JCB biowrites

Scientists Decode How Neurons Ride Their Way To The Final Destination

GIZMODO India -- The neuron is the basic working unit of the brain. It is a specialized cell designed to transmit information to other nerve cells, muscle, or gland cells. According to a study published in the Journal of Cell Biology, the basic functions of human beings is depended on the journey of neurons getting to where they need to go, and making correct connections once they arrive. This phenomenon ensures that our eyes can see, our ears can hear, our fingers can touch, and so on. (more)

Study shows how neurons reach their final destinations

Science News -- A new study from Drexel University researchers shows that the sliding movements of a small group of intracellular structures -- called microtubules -- play a key role in keeping neurons on a smooth, proper trajectory. The study, published this month in The Journal of Cell Biology, focuses on microtubules and the molecular motor proteins that generate forces on these intracellular structures. (more)

ASCB 2015: Happy Xmas (Organelle War is Over)

Well… they probably aren’t over, exactly. I’m sure the organelle wars – the ongoing Twitter debate over which organelle is the most important* – will continue for some time. But, judging by the presentations at this year’s ASCB meeting in San Diego, mitochondria seem to have the upper hand at the moment.

Given the wide variety of mitochondrial functions, including energy metabolism, amino acid and lipid synthesis, apoptosis, and immune signaling, it’s no surprise that the organelle is coming under increased scrutiny for its role in cancer cell biology. Indeed, this was the subject of a special Emerging Topic Symposium on Monday night, which featured talks from Susanne Rafelski on the importance of analyzing mitochondrial network dynamics and topology, Gerald Shadel on the stress responses induced by mitochondrial DNA, Christian Metallo on the mitochondria’s biosynthetic role, and Jerry Chipuk on the essential role of mitochondrial division in Ras-induced transformation.

Earlier in the day, mitochondria also dominated the minisymposium on Organelle Dynamics, Structure and Function, with the majority of talks focusing on either the organization of the mitochondrial inner membrane, or on the complex interplay between GTPases, actin, and the Endoplasmic Reticulum in controlling mitochondrial fission.

The session did give space to a lesser known participant in the organelle wars, however. The pyrenoid is a tiny organelle embedded within the chloroplasts of algae and hornworts. It serves to concentrate carbon dioxide so that the enzyme RuBisCo can more efficiently fix atmospheric carbon into organic sugars. (RuBisCo is thought to be the most abundant enzyme in the world, responsible for fixing over 400 billion tons of CO₂ per year). Martin Jonikas (Carnegie Institution of Science, Stanford) described his lab’s efforts to characterize components of the Chlamydomonas pyrenoid and determine their role in the organelle’s assembly. Jonikas also has the ambitious long-term goal of introducing pyrenoids into higher plants in order to enhance their crop yields. I think this video explains it all nicely:

It’s certainly an impressive shot in the organelle wars. To your battle stations, everyone!

 

*Spoiler alert: It's actually the Golgi Apparatus.

Top tomogram image of mitochondrial membrane organization © 2009 Rabl et al.

ASCB 2015: Cells on the move

On Sunday afternoon at ASCB 2015, I attended the minisymposium on Cell Migration in Tissues. It was a terrific session that covered a wide range of migratory behaviors in development, disease, and repair. Here, I’ll focus on the stories that have already been published, though there was plenty of great unpublished work presented as well.

Celeste Nelson (Princeton) described the use of microfabricated tissues and 3D traction force microscopy to study the forces generated by mammary epithelial cells during branching morphogenesis, demonstrating that branch extension is associated with high contractile forces at the leading edge of new branches. These forces pull on the surrounding extracellular matrix and align its fibers into tracks that guide the collective migration of the mammary cells as they form the new branch.

David Matus (Stony Brook) discussed his recent paper exploring the mechanisms that control anchor cell invasion in C. elegans. During the worm’s development, this specialized uterine cell breaks through a basement membrane to connect to the underlying vulval tissue. Because this event can be visualized by live imaging in vivo, it’s a terrific model system for studying cell invasion (a key step in cancer metastasis). Matus and colleagues found that anchor cells must arrest in G1 before they can become invasive; in the absence of the transcription factor NHR-67, cells continue to proliferate and don’t invade. It will certainly be interesting to see if similar rules apply in cancer, such that metastasis is driven by non-proliferative tumor cells.

Eliah Shamir, from Andrew Ewald’s lab at Johns Hopkins School of Medicine, gave a terrific talk expanding on her 2014 JCB paper describing the role of the transcription factor Twist1 in promoting the dissemination of single cells from 3D organotypic cultures (and the surprising finding that, contrary to the usual model of epithelial-to-mesenchymal transitions, the disseminating cells retain their epithelial character and that the cell adhesion molecule E-cadherin promotes their dispersal).

Bong Hwan Sung, from Alissa Weaver’s lab at Vanderbilt University School of Medicine gave a fascinating presentation describing how cancer cells enhance their directional migration through tissues by secreting exosomes. These small, extracellular vesicles are coated with the extracellular matrix protein fibronectin and so they promote adhesion assembly and stabilize cell protrusions.

IVM muscle regeneration from ASCB on Vimeo.

And Micah Webster, from Chen-Ming Fan’s group at the Carnegie Institution of Science, described his hot-off-the-press paper examining the in vivo movements of satellite stem cells during muscle regeneration. When muscle fibers are injured, they degenerate until all that remains are remnants of the basal lamina that surrounded them. Webster et al. found that these “ghost fibers” guide the migration and proliferation of satellite cells as they repair the injured muscle. The stem cells migrated back and forth along the long axis of ghost fibers (see the video above), and divided in this direction as well. Webster and colleagues think that this may help the cells spread out evenly so that they can then fuse together and differentiate into a new muscle fiber.

Intravital imaging video of satellite cells during muscle regeneration courtesy of Micah Webster et al.

Top image of Twist1-expressing cells (green) disseminating from an explanted mammary duct © 2014 Shamir et al.

Everything you need to know about image screening at Rockefeller University Press in 10 posts

#10. The big (and now beautiful) picture

This post is part of a weekly series about image screening. All published posts can be found on this page.

That’s it! We hope that our tips will help you prepare beautiful, high-resolution figures, and that we have convinced you to pay close attention to image quality from the time you acquire the data to the moment you’re submitting the paper. If you need to go back to specific posts, here is the round-up:

• Figure and image resolution
• Scanning and exporting image data
• Image file format
• Figure-making software
• Importing image data into a figure
• Micrograph image data manipulations
• Modifying image contrast and other gel image manipulations
• Safe-keeping the original data

And in case of doubt, please feel free to contact us at jcellbiol@rockefeller.edu – we are happy to discuss these questions anytime. Best of luck to you all with experiments and we hope to see the fruits of this labor in the pages of JCB, JEM, or JGP very soon!

Everything you need to know about image screening at Rockefeller University Press in 10 posts

#9. Safe-keeping the original data

This post is part of a weekly series about image screening. All published posts can be found on this page.

As you now know, Rockefeller University Press journals (JGP, JCB and JEM) conduct routine figure checks on all editorially accepted manuscripts. We check for figure and image quality (or “resolution”) as well as various alterations, such as contrast adjustment or manipulation of image elements.

Resolution issue? Easy: these are most often quickly corrected by properly inserting an image file into a figure or by re-exporting it to a loss-less file type that properly stores and displays the high level of detail of the image.

What if the issue is more complicated? In those rare cases, the most direct and easiest way to define whether the image or figure quality could be acceptable or whether a manipulation falls within what we allow is to go back to the original image data and to determine whether any information was lost by the adjustments made to the image.

We cannot stress enough the importance of properly storing, organizing, and making accessible primary research data as first acquired. It’s crucial to be able to return to the original results to back-up the research or to further an analysis, as highlighted by the many recent discussions over research reproducibility. And it is our policy that the primary data must be made available to the editors upon request at any point in the editorial process.

Please feel free to reach out (jcellbiol@rockefeller.edu) if you have any questions, we are happy to discuss our policy and/or case-by-case scenarios anytime.

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Everything you need to know about image screening at Rockefeller University Press in 10 posts

#8. Gel image alterations – what’s acceptable?

This post is part of a weekly series about image screening. All published posts can be found on this page.

When conducting our routine figure screen, our production and editorial team carefully examines all gel images for resolution, but also for any other type of alteration. Our rule is that “no specific feature within an image may be enhanced, obscured, moved, removed, or introduced.” In particular, we watch for the following alterations:

• Splicing lanes out of a gel is permitted if consistent throughout panels, disclosed in the figure legend and represented in the figure by a clearly visible line. We believe, however, that all samples blotted for a protein of interest must come from the same membrane/gel as those blotted for a loading control, so inconsistent splicing between loading control and protein of interest is not accepted, and we will ask you to revise the figure if we observe this type of inconsistency.

 

 

• Duplication of panels and deletion/addition of bands constitute misrepresentations of the original data and are not appropriate. (We’ll get into what we would do if we found such issues in a JCB submission in our next post.) Examples are shown here.

 

• Background cleaning or brightness/contrast adjustments (examples here) cannot be done to the extent that all background information has been lost or that specific elements are obscured or enhanced. For instance, although non-specific bands might not be relevant to you or to the paper’s conclusions, altering them constitutes a misrepresentation of the primary data and goes against our policy. It provides the false impression of a different (often cleaner) background. Importantly, non-specific bands or signal might not mean anything in the context of your investigation, but they might be biologically meaningful to another researcher, now or in the future.

 

Overall, these rules are largely based on good scientific behavior and common sense: you would want to see the blot as first obtained by the researcher doing the experiment in order to accurately interpret the results. We simply want to afford our readers the same opportunity. And while some adjustments are absolutely acceptable and do not alter the interpretation of the data, our screening is here to make sure that we only publish figures that you can trust are an accurate depiction of the primary results. In our next installment, we will discuss a related and very important aspect of proper figure-making: keeping the original data as first acquired for a long, long time. More next week.

Everything you need to know about image screening at Rockefeller University Press in 10 posts

#7. What is appropriate or inappropriate micrograph manipulation?

This post is part of a weekly series about image screening. All published posts can be found on this page.

At JCB and Rockefeller University Press, we still believe that the data presented in a published manuscript must accurately represent the original data acquired. If a reader does not see what you saw when first obtaining these results, it means that the data are not displayed in a reliable fashion. Reproducibility issues are too frequent, important, and costly not to try our best to accurately depict experimental findings in publications. JCB’s stance is therefore firm, and deliberate alterations that affect data interpretation are not permitted. This is why, during our routine figure screening, we pay close attention to potential misrepresentations or manipulations of the data. Some turn out to be harmless: it can be ok to rotate or crop a micrograph so as to align it with others, and although we prefer to have a false background stand out in a different color so as to make the image boundaries clearly visible, such alterations are minor acceptable changes that we can easily deal with without bothering you.

However, other manipulations are considered more serious and are not permitted:

• Misrepresentation of a microscope field (as shown here): we hope to see in a figure what you saw through the microscope (in one field). Copying/pasting, removing, or repositioning cells or other elements are not allowed.
• Selectively enhancing a specific element in an image using uneven brightness/contrast or coloring adjustments (as exemplified here): for instance, filling gold particles with black color so as to emphasize them is not allowed. Similarly, brightness adjustments must be made to the entire image and not be confined to a specific part to enhance or erase particular elements.

We are happy to discuss these issues and examples as needed, and, if a question arises, please feel free to contact us at jcellbiol@rockefeller.edu. In our next installment, we’ll tackle manipulations of the other main type of image data: gels.

Everything you need to know about image screening at Rockefeller University Press in 10 posts

#6. How to bring images into your figure and how to handle them once they are there

This post is part of a weekly series about image screening. All published posts can be found on this page.

Now that you have the document and resolution settings of your new figure file defined, it is time to add in images. When making a figure, there are multiple straightforward ways to insert an image (say, a micrograph or gel), and this is particularly relevant for users of the Adobe Creative Suite. However, we have found that some ways are better than others when it comes to preserving the full resolution of the image. We have noticed a number of “placement” issues into Adobe Photoshop or Illustrator that result in overall lower quality insufficient for figure-screening – even if the imported image was originally of sufficient resolution. To properly insert an image into a figure, we recommend using one of two ways:       

-          Open the figure file and the image data you would like to insert into the figure side-by-side and simply drag the image into the figure. See here for a quick video demonstrating these steps.

-          Alternatively, you can open the figure file; click on the “Place” option from the “File” menu and select the image you would like to insert into the figure file. You will have the option to transform (scale, reposition, rotate, etc.) the file before committing to its placement. If you’re placing a PDF, EPS, or Adobe Illustrator file, we also recommend that you select the anti-alias option in the options bar. Here's a quick video summing up the steps involved in this process.

When inserting an image into a figure, beware of transformations: shrinking or enlarging adds or removes pixels and can significantly change the appearance of an image. We also recommend keeping the original aspect ratio – stretching or squishing an image will impact its rendering and affect its resolution.

And that’s it! With a couple of clicks (and tricks), your image data are now safely inserted into your figure. Next up: how much can you adjust image data when making the figure and which image manipulations are considered acceptable at JCB?

Everything you need to know about image screening at Rockefeller University Press in 10 posts

#5. It is time to make the actual figure: I see you scrolling to the Powerpoint icon on your desktop…

This post is part of a weekly series about image screening. All published posts can be found on this page.

…and here is why it is a bad idea. Powerpoint (or Keynote) is a wonderful presentation tool. It allows you to give splendid lab meetings and to dazzle competitors at conferences. It is free and widely accessible and easy to use and everybody is comfortable with it. Unfortunately, however, it does not produce proper high-resolution figures that are appropriate for publication and printing and cannot be used to archive data at high resolution. Slides or figures made using Adobe Creative Suite are easily converted and opened in Powerpoint, but the reverse sadly rarely works. Figures created in Powerpoint can be exported to TIFF or EPS files, but they will be low resolution (72 dpi) and will fail to meet printing requirements (and routine screening procedures). Even using tricks (saving as EMF, PDF, or other) will result in insufficient quality when time comes to send your TIFF/EPS/AI figure files to the journal of your dreams. Appropriate figure-making software includes the Adobe Creative suite, CorelDRAW, Inkscape, OMERO.figure, and others. (If you are not familiar with OMERO yet, it is a free online platform from The Open Microscopy Environment allowing visualization, management, and analysis of microscopy images. It supports a very large number of microscope file formats and is designed to safely store, view, and export high-resolution micrographs and, thanks to its figure-making tools, entire figures. Full disclosure: as you may know, JCB partnered with Glencoe Software, Inc. to develop the JCB DataViewer using technology from The Open Microscopy Environment.)

If you have any doubt as to whether software is appropriate, please feel free to send a test file to us and we’ll happily check whether it meets our requirements and explain how to move forward from there.

Now that you’re set on using proper software and have all your data ready, how do you make sure you’re not improperly adding images to the figure files? Check back next week!