Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Photobacterium profundum under Pressure:A MS-Based Label-Free Quantitative Proteomics Study

Photobacterium profundum SS9 is a Gram-negative bacterium, originally collected from the Sulu Sea. Its genome consists of two chromosomes and a 80 kb plasmid. Although it can grow under a wide range of pressures, P. profundum grows optimally at 28 MPa and 15°C. Its ability to grow at atmospheric pressure allows for both easy genetic manipulation and culture, making it a model organism to study piezophily. Here, we report a shotgun proteomic analysis of P. profundum grown at atmospheric compared to high pressure using label-free quantitation and mass spectrometry analysis. We have identified differentially expressed proteins involved in high pressure adaptation, which have been previously reported using other methods. Proteins involved in key metabolic pathways were also identified as being differentially expressed. Proteins involved in the glycolysis/gluconeogenesis pathway were up-regulated at high pressure. Conversely, several proteins involved in the oxidative phosphorylation pathway were up-regulated at atmospheric pressure. Some of the proteins that were differentially identified are regulated directly in response to the physical impact of pressure. The expression of some proteins involved in nutrient transport or assimilation, are likely to be directly regulated by pressure. In a natural environment, different hydrostatic pressures represent distinct ecosystems with their own particular nutrient limitations and abundances. However, the only variable considered in this study was atmospheric pressure

Plasma Proteomic Profiling in HIV-1 Infected Methamphetamine Abusers

We wanted to determine whether methamphetamine use affects a subset of plasma proteins in HIV-infected persons. Plasma samples from two visits were identified for subjects from four groups: HIV+, ongoing, persistent METH use; HIV+, short-term METH abstinent; HIV+, long term METH abstinence; HIV negative, no history of METH use. Among 390 proteins identified, 28 showed significant changes in expression in the HIV+/persistent METH+ group over the two visits, which were not attributable to HIV itself. These proteins were involved in complement, coagulation pathways and oxidative stress. Continuous METH use is an unstable condition, altering levels of a number of plasma proteins

Salinity and Simulated Herbivory Influence Spartina alterniflora Traits and Defense Strategy

Sea level rise is expected to push saline waters into previously fresher regions of estuaries, and higher salinities may expose oligohaline marshes to invertebrate herbivores typically constrained by salinity. The smooth cordgrass, Spartina alterniflora (syn. Sporobolus alterniflorus), can defend itself against herbivores in polyhaline marshes, however it is not known if S. alterniflora’s defense varies along the mesohaline to oligohaline marsh gradient in estuaries. I found that S. alterniflora from a mesohaline marsh is better defended than plants from an oligohaline marsh, supporting the optimal defense theory. Higher salinity treatments lowered carbon content, C:N, and new stem biomass production, traits associated with a tolerance strategy, suggesting that salinity may mediate the defense response of S. alterniflora. Further, simulated herbivory increased the nitrogen content and decreased C:N of S. alterniflora. This indicates that grazing may increase S. alterniflora susceptibility to future herbivory via improved forage quality. Simulated herbivory also decreased both belowground and new stem biomass production, highlighting a potential pathway in which herbivory can indirectly facilitate marsh loss, as S. alterniflora biomass is critical for vertical accretion and marsh stability under future sea level rise scenarios

The synthetic bacterial lipopeptide Pam3CSK4 modulates respiratory syncytial virus infection independent of TLR activation

Respiratory syncytial virus (RSV) is an important cause of acute respiratory disease in infants, immunocompromised subjects and the elderly. However, it is unclear why most primary RSV infections are associated with relatively mild symptoms, whereas some result in severe lower respiratory tract infections and bronchiolitis. Since RSV hospitalization has been associated with respiratory bacterial co-infections, we have tested if bacterial Toll-like receptor (TLR) agonists influence RSVA2- GFP infection in human primary cells or cell lines. The synthetic bacterial lipopeptide Pam3-Cys-Ser-Lys4 (Pam3CSK4), the prototype ligand for the heterodimeric TLR1/TLR2 complex, enhanced RSV infection in primary epithelial, myeloid and lymphoid cells. Surprisingly, enhancement was optimal when lipopeptides and virus were added simultaneously, whereas addition of Pam3CSK4 immediately after infection had no effect. We have identified two structurally related lipopeptides without TLR-signaling capacity that also modulate RSV infection, whereas Pam3CSK4-reminiscent TLR1/2 agonists did not, and conclude that modulation of infection is independent of TLR activation. A similar TLR-independent enhancement of infection could also be demonstrated for wild-type RSV strains, and for HIV-1, measles virus and human metapneumovirus. We show that the effect of Pam3CSK4 is primarily mediated by enhanced binding of RSV to its target cells. The Npalmitoylated cystein

Vertical distribution of fish larvae in the Canaries-African coastal transition zone, in summer

13 pages, 6 figures, 2 tables.-- Printed version published Jul 2006.This study reports the vertical distribution of fish larvae during the 1999 summer upwelling season in the Canaries-African Coastal Transition Zone (the Canaries-ACTZ). The transition between the African coastal upwelling and the typical subtropical offshore conditions is a region of intense mesoscale activity that supports a larval fish population dominated by African neritic species. During the study, the thermal stratification extended almost to the surface everywhere, and the surface mixed layer was typically shallow or non-existent. Upwelling occurred on the African shelf in a limited coastal sub-area of our sampling. The vertical distributions of the entire larval fish population, as well as of individual species, were independent of the seasonal thermocline. Fish larvae and mesozooplankton were concentrated at intermediate depths regardless of the thermocline position, probably because of its weak signature and spatial and temporal variability. Day/night vertical distributions suggest that some species did not perform diel vertical migration (DVM), whereas others showed either type I DVM or type II DVM. The opposing DVM patterns of different species compensate for each other resulting in no net DVM for the larval fish population as a whole.Fieldwork was carried out as part of the CANIGO project, funded by the EU, and of the "Pelagic (EU-CICYT 1FD97-1084)" project from the Spanish Ministry of Education and the European Union

When workplace unionism in global value chains does not function well : exploring the impediments

Improving working conditions at the bottom of global value chains has become a central issue in our global economy. In this battle, trade unionism has been presented as a way for workers to make their voices heard. Therefore, it is strongly promoted by most social standards. However, establishing a well-functioning trade union is not as obvious as it may seem. Using a comparative case study approach, we examine impediments to farm-level unionism in the cut flower industry in Ethiopia. For this purpose, we propose an integrated framework combining two lenses, namely a vertical one (governance and structure of global value chains) and a horizontal one (socio-economic context). We identify 10 impediments that point to three major dimensions contributing to unionisation. These three dimensions include awareness of and interest from workers, legitimacy of trade unions, and capacity of trade unions to act. Furthermore, our results suggest that private social standards may, in certain cases, be counterproductive for the efficient functioning of trade unions. Although we argue that there is no ‘quick fix’ solution to weak workplace unionism at the bottom of global value chains, we stress the importance of considering the dynamics of, and interactions between, the impediments when designing potential support measures that mitigate negative impacts