(s) on the anatomy of your organism and at least one person who has some coding experience, and you can build an ontology for your data. The tools in the field are easy to use (Web Protégé, Git Hub and Google Sheets) and are becoming increasingly accessible with the ontology-development-kit (Matentzoglu, 2021), ROBOT (Jackson et al., 2019), and COGs (https://github.com/ontodev/cogs).
When’s the best time to build an anatomy ontology?
It is never too soon to put frameworks in place to organize and connect big data. For example, a growing number of labs use the planarian flatworm Schmidtea mediterranea as a research organism to model regeneration and stem cell biology, but there are still far fewer when compared to labs using Drosophila or C. elegans. Searching Pubmed for “Drosophila”, “C.elegans”, and “Planaria” yields 113,316; 35,030; and 1,884 papers, respectively. Going back to our original 5 paper a day example, it would take one person 62 years to read all of the Drosophila papers, 19 years to read all of the C. elegans papers, and just over a single year to read all of the Planaria papers. For the planarian field, this meant we were at a point where our data and information base was manageably small for a team of curators to capture all the anatomical terms needed for an ontology. As a general rule of thumb, it is a good time to build an ontology for data organization when the published record is still small enough for humans to read and process. That way, we ensure we can capture old data, as well as promote and ensure that future data can be integrated into a unified framework.
Why we need to use ontologies to organize big data:
If you’ll allow a somewhat geeky paraphrase, with big data, comes great responsibility. How do we handle big data responsibly? Efficiently? And in a way that is accessible and reusable? Luckily, we already have a framework in the form of FAIR. FAIR data practices insist that data be Findable, Accessible, Interoperable, and Reproducible (Wilkinson et al., 2016). When data is acquired and handled according to FAIR practices, everyone wins. Anatomy ontologies are Findable and Accessible when available through the Ontology Lookup Service (Jupp et al., 2015), are interoperable when using relationships found in the Relationship Ontology, and are Reproducible when reported in adherence to the Minimum Information for Reporting an Ontology (MIRO) practices (Matentzoglu et al., 2018). Adhering to FAIR practices while annotating anatomical data using an ontology ensures that all folks can access research and data more easily, source data has an opportunity to gather more citations, and importantly we all get more accessible science for our money.
Anatomy ontologies are the difference between hoarding data in piles versus curating and organizing biological data into a searchable library. Building an anatomy ontology for a research organism may seem like a big undertaking, but it is a necessary investment in the community, a tool everyone can benefit from. Consider our own experience: if two biologists and someone who scripts could build an anatomy ontology with help from the great community at the Open Biological and Biomedical Ontologies (OBO)foundry, so can you.
References
Chibucos, M. C., Mungall, C. J., Balakrishnan, R., Christie, K. R., Huntley, R. P., White, O., Blake, J. A., Lewis, S. E. and Giglio, M. (2014). Standardized description of scientific evidence using the Evidence Ontology (ECO). Database 2014,.
Conan Doyle, S. A. (1885). The Great Kleinplatz Experiment. The New York Times.
Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008). ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–50.
Gonçalves, R. S., Horridge, M., Li, R., Liu, Y., Musen, M. A., Nyulas, C. I., Obamos, E., Shrouty, D. and Temple, D. (2019). Use of OWL and Semantic Web Technologies at Pinterest. arXiv [cs.CL].
Haendel, M., Gkoutos, G., Lewis, S. and Mungall, C. (2009). Uberon: towards a comprehensive multi-species anatomy ontology. Nature Precedings 1–1.
Hotta, K., Dauga, D. and Manni, L. (2020). The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis. Sci. Rep.10, 17916.
Jackson, R. C., Balhoff, J. P., Douglass, E., Harris, N. L., Mungall, C. J. and Overton, J. A. (2019). ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics20, 407.
Jupp, S., Burdett, T., Leroy, C. and Parkinson, H. E. (2015). A new Ontology Lookup Service at EMBL-EBI. SWAT4LS2, 118–119.
Matentzoglu, N. (2021). INCATools/ontology-development-kit: June 2020 release.
Matentzoglu, N., Malone, J., Mungall, C. and Stevens, R. (2018). MIRO: guidelines for minimum information for the reporting of an ontology. J. Biomed. Semantics9, 6.
Nowotarski, S. H., Davies, E. L., Robb, S. M. C., Ross, E. J., Matentzoglu, N., Doddihal, V., Mir, M., McClain, M. and Sánchez Alvarado, A. (2021). Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. Development148,.
Osumi-Sutherland, D., Costa, M., Court, R. and O’Kane, C. J. (2014). Virtual Fly Brain – Using OWL to support the mapping and genetic dissection of the Drosophila brain. CEUR Workshop Proc.1265, 85–96.
The Gene Ontology Consortium (2019). The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res.47, D330–D338.
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci Data3, 160018.
The Human Cell Atlas (HCA) Developmental and Pediatric Cell Atlas meeting will be held August 25-27, 2021 online. Free registration up to and during the meeting is available at https://devped2021.humancellatlas.org/
This meeting will bring together diverse communities of scientists to plan how to map human development from conception to adolescence, and how to apply this knowledge to address important scientific and clinical challenges. We are particularly looking to engage developmental biologists and pediatric community members, as well as computational biologists, single-cell and imaging genomics experts, clinicians and ethicists who are interested in forging new collaborations to support this effort.
We have an amazing presenter line up, including: Hans Clevers, Kat Hadjantonakis, Muzz Haniffa, Aviv Regev, Sarah Teichmann, Sten Linnarsson, Deanne Taylor, Amos Tanay, and Barbara Treutlein. The meeting also will feature lightning talks, poster sessions and an ethics panel led by Bartha Knoppers and Jonah Cool, with panelists Helen Firth, Dimitri Patrinos, Vasiliki Rahimzadeh and Deanne Taylor.
To help participants connect around key research areas, a large part of the meeting will involve scientific discussion at breakout sessions covering the following topics:
Regulatory mechanisms in development (led by James Briscoe and Jesse Gillis)
Single cell genetics to highlight genes, pathways, cell types and tissues (led by Gray Camp and Xiao Chen)
Understanding cellular decision-making during development (led by Anne Grapin-Botton and Cantas Alev)
Imaging and spatial omics technologies and applications (led by Ali Erturk and Hiroki Ueda)
Lineage tracing, recording, clonal evolution, tagging and its applications (led by Samantha Morris and Nozomu Yachie)
Abnormal development in humans (led by Heather Etchevers and Stéphane Zaffran)
Clinical genetics – use of development and pediatric single-cell atlas data to identify disease causing variants in patients (led by Sarah Henrickson and Helen Firth)
Regenerative medicine (led by Guoji Guo and Jason Rock)
Developmental origins of health outcomes over a lifespan/Challenges of studying an organ from development to aging at the single cell level (led by Kricket Seidman and Arnold Kriegstein)
The ethics of working with human developmental and pediatric samples (led by Bartha Knoppers and Jonah Cool)
This meeting is generously supported by University of Toronto’s Medicine by Design program, the Children’s Hospital of Philadelphia, Cincinnati Children’s hospital, the Hospital for Sick Children, Toronto, Genome Canada, the Development journal, and the McLaughlin Centre at the University of Toronto. HCA gratefully acknowledges the Chan Zuckerberg Initiative and the Klarman Family Foundation for additional organizational support.
(No Ratings Yet)
Loading...
