21 posts · 3,771 views
A blog on fluorescent microscopy in biological research
Gal Haimovich
21 posts
Sort by: Latest Post, Most Popular
View by: Condensed, Full
- May 23, 2013
- 12:44 PM
- 13 views
If you chew that mRNA, you must make a new one!
by Gal Haimovich in Green Fluorescent Blog
Gene expression is very complex. My paper, which was published in Cell today, just shows that it is more complicated than previously realized. Traditionally, eukaryotic gene expression is divided into five steps: Transcription (mRNA synthesis): this step is subdivided into … Continue reading →... Read more »
Haimovich, G., Medina, D., Causse, S., Garber, M., Millán-Zambrano, G., Barkai, O., Chávez, S., Pérez-Ortín, J., Darzacq, X., & Choder, M. (2013) Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis. Cell, 153(5), 1000-1011. DOI: 10.1016/j.cell.2013.05.012
Haimovich G, Choder M, Singer RH, & Trcek T. (2013) The fate of the messenger is pre-determined: A new model for regulation of gene expression. Biochimica et biophysica acta, 1829(6-7), 643-53. PMID: 23337853
- May 14, 2013
- 03:33 PM
- 32 views
Those repair crews work fast!
by Gal Haimovich in Green Fluorescent Blog
Super-resolution microscopy can potentially allow imaging of single protein molecules. A new paper now tracks single Pol and Lig proteins in E. coli, as they repair DNA damage. The researchers replaced the endogenous proteins with proteins tagged with a photoactivatable mCherry (PAmCherry). … Continue reading →... Read more »
Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, & Kapanidis AN. (2013) Single-molecule DNA repair in live bacteria. Proceedings of the National Academy of Sciences of the United States of America, 110(20), 8063-8068. PMID: 23630273
- April 30, 2013
- 10:56 AM
- 54 views
New and improved – the next generation of GFP?
by Gal Haimovich in Green Fluorescent Blog
A new and improved green fluorescent protein, named mNeonGreen, was developed. It was engineered from a Yellow fluorescent protein (LanYFP) that was isolated from the cephalochordate Branchiostoma lanceolatum. Therefore, LanYFP is genetically unrelated to the commonly used Aequorea victoria GFP. LanYFP has … Continue reading →... Read more »
Shaner NC, Lambert GG, Chammas A, Ni Y, Cranfill PJ, Baird MA, Sell BR, Allen JR, Day RN, Israelsson M.... (2013) A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nature methods, 407-409. PMID: 23524392
- April 25, 2013
- 05:10 PM
- 63 views
FISH-Quant: the sequel
by Gal Haimovich in Green Fluorescent Blog
As promised, I started using FISH-Quant to analyze my FISH images. I must say that I enjoy using FQ much better than the previous program that was developed by one of my lab members. I find FQ more intuitive, more informative, … Continue reading →... Read more »
Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E., Darzacq, X., & Zimmer, C. (2013) FISH-quant: automatic counting of transcripts in 3D FISH images. Nature Methods, 10(4), 277-278. DOI: 10.1038/nmeth.2406
- April 11, 2013
- 11:02 AM
- 104 views
Looking through the brain with CLARITY!
by Gal Haimovich in Green Fluorescent Blog
Imaging single-layers of cells is very easy since the light can penetrate the cells quite easily. Imaging a tissue sample of several layers of cells is more difficult, because the passage of light is gradually block. To image a whole organ … Continue reading →... Read more »
Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A., Davidson, T., Mirzabekov, J., Zalocusky, K., Mattis, J., Denisin, A.... (2013) Structural and molecular interrogation of intact biological systems. Nature. DOI: 10.1038/nature12107
- March 29, 2013
- 11:43 AM
- 108 views
FISH-quant, a new RNA-FISH analysis tool
by Gal Haimovich in Green Fluorescent Blog
RNA FISH is a powerfull tool to measure not only the amount of mature mRNAs in the cytoplasm (or other compartments) but also to asses the amount of nascent transcripts that are still at the transcription site. These nascent transcripts are RNAs … Continue reading →... Read more »
Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E., Darzacq, X., & Zimmer, C. (2013) FISH-quant: automatic counting of transcripts in 3D FISH images. Nature Methods, 10(4), 277-278. DOI: 10.1038/nmeth.2406
- February 21, 2013
- 08:19 AM
- 155 views
RNAScope – a new FISH in the sea
by Gal Haimovich in Green Fluorescent Blog
I recently started a collaboration that involves the use of the RNAScope method. So here’s a short overview of the method. FISH is a very useful method to observe and quantify specific RNA species in situ. Yet, a major issue … Continue reading →... Read more »
Wang F, Flanagan J, Su N, Wang LC, Bui S, Nielson A, Wu X, Vo HT, Ma XJ, & Luo Y. (2012) RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. The Journal of molecular diagnostics : JMD, 14(1), 22-9. PMID: 22166544
- February 13, 2013
- 09:00 AM
- 106 views
A new probe may enable researchers to identify drug resistant influenza viruses
by Gal Haimovich in Green Fluorescent Blog
Flu has always been a public scare issue, the latest being the “swine flu” (a.k.a H1N1 strain). One of the problems with the influenza virus is that its genome is composed of 7-8 separate pieces of RNA (an unusual case, … Continue reading →... Read more »
Tsai CS, Yen HY, Lin MI, Tsai TI, Wang SY, Huang WI, Hsu TL, Cheng YS, Fang JM, & Wong CH. (2013) Cell-permeable probe for identification and imaging of sialidases. Proceedings of the National Academy of Sciences of the United States of America, 110(7), 2466-2471. PMID: 23359711
- February 11, 2013
- 08:00 AM
- 203 views
Watching Neurons in action
by Gal Haimovich in Green Fluorescent Blog
Fluorescent sensors are important tools that can allow real-time, live, single molecule imaging of microscopic millisecond scale events. It is even better if these sensors are genetically encoded sensors (i.e. fluorescent proteins). We have already encountered the pH sensors pHluorin and … Continue reading →... Read more »
Marvin JS, Borghuis BG, Tian L, Cichon J, Harnett MT, Akerboom J, Gordus A, Renninger SL, Chen TW, Bargmann CI.... (2013) An optimized fluorescent probe for visualizing glutamate neurotransmission. Nature methods, 10(2), 162-70. PMID: 23314171
- January 7, 2013
- 01:57 PM
- 144 views
Two colors, single mRNA, and a multitude of transcription rates
by Gal Haimovich in Green Fluorescent Blog
Imaging single mRNA molecules in live cells has proved to be very useful in studying mRNA localization, as well as mRNA transcription. Specifically, by using the MS2-like systems, it is possible to follow the synthesis of single mRNAs, thus determining … Continue reading →... Read more »
Larson DR, Zenklusen D, Wu B, Chao JA, & Singer RH. (2011) Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science (New York, N.Y.), 332(6028), 475-8. PMID: 21512033
Hocine S, Raymond P, Zenklusen D, Chao JA, & Singer RH. (2012) Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nature methods. PMID: 23263691
- December 18, 2012
- 03:00 PM
- 128 views
Put that mRNA where you want it
by Gal Haimovich in Green Fluorescent Blog
How do you determine the localization of a single mRNA molecule in a living cell? Better yet – can you bring that mRNA where you want it? I have briefly mentioned the MS2 system a while back. Essentially, The MS2 system to … Continue reading →... Read more »
Katz ZB, Wells AL, Park HY, Wu B, Shenoy SM, & Singer RH. (2012) β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes , 26(17), 1885-90. PMID: 22948660
Wu B, Chao JA, & Singer RH. (2012) Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells. Biophysical journal, 102(12), 2936-44. PMID: 22735544
Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, Chao JA, Park HY, de Turris V, Lopez-Jones M, & Singer RH. (2011) A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nature methods, 8(2), 165-70. PMID: 21240280
- November 12, 2012
- 04:21 PM
- 200 views
Folding and maturation (part 3) – fluorescent timers
by Gal Haimovich in Green Fluorescent Blog
In the previous two posts, I described the directed evolution of fast folding fluorescent proteins. But why is it important? Why do we need fast folding GFP? Why do we need to know the maturation time? For most applications, it … Continue reading →... Read more »
Khmelinskii A, Keller PJ, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G.... (2012) Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nature biotechnology, 30(7), 708-14. PMID: 22729030
- October 17, 2012
- 03:13 PM
- 256 views
Folding and maturation, or how to evolve your own GFP (part 2)
by Gal Haimovich in Green Fluorescent Blog
In part 1 I discussed the directed evolution of fast-folding GFPs. These were developed for specific purposes of improving the solubility, stability and folding of the protein. Now, I will discuss the maturation step and how it was measured for … Continue reading →... Read more »
Iizuka R, Yamagishi-Shirasaki M, & Funatsu T. (2011) Kinetic study of de novo chromophore maturation of fluorescent proteins. Analytical biochemistry, 414(2), 173-8. PMID: 21459075
Yoo TH, Link AJ, & Tirrell DA. (2007) Evolution of a fluorinated green fluorescent protein. Proceedings of the National Academy of Sciences of the United States of America, 104(35), 13887-90. PMID: 17717085
- August 1, 2012
- 10:05 AM
- 264 views
Folding and maturation, or how to evolve your own GFP (part 1)
by Gal Haimovich in Green Fluorescent Blog
GFP is one of the most widely used proteins in research. Its usefulness has advanced our understanding of biology in huge leaps forward. One of the greatest advantages of GFP is that the chromophore is formed in an autocatalytyic manner, … Continue reading →... Read more »
Crameri A, Whitehorn EA, Tate E, & Stemmer WP. (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nature biotechnology, 14(3), 315-9. PMID: 9630892
Pédelacq JD, Cabantous S, Tran T, Terwilliger TC, & Waldo GS. (2006) Engineering and characterization of a superfolder green fluorescent protein. Nature biotechnology, 24(1), 79-88. PMID: 16369541
Lawrence MS, Phillips KJ, & Liu DR. (2007) Supercharging proteins can impart unusual resilience. Journal of the American Chemical Society, 129(33), 10110-2. PMID: 17665911
Fisher AC, & DeLisa MP. (2008) Laboratory evolution of fast-folding green fluorescent protein using secretory pathway quality control. PloS one, 3(6). PMID: 18545653
- July 22, 2012
- 08:00 AM
- 299 views
Virtual cell biology
by Gal Haimovich in Green Fluorescent Blog
Ever wondered how all the processes inside a living cell work together as one system, in real time? How they all collaborate with each other, affect each other? Well, wonder no more. Researchers from Stanford U. and the Craig Venter … Continue reading →... Read more »
Jonathan R. Karr1, Jayodita C. Sanghvi, Derek N. Macklin, Miriam V. Gutschow, Jared M. Jacobs, Benjamin Bolival Jr., Nacyra Assad-Garcia, John I. Glass, & Markus W. Covert. (2012) A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell, 150(2), 389-401. DOI: 10.1016/j.cell.2012.05.044
- July 18, 2012
- 04:52 PM
- 257 views
New model for gene birth
by Gal Haimovich in Green Fluorescent Blog
I decided to deviate from the regular fluorescent content and discuss a new paper just publish in Nature, entitled “Proto-genes and de novo gene birth“. Once upon a time, life was simple. We knew that we had X genes; that … Continue reading →... Read more »
Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B.... (2012) Proto-genes and de novo gene birth. Nature, 370-374. PMID: 22722833
- July 5, 2012
- 09:41 PM
- 282 views
Nature methods special issue (Part IV): systems biology in single cells
by Gal Haimovich in Green Fluorescent Blog
Systems biology is a field that aims to understand the behavior and interactions between multiple biological components, in a quantitative manner. Thus, systems biology routinely uses “-omics” analyses, on whole cell populations, yielding an average behavior of heterogenic populations. Little … Continue reading →... Read more »
Lubeck E, & Cai L. (2012) Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nature methods, 9(7), 743-748. PMID: 22660740
- July 4, 2012
- 01:13 PM
- 365 views
Nature methods special issue: focus on bioimage informatics (Part III)
by Gal Haimovich in Green Fluorescent Blog
Continuing with the Brief communications section: Rapid, accurate particle tracking by calculation of radial symmetry centers Tracking single particles is a major challenge, since in many cases the particles are smaller than the pixel size. Several image analysis methods … Continue reading →... Read more »
Parthasarathy R. (2012) Rapid, accurate particle tracking by calculation of radial symmetry centers. Nature methods. PMID: 22688415
Zhang M, Chang H, Zhang Y, Yu J, Wu L, Ji W, Chen J, Liu B, Lu J, Liu Y.... (2012) Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nature methods, 9(7), 727-729. PMID: 22581370
Krzic U, Gunther S, Saunders TE, Streichan SJ, & Hufnagel L. (2012) Multiview light-sheet microscope for rapid in toto imaging. Nature methods, 9(7), 730-733. PMID: 22660739
- July 1, 2012
- 02:26 PM
- 256 views
Nature methods special issue: focus on bioimage informatics (Part II)
by Gal Haimovich in Green Fluorescent Blog
In the second part of this series, I review four “Brief communicaions” papers. Unsupervised modeling of cell morphology dynamics for time-lapse microscopy This work, from the lab of Daniel Gerlich, provides a tool for automatic prediction and annotation of cell … Continue reading →... Read more »
Zhong Q, Busetto AG, Fededa JP, Buhmann JM, & Gerlich DW. (2012) Unsupervised modeling of cell morphology dynamics for time-lapse microscopy. Nature methods. PMID: 22635062
Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE.... (2012) An image analysis toolbox for high-throughput C. elegans assays. Nature methods, 9(7), 714-716. PMID: 22522656
Saalfeld S, Fetter R, Cardona A, & Tomancak P. (2012) Elastic volume reconstruction from series of ultra-thin microscopy sections. Nature methods, 9(7), 717-720. PMID: 22688414
Zhu L, Zhang W, Elnatan D, & Huang B. (2012) Faster STORM using compressed sensing. Nature methods, 9(7), 721-723. PMID: 22522657
- June 29, 2012
- 10:11 PM
- 241 views
Nature methods special issue: focus on bioimage informatics (Part I )
by Gal Haimovich in Green Fluorescent Blog
The July issue of Nature Methods is dedicated to microscopy. Actually, to quantitative microscopy. As the editor points out, Microscopy started as a qualitative method to visualize structures and movement of single cells and organelles. With advancement of optics on … Continue reading →... Read more »
Lelek M, Di Nunzio F, Henriques R, Charneau P, Arhel N, & Zimmer C. (2012) Superresolution imaging of HIV in infected cells with FlAsH-PALM. Proceedings of the National Academy of Sciences of the United States of America, 109(22), 8564-9. PMID: 22586087
Small A. (2012) Faster and more versatile tools for super-resolution fluorescence microscopy. Nature methods, 9(7), 655-6. PMID: 22743767
Weber M, & Huisken J. (2012) Omnidirectional microscopy. Nature methods, 9(7), 656-7. PMID: 22743768
Myers G. (2012) Why bioimage informatics matters. Nature methods, 9(7), 659-60. PMID: 22743769
Cardona A, & Tomancak P. (2012) Current challenges in open-source bioimage informatics. Nature methods, 9(7), 661-5. PMID: 22743770
Carpenter AE, Kamentsky L, & Eliceiri KW. (2012) A call for bioimaging software usability. Nature methods, 9(7), 666-70. PMID: 22743771
Caroline A Schneider, Wayne S Rasband, & Kevin W Eliceiri. (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 671-675. DOI: 10.1038/nmeth.2089
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B.... (2012) Fiji: an open-source platform for biological-image analysis. Nature methods, 9(7), 676-82. PMID: 22743772
Kankaanpää P, Paavolainen L, Tiitta S, Karjalainen M, Päivärinne J, Nieminen J, Marjomäki V, Heino J, & White DJ. (2012) BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nature methods, 9(7), 683-9. PMID: 22743773
de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y.... (2012) Icy: an open bioimage informatics platform for extended reproducible research. Nature methods, 9(7), 690-6. PMID: 22743774
Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B.... (2012) Biological imaging software tools. Nature methods, 9(7), 697-710. PMID: 22743775
topics
join us!
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
