J. K. Wickiser Lab

Posts Tagged ‘Cell Biology’

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Giant amoebas under the ocean

Monday, November 7, 2011

Brought up from deep sea studies, these amoeba are absolutely huge!

http://latimesblogs.latimes.com/nationnow/2011/10/giant-amoeba-found-mariana-trench-beneath-the-sea.html

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Network Science – making even Slime Molds sexy

Thursday, October 6, 2011

Slime molds don’t sound very exciting but researchers are using them to optimize networks ranging from highway systems to disasters emergency response procedures. In this recent NYT Science Times piece, the research of several prominent labs is showcased.

In short, these organisms live as individual soil-dwelling cells and are content to survive on their basic food source: bacteria. But when food becomes scarce, these individuals send a chemical signal out to each other and a major change in physiology and strategy takes place. Some cells will sacrifice themselves for the great good of the group by filling themselves up with a carbohydrate that stiffens them (causing death). These cells serve as a scaffold support so that other cells can use this stalk as a structure to form spores, or cellular life rafts, that are capable of weathering the starvation conditions. Only when food becomes plentiful do the spores change back into individual cells to form a new colony.

The Bionetworks group in the Network Science Center is currently studying the modes of communication between cells as they respond not only to starvation conditions, but chemical contaminants of military interest as well.

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An RNA aptamer “version” of GFP

Friday, September 16, 2011

Cool story bro: Someone wanted to track specific transcripts in vivo so they evolved an aptamer to bind a crippled fluorophore and in doing so, activate it. Yeah. Category: Things I wish I had invented.

Here’s the paper.

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Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins.

Wednesday, August 24, 2011

Here are two reviews of a cool paper detailing synthetic RNA switches in the cell.

“I found this paper interesting because the authors describe an innovative step towards engineering a regulatory system that can change the expression of targeted genes.

More importantly, their system senses specific endogenous signals defined by users and responds by directing the cells to an alternative behavior. Indeed, they showed that endogenous signalling pathways can be rerouted to induce novel cellular phenotypes, including apoptosis. Their sensing device is an RNA aptamer that, upon binding to a specific protein, changes its structure and function to modulate the alternative spicing of the gene in which it has been inserted. Their work emphasizes the efficacy and versatility of RNA aptamers for engineering gene regulation systems and hence for gene therapy.
Competing interests: None declared”

Cite this evaluation
DesGroseillers L: “I found this paper interesting because the authors describe an innovative step towards engineering a…” Evaluation of: [Culler SJ et al. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010 Nov 26; 330(6008):1251-5; doi: 10.1126/science.1192128]. Faculty of 1000, 03 Feb 2011. F1000.com/7626956

“Molecular biologists usually alter cellular functions by overexpressing, mutating, or knocking down components of transcription factor and signal transduction networks. However, a method for reprogramming cellular behavior in response to any user-defined component of endogenous signaling networks would provide an important tool both for measuring the activities of these networks and using them to tailor cellular function. Culler et al. have managed to devise such a method by engineering what they call, “RNA-based sensing actuation devices”.

Basically, these devices comprise a three-exon mini-gene with two introns. The middle exon includes a translational stop codon that prevents translation of the open reading frame (ORF) encoded in the 3’-most exon. The critical component in this system is an RNA aptamer incorporated into the intronic sequences flanking the middle exon. The aptamer is first generated by in vitro selection to bind to a specific protein ligand. The authors show that association of the specific ligand with the inserted aptamer can act to alternatively splice the mini-gene such that the middle exon containing the stop codon is either included or excluded. The mechanism through which aptamer-ligand interaction influences splicing is unclear and the exact position of the aptamer within the intronic sequences required to trigger alternative splicing must be determined empirically for each aptamer. In principle, these devices could be employed to sense any endogenous protein and to respond by expressing any protein encoded in the 3’ exon ORF.

The authors provide several compelling demonstrations that their sensing devices work quite well. For example, inclusion of an aptamer that binds phage MS2 coat protein results in expression of the green florescent protein (GFP) signal encoded in the 3’ exon ORF in response to expression of the coat protein. Moreover, treatment of cells with exogenous factors that stimulate endogenous nuclear factor kappa B (NFkB)- or Wnt-signaling pathways also produce a robust GFP signal from mini-genes with aptamers binding NFkB p65 or beta-catenin, respectively. They also show that insertion of two aptamers can increase the response and that, at least in some cases, multiple ligands act to evoke a synergistic response. Lastly, they demonstrate that the system can be employed to regulate cell fate decisions. Thus, a mini-gene designed to ‘sense’ beta-catenin and produce the herpes simplex virus thymidine kinase from the 3’ ORF will trigger cell death in the presence of Wnt ligand and the pro-drug Ganciclovir.

This work underscores the versatility of RNA as both a biological sensor and regulator and suggests that the engineering of synthetic networks is within reach (also see related perspective by Liu and Arkin {1}).

References:
{1} Liu and Arkin, Science 2010, 330:1185-6 [PMID:21109657].
Competing interests: None declared”

Cite this evaluation
Eisenman R: “Molecular biologists usually alter cellular functions by overexpressing, mutating, or knocking down components of transcription…” Evaluation of: [Culler SJ et al. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 2010 Nov 26; 330(6008):1251-5; doi: 10.1126/science.1192128]. Faculty of 1000, 19 Jan 2011. F1000.com/7626956

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Cool meeting in the near future.

Monday, August 22, 2011

NYAS meeting on synthetic biology.

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Meet the scientists of JKW Lab

Tuesday, August 9, 2011

Hi my name is Hannah Lachance and I am a laboratory technician in the JKW lab. The main project I am working on involves studying how organisms such as E. coli and B. subtilis react to RDX exposure.

Techniques I use in these experiments includes growing cell cultures in various mediums, extracting RNA and DNA, running reverse transcriptions in order to obtain cDNA, using organism specific primers to run PCR and QPCR and performing gel electrophoresis. I highly enjoy working in the lab because it helps reinforce all that I have learned in school in a very practical and meaningful way. In addition, I get to work with amazing people and have fun while learning and accumulating valuable skills.

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Naturally Obsessed: The making of a scientist

Wednesday, April 14, 2010

Too cool. I might be letting people know a little too much about me by admitting that I’ve watched it twice and it motivates me to knock out bench work.

http://www.thirteen.org/naturally-obsessed/

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Imagine the cool hyperbaric biology in this beast

Wednesday, March 31, 2010

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Polymerization – a caveat to Condensation

Friday, March 20, 2009

I remember that I did not make the point that a condensation reaction requires the production of a small molecule and that the molecule doesn’t have to be water.  In the case of nucleic acid polymerization, inorganic pyrophosphate, or PPi (the beta and gamma phosphates from the triphosphate precursor), is produced as the NMP is incorporated into the nascent chain.

Check out this transcription video but take care to note that this is a cartoon and the authors chose to show DNA as a tube rather than a double helix that gets separated in a transcription bubble as the polymerase proceeds.

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Virus Research Paper

Friday, March 20, 2009

The course website has been updated so that the Research Paper hyperlink works.  Read the document to get an idea of what is expected of you.
Trustworthy sources — the best is PubMed, although our library’s subscription list is spotty at best so many of the papers you will try and access will be unavailable.  But that shouldn’t stop you from trying as most everything on PubMed is infinitely more trustworthy than standard Google fare.

If the lack of subscriptions is annoying you can go to PubMed Central, an online repository of public-accessible journal articles.  It’s basically PubMed without some of the newest articles.

You want to stick with reviews, at least at first (click the tab titled “Review” or include the word “review” in your search parameter, e.g. “smallpox review vaccine” or “HIV AZT review”).  Find a couple of review titles that interest you and then sit down and read them.  The danger here is that many of these reviews are very well written and you might find yourself adopting phrases and sentences rather than just adopting the ideas presented and fashioning your own interpretation and presentation of the material.

Also think of figures that you might generate to help describe the virus, the cell biology, and the biochemistry involved with that virus.  You might also choose to concentrate on therapeutics for a particular virus.  What are they?  What is the mechanism?  What is the target?  Give us molecular details.

Hope this helps.

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