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1.  Biodegradation of Polyester Polyurethane by Endophytic Fungi▿ 
Applied and Environmental Microbiology  2011;77(17):6076-6084.
Bioremediation is an important approach to waste reduction that relies on biological processes to break down a variety of pollutants. This is made possible by the vast metabolic diversity of the microbial world. To explore this diversity for the breakdown of plastic, we screened several dozen endophytic fungi for their ability to degrade the synthetic polymer polyester polyurethane (PUR). Several organisms demonstrated the ability to efficiently degrade PUR in both solid and liquid suspensions. Particularly robust activity was observed among several isolates in the genus Pestalotiopsis, although it was not a universal feature of this genus. Two Pestalotiopsis microspora isolates were uniquely able to grow on PUR as the sole carbon source under both aerobic and anaerobic conditions. Molecular characterization of this activity suggests that a serine hydrolase is responsible for degradation of PUR. The broad distribution of activity observed and the unprecedented case of anaerobic growth using PUR as the sole carbon source suggest that endophytes are a promising source of biodiversity from which to screen for metabolic properties useful for bioremediation.
doi:10.1128/AEM.00521-11
PMCID: PMC3165411  PMID: 21764951
2.  Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays 
BMC Genomics  2010;11:383.
Background
Tiling arrays have been the tool of choice for probing an organism's transcriptome without prior assumptions about the transcribed regions, but RNA-Seq is becoming a viable alternative as the costs of sequencing continue to decrease. Understanding the relative merits of these technologies will help researchers select the appropriate technology for their needs.
Results
Here, we compare these two platforms using a matched sample of poly(A)-enriched RNA isolated from the second larval stage of C. elegans. We find that the raw signals from these two technologies are reasonably well correlated but that RNA-Seq outperforms tiling arrays in several respects, notably in exon boundary detection and dynamic range of expression. By exploring the accuracy of sequencing as a function of depth of coverage, we found that about 4 million reads are required to match the sensitivity of two tiling array replicates. The effects of cross-hybridization were analyzed using a "nearest neighbor" classifier applied to array probes; we describe a method for determining potential "black list" regions whose signals are unreliable. Finally, we propose a strategy for using RNA-Seq data as a gold standard set to calibrate tiling array data. All tiling array and RNA-Seq data sets have been submitted to the modENCODE Data Coordinating Center.
Conclusions
Tiling arrays effectively detect transcript expression levels at a low cost for many species while RNA-Seq provides greater accuracy in several regards. Researchers will need to carefully select the technology appropriate to the biological investigations they are undertaking. It will also be important to reconsider a comparison such as ours as sequencing technologies continue to evolve.
doi:10.1186/1471-2164-11-383
PMCID: PMC3091629  PMID: 20565764
3.  THE RNA POLYMERASE “SWITCH REGION” IS A TARGET FOR INHIBITORS 
Cell  2008;135(2):295-307.
Summary
We report the target, biochemical basis, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the α-pyrone antibiotic myxopyronin (Myx). We show that Myx interacts with the RNAP “switch region,” the hinge that mediates opening and closing of the RNAP active-center cleft. We show that Myx prevents interaction of RNAP with promoter DNA. We present a crystal structure that defines contacts between Myx and RNAP and defines effects of Myx on RNAP conformation. We propose that Myx functions by preventing opening of the RNAP active-center cleft to permit entry of DNA during transcription initiation (“hinge jamming”). We establish further that the structurally related α-pyrone antibiotic corallopyronin and the structurally unrelated macrocyclic-lactone antibiotic ripostatin function through the same target and same mechanism. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.
doi:10.1016/j.cell.2008.09.033
PMCID: PMC2580802  PMID: 18957204

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