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Friday, July 14, 2006

CoLocalizer Pro in the Journal of Biological Chemistry paper


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".

Sunday, July 02, 2006

American Journal of Physiology paper cites CoLocalizer Pro software


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.

Saturday, June 03, 2006

Journal of Immunology paper reports data obtained using CoLocalizer Pro


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.

Sunday, February 19, 2006

Review article in the works

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.

Tuesday, December 20, 2005

CoLocalizer Pro is an Apple.com featured download


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.

Sunday, October 30, 2005

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


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.

Sunday, September 18, 2005

CoLocalizer Express released!


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.

Tuesday, August 23, 2005

Our latest paper appeared In Microscopy Research and Technique

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.

Wednesday, July 06, 2005

New look of CoLocalization Research Software web site


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

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.

Thursday, June 30, 2005

New application under development

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.

Friday, June 17, 2005

CoLocalizer Pro 1.3 is available!

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.

Tuesday, June 07, 2005

Ready your images for CoLocalizer Pro 1.3

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.

Wednesday, May 04, 2005

Microscopy Research and Technique (MRT) accepts our newest paper

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.

Friday, April 22, 2005

CoLocalizer Pro 1.2.1 released

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.

Monday, February 07, 2005

Very interesting paper appeared in Blood

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).

Tuesday, January 25, 2005

CoLocalizer Pro 1.2 released

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.

Friday, December 10, 2004

Demoing CoLocalizer Pro to colleagues

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.

Sunday, November 21, 2004

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

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.