Development invites you to submit your latest research to our upcoming special issue: Imaging development, stem cells and regeneration.
Imaging-based approaches have long played a role in the field of developmental biology. However, recent technical advances now provide us with the ability to visualise cell and developmental processes at extraordinary resolution and in real-time. From progress in light sheet and super-resolution microscopy, to the development of tissue-clearing techniques and sophisticated image analysis platforms, we are now able to capture and quantitatively analyse the beauty and dynamics of development across different scales – from individual molecules and cells, to complete tissues and embryos. This Special Issue aims to showcase articles that, at their core, have applied such advanced techniques in innovative ways to further our understanding of developmental and regenerative processes. We also encourage the submission of articles that report the development or application of a novel imaging-based technique.
Prospective authors are welcome to send pre-submission enquiries to dev.specialissue@biologists.com. We also invite proposals for Review articles: if you are interested in contributing a Review, please send a summary of your proposed article to us by 15 December 2020.
The Special Issue will be published in mid-2021 (although note that, in our new continuous publication model, we will aim to publish your article as soon as it is accepted*). The issue will be widely promoted online and at key global conferences, guaranteeing maximum exposure for your work.
For information about article types and manuscript preparation, please refer to our author guidelines. To submit your article, visit our online submission system; please highlight in your cover letter that the submission is to be considered for this Special Issue.
The deadline for submitting articles is 30 March 2021.
Why choose Development?
Submissions handled by expert Academic Editors
Competitive decision speeds and rapid publication
Format-free submission
Strong commitment at first decision – over 95% of invited revisions accepted
Free to publish – no page or colour charges, no hidden fees
Easy one-click transfer option to Biology Open
Not-for-profit publisher
* Please note that not all articles accepted for publication will be included in the Special Issue; they may instead be published in earlier or later issues of the journal based on timing and editorial discretion.
Oleic acid triggers hippocampal neurogenesis by binding to TLX/NR2E1
Prasanna Kandel, Fatih Semerci, Aleksandar Bajic, Dodge Baluya, LiHua Ma, Kevin Chen, Austin Cao, Tipwarin Phongmekhin, Nick Matinyan, William Choi, Alba Jiménez-Panizo, Srinivas Chamakuri, Idris O. Raji, Lyra Chang, Pablo Fuentes-Prior, Kevin R. MacKenzie, Caroline L. Benn, Eva Estébanez-Perpiñá, Koen Venken, David D. Moore, Damian W. Young, Mirjana Maletic-Savatic
Cardiac Sex Differences are Established Prior to Gonad Formation
Wei Shi, Xinlei Sheng, Kerry M. Dorr, Josiah E. Hutton, Haley A. Davies, Tia D. Andrade, Todd M. Greco, Yutaka Hashimoto, Joel D. Federspiel, Zachary L. Robbe, Xuqi Chen, Arthur P. Arnold, Ileana M. Cristea, Frank L. Conlon
Olig3 acts as a master regulator of cerebellar development
Elijah D. Lowenstein, Aleksandra Rusanova, Jonas Stelzer, Marc Hernaiz-Llorens, Adrian E. Schroer, Ekaterina Epifanova, Francesca Bladt, Eser Göksu Isik, Shiqi Jia, Victor Tarabykin, Luis R. Hernandez-Miranda
Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential
Ge Guo, Giuliano Giuseppe Stirparo, Stanley Strawbridge, Daniel Spindlow, Jian Yang, James Clarke, Anish Dattani, Ayaka Yanagida, Meng Amy Li, Sam Myers, Buse Nurten Özel, Jennifer Nichols, Austin Smith
A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals
Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Sunita L. D’Souza, Arjun Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen Lynch, Katherine Michelis, Neelima Tangirala, Himali Weerahandi, David C. Thomas, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C Schürer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar
Cathepsin K maintains the number of lymphocytes in vivo
Renate Hausinger, Marianne Hackl, Ana Jardon-Alvarez, Miriam Kehr, Sandra Romero Marquez, Franziska Hettler, Christian Kehr, Sandra Grziwok, Christina Schreck, Christian Peschel, Rouzanna Istvanffy, Robert A.J. Oostendorp
Early Stem Cell Aging in the Mature Brain
Albina Ibrayeva, Maxwell Bay, Elbert Pu, David Jörg, Lei Peng, Heechul Jun, Naibo Zhang, Daniel Aaron, Congrui Lin, Galen Resler, Axel Hidalgo, Mi-Hyeon Jang, Benjamin D. Simons, Michael A. Bonaguidi
Cell size is a determinant of stem cell potential during aging
Jette Lengefeld, Chia-Wei Cheng, Pema Maretich, Melanie R. McReynolds, Marguerite Blair, Hannah Hagen, Emily J Sullivan, Kyra Majors, Christina Roberts, Joon Ho Kang, Joachim Steiner, Teemu P Miettinen, Scott Manalis, Adam Antebi, Jacqueline Lees, Laurie Boyer, Omer H. Yilmaz, Angelika Amon
Endogenous Galectin-3 is Required for Skeletal Muscle Repair
Daniel Giuliano Cerri, Lilian Cataldi Rodrigues, Vani Maria Alves, Juliano Machado, Víctor Alexandre Félix Bastos, Isis do Carmo Kettelhut, Luciane Carla Alberici, Sean R. Stowell, Maria Cristina R. Costa, Richard D. Cummings, Marcelo Dias-Baruffi
A CRISPR-Cas9–engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions
Miguel Rodríguez de los Santos, Marion Rivalan, Friederike S. David, Alexander Stumpf, Julika Pitsch, Despina Tsortouktzidis, Laura Moreno Velasquez, Anne Voigt, Karl Schilling, Daniele Mattei, Melissa Long, Guido Vogt, Alexej Knaus, Björn Fischer-Zirnsak, Lars Wittler, Bernd Timmermann, Peter N. Robinson, Denise Horn, Stefan Mundlos, Uwe Kornak, Albert J. Becker, Dietmar Schmitz, York Winter, Peter M. Krawitz
Patient iPSC-astrocytes show transcriptional and functional dysregulation in schizophrenia
Marja Koskuvi, Šárka Lehtonen, Kalevi Trontti, Meike Keuters, Ying Chieh Wu, Hennariikka Koivisto, Anastasia Ludwig, Lidiia Plotnikova, Pekka L. J. Virtanen, Noora Räsänen, Satu Kaipainen, Ida Hyötyläinen, Hiramani Dhungana, Raisa Giniatullina, Ilkka Ojansuu, Olli Vaurio, Tyrone D. Cannon, Jouko Lönnqvist, Sebastian Therman, Jaana Suvisaari, Jaakko Kaprio, Markku Lähteenvuo, Jussi Tohka, Rashid Giniatullin, Claudio Rivera, Iiris Hovatta, Heikki Tanila, Jari Tiihonen, Jari Koistinaho
A comprehensive overview of computational tools for RNA-seq analysis
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Lana S. Martin, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Pawel P Labaj, Serghei Mangul
Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature
Clarissa F. D. Carneiro, Victor G. S. Queiroz, Thiago C. Moulin, Carlos A. M. Carvalho, Clarissa B. Haas, Danielle Rayêe, David E. Henshall, Evandro A. De-Souza, Felippe E. Amorim, Flávia Z. Boos, Gerson D. Guercio, Igor R. Costa, Karina L. Hajdu, Lieve van Egmond, Martin Modrák, Pedro B. Tan, Richard J. Abdill, Steven J. Burgess, Sylvia F. S. Guerra, Vanessa T. Bortoluzzi, Olavo B. Amaral
The study of regenerative biology aims to elucidate the innate ability of organisms to repair tissues or organs after they have been removed or damaged. During vertebrate regeneration, tissue damage causes the immediate release of signals that initiate wound closure and initiate regeneration. This project uses larval zebrafish to study how cells respond to when the epithelia is damaged. Zebrafish repair wounds quickly and efficiently, and their small size and transparency allow us to follow cell behaviour easily. Our previous research found that there are very surprising movements of cells over the first few hours after damage, and this current project aims to understand the forces involved in these movements and the signals that orchestrate the wound response. We plan to image fluorescently labelled cells over time to give positional data across the fish using a custom built lightsheet microscope. Data sets will be analysed using physical and computational modelling to calculate passive and active forces such as compression, stretching, shear and friction. Once a physical model of whole animal cell movement is established we will interrogate our predictions by manipulating known early wound signals.
Funding Notes
White Rose BBSRC Doctoral Training Partnership in Mechanistic Biology
4 year fully-funded programme of integrated research and skills training, starting October 2021:
• Research Council Stipend (estimated £15,600 per year)
• Tuition Fees at the UK fee rate (£4,473 per year)
• Research support and training grant (RTSG)
Please note: international tuition fees for 2021 entry are £23,750
To Apply:
Informal inquiries: h.roehl@sheffield.ac.uk
The deadline for applications will be the 10th January 2021 with selection of final candidates for interview shortly after.
Updated 30 October . Let us know if we missed anything
Various organisations and looser assemblies of locked down researchers have begun to put together online seminar and talk series, many of which are open to anyone (usually with registration), and many of which also have previous talks recorded.
Here’s a list of what we’ve found recently, developmental biology and adjacent – please let us know if we missed anything so we can keep it up to date. For upcoming virtual developmental biology conferences/symposia, see our recently updated Events calendar page.
Big news from us is Development presents…, the webinar series hosted each month by a different Development Editor which will be a platform for early career researchers to share their work. As well as the talks, you also have the chance to meet the speakers and other participants at interactive video tables – giving the developmental biology community the chance to network virtually.
Talking about promoting early career researchers, the Society for Developmental Biology in the USA is running a monthly postdoc seminar series. Next one is November 13, speakers TBD (you can see recordings of the October session with Michael Piacentino and Natasha O’Brown on the homepage).
The role of the next generation sequencing (NGS) specialist is to ensure daily operations at the Genomics Platform and to support researchers at two centres working on fundamental biological mechanism, the Novo Nordisk Centres for Protein Research (CPR) and Stem Cell Biology (DanStem), with expertise in functional genomics and single-cell sequencing applications. The advertised job is an exciting opportunity for strong candidates with a background in genomics technology to establish themselves in the field of genomics services. The genomics platform represents a joint venture that bridges the vibrant scientific environment that spans DanStem and the CPR and is central to scientific activities in both centers.
Background
DanStem addresses fundamental research questions in stem cell and developmental biology and has activities focused on the translation of promising basic research results into new therapeutic strategies for cancer and chronic diseases. DanStem is a vibrant, internationally diverse and ambitious research center with state-of-the-art facilities. The setting is ideally suited for seamless collaboration and exchange with other centers and departments of the Faculty and Copenhagen science community.
CPR promotes basic and applied research on human proteins of medical relevance. CPR spans broad areas of protein research, ranging from structural and mechanistic understanding of proteins and their cellular functions in chromatin biology and genome maintenance, to development of clinical applications of proteomics and systems biology. The vision of CPR is to combine the power of integrative protein technologies and their application to accelerate understanding of the biological processes underlying health and disease.
The genomics platform was established in 2017 by DanStem and CPR and is run by a sequencing specialist and a bioinformatics specialist. We are seeking a highly motivated and ambitious candidate to join the platform as sequencing specialist with a focus on user support, method development and training. The genomics platform has access to its own NextSeq500, an Agilent Bravo, Fragment analysers and other necessary genomics equipment. Groups at CPR and DanStem are seeing a steady increase in genomics based experiments and assays that massively benefit from input and advice by the combined expertise of the genomics platform. The advertised job is an exciting opportunity for strong candidates to establish themselves in the field of genomics services in an exciting scientific environment provided by our well-established centers.
Job description
The role of the next generation sequencing (NGS) specialist is to ensure daily operations of the wet lab part of Genomics Platform. The tasks include: Supporting experimental design and advising potential users, training and assistance on library preparations (DNA and RNA based), running and overseeing the NextSeq500 sequencer, training the users on platform instruments (e.g. Fragment Analyser, liquid handling robot), providing advice on genomics tools and troubleshooting. It also includes ordering, stocking and supplying consumables specific to the genomics platform. Importantly, the applicant will be expected to introduce and support the establishment of new genomics applications as a service in collaboration with users.
Your profile
A degree in biotechnology, molecular biology, or appropriate biological or biomedical science with either PhD or MSc.
Theoretical and practical knowledge of NGS sample preparation workflows and applications.
Previous experience with NGS bioinformatics is a plus.
Team oriented communication style and ability to manage experiment associated cost transparently and efficiently
Good English communication skills, both oral and written, are required.
Ability to connect and actively participate in exchange with other genomics platforms nationally and internationally
We offer
Stimulating, challenging and multifaceted research environment
A combination of active scientific service platforms to interact and to develop ideas together and expand available methodology at CPR and DanStem
Possibility for continued education and training
Attractive employment conditions
Central located workplace.
Employment conditions
The employment is a permanent position and is scheduled to start 1 March 2021 or upon agreement with the chosen candidate. The place of work is at DanStem, University of Copenhagen, Blegdamsvej 3B, Copenhagen. Salary, pension and terms of employment are in accordance with the provisions of the collective agreement between the Danish Government and AC (the Danish Confederation of Professional Associations).
In addition to the basic salary, a monthly contribution to a pension fund is added (17.1% of the salary) and depending on qualifications, a supplement may be negotiated.
The employment will be as Research consultant (Specialkonsulent) depending on the selected candidate’s experiences and qualifications and the working time are 37 hours per week on average.
Application
Your application must be submitted in English by clicking “Apply now” below and must include:
Motivation letter
Curriculum vitae incl. education, experience, previous employments, language skills and other relevant skills
Copy of diplomas/degree certificate(s).
Only applications received in time and consisting of the above listed documents will be considered. Applications and/or any material received after the deadline will not be taken into consideration.
Deadline for applications: 9 December 2020.
Questions
For further information about the position, please contact Professor Joshua Brickman by e-mail: joshua.brickman@sund.ku.dk.
The Faculty of Health and Medical Sciences comprises approximately 7,850 students, 1,700 PhD students and 4,800 employees. The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community. The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.
The new Center for Stem Cell & Organoid Medicine (CuSTOM) at Cincinnati Children’s Hospital Medical Center (CCHMC) is launching a major new initiative to recruit outstanding tenure-track or tenured faculty at the Assistant to Associate Professor level.
CuSTOM (www.cincinnatichildrens.org/custom ) is a multi-disciplinary center of excellence integrating developmental and stem cell biologists, clinicians, bioengineers and entrepreneurs with the common goal of accelerating discovery and facilitating bench-to-bedside translation of organoid technology and regenerative medicine. Faculty in CuSTOM benefit from the unique environment and resources to studies of human development, disease and regenerative medicine using pluripotent stem cell and organoid platforms.
CCHMC is a leader in organoid biology and one of the top ranked pediatric research centers in the world, providing a unique environment for basic and translational research. Among pediatric institutions CCHMC is the third-highest ranking recipient of research grants from the National Institutes of Health. CCHMC continues to make major investments in research supporting discovery with 1.4 million square feet of research space and subsidized state-of-the-art core facilities including a human pluripotent stem cell facility, CRISPR genome editing, high-throughput DNA analysis, biomedical informatics, a Nikon Center of Excellence imaging core and much more.
We invite applications from innovative and collaborative investigators focused on basic or translational research in human development and/or disease using stem cells or organoid models. Successful candidates must hold the PhD, MD, or MD/PhD degrees, and will have a vibrant research program with an outstanding publication record.
Applicants should submit their curriculum vitae, two to three page research statement focused on future plans, and contact information for three people who will provide letters of recommendation to CuSTOM@cchmc.org. Applications must be submitted by December 1st, 2020
The Cincinnati Children’s Hospital Medical Center, and the University of Cincinnati are Affirmative Action/Equal Opportunity Employers, fostering diversity and inclusion. Qualified women and minority candidates are especially encouraged to apply.
To develop remedial strategies for neurodegeneration in age and disease, we need to improve our understanding of the cell biology of neurons – in particular their axons. Axons are the cable-like, up-to-meter long processes of neurons that wire our nervous system (Fig.1); we lose 40% of axons towards high age and they are key target sites for degenerative processes (Fig.2).
Fig.3 Click to see original
The overarching aim of this project is therefore to gain a better understanding of the architecture of axons and how it evolved from invertebrates to mammals. For this, we focus on the bundles of microtubules (MTs; Fig.3) that extend through the entire axon; they provide the structural backbones of axons and highways for life-sustaining cargo transport and organelle dynamics. Therefore, our studies of the mechanisms that uphold these MT bundles [Refs.1,2] aim to advance our understanding of axon architecture and how they are maintained long-term (Fig.4).
Fig.4 Click to see original
Here we focus on the role of so-called MT cross-linker proteins, expected to hold MTs in parallel bundled arrangements (Figs.3,5). Cross-linkage was one of the first mechanisms proposed to explain axonal MT bundle conformation, and proposed cross-linkers such as Tau or MAP1B have close links to neurodegeneration including Alzheimer’s disease. However, the experimental evidence and molecular understanding of MT cross-linkage is surprisingly sparse [reviewed in Refs. 2,4], leaving an important gap in our understanding of axon architecture and maintenance.
Fig.5 Click for further information
We are particularly interested in MAP1B which plays conserved roles in MT bundle architecture from invertebrates to humans, whilst showing a very particular evolutionary profile (Fig.6): the N- and C-terminal domains have proposed actin-binding properties and are well-conserved throughout the animal kingdom, whereas the middle region is highly variable: it is extremely long (>4,500 aa) in many arthropods correlating with wider spacing of their MTs, whereas other animals including mammals have short forms (1,687 aa in humans) correlating with narrower spacing and the presence of neurofilaments (absent in arthropods). Furthermore, the middle region undergoes rapid change, with sequences not conserved even between closely related species (e.g. Drosophila melanogaster and D. grimshawi flies from the same family). Our detailed studies of MAP1B and its homologues will be doubly beneficial: they will bring important new understanding of mechanisms underpinning evolution, as well as of axon architecture providing information that is also relevant for work on axon degeneration.
During this project, we will capitalise on Matthew Ronshaugen‘s expertise in evolutionary biology to perform phylogenetic analyses of MAP1B and its homologues, aiming to extract concepts and rules that explain MAP1B’s evolutionary behaviour, and develop experimentally testable working hypotheses. Experiments will build on Andreas Prokop‘s expertise on axon structure and MT regulation using Drosophila neurons as a genetically amenable system for fast and efficient experimentation; thus, we will modify the fly MAP1B gene to test our phylogenetics-derived hypotheses. Many experiments will involve electron microscopy for which Karl Kadler is a long-standing expert; EM will reveal structural aberrations, subcellular positions of MAP1B and changes in MT spacing.
Detailed project description
Obj. 1: To understand the evolution of MAP1B homologues: We will perform in-depth evolutionary analysis of the MAP1B protein family by (a) collecting full length MAP1B protein sequences from a broad set of metazoan animal species, (b) building an accurate protein alignment and (c) establishing a stable phylogeny for MAP1B. We will examine how selection has acted on MAP1B domains, for example whether rapid middle region variations are due to neutral drift or possibly positive selection acting to diversify MAP1B crosslinking function and neuronal morphology. Finally, we will use a bioinformatic approach to identify conserved motifs, predict functions based on structure and homology, and examine their gain and loss throughout the MAP1B evolutionary history. Our results will inform the genetic structure function analysis described in Obj. 3 to examine how sequence conservation and divergence within MAP1B proteins correlate with changes in neuronal morphology.
Fig.6 Click image to see original
Obj. 2: To establish the mechanisms of Drosophila MAP1B in MT cross-linkage: We will test whether the fly MAP1B is positioned in between MTs and whether it imposes a constant MT-MT spacing in this position. For this, we will perform EM studies using MT contrast enhancement (lanthanum or tannic acid) in combination with MAP1B detectable via a central enzymatic APEX2 tag (generated via CRISPR/Cas9). We know that the conserved N- and C-terminal domains of fly MAP1B are functionally relevant but have no knowledge of the underlying mechanisms [Ref. 3]. We will establish whether they directly bind MTs using biochemical pull-down strategies.
Fig.7 Examples of MT profiles (arrow heads) in axonal cross-sections in the Drosophila CNS (A) and peripheral nerve (B).
Obj. 3: To functionally assess the meaning of evolutionary changes: Using readouts established during Obj. 2, we will introduce changes to fly MAP1B and assess their impacts on axon structure. We already hold constructs of rat MAP1B and mini constructs of fly MAP1B (containing only N- and C-terminal domains) which will be expressed and tested in MAP1B-deficient background to assess changes, for example in MT spacing. We will build on our phylogenetic analyses and use gene blocks strategies to generate and then analyse interspecies hybrid versions of MAP1B; for example we will assess whether the exchange of the middle region has a structural impact.
Taken together, we will establish how MAP1B proteins contribute to the bundled conformation of axonal MTs across the animal kingdom, and why part of this molecule has undergone such a severe change. This will provide new insights into evolutionary mechanisms and relevant understanding of neurodegenerative processes. This project is therefore highly interdisciplinary and provides training opportunities including phylogenetic in silico analyses, molecular biology, classical genetics, biochemistry and electron microscopy.
References
Hahn, I., Voelzmann, A., Parkin, J., Fuelle, J. B., Slater, P. G., Lowery, L. A., Sanchez-Soriano, N., Prokop, A. (2020). Tau, XMAP215/Msps and Eb1 jointly regulate microtubule polymerisation and bundle formation in axons. bioRxiv, 2020.08.19.257808 — [LINK]
Hahn, I., Voelzmann, A., Liew, Y.-T., Costa-Gomes, B., Prokop, A. (2019). The model of local axon homeostasis – explaining the role and regulation of microtubule bundles in axon maintenance and pathology Neural Dev 14, 10.1186/s13064-019-0134-0 — [LINK]
Hummel, T., Krukkert, K., Roos, J., Davis, G., Klämbt, C. (2000). Drosophila Futsch/22C10 is a MAP1B-like protein required for dendritic and axonal development. Neuron 26, 357-370 — [LINK]
Prokop, A. (2020). Cytoskeletal organization of axons in vertebrates and invertebrates. J Cell Biol 219, e201912081 — [LINK]
Qu, Y.*, Hahn, I.*, Lees, M., Parkin, J., Voelzmann, A., Dorey, K., Rathbone, A., Friel, C., Allan, V., Okenve Ramos, P., Sánchez-Soriano, N., Prokop, A. (2019). Efa6 regulates axon growth, branching and maintenance by eliminating off-track microtubules at the cortex. eLife 8, e50319 — [LINK]
In my visual communication classes students increasingly want to learn how to make graphical abstracts. Below I summarized a few key points
What are Graphical abstracts?
Graphical abstracts are increasingly common to explain biomedical concepts and research results. “Summary slides” have been for long been used in talks or lectures. Today, graphical abstracts are omnipresent a thumbnail previews in online publications, and are also used in posters, on lab websites, and in research grant applications.
The key element of every graphical abstract are pictograms-like visualizations or icons. With text and arrows, the pictograms are then arranged into a sequential narrative or ‘story’. A consistent color scheme and clear layout help to orienting the audiences. Below are a few quick suggestions to help you design a graphical abstract quickly.
One main message
Before starting the design process, spend a good amount of time brainstorming the key message to get across. I personally do this by doodling on paper and discussing with peers. Without a clear main message, it will be impossible to design a good graphical abstract.
Pictograms as visual elements
Pictograms have long been used in science and in the early 20th century, Otto Neurath and Gerd Arntz started to systemically designed icons for communicating data to broad audiences. The past decade saw an explosion of new pictograms such as emoticons in social media.
A new resource for pictograms is fontawesome, a unicode-based icon library that can be installed locally as a font. The font can then be used in e.g. PowerPoint or Illustrator to directly “write” pictograms. Alternatively, pictograms can be accessed online and downloaded (svg, png). A larger collection is available at the Nounproject. Here, designers can upload icons for re-use with attribution. Scientific pictograms for free re-use are collected at the EBI reactome icon library. This site allows upload of user-designed pictograms for sharing with the scientific community.
In a graphical abstract, the pictograms used should have a similar overall appearance. Ensure that colors, line widths, and level of detail are comparable in all used icons. Best practice would be to use pictograms from one designer or one source only. And: start your own personal collection, chances are you might need them again!
All pictograms used have similar overall appearance (color, size, design)
Bad combination of pictogram, all pictograms have different appearance
Layout: Dimensions
Layout describes the organization of visual elements on the page. First, consider the dimensions of your page: a graphical abstract for a journal website most often is square, while rectangle stretching across the entire page might be a better use of space for a graphical abstract in a grant application with limited word number.
Dimensions for Graphical Abstracts: square is often required by journals and works well online. Rectangle is easier for slides, posters etc. Adapt dimension when including Graphical Abstract in text.
Layout: Reading direction
The layout should provide a clear entry into the graphical abstract and a clear end. Typically, we read from left to right, and top to bottom. The visual elements should be arranged along the chosen reading direction.
For depiction of linear processes, which have a clear beginning and end, organization from left to right is most suitable: time is usually shown as the independent variable on the x-axis f graphs. Linea processes may be procedures, such as a methodical pipeline, or cellular events such as cell division, embryo development, or disease progression. For depiction of cyclic events, for example daily, annual or metabolic processes, consider a circular layout; for static events, e.g. contrasting two scenarios or providing two levels of details for one scenario, consider two parallel or nested organization.
Different layouts for Graphical Abstracts that have a clear start and end.
Arrows
Arrows (and lines) have several roles in graphical abstracts. First, arrows reinforce a reading direction that is already visually defined by a layout, or point out an exception from the reading direction. Second, arrows often indicate motion: a molecule passes a membrane, a cell migrates into a tissue, animals flock to food source. And third, arrows are used for labeling structures or regions of interest. Here, the arrow may be replaced by a simple line. Depending on the arrow head, the meaning can also change to showing an inhibition or forking etc.
It is important to clearly signal to the audience the intention of an arrow and, if two types of arrows are used in parallel, to contrast them visually. Note how changing the context of an arrow can also change its perceived meaning.
Different arrow types and arrow usage in Graphical Abstracts
Text
Understanding of complex scenarios is easiest when text and visual are used in synergy (Mayer RE 2002; Hegarty, 1993). First, text is used to substitute for pictograms where these are no available (e.g. specific molecules: ‘acetylcholine’). Second, text also serves to label pictograms that are otherwise ambiguous (e.g. a circle for ‘cell’, ‘bacteria’, ‘nucleus’), Third, text also enforces the meaning of an arrow: an upward arrow could indicate ‘move up’, ‘increase’ or ‘good’, or a circular arrow could be day, year or life cycle. Last, text often provides further explanations. Here it is critical that the it remains short and without jargon and sparse abbreviations.
Colors
As in all visualizations, colors are used in graphical abstracts to highlight and contrast, to encode numerical data, or to show the natural appearance of a visualized object. It is key to use colors consistently. A change in color is perceived as a change in meaning. Also use color sparsely as color always draws attention of the audiences, and might eclipse the key take home message of the graphical abstract.
For picking harmonious colors schemes use e.g. http://paletton.com. Colors schemes can be based on adjacent colors to appear harmonious or on complementary colors to contrast scenarios.
Color can highlight, encode numbers, or show natural appearance in Graphical Abstracts. Careful with color choice when using a background color!
Making of… Tools!
Graphical abstracts can, like a poster, be prepared with vector-design software (Illustrator, Inkjet, CorelDraw) or software for preparing slides (Powerpoint, Keynote). In both cases, pictograms can be included as images (png, tiff) or .svg files. https://biorender.com/ allows a web-based, drag-and-drop design of slides with a harmonious overall layout and biomedically relevant pictograms. For an annual fee, users can export graphical abstracts/figures in publication quality resolution.
Finish by…
Design is an iterative process of adjusting and assessing. A common problem in graphical abstracts is an unclear reading directions (Hullman and Bach): assess if your graphical abstract support a visual hierarchy with text, lines, and arrows. Often, elements are not connected to the rest of the graphical abstract, which forces readers to guess. Confusing also arises from inconsistent visual style: are your pictograms similar in detail? Do arrow with the same meaning have same appearance? Are colors used sparsely and consistently?
As always, source feedback from colleagues, ask them to tell you back what they see!
Tversky B. Lines, Blobs, Crosses and Arrows: Diagrammatic Communication with Schematic Figures. In: M. Anderson, P. Cheng, and V. Haarslev (Eds.): Diagrams 2000, LNAI 1889, pp. 221-230, 2000. Springer-Verlag Berlin Heidelberg.
Hullman J and Bach B. Picturing Science: Design Patterns in Graphical Abstracts. In: P. Chapman et al. (Eds.): Diagrams 2018, LNAI 10871, pp. 183–200, 2018. https://doi.org/10.1007/978-3-319-91376-6_19
Hegarty, M., Just, M.A.: Constructing mental models of machines from text and diagrams. J. Mem. Lang. 32, 717–742 (1993)
Myosin is a major component of the sarcomeres of muscle, but its roles during muscle development are still relatively poorly understood. A new paper in Development investigates the function of a developmentally expressed myosin heavy chain isoform during mice myogenesis. We caught up with the paper’s four co-first authors, Megha Agarwal, Akashi Sharma, Pankaj Kumar and Amit Kumar, and their supervisor Sam Mathew (Associate Professor in the Regional Centre for Biotechnology in Faridabad, India) to find out more about the project.
Sam, Megha, Pankaj, Akashi and Amit (L to R).
Sam, can you give us your scientific biography and the questions your lab is trying to answer?
I did my Bachelor’s and Master’s degree in Zoology in Kerala, India, and then got my first experience in research working as a research assistant for a year in Bangalore, in a lab that used Drosophila to study circadian rhythms. Soon after, in 2001, I joined the graduate program in Genetics and Functional Genomics at the University of Cologne, Germany. I joined Maria Leptin’s lab for my graduate work, trying to characterize a genomic region involved in gastrulation in Drosophila. Maria’s mentorship style of giving students a free hand helped me develop ideas and grow as a scientist. I got interested in understanding developmental processes using genetic tools and, although it took a while, this work led to the identification of the role of the TNF-Receptor Associated Factor 4 (TRAF4) in Drosophila gastrulation. I continued with Maria for 2 years as a postdoctoral fellow to complete this work and then wanted to switch to a vertebrate model. Thus, I joined Gabrielle Kardon at the University of Utah, USA, where she was using mouse models to understand the role of connective tissue fibroblasts in skeletal muscle development and regeneration. Using mouse genetics, we showed that Tcf4 is a marker of connective tissue fibroblasts and that Tcf4+ connective tissue fibroblasts are important regulators of muscle development and differentiation, especially regulating maturation of muscle fibre type. This is where I came across myosin heavy chain-embryonic (MyHC-emb), which we used as a marker for developing myofibres. Delving into the literature, I found that not much was known about MyHC-emb function even though it was used routinely as a marker for terminally differentiated myofibres during development and for regenerating fibres in adults. This led to discussions with Gabrielle, who was generous enough to allow me to start generating a targeted mouse model, which is an important tool used in the current work.
We are pursuing three main research directions in my lab: first, we are trying to understand the specific functions of developmental myosin heavy chains (MyHCs) and how mutations in these MyHCs lead to congenital diseases. Second, we are interested in how skeletal muscle differentiation occurs during development and stem cell-mediated regeneration, and are trying to identify genes and regulatory sequences involved in this. Third, we are working on signalling pathways that are misregulated and lead to the formation of a cancer type called rhabdomyosarcoma, in which the tumour cells exhibit muscle-cell characteristics. We use Drosophila, mouse and cell culture models, and employ imaging, biochemical methods and genetic tools to address all of these questions.
How did the four of you come to work in Sam’s lab, and what questions drive your research?
MA I was very clear that I wanted to work on stem cells for my PhD. I had already worked on mesenchymal stem cells during my Master’s degree project and was fascinated by how smart these cells are. How stem cells serve as a maintenance and repair resource for the entire body is something that has interested me all along. After checking out a few labs, I decided to join Sam’s since it provided me with a great opportunity to study stem cells and their behaviour during animal development and adult tissue regeneration. Since this research topic is something close to my heart, it has been easy to keep myself motivated.
AS I joined as a project fellow in Sam’s lab in 2014 and within 4 months I started my PhD with him! From my college days, I was interested in the processes of embryonic development that make an entire organism from a single cell. While working with Sam as a project fellow, I got an opportunity to develop a deeper understanding of the developmental processes that lead to muscle formation. Different muscles in our body have distinct muscle fibre type composition; however, all fibres express MyHC-emb during embryonic development. I was intrigued and wanted to explore more about this MyHC isoform and decipher the functional importance of MyHC-emb.
PK Before joining Sam’s lab, I briefly worked on Leishmania, a parasitic protozoan that causes kala-azar (visceral leishmaniasis) in humans. I discovered how intriguing animal development is while preparing for my PhD fellowship exams. Therefore, I scouted around for labs working on animal development and joined Sam when he was in the early phase of setting up his lab at RCB. My research is driven by a quest to understand the complexities underlying gene regulation during animal development and tissue regeneration.
Cross-sections through the shank of postnatal day 0 wild-type (right) and Myh3 knockout (left) mice, showing MyHC-slow (red), laminin (green) and DAPI (blue).
AK I joined Sam’s lab with a deep interest in studying development, as it has always fascinated me. I worked extensively on fetal tissues during my doctoral training. Sam explained some of the observations he made on the myosins and how human muscle defects are recapitulated in myosin heavy chain knockout mouse models. This was exciting and I was keen to understand the role of myosins during development and regeneration.
How much was known about the role of the developmental MyHCs before your work?
MA, AS, PK, AK & SM Developmental MyHCs were discovered in the 1980s and although they were found to be expressed during development and regeneration, not much has been known about their function since then. A few studies on the regulation of their expression were carried out during the 1990s and early 2000s. Then in 2006, Michael Bamshad’s lab identified that mutations in the MYH3 gene, which codes for MyHC-emb, lead to Freeman–Sheldon and Sheldon–Hall congenital contracture syndromes, indicating that developmental MyHCs – and MyHC-emb specifically – have important functions. Surprisingly, animal models for studying and understanding the mechanisms underlying these syndromes were not pursued or were unsuccessful. This was in contrast to adult MyHCs, for which knockout mice for two isoforms were generated and characterized successfully in the 1990s by Leslie Leinwand’s lab. This provided us an opportunity to explore the roles played by developmental MHCs.
Can you give us the key results of the paper in a paragraph?
MA, AS, PK, AK & SM In this paper, we describe the role of MyHC-emb in skeletal muscle development. By generating and making use of conditional targeted and null mouse alleles for Myh3, we characterize the role of MyHC-emb during embryonic, fetal and neonatal myogenesis. There are four key findings that we describe in this paper. First, we find that MyHC-emb has dual cell-autonomous and non-cell-autonomous roles during muscle development. MyHC-emb is expressed in myofibres, and in a cell-autonomous manner regulates muscle fibre type, fibre number and fibre size. In a non-cell-autonomous manner it regulates the rate of differentiation of myogenic progenitors and myoblasts during embryonic and fetal myogenesis (cells in which it is not expressed). Second, we identify fibroblast growthfactor (FGF) as the secreted signal from myofibres that mediates the non-cell-autonomous effects of MyHC-emb on muscle progenitors and myoblasts. Third, we find that, although MyHC-emb is expressed in all myofibres during development, different muscles respond differently to MyHC-emb loss. Fourth, adult mice null for Myh3 exhibit scoliosis, a phenotype seen in individuals with Freeman–Sheldon Syndrome, a congenital muscle contracture syndrome in which MYH3 is mutated. Thus, this work highlights the role of developmental MyHCs during development and how their loss of function leads to abnormalities.
Why do you think MyHC-emb has distinct effects in different muscle types?
MA, AS, PK, AK & SM This was a surprising finding since, to our knowledge, MyHC-emb is expressed by all myofibres during development. We believe that the distinct effects loss of MyHC-emb has on different muscles is down to unique fibre-type composition and metabolic characteristics, which in turn are determined by the anatomical location and functional needs of the specific muscle. We think that these differences between muscles are reflected in the distinct effects we observe upon loss of MyHC-emb.
How do you think an intracellular component of the sarcomere could act non-autonomously?
MA, AS, PK, AK & SM This was a puzzle for us until we came across some publications showing that the FGF pathway mediates differentiation and maintenance of the stem cell pool. FGFR4, a receptor in the FGF pathway, is important in regulating the rate of differentiation of myogenic progenitors and myoblasts during development, which are the cell populations that were affected upon loss of MyHC-emb. This led to additional experiments to test whether FGF signalling mediates the non-cell-autonomous effects of MyHC-emb on myogenic progenitors and myoblasts, which was indeed found to be the case. How MyHC-emb within myofibres controls the levels of FGF secreted by myofibres is a question we have been trying to find answers for, but have not been successful. This could hint at some novel function of MyHC-emb, which might be independent of its role in the sarcomere. Interestingly, Leslie Leinwand’s lab reported in 2003 that MyHC-emb is one of three MyHCs that are expressed in non-myogenic cell types such as pulmonary myofibroblasts, indicating that MyHCs may have functions that are not restricted to skeletal muscle cells.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
MA While deciphering the non-cell-autonomous effect of MyHC-emb on muscle progenitors, we hypothesized that it is mediated by FGFs. My eureka moment was when I successfully figured out, by mass spectrometric analysis, that secreted FGF levels are altered upon knockdown of MyHC-emb. This led us to the mechanism of how MyHC-emb regulates muscle differentiation non-cell-autonomously, confirming and validating our hypothesis.
AS One of our first in vivo experiments was to investigate the effect of loss of MyHC-emb on other MyHC isoforms. I was full of curiosity while performing the immunostaining for other MyHCs on Myh3 knockout samples. I think finding more MyHC-slow+ fibres in Myh3 knockout muscles was a result I can never forget.
PK Two moments actually, both related to when I was quantifying data: first when I found that the muscle progenitor numbers reduced significantly upon Myh3 knockout, and second when FGF supplementation led to a rescue of the progenitor numbers in vitro.
AK To me, corroborating the in vivo results from the Myh3 knockout mice using C2C12 myogenic cells in vitro was highly satisfying. The in vitro system proved really handy for the demonstration of the non-cell-autonomous effect of MyHC-emb.
And what about the flipside: any moments of frustration or despair?
MA I started working on this project about 5 years ago and there were several instances when I got frustrated. For a while, we had difficulty in explaining the MyHC-emb loss-of-function phenotype, especially the mechanism of how MyHC-emb regulates muscle stem cells. Although we followed several directions, most were unsuccessful until we came upon FGF signalling. I think many of these failed experiments formed the basis of this manuscript and I kept going because, as Steve Jobs said, I considered what I do to be great work!
AS Not really a specific moment, but in the early days of the project, we did not have an animal facility on campus and were reliant on the samples brought by Sam from the laboratory of our collaborator, Gabrielle Kardon, at the University of Utah. This meant that every sample was precious and there were times when I had to wait for several months to get samples for new experiments, which was frustrating.
PK I faced some frustrating moments with the muscle-fibre size quantification. This was mainly related to finding a reliable software application that would make these measurements accurately. These problems went away after we came across a software application called SMASH, which was developed precisely for muscle fibre measurements.
AK I remember that one of the challenging moments early on was to draw an understanding of the sequence of events affecting normal myogenesis in the absence of MyHC-emb, and to identify the mechanisms underlying them. This led to testing a lot of possibilities without success, which for a while was frustrating.
So what next for the four of you after this paper?
MA This PhD training with all its ups and downs has helped me decide that research is what I want to do. Although there might be difficulties in research, with constant effort one can definitely achieve good results. I am keen to switch fields and am on the lookout for a postdoctoral position in computational modelling and bioinformatics.
AS I am currently working on other projects and plan to complete my PhD soon. In addition to skeletal muscle, I am also interested in the cardiac and smooth muscle. I would like to pursue postdoctoral research in the development of any or all of these three muscles.
PK I am also working on another project in the lab, related to the regulation of myogenesis. I am trying to complete this work and will be looking for postdoctoral opportunities in developmental biology, with translational relevance.
AK I left the lab in 2016, when this paper had started to take shape. I am now a postdoctoral fellow at the University of California Los Angeles, working on haematopoietic stem cells and cancer from a gene regulation perspective.
Where will this work take the Mathew lab?
SM This work originated when I was working as a postdoctoral fellow and I remember starting work on the gene-targeting construct almost 10 years ago! There have been a few milestones along the way, such as successfully identifying the gene-targeted mice, initial characterization of the knockout mice, moving to India and becoming an independent investigator, getting the mice shipped to India and now getting the work published. Although it took a while to get this paper out, we should now be able to come out with more interesting results, especially with respect to MyHC-emb in muscle regeneration. We are also keen to understand the precise mechanisms that underlie the phenotypes seen in individuals with Freeman–Sheldon Syndrome. I think skeletal muscle development, regeneration and homeostasis are all research areas with immense translational significance and hope to continue making new discoveries in these fields.
Am I right in thinking there is an increasing amount of developmental biology going on in India at the moment? As someone who left India for your PhD and postdoc but then returned to set up your own lab, what has your experience been like?
SM Yes, I think it is true. Actually, there are a lot of relatively young investigators, working in diverse areas, who set up their labs in the past 10-15 years. In my opinion, this resulted from several new research institutes being set up and an increase in funding over this period. Coming back to developmental biology in India, we have a set of diverse researchers working on different model systems, who are doing well. We also have an Indian Society for Developmental Biology with an ever-increasing number of members.
Returning to India was a decision I made after being abroad for more than 12 years. Although it took some getting used to, it is a decision I am quite happy with. Since I joined a relatively new research institute, some amount of time was spent initially on ordering equipment and getting facilities up and running. Some of the flexible funding I received, especially from the Wellcome Trust DBT India Alliance, really helped run the project during the initial days, when I had to travel to Gabrielle’s lab to carry out the mouse work. I have been lucky to work with some really smart, talented and dedicated graduate students and postdoctoral fellows, and mentoring them has been a lot of fun.
There are many labs working on developmental biology today in India
Finally, let’s move outside the lab – what do you like to do in your spare time in Faridabad?
MA When I have free time, I like to work out in the gym. I also like to go out shopping with friends.
AS Our campus in Faridabad is a really beautiful place, and I like to spend my leisure time enjoying the beauty of nature around me, while reading books.
PK I like playing badminton, going out with friends and especially visiting my cousins to enjoy home-cooked food!
AK I remember how we used to go out together with the lab for lunch, and also remember a trip to the Himalayan mountains for hiking and fun. Currently, I am in Los Angeles, where I like to try out different cuisines and go on long drives over weekends.
SM I like spending time with family and friends in my spare time. I also like to travel; Faridabad is close to a lot of places with historical significance, which I try to visit.
The Biology Department of Boston College seeks to recruit a tenure-track faculty member with research and teaching interests in the area of Cell & Developmental Biology.
The ideal candidate is expected to establish a rigorous, externally funded research program that contributes to, or complements, current strengths in using in vivo model systems to answer fundamental questions in cell and developmental biology. The successful candidate will receive a highly competitive startup package including research and equipment funds and laboratory space, IT/computational support, grant preparation and management assistance, and access to shared resources and state-of-the-art core facilities including imaging/microscopy (including super-resolution microscopy), NexGen sequencing, flow-cytometry/FACS, NMR, and mass-spectrometry. Finally, all new faculty members receive active and dedicated mentoring to help ensure success at Boston College.
In alignment with the University’s goal of building a culturally diverse, equitable and inclusive academic community, we are seeking individuals who are committed to the advancement of historically underrepresented and marginalized communities in the sciences. In addition, the successful candidate must have a strong record of research productivity, and a desire to teach, advise and mentor graduate students and undergraduate students in the biosciences.
The Biology Department is home to a dynamic research community embedded in a highly ranked, liberal arts university campus located close to downtown Boston and Cambridge. The surrounding region constitutes a global research hub, comprising numerous universities, research institutes, biotechnology firms and pharmaceutical companies. The Biology Department hosts a graduate program in the biosciences; provides lecture and laboratory courses and research opportunities for undergraduates majoring in biology and biochemistry; and actively participates in the Gateway Scholar’s Program for underserved minorities and first-generation college students majoring in STEM fields at Boston College. Faculty and their research teams also have access to new facilities and interdisciplinary collaborations provided by The Schiller Institute for Integrated Science and Society.
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