Our research investigates the fundamental question of how cardiac cells sense and respond to their environment. We seek to understand the mechanisms underlying the regulation of morphogenetic and identity transformations that occur during development and disease. We use the assembly of the heart tube in zebrafish as our model with which to elucidate these mechanisms. Some of the specific research questions we are interested in include: How do multiple tissues interact to regulate large movements and biomechanical force? How do dynamic changes in the extracellular matrix regulate cardiac morphogenesis? How is lumen formation intrinsically and extrinsically encoded? and How is the plasticity of cardiovascular identity regulated? To answer these questions, we take an interdisciplinary approach, combining the genetic and live-imaging strengths of zebrafish with both biomechanics and systems-level methodologies.
If you are interested in joining our lab as a PhD student, please contact us directly at josh@olemiss.edu.
-Additional positions, including a rotation program, are also available in our interdisciplinary graduate program in the department of Biology at the University of Mississippi. For more information about our graduate program including rotations please see biology.olemiss.edu
We seek a biocurator to join the FlyBase group at the University of Cambridge, UK. If you are looking for a fulfilling, fly-related career away from the lab, and enjoy the challenge of organizing complex data clearly and concisely, then this is the job for you!
FlyBase curators extract biological information from scientific articles about the model organism Drosophila melanogaster, recording and organizing these data in template forms and graphical interfaces. Phenotype curators focus on data that illuminate the function of genes based on their mutant phenotypes and genetic interactions. All curated data are subsequently integrated into our central database and made freely available via the FlyBase website.
Additional responsibilities of phenotype curators include: developing strategies/tools to improve curation; enhancing data display/querying on the website; and interacting with the research community through HelpMail and presentations/help desks at research conferences. Curators also contribute to FlyBase publications and have the opportunity to develop computational skills (e.g. Unix, scripting, SQL).
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.
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We look back over the first 20 episodes of Genetics Unzipped to select some of our favourite bits that you might have missed.