Vadim's Blog

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

2011-09-16T02:00:00.001-07:00

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

2011-02-18T05:41:00.000-08:00

Acquired with Nikon. Stitched in Photoshop. Enhanced in Aperture.

Shinjuku Station

2010-11-12T03:37:00.000-08:00

Shinjuku Station (Tokyo). Acquired using Nikon D60, stitched in Photoshop CS5.

Kochi City Scape

2010-04-25T22:10:00.000-07:00

View from the castle. Acquired with Nikon. Stitched in Photoshop. Adjusted in Aperture.

Sakura

2010-04-08T00:13:00.001-07:00

Colocalization and cancer cells

2010-03-17T17:41:00.001-07:00

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

2010-01-17T16:19:00.000-08:00

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

2009-11-07T20:10:00.000-08:00

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

2009-09-22T21:35:00.000-07:00

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

2009-09-05T00:43:00.000-07:00

Tuscany: Pisa

2009-09-05T00:40:00.000-07:00

Tuscany: Villas

2009-09-04T02:42:00.001-07:00

Tuscany: Bachus

2009-09-03T06:07:00.001-07:00

Tuscany: Wine Grapes

2009-09-03T06:06:00.001-07:00

Tuscany: Lucca

2009-09-03T06:00:00.000-07:00

Tuscany: Panorama of Lucca

2009-09-03T05:56:00.000-07:00

Tuscany: Hills

2009-09-03T05:54:00.001-07:00

CoLocalizer Pro 2.5.1 is an Apple.com Staff Pick

2009-07-24T00:21:00.000-07:00

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

2009-07-18T05:15:00.001-07:00

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

2009-05-20T18:49:00.001-07:00

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

2008-12-07T15:53:00.000-08:00

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

2008-11-07T21:59:00.001-08:00

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

2008-07-11T01:22:00.000-07:00

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.

Pictures from Switzerland: Freddie Mercury Sites

2008-02-24T06:10:00.000-08:00

Pictures from Switzerland: Montreux

2008-02-21T00:40:00.000-08:00

Pictures from Switzerland: Lucerne

2008-02-11T01:58:00.000-08:00

Pictures from Switzerland: Lugano

2008-01-27T04:53:00.000-08:00

Pictures from Switzerland: Bern

2008-01-24T21:28:00.000-08:00

Pictures from Switzerland: mountains & valleys

2008-01-22T19:22:00.000-08:00

Pictures from Switzerland: Zurich

2008-01-22T05:17:00.000-08:00

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

2007-12-12T19:00:00.000-08:00

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

2007-11-26T18:42:00.000-08:00

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

2007-11-21T22:57:00.000-08:00

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

2007-10-23T00:13:00.000-07:00

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

2007-09-21T21:20:00.000-07:00

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

2007-08-29T06:42:00.000-07:00

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

2007-07-31T02:55:00.000-07:00

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.

Colocalization of zymogens with lysosomal hydrolases

2007-06-18T00:32:00.000-07:00

Observation of colocalziation played central role in understanding of the cause-effect relatioships between zymogen activation and other early events in secretagogue-induced acute pancreatitis. CoLocalizer Pro software was used by Dr. Van Acker and colleagues from Tufts-New England Medical Center in Boston to show that inhibition of cathepsin B by pre-treatment with CA-074me prevents intrapancreatic zymogen activation and reduces organellar fragility but it does not alter the caerulein-induced co-localization phenomenon or sub-cellular F-actin redistribution or prevent caerulein-induced activation of NF-B, ERK 1/2, and JNK, or up-regulated expression of cyto-chemokines. The authors concluded (a) that the co-localization phenomenon, F-actin redistribution, activation of pro-inflammatory transcription factors, and up-regulated expression of cyto-chemokines are not the result of zymogen activation, and (b) that these early events in pancreatitis are not dependent upon cathepsin B activity. The paper appeared in in American Journal of Physiology (Gastrointestinal and Liver Physiology), an official journal of The American Physiological Society ((2007) 292 G1738-G1746).

American Journal of Pathology paper cites CoLocalizer Express software

2007-03-12T22:05:00.000-07:00

Dr. Rocker and colleagues from departments of biophysics and cardiology at the University of Ulm and physics at the University of Illinois at Urbana–Champaign published interesting article about enhancement of the affinity of C-reactive protein toward FcgammaRI by the gamma-chain. The publication appeared in American Journal of Pathology (2007) 170:755-763, an official journal of the American Society for Investigative Pathology. This study investigates C-reactive protein (CRP), the prototype human acute phase protein, which is widely regarded as a key player in cardiovascular disease. Taking into consideration the structure of CRP, the study concludes that multivalent binding and receptor clustering are crucially involved in the interaction of CRP with nucleated cells. The article cite CoLocalizer Express software, wich has been used to understand the details of the studies processes.

Activation-induced endocytosis of the raft-associated transmembrane adaptor protein LAB/NTAL in B lymphocytes

2007-02-06T17:28:00.000-08:00

International Immunology (Int Immunol (2007) 19:19-30), new but already highly respected journal in the field of immunology, published interesting article about role of activation-induced endocytosis of the raft-associated transmembrane adaptor protein Linker for activation of B cell (LAB)/non-T cell activation linker (NTAL) in B lymphocytes in internalization of the B cell receptor (BCR). The authors lead by Dr. Deans from Department of Biochemistry and Molecular Biology at the University of Calgary used a complex methodological approach, which included quantitative colocalization analysis using CoLocalizer Pro software. The paper sheds light onto the role of LAB/NTAL in the internalization of BCR and describes intrinsic details of this process. Congratulations to the authors on this elegant study.

Regulation of adenylyl cyclase in cultured cardiac myocytes

2007-01-29T19:56:00.000-08:00

Journal of Biological Chemistry (JBC) editors seem to like quantitative colocalization analysis, because the journal published three articles which employed CoLocalizer Pro software in 2006 alone. This is very encouraging, because JBC is one of the best journals in the medico-biological field. The paper which I did not mention here yet is written by Dr. Head and colleagues from the University of California in San Diego (J Biol Chem (2006) 281:38730-38737). It reports about regulation of localization of adenylyl cyclase in cultured cardiac myocytes. In an elegant way, Dr. Head and coworkers showed that microtubules and actin filaments restrict formation of cyclic AMP by regulating the localization and interaction of G protein-coupled receptors with adenylyl cyclase in lipid rafts/caveolae. The paper is an interesting read.

CoLocalizer Express 1.2 released!

2007-01-04T07:30:00.000-08:00

We have updated CoLocalizer Express to version 1.2. This update is a universal binary version. It includes updates to the Help and User Guides and to the License Agreement. It can be downloaded here: http://homepage.mac.com/colocalizerpro/purchasesupport.html. Enjoy!

CoLocalizer Pro papers keep coming...

2006-12-13T02:41:00.000-08:00

Dr. Osvaldo Rey and colleagues from the University of California at Los Angeles published a very interesting paper about the role of calcium-sensing receptor (CaR) in the generation of transient Ca2+ oscillations. Dr. Rey used CoLocalizer Pro software to elegantly quantify the colocalization of CaR and transient receptor potential gene, TRPC1, according to Manders' overlap coefficient. They employed CoLocalizer Pro to quantify colocalization of CaR and TRPC1 and presented corresponding scatter grams. The paper is a good read and leaves a very positive impression. The paper appeared in the Journal of Biological Chemistry (281:38730-38737 (2006), one of the best journals in the medico-biological field.

To do or not to do

2006-12-10T17:55:00.000-08:00

A number of researchers contacted CoLocalization Research Software Support lately and said they tried either CoLocalizer Pro or Express versions of colocalziation analysis software and the results of colocalization coefficients were not what they expected. They wondered why is this so and what should they do to obtain more suitable calculations. After asking them few questions about the way they prepared samples and how they used confocal microscopes, it became clear that their images were simply unusable for quantitation purposes. For these images, even calculations which seem correct will no doubts be erroneous. We put together some simple guidelines for researchers using confocal microscopy and doing quantitative colocalziation analysis so that they can avoid mistakes in future. Here they are:

Sample preparation:
- Make sure that the used antibodies are specific and do not cross-react.
- Choose fluorophores with well-separated excitation and emission spectra.
- Use the same mounting medium for the samples you will be comparing.
- Try to avoid using anti-fading reagents, as they can increase background fluorescence.

Microscope set-up:
- Use plan apochromatic lenses to reduce chromatic shift.
- Use optimized emission filters to maximize emission collection while avoiding bleed-through effect.
- Use the same objective lens for the samples you will be comparing.
- Make sure that the size of microscope pinhole is properly set.

Image acquisition and handling:
- Acquire images sequentially to minimize bleed-through effect.
- Do not acquire too bright and too contrast images, as it will result in their saturation.
- Do not manipulate images in graphics-editing programs, as it may ruin usability of your images for quantitation.
- Do not resave files in any other format than TIFF. It may cause loss of original image data needed to perform calculations.

If you have not followed one of these guidelines, just don`t use your images for calculating colocalization. You will not get reliable results.

CoLocalizer Pro 2 released!

2006-11-22T00:47:00.000-08:00

We upgraded CoLocalizer Pro to version 2. New version of CoLocalizer Pro is a significant improvement over the previous one. CoLocalizer Pro 2 adds one of the most requested features: the ability to reveal colocalized and selected pixels. The upgrade is free to all registered users! It can be downloaded here: http://homepage.mac.com/colocalizerpro/purchasesupport.html

Colocalization studies performed using multidimensional microscopic robot technology

2006-10-10T19:52:00.000-07:00

October issue of Nature Biotechnology published an article about the latest trend in studying the high-throughput protein colocalization studies: multidimensional microscopic robot technology. The technology consists of cycles of fluorescence tagging, imaging and bleaching in situ. It is said that the technology combines three advances: a) a fluorescence technique capable of mapping hundreads of different proteins in one tissue section or sample, b) a method selecting the most prominent combinatorial molecular patterns by representing the data as binary vectors, c) and a system for imaging the distribution of these protein clusters in a so called toponome map. It is claimed that this approach is able to reveal rules of hierarchical protein network organization, in which state-specific lead proteins control protein network topology and function.

The method is relied on a so called multi-epitope-ligand cartography (MELC), that can map the location of several proteins in the one samlel of cells or tissue using sequential rounds of fluorescent detection in situ. Importantly, it appears that MELC can be used to show when and where proteins colocalize in cellular or tissue compartments, which proteins are excluded, how these associations are altered by pathology and how proteins are functionally interrelated.

MELC appears to be a significant step forward in colocalization analysis, because it enables obtaining considerably more reliable images for latter use with colocalization analysis software. It would be interesting to see whether these images will still require background correction, a critical step performed by the current software.

Study colocalized antigens? Make sure you`ve got CoLocalizer...!

2006-09-19T06:53:00.000-07:00

A whole lot of new researchers doing confocal microscopy will now learn about amazing capabilities of CoLocalizer Pro and CoLocalizer Express! Microscopy and Analysis, the premier international journal for users of microscopical, analytical and imaging equipment with 46,000 subscribers and 120,000 readers worldwide, in its special issue dedicated to "Light Microscopy in the Life Sciences" published our review article about quantitative colocalzition analysis. The article describes the applicability of our colocalization analysis software for studying dynamics of cellular responses: Microscopy and Analysis 2006, September. For the convenience of users, we included table with characteristics of coefficients used to estimate colocalization. We describe the range of their values and give tips on how they should be applied.

Another American Journal of Physiology paper empoyed CoLocalizer Pro software

2006-08-19T01:23:00.000-07:00

Dr. Tstutsumi and colleagues from University of California in San Diego reported results of their study about role of 12-lipoxygenase in volatile anesthetic-induced delayed preconditioning in mice. Researchers tested the hypothesis that expression and activity of 12-LO mediate delayed cardiac protection induced by isoflurane in the mouse heart in vivo. Among other tools, CoLocalizer Pro software was used in this study to find out that 12-LO is an important mediator of isoflurane-induced delayed preconditioning. Am J Physiol Heart Circ Physiol 2006, 291:H979-H983.

CoLocalizer Pro in the Journal of Biological Chemistry paper

2006-07-14T03:24:00.000-07:00

Dr. Sweaney and colleagues from University of California in San Diego published interesting paper about the mechansim of fibroblast-myofibroblast transformation. The paper appeared in Journal of Biological Chemistry (JBC), one of the best and highly credited medico-biological journals J Biol Chem 2006 281:17173-17179. Fibroblast-myofibroblast transformation is a critical event for enhanced extracellular matrix deposition. It involves formation of an actin stress fiber contractile apparatus that radiates from focal adhesions (FA) in the plasma membrane. The researchers used adult rat cardiac fibroblasts to examine distribution and expression of adenyly cyclase (AC), phospho-cav-1, and FA proteins to define mechanisms that link increases in cAMP to caveolin-1 phosphorylation, actin/FA assembly, and fibroblast-myofibroblast transformation. The authors detected AC in both cav-1 and phospho-cav-1 immunoprecipitates, but FA kinase (FAK), phospho-FAK (FAK Tyr-397), paxillin, and vinculin were detected only in phospho-cav-1 immunoprecipitates. Treatment with the AC activator forskolin or a cAMP analog increased cav-1 phosphorylation but decreased FAK Tyr-397 phosphorylation in a cAMP-dependent protein kinase-dependent manner. These events preceded actin cytoskeletal disruption, an effect that was blocked by small interfering RNA knock-down of cav-1. Inhibition of protein tyrosine phosphatase 1B abrogated cAMP-mediated disruption of actin cytoskeleton, cav-1 phosphorylation, and FAK Tyr-397 dephosphorylation. CoLocalizer Pro software was used to make important conclusions about functional significance of phospho-caveolin-1. According to the authors "the data define a novel organization of signaling molecules that regulate fibroblasts: scaffolding of AC by phospho-cav-1 at FA sites in a caveolae-free microdomain along with components that mediate inhibition of actin/FA assembly and fibroblast-myofibroblast transformation via increases in cAMP".

American Journal of Physiology paper cites CoLocalizer Pro software

2006-07-02T06:11:00.000-07:00

Dr. Patel and colleagues from University of California in San Diego reported results of their interesting study about the role of caveolar microdomains and δ-opioid receptors in protection of adult rat cardiac myocytes from ischemic cell death. They tested the hypothesis that that opioid receptors (OR), which are capable of producing cardiac protection in vivo, promote cardiac protection in cardiac myocytes in a caveolae-dependent manner. The authors used tools of quantitative colocalization to determine colocalization of DOR with caveolin-3 (Cav-3), a structural component of caveolae in muscle cells. CoLocalizer Pro software was used for this task. They also investigated the effect of the treatment with methyl-β-cyclodextrin (MβCD), which binds cholesterol and disrupts caveolae. It was found that MβCD fully attenuated the protective effects of ischemic preconditioning or SNC-121, a selective DOR agonist, resulting in cell death comparable to that of the ischemic group. By contrast, SNC-induced protection was not abrogated in cells incubated with cholesterol-saturated MCD, which maintained caveolae structure and function. This article suggests a key role for caveolae, perhaps through enrichment of signaling molecules, in contributing to protection of cardiac myocytes from ischemic damage. Am J Physiol Heart Circ Physiol 2006, 291:H344-H350.

Journal of Immunology paper reports data obtained using CoLocalizer Pro

2006-06-03T05:42:00.000-07:00

Dr. Cario and colleagues from Division of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany, and Harvard and University of Massachusetts Medical Schools published intersting article about trypsin-sensitive modulation of intestinal epithelial MD-2 as mechanism of lipopolysaccharide tolerance. The paper appeared in Journal of Immunology, one of the best journals in the medico-biological field.

The article characterized the expression and subcellular distribution of intestinal epithelial MD-2 and delineated potential functional interactions with trypsin and then alteration in inflammatory bowel disease (IBD). The authors obtained confocal images using Zeiss LSM510 and then quantified the extent of colocalization in the sections using CoLocalizer Pro software. Pearson’s correlation and the Manders’ overlap coefficients were employed.

It was concluded that endoplasmic reticulum-associated MD-2 expression in IBD may be altered by ileal protease in inflammation, leading to impaired LPS recognition and hyporesponsiveness through MD-2 proteolysis in IEC, thus implying a physiologic mechanism that helps maintain LPS tolerance in the intestine. J Immunol 2006, 176:4258-4266.

Review article in the works

2006-02-19T21:10:00.000-08:00

I am working on a review article about quantitative colocalization analysis. We have accumulated significant knowledge about this subject over the last two years and I am convinced that such article is needed for the research community. I will be giving theoretical background of this research technique, summarizing tips on how it should be used properly, and provide practical examples of its applicability.

CoLocalizer Pro is an Apple.com featured download

2005-12-20T21:10:00.000-08:00

CoLocalizer Pro version 1.4 is a featured download on Math & Science page of Apple.com Downloads page. We hope that many more researchers will now learn about our software and use it for their studies with great success.

CoLocalizer Pro is used to obtain data published in The Journal of Clinical Investigation

2005-10-30T03:34:00.000-08:00

The Journal of Clinical Investigation (J Clin Invest (2005) 115:2716-2730) published interesting paper finding out that atrial natriuretic peptide promotes cardiomyocyte survival by cGMP-dependent nuclear accumulation of zyxin and Akt. The study reports that zyxin and activated Akt participate in a cGMP-dependent signaling cascade leading from ANP receptors to nuclear accumulation of both molecules. It is concluded that nuclear accumulation of zyxin and activated Akt may represent a fundamental mechanism that facilitates nuclear-signal transduction and potentiates cell survival. The paper is written by the Mark Sussman`s team from San Diego State University Heart Institute. Dr. Sussman and colleagues used CoLocalizer Pro software for quantifying TUNEL positive nuclei. The Journal of Clinical Investigation (JCI) is a top-tier journal publishing biologically significant findings with clinical relevance. Published since 1924, the JCI has a 2004 Impact Factor of 14.204.

CoLocalizer Express released!

2005-09-18T22:21:00.000-07:00

We have released new application, CoLocalizer Express. It is a lite version of CoLocalizer Pro. CoLocalizer Express suits best to labs on little budget. It employs power and flexibility of CoLocalizer Pro and guarantees that you will obtain your calculation results very quickly. If you do not need image viewing capabilities of CoLocalizer Pro and can be satisfied with saving results in a simple way, CoLocalizer Express is a program for you. Standard Single-User license of CoLocalizer Express costs $99 (US), Academic Single-User license costs $89 (US). Lab license sells for $249 (US). Similarly to CoLocalizer Pro, you may try CoLocalizer Express for 1 week before purchasing its license.

Our latest paper appeared In Microscopy Research and Technique

2005-08-23T00:43:00.000-07:00

Microscopy Research and Technique (MRT) in its June issue published our paper entitled "Experimental LPS-induced cholestasis alters subcellular distribution and affects colocalization of Mrp2 and Bsep proteins: a quantitative colocalization study". You can read it here:
http://www3.interscience.wiley.com/cgi-bin/abstract/110573293/ABSTRACT
Interesting thing about this article is that, in addition to Pearson's correlation coefficient and Overlap coefficient according to Manders, we used this time Overlap coefficients k1 and k2 as well to present the significance of the changes of colocalization of Mrp2 and Bsep proteins in dynamics of pathological process. MRT made a proper layout of tables and graphs in the paper so that the significance of our data is easily seen. MRT is a leading journal in the field of modern microscopy and we hope that our article will attract attention of many specialists in the field.

New look of CoLocalization Research Software web site

2005-07-06T22:26:00.000-07:00

As we are preparing new application, CoLocalizer Express, we have decided to refresh our site. We included more information, such as about us, frequently asked questions, support, and much more. We have also added News section as well as created space for special announcements. Special announcement at this time is start of the BACK TO THE LAB campaign.

BACK TO THE LAB campaign, Lab licensing

2005-07-06T22:02:00.000-07:00

We kicked off CoLocalizer Pro BACK TO THE LAB campaign and introduced its Lab licensing. Users who register CoLocalzier Pro before August 31, 2005 are eligible for 10% discount. Under requests, we have also introduced new Lab licensing. Lab license costs $899 (USD) and is offered to labs where several researchers require the software. It allows full access to the features of the program for all members of a lab. We strongly recommend to users who emailed us and asked about Multi-User discount option consider it as this is the smartest CoLocalizer Pro registration money can buy.

New application under development

2005-06-30T22:45:00.000-07:00

We decided to create a new application. We named it CoLocalizer Express. It will be a lite version of CoLocalizer Pro designed specifically for the labs on little budget. It will be priced under $100 (US). In addition, we will also offer a discounted Multi-User license, a Lab license. This license will allow full access to the features of the program for all members of a lab.

CoLocalizer Pro 1.3 is available!

2005-06-17T21:28:00.000-07:00

We have released CoLocalizer Pro 1.3. It is a free update to all registered users and has an important new feature, Merge. In addition, we rearranged built-in Help making it even easier to navigate, and added more information about analyzed image file to Show Info window. With this release, CoLocalizer Pro positions itself as a powerful application for the researchers working on the cutting-edge of cellular and molecular biology. If you like this release, help spread a word about it. If you have any questions, please email our Support Team.

Ready your images for CoLocalizer Pro 1.3

2005-06-07T01:28:00.000-07:00

We are putting finishing touches on CoLocalizer Pro version 1.3. This version will bring an important new feature, Merge. Previously, CoLocalizer Pro users who save results of colocalization experiments as single channel images needed to use other apps to merger them into one before importing into CoLocalizer Pro. Starting from version 1.3, they can do it easily and smoothly with CoLocalizer Pro.

CoLocalizer Pro 1.3 runs flawlessly on Mac OS X 10.4 Tiger. Our registered users who upgraded to Tiger will have no problem running this new version of CoLocalizer Pro (as well as all previous versions).

CoLocalizer Pro 1.3 will be a completely free update. I am convinced that everyone will love this release.

Microscopy Research and Technique (MRT) accepts our newest paper

2005-05-04T21:23:00.000-07:00

Our paper entitled "Experimental LPS-induced cholestais alters subcellular distribution and affects colocalization of Mrp2 and Bsep proteins: a quantitative colocalization study" has been accepted for publication in Microscopy Research and Technique (MRT). This respected international journal publishes articles on all aspects of advanced microscopy in the biological, clinical, chemical, and materials sciences. MRT attracts attention of researchers looking for new, reliable, and advanced tools for their microscopy studies. We are very pleased that many new investigators will be able to see the usefulness of CoLocalizer Pro software for their studies.

CoLocalizer Pro 1.2.1 released

2005-04-22T18:07:00.000-07:00

We have updated CoLocalizer Pro to version 1.2.1. This update fixes the m2 coefficient issue. We recommend to all CoLocalizer Pro registered users download and install this update. Enjoy.

Very interesting paper appeared in Blood

2005-02-07T01:09:00.000-08:00

Dr. Brian Eliceiri, Registered User of CoLocalizer Pro from the Institute for Molecular Medicine in La Jolla, CA, and his colleagues published interesting study about the dependency of tumor metastasis, not tumor growth, on Src-mediated vascular permeability. Src, the non-receptor tyrosine kinase, plays an essential role in specific VEGF (vascular endothelial growth factor/vascular permeability (VP) factor) pathway signaling responses. The authors used CoLocalizer Pro software to quantify colocalization of fibrin/FDPs and CD31, markers of vascular endothelial cells, in perivascular spaces of tumors of control (src +/- and wildtype) and src -/- mice. A conclusive difference of the degree of colocalization of them was found. The study suggests that there are defects in VP in the primary site of Src-deficient mice and that there may be an essential role for Src and Src-mediated VP in tumor metastasis to the lung. The paper appeared in Blood (2005, 105: 1508-1514), a highly respected Journal of the American Society of Hematology (Impact Factor 10.12, 2003).

CoLocalizer Pro 1.2 released

2005-01-25T21:48:00.000-08:00

We have just released CoLocalizer Pro version 1.2. In this version, we listened to the majority of our users` requests and gave more options for background correction! Background correction has now Auto and Manual modes. In the Manual mode, there are three presets depending upon the image pattern: Average Contrast and Fluorescence, Low Contrast, and Weak Fluorescence. Auto mode should be used by users whose images do not require a very precise correction and should work for the majority of them. It should appeal to the users who want get things done really quickly. For other images and more precision, use Manual mode. We also made several minor enhancements, updated documentation, and tweaked the interface. Enjoy.

Demoing CoLocalizer Pro to colleagues

2004-12-10T05:56:00.000-08:00

Two colleagues from Kyoto University visited me today for taking a look at CoLocalizer Pro and trying it out on their images. First of all both of them said it is really great to have a tool that works without a confocal microscope. The guys were excited and looked like they loved the software. Gave me a bunch of images they wanted to analyze and kept asking how to get things done. Asked me a lot of questions about background correction and tried doing correction themselves. They said they are going to buy the software for their labs and recommend it to collaborators. Then they went on telling me why the program is so useful and what they want to see improved and updated. It was great to see people sharing their views to make the program even better.

How the idea to create computer software for quantitative colocalization analysis came out

2004-11-21T23:52:00.000-08:00

Hello Everybody! I have been using confocal microscopes for years and wanted to be able to perform reliable analysis of the colocalization of antigens on my samples. I also wanted to do it on my PowerBook, not on anemic Windows computers bundled with the microscopes. I started researching for the appropriate software, but found nothing, not a single title. Well, I teamed up with friends, and together we have created CoLocalizer Pro, a computer software for quantitative analysis of multicolor confocal fluorescence images. We wanted it to be used by our collaborators and the people we know, as well as by many others we don`t. On April 24, after more than 10 months of development, we offered CoLocalizer Pro to the scientific community worldwide. Its journey to the labs has begun.