18th Cell Cyclist Newsletter

Screen Shot 2016-06-20 at 10.09.40Dear Cell Cyclists,

Summer has hit Sweden, so it’s actually not the right time to spend locked-up  in the lab doing microscopy. However, I collated 4 nice resources around the topic high-content fluorescent microscopy covering the whole range from basic concepts in microscopy to advanced image analysis.

1. A video crash course to microscopy and digital images. Introducing concepts as brightness/contrast, bit-depth, gamma, LUTs, compression, file formats…

Introduction to Digital Images

2. A very nice paper introducing quantitative analysis of fluorescence microscopy images for cell-based screening
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791844/

3. A great introduction to microscopy-based high-content screening
http://www.sciencedirect.com/science/article/pii/S0092867415014877

4. And finally a paper describing how to automatically identify image acquisition artifacts such as dirt or out-of-focus images (providing also a CellProfiler pipeline)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593271/

Cheers,
Erik

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17th Cell Cyclist Newsletter

456493667-Going-up-300x300Dear Cell Cyclists,

It’s been a while since my last post, because I transitioned from the East to the West coast of Sweden. I focused on the new city and my new role, but that didn’t stop me from collecting sciency links and tools, today all around publishing and leading a research team.

1. I’d like to recommend the Naturejobs faculty series – 13 great pieces for new and aspiring faculty members to flourish in their positions.
http://blogs.nature.com/naturejobs/tag/faculty-series/

2. Also from Naturejobs 10 tips on time management and lab organization.
http://blogs.nature.com/naturejobs/2016/01/25/the-faculty-series-top-10-tips-on-managing-your-time-as-a-pi?WT.ec_id=NATUREJOBS-20160204

3. Publish or Perish is a software program that retrieves, formats and analyzes your publications and research impact. Really helpful when writing grant or job applications.
http://www.harzing.com/resources/publish-or-perish

4. In a similar direction, Tony Hyman’s recent talk in Stockholm on publishing and perishing 😉

Cheers,
Erik

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16th Cell Cyclist Newsletter

SONY DSC

Dear Cell Cyclists,

God fortsättning! That’s what people wish each other at the beginning of a New Year in Sweden. Literally it translates to ‘good continuation’ which I freely translate to  ‘Go on, continue as you did before, and good luck with that’. And that’s what I’ll do.

1. To start the year on a positive note, here comes a great reminder on why being a scientist is one of the best jobs in the world.
http://gu.com/p/4fhmd/stw

2. ‘Stats the way I like it’ – Helps you understand your everyday statistics. Funny and simple. (Thanks Helena)
http://statsthewayilikeit.com/

3. FACS and flow cytometry data can be quite complex. Here you find some tips for handling and presenting it.
http://bitesizebio.com/26007/spot-the-difference-5-ways-to-improve-the-presentation-of-your-flow-cytometry-data/#

4. Finally, Nature reviewed the many different options of reference-management software. For me, Mendeley has been the favorite choice for some time.
http://www.nature.com/news/eight-ways-to-clean-a-digital-library-1.18695?WT.mc_id=TWT_NatureNews

Cheers,
Erik

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15th Cell Cyclist Newsletter

Dear Cell Cyclists,Spumavirus_virion

Before everybody leaves for some well-deserved Christmas vacation four links to sciency resources collected from the past weeks.

1. ViralZone is a great resources for every virologist. Currently it provides 532 Virus description pages (including Foamy Viruses) and 216 pages on viral molecular biology.
http://viralzone.expasy.org/viralzone/all_by_species/10.html

2. The Library Genesis Project is a search engine for scientific articles and books, which allows access to otherwise paywalled content. So if you can’t access a paper through your institution – this is bit like Napster but pirating scientific papers. (Thanks Pim)
http://gen.lib.rus.ec/

3. Creating box and whisker plots in Excel can be a bit tricky. So, on this page you can find a nice tool to help you out. (Thanks Lorenzo)
http://boxplot.tyerslab.com

4. What to do when your manuscript gets rejected? – A novel, not-fully serious approach to editorial rejection letters.
http://www.bmj.com/content/351/bmj.h6326

Merry Christmas,
Erik

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14th Cell Cyclist Newsletter

layout0Dear Cell Cyclists,

Today I’d like to share some interesting reads addressing the non-experimental aspects of science work – namely publications, grants, setting up a group and leading it.

1. Starting on a somewhat sad note, this blog piece analyzes the (rather long) time it takes from submission to publication: ‘Waiting to Happen: Publication lag times in Cell Biology Journals’
https://quantixed.wordpress.com/2015/03/09/waiting-to-happen-publication-lag-times-in-cell-biology-journals/

2. One thing manuscripts and grants have in common is the high rate of rejection. Here you can find recent grant success rates compiled by Alexis Verger.
https://docs.google.com/spreadsheets/d/1Zt_Hx8RJw1-w3rTr5HL1AGrsX5g4QirWIn2Eyo4dykc/edit?pli=1#gid=1442547813

If your grants were rejected…

3. How to give and receive grant feedback.
https://theresearchwhisperer.wordpress.com/2015/09/29/grant-feedback/#more-3948

On the other hand, if your grants were successful…

4. How to negotiate a lab startup budget.
http://blog.addgene.org/how-to-negotiate-a-successful-lab-start-up-budget

5. Advice for new PIs. (Quite relevant for postdocs as well.)
https://quantixed.wordpress.com/2015/06/22/tips-from-the-blog-v-advice-for-new-pis/

6. And, how to stand out in academic scientific research.
https://biomickwatson.wordpress.com/2014/04/27/how-to-stand-out-in-academic-scientific-research/

Cheers,
Erik

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13th Cell Cyclist Newsletter

fpcolorpalettefigure7Dear Cell Cyclists,

Today it’s a lot about fluorescence, colors and imaging, both for microscopy and flow cytometry.

1. The Michael-Davidson Fluorescent Protein Collection “[…] has every fluorescent protein under the sun, from the standard oldies but goodies (e.g. EGFP and YFP) to the new and improved fruit colors (e.g. apple, papaya, and tomato) and the photoactivatable fluors (e.g. Phamret and Dendra).” More than 300 backbones at your fingertips on addgene.
https://www.addgene.org/fluorescent-proteins/davidson/

2. In line, Michael’s lab webpage provides a very, very, very extensive resource on fluorescence microscopy, discussing techniques, trouble-shooting, microscopes, lamps, filters, cameras, detectors, lasers, proteins, fluorophores, probes, live-cell, FRET, FLIM, confocal, TIRF, FISH… you name it.
http://micro.magnet.fsu.edu/primer/techniques/fluorescence/fluorhome.html
http://micro.magnet.fsu.edu/primer/webresources.html

3. A DNA dye perfect for live imaging: Far-red, cell-permeable and with minimal toxicity.
http://www.nature.com/ncomms/2015/151001/ncomms9497/full/ncomms9497.html

4. A nice collection of flow cytometry resources on abcam, including protocols for staining, how to do compensation, immune-phenotyping, FACS or cell cycle analysis.
http://www.abcam.com/tag/flow%20cyt

5. Finally, for the people at KI: A simple “one-click” plugin for Google Chrome to allow full-access to scientific articles through the KI-library proxy.
https://chrome.google.com/webstore/detail/karolinska-proxy-kib-by-n/ofhedjhogoljknalddgomihcooamfehj

Cheers,
Erik

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12th Cell Cyclist Newsletter

Dear Cell Cyclists,truth-vigilantes-retractions

Hope everybody had as nice of a summer break as I did. Back in the lab here are some links, articles and papers that came up interesting during the time.

1. My favorite for the start, a scientific analysis and discussion on why it is difficult to do science right.
http://fivethirtyeight.com/features/science-isnt-broken/

2. A nice review novel fluorescent protein technologies by the Campbell lab.
http://www.sciencedirect.com/science/article/pii/S1367593115000435

3. In line, (not only) for the molecular virologists, a very good review about the special requirements of fluorescent proteins in virology – “Going viral with Fluorescent Proteins”.
http://jvi.asm.org/content/early/2015/07/16/JVI.03489-13.full.pdf+html

4. To postdoc or not to postdoc? – How To Know If You Should Leave Academia? A somewhat controversial, but interesting article with a nice infographic.
http://www.nextscientist.com/leave-academia-before-postdocs/

5. Finally, sounds simple, but it’s certainly worth a re-read for anybody reviewing papers: Ten simple rules for reviewing papers.
http://www.molbiolcell.org/content/22/5/525.full#sec-3

Cheers,
Erik

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11th Cell Cyclist Newsletter

Dear Cell Cyclists,url

Today I like to share four five interesting new imaging tools and publications. I also like to highlight again Kurt’s (outstanding) microscopy blog that features a monthly microscopy paper roundup.

1. CRISPR-based multicolor labeling of chromosomal loci in human cells
http://www.pnas.org/content/112/10/3002.full

2. Similar to a technique previously developed by the Kirschner lab and our lab, Roukos and colleagues present an approach for cell cycle staging of individual cells by measuring their DNA content by fluorescence microscopy
http://www.nature.com/nprot/journal/v10/n2/full/nprot.2015.016.html

3. Introducing MERFISH, a multiplex technique to measure thousands of different RNAs from different genes in a single cell
http://www.sciencemag.org/content/348/6233/aaa6090.abstract

4. A nice ImageJ plugin to quantify cell migration, protrusions, and fluorescence intensities from live-cell imaging data
http://jcb.rupress.org/content/209/1/163

5. (Added on May 29) Just finished the blog post and promptly another cool paper comes to my attention: “Smith et al. describe a microscopy technique that instantaneously captures 3D images of live cells, allowing them to track the movement of single mRNAs in the nucleus” They call it a SMRTer way to track molecules.
http://jcb.rupress.org/content/209/4/609

Cheers,
Erik

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10th Cell Cyclist Newsletter

Dear Cell Cyclists,BrzqD3cIEAAxfmW

Currently I’m keeping myself occupied with paper writing. In line some articles and resources on selling your story, making great figures and getting your ideas out there:

1. Let’s start with a nice perspective on how much you should and need to sell your science and how far to develop a story before submitting.
https://quantixed.wordpress.com/2015/04/28/middle-of-the-road-pitching-your-paper/

2. As figures are the essence of a paper, a repost of this article on better figures from the PLoS ‘Ten simple rules’ series.
http://journals.plos.org/ploscollections/article?id=10.1371/journal.pcbi.1003833

3. “Most bar graphs provided little more information than a table.” – A case for the less frequent use of bar graphs and better data presentation.
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128
The authors also provide a helpful template for easy creation of scatter plots in Excel.
https://www.ctspedia.org/do/view/CTSpedia/TemplateTesting

4. Ideally your paper has a single super-strong, self-explanatory figure. ‘The Data Visualisation Catalogue’ is a great tool to chose the right plot for your data.
http://datavizcatalogue.com/

5. Finally, ‘The Journal of Brief Ideas’ provides a platform for all those like me, coming up with many ideas, but can’t possibly do all the pipetting necessary to explore them.
http://beta.briefideas.org/ideas/17b997da912f99ce9988a47f42b52692

Have a nice long weekend! I’m off kayaking in the Stockholm archipelago 🙂
Cheers,
Erik

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9th Cell Cyclist Newsletter

Dear Cell Cyclists,9780465022229_p0_v1_s260x420

Spring has hit Stockholm and many things are going on in the last weeks. And it’s time again to share some interesting resources with you. As it’s Friday today, I chose some easier ‘weekend’ reads. Let me know if you like them.

1. Bigger is not better when it comes to lab size. – An interesting analysis on what’s the perfect lab size and the contributions of different lab members.
http://www.nature.com/news/bigger-is-not-better-when-it-comes-to-lab-size-1.16866

2. I couldn’t stop exploring this interactive timeline visualizing milestones of cancer research and discovery in the past 250 years.
http://www.cancer.gov/researchandfunding/progress/250-years-advances

3. The National Cancer Institute also provides an extensive cancer drug dictionary at:
http://www.cancer.gov/drugdictionary

4. And as another cancer feature, a thought-provoking article discussing the possibility of genetic cancer resistance.
http://www.the-scientist.com/?articles.view/articleNo/42469/title/Resisting-Cancer/

5. An excellent read for every researcher and one of my favorite science books: ‘A PhD is not enough! – A Guide to Survival in Science’ You could download it, but buying it supports the author, a scientist.

Cheers,
Erik

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