Green Fluorescent Blog

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42 posts · 21,850 views

A blog on fluorescent microscopy in biological research

Gal Haimovich
42 posts

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  • April 14, 2015
  • 03:36 PM
  • 270 views

Tracking membranes by imaging – mCLING and surface glycans

by Gal Haimovich in Green Fluorescent Blog

Living cells exhibit many types of membranes which participate in most biological precesses, one way or another. Imaging membranes is usually acheived by two types of reagents: chemical dyes or fluorescent proteins that are targeted to the membrane itself or … Continue reading →... Read more »

Jiang H, English BP, Hazan RB, Wu P, & Ovryn B. (2015) Tracking surface glycans on live cancer cells with single-molecule sensitivity. Angewandte Chemie (International ed. in English), 54(6), 1765-9. PMID: 25515330  

Revelo NH, Kamin D, Truckenbrodt S, Wong AB, Reuter-Jessen K, Reisinger E, Moser T, & Rizzoli SO. (2014) A new probe for super-resolution imaging of membranes elucidates trafficking pathways. The Journal of cell biology, 205(4), 591-606. PMID: 24862576  

  • March 23, 2015
  • 12:39 PM
  • 237 views

Visualizing translation: insert TRICK pun here

by Gal Haimovich in Green Fluorescent Blog

Unlike transcription, it is much harder to image translation at the single molecule level. The reasons are numerous. For starters, transcription sites (TS) are fairly immobile, whereas mRNAs, ribosomes and proteins move freely in the cytoplasm, often very fast. Then … Continue reading →... Read more »

Halstead JM, Lionnet T, Wilbertz JH, Wippich F, Ephrussi A, Singer RH, & Chao JA. (2015) Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals. Science (New York, N.Y.), 347(6228), 1367-671. PMID: 25792328  

Dieterich DC, Hodas JJ, Gouzer G, Shadrin IY, Ngo JT, Triller A, Tirrell DA, & Schuman EM. (2010) In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons. Nature neuroscience, 13(7), 897-905. PMID: 20543841  

Rodriguez, A., Shenoy, S., Singer, R., & Condeelis, J. (2006) Visualization of mRNA translation in living cells. The Journal of Cell Biology, 175(1), 67-76. DOI: 10.1083/jcb.200512137  

  • January 28, 2015
  • 07:48 AM
  • 236 views

Transcription caught on camera part 2: Fab-ulous Histones

by Gal Haimovich in Green Fluorescent Blog

In eukaryotes, the DNA is packages tightly in nucleosomes, which are composed primarily out of histone proteins. There are four major types of histones (1,2,3 & 4). Extensive work has been done on how histones facilitate and regulate transcription. It … Continue reading →... Read more »

Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG.... (2014) Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature, 516(7530), 272-5. PMID: 25252976  

  • January 4, 2015
  • 07:46 AM
  • 323 views

In the right place at the right time: visualizing and understanding mRNA localization

by Gal Haimovich in Green Fluorescent Blog

The title of this post is also the title of a review paper that I co-authored  with Adina Buxbaum, a recently graduated PhD student from Rob Singer’s lab. The review was published last week in Nature Reviews Molecular Cell biology. … Continue reading →... Read more »

  • December 15, 2014
  • 02:39 AM
  • 305 views

Transcription caught on camera part 1: Halo transcription factors

by Gal Haimovich in Green Fluorescent Blog

Transcription factors (TFs) have a fundamental role is regulating gene expression. The basic model, based on numerous biochemical analyses, have determined where TFs bind (usually at specific sites at or near promoters), when they bind the DNA (at a resolution … Continue reading →... Read more »

Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, Legant W, Dahan M, Lionnet T, Betzig E.... (2014) Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell, 156(6), 1274-85. PMID: 24630727  

  • June 20, 2014
  • 12:57 PM
  • 465 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
  • 435 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
  • 519 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
  • 471 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
  • 826 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
  • 551 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
  • 457 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
  • 410 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
  • 455 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
  • 486 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
  • 522 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
  • 592 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
  • 711 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
  • 522 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
  • 617 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 »

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