Our paper studying the evolution of cancer cell organotropism using a zebrafish xenograft model is now in press at Cell Systems! I am particularly excited about the use of zebrafish systems to interrogate dynamic events in vivo. Thanks to all of the coauthors on the paper - the variety of techniques that we were able to bring to this study greatly enhanced the work.
Congratulations to Dr. Rory Staunton, Dr. Woong Young So, and Dr. Kandice Tanner on the publication of our paper studying cell mechanics in 3D! The study found that malignant breast cancer cells are mechanically plastic and are stiffer than the local microenvironment when cultured in 3D. In contrast, nonmalignant cells more closely match the mechanics of the local ECM. The study can be found here.
Congratulations to Chris Yankaskas, Kostas Konstantopoulos, and all of my co-authors on the publication of a study in Nature Biomedical Engineering showing that a microfluidic chip can be used to predict the metastatic propensity of a breast cancer cell sample! The study presents an elegant use of our patented microfluidic migration chip to offer a prediction about whether a population of cancer cells is likely to metastasize and characterize the properties of this highly metastatic subpopulation. Read a commentary about the study here.
My postdoctoral advisor, Dr. Kandice Tanner, was recently interviewed by Physics Today about her career path and research. She is a fantastic scientist and mentor, and it is worth a read! Find it here. Her research (and one of our images of cancer cells metastasizing in zebrafish) was also featured in an article in Physics Today about physical and mathematical approaches to study cancer. Dr. Kandice Tanner
Credit: NIH Medical Arts Today, I went to an interesting seminar presented by Christian Dietz from Konstantz University and KNIME. He presented his work on using KNIME for image processing applications. KNIME is open-source (free!) software where "nodes" can be connected to perform a prescribed task. It is kind of like macros or plugins in ImageJ, where you automate things to run a series of operations on a set of images. What I found interesting about KNIME was that it serves as a sort of translator, loading data from a variety of sources and then pulling from different image processing tools (ImageJ, CellProlifer, Python, etc.) as dictated by the user, all in one central graphical interface. I plan on trying it out for some image processing applications to see how it compares to running things in ImageJ directly.
In a recent commentary published in the Journal of Cell Biology (JCB), editors Kenneth M. Yamada and Alan Hall wrote about the problem of reproducibility in cell biology studies. Yamada and Hall cite various articles stating that results from cell biology were able to be reproduced as little as 50% (and potentially down to 25%) of the time. Besides causing a loss of public trust in biomedical research that could result in funding cuts, a lack of reproducible results severely hinders translation of basic research to the clinic.
Scientific research is only meaningful if it is communicated clearly and is seen (and understood, and accepted) by the larger scientific community. Useful insights into preparing papers and figures can be gained by examining how some of the world's most successful researchers go about these tasks.
George M. Whitesides, the astoundingly productive professor of Chemistry and Chemical Biology at Harvard University, has generated a number of guides for paper preparation. These guides focus on the ideas and structure of a paper more than the contained prose. A video produced by the American Chemical Society about writing a paper is available here, along with a presentation on scientific paper writing. A more formal summation of Whitesides' ideas is available in an article originally published in the Advanced Materials. Clearly, writing a scientific paper is closely linked to the data and figures that the paper presents. Figures should reflect the results of an experiment, not the interpretation of those results. To this effect, Mike Rossner and Kenneth M. Yamada have published a paper on the dangers of image manipulation. The paper is a very helpful guide for young researchers to see what is and is not allowed when preparing figures for publication. There are a number of very useful guides online for using ImageJ. Basic ImageJ setup requirements and commonly used commands are collected here in a document written by G. von Dassow. A technique for drawing items in ImageJ using overlays can be found here. This method, summarized by Chris Ambrose, presents an alternative, non-destructive technique for annotating images than the one I presented in my guide for creating publication-quality videos in ImageJ.
Additionally, a great guide for preparing publication-quality figures using free software can be found in this guide, which was written by Benjamin Nanes. Hopefully you find these resources useful!
I am currently looking for a post-doctoral research position in the fields of tumor immunology, tissue engineering, and/or microfluidics in the Baltimore/Washington region. Please contact me if you're looking for someone for your lab or know of any openings!
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AuthorColin Paul is a CRTA Fellow at the National Cancer Institute, National Institutes of Health. Archives
August 2019
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