J. K. Wickiser Lab

Posts Tagged ‘Current Literature’

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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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Patenting Genes and naturally occuring small molecules

Friday, November 4, 2011

Interesting piece by NPR on the patenting of natural products:

http://www.npr.org/2011/10/24/141429392/deadly-monopolies-patenting-the-human-body?sc=fb&cc=fp

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Enzymatic networks

Monday, October 17, 2011

This group analyzes enzyme networks for robustness and dynamics.

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The essential genome of a bacterium: wants versus needs.

Tuesday, October 11, 2011

Lucy Shaprio and colleagues have identifed the minimal set of genes required for caulobacter to thrive on rich media. This work will help others bioengineer the organism to function in a variety of roles involving the production of small molecule metabolites and the generation of biosensor systems.

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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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Top 7 papers in Molecular Biology from F1000

Monday, September 12, 2011

Here are the top 7 papers in Molecular Biology ranked by F1000. Roger Tsien keeps hitting them out of the park. Cool stuff.

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In silico selection of RNA aptamers.

Sunday, August 21, 2011

Here is a review of some interesting work in the evolution of aptamers in the test tube.

“In this paper, Chushak and Stone develop a new method for more efficient RNA screening.

Many systematic efforts for the design of RNAs with tailored functions have been reported in recent years, and some of these novel RNAs have important technological and medical applications. Indeed, in vitro selection technology has been widely used for this purpose and has been successful at discovering new synthetic RNAs with high affinity and selectivity to a range of targets, including antibiotics and proteins. However, practice quickly revealed that RNA random pools are not structurally diverse and, in fact, that complex motifs are rare. Because random pool generation and analysis lends itself to computation, many computational frameworks have also been developed to mimic in vitro selection in silico. Challenges in such efforts remain the large size of sequence pools and the development of efficient ways to evaluate function of the generated candidates. As parallel networks of computers are more readily available, the size challenge can be surmounted, for example, as reported in a recent computational approach that combined nucleotide transition probability matrices, motif filtering, and supercomputing {1,2}. However, the second challenge of assessing functionality from 3D structures remains. Chushak and Stone combine ideas of directed evolution and those above in a multi-step large-pool generation approach by selecting RNA aptamers based on 2D pattern searching, 3D structure generation, and screening for target binding using docking programs. They show that an initial set of order 10^{13} to 10^{14} candidates can be reduced by nine orders of magnitude with this approach. The resulting candidates can serve viable candidates for further experimentation by in vitro technology or microarray applications for aptamer design.

NB: I am an author on refs {1,2}.

References:
{1} Kim et al. RNA 2007, 13:478-92 [PMID:17322501].
{2} Kim et al. Nucleic Acids Res 2010, 38:e139 [PMID:20448026].
Competing interests: None declared”

Cite this evaluation
Schlick T: “In this paper, Chushak and Stone develop a new method for more efficient RNA screening…” Evaluation of: [Chushak Y, Stone MO. In silico selection of RNA aptamers. Nucleic Acids Res. 2009 Jul; 37(12):e87; doi: 10.1093/nar/gkp408]. Faculty of 1000, 28 Mar 2011. F1000.com/1255974

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High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

Friday, August 19, 2011

Here’s an evaluation of from the Faculty of 1000.

“Here is a method for determining, in a single experiment, rates of synthesis and decay of mRNAs, individually or genome-wide.

Modifying previously published procedures, the authors use 4-thiouridine (4-thio-U) for pulse-labeling newly synthesized RNA in mammalian cells. After RNA isolation, RNA containing 4-thio-U is selectively biotinylated. This newly synthesized RNA is separated from ‘old’ RNA, and all three fractions — total, new and old — can be analyzed, e.g. by microarrays. Rates of synthesis and decay are obtained from simple equations. The method can potentially replace separate determinations of synthesis and decay rates. Nuclear run-on experiments to determine rates of synthesis are tedious and based on assumptions. Actinomycin-D time courses for analysis of RNA decay run the risk of interfering with the process that is to be measured and cannot measure long half-lives reliably. Actinomycin-D can be avoided through the use of regulated promoters, but this almost invariably requires a separate construct to be made for every transcript to be examined. 4-thio-U labeling looks like an attractive alternative.

For a recent application of the procedure and its adaptation to Saccharomyces cerevisiae, please see ref. {1}.

References:
{1} Miller et al. Mol Syst Biol 2011, 7:458 [PMID:21206491].
Competing interests: None declared”

Citation:
Wahle E: “Here is a method for determining, in a single experiment, rates of synthesis and decay…” Evaluation of: [Dölken L et al. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA. 2008 Sep; 14(9):1959-72; doi: 10.1261/rna.1136108]. Faculty of 1000, 18 Apr 2011. F1000.com/9679960

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Modification of gene duplicability during the evolution of protein interaction network

Thursday, August 18, 2011

From a review of this paper in the Faculty of 1000.

“This paper is interesting as it highlights important aspects of gene duplicability and the maintenance of network structures throughout evolution. It reports the differences found in human networks, which have important consequences for disease.

Previous studies have shown that, in most species, highly connected proteins in protein-protein interaction networks are usually singleton proteins, while, in mouse and human, highly connected developmental proteins are usually duplicated genes. Here, the authors look at duplication and networks for proteins originating at different points in the evolutionary tree. They find that, although there are a core of ancient singleton genes that maintain a high connectivity in all four organisms studied (human, fly, yeast and Escherichia coli), there are genes that arose from duplication after the metazoan or vertebrate splits, which are highly connected hubs. They show that these duplicated genes tend to have regulatory functions, while the singleton hubs tend to have basic cellular functions. They look further into these duplicated hubs and find that they tend to have arisen from whole genome duplication, or have micro (mi)RNA targets, or have tissue-specific expression, all of which provide some sort of gene-dosage balance to the network, thus maintaining the network structure. They previously reported that cancer genes are more often singleton hubs, and show here that cancer genes can also be duplicated hubs that arose within the metazoan branch.
Competing interests: None declared”

Citation: Mulder N: “This paper is interesting as it highlights important aspects of gene duplicability and the maintenance…” Evaluation of: [D'Antonio M, Ciccarelli FD. Modification of gene duplicability during the evolution of protein interaction network. PLoS Comput Biol. 2011 Apr; 7(4):e1002029; doi: 10.1371/journal.pcbi.1002029]. Faculty of 1000, 16 May 2011. F1000.com/10521956

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Oxidative stress response and gene expression with atrazine exposure in adult female zebrafish

Friday, August 12, 2011

From Hannah Lachance as she was perusing the literature: Atrazine (ATZ) is a herbicide that runs off from agricultural facilities into the ground and surface water sources. ATZ is suspected to be a cause of oxidative stress in fish because it interferes with reactive oxygen species (ROS) production and different endpoints. Fish species, such as Zebrafish have an antioxidant defense system that helps them limit damage from oxidative stress. Therefore, measuring antioxidant enzyme activity was used to measure oxidative stress levels. This study analyzed the liver and ovaries of adult female zebra fish to determine oxidative stress levels caused by ATZ. The oxidative stress levels we determined by the MDA and GSH content as well as by the activities of SOD and CAT. Oxidation stress levels were also measured by analyzing the gene expression of Cu/Zn-Sod, Mn-Sod, Cat, and Gpx which are antioxidant proteins. The ROS production, the respiratory chain, and ATP synthase in the liver were also monitored through analyzing the transcription of mitochondrial inner membrane genes related to these processes. The subjects of this experiment were 5 month-old, healthy, female zebrafish weighing between 0.08g and 0.52g that were randomly selected for the different experimental and control groups . All the fish were kept on a 14h light/10h dark cycle and feed brine shrimp two times a day. The experimental groups based on the different concentrations of ATZ; 1,10, 100, and 1000ug L-1 of ATZ were in water containing 0.2% acetone. The control group was in water with 0.2% acetone and no ATZ. Each experimental group consisted of 10 fish in 3L of the water ATZ mixture. The zebrafish were exposed to the solutions for 14 days after which the livers and ovaries were harvested and divided into pooled samples; 4 pooled samples for enzyme extraction and biochemical analysis, 4 pooled samples for RNA extraction and mRNA transcription analysis. RNA was isolated from the liver and ovaries using TRIzol. In order to verify the quality of the RNA, gels containing 1% agarose formaldehyde gel and the 260nm/280nm ratio were used. cDNA was then synthesized through a reverse transcriptase kit. PCR and Q-PCR (using syber green and ∆∆Ct) were preformed and oligonucleotide primers were used to detect the gene expression of the oxidative stress indicators. The results showed that the SOD and CAT activity increased sequentially (low concentration to high concentration) in the liver but not so much in the ovaries. GSH levels decreased and MDA levels increased in a dose dependent manner in the liver but on the GSH levels changed in the ovaries. mRNA levels of Mn -Sod and Cu/Zn- Sod increased significantly in the liver but neither changed in the ovaries. Cat and Gpx increased at the 100ug L-1 level in the liver but no change in the ovaries. This suggest that the ovaries are less susceptible to oxidative stress caused by ATZ. Bcl-2 decreased and Ucp-2 increased yet Ndi, Coxl, and ATPo6 showed no signs of change. All of these results show that the liver is actively reacting to the ATZ trying to prevent oxidative stress.

Zebrafish

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