Gal Haimovich

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  • September 1, 2016
  • 06:52 AM

Roger Tsien – the scientist that colored our research

by Gal Haimovich in Green Fluorescent Blog

Roger Tsien died a few days ago, at the relatively young age of 64. He was a UCSD scientist, a Nobel laureate and he was one of the first to see the significance and usefulness of GFP. I’ve never met him. … Continue reading →... Read more »

  • June 29, 2016
  • 08:01 AM

Design guidlines for tandem fluorescent timers

by Gal Haimovich in Green Fluorescent Blog

Almost 4 years ago, I wrote a post on tandem fluorescent timers (tFTs). The idea is to have two different fluorescent proteins fused together to the protein of interest. In the paper from 4 years ago, it was superfolder GFP … Continue reading →... Read more »

Khmelinskii A, Meurer M, Ho CT, Besenbeck B, Füller J, Lemberg MK, Bukau B, Mogk A, & Knop M. (2016) Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers. Molecular biology of the cell, 27(2), 360-70. PMID: 26609072  

  • June 5, 2016
  • 02:03 PM

Counting exosome secretion

by Gal Haimovich in Green Fluorescent Blog

Last month I wrote a post about exosome internalization by recipient cells.  One of the topics I discussed was the lack of good quantitative data in the exosomal field, and what the current data tells us about the efficiency and … Continue reading →... Read more »

  • May 31, 2016
  • 05:17 AM

Imaging translation of single mRNAs in live cells

by Gal Haimovich in Green Fluorescent Blog

Translating the information encoded in mRNAs into proteins is one of the most basic processes in biology. The mechanism requires a machinery (i.e. ribosomes) and components (mRNA template, charged tRNAs, regulatory factors, energy) that are shared by all organisms on … Continue reading →... Read more »

  • May 9, 2016
  • 06:39 AM

The wild ride of the exosomes

by Gal Haimovich in Green Fluorescent Blog

Exosomes are extracellular vesicles that are thought to mediate cell-to-cell communication in eukaryotes. Briefly, exosomes are 50-100 nanometer (nm) sized vesicles produced by the endosomal system. They are exported out of the cell and can be found in every bodily … Continue reading →... Read more »

Heusermann W, Hean J, Trojer D, Steib E, von Bueren S, Graff-Meyer A, Genoud C, Martin K, Pizzato N, Voshol J.... (2016) Exosomes surf on filopodia to enter cells at endocytic hot spots, traffic within endosomes, and are targeted to the ER. The Journal of cell biology, 213(2), 173-84. PMID: 27114500  

Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, & Théry C. (2016) Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proceedings of the National Academy of Sciences of the United States of America, 113(8). PMID: 26858453  

Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN.... (2014) Quantitative and stoichiometric analysis of the microRNA content of exosomes. Proceedings of the National Academy of Sciences of the United States of America, 111(41), 14888-93. PMID: 25267620  

Tian T, Zhu YL, Hu FH, Wang YY, Huang NP, & Xiao ZD. (2013) Dynamics of exosome internalization and trafficking. Journal of cellular physiology, 228(7), 1487-95. PMID: 23254476  

Kanada M, Bachmann MH, Hardy JW, Frimannson DO, Bronsart L, Wang A, Sylvester MD, Schmidt TL, Kaspar RL, Butte MJ.... (2015) Differential fates of biomolecules delivered to target cells via extracellular vesicles. Proceedings of the National Academy of Sciences of the United States of America, 112(12). PMID: 25713383  

  • April 19, 2016
  • 12:41 PM

Does bound MS2 coat protein inhibit mRNA decay?

by Gal Haimovich in Green Fluorescent Blog

Roy Parker recently sent a  “Letter to the Editor“, published in RNA journal, in which he suggested that the MS2 system might not be best suited for live imaging of mRNA in budding yeast. According to Parker, the MS2 system … Continue reading →... Read more »

  • April 4, 2016
  • 02:41 PM

Imaging with CRISPR/Cas9

by Gal Haimovich in Green Fluorescent Blog

The hottest buzz-word in biology today is CRISPR: an adaptive immune system in bacteria and archea. At its basis is a nuclease, named Cas9, which is targeted to DNA by a short single-guide RNA (sgRNA). This turned out to be … Continue reading →... Read more »

Deng W, Shi X, Tjian R, Lionnet T, & Singer RH. (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proceedings of the National Academy of Sciences of the United States of America, 112(38), 11870-5. PMID: 26324940  

Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, & Yeo GW. (2016) Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell, 1-9. PMID: 26997482  

  • January 4, 2016
  • 11:56 AM

ASCB15 – part 3

by Gal Haimovich in Green Fluorescent Blog

(part 1, part 2) I ended part 2 Monday night. It was an exciting day with many excellent talks, but the best talk (mine, of course!) was due the next day. Tuesday started with the seminar on engineering cells and … Continue reading →... Read more »

Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, & Herr AE. (2014) Single-cell western blotting. Nature methods, 11(7), 749-55. PMID: 24880876  

  • December 31, 2015
  • 03:10 AM

ASCB15 – part 2

by Gal Haimovich in Green Fluorescent Blog

I ended Part 1 after the morning session on pushing the boundaries of imaging. After the amazing talks on imaging, I browsed the halls, visited some exhibitors, sampled a couple of exhibitor tech-talks. I later went to a mycrosymposium (#2: signaling … Continue reading →... Read more »

Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D.... (2015) In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. The Journal of cell biology, 211(6), 1121-30. PMID: 26694837  

Nelles DA, Fang MY, Aigner S, & Yeo GW. (2015) Applications of Cas9 as an RNA-programmed RNA-binding protein. BioEssays : news and reviews in molecular, cellular and developmental biology, 37(7), 732-9. PMID: 25880497  

Vale RD. (2015) Accelerating scientific publication in biology. Proceedings of the National Academy of Sciences of the United States of America, 112(44), 13439-46. PMID: 26508643  

  • November 18, 2015
  • 12:42 PM

New data on SmartFlare – do they detect mRNA?

by Gal Haimovich in Green Fluorescent Blog

Almost exactly a year ago, I wrote a post regarding my concerns with SmartFlare, supposedly a novel method for live imaging of RNA in cells. In a nutshell, SmartFlare are gold nanoparticles covered in oligos specific to a certain mRNA … Continue reading →... Read more »

David Mason,, Gemma Carolan,, Marie Held,, Joan Comenge,, & Raphael Levy. (2015) The Spherical Nucleic Acids mRNA Detection Paradox. ScienceOpen Research. DOI: 10.14293/S2199-1006.1.SOR-CHEM.AZ1MJU.v1  

  • April 14, 2015
  • 03:36 PM

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

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

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

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

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

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

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

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

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

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  

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