Green Fluorescent Blog

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37 posts · 15,553 views

A blog on fluorescent microscopy in biological research

Gal Haimovich
37 posts

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  • June 20, 2014
  • 12:57 PM
  • 233 views

Eliminating mutated mitochondria during in-vitro fertilization

by Gal Haimovich in Green Fluorescent Blog

There are several genetic diseases which originate not from mutations in the nuclear genome but mutations in the mitochondrial genome. In humans, the threshold for disease occurrence is if 60% of the mitochondria has mutated mitochondrial DNA (mtDNA) (a mixed … Continue reading →... Read more »

  • May 7, 2014
  • 09:30 PM
  • 247 views

The next evolutionary step

by Gal Haimovich in Green Fluorescent Blog

Human have always tried to improve on nature, from domestication of plants & animals through directed evolution in the test tube and GMO and up to Craig Venter’s synthetic bacteria and the expansion of the genetic code. Today, another step was taken … Continue reading →... Read more »

Malyshev, D., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J., Corrêa, I., & Romesberg, F. (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature. DOI: 10.1038/nature13314  

  • March 23, 2014
  • 05:28 PM
  • 323 views

sequencing localized RNA in single cells by FISH

by Gal Haimovich in Green Fluorescent Blog

To celebrate the 2-year anniversary of this blog, lets talk about the new Science paper in which the authors claim to performs in situ single cell, single molecule  RNA sequencing. So what’s the big deal? Well, RNA sequencing (RNA-Seq) has become a … Continue reading →... Read more »

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R.... (2014) Highly multiplexed subcellular RNA sequencing in situ. Science (New York, N.Y.), 343(6177), 1360-3. PMID: 24578530  

  • March 17, 2014
  • 12:04 PM
  • 311 views

This month’s Nature methods (part 2): optogenetics

by Gal Haimovich in Green Fluorescent Blog

Optogenetic tools are light-sensitive genetically encoded proteins that, upon light activation, affect a molecular change in the cells. In the previous post I described an optogenetic system to induce transcription. However, the most common use is of channelrhodopsin (ChR) molecules, that alter … Continue reading →... Read more »

Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z.... (2014) Independent optical excitation of distinct neural populations. Nature methods, 11(3), 338-46. PMID: 24509633  

  • March 3, 2014
  • 08:08 PM
  • 615 views

this-months-nature-methods-part-1: Spinach, blue transcription & photoacoustic imaging

by Gal Haimovich in Green Fluorescent Blog

This month’s Nature Methods issue has several interesting imaging items & articles, including two super-resolution reviews, two optogenetics articles, and more. This post will be dedicated to three items in the “tools in brief” section. Blue transcription Optogenetics usually refers to … Continue reading →... Read more »

Tools in brief. (2014) Imaging: Activatable photoacoustic probes. Nature Methods, 11(3), 230-230. DOI: 10.1038/nmeth.2868  

Motta-Mena LB, Reade A, Mallory MJ, Glantz S, Weiner OD, Lynch KW, & Gardner KH. (2014) An optogenetic gene expression system with rapid activation and deactivation kinetics. Nature chemical biology, 10(3), 196-202. PMID: 24413462  

Song W, Strack RL, Svensen N, & Jaffrey SR. (2014) Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach. Journal of the American Chemical Society, 136(4), 1198-201. PMID: 24393009  

  • February 18, 2014
  • 07:55 PM
  • 376 views

Looking at single mRNAs in neurons hints at memory formation

by Gal Haimovich in Green Fluorescent Blog

It is postulated that learning and memory are modulated by synaptic plasticity – molecular changes  that result in changes in the synapse morphology and signaling capacity. Local protein translation is considered important for synaptic plasticity. Two works from our lab … Continue reading →... Read more »

Park HY, Lim H, Yoon YJ, Follenzi A, Nwokafor C, Lopez-Jones M, Meng X, & Singer RH. (2014) Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science (New York, N.Y.), 343(6169), 422-4. PMID: 24458643  

  • January 16, 2014
  • 01:11 PM
  • 288 views

Don’t eat this FISH-STIC

by Gal Haimovich in Green Fluorescent Blog

single molecule FISH (smFISH) is a great way to detect single RNA molecules in fixed cells. The “traditional” FISH uses fluorescently labeled oligonucleotides which directly hybridize with the target RNA sequence. The two most common approaches are the use of 1-5 50-mer oligos, that are … Continue reading →... Read more »

  • January 13, 2014
  • 07:47 PM
  • 255 views

When two halves equal zero (background)

by Gal Haimovich in Green Fluorescent Blog

Fluorescent imaging is all about the contrast between the signal and the background. For imaging to be successful, the signal should be clear above the background. Background fluorescence can come from free/non-specific fluorescent probe, autofluorescence, and out of focus fluorescence. There … Continue reading →... Read more »

  • December 28, 2013
  • 03:39 PM
  • 314 views

The microscope’s light may affect your experiment

by Gal Haimovich in Green Fluorescent Blog

The conditions used for microscopy are often not “physiological” conditions. If we are talking about live imaging, then the cells are usually in culture, placed on a glass surface and grown in an artificial media. In many cases, we use … Continue reading →... Read more »

Robertson JB, Davis CR, & Johnson CH. (2013) Visible light alters yeast metabolic rhythms by inhibiting respiration. Proceedings of the National Academy of Sciences of the United States of America, 110(52), 21130-5. PMID: 24297928  

  • September 21, 2013
  • 07:31 PM
  • 328 views

Silicon nanocrystals – the next generation of fluorescent dyes?

by Gal Haimovich in Green Fluorescent Blog

Fluorescent microscopy is the only current method to follow biological structures and molecules in real-time in live specimens. Many advances were made but there are still a few problems with present fluorescent probes. Photobleaching (permanent disappearance of the fluorescent signal due … Continue reading →... Read more »

Nishimura H, Ritchie K, Kasai RS, Goto M, Morone N, Sugimura H, Tanaka K, Sase I, Yoshimura A, Nakano Y.... (2013) Biocompatible fluorescent silicon nanocrystals for single-molecule tracking and fluorescence imaging. The Journal of cell biology, 202(6), 967-83. PMID: 24043702  

  • September 6, 2013
  • 04:06 PM
  • 375 views

Imaging gene expression – methods & protocols

by Gal Haimovich in Green Fluorescent Blog

A new book in the “Methods in molecular biology” series, recently published, contains 23 imaging protocols in three major research areas: gene expression & RNA dynamics, genome & chromatin dynamics, and nuclear process & structures. This is a fairly good … Continue reading →... Read more »

Yaron Shav-Tal (Ed.). (2013) Imaging Gene Expression Methods and protocols. Methods in Molecular Biology/ Humana Press, Springer Science Business Media, LLC. DOI: 10.1007/978-1-62703-526-2  

  • September 2, 2013
  • 08:31 AM
  • 374 views

High res imaging of DNA double strand breaks: Clearing the nucleus or marking the spot

by Gal Haimovich in Green Fluorescent Blog

DNA can be damaged in many ways. Consequently, there are numerous mechanisms to repair it. It is a fascinating field full of innovative concepts (“DNA repair” was my favorite course during my undergrad studies).  Double strand breaks (DSBs) are considered the … Continue reading →... Read more »

Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, & Misteli T. (2013) Spatial dynamics of chromosome translocations in living cells. Science (New York, N.Y.), 341(6146), 660-4. PMID: 23929981  

Schermelleh L, Heintzmann R, & Leonhardt H. (2010) A guide to super-resolution fluorescence microscopy. The Journal of cell biology, 190(2), 165-75. PMID: 20643879  

  • August 9, 2013
  • 12:35 PM
  • 458 views

Nuclear pore complex at super resolution

by Gal Haimovich in Green Fluorescent Blog

It is very difficult to decipher the spatial arrangement of proteins in a given complex. The most common methods are X-ray crystallography (which is very difficult to achieve for single proteins, let alone complexes), cryo-electron microscopy  and electron tomography (ditto) … Continue reading →... Read more »

Szymborska A, de Marco A, Daigle N, Cordes VC, Briggs JA, & Ellenberg J. (2013) Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging. Science (New York, N.Y.), 341(6146), 655-658. PMID: 23845946  

Schermelleh L, Heintzmann R, & Leonhardt H. (2010) A guide to super-resolution fluorescence microscopy. The Journal of cell biology, 190(2), 165-75. PMID: 20643879  

  • August 5, 2013
  • 08:30 AM
  • 391 views

Green Fluorescent sushi

by Gal Haimovich in Green Fluorescent Blog

Fluorescent proteins have been isolated from invertebrate species only, until now.  A group of researchers from Japan isolated a green fluorescent protein from the freshwater eel called Unagi (yes, the same Unagi used for sushi). The protein, named UnaG, is smaller … Continue reading →... Read more »

Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, & Miyawaki A. (2013) A bilirubin-inducible fluorescent protein from eel muscle. Cell, 153(7), 1602-11. PMID: 23768684  

  • June 13, 2013
  • 03:53 PM
  • 491 views

Cells reach out their “hands” to create new limbs

by Gal Haimovich in Green Fluorescent Blog

Communication between cells takes many forms. There could be communication by sending out microvesicles with important messages inside, by sending out free molecules (like hormones) or by special structures (e.g. synapses). Sonic hedgehog (SHH) is a signaling protein that is important … Continue reading →... Read more »

  • June 4, 2013
  • 02:48 PM
  • 487 views

Malaria parasites send each other genes

by Gal Haimovich in Green Fluorescent Blog

Communication between cells takes many forms. There could be communication by direct contact, by sending out free molecules (like hormones) or by special structures (e.g. synapses). But how can parasites, that dwell inside their host cell, communicate with one another? … Continue reading →... Read more »

Regev-Rudzki N, Wilson DW, Carvalho TG, Sisquella X, Coleman BM, Rug M, Bursac D, Angrisano F, Gee M, Hill AF.... (2013) Cell-Cell Communication between Malaria-Infected Red Blood Cells via Exosome-like Vesicles. Cell, 153(5), 1120-33. PMID: 23683579  

  • May 23, 2013
  • 12:44 PM
  • 399 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  

  • May 14, 2013
  • 03:33 PM
  • 329 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
  • 471 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
  • 392 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  

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