I am pleased to announce a new collaborative interest initiative called DevoWormML, based on work being done in the DevoWorm group. DevoWormML will meet on a weekly basis, and explore the application of machine learning and artificial intelligence to problems in developmental biology. These applications can be geared towards the analysis of imaging data, gaining a better understanding of thought experiments, or anything else relevant to the community.
While “ML” stands for machine learning, participation can include various types of intelligent systems approaches. Our goal is to stimulate interest in new techniques, discover new research domains, and establish new collaborations. Guests are welcome to attend, so if you know an interested colleague, feel free to direct them our way.
Meetings will be Wednesdays at 1pm UTC on Google Meet. Discussions will also take place on the #devowormml channel of OpenWorm Slack (request an invitation). We will discuss organizational details at our first meeting on September 4. If you cannot make this time but are still interested in participating, please contact me. Hope to see you there!
Deficiency in the endocytic adaptor protein PHETA1/2 impairs renal and craniofacial development
Kristin M. Ates, Tong Wang, Trevor Moreland, Rajalakshmi Veeranan-Karmegam, Priya Anand, Wolfgang Wenzel, Hyung-Goo Kim, Lynne A. Wolfe, Joshi Stephen, David R. Adams, Thomas Markello, Cynthia J. Tifft, William A. Gahl, Graydon B. Gonsalvez, May Christine Malicdan, Heather Flanagan-Steet, Y. Albert Pan
The enteric nervous system of the human and mouse colon at a single-cell resolution
Eugene Drokhlyansky, Christopher S. Smillie, Nicholas Van Wittenberghe, Maria Ericsson, Gabriel K. Griffin, Danielle Dionne, Michael S. Cuoco, Max N. Goder-Reiser, Tatyana Sharova, Andrew J. Aguirre, Genevieve M. Boland, Daniel Graham, Orit Rozenblatt-Rosen, Ramnik J. Xavier, Aviv Regev
The skin’s germinative layer from Joost, et al.’s preprint
A molecular cell atlas of the human lung from single cell RNA sequencing
Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V. Sit, Stephen Chang, Stephanie D. Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B. Shrager, Ross J. Metzger, Christin S. Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake, Mark A. Krasnow
Generation of human neural retina transcriptome atlas by single cell RNA sequencing
Samuel W. Lukowski, Camden Y. Lo, Alexei Sharov, Quan H. Nguyen, Lyujie Fang, Sandy S.C. Hung, Ling Zhu, Ting Zhang, Tu Nguyen, Anne Senabouth, Jafar S. Jabbari, Emily Welby, Jane C. Sowden, Hayley S. Waugh, Adrienne Mackey, Graeme Pollock, Trevor D. Lamb, Peng-Yuan Wang, Alex W. Hewitt, Mark Gillies, Joseph E. Powell, Raymond C.B. Wong
DUX4 regulates oocyte to embryo transition in human
Sanna Vuoristo, Christel Hydén-Granskog, Masahito Yoshihara, Lisa Gawriyski, Anastassius Damdimopoulos, Shruti Bhagat, Kosuke Hashimoto, Kaarel Krjutškov, Sini Ezer, Priit Paluoja, Karolina Lundin, Pauliina Paloviita, Gaëlle Recher, Vipin Ranga, Tomi Airenne, Mahlet Tamirat, Eeva-Mari Jouhilahti, Timo Otonkoski, Juha S. Tapanainen, Hideya Kawaji, Yasuhiro Murakawa, Thomas R. Bürglin, Markku Varjosalo, Mark S. Johnson, Timo Tuuri, Shintaro Katayama, Juha Kere
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Guanjue Xiang, Cheryl A. Keller, Elisabeth Heuston, Belinda M. Giardine, Lin An, Alexander Q. Wixom, Amber Miller, April Cockburn, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David Bodine, Shaun Mahony, James Taylor, Gerd A. Blobel, Mitchell J. Weiss, Yong Cheng, Feng Yue, Jim Hughes, Douglas R. Higgs, Yu Zhang, Ross C. Hardison
Modeling and treating GRIN2A developmental and epileptic encephalopathy in mice
Ariadna Amador, Christopher D. Bostick, Heather Olson, Jurrian Peters, Chad R. Camp, Daniel Krizay, Wenjuan Chen, Wei Han, Weiting Tang, Ayla Kanber, Sukhan Kim, Jia Jie Teoh, Sabrina Petri, Hunki Paek, Ana Kim, Cathleen M. Lutz, Mu Yang, Scott J. Myers, Subhrajit Bhattacharya, Hongjie Yuan, David B. Goldstein, Annapurna Poduri, Michael J. Boland, Stephen F. Traynelis, Wayne N. Frankel
Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells
Eleazar Rodriguez, Jonathan Chevalier, Jakob Olsen, Jeppe Ansbøl, Vaitsa Kapousidou, Zhangli Zuo, Steingrim Svenning, Christian Loefke, Stefanie Koemeda, Pedro Serrano Drozdowskyj, Jakub Jez, Gerhard Durnberger, Fabian Kuenzl, Michael Schutzbier, Karl Mechtler, Signe Lolle, Yasin Dagdas, Morten Petersen
Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid
Mark Zander, Mathew G. Lewsey, Natalie M. Clark, Lingling Yin, Anna Bartlett, J. Paola Saldierna Guzmán, Elizabeth Hann, Amber E. Langford, Bruce Jow, Aaron Wise, Joseph R. Nery, Huaming Chen, Ziv Bar-Joseph, Justin W. Walley, Roberto Solano, Joseph R. Ecker
The importance of barrier-free use of colors in images and graphs has been highlighted in letters to editors (Miall, 2007), papers (Geissbuehler and Lasser, 2013, Levine, 2009), editorials (anonymous, 2007), columns (Wong, 2011) and on numerous web pages. One of the recommendations is to use a color blindness simulator. Having a color vision deficiency myself, I cannot judge whether these tools work well. Nevertheless, a trial-and-error based approach seems rather inefficient. Instead, the use of (a number of) default color blind friendly palettes would be much more straightforward. For instance, green and magenta colors are the default choice for the production of color blind friendly overlays of fluorescence images. Below, I discuss a number of color palettes that are suitable for coloring graphical elements in plots. I think that people with a color vision deficiency would benefit from the implementation of these palettes in software for data visualization.
Qualitative color schemes
A quantitative color scheme is used when numbers need to be represented by colors. This conversion is done with a Look-Up Table (LUT). For more information on (colorblind-friendly) LUTs see this blog and this paper. Here, I talk about qualitative color schemes, which use colors to label different categories. The number of distinct categories define the number of unique colors that are needed. Ideally, these color can be distinguished by everybody.
For up to four categories, it is rather straightforward to come up with a set of colors that are easy to distinguish. Still, it does make sense to choose the colors from a color blind friendly color scheme. When 5-8 colors are needed to uniquely label different categories, it is a considerable challenge to find a suitable color palette. Beyond 8, it is close to impossible to find colors that can be readily distinguished. In these cases, alternative labeling methods are recommended. Below, several color blind friendly qualitative color schemes are described and four of those are shown in figure 1.
Color blind friendly palettes
Masataka Okabe and Kei Ito have proposed a palette of 8 colors on their website Color Universal Design (CUD). This palette is a “Set of colors that is unambiguous both to colorblinds and non-colorblinds”. The use of this palette is supported by others (Wong, 2011; Levine, 2009) and it is the default scale for the book “Fundamentals of Data Visualization” by Claus Wilke.
Martin Krzywinski has a website with 12- and 15-color palettes that offer more choices. Personally, I have difficulty with distinguishing several of these colors. Also, it is recommended to use no more than 8 different colors. Therefore, these palettes will not be taken along.
Paul Tol has created several qualitative color schemes that are color blind friendly. These palettes have 5-10 colors (including grey) and vary in darkness.
Figure 1: An overview of qualitative, color blind friendly palettes. The figure was produced with an R-script that defines and plots the palettes (doi: 10.5281/zenodo.3381072).
Choosing a color scheme
Which of the palettes is the best? This is hard to say for several reasons. Colors look different when printed, shown on a screen, or projected with a beamer. Next to this, size, structure and position of the objects will determine whether the categories can be distinguished. As a consequence, it is probably impossible to come up with a single universal color palette. I think that the palette designed by Okabe&Ito is a good first choice. Still, it is a good idea to see how different palettes perform when they are used in realistic data visualizations. As an example, figure 2 shows four plots in which the different color blind friendly palettes are used to label 6 lines.
Figure 2: The color palettes shown in figure 1 are used to uniquely label 6 different lines in a realistic data visualization. The graphs are with made with PlotTwist.
The palettes shown in figure 1 are implemented in the webtool PlotTwist (Goedhart, 2019). PlotTwist is a freely available online tool for plotting and annotating time-series data. It enables anyone to experiment with the color blind friendly palettes and apply them to lineplots. I encourage you to share your opinion on these (or any other) palettes and how they perform (especially if you have a color vision deficiency). To do so, you may leave a reply below or share your thoughts on twitter. Ultimately, I hope to see more data visualizations that pass a color blindness test with flying colors.
Recommendations
I will end with some recommendations aimed at improving graphs that use color:
-Use a color blind friendly palette by default.
-Use thick lines or large symbols to make it easier to correctly identify and map the color to a legend.
-In addition to colors, consider the use of patterns or labels to distinguish between categories.
We look back over the first 20 episodes of Genetics Unzipped to select some of our favourite bits that you might have missed.
There’s the tale of Esther Lederberg, whose contributions to science were overshadowed by her Nobel prize-winning husband, as well as an unexpected connection between the New England witch trials and Huntington’s disease.
Mary-Claire King describes how she stumbled into science, fell in love with genetics and went on to make groundbreaking discoveries. Finally, professional pyromaniac Fran Scott explains the importance of fire for human evolution.
If you enjoy the show, please do rate and review and spread the word. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com
The Company of Biologists’ journals – Development, Journal of Cell Science, Journal of Experimental Biology andDisease Models & Mechanisms – offer Travelling Fellowships of up to £3,000 to graduate students and post-doctoral researchers wishing to make collaborative visits to other laboratories. These are designed to offset the cost of travel and other expenses. There is no restriction on nationality.
They really are an amazing opportunity for ECRs to learn new things, meet new people and travel to new places.
The current round of Travelling Fellowships closes on 30 May (for travel after 11 July 2022)
Position Summary: The Marine Biological Laboratory seeks a motivated, creative and innovative Research Assistant or Research Associate to join the laboratories of Kristin Gribble and David Mark Welch in the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution. Our research combines comparative genomics, biochemistry, and life history to study aging, maternal effects, and DNA damage prevention and repair using rotifers, a novel aquatic invertebrate model system for studies of aging, neurobiology, genome evolution, and ecology. The successful candidate will develop genome editing techniques in rotifers, including CRISPR/Cas9, as part of a broad initiative at the MBL to advance new aquatic and marine models for biological discovery. Research will take place in the Bay Paul Center, with extensive DNA sequencing and bioinformatic resources, and in the NSF-funded Genome Editing Facility in the Marine Resources Center, where MBL scientists are developing new genetic and genomic tools for a wide range of marine invertebrates. We invite individuals with experience in genome editing in other animals to join this expanding program.
Basic Qualifications: Research Assistant applicants should have a B.A., B.S., or Master’s degree in biology, cell/molecular biology, biochemistry, or a related field. Research Associate applicants should hold a Ph.D. or have commensurate laboratory experience. This position requires proficiency and previous experience in molecular biology, microscopy, microinjection, and CRISPR/Cas9 methodology. We are seeking an independent, organized, enthusiastic, and productive individual with robust problem solving skills. Excellent interpersonal skills, attention to detail, and a strong work ethic are essential. Position level and salary will depend upon education and experience.
Preferred Qualifications: The ideal candidate will have working familiarity with RNAi and transgenic protocols. Proficiency in bioinformatics is a plus. Previous experience in established animal model or in non-model systems is preferred.
Physical Requirements: Ability to work with biohazardous chemicals using proper personal protective equipment. Occasional lifting of heavy objects (<30 lbs).
Special Instructions: Please apply on the MBL website and submit the following three items with your application:
(1) Cover letter describing your experience, research goals, specific interest in joining our group, and what you would contribute to the project
(2) CV/resume
(3) Contact information for 3-4 references (Please do not send letters at this time; we will contact references directly).
The Marine Biological Laboratory seeks a highly motivated individual to join the laboratory of Dr. Kristin Gribble in the position of Research Assistant I, II, or III.The successful applicant will contribute to our projects on the biology of aging, maternal effects on offspring health and lifespan, life history, evolution, and ecology using an aquatic invertebrate model system. The Gribble lab is housed within the Josephine Bay Paul Center, a collaborative research group addressing questions of microbial diversity, molecular evolution, and comparative genomics. Information about our research may be found at: http://mbl.edu/jbpc/gribble
Additional Information:
Responsibilities for this position include, but are not limited to, designing and conducting experiments, rotifer and phytoplankton culture, PCR, qPCR, protein extraction and analysis, microscopy, data entry and analysis, and general laboratory maintenance and organization. This position requires occasional work on weekends to accomplish long-term life table experiments. The position will be for one year but may be extended beyond this period contingent upon progress and funding.
Basic Qualifications:
Applicants should have a B.A./B.S., or M.A/M.S. in biology, cell/molecular biology, biochemistry, or a related field. This position requires an independent, organized, and self-motivated individual with robust problem-solving skills. Excellent written, verbal, and interpersonal skills; attention to detail; and a strong work ethic are essential. Position level and salary will depend upon education and experience.
Preferred Qualifications:
The ideal candidate will have one or more years of experience working in a research laboratory and will be familiar with standard laboratory practices and equipment. Previous experience with DNA, RNA, and protein extractions; next-generation sequencing library construction; PCR and qPCR; protein analysis; RNAi; microscopy; and bioinformatics is preferred. An understanding of basic molecular biology concepts is important.
Instructions:
Please apply on the MBL website and provide the following required documents:
Cover letter describing your interests, skills, prior research experience, and motivation for joining the lab;
Curriculum vitae;
The names and contact information for three references (Please do not send letters at this time; we will contact references directly).
The goal of Dr. Sanchez-Gurmaches lab is to understand the mechanisms that drive the normal and pathological formation and function of distinct types of adipocytes with the long-term goal of finding new therapeutic approaches to prevent or treat obesity and type 2 diabetes. For this we are using a wide variety of mouse genetic models to study adipocyte stem cells in different fat depots, induced pluripotent stem cells (iPSC) models, human clinical fat samples, single cell-omic tools, CRISPR screenings, omics approaches and functional in vivo and in vitro studies among others, following our recent findings (Cell Metabolism 2012, Nature Comm 2014, Stem Cell Reports 2015, Cell Metabolism 2018, Molecular Metabolism 2019).
We are seeking applicants, with a recent Ph.D. or equivalent, who have peer review publications, high capacity for independent thinking, collaborative work, and problem solving and show motivation and implication for the area of research. Candidates with strong experience in mouse study as in vivo model, cell culture techniques, molecular biology, biochemistry, metabolism, immunology and/or, microscopy are encouraged to apply. Interested applicants, please send your CV and a statement of research interests to juan.sanchezgurmaches@cchmc.org.
The laboratory of Drs. Sally A. Moody and Andre Tavares at the George Washington University School of Medicine and Health Sciences (https://smhs.gwu.edu/moody-lab/) seeks a beginning Postdoctoral Scientist to study aspects of craniofacial development using Xenopus and mouse. Studies will include evaluation of craniofacial phenotypes and transcriptional regulation. Techniques include embryo manipulations, qPCR, in-situ hybridization, RNA-seq, cell culture, and histology. Experience in developmental biology, embryological manipulations, molecular biology techniques and cell culture are preferred. Qualified candidates will hold a Ph.D. in Developmental Biology or related discipline. Degree must be conferred by the start date of the position. Term is for 2 years, and salary will be equivalent to NIH postdoctoral trainee stipends based on years of experience. To apply, please go to: http://www.gwu.jobs/postings/69978.
The Section of Developmental Biology at the University of Colorado School of Medicine, with support from the Gates Frontiers Fund, is inviting applications for our Postdoctoral Training Program. Member labs in the program use diverse model systems to address a broad range of questions in the areas of Developmental Biology, Disease Modeling and Regenerative Medicine:
Bruce Appel, PhD, Professor and Diane G. Wallach Chair of Pediatric Stem Cell Biology; website: https://www.appellab.com
We investigate genetic, cellular and molecular mechanisms of neural development using zebrafish as a model system. In particular, we investigate how neural progenitor cells are specified for neuronal and glial cell fates and mechanisms that regulate myelin plasticity in response to brain activity.
Ravanelli AM, and Appel, B. Genes & Development 29:2504-2515. PMCID: PMC4691953.
The Bates lab uses human, mouse, and fly genetics to understand how cells coordinate to develop into complex structures like the human brain and face or a fly wing. Specifically, we are trying to understand how ion channels contribute to developmental signaling and how the cytoskeleton is regulated to build a brain.
Dahal, GR, S. Pradhan, EA Bates. Development 2017 144:2771-2783. Doi:10.1242/dev146647. PMID: 28684627
We use the zebrafish as our main model to understand the causes of congenital diseases affecting mesodermal organs. Our work combines gene-regulatory element discovery, genotype-phenotype association studies, and novel zebrafish-based models for pediatric diseases. We further develop new approaches for genome editing in zebrafish and beyond.
Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E, Zaugg J, Weber LM, Catena R, Jinek M, Robinson MD, Mosimann C. Development. 2016 Jun 1;143(11):2025-37. PMID: 27130213
Lindsay H, Burger A, Biyong B, Felker A, Hess C, Zaugg J, Chiavacci E, Anders C, Jinek M, Mosimann C, Robinson MD. Nat Biotechnol. 2016 Jul 12;34(7):701-2. PMID: 27404876
Peter Dempsey, PhD, Associate Professor
The Dempsey lab studies the development and function of epithelial cells in gastrointestinal tract during normal physiology and disease. In particular, we are interested in how extracellular signals regulate intestinal homeostasis and the role of cellular plasticity during intestinal regeneration and in colitis-associated cancer. We use genetically engineered mouse models and both adult and iPS-derived intestinal stem cell enteroid cultures to study these events.
Feng Y, Tsai YH, Xiao W, Ralls MW, Stoeck A, Wilson CL, Raines EW, Teitelbaum DH, Dempsey PJ. Mol Cell Biol. 2015 Nov;35(21):3604-21.
Tsai YH, VanDussen KL, Sawey ET, Wade AW, Kasper C, Rakshit S, Bhatt RG, Stoeck A, Maillard I, Crawford HC, Samuelson LC, Dempsey PJ. Gastroenterology. 2014 Oct;147(4):822-834.
Caleb Doll, PhD, Research Assistant Professor
We study developmental myelination in zebrafish larvae, with focus on the mechanisms underlying local production of proteins in nascent myelin sheaths. We use cell type specific methods to visualize and manipulate RNA binding proteins and associated mRNA targets during oligodendrocyte development.
Doll, C, Yergert, K, Appel, B. bioRxiv; doi: 10.1101/669895
Santos Franco, PhD, Assistant Professor and Boettcher Investigator; website:www.francolabcu.org
The Franco Lab uses mouse models to study several aspects of brain development. We are particularly interested in understanding early brain patterning, cell fate specification of neural stem cells, neuronal migration, dendrite formation and synaptogenesis.
Winkler CC, Yabut OR, Fregoso SP, Gomez HG, Dwyer BE, Pleasure SJ, Franco SJ. (2018) J Neurosci. Jun 6;38(23):5237-5250. PMID: 29739868
• Fregoso SP, Dwyer BE, Franco SJ. (2019) Development. Mar 7;146(5). PMID: 30770393
• Gutierrez MA, Dwyer BE, Franco SJ. (2019) eNeuro. May 7;6(2). PMID: 31073541
Christian Mosimann, PhD, Associate Professor and Johnson Endowed Chair in Heart Development Research
Our lab studies the mechanisms of cell fate determination during development and congenital disease, with particular focus on the origins of mesodermal cell types and of the cardiovascular system. We combine transgenic, genome editing, single-cell, and live-imaging approaches using the zebrafish as our principal model and engage in several cross-species collaborations.
Felker A, Prummel KD, Merks AM, Mickoleit M, Brombacher EC, Huisken J, Panáková D, Mosimann C.; Nat Commun.2018 May 21;9(1):2001. PMID: 29784942
Cantù C, Felker A, Zimmerli D, et al.; Genes Dev. 2018 Nov 1;32(21-22):1443-1458. PMID: 30366904
Our group uses zebrafish to study transcriptional and epigenetic control of key transitions during embryogenesis. We are particularly interested in understanding the onset of zygotic gene expression at the maternal-to-zygotic transition and in the initiation of neural gene expression in the embryonic ectoderm.
S.-K. Choe, F. Ladam and C. G. Sagerström. Developmental Cell 28:203-211. PMID:24480644
F. Ladam, W. Stanney III, I. J. Donaldson, N. Bobola and C. G. Sagerström. eLife2018;7:e36144. PMID: 29911973
The Siegenthaler lab is focused on identifying cellular and molecular mechanisms regulating development and adult function of the CNS vasculature and the meninges. In pursuit of this goal, we utilize mouse genetics to specifically target meningeal and vascular cell populations and perturb signaling pathways of interest (retinoic acid, Wnt-beta-catenin), advanced imaging modalities, cell culture and transcriptional profiling. We have recently completed a first ever single cell transcriptome analysis of the developing meninges; this valuable tool will aid in studying the development of meningeal fibroblast populations and exploring interactions of fibroblasts with meninges-located vasculature and immune populations as well as the developing and adult CNS.
Bonney, S, Dennison, BJC, Wendlandt, M, Siegenthaler, JA. Frontiers in Cellular Neuroscience,
Kelly Sullivan, PhD, Assistant Professor and Boettcher Investigator
Our lab is interested in how an extra copy of chromosome 21 gives rise to the condition known as Down syndrome. We use a combination of primary samples, cell culture, and mouse models, to understand how aberrant interferon signaling affects development and contributes to pathophysiology in Down syndrome.
Sullivan KD*, Lewis HC, Hill AA, Pandey A, Jackson LP, Cabral JM, Smith KP, Liggett LA, Gomez EB, Galbraith MD, DeGregori J, Espinosa JM*. Elife. PMID:27472900, PMCID: PMC5012864 *Co-corresponding Author
Powers RK, Culp-Hill R, Ludwig MP, Smith KP, Waugh KA, Minter R, Tuttle, KD, Lewis HC, Rachubinski AL, Granrath RE, Carmona-Iragui M, Wilkerson RB, Kahn DE, Joshi M, Lleo A, Blesa R, Fortea J, D’Alessandro A, Costello JC, Sullivan KD*, Espinosa JM*. Biorxiv 403642 *Co-corresponding Author
The Training Program provides a mechanism for postdoctoral trainees to mature into successful independent researchers in Developmental Biology and Regenerative Medicine. Trainees are provided salary support in accordance with the NIH pay scale and the University of Colorado offers a full benefits package. Successful applicants will be appointed as Gates Fellows with initial appointments made for one year and continued support contingent on satisfactory progress. The Program also provides each trainee with a mentoring committee, funds to attend conferences/courses and networking opportunities in the form of interactions with visiting scientists, national/international collaborations, journal clubs, research interest groups and annual retreats. Interested trainees will also be given opportunities to teach and mentor students as well as to improve writing skills.
Applicants must have a PhD degree and less than two years of postdoctoral experience as of September 1, 2019. Interested candidates should submit 1) a statement explaining their interest in the Program and indicating their preferred host lab (2-page maximum), 2) a CV and 3) arrange to have three reference letters sent. Review of applications will begin immediately and finalists will be invited for on-campus interviews. We anticipate filling four positions and interviews will continue until the positions are filled.
Questions and applications should be submitted by email to Dr. Charles Sagerström, Director of the Postdoctoral Training Program, at charles.sagerstrom@cuanschutz.edu
(1 votes)
Loading...
(No Ratings Yet)
(33 votes)
We look back over the first 20 episodes of Genetics Unzipped to select some of our favourite bits that you might have missed.