November 15, 2013  |  User Stories

Cytobank User Stories: Adam Litterman

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow and mass cytometry.

This time we interview Adam Litterman, a Ph.D. Candidate of the Microbiology, Immunology and Cancer Biology graduate program in Dr. David Largaespada’s lab at the University of Minnesota. Some of his work was recently published in the Journal of Immunology and was analyzed using Cytobank.

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What are you excited about in science? What is your scientific vision?
Adam Litterman - Ph.D. student at University of Minnesota
Adam Litterman – Ph.D. student at University of Minnesota

I am excited about understanding how gene expression is controlled in T cells. This is for a couple reasons. First of all, T cells have a hand in a large number of disease processes: autoimmunity, infectious diseases, vaccinations, cancer, etc., all these diseases could see improved outcomes stemming from better understanding of how T cells work. Second, T cells are an exciting, emerging new type of therapeutic, different in kind from regular drugs or biologics, for cancer and other diseases too. Finally, T cells are a great model system for understanding cellular differentiation and plasticity: naive T cells can take on a number of fairly well characterized fates based on information from their environment. I see a lot of work left to do to try to understand how T cells make those decisions, and ultimately to try to manipulate those decisions for therapeutic purposes. More »

November 1, 2013  |  Uncategorized

Cytobank Remembers Leonard Herzenberg

Leonard ‘Len’ Herzenberg, a world renowned scientist, innovator, and mentor, passed away on October 27 at the age of 81 after a brief illness. In cooperation with his wife and scientific partner, Lee Herzenberg, he brought the power of flow cytometry to the field of immunology, developed fluorescence activated cell sorting, and mentored some of the most influential figures in flow cytometry today – including Garry Nolan, out of whose lab Cytobank was formed.

Several of us at Cytobank have spent time at the Stanford Shared FACS Facility working on projects and can intimately appreciate Len Herzenberg’s contributions to the field in both instrumentation and the pervasive attitude of openness. The cytometry community has always been open and inclusive – labs and core facilities strive to educate new users and spread cytometry expertise as far as possible. These ideals were instilled in the community by the founders and pioneers of flow cytometry, and Len played a large role in the process. This was evident in the way he handled the distribution of early hybridomas (a term he coined during a sabbatical in César Milstein’s laboratory) – open and available to anyone who asked.

As we reflect on Len’s contributions to the field, we’d like to highlight a memorial written by Mario Roederer and a video interview  performed by him of both Lee and Len Herzenberg. If you’d like to read more about Lee and Len’s life and scientific journey from Brooklyn College, to Cal Tech, the Pasteur Institute, the NIH, and then finally to Stanford, please visit their lab’s website where the article “A Tale of Two Lives Intertwined” is hosted.

Our condolences go out to Lee and the rest of the Herzenberg family – the world has lost a great man and he’ll be missed, both in the corridors of Stanford and in the scientific community at large.

[Edit-Dec2013] We’d like to likewise share a thoughtful memorial of Len Herzenberg offered by Garry Nolan.

October 29, 2013  |  Announcements

New FCS File Concatenation tool

Cytobank has a new section of our website dedicated to utilities designed to make interacting with data easier. The first program featured here will be a concatenation tool for combining multiple FCS files into a single file, while maintaining keywords and compatibility with Cytobank. This can be an issue when working with files generated by the Fluidigm CyTOF, as starting and stopping a run several times over the course of a single tube is not uncommon. Several other publicly available concatenation tools exist but many of them change the FCS file in subtle ways and thereby cause issues when uploading those files to Cytobank. Our new FCS file concatenation tool produces cleanly concatenated files that work seamlessly with Cytobank. If you would like help getting started with the tool or encounter any problems with installation or execution, read more on our knowledgebase. More »

September 30, 2013  |  User Stories

Cytobank User Stories: Emilie Decaup

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow and mass cytometry.

This time we interview Emilie Decaup, a Ph.D. Student at Toulouse University whose work on follicular lymphoma was recently published in the Journal of Blood Cancer.

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What are you excited about in science? What is your scientific vision?
Emilie Decaup - Ph.D. Student at Toulouse University
Emilie Decaup – Ph.D. Student at Toulouse University

I am really excited by cancer research. There is so much to do and to discover particularly for therapy. It is a domain in perpetual evolution with ever new therapeutic targets and drugs. Technological advances in biomedical research allow us to learn more. Flow cytometry is a technique that I particularly appreciate because it is really powerful especially for studying mechanisms of action of therapeutic agents like monoclonal antibodies. New technical approaches like fluorescent cell barcoding simplify experiments with lot of samples and allow straightforward drug screening. I think that technological advances will allow researchers to be more efficient. More »

August 31, 2013  |  Education

Cytometry for Interns II

Previously on my first blog post, I had written about the fluorescence PBMC experiment. Since then, I performed the same experiment on CyTOF. The setup of this experiment was easier due to my previous experience. However, it was my first time running the experiment on a mass cytometer. This link includes details on how the CyTOF machine works and also how data is collected.

Some of the materials were similar to those of the fluorescence experiment, including the stimulations. The protocol for the 17-parameter experiment can be found here.
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August 31, 2013  |  User Stories

Cytobank User Stories: Manfred Claassen, Ph.D.

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow and mass cytometry.

This time we interview Manfred Claassen, Ph.D., an Assistant Professor for Computational Biology at the Institute for Molecular Systems Biology at ETH Zurich, Switzerland.

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What are you excited about in science? What is your scientific vision?
Manfred Claassen, Ph.D. - Assistant Professor ETH Zurich
Manfred Claassen, Ph.D. – Assistant Professor ETH Zurich

I am deeply impressed by the power of interdisciplinary approaches to elegantly, concisely and yet conclusively describe seemingly overwhelming complex biological phenomena and diseases by means of well-established scientific and sound mathematical principles. We are living in a time where the technological advances in biology enable us to map out these phenomena at ever increasing breadth and resolution. I believe that in the future we will be able to generically make use of these technologies to routinely draw scientific conclusions or design clinical interventions. To achieve this goal we still have to develop an appropriate language to describe and simulate complex biological systems at the right scale. It will be exciting to contribute to this endeavor. More »

July 31, 2013  |  User Stories

Cytobank User Stories: Benjamin Spurgeon

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of flow and mass cytometry.

This time we interview Benjamin Spurgeon a PhD student in Professor Khalid Naseem’s Thrombosis & Hemostasis Research Laboratory at the Centre for Cardiovascular and Metabolic Research, Hull York Medical School, Hull, UK.

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What are you excited about in science? What is your scientific vision?
Benjamin Spurgeon - PhD student
Benjamin Spurgeon – PhD student

I am particularly excited about the development of methods for the identification of novel therapeutic agents. Flow cytometry provides a powerful platform for drug screening because of its inherent capability to discern specific cell populations from heterogeneous mixtures. Using flow cytometry, we can therefore evaluate the efficacy of drug compounds in the physiologic milieu of whole blood. Additionally, flow cytometry can be (and is being) used to assess the efficacy of therapeutic regimens. My vision concerns the development of flow cytometry systems suitable for rapid and convenient monitoring of drug therapies. More »

July 31, 2013  |  Education, Flow Cytometry

Cytometry for Interns

As a summer intern at Cytobank, the past few months have been busy and interesting to say the least. I am currently an undergraduate from the University of Redlands in Southern California. Although I have only been exposed to two years of introductory science courses, I have found that not only has it been easy to adjust to the research environment at the Nolan Lab at Stanford and the collegial atmosphere of Cytobank Inc, it has also been remarkably manageable to learn about flow cytometry.

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