CoLocalizer Pro 2.5.1 is an Apple.com Staff Pick

For those visiting Math & Science page of Apple.com, there is an information about CoLocalizer Pro. Apple.com classified it as a Staff Pick.

Colocalization? No, false presentation

I recently came across an article in the Journal of Cell Biology (JCB) entitled "Quantitative proteomics identifies a Dab2/integrin module regulating cell migration" (JCB 2009; 186:99–111). Finding images with colocalization in it, I expected them to be analyzed quantitatively as well. That was a wishful thinking. On Figure 5 of the article, Teckchandani et al. counted the number of colocalized and non-colocalized particles of Dab2 an integrinbeta1 and made conclusions about their ratio in ventral versus dorsal surfaces. How they determined coloalized particles? Visually. Non-colocalized ones? Also visually. How did they compare them? Visually as well! What a visual (and totally erroneous) approach! Ironically, the paper uses word "quantitative" in the title. But that is not for quantifying colocalization, that's for other things. Why? This is a good question.

Replying to my inquiry, Dr. Cooper of Fred Hutchinson Cancer Research Center shared a truly contemporary and very scientific attiude by saying that he believes only in what he sees and never relies on a "clever computer stuff". Is this disbelief applicable to the mentioned above paper he co-authored as well?

It is known that JCB not only sets trends in cell and molecular biological research, but also devotes a meaningful portion of its pages to the articles describing how to interpret and analyze biological imagery. It also explains the benefits of quantification of data and encourages readers to use it in their research. Worth mentioning in this regard are "Seeing is believing?" (JCB 2006; 172:9-18) and a very recent "Accuracy and precision in quantitative fluorescence microscopy" (JCB 2009; 185:1135-1148). So why JCB published a paper that ignores its own policies? This is an another good question.

Conclusion? Some people who publish their efforts in JCB should probably read the journal as well ... or choose a less visible venue for their misguiding publications.

New review came out

We have written a new review "Recent advances in quantitative colocalization analysis: focus on neuroscience" for "Progress in Histochemistry and Cytochemistry". The review summarizes latest information about applications of quantitative colocalization in the field of neuroscience.

Many thanks to the authors of excellent cited papers with whom we discussed their findings during preparation of the manuscript.

CoLocalization Research Software releases CoLocalizer Pro 2.5

CoLocalization Research Software released CoLocalizer Pro 2.5, a major update to its popular scientific imaging application. CoLocalizer Pro is now used by leading research organizations worldwide. Its customers work in various scientific and commercial institutions. Among them are Genentech, Nestle Corporation, as well as distinguished research laboratories at Harvard University, UC Berkeley, MIT, Columbia University, UC San Diego, UCLA School of Medicine, La Jolla Institute of Molecular Medicine, Mount Sinai School of Medicine, McGill University, University of Tokyo, and many others.

This update adds more viewing capabilities, improves check for update functionality, and introduces a very elegant personalized licensing feature. It is free to all users of CoLocalizer Pro 2.0. Users of earlier versions can upgrade for a fee.

The update can be downloaded here. For more details visit the site of CoLocalization Research Software.

MacResearch praises CoLocalizer Pro

MacResearch, a website dedicated to the use of Macs in research, posted CoLocalizer Pro software review.

The review describes the purpose of using CoLocalizer Pro in medico-biological field and explains why it is significantly better than any other types of software that can count colocalization. In particular, it is clarified that using confocal images for quantitative colocalization analysis without corrected background usually results in overestimation of colocalization.

Description of software is very informative yet very concise. The review is a remarkably useful bit of knowledge for all researchers who obtain and analyze confocal images with colocalization.

Quantitative Colocalization Analysis Protocol

Current Protocols in Cell Biology, the best and the most popular compilation of protocols in cell biology field, published protocol describing how to perform quantitative colocalization analysis of confocal fluorescence microscopy images.

The protocol can be accessed here

This protocol is the most comprehensive source of practically-oriented information in the field of quantitative colocalization analysis. Researchers studying colocalization will find it absolutely indispensable.

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Deconvolution of the cellular oxidative stress response with organelle-specific peptide conjugates

Chemistry & Biology, one of the journals of the famous Cell Press publishing group (2007, 14:923-930), published an article which uses CoLocalizer Pro software to analyze images and thus help to understand the mechanism of oxidative stress response. One of the images presented in the paper was selected to be the issue cover.

Review on quantitative colocalization analysis

Acta Histochemica et Cytochemica, an Official Journal of the Japan Society of Histochemistry and Cytochemistry, published our review on quantitative colocalization analysis. The review is entitled "Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena" (Acta Histochem Cytochem 2007 40:101-111). This is the most comprehensive review on this subject available. It should be very helpful to the beginners and to those familiar with the technique alike, as it not only gives the basics of the colocalization theory, but provides examples of the practical use of quantitative colocalization analysis as well.

Interesting paper appeared in Journal of Clinical Investigation

Journal of Clinical Investigation (Impact Factor 16 in 2006), published a very interesting paper about requirement of Foxo3 (forkhead box O3) for the regulation of oxidative stress in erythropoiesis (J. Clin. Invest. 117:2133-2144 (2007). The study is a collaborative effort performed by Dr D Marinkovic and colleagues from Departments of Gene and Cell Medicine, Mount Sinai School of Medicine, New York, USA, Laboratory Medicine, Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA, Black Family Stem Cell Institute, and Departments of Molecular, Cell, and Developmental Biology, and Medicine, Division of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, New York, USA.

The study found that Foxo3-deficient erythrocytes exhibited decreased expression of ROS scavenging enzymes and had a ROS-mediated shortened lifespan and evidence of oxidative damage. Furthermore, loss of Foxo3 induced mitotic arrest in erythroid precursor cells, leading to a significant decrease in the rate of in vivo erythroid maturation. We identified ROS-mediated upregulation of p21CIP1/WAF1/Sdi1 (also known as Cdkn1a) as a major contributor to the interference with cell cycle progression in Foxo3-deficient erythroid precursor cells. These findings establish an essential nonredundant function for Foxo3 in the regulation of oxidative stress, cell cycle, maturation, and lifespan of erythroid cells. These results may have an impact on the understanding of human disorders in which ROS play a role. The study used CoLocalizer Pro software to perform quantification of immunofluorescence images and employed Manders' coefficient to obtain important conclusions.

Interesting article published by PNAS

Proceedings of the National Academy of Sciences the United States of America (PNAS), one of the most respected and highly acclaimed scientific journals, published in its June issue (104: 10205-10210, 2007) a very interesting article about involvement of host cellular multivesicular body functions in hepatitis B virus budding. The paper was written by Dr. Watanabe and colleagues from Institute for Molecular Virology, McArdle Laboratory for Cancer Research and Howard Hughes Medical Institute, University of Wisconsin, Madison. The authors found that host multivesicular bodies (MVBs) functions are required for efficient budding and release of enveloped Hepatitis B virus (HBV) virions and may be a valuable target for HBV control. Moreover, HBV enveloped virions, enveloped subviral particles, and unenveloped nucleocapsids are all released by distinct pathways with separate host factor requirements. The study elegantly used CoLocalizer Pro software to estimate colocalization of HBV envelope protein with class E proteins in Huh-7 cells.

Zymogen activation and other early events in secretagogue-induced acute pancreatitis

Dr. Van Ecker and collaborators from Tufts-New England Medical Center and Tufts University School of Medicine in Boston published a very interesting article about cause-effect relationships between zymogen activation and other early events in secretagogue-induced acute pancreatitis. The article appered in American Journal of Physiology Gastrointestinal and Liver Physiology (292: G1738-G1746, 2007). It was concluded: 1) that the colocalization phenomenon, F-actin redistribution, activation of proinflammatory transcription factors, and upregulated expression of cytochemokines are not the results of zymogen activation, and 2) that these early events in pancreatitis are not dependent on cathepsin B activity. In contrast, zymogen activation and increased subcellular organellar fragility during caerulein-induced pancreatitis are dependent on cathepsin B activity. The authors made a very good use of CoLocalizer Pro software to obtain these important results.

Tyrosine phosphorylation and lipid raft association of pseudorabies virus

Virology, the leading source of new information in its field (2007 362:60-66), published an article of Dr. Desplanques and colleagues from Ghen University, Belgium, on tyrosine phosphorylation and association of lipid raft of pseudorabies virus (PRV) glycoprotein E during antibody-mediated capping. It was found that PRV gE-mediated viral capping process results in increased Src kinase-mediated tyrosine phosphorylation of the cytoplasmic domain of gE and that a fraction of gE associates with lipid rafts, all very reminiscent of immunoreceptor capping. These results provide evidence that gE-mediated capping is a viral mimicry of immunoreceptor capping. The authors made a good use of CoLocalizer Pro software not only performing calculations of various colocalization coefficients, but analyzing scatter grams of images as well. Interesting that images used for quantification of colocalization in this study were selected for the journal issue cover. Good job!

Ethanol consumption alters expression and colocalization of bile salt export pump and multidrug resistance protein 2 in the rat

Histochemistry & Cell Biology (2007, 127:503-512), an Official Journal of the Society for Histochemistry, published our article on the effect of ethanol toward bile salt export pump and multidrug resistance protein 2. In this paper, we calculated several colocalization coefficients to understand the changes occurring in hepatocytes in greater details. We believe that this article should be of significant interest not only to basic science researchers, but to clinicians dealing with alcohol abuse as well.