Last Sunday evening found me sitting in the BBC Cambridge radio studio, headphones on and mic in front of me, talking about developmental and stem cell biology with Dr. Chris Smith, better known as the naked scientist. Fortunately, both of us were fully clothed. For those of you who aren’t familiar with The Naked Scientists, it’s an award-winning radio show and podcast that discusses the latest scientific research, answers questions on diverse scientific topics from listeners, and generally aims to make science more accessible to the general public. I’d met Chris a few weeks earlier to talk about a program he was planning that would link developmental and stem cell biology to regenerative medicine, and he asked whether I’d be willing to contribute to the show – providing an introduction and commentary to the interviews he was conducting. Hence the headphones and mic.
Having never been in a radio studio before, let alone appeared on live radio, I found the experience fascinating and daunting in equal measure. How did the whole thing work? What if I said something stupid? Fortunately, Chris and Tom (Crawford – the producer working on this show) were great at putting me at ease and guiding me through the program. And I think (hope!) the end result makes for an interesting listen. In the show, you’ll hear Roger Barker talking about his plans for a clinical trial for Parkinson’s Disease using embryonic stem cell-derived dopaminergic neurons, Hans Clevers discussing how gut organoids can be used for personalised drug testing, and Don Ingber on his amazing organ-on-a-chip technology. Plus Chris and me trying to pull these threads together and provide a perspective on where the field is going.
You can find the full show here; our discussion starts around 25 minutes in, but I’d actually encourage you to listen to the whole thing – which covers topics as diverse as heroin addiction, why airplane travel is likely to get more turbulent, and what determines whether something will ‘go viral’.
Regeneration, the ability to restore lost parts of the body, is a widespread phenomenon in animals. Whilst this ability is somehow limited in classical developmental model organisms, a variety of animals are able to regenerate complex structures, such as limbs or important parts of their body. Regeneration is often based on the presence of populations of stem cells which are either pluripotent and able to regenerate all tissues, or multipotent with a much more restricted potential. Regeneration can also rely on local cell dedifferentiation processes by which differentiated cells are reprogramed into proliferating progenitor or stem cells.
In the our team (Stem Cells, Development and Evolution team), we use the emerging developmental biology annelid model Platynereis dumerilii to investigate the evolution of stem cells and regeneration. Platynereis worms are able to grow and regenerate their posterior (caudal) part following posterior amputation during most of their life. These two abilities end when the worms become sexually mature and are dependent on the presence of a brain hormone (methylfarnesoate) that blocks sexual maturation. In the frame of a collaborative ANR-FWF funded project with the team of Florian Raible (Origin and Diversification of Hormone Systems, MFPL Vienna, Austria), the postdoctoral fellow will study, using cellular and molecular approaches, how the brain hormone controls the growth and regeneration abilities of Platynereis worms, and participate to the molecular and cellular characterization of the regeneration process.
The Vervoort team belongs to the Institut Jacques Monod (IJM) in Paris (France). The IJM is a leading French biological research institute, comprising about 30 interactive research groups and high-quality technological facilities, including a cutting-edge imaging platform. The working language at the IJM is English, and knowledge of French is therefore not a prerequisite for this position. Successful candidates will collaborate with a dynamic team of developmental, cellular and evolutionary biologists at both the IJM and MFPL.
Starting date is flexible but should be around September 2017 onwards and is funded initially for 14 months. The successful applicant must have, or be in the process of completing, a PhD thesis in a relevant research area and not more than two years of postdoctoral experience. Desirable qualifications include expertise in molecular biology, immunohistochemistry, qPCR, and DNA sequence analysis. Potential candidates should send their application by e-mail to michel.vervoort@ijm.fr with a statement of interests and expertise, a Curriculum Vitae and contact information from two referees. The position will remain open until filled; however, applications received by May 30th will be given priority. Please contact Michel Vervoort for more information.
We are seeking an enthusiastic and motivated Postdoctoral Research Scholar to join research projects investigating the molecular basis of neurodevelopmental disorders in the laboratory of Kristen L. Kroll at Washington University School of Medicine. Working in collaboration with Washington University’s Intellectual and Developmental Disabilities Research Center (http://iddrc.wustl.edu/About/MissionOverview), we use directed differentiation of human pluripotent stem cells (embryonic stem cells and patient-derived induced pluripotent stem cells), mouse models, and a wide range of cellular, molecular, biochemical, and genomic approaches, to define gene regulatory networks that control neural cell fate acquisition and the specification and differentiation of specific neuronal cell types, such as cortical interneurons. We are defining roles for epigenetic regulation in controlling these networks and identifying mechanisms by which their dysregulation alters neural development and function and contributes to neurodevelopmental disorders, including inherited epilepsies, autism spectrum disorder, and neural tube defects.
For additional information about our ongoing work and research interests, please see: http://krolllab.wustl.edu/
Setting/Salary/Benefits:
Our laboratory is in an academic setting in the Department of Developmental Biology at Washington University School of Medicine (St. Louis), an internationally recognized research institution with a dynamic research environment and extensive infrastructural and core facility support. Postdoctoral appointees at Washington University receive a starting salary based on the NIH NRSA guidelines and a generous benefit package. Complete information on the benefit package is located on the WUSM Human Resources Benefits Website (http://medschoolhr.wustl.edu). The St. Louis area combines the attractions of a major city with family-friendly and affordable lifestyle opportunities (https://explorestlouis.com/)
Qualifications:
Candidates should hold a recent PhD with less than 2 years of prior post-doctoral experience. Preference will be given to applicants with a strong interest in and research training relevant to the areas of neural development, stem cell biology, and transcriptional or epigenetic regulation. US citizens are preferred. Interested candidates should send a CV/names of references by email to kkroll@wustl.edu or by regular mail to Kristen L. Kroll, Washington University School of Medicine, Campus Box 8103, 660 S. Euclid Ave, St. Louis, MO 63110.
A postdoctoral position is available in the laboratory of Dr. Martin Basch to study the regenerative potential of the stria vascularis in cases of congenital deafness. Highly motivated, creative and enthusiastic individuals are particularly invited to apply.
Qualifications include a PhD in developmental biology, neuroscience, cell biology or related field. Priority will be given to candidates with experience in cell culture and basic molecular biology. Mouse genetics and/or neonate mouse surgery skills are desired but not required.
Our laboratory is part of the Hearing Research Program, at Case Western Reserve University School of Medicine. Currently the program involves five Research Faculty PIs and Physician Scientists with key areas of research, which include molecular otology, otitis media, congenital/acquired hearing loss, inner ear development, and hair cell biology. The strength of our program is enhanced by an excellent interdisciplinary and collaborative intellectual environment at Case.
Interested candidates should submit their CV and a letter of application (including a brief description of previous research experience and a statement of interests) to: Martin Basch Ph.D. at mlb202@case.edu.
For more information on our laboratory, please visit our website at http://www.baschlab.org
In employment, as in education, Case Western Reserve University is committed to Equal Opportunity and Diversity. Women, veterans, members of underrepresented minority groups, and individuals with disabilities are encouraged to apply.
Case Western Reserve University provides reasonable accommodations to applicants with disabilities. Applicants requiring a reasonable accommodation for any part of the application and hiring process should contact the Office of Inclusion, Diversity and Equal Opportunity at 216-368-8877 to request a reasonable accommodation. Determinations as to granting reasonable accommodations for any applicant will be made on a case-by-case basis
The Beddington Medal is the BSDB’s major commendation to promising young biologists, awarded for the best PhD thesis in Developmental Biology defended in the year previous to the award. Rosa Beddington was one of the greatest talents and inspirational leaders in the field of developmental biology. Rosa made an enormous contribution to the field in general and to the BSDB in particular, so it seemed entirely appropriate that the Society should establish a lasting memorial to her. The design of the medal, mice on a stylised DNA helix, is from artwork by Rosa herself. For further medal and award winners at the 2017 Spring Meeting see here.
The BSDB congratulates the 2017 Beddington Medal winner Erik Clark. Erik did his BA in Biological Sciences at the University of Oxford (1st in his year group) and his MSc in Bioinformatics & Theoretical Systems Biology at Imperial College London where he worked on the project entitled “Evolution of Mutation Rate in Fluctuating Environments”. He then moved on to do his PhD within the BBSRC Genes to Organisms Program supervised by Michael Akam at the Department of Zoology, University of Cambridge, where he worked on his project entitled “The Drosophila Pair-Rule System” and where he continues to work now. Erik won an impressive number of prizes, fellowships and grant awards, including the Gibbs Prize in Animal Biology (Univ. Oxford, 2011), an Isaac Newton Trust Research Grant (2016-17), a Junior Research Fellowship (Trinity College, Cambridge) and he is co-investigator on a BBSRC research grant (2017-20).
His Beddington Medal talk described the outcome of his most successful PhD project. About the background Erik explained: “The Drosophila segmentation cascade is a paradigmatic example of a developmental gene regulatory network, used to gain insight into transcriptional regulation in all animals… Using spatial information from graded domains of “gap” gene expression, seven “pair-rule” genes are expressed in periodic patterns of seven stripes each .. [which] then work in combination to specify precisely-phased 14 stripe patterns of “segment polarity” genes. These output patterns form the template for the segmental organisation of the insect body…[Although] the pair-rule genes have been studied in Drosophila for over 30 years,… there is still no good systems-level understanding of their regulatory interactions“.
In his thesis, Erik used a combination of modelling and experiment to reverse-engineer the structure of the Drosophila pair-rule network and understand how it generates expression dynamics that lead to the patterning of segmental boundaries. He set out to collect a complete time-resolved dataset of relative expression for all pairwise combinations of the 7 pair-rule genes in wild type embryos (see Figure), and a partial dataset for a number of mutant genotypes. Using these data he defined how the regulatory interactions of pair-rule genes change at the mid-cellularisation stage, and identified odd-paired as a temporally regulated factor responsible for these network changes. As an outcome of his work, Erik proposes that that spatial resolution emerges from temporal dynamics, rather than static positional information.
A further part of his thesis proposes that the standard model for how parasegment boundaries are specified, by the interpretation of local gradients of Even-skipped protein, may not be correct. He suggests instead that the shifting of even-skipped stripes across the field of cells in the blastoderm, driven by dynamic gap gene expression, coupled with the temporal control of network interactions, may generate the key offsets in downstream gene expression, and this is an entirely novel idea.
To illustrate Erik’s path to success, Michael Akam writes: “Unlike any other student I have had, Erik spent pretty much the whole of his first year reading. He worked through the entire literature on Drosophila segmentation (spanning 30 years and hundreds of papers), assessing the claims made on the basis of the data presented, and with the advantage of hindsight that the original authors lacked. I suspect he has a more detailed and critical knowledge of this literature than any other researcher.” Michael concludes his support letter with the words: “Erik’s work is strikingly original, and represents a major innovation in thinking about Drosophila segmentation.”
Erik’s publications so far:
Clark, E. (2017) ‘Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation’. bioRxiv: 1101/099671
Clark E & Akam M (2016). Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network. eLife: 7554/eLife.18215
Clark E. & Akam M. Drosophila pair-rule gene double FISH Data (data from Clark & Akam 2016). org:10.5061/dryad.cg35k 2016
BertaVerd, ErikClark, Karl R.Wotton, HildeJanssens, EvaJimenez-Guri, AntonCrombach, JohannesJaeger (2017). A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. bioRxiv: 10.1101/068072
A large-scale study of DMDD data has shown that inactivating the same gene in mouse embryos that are virtually genetically identical can result in a wide range and severity of physical abnormalities. This suggests that the relationship between gene mutation and embryo development is more complex than previously thought.
A comparison of two embryos that are both missing the embryonic lethal gene Coro1c. The embryo on the right has abnormal viscerocranium (facial skeleton) morphology, while the embryo on the left does not.
The study considered 220 mouse embryos, each with one of 42 different genes inactivated. These genes are part of a set known as ‘embryonic lethal’, because they are so crucial to development that an embryo missing any one of them can’t survive to birth. Studying these genes can help us understand how embryos develop, why some miscarry and why some mutations can lead to abnormalities.
Here are the highlights from the current issue of Development:
A new niche for human HSCs
Human haematopoiesis occurs at various anatomical sites throughout development, including the yolk sac, the aorta-gonad-mesonephros region, the liver, the placenta and the bone marrow. Cells marked by high expression of CD34 and low CD45 – suggestive of possible HSCs – have been reported in human fetal membranes; however, their exact niche as well as their functional capacity remain untested. In this issue (p. 1399), Alicia Bárcena and colleagues isolate and interrogate this putative HSC population, and demonstrate for the first time that the human chorion contains transplantable, definitive HSCs. The authors carefully separate the chorion and the amnion, and show via fluorescence-activated cell sorting that only the chorion contains the putative HSCs, and only from 15 weeks of gestation. The cells display markers of HSC and primitive haematopoietic progenitors, such as little CD38 and CD133, low levels of CD117 and CD4, and medium to high levels of HLA-DR, CD31, CD90, CD95, TIE2 and CD71. Cells co-expressing CD34 and CD45 antigens are found either in association with mesenchymal stromal cells or with endothelial cells of chorion vasculature . Using in vivo xenotransplantations, the authors demonstrated that the CD34++ CD45low cells possess multilineage long-term HSC activity specifically between weeks 15 and 24 of gestation. This study reveals novel insight into an unexpected niche for HSCs during human development.
How the stomach gets its curve
Left-right asymmetry is a common feature of many organs, and is crucial for their function. The stomach is one such organ, with marked curvature on the left compared with the right, resulting in a distinctive shape that is highly conserved among vertebrates. Although it is well established that activation of Nodal controls left-right asymmetry of visceral organs, the cell- and tissue-level morphogenetic mechanisms that drive this phenomenon are poorly understood, especially in the stomach. Now, on p. 1477, Nanette Nascone-Yoder and colleagues shed light on the mechanisms that drive left-right asymmetric development of the stomach in both mouse and Xenopus embryos. The authors start with a gross examination of stomach curvature during development and compare their findings with two proposed models: a rotation model and an asymmetric growth model. They find no evidence for the former, and therefore suggest that the stomach acquires its asymmetry by an intrinsic mechanism. In support of this, the authors show that there is an asymmetric thickness of the left and right stomach wall, which depends on intact cilia and Nodal signalling as both Foxj1 mutant mouse embryos and Xenopus embryos treated with a Nodal inhibitor show a loss of this asymmetry. The authors show a role for Pitx2 in this process by overexpressing Pitx2 on the right side or knocking down Pitx2, both of which affect stomach curvature in Xenopus. This study demonstrates that asymmetric morphogenesis of the stomach in frogs and mice is driven by FoxJ1-Nodal-Pitx2-dependent asymmetric remodelling of the gastric epithelium on the left side.
Liverworts breathe easy
The vast majority of land plants regulate gas exchange through their stomata – tiny pores usually found on the underside of leaves. The liverwort plant group Marchantiidae is an exception, as it lacks stomata and instead breathes through air pore complexes. This is an important evolutionary adaptation, and yet the mechanisms that regulate air pore complex development in Marchantiidae remain unknown. In this issue (p. 1472), Victor Jones and Liam Dolan identify the zinc finger protein MpWIP as necessary for the morphogenesis of the air pore complex in the epidermis of Marchantia polymorpha. The gene was first identified through a mutagenesis screen, in which overexpression led to the presence of ectopic rhizoids on the dorsal epidermis. Using a construct containing the MpWIP promoter fused to a reporter gene, the authors show that MpWIP is expressed both ventrally and dorsally and that the dorsal expression pattern is within the developing air pore complex cells. To determine whether MpWIP is required for air pore development, the authors use artificial microRNAs to generate plants with reduced expression of MpWIP, which results in defects in air pore complex morphology. Based on chimeric dominant repressor and activator versions of MpWIP expressed separately in transgenic plants, the authors provide some evidence for the possible role of MpWIP as a transcriptional repressor. This study identifies, for the first time, a gene that regulates the development of the air pore complex, which is an important evolutionary innovation in liverworts as an alternative to stomata.
Specialised fibroblasts maintain the nipple epidermis
The skin is the body’s largest organ, and is the first line of defence against the external environment. The epidermis – the outermost layer of the skin – is highly specialised and often exhibits unique characteristics depending on its anatomical location and the function it serves. It has long been known that this specialisation is dependent on inductive signals that originate from underlying fibroblasts; however, the exact nature of the signals and their role in maintaining the epidermis is only just starting to emerge. In this issue (p. 1498), John Foley and colleagues identify an oestrogen-regulated TGFβ signalling pathway that is crucial for the maintenance of the highly specialised nipple epidermis. Using a series of grafting experiments, the authors show that fibroblasts taken from the nipple-like skin of mice can induce reprogramming of trunk keratinocytes into nipple-like epidermis. Transcriptional profiling of the nipple-like fibroblasts identifies oestrogen signalling as a strong candidate factor for the maintenance of the nipple epidermis and, indeed, ablation of oestrogen signalling in ovariectomised mice results in an abnormally thin nipple epidermis. The authors further identify Tgfb1 as a direct target of oestrogen signalling and show how ectopic treatment of TGFβ1 protein into the connective tissue of the nipple causes a decrease in epidermal proliferation and a thinning of the nipple epidermis. Taken together, these data represent an important step forward in understanding the signalling network that maintains the specialisation of the nipple epidermis.
PLUS:
Stem cell therapies for retinal diseases: recapitulating development to replace degenerated cells
Retinal degenerative diseases are the leading causes of blindness worldwide. In their Review article, Sally Temple and colleagues review stem cell-based therapies for retinal diseases, describing the challenges involved and discussing how basic developmental studies have contributed to and are needed to advance clinical goals.
Prostate organogenesis: tissue induction, hormonal regulation and cell type specification
Prostate organogenesis is a complex process that is regulated by androgens and subsequent mesenchyme-epithelial interactions. In their Review article, Roxanne Toivanen and Michael Shen provide a comprehensive overview of prostate development, focusing on recent findings regarding sexual dimorphism, bud induction, branching morphogenesis and cellular differentiation.
As every year, the Spring meeting was the time of awards and medals! This year, we had awardees of three societies who are listed below. For those wanting to have a look at the topics of talks and posters presented at the meeting, please download the abstract book here. Watch the movies of the BSDB award winners below.
1st BSDB PhD Poster Prize winner (Attendance at SDB 76th Annual Meeting, Minneapolis): Claire Bromley (Kings College London) – Poster 25 “Investigating biomechanical forces in zebrafish brain morphogenesis“
1st BSCB PhD Poster Prize winner (visit to 2017 ASCB/EMBO meeting, Philadelphia): Christina Dix (University College London) – poster 5 “Adhesion, not cortical tension, is vital for successful cytokinesis in RPE-1 cells“
1st Genetics Society (£100 cash prize sponsored by BioMed Central): Alexandra Buffry (Oxford Brookes University) – Poster 182 “Investigating gene regulatory network architecture and evolution in different developmental contexts“
2nd BSDB PhD Poster Prize (£100 cash prize sponsored by BioMed Central): Ariadna Gador Navarro-Aragall (UCL Institute of Ophthalmology) – Poster 86 “SEMA3E and SEMA3C Cooperate to establish vascular boundaries“
2nd BSCB PhD Poster Prize (£100 cash prize sponsored by BioMed Central): Sophie Adams (Barts Cancer Institute) – Poster 32 “‘Exosome signatures’ as biomarkers for centrosome-targeted therapy in pancreatic ductal adenocarcinoma (PDAC)“
► Postdoc Poster Prizes
1st BSDB Prize (£200 cash prize sponsored by BioMed Central): Carla Mulas (University of Cambridge) – Poster 129 “Functional characterisation of metachronous cell state transitions“
1st BSCB Prize (£100 Cash prize sponsored by BioMed Central): Girish Mali (MRC Laboratory of Molecular Biology) – Poster 47 “Assembly Mechanisms of Dynein Motors“
1st Genetics Society (£100 bank transfer sponsored by BioMed Central): Laura Molina-Garicia (University College London) – Poster 122 “Sexy learning in C. elegans”
2nd BSDB Prize (£100 cash prize sponsored by BioMed Central): Hadi Boukhatmi (University of Cambridge) – Poster 92 “Molecular logic behind Satellite cells specification in Drosophila”
► Others
Genetics Society Overall Poster Prize (Junior Scientist Conference Grant, Scheme A): Alewo Idoko-Akoh (The Roslin Institute) – Poster 185 “CXCR4 and c-Kit signalling are required for directed migration of chicken primordial germ cells through the chick embryonic vascular system“
BSDB Honorary Mention (Certificate): Eva Higginbotham (University of Cambridge) -Poster 114 “Neurotransmitter specification in the ventral nerve cord of Drosophila melanogaster”
Macrophages are usually associated with immunity, but have increasingly appreciated functions in development and homeostasis. This week we meet the authors of a recent Science paper that identified a role for macrophages in zebrafish stripe patterning, revealing a remarkable ‘relay’ mechanism whereby macrophages help one type of cell signal to another via cytoplasmic extensions. Postdoc Dae Seok Eom and his supervisor David Parichy, recently appointed Pratt-Ivy Foundation Distinguished Professor of Morphogenesis at the University of Virginia, told us more.
David, can you give us your scientific biography and the questions your lab is interested in?
DP I started out in ecology and evolution as an undergrad at Reed College, studying maternal effects on tadpole growth and survivorship for four years with Bob Kaplan. With that experience I applied to E&E Ph.D. programs and ended up accepting an offer from Population Biology at UC Davis, with Brad Shaffer, a systematist and organismal biologist studying biogeography of salamander populations. But between when I applied and when I got there, I became more and more interested in developmental mechanisms and how they evolve. So I was really lucky that Brad has diverse interests and that Carol Erickson—a developmental biologist working on neural crest—was willing to serve as a co-advisor. For my dissertation I focused on the cellular bases for salamander pigment pattern development and evolution. Those are great animals, but the molecular biology and genetics were difficult at the time. So I switched to zebrafish and its relatives for my postdoc with Steve Johnson at Wash U Medical School in St. Louis. In Steve’s lab, we identified some of the mechanisms underlying the development of stripes and other patterns, and I carried this program into my independent career.
My lab has broad interests but an organizing theme has always been to understand the genes and cell behaviors underlying adult phenotypes, and how changes in developmental genetic mechanisms contribute to variation within and among species. We continue to work on pigment patterns, but we also want to know what regulates the stem cells that give rise to adult pigment cells and how “local” cellular mechanisms intersect with “global” endocrine control during development, homeostasis and regeneration. But our interests are wide-ranging so we’ve also worked on topics including skeletal development, zebrafish natural history, and the behavioural significance and cognitive processing of pigmentation. Right now we are doing a lot of work to understand scale morphogenesis and patterning in fish, and we’ve even started working on salamanders again, both pigment and regeneration.
The macrophage depletion phenotype, from Figure 1, Eom & Parichy, 2017.
And Dae Seok, how did you come to join David’s lab?
DSE Actually, when I was at PhD training at the University of Texas at Austin, Dave was a faculty of my department, and I was interested in his work, but by then he was then planning to move to the University of Washington. While I was finishing my PhD training, my wife started her PhD at UW, so I had to find a postdoc position in Seattle. I realised Dave was there, and it was obviously a great second chance to work with him – and he accepted.
Aside from aesthetics, what makes zebrafish stripe development an attractive developmental model?
DP When I was a grad student, I wanted to find a system that could be studied from many different angles—molecular through organismal. And this was why I ended up focusing on pigmentation. For anyone with broad interests it’s just a natural: there’s a deep literature on pigment cells and pattern going back to the turn of the last century, the cells are visible even in the living organism as the phenotype is developing, the patterns themselves often have profound ecological significance, and there’s tremendous diversity of pattern across even closely related species. Of course there are also a variety of pigmentary disorders, including melanoma, and pigment cells develop and regenerate from stem cells—so there is obvious biomedical utility in studying pigment cells, especially with a system like zebrafish in which the genetic and cellular mechanisms are so accessible.
A macrophage drags an airineme to a melanocyte. Eom & Parichy, 2017.
Can you give us the key results of the paper in a paragraph?
DP We showed previously that consolidation of melanophores into adult stripes depends on interactions between these cells and xanthoblasts, the precursors of yellow xanthophores. During a specific stage of stripe development, xanthoblasts that happen to be present in future stripe regions extend very long, thin and meandering filopodia-like processes with membraneous vesicles at their tips. We called these projections “airinemes” after Iris—messenger of the gods—and Sir George Airy, who described limits on optical resolution, because the projections are such a pain to visualize. We saw airinemes “dock” with melanophores, and we found that blocking airineme extension prevented melanophores from consolidating properly into stripes, at least in part because of a defect in Delta-Notch signalling.
“Weird biology”
In Dae Seok’s new paper, we show that airineme extension and vesicle delivery depend on macrophages that are cruising around the local tissue environment. The macrophages recognize surface blebs on xanthoblasts and try to engulf them but continue to wander, pulling a membrane filament from the xanthoblast as they go. Eventually they wander across a melanophore and the vesicle and filament are deposited on the melanophore surface. If we get rid of macrophages, we prevent airineme extension and melanophores remain dispersed. Weird biology.
What convinced you to deplete macrophages in the first place? It might not seem like the most obvious place to look for patterning regulators…
DSE The idea initially came from the question of what would happen to unbound airineme vesicles. When xanthoblasts don’t meet the target melanophores, airineme vesicles detach from the airineme filaments and wander away. We knew the vesicles carry DeltaC and possibly other signalling molecules. Thus, these unbound vesicles should be somehow eliminated. The question then was what cell types can do that? One of the answers was the macrophage.
DP Plus we could constantly see macrophages wandering around in Dae Seok’s movies. How could we not try getting rid of them?
Airineme vesicle associated with melanophore membrane, from Fig. 4, Eom & Parichy, 2017.
Is there anything in the macrophage-depleted fish to suggest that other patterning or morphogenetic events may be affected, or is this just tissue specific?
DP We’re only starting to investigate roles for macrophages as well as airinemes in other tissues. Because macrophages wander all over, you could imagine a whole variety of possibilities for diffusion-like dissemination—or regulated attenuation—of signals in other contexts. The more people look, the more interesting things macrophages seem to do.
Can you hazard a guess as to whether you think the macrophages actively select signalling targets or just wander around randomly?
DSE We have no idea at this time but my guess is macrophages constantly probe the environment, and signals from the airineme vesicles instruct macrophages to detect the targets and drop the vesicles while they are randomly wandering around.
DP Yes, because Dae Seok showed that targeting is specific to a subset of melanophores, there has to be some sort of airineme vesicle–melanophore recognition system. It will be interesting to see whether this is somehow instructive to the macrophage itself or whether the macrophage is simply trying to eat the vesicle and can’t manage to do so, and therefore the vesicle gets displayed at the cell surface often enough that it can stick to a melanophore as its carrier macrophage wanders along.
When doing the research, was there a particularly exciting result or eureka moment that has stayed with you?
DSE I do not have good explanation for it, but I had very strong gut feeling that there are something going on between macrophages and airinemes. So of course, my most exciting moment was when I saw the macrophages interacting with extending airinemes.
Xanthoblast airinemes. Eom and Parichy, 2017.
And what about the flipside: any moments of frustration or despair?
DSE Our original plan was to add additional mechanisms of airineme vesicle-macrophage interactions beside phosphatidylserine, as we have several additional candidates. We ran into technical problems for this first paper but are now working on it again.
What next for you following this work?
DSE We have many questions about airineme-macrophage interactions, for example, what other signalling molecules carried in the airineme vesicles and how macrophages know what the targets are. I’m very excited about using our new super-resolution microscopes – they will open up many new possibilities.
“Our new super-resolution microscopes will open up many new possibilities.”
And where will this discovery take the Parichy lab?
DP Of course we’ll continue to pursue the mechanisms underlying this signalling relay in zebrafish pigment pattern formation. And we’d really like to know how these and other interactions have evolved to generate the very different patterns we see in Danio and beyond. But you know, a lot depends on the interests of the grads and postdocs who come to my lab. I just try to foster an intellectual environment and provide the resources to let people explore and go where the science leads. When we decided eight years ago to invest in live imaging we didn’t know what we’d find and we certainly didn’t expect this. So I’d be hesitant to make firm predictions.
Finally – what do you get up to outside of the lab when you are not playing with fish?
DSE One of my favourite things to do is visiting local breweries. My wife and I have a Saturday routine of having a lunch at a brewery, and then heading to the lab.
DP Legos. I like to spend as much time as I can with my four year old and my wife. So we do a lot of legos, trains and construction. Helicopters are big, too.
Our latest monthly trawl for developmental biology (and other cool) preprints. See June’s introductory post for background, and let us know if we missed anything
March was (yet) another bumper month for life sciences preprints. A glance at some of the names of last authors – Daniel St. Johnston, Denise Montell, Dennis Duboule, Roberto Mayor, Fiona Watt – shows that preprints are being embraced by established as well as early career scientists. The content itself covers every base in developmental biology, as well as a lot of exciting cell biology and modelling relevant for development, and an acronym-rich list of tools and resources.
The Molecular Link Between Auxin And ROS-Mediated Polar Growth. Silvina Mangano, Silvina Paola Denita-Juarez, Hee-Seung Choi, Eliana Marzol, Youra Hwang, Philippe Ranocha, Silvia M Velasquez, Jorge P Muschietti, Christophe Dunand, Hyung-Taeg Cho, Jose M Estevez
Alignment of X. tropicalis and the X. laevis L and S subgenomes, from Elurbe, et al.
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Dei M. Elurbe, Sarita S. Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Ozren Bogdanovic, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra
Looking for LGR5+ cells in the adult duodenum, from Dame, et al.
Identification, Isolation, and Characterization of Human LGR5-positive Colon Adenoma Cells. Michael K Dame, Durga Attili, Shannon D McClintock, Priya H Dedhia, Peter Ouilette, Olaf Hardt, Alana M Chin, Xiang Xue, Julie Laliberte, Erica L Katz, Gina M Newsome, David Hill, Alyssa Miller, David Agorku, Christopher H Altheim, Andreas Bosio, Becky Simon, Linda C Samuelson, Jay A Stoerker, Henry D Appelman, James Varani, Max S Wicha, Dean E Brenner, Yatrik M Shah, Jason R Spence, Justin A Colacino
An Algorithm for Cellular Reprogramming. Scott Ronquist, Geoff Patterson, Markus Brown, Haiming Chen, Anthony Bloch, Lindsey Muir, Roger Brockett, Indika Rajapakse
Rapid Sequential In Situ Multiplexing With DNA-Exchange-Imaging. Yu Wang, Johannes B Woehrstein, Noah Donoghue, Mingjie Dai, Maier S Avendano, Ron C.J. Schackmann, Shan Shan Wang, Paul W Tillberg, Demian Park, Sylvain W Lapan, Edward S Boyden, Joan S Brugge, Pascal S Kaeser, George M Church, Sarit S Agasti, Ralf Jungmann, Peng Yin
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The 
His Beddington Medal talk described the outcome of his most successful PhD project. About the background Erik explained: “The Drosophila segmentation cascade is a paradigmatic example of a developmental gene regulatory network, used to gain insight into transcriptional regulation in all animals… Using spatial information from graded domains of “gap” gene expression, seven “pair-rule” genes are expressed in periodic patterns of seven stripes each .. [which] then work in combination to specify precisely-phased 14 stripe patterns of “segment polarity” genes. These output patterns form the template for the segmental organisation of the insect body…[Although] the pair-rule genes have been studied in Drosophila for over 30 years,… there is still no good systems-level understanding of their regulatory interactions“.
Retinal degenerative diseases are the leading causes of blindness worldwide. In their 
Prostate organogenesis is a complex process that is regulated by androgens and subsequent mesenchyme-epithelial interactions. In their 
As every year, the 
