"Comedians in Cars Getting Coffee" heading for Season 2!

According to the recent The New York Times report, web series Comedians in Cars Getting Coffee is heading for Season 2! This is great news for all who liked the show!

"Comedians in Cars Getting Coffee"

Just recently stumbled upon a new internet project from a sitcom superstar Jerry Seinfeld called Comedians in Cars Getting Coffee. As its name implies, its about comedians in cars getting coffee. In series of short (10 min or so long episodes) Mr. Seinfeld picks up a fellow comedian in a car and they go for lunch laughing and talking.

In many aspects it reminds of a well established British internet series Carpool, instead that, fortunately, Jerry does not drive Toyota Prius and chooses vintage cars (just two Porsches featured so far if you know what I mean) instead.

As one may expect, the first episode featured his fellow comedian and Seinfeld co-creator Larry David. The upcoming 10th episode will remind of another Seinfeld star Michael Richards (Kramer). Although not all his guests are equally sharp and entertaining, I found these little episodes a real treat to watch. Give them a try!

"Beyond the limit of histochemistry"

Poster of 14th ICHC at the entrance of Kyoto International Conference Hall.

14th International Congress of Histochemistry and Cytochemistry (ICHC) came and went and I am taking a few moments to reflect. It was my third ICHC (previous two were in Kyoto in 1996 and in Gdansk in 2008) and it is my impression that this one was probably the best in terms of both organization and attendance. Most importantly, due to recent breakthrough developments in microscopy instrumentation, the Congress was fortunate to have a common topic/theme that united many of its presentations and became a Congress key, which was super resolution. For those not very familiar, super resolution microscopes operate above the diffraction limit of light and allow to see structures at the resolution of 10 nm (compared to 220-250 nm in conventional (including confocal) fluorescence microscopes), which is nothing short of revolutionary.

   Congress started with a keynote lecture delivered by Dr. Lippincott-Schwartz from NIH. She talked about new optical probes, imaging strategies, and technical innovations. Although Congress attendees were certainly familiar that Dr. Lippincott-Schwartz is a pioneer of super resolution microscopy and more or less knew what to expect from the lecture, it was my feeling that many of them were blown away by the dynamics of the imagery she had shown and the presentation logic of her talk. I personally was impressed the most by the extent of integration of various disciplines in her studies. Researchers talk about the need for interdisciplinary approach in contemporary medico-biological science for quite some time now. But we don't see too many examples. In this case, everything was there in full bloom.

   Speaking about our workshop on quantitative methods in histochemistry and cytochemistry, we had more attendees that I expected and all three presentations went really well. We also had very lively discussions. Both Dr. Wollscheid  and Dr. Seitz are experienced and dedicated presenters and they tried to pack in their talks as much information as possible. I was glad to speak about quantification of spatial correlation of fluorescent markers mostly based on our recently published Nature Protocols paper. All three talks of us covered different areas of quantification techniques and that was the very idea of the workshop.

The next ICHC Congress will take place in Istanbul, Turkey, in 2016. I wonder what will become a key topic there?

14th International Congress of Histochemistry & Cytochemistry

From August 26th to 29th I'll be attending 14th International Congress of Histochemistry & Cytochemistry in Kyoto. This going to be my second International Histochemistry & Cytochemistry Congress in this marvelous Japanese city. First one was back in 1996, soon after I came to Japan. This time I am organizing a workshop dedicated to modern quantitative methodologies. Two outstanding European researchers working in Switzerland, Drs. Bernd Wollscheid and Arne Seitz from renown ETH Zurich and EPFL Lausanne, respectively, will be joining me at the workshop. Dr. Wollscheid will be talking about chemoproteomic technology for the ligand-based receptor identification on living cells and tissues, while Dr. Seitz will be focusing on the strategy to test fluorophores stability for typical histological samples. I will be presenting latest developments in the field of quantification of colocalization. I am glad to mention that I was able to obtain financial support for both Dr. Wollscheid's and Dr. Seitz's travel.

I am quite looking forward to the Congress, because there should be really interesting presentations there, as well as, because, as people who visited this old Japanese city even once may say, there is no any other place in the world like Kyoto.

P.S. Picture above: Kinkaku-ji (Temple of the Golden Pavilion), one of the most popular buildings in Japan and one of the World Heritage Sites.

Editorial Board of Scientific Reports

I recently joined Editorial Board of Scientific Reports, new online and open access journal from the publishers of Nature. It covers all areas of the natural sciences. As a member of Nature Publishing Group (NPG), Scientific Reports publishes technically sound, original research papers of interest to specialists within their field and without barriers to access. I am affiliated with the Cell Biology section of the Board.

To ensure rapid peer review and publication of research, Scientific Reports relies on an external Editorial Board and a streamlined peer-review system. An internal publishing team works with the board and authors to make sure that accepted manuscripts are processed for publication as quickly and smoothly as possible.

In addition, Scientific Reports leverages the tools, technology and experience of NPG to ensure that published manuscripts are enhanced by innovative web technologies. All papers are archived in PubMed Central.

I look forward to help making Scientific Reports an another NPG success.

Nature Protocols publishes our paper and presents it as a featured protocol

I am very pleased to report that Nature Protocols published our protocol dedicated to quantification of spatial correlations of fluorescent markers. Delightfully, editors of the journal presented it as a featured protocol. In the published protocol, we examined interactions of proteins by detecting their overlap using fluorescent markers. The observed overlap was then quantified to serve as a measure of spatial correlation. We reduced the contribution of the background in the images to be analyzed using CoLocalizer Pro and a custom software created by Dr. Yong Wu of UCLA. Colocalization was estimated using protein proximity index (PPI) and a correlation coefficient. PPI provided separate values of colocalization for each channel, while correlation coefficient determined the overall colocalization. We used computer-simulated and real biological images to showcase how the protocol works. The protocol minimizes human bias and can be universally applied to various cell types in which there is the need to understand protein-protein interactions. We encourage cell and molecular biologists studying protein-protein interactions to include our protocol to the arsenal of their research tools.

Milan. Piazza del Duomo. December 28th, 2010

Lens: AF-S DX NIKKOR 18-55mm f/3.5-5.6G VR. Stitched with Adobe Photoshop CS5. Enhanced with Apple Aperture 2.

Shinjuku Station

Shinjuku Station (Tokyo). Lens: AF-S DX NIKKOR 18-55mm f/3.5-5.6G VR. Stitched with Adobe Photoshop CS5.

Kochi City Scape

View from the castle. Lens: AF-S DX NIKKOR 18-55mm f/3.5-5.6G VR. Stitched with Adobe Photoshop. Enhanced with Apple Aperture.

Sakura

Lens: AF-S DX NIKKOR 35mm f/1.8G.

Colocalization and cancer cells

A rapidly growing evidence suggests the possibility of the link between changes of the degree of colocalization of various antigens in the cells and the spectrum of their malignant properties. This is hardly surprising, since it has been known for a long time that various proteins are overexpressed in cancers. Discordant overexpression of colocalized proteins should inevitably result in the shift of their colocalization properties.

A recent study that caught my attention described overexpression of adenylate cyclase-associated protein 1 (CAP1) in pancreatic cancers. Fluorescence microscopy showed colocalization of CAP1 with actin to the edge of lamellipodia. Knockdown of CAP1 by the RNA interference technique resulted in the reduction of lamellipodia formation, hence colocalization as well, and motility and invasion properties of pancreatic cancer cells. Interestingly, the authors concluded that this is the first report that demonstrated the overexpression of CAP1 in pancreatic cancer cells and suggested the involvement of CAP1 in their aggressive behavior. Thus, the described observation of colocalization of CAP1 with actin served to identify CAP1 as a marker for this type of cancer as well as determined its usefulness for prognosis. Since quantification of colocalization not only proves its existence objectively, but also provides many important additional details about it (dynamical changes, contribution to colocalization of a particular antigen/channel, etc.), it is natural to expect that the use of this methodology should significantly extend the significance of these and similar observations by making them less descriptive and much more factually-based. In addition to the peripheral proteins, it can be expected that changes of the degree of colocalization can have diagnostic and prognostic values when examined in the nuclei of tumor cells, such as for example colocalization of promyelocytic leukemia (PML) bodies with telomeres (Cancer Res 2007;67:7072).

It should be mentioned, however, that the use of quantification requires a certain level of methodological knowledge and skills to ensure that it is executed correctly. It is also critical to ensure that images for analysis are properly acquired and processed prior to quantification. Fortunately, this issue received a much required attention of late with the appearance of several high quality articles stressing the importance of accuracy and precision in quantitative fluorescence microscopy and even describing a specialized quantitative colocalization analysis protocol. An another important thing worth noting is that, to be actually useful for diagnostics, quantification of colocalization should be at least semi-automated. This can be addressed by employing the latest software tools when, for example, the whole workflow of image analysis is saved as a preset or even as an action (similar to the Photoshop action), which then can be re-used and re-applied easily and quickly on as many images as needed. The critical issue here is to ensure that all images are prepared for the analysis and then analyzed in exactly the same fashion so that the results of calculations are easily reproduceable and fully comparable.

To conclude, we will likely see a noticeable increase in the number of studies attempting to use quantification of colocalization in tumors for diagnostic and prognostic purposes in the near future. Lets hope they adhere to the methodological guidelines and report really promising and applicable observations.

Haiti Indie Relief

CoLocalization Research Software will be participating in the Indie Relief effort to gather money for Haiti earthquake victims. Indie Relief will take place on January 20th: http://www.indierelief.com/.

CoLocalizer Express and Macnification combine forces

CoLocalization Research Software and Orbicule joined forces to offer CoLocalizer Express and Macnification in a bundle. The bundle combines two of the best applications for analysis of microscopy images created for the Macintosh platform. It is also an excellent match in terms of the applications' features, reliability, and ease of use.

Importantly, the bundle is offered at a very affordable price. For a limited time, the licenses of both applications can be purchased for an amazing EUR 199. That's a saving of EUR 30!

Macnification, CoLocalizer's good companion

In addition to quantifying colocalization, you can also asses other morphological parameters of your images, such as to measure and analyze the size of the cells and their different components. This comes in very handy to properly understand the significance of colocalization calculations. The best way to perform these types of measurements it is to use Macnification, a scientific application for organizing, editing, and analyzing of medico-biological imagery. Macnification lets you create folders where you can store your images, analyze them, and master image meta data. It also handles microscopic images in the variety of specialized file formats.

It is worth mentioning that Macnification is a 2008 Mac Design Award Winner for Best Mac OS X User Experience. As can be expected, it provides outstanding look and feel of the best breed of Macintosh software and guarantees an exquisite user experience.

Tuscany: Panorama of Florence

Tuscany: Pisa

Tuscany: Villas

Tuscany: Bachus

Tuscany: Wine Grapes

Tuscany: Lucca