The seventh episode of Made the Same Way, a podcast produced by the Wellcome-funded Human Developmental Biology Initiative, features sociologist and writer Marieke Bigg discussing the ethics of research with early human embryos with Mancunian poet and rapper Meduulla. The pair discuss the legacy of Anne McLaren and muse on future implications of this area of research.
At the end of the episode, the pair collaborate on an original piece of music inspired by their conversation.
“What things can we consider to be right and wrong, and who makes that decision?”
– Meduulla
About the participants
Marieke Bigg writes about bodies and culture. She holds a PhD in Sociology from the University of Cambridge, where she studied the technological transformation of human reproduction, with a focus on Dr Anne McLaren’s role in the human embryo research debates. She now writes both non-fiction and fiction about the cultural dimensions of biology and bodies. In addition to her books, Marieke writes freelance, hosts podcasts and panels, and collaborates with scientists and biologists to discuss and produce art that conjures new social worlds.
Hailing from North Manchester, Meduulla is a 23 year old Zimbabwean-born Rapper, Poet and DJ paving her way through the UK rap scene. Meduulla marries her modern flows and witty lyrics with jazz inspired hip hop instrumentals to create music that reflects the present day whilst carrying a nostalgic air.
Despite having been a writer for 10 years, she only released her first single in 2021 which then led to her appearance on BBC’s The Rap Game UK as a finalist. Her independently released single, Mish Muulla was selected as Track of the Week on BBC 1Xtra Radio,resulting in Meduulla performing at Reading and Leeds Festival in 2022. The wordsmith is a 2023 Sound and Music Seed Award recipient and her poetry won first prize in TogetherintheUK’s migrant writers competition. Her passion for using her lyricism as a force of positive change continues to be recognised by various cultural organisations.
In 2023, Meduulla will release her debut project entitled Oblongata.
Please subscribe and listen to Made the Same Way on Apple podcasts, Spotify, or wherever you get your podcasts. If you enjoy the podcast, please rate and review us on Apple podcasts to help others find us!
Gender problems in STEM are familiar to women researchers in every corner of the world. Japan is no exception. In a culture that seeks harmony and balance with people around, where conflict is avoided at all costs, it is often difficult to express someone’s needs. Social pressure is working in very subtle ways. You have an event in a room with photos of the previous heads of the department, twenty or thirty of them, which are all men; you go to a conference and see the overwhelming majority of the keynote speakers being male researchers; you notice the appointed leaders of the diversity and inclusion groups are mostly male when the volunteer groups have hardly any. The hours researchers stay in the laboratory make you feel like you are reliving the same day again and again; the boisterous communication style and jokes and comments are too harsh for you. The passion you once had for research is slowly withering away, leaving you with the feeling of unhappiness and unworthiness, and you give up, thinking that you are not made for this work, you are not a good fit, with a question in your mind: “How did I end up here?”.
I was lucky to grow up in a bubble where science was never gendered, there were no sciences that were inherently for women or men, and there were no subjects that some genders were naturally bad at. My parents were working in science-related areas, and they would divide school subjects between them. My mother would help me with mathematics, chemistry, and biology. My father with English, physics, and music. So, it never occurred to me that there was a need for societies supporting women researchers until I moved to Japan. My intrinsic belief that science is for everyone was challenged by a different culture, where many people of both genders believed otherwise for one reason or another. The confusion and frustration led me to research the problem (what else a scientist can do!?). And what I discovered – amazed me.
The universities in Europe and North America have women in STEM organisations active on social media, organising events, inviting young women scientists, actively connecting, and searching for opportunities to widen the network. These societies are vocal and visible, making the world know they exist. They constantly push for change. There are university-based workshops, training programs, and symposiums specifically for women in research. There is this feeling of women researchers trying to unite and support each other, pave the way for future generations, and improve the working environment.
I wished something like this existed in Japan. Most of the groups I found were quite exclusive: only for students, or mainly in Japanese, with no easily accessible information on how to join and what kind of events they are planning. There was little presence on social media, and you would need to make a targeted search to find them. I rarely hear about women researchers-oriented events or workshops, and yet to hear about women researcher-oriented training university programs.
So, I searched for women researchers’ communities outside the university and found ‘’Women in Science Japan’’, the young community founded by Elizabeth Oda, Dr. Sarah K. Abe and Lauren Hartz in 2019. I looked through their website and joined on the spot. I had a chance to talk with one of the co-founders, Elizabeth, and asked her about the motivation behind creating “Women in Science Japan”:
I and my co-founders created this community to address what we have witnessed as gender inequality in Japan, both the statistics you can often hear in the media and micro- and macroaggressions women experience. We also wanted to start with students and give a voice to students in high schools and universities. Because we knew both from the literature and from our own experience that in Japan, there are many negative stereotypes around women pursuing STEM and girls are discouraged from pursuing these fields from the young age.
Elizabeth says that one of the reasons most people join “Women in Science Japan”, and the one she thinks is very important for the future of the community and hopes to improve – is a mentorship program. That was one of my reasons for joining too. Even without talking about being an international researcher in a country that doesn’t speak your native language and has completely different social structures, finding your way in a field that wasn’t designed for you is difficult. I often feel that mentoring comes naturally to male researchers, whereas women researchers need it even more but receive it very rarely and are expected to figure out many things on their own. The community evolved, and apart from students, it started to focus more on early-career women. Elizabeth notes that it was important to create a space where members can be vulnerable, authentic, and empowered, without the fear of retribution, discipline or ostracisation, to feel heard and to have someone else say, “You are experiencing that too? I thought it was just me.”
The reality is that gender inequality is a systemic problem that an individual person can’t solve, so the idea was to create a culture that is more aware of the issues, willing to discuss the issues, face the issues, and hopefully raise these issues outside of the Women in Science Japan community.
Women in Science Japan now unites scientists, educators, women working in start-ups and the corporate world, and students at high schools and universities. Geology, biology, engineering, IT – all fields of science are welcome. And it is beautiful. It is invigorating to have such diversity, to be with people from all walks of life, with different backgrounds and different life stories. It is empowering and inspiring to hear what fellow members have overcome and where they are heading. It is not easy to be vulnerable and share your story, but if the person decides to do it – it is a treasure, a path for growth for both the person sharing and the person listening.
Women in Science Japan offers various activities: career-related events, mentorship mentioned earlier, casual events, and the book club (!). Elizabeth says that the book club is one of the things she is proud of. The book is chosen by members interested in joining the club and is related to gender inequality, science, and Japan. Currently, the book club is reading “How to Be an Inclusive Leader: Your Role in Creating Cultures of Belonging Where Everyone Can Thrive” by Jennifer Brown, which touches on diversity, equity, and inclusion. Being a part of the book club is a fantastic experience for me. The same text often generates different responses in different people, and this experience is the diversity in action. It is eye-opening to hear what people think and how the same words are heard differently because of the different backgrounds. Reading the book together, rather than alone, creates deep conversations, challenges to see the text from different angles and helps to navigate difficult questions.
I think we can only overcome our hardships and glass ceilings by holding each other’s hands and supporting and helping each other. This is one of the things Women in Science Japan is trying to achieve, a support system to help members to navigate complicated work situations or decisions, get feedback, provide clarity about career paths, and create a network that helps to build their businesses or solve work-related problems, or for international members to settle in Japan. And I wanted to use my chances to speak to the world and encourage women researchers to unite, to join communities like “Women in Science Japan”, to create new communities of like-minded people, say for women scientists in developmental biology or tissue engineering, or working on a specific problem. To be visible, vocal, advocate for your needs, become more confident, and create a welcoming future for the new generations of women in science. Or make a safe space for sharing your thoughts, finding your way, and knowing that you are not alone.
You are very welcome to join “Women in Science Japan” if you are currently working in science-related areas in Japan.
But if you are in countries other than Japan, here are some links that can get you started on your journey of finding a safe space. (Thank you to my fellow correspondents, The Node community manager, and my friends for helping me with this list.)
“Cancer rates vary wildly across the world, and we don’t know why. To solve this mystery, scientists are tracking down causes of cancer by the fingerprints they leave in the genome”
Dr Kat Arney
In the latest episode of the Genetics Unzipped podcast, we’re chasing down the perpetrator of a scientific Whodunnit with the DNA detectives – the Mutographs of Cancer team, who are on the hunt for the causes of cancer
In sixth episode of HDBI’s podcast, Made the Same Way, scientist Katie Long explores the topic of human brain development with spoken word artist Harmony.
At the end of the episode, Harmony creates an original spoken word piece based on their conversation.
If we look at every single person’s brain, most of these wrinkles will be in the same place.”
-Katie Long
About the participants
Katie’s labhas been at King’s College London since 2019, and their research focuses on how the human neocortex develops with the correct size, shape and organisation. To address this they use an interdisciplinary approach using human fetal cortex tissue models to look at the cellular and mechanical mechanisms that drive the development of the human neocortex, including the formation of the folds present on the surface of the neocortex, and how dysregulation of these functions can lead to neurodevelopmental disorders. They also use our human fetal tissue culture models to investigate the effect of injury on the developing human brain.
In her spare time, Katie likes to get outdoors and she is a keen cyclist and runner.
Harmony is a spoken word artist who has been interested in the arts since she watched her first movie.
Please subscribe and listen to Made the Same Way on Apple podcasts, Spotify, or wherever you get your podcasts. If you enjoy the podcast, please rate and review us on Apple podcasts to help others find us!
The lab is located in the Cochin Institute (14th arrondissement of Paris), in between la Butte aux Cailles and Montparnasse.
2. Research summary
Antoine: We use the cranial neural crest as a model to understand how cell fate decision and cell plasticity are regulated during embryogenesis. This population presents a remarkable differentiation potential as it gives rise to the entire peripheral nervous system and to most of the craniofacial skeleton. We are also testing whether cranial neural crest plasticity could be harnessed to enhance postnatal bone regeneration.
The Zalc Lab
3. Can you give us a lab roll call, with a sentence including what each person works on and career stage
Jean-Christophe: Engineer – trust in sphere, spend money the PI collect, love, and hate expectation
Saverio: Master2 student – trying to understand neural crest regionalization: cares for his many little spheres, gets happy when they behave nicely, starts shouting in Italian when they do random stuff just to annoy him.
Martina: Master2 student – trying to not get crazy when she obtains just 5 ng/ul of RNA from 150 spheres, in love with multichannel pipettes
Laura: Postdoc – juggles with differentiating spheres, sees the light at the scope, pipets hard at the bench, wants to understand the tuning of Oct4 for cell plasticity, is driven by curiosity
Antoine: PI – does the paperwork, have multiple meetings every day, jumps and/or dance when new data arrive
4. Favourite technique, and why?
Antoine: Depends on the question we are asking.
If I had to choose it will be genetic lineage tracing. The embryo being the best teacher, this technic provides a clear understanding of the decision made by the cells, and it generates great images.
Then RNA in situ hybridization, works beautifully on whole embryo or sections. Allows to the questions what are cells asking before, during and after they made a choice.
5. Apart from your own research, what are you most excited about in developmental and stem cell biology
Antoine: We are reaching a stage where we are done naming things. We are now able to understand development with equations. The advances of single cell omics will soon allow us to reconstruct an entire embryo in sillico. With this, it will be possible to predict how an environmental or genetic perturbation affects development. This will also allow us to generate several scenarios to rescue the defect, which can be much later than when the problem occurs.
I’m also really excited by the rapid progress made with organoïds. I was skeptical at first, but this is becoming an excellent tool to study basic cell behavior and logic.
6. How do you approach managing your group and all the different tasks required in your job?
Antoine: This is a learning process… I’m a strong believer that science must be fun! We spend so much time and effort doing it we should at least enjoy the process. For it to be fun, this implies scientific rigor, work ethics, good technical skills and simply being humane.
I’m still learning about the different task required by the job! Using the one thing I learnt during my PhD and postdoc which is learning how to learn. Thankfully, I have greats colleagues in the Institute that can help with this!
7. What is the best thing about where you work?
Jean-Christophe: Multiplicity of help you can hope and offer.
Saverio: Everything in the lab is brand new so every little step feels like a big achievement!
Martina: There is always chocolate!
Laura: The Institute is included in the Université Paris-city network which gives access to all exciting seminars occurring in the network.
Antoine: The Cochin Institute is multidisciplinary which means I learn a lot about various topics which stimulates creativity and open the way to great collaborations on various topics
8. What’s there to do outside of the lab?
Jean-Christophe: Why do you want to do things outside of the lab? Are you not happy here?
Saverio: If you work in research, try climbing. You will meet so many colleagues that you will feel like you never left the lab. Bring your friends!
Martina: Many sunsets along the Seine with a beer.
Laura: We are in Paris, a lot of culture, art, good coffee, much more.
Antoine: Paris is outside the lab, there’s plenty to do! I take care of my kids, which is a second job on itself, and spend time with my family. When I have time, I try to keep doing photography, keeping an eye and the dynamic Parisian Street Art scene.
Browse through other ‘Lab meeting’ posts featuring developmental and stem cell biology labs around the world.
In our latest SciArt profile we hear from Ivana Henry, a science communicator and illustrator with a background in developmental genetics. Ivana enjoys creating 3D visualisations of scientific concepts in molecular biology and genetics.
Where are you originally from and what do you work on now?
I was born in beautiful southern Czech Republic and studied genetics at the University of South Bohemia. After completing a PhD in developmental genetics in Bayreuth (Germany), I undertook a postdoc at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden (Germany). I studied the role of planar cell polarity in tissue/organ development using the Drosophila ovary as a model. Later on, I studied how force generation moves tissues. I also developed light-sheet microscopy imaging approaches to study subcellular processes in curved epithelia. At this time, I found my love of scientific illustration and 3D visualisation and started to offer scientific illustration services. I currently work as a laboratory manager at the MRC Laboratory of Molecular Biology in Cambridge in the UK.
2D illustration showing a comparison of embryo development (Tribolium vs Drosophila)
Were you always going to be a scientist?
I don’t think so. As a child I liked all school subjects, so I think I probably wanted to be a teacher first. I liked art, languages, history, literature, and my interest in biology and chemistry came later. It was at secondary school/gymnasium that I discovered Louis Pasteur, Darwin’s theory and then molecular biology and genetics. I took part in biology Olympiads and became curious about insects and plants. The idea of becoming a scientist may have started to take shape in grammar school, but I didn’t seriously consider it until I was at university.
A detail of a graphical summary indicating a difference between the expression of the circadian clock genes in the summer and in the winter. Drosophila adult is digitally painted.
And what about art- have you always enjoyed it?
Yes, I always enjoyed art. As much as I loved going to natural history museums, I also loved going to art museums. Later on, I couldn’t resist visiting art museums in various destinations when I was at scientific conferences. Art simply has been always part of my life. It started with drawing portraits of my family and led to drawing portraits of my whole gymnasium class. But I never thought I was an artist or that I’d like to become one. I was drawn to the world of molecular biology and genetics. I wanted to understand how things work. But art comes through in different forms in my scientific journey. When I was at university, I used to draw an overview of the study material for each subject I was studying. This helped me to commit newly acquired knowledge into long-term memory. I think it is important to visualise scientific knowledge and I find it easier to remember information in the form of a picture rather than as long scientific text.
Digital drawings of a kidney showing nephron and glomerulus (on the left) and a cardiomyocyte (on the right).
What and who are your most important artistic influences?
One of my favourite artists is our Czech Art Nouveau artist, Alphonse Mucha. I like his detailed graphic and illustrative style and admire his dreamy paintings of The Slavic Epic on such a large scale. I’m not sure this influence is visible in my art, but his works often serve as my inspiration. I also very much like Impressionism, especially Claude Monet and his later paintings, including the Water Lilies series as they are almost abstract art. Bright and complementary colours used by impressionists usually reflect in my colour code.
In addition, I’m often inspired by new digital approaches from contemporary 3D artists and several renowned biomedical studios creating visuals for industry / the medical field.
A metaphorical digital drawing of the physical forces that play a crucial role in shaping animal tissues and organs. This illustration shows the actomyosin filament (pink thread) that drives tissue fluidization during epithelial gap closure in embryogenesis or wound healing. Similarly, holes in old socks can be sewn together.3D visualisation of antibody molecules (heavy chains in dark blue and light chains in light blue) detecting antigens (green)
How do you make your art?
I usually draw an initial concept as a pencil sketch, creating different versions. I present these to my client and then convert the preferred version into digital form. The final digital version depends very much on the subject and what it will be used for. I usually create vector graphic illustrations for graphical summaries/abstracts, adding final digital/painting touches. I also create 3D visuals using 3D software, which are best suited for presentations, websites and cover art where you want to engage your audience.
Digital drawing of Thomas H. Morgan
Does your art influence your science at all, or are they separate worlds?
When I was doing my own research, it was probably a direct influence. I don’t know if you could call it art, but much like at university, I used drawings to summarise my findings and it helped me to put them into a bigger picture/see what direction to take next. It usually forced me to simplify and focus on the main points. Now it is more my relaxation/hobby time. I do enjoy the process of translating a key scientific message into a visual form. It is not classical art per se, but it does require certain ability to come up with an original idea that leads to a visually pleasing and self-explanatory design that attracts your audience.
3D visualization of a ‘springing’ neuron
What are you thinking of working on next?
I’m looking forward to the art and craft show at our institute, where I plan to show some of my art made with traditional painting materials. It is a hobby that forces me to leave my computer screen and gives me new ideas for digital art. I also hope to have more time to update my website and to launch more products incorporating my scientific designs.
Artworks were created using the Fluid Art technique to evoke the abstract representation of plant tissue. Both 40x40cm on deep edged canvas. These were created for the 2022 exhibition.
Dr Taiichi Tsuyama, Professor Tadashi Uemura and colleagues from Kyoto University recently published a paper in Development entitled ‘Dynamic de novo adipose tissue development during metamorphosis in Drosophila melanogaster‘, identifying the precursor cells that give rise to the adult fat body in Drosophila. We caught up with the authors to learn more about the story behind this work.
What were known about the origin and developmental processes of adult adipose tissue in fruit flies before your work? At the start of this project, many fly people knew that the adult fat body (AFB) exists in adult flies immediately after eclosion; however, only several studies tried to reveal the developmental aspects of the AFB in detail. Using transplantation techniques, Lawrence and Johnston (1986) reported that the AFB is mesodermal in embryonic origin. Hoshizaki et al. (1995) tackled the origin of the AFB using histochemical techniques with state-of-the-art genetic reporter lines in those days. The Hoshizaki paper has been one of the best references for the development of the AFB for about 30 years. However, it had been cited only ~30 times by 2021 despite many studies employing the mature AFB to study fat metabolism in adult flies. No previous study had identified precursor cells of AFB and characterized their cellular dynamics underlying AFB formation.
Why is this such a challenge to unravel? We think a major obstacle was the lack of genetic tools that specifically control gene expression in the AFB but not in the larval fat body (LFB). The larval fat body cells, which are generated in the embryo, persist during metamorphosis and locate near the AFB in young adult flies. Thus, genetic tools specific to the AFB are required to unravel the developmental progress of the AFB. Our interest in the adult fat body might be kind of serendipitous. One central theme in our laboratory has been how neuronal dendritic arbors achieve their complex and diverse morphological patterns and how they undergo remodeling during metamorphosis (for example, Shimono et al. 2014; Tsuyama et al. 2017). When we had attempted to study how systemic communications affect the metamorphic remodeling of dendritic trees in flies, we noticed that there were no good tools to control gene expression in larval and adult fat cells individually during metamorphosis. It prompted us to establish new genetic tools, which enabled us to visualize the developmental progression of the AFB in metamorphic flies.
Can you summarise your key findings? We identified precursor cells that give rise to the AFB and delineated their dynamic cellular behaviors at the single-cell resolution (Figure 1; Tsuyama et al. 2023). These precursor cells emigrate from the thorax with polarized cell shapes and oriented motility, and undergo a long journey to disperse to the abdomen and head. After this spatiotemporal large-scale migration, these cells adhere to each other, assembling into the AFB with a sheet-like architecture. Cell proliferation takes place continuously during and after the migration to make up one of the largest tissues in the abdomen of adult flies. Another intriguing behavior is homotypic cell fusion after the sheet formation, resulting in the formation of multinucleated adult fat cells. We also tested the roles of candidate genes and found that Ecdysone Receptor (EcR), a steroid hormone receptor critical for the metamorphic progression of insects, and the GATA-factor transcription factor Serpent support AFB organogenesis.
Adult fat body precursor cells undergo a long journey to disperse across the whole body. Schematic illustrations of AFBp migration pathways in the fly (A,B). While our data support the notion that AFBp cells originate from thoracic segments, the detailed site of origin is still unclear. (C) Timeline of fly AFB development during metamorphosis (h: hours after puparium formation). Numbers in text boxes refer to numbers in A and B.
Are you surprised that the adult fat body precursor cells have to migrate over a long-distance from the thorax to disperse across the body? Yes. The migration-based distribution strategy makes a striking contrast with those of other mesodermal organs. Larval fat cells and muscle precursors differentiate in a segmentally-repeated manner in the embryo. Adult muscles, another class of mesodermal tissue that undergo metamorphic remodeling, are also locally generated during metamorphosis. Thus, such on-site differentiation is likely to be the canonical mechanism for the broad distribution of mesodermal organs in the fly; in contrast, the long journey of the AFB precursors appears to be exceptional.
When doing the research, did you have any particular result or eureka moment that has stuck with you? We experienced at least two eureka moments in our searches for Gal4 driver stocks that can induce gene expression in the AFB. After establishing new Gal80 lines, which block Gal4 activity in larval fat cells, we tested various known fat-body Gal4 drivers with our Gal80 lines and found that the c833-Gal4 driver could visualize migrating adult fat precursor cells. Then, in our additional search for Gal4 lines related to mesodermal genes, two svp Gal4 strains exhibited persistent Gal4 expression from early in the AFB lineage onward when used with lineage tracing tools. The moment when we saw the precursor cells migrating from the thorax into the abdomen was memorable indeed (Movie 2 in Tsuyama et al. 2023).
And what about the flipside: any moments of frustration or despair? With the new Gal4-based tools, we started lots of imaging with fluorescent protein markers and got a rough picture of the developmental progression of the AFB. Then, we examined whether wildtype flies without protein markers start to deposit lipid droplets at the same stage using Nile Red (a lipid stain); however, we were puzzled to find that various wildtype flies exhibited reduction or absence of Nile Red-positive lipid droplets with variable degrees of penetrance late in metamorphosis. We suspected that fluorescent markers might affect the developmental timings of the AFB but finally found that various fly stocks, including a widely used wildtype strain Canton-S, showed disorganized or lost AFB tissues with approximately 30% (!) penetrance even in the mature adult stage. We first could not come up with such an idea that a major tissue is occasionally lost in wildtype flies. This finding prompted us to examine defects in AFB development in a collection of inbred lines, Drosophila Genetic Reference Panel, performed by Yusaku Hayashi. Our results strongly suggest that the aberrant AFB development observed in those wildtype genetic backgrounds might be due to genetic variations, and we are attempting to characterize novel candidates of genes controlling AFB development as our ongoing study.
Where will this story take the lab? Tadashi Uemura: So far as a separate project, I have been studying long-term effects of nutritional environments during larval stages on the reproduction and lifespan of adult flies. The background of that project and a potential link with our study on AFB development are the following: massive and rapid growth of juveniles is heavily influenced by the quality and quantity of nutrients consumed. The impact of the nutritional environment in the early life (the nutrition history) is not restricted to that stage; the nutrition history exerts long-term effects on adult health in the later life. I have been investigating on underlying mechanisms including identification of the key cell where the history is stored, and the AFB precursor could be one of such candidate cells.
Taiichi, what brought to you join Prof. Uemura’s lab? And what is next for you after this paper? When I was a senior undergraduate student, I studied molecular mechanisms underlying plant-microbe symbiotic interactions using Lotus japonicus (supervised by Dr. Shingo Hata; I never imagined that studying gut-microbe and plant-microbe interactions is so trending now!). Reading papers with whole plants brought up my interest on molecular genetics. I was also interested in morphogenesis of cells. At that time, Uemura-san’s lab had been studying the molecular basis of dendritic morphogenesis using fly molecular genetics. So, I thought it might be the best place to join as a graduate student. After some studies on how aberrant ATP metabolism due to mitochondrial dysfunction causes the loss of dendritic trees of sensory neurons as my doctoral project (Tsuyama et al., 2017), we started this study on the development of the AFB. Even though these projects took a whole lot of time, Uemura-san generously and continuously supported my thoughts and plans. Recently, I have been focusing on ATP metabolism by developing genetic tools to manipulate energetic metabolism and structural analyses of proteins related to ATP metabolism in Prof. Ken Yokoyama’s laboratory at Kyoto Sangyo University.
References Lawrence, P. A. and Johnston, P. (1986). Observations on cell lineage of internal organs of Drosophila. Journal of embryology and experimental morphology 91, 251–66.
Hoshizaki, D. K., Lunz, R., Johnson, W. and Ghosh, M. (1995). Identification of fat-cell enhancer activity in Drosophila melanogaster using P-element enhancer traps. Genome 38, 497–506.
Shimono, K., Fujishima, K., Nomura, T., Ohashi, M., Usui, T., Kengaku, M., Toyoda, A. and Uemura, T. (2014). An evolutionarily conserved protein CHORD regulates scaling of dendritic arbors with body size. Scientific Reports 4, 4415.
Tsuyama, T., Tsubouchi, A., Usui, T., Imamura, H. and Uemura, T. (2017). Mitochondrial dysfunction induces dendritic loss via eIF2α phosphorylation. Journal of Cell Biology 216 (3), 815–834, jcb.201604065.
Tsuyama, T., Hayashi, Y., Komai, H., Shimono, K. and Uemura, T. (2023). Dynamic de novo adipose tissue development during metamorphosis in Drosophila melanogaster. Development 150 (10): dev200815.
Our June webinar will be chaired by Development’s Editor-in-Chief, James Briscoe (The Crick), and features three early-career researchers investigating growth and morphogenesis. The webinar will be held using Zoom with a Q&A session after each talk.
Wednesday 21 June 2023 – 16:00 BST
Patricio Pérez-Henríquez (University of California, Riverside) ‘PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons’
Stefania Tavano (MedUni Vienna) ‘You shall not pass! How ectoderm patterning modulates lateral mesendoderm migration in the early zebrafish gastrula’
Stefan Harmansa (IBDM and Turing Center for Living Systems) ‘Morphogenesis in a growing shell’
Doing great science depends on teamwork, whether this is within the lab or in collaboration with other labs. However, sometimes the resources that support our work can be overlooked. Our ‘Featured resource’ series aims to shine a light on these unsung heroes of the science world. In our latest article, we hear from Denis Bienroth, who describes the work of VR-Omics.
What is VR-Omics?
VR-Omics is a computational framework that analyses, visualises, explores, and interprets spatially resolved transcriptomics (SRT) data. It supports SRT data from various technologies, including sequencing-based and imaging-based platforms. Notably, VR-Omics is the first tool to analyse and visualise SRT data in both 2D desktop and virtual reality (VR) environments. It incorporates an automated workflow for data preprocessing and spatial mining. Additionally, VR-Omics is available at our VR-Omics Website. It is an open-source software, ensuring accessibility for all users. This platform is highly valuable for researchers as it also facilitates cross-platform comparisons, particularly when deploying different SRT technologies.
The VR-Omics Introduction Video showcases a comprehensive array of SRT Methods, providing an overview of all the options available.
What inspired VR-Omics’ development and its target challenges?
The development of VR-Omics was inspired by the realisation that existing tools for spatially resolved transcriptomics (SRT) data analysis required a high level of computational knowledge, making them inaccessible to many biologists. We aimed to create a solution that empowers researchers by providing a user-friendly graphical user interface (GUI) and eliminating the need for extensive computational expertise. VR-Omics puts the power back in the hands of biologists, allowing them to easily work with their own data and explore the fascinating world of gene expression landscapes.
Which SRT methods are currently supported?
VR-Omics currently supports a variety of spatially resolved transcriptomics (SRT) methods, including both sequencing-based and imaging-based technologies. The supported sequencing-based SRT methods include Visium from 10X Genomics, Tomo-seq, and STOmics from BGI. In terms of imaging-based SRT methods, VR-Omics supports Xenium from 10X Genomics and MERFISH from Vizgen. Additionally, VR-Omics allows for the analysis of custom SRT data, providing flexibility for users who are using their own spatial transcriptomics data not suitable with any of the aforementioned vendors. It’s worth mentioning that CosMx by Nanostring will also be available in VR-Omics shortly, further expanding the range of supported SRT methods. The wide range of supported SRT methods in VR-Omics ensures its compatibility with diverse experimental setups, enabling researchers to analyse and visualise their spatial data effectively.
Figure 1: Visualisation of different Spatial Transcriptomics data sets using VR-Omics. a) 3D Dataset of Human Developing Heart1 (Visium – 10X Genomics) as VR environment. b) Mouse Brain Receptor Map2 (MERFISH – Vizgen) c) Mouse Brain Coronal Section3 (Visium – 10X Genomics) d) Zebrafish Embryo SS154 (Tomo-Seq) e) Breast Cancer Tumour Section5 (Xenium – 10X Genomics)
How can biologists’ access and utilise VR-Omics for their research?
VR-Omics empowers biologists to improve their research and make significant findings by providing an immersive and intuitive platform for spatially resolved transcriptomics (SRT) data analysis. Its visualisation capabilities enable a deeper understanding of gene expression landscapes, while cross-platform compatibility facilitates collaboration and data comparison. By streamlining workflows and eliminating computational complexities, VR-Omics allows researchers to focus on interpreting their data and uncovering valuable insights, ultimately accelerating scientific progress in diverse fields. VR-Omics is available at our VR-Omics Website.
Can I use VR-Omics with my own data?
Absolutely! VR-Omics is specifically designed to empower you to use your own data. It seamlessly supports spatially resolved transcriptomics (SRT) data generated through sequencing-based or imaging-based technologies, ensuring compatibility with multiple SRT platforms. Once loaded, VR-Omics streamlines the analysis process with its integrated workflow, automating tasks such as clustering, filtering, and spatial variable gene analysis. This means you can effortlessly explore and gain valuable insights from your data.
Can I export my findings to share them with my colleagues?
VR-Omics provides convenient export options for sharing your findings. You can export the output of the automated workflow, including plots, CSV files, and HDF files for downstream analysis. Additionally, the software allows you to export data directly from the Visualiser, such as gene lists, selected Regions of Interest (ROIs), screenshots, and videos. These versatile export capabilities enable you to easily share your results and collaborate effectively with your colleagues.
How can I explore my spatial data with VR-Omics?
With VR-Omics’ Visualiser feature, you can explore your spatial data on your desktop or in an immersive virtual reality (VR) environment. It supports side-by-side gene comparisons, merging gene expression patterns in one slide, and overlaying 3D objects for improved orientation. The Figure Viewer allows real-time interaction with output plots. VR-Omics offers a range of powerful tools to enhance your exploration and analysis of spatial data.
Creating 3D dataset from sequential Visium slides and exploration of the 3D data using VR-Omics.
What if I don’t know how to process my data? Do I need computational knowledge to run VR-Omics?
Not at all! VR-Omics is designed to be user-friendly and accessible, even for those without extensive computational knowledge. Its integrated workflow automates essential processing steps, allowing you to analyse your data without requiring deep computational expertise. With VR-Omics, you can easily load your data and navigate the intuitive graphical user interface (GUI) for seamless data processing and analysis. It empowers biologists to explore and interpret their spatial transcriptomics data effortlessly, regardless of their computational background.
Can VR-Omics facilitate the creation and exploration of 3D spatial data?
Certainly! VR-Omics is specifically designed to facilitate the creation and exploration of 3D spatial data. While many platforms are limited to visualising individual sections from a single spatially resolved transcriptomics (SRT) experiment, VR-Omics takes it a step further. It enables you to seamlessly navigate through multiple sections, such as serial sections of the same tissue, for a more comprehensive understanding of spatial gene expression patterns in three-dimensional space. With the immersive capabilities of virtual reality (VR), VR-Omics provides an enhanced environment to study complex biological systems and unravel intricate spatial relationships. It empowers researchers to delve into the three-dimensional landscape of their SRT data, gaining deeper insights into the biology of the system under study.
VR-Omics Features of the Visualiser to explore and mining of spatial data. Gene search (Heatmap and Binary); Side-By-Side comparison and merge function; ROI selection; Cluster visualisation and environment customisation on desktop or VR.
What are the next plans and features for VR-Omics?
The future of VR-Omics is driven by our commitment to constant improvement and expanding its capabilities. Our plans include incorporating new spatially resolved transcriptomics (SRT) methods, such as Nanostring (CosMx), to broaden the range of compatible technologies. We are dedicated to staying up to date with the latest algorithms and packages used in the literature, ensuring that the Automated Workflow remains robust and relevant. Additionally, we are excited to introduce new features, to enhance the user experience and analysis possibilities. Our goal is to continuously evolve VR-Omics, incorporating user feedback and advancements in the field, to provide a cutting-edge software solution for spatial data analysis.
What are the benefits of using VR for spatial data work, and can I use VR-Omics without VR?
VR-Omics offers the flexibility to work with or without VR hardware, allowing users to choose their preferred mode of interaction. While VR provides an immersive experience for spatial data exploration, the benefits go beyond visualisation. In a virtual reality environment, users can effectively navigate and analyse complex 3D spatial structures, revealing hidden patterns, identifying spatial co-expression relationships, and gaining new insights into biological phenomena. However, even without VR, VR-Omics provides powerful analysis and visualisation tools, ensuring that users can effectively analyse and interpret spatial data. Whether in VR or non-VR mode, VR-Omics empowers researchers to unlock the full potential of their spatial data.
What if a necessary feature is missing in VR-Omics Visualiser or the Automated Workflow that would benefit my project?
We highly value user feedback and are dedicated to continuously improving VR-Omics based on the needs of our users, particularly biologists working with spatial data. If you find that there is a missing feature or a step in the Automated Workflow that would benefit your project, we are always eager to hear your suggestions. We actively seek input from users and encourage collaboration to enhance the software’s functionality. By engaging with the community, we aim to incorporate new features and improvements that address the specific requirements of our users. Your input is invaluable, and we are committed to making VR-Omics a powerful and user-friendly tool for spatial data analysis.
What if I have any questions, is VR-Omics documented and supported?
If you have any questions or need assistance while using VR-Omics, you can rely on its Documentation and support resources. VR-Omics is well-documented, providing detailed guides, tutorials, and documentation that explain its features and functionality. Additionally, the VR-Omics team is available to help address any queries or issues you may encounter. They are committed to providing support and ensuring a smooth user experience with the software. Shot us an email (denis.bienroth@mcri.edu.au) if you have any questions or inquiries.
References
1: Asp, M. et al. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell179, (2019).
4: Junker, J. P. et al. Genome-wide RNA Tomography in the Zebrafish Embryo. Cell, 662–675 (2014).
5: High resolution mapping of the breast cancer tumour microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue, https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
We are happy to announce the 2nd edition of the EMBO workshop “The Evolution of Animal Genomes”.
The event will take place in Seville (Spain), from 18-21 September 2023 (Registration and abstract deadline: 12th July 2023)
Genome evolution represents the basis of species adaptation to changing environments and habitats. Recent breakthroughs in sequencing technologies resulted in the acquisition of complete genome information for an increasing number of animal species, propelling the field of evolutionary genomics into a new era of discovery. Yet, our limited capacity to interpret genome variation hinders our understanding on how phenotypical changes drive adaptation. This urges the development of novel strategies to reconcile genomic sequence and function, for which a proper integration of cell-specific gene programs, non-coding regulation and 3D chromatin organization becomes essential. Further, establishing causal relationships between genome mutations and phenotypes still remains a major challenge in the field. Within this context, novel synthetic biology approaches are emerging as a means to understand developmental processes in the context of evolution. The aim of this EMBO workshop is to bring together international scientists with distinct, but complementary expertises on interpreting genome variation, on mechanisms of gene regulation and on in vivo synthetic biology approaches. This allows a comprehensive overview that goes from fundamental principles encoded in genomes to their ultimate biological significance on the formation of living, evolving organisms.
An exciting line-up of speakers (keynote lectures by Edith Heard, Mike Levine and Neil Shubin) will cover the following topics:
– Genomics of ecological adaptation – Evolution of cell types – Mechanisms of regulatory variation – 3D genome organization and structure – Synthetic biology approaches to model evolution
There will be short talks selected from abstracts, as well as ample time for networking.
Fee waiver, travel and childcare grants available.
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