Use of Short Amino Acid Motifs in the Computational Analysis of Protein Diversity and Function

The explosion of whole genome sequence and environmental sequence data afford us the opportunity to explore protein diversity and protein function. This is particularly exciting given the nascent field of synthetic biology. A comprehensive computational analysis of extant proteins is needed in order to define the limitations on protein structure and diversity from a bioengineering perspective. This paper focuses on defining an upper limit for protein diversity using computational approaches derived from linguistic analyses. These methods are used to make a prediction on the upper limit of unique proteins and number of highly conserved motifs. Motifs deemed highly conserved will, more than likely represent important structural components of basic proteins. Results were gathered from two large data sets: all of the currently available microbial genome sequences available from NCBI and the Global Ocean Survey data set. There were 6.6 million unique proteins at 95% amino acid identity. The majority of unique motifs in these data sets were only found once. The motifs deemed highly conserved in lifestyle groupings of organisms and individual organisms were analyzed for function based on a conserved domain search. The importance between pathogenicity and cell motility and secretion related genes and proteins was observed. These motifs represent potential new drug targets or areas of future experimentation

Kinomic Profiling of Electromagnetic Navigational Bronchoscopy Specimens: A New Approach for Personalized Medicine

Purpose Researchers are currently seeking relevant lung cancer biomarkers in order to make informed decisions regarding therapeutic selection for patients in so-called “precision medicine.” However, there are challenges to obtaining adequate lung cancer tissue for molecular analyses. Furthermore, current molecular testing of tumors at the genomic or transcriptomic level are very indirect measures of biological response to a drug, particularly for small molecule inhibitors that target kinases. Kinase activity profiling is therefore theorized to be more reflective of in vivo biology than many current molecular analysis techniques. As a result, this study seeks to prove the feasibility of combining a novel minimally invasive biopsy technique that expands the number of lesions amenable for biopsy with subsequent ex vivo kinase activity analysis. Methods Eight patients with lung lesions of varying location and size were biopsied using the novel electromagnetic navigational bronchoscopy (ENB) technique. Basal kinase activity (kinomic) profiles and ex vivo interrogation of samples in combination with tyrosine kinase inhibitors erlotinib, crizotinib, and lapatinib were performed by PamStation 12 microarray analysis. Results Kinomic profiling qualitatively identified patient specific kinase activity profiles as well as patient and drug specific changes in kinase activity profiles following exposure to inhibitor. Thus, the study has verified the feasibility of ENB as a method for obtaining tissue in adequate quantities for kinomic analysis and has demonstrated the possible use of this tissue acquisition and analysis technique as a method for future study of lung cancer biomarkers. Conclusions We demonstrate the feasibility of using ENB-derived biopsies to perform kinase activity assessment in lung cancer patients

The significance of nitrogen cost minimization in proteomes of marine microorganisms

Marine microorganisms thrive under low levels of nitrogen (N). N cost minimization is a major selective pressure imprinted on open-ocean microorganism genomes. Here we show that amino-acid sequences from the open ocean are reduced in N, but increased in average mass compared with coastal-ocean microorganisms. Nutrient limitation exerts significant pressure on organisms supporting the trade-off between N cost minimization and increased average mass of amino acids that is a function of increased A+T codon usage. N cost minimization, especially of highly expressed proteins, reduces the total cellular N budget by 2.7–10% this minimization in combination with reduction in genome size and cell size is an evolutionary adaptation to nutrient limitation. The biogeochemical and evolutionary precedent for these findings suggests that N limitation is a stronger selective force in the ocean than biosynthetic costs and is an important evolutionary strategy in resource-limited ecosystems

A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 6 (2012): 1901-1915, doi:10.1038/ismej.2012.31.Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean’ mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.CSR was supported by an NSF Postdoctoral Fellowship in Biological Informatics (DBI-0532893). The research was supported by National Science Foundation awards: ANT 0632389 (to AEM and JJG), and ANT 0632278 and 0217282 (to HWD), all from the Antarctic Organisms and Ecosystems Program

Hepatitis C virus Genie: A web 2.0 interpretation and analytics platform for the Versant Hepatitis C virus genotype Line Probe Assay version 2.0

Context: Hepatitis C virus (HCV) genotyping at our institution is performed using the Versant HCV genotype 2.0 Line Probe Assay (LiPA). The last steps of this procedure are manual, laborious, and error-prone process that involves the comparison of the banding pattern on a test strip to a physical reference table. Aim: We developed a web-based HCV genotype interpretation platform that utilizes a scanned image to generate the genotypes, thus minimizing interpretation time and reducing error. Subjects and Methods: HCV Genie 2 utilizes a database of banding patterns in conjuncture with image analysis algorithms to determine the genotype for any number of scanned LiPA strips. HCV Genie 2 is built with client-side JavaScript; allowing the program to run in the user' browser rather than on an unknown server, essentially eliminating data and patient privacy concerns. Results: HCV Genie 2 was tested over 2 months and proved identical to human expert interpretation for 148 samples (>1000 bands identified). Manual intervention was required only for two faint bands and one false-positive band; this was done utilizing the built-in-user interface. Utilizing the original method, the trained laboratory technician interpretation time for 16 samples was 13.8 (±0.96) min as compared to 5.0 (±1.09) min with HCV Genie 2, a 63.8% decrease. In addition to the time savings, the new method provides an additional validation step, which decreases the potential for errors. Conclusions: Our institution has moved exclusively to utilize the new techniques and tools described here. Both experienced technicians and the molecular pathologists at our institution prefer the workflow using HCV Genie. It is easier for the technicians to prepare and document, and the pathologists are more rapidly able to review and confirm results. The use of this tool will lead to increase the quality of patient care delivered through this test methodology by decreasing the potential for error. The algorithms developed here can be ported to similar band identification platforms, most directly to other LiPAs

Correction: Kinomic Profiling of Electromagnetic Navigational Bronchoscopy Specimens: A New Approach for Personalized Medicine.

[This corrects the article DOI: 10.1371/journal.pone.0116388.]

Basal kinomic activity profiles.

<p>Unsupervised hierarchical clustering of basal (untreated) tyrosine kinomic profiles displaying log transformed slope-exposure for (<b>A</b>) all 144 peptides and (<b>B</b>) as change from sample mean and filtered for variance >1. Red in (A) indicates relative increased signal and in (B) indicates an increase from sample mean. Blue indicates the opposite. Blue arrowhead points to red line denoting dendrogram separation. (<b>C</b>) Western blotting of GAPDH and Actin is shown with sample concentration indicated for each patient.</p

<i>Ex vivo</i> drug response profile.

<p>Displays <i>ex</i><i>vivo</i> drug response profiles as (A) a heatmap of kinase activity (log signal values) change from untreated, clustered by row, of altered phosphopeptides per patient, per dose at 20 nM, 0.5 µM or 20 µM. (B) <i>Ex vivo</i> prewash kinetic peptide phosphorylation (y axis per cell) over time (x axis per cell) of selected peptides in the selected samples, in response to indicated drugs at 20 µM. Blue lines denote untreated, and green lines indicate treated phosphorylation curves.</p

Patient characteristics and tumor evaluation.

<p>M-male; F-female; NSCLC-non small cell lung cancer; MD-PD-moderately differentiated to poorly differentiated; SBRT-stereotactic body radiotherapy.</p><p>Patient characteristics and tumor evaluation.</p