Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.

Shotgun proteomics aims to identify and quantify the thousands of proteins in complex mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid chromatography coupled with tandem mass spectrometry and typically generates hundreds of thousands of mass spectra that require specialized computational environments for data analysis. PatternLab for proteomics is a unified computational environment for analyzing shotgun proteomic data. PatternLab V (PLV) is the most comprehensive and crucial update so far, the result of intensive interaction with the proteomics community over several years. All PLV modules have been optimized and its graphical user interface has been completely updated for improved user experience. Major improvements were made to all aspects of the software, ranging from boosting the number of protein identifications to faster extraction of ion chromatograms. PLV provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing for both labeled and label-free quantitation. The PepExplorer module can even pinpoint de novo sequenced peptides not already present in the database. PLV is of broad applicability and therefore suitable for challenging experimental setups, such as time-course experiments and data handling from unsequenced organisms. PLV interfaces with widely adopted software and community initiatives, e.g., Comet, Skyline, PEAKS and PRIDE. It is freely available at http://www.patternlabforproteomics.org .

Proteomics pinpoints alterations in grade I meningiomas of male versus female patients.

Meningiomas are among the most common primary tumors of the central nervous system (CNS) and originate from the arachnoid or meningothelial cells of the meninges. Surgery is the first option of treatment, but depending on the location and invasion patterns, complete removal of the tumor is not always feasible. Reports indicate many differences in meningiomas from male versus female patients; for example, incidence is higher in females, whereas males usually develop the malignant and more aggressive type. With this as motivation, we used shotgun proteomics to compare the proteomic profile of grade I meningioma biopsies of male and female patients. Our results listed several differentially abundant proteins between the two groups; some examples are S100-A4 and proteins involved in RNA splicing events. For males, we identified enriched pathways for cell-matrix organization and for females, pathways related to RNA transporting and processing. We believe our findings contribute to the understanding of the molecular differences between grade I meningiomas of female and male patients.

The ribosome assembly factor Nop53 controls association of the RNA exosome with pre-60S particles in yeast.

Eukaryotic ribosomal biogenesis is a high-energy-demanding and complex process that requires hundreds of trans-acting factors to dynamically build the highly-organized 40S and 60S subunits. Each ribonucleoprotein complex comprises specific rRNAs and ribosomal proteins that are organized into functional domains. The RNA exosome complex plays a crucial role as one of the pre-60S-processing factors, because it is the RNase responsible for processing the 7S pre-rRNA to the mature 5.8S rRNA. The yeast pre-60S assembly factor Nop53 has previously been shown to associate with the nucleoplasmic pre-60S in a region containing the "foot" structure assembled around the 3' end of the 7S pre-rRNA. Nop53 interacts with 25S rRNA and with several 60S assembly factors, including the RNA exosome, specifically, with its catalytic subunit Rrp6 and with the exosome-associated RNA helicase Mtr4. Nop53 is therefore considered the adaptor responsible for recruiting the exosome complex for 7S processing. Here, using proteomics-based approaches in budding yeast to analyze the effects of Nop53 on the exosome interactome, we found that the exosome binds pre-ribosomal complexes early during the ribosome maturation pathway. We also identified interactions through which Nop53 modulates exosome activity in the context of 60S maturation and provide evidence that in addition to recruiting the exosome, Nop53 may also be important for positioning the exosome during 7S processing. On the basis of these findings, we propose that the exosome is recruited much earlier during ribosome assembly than previously thought, suggesting the existence of additional interactions that remain to be described.

Phytoseiid mites (Acari: Phytoseiidae) associated with tropical ornamental plants, with a checklist and a key to the species of Bahia, Brazil.

Twenty-four papers refer to phytoseiid mites from different plant species in the state of Bahia, northeastern Brazil, but none of those refer to taxonomic surveys on ornamental plants. The aim of this study was to determine phytoseiids from tropical ornamentals in the southern coastal region of Bahia state, as well as to present a checklist and an identification key to the species recorded in that state. Samples were collected at eight localities of five municipalities. A total of seventeen species in nine genera was found on fifteen plant species of the families Costaceae, Heliconiaceae, Musaceae and Zingiberaceae. The most frequent and abundant phytoseiid species were Iphiseiodes metapodalis (El-Banhawy), Amblyseius operculatus De Leon and Iphiseiodes zuluagai Denmark & Muma, respectively. The checklist and the identification key to the Phytoseiidae species of Bahia were prepared based on the published literature.

Quantitative proteomic analysis of the Saccharomyces cerevisiae industrial strains CAT-1 and PE-2.

Brazilian ethanol fermentation process commonly uses baker's yeast as inoculum. In recent years, wild type yeast strains have been widely adopted. The two more successful examples are PE-2 and CAT-1, currently employed in Brazilian distilleries. In the present study, we analyzed how these strains compete for nutrients in the same environment and compared the potential characteristics which affect their performance by applying quantitative proteomics methods. Through the use of isobaric tagging, it was possible to compare protein abundances between both strains during the fermentation process. Our results revealed a better fermentation performance and robustness of CAT-1 strain. The proteomic results demonstrated many possible features that may be linked to the improved fermentation traits of the CAT-1. Proteins involved in response to oxidative stress (Sod1 and Trx1) and trehalose synthesis (Tps3) were more abundant in CAT-1 than in PE-2 after a fermentation batch. Tolerance to oxidative stress and trehalose accumulation were subsequently demonstrated to be enhanced for CAT-1, corroborating the comparative proteomic results. The importance of trehalose and the antioxidant system was confirmed by using mutant stains deleted in Sod1, Trx1 or Tps3. These deletions impaired fermentation performance, strengthening the idea that the abilities of accumulating high levels of trehalose and coping with oxidative stress are crucial for improving fermentation. SIGNIFICANCE: The importance of the present works emerges from the necessity to better understand the peculiar biological features from two important bioethanol industrial strains of Saccharomyces cerevisiae during batch fermentation. We applied an iTRAQ-based quantitative proteomics analysis to compare these two important strains during batch fermentation and identified possible features involved in the fermentation performance. The results provided by this work will serve as an initial framework for future investigations on the biology of both strains.