MS/MS studies on the selective on-line detection of sesquiterpenes using a Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS)

A Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS) was used to investigate the feasibility of selective on-line detection of a series of seven sesquiterpenes (SQTs). These SQTs were chemically ionized by either H3O+ or NO+ reagent ions in the FA, resulting among others in protonated SQT and SQT molecular ions, respectively. These and other Chemical Ionization (CI) product ions were subsequently subjected to dissociation by collisions with Ar atoms in the collision cell of the tandem mass spectrometer. The fragmentation spectra show similarities with mass spectra obtained for these compounds with other instruments such as a Proton Transfer Reaction-Linear Ion Trap (PTR-LIT), a Proton Transfer Reaction-Mass Spectrometer (PTR-MS), a Triple Quadrupole-Mass Spectrometer (QqQ-MS) and a Selected Ion Flow Tube-Mass Spectrometer (SIFT-MS). Fragmentation of protonated SQT is characterized by fragment ions at the same masses but with different intensities for the individual SQT. Distinction of SQTs is based on well-chosen intensity ratios and collision energies. The fragmentation patterns of SQT molecular ions show specific fragment ion tracers at m/z 119, m/z 162, m/z 137 and m/z 131 for alpha-cedrene, delta-neoclovene, isolongifolene and alpha-humulene, respectively. Consequently, chemical ionization of SQT by NO+, followed by MS/MS of SQT(+) seems to open a way for selective quantification of SQTs in mixtures

Structural and functional consequences of c-N-Ras constitutively associated with intact mitochondria

AbstractWe demonstrate that both c-N-Ras and c-K(B)-Ras are constitutively associated with purified mitochondria. c-K(B)-Ras is associated with the mitochondrial outer membrane, and c-N-Ras is associated with both the outer membrane and inner mitochondrial compartments. The mitochondrial morphology is abnormal in both c-N-Ras negative and K-Ras negative cells. Normal mitochondrial morphology was restored by targeting N-Ras to both the inner and outer mitochondrial compartments, or by ectopically expressing c-K(B)-Ras. Impaired mitochondrial function can result in increased CHOP and NFκB activity, typical for a retrograde signaling response. Both are constitutively elevated in the N-Ras negative cells, but not in the K-Ras negative background, and are restored by c-N-Ras targeted exclusively to the inner mitochondrial compartment. Surprisingly, both targeting and the ability to functionally reduce retrograde transcriptional activity were found to be independent of c-N-Ras farnesylation. Overall, these data demonstrate for the first time a (1) farnesylation independent function for c-N-Ras and (2) that N-Ras within the inner mitochondrial compartment is an essential component of the retrograde signaling system between the mitochondria and nucleus

Environmental stress is the major cause of transcriptomic and proteomic changes in GM and non-GM plants

The approval of genetically modified (GM) crops is preceded by years of intensive research to demonstrate safety to humans and environment. We recently showed that in vitro culture stress is the major factor influencing proteomic differences of GM vs. non-GM plants. This made us question the number of generations needed to erase such “memory”. We also wondered about the relevance of alterations promoted by transgenesis as compared to environment-induced ones. Here we followed three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout eight generations after transgenesis combining proteomics and transcriptomics, and further analyzed their response to salinity stress on the F6 generation. Our results show that: (a) differences promoted during genetic modification are mainly short-term physiological changes, attenuating throughout generations, and (b) environmental stress may cause far more proteomic/transcriptomic alterations than transgenesis. Based on our data, we question what is really relevant in risk assessment design for GM food crops.This work was supported by Fundação para a Ciência e a Tecnologia (FCT) Project PTDC/EBB-BIO/098983/2008 and research unit GREEN-it “Bioresources for Sustainability” (UID/Multi/04551/2013). S.N. acknowledges funding from King Abdullah University of Science and Technology (KAUST).info:eu-repo/semantics/publishedVersio

Proteomic analysis of three Coffee Leaf Rust races with different pathogenic behavior

info:eu-repo/semantics/publishedVersio

Flowering under stress: phenomics and proteomics approaches to chickpea grain yield and quality.

Chickpea (Cicer arietinum) is a major player in the FAO Zero Hunger program “toolkit”. It is the second most cultivated food legume, a source of sustainable protein (and other nutrients) and contributes to improved soil health and lower fertilization input. Grain yield, seed protein content and nutritional quality were found to be largely affected by Genotype x Environment. In the Mediterranean regions, higher frequency, intensity and duration of droughts, as well as hotter droughts are being registered, thus interfering with agroecosystems’ structure, composition, and functions. A controlled conditions assay (non-invasive phenotyping@PhenoLab) was undertaken in two genotypes from the Portuguese chickpea breeding program (Elvas, INIAV). Results revealed that high temperature (32º C during the reproductive phase) and water regime (40% vs 10% soil water content) play a significant role in chickpea development, seed production and composition, and protein content. As seed biochemical signatures allow to discriminate between genotypes, the power protein-based methodologies in genotype assessment are highlighted. Because some proteins can resist gastrointestinal digestion and influence human health, the processed seed proteome (i.e. following soaking, boiling and in-vitro digestion) in three consecutive years was further analysed in field-grown chickpeas (Elvas, INIAV). The seed proteome was found to be highly conserved, with minor changes being attributed to the seed development conditions. Furthermore, in vitro digestion efficiently removed many anti-nutritional proteins. Combined phenotyping and omic´s approaches contribute to the mechanistic knowledge of how severe terminal drought and high temperature modulate sink capacity and productivity (yield and quality). The integrated use of phenomics and omics methodologies has significant potential to increase our understanding of plant growth and development and, thus, an efficient, knowledge-based management of crops and resources.Work supported by EMPHASIS-GO (HORIZON-INFRA-2021-DEV-02 contract n. 101079772), by the European Plant Phenotyping Network 2020 (EXCELLENT SCIENCE - Research Infrastructures contract n. 731013) and by national funds from FCT - Fundação para a Ciência e a Tecnologia, I.P. namelly: UCIBIO – Research Unit on Applied Molecular Biosciences (FCT UIDP/04378/2020; FCT UIDB/04378/ 2020); 4HB - Associate Laboratory Institute for Health and Bioeconomy (FCT LA/P/0140/2020); LEAF – Linking Landscape, Environment, Agriculture and Food (FCT UID/AGR/04129/2020); PhD fellowship SFRH/BD/70345/2010.info:eu-repo/semantics/publishedVersio

On the well-posedness for the Ideal MHD equations in the Triebel-Lizorkin spaces

In this paper, we prove the local well-posedness for the Ideal MHD equations in the Triebel-Lizorkin spaces and obtain blow-up criterion of smooth solutions. Specially, we fill a gap in a step of the proof of the local well-posedness part for the incompressible Euler equation in \cite{Chae1}.Comment: 16page

The relative importance of phytoplankton aggregates and zooplankton fecal pellets to carbon export: insights from free-drifting sediment trap deployments in naturally iron-fertilised waters near the Kerguelen Plateau

The first KErguelen Ocean and Plateau compared Study (KEOPS1), conducted in the naturally iron-fertilised Kerguelen bloom, demonstrated that fecal material was the main pathway for exporting carbon to the deep ocean during summer (January–February 2005), suggesting a limited role of direct export via phytodetrital aggregates. The KEOPS2 project reinvestigated this issue during the spring bloom initiation (October–November 2011), when zooplankton communities may exert limited grazing pressure, and further explored the link between carbon flux, export efficiency and dominant sinking particles depending upon surface plankton community structure. Sinking particles were collected in polyacrylamide gel-filled and standard free-drifting sediment traps (PPS3/3), deployed at six stations between 100 and 400 m, to examine flux composition, particle origin and their size distributions. Results revealed an important contribution of phytodetrital aggregates (49 ± 10 and 45 ± 22% of the total number and volume of particles respectively, all stations and depths averaged). This high contribution dropped when converted to carbon content (30 ± 16% of total carbon, all stations and depths averaged), with cylindrical fecal pellets then representing the dominant fraction (56 ± 19%).At 100 and 200 m depth, iron- and biomass-enriched sites exhibited the highest carbon fluxes (maxima of 180 and 84 ± 27 mg C m-2 d-1, based on gel and PPS3/3 trap collection respectively), especially where large fecal pellets dominated over phytodetrital aggregates. Below these depths, carbon fluxes decreased (48 ± 21% decrease on average between 200 and 400 m), and mixed aggregates composed of phytodetritus and fecal matter dominated, suggesting an important role played by physical aggregation in deep carbon export.Export efficiencies determined from gels, PPS3/3 traps and 234Th disequilibria (200 m carbon flux/net primary productivity) were negatively correlated to net primary productivity with observed decreases from ~ 0.2 at low-iron sites to ~ 0.02 at high-iron sites. Varying phytoplankton communities and grazing pressure appear to explain this negative relationship. Our work emphasises the need to consider detailed plankton communities to accurately identify the controls on carbon export efficiency, which appear to include small spatio-temporal variations in ecosystem structure

The Beale-Kato-Majda criterion to the 3D Magneto-hydrodynamics equations

We study the blow-up criterion of smooth solutions to the 3D MHD equations. By means of the Littlewood-Paley decomposition, we prove a Beale-Kato-Majda type blow-up criterion of smooth solutions via the vorticity of velocity only, i. e. \sup_{j\in\Z}\int_0^T\|\Delta_j(\na\times u)\|_\infty dt, where $\Delta_j$ is a frequency localization on $|\xi|\approx 2^j$.Comment: 12page

Chemometric perspectives on plankton community responses to natural iron fertilisation over and downstream of the Kerguelen Plateau in the Southern Ocean

International audienceWe examined phytoplankton community responses to natural iron fertilisation at 32 sites over and downstream from the Kerguelen Plateau in the Southern Ocean during the austral spring bloom in October–November 2011. The community structure was estimated from chemical and isotopic measurements (particulate organic carbon – POC; 13C-POC; particulate nitrogen – PN; 15N-PN; and biogenic silica – BSi) on size-fractionated samples from surface waters (300, 210, 50, 20, 5, and 1 μm fractions). Higher values of 13C-POC (vs. co-located 13C values for dissolved inorganic carbon – DIC) were taken as indicative of faster growth rates and higher values of 15N-PN (vs. co-located 15N-NO3 source values) as indicative of greater nitrate use (rather than ammonium use, i.e. higher f ratios).Community responses varied in relation to both regional circulation and the advance of the bloom. Iron-fertilised waters over the plateau developed dominance by very large diatoms (50–210 μm) with high BSi / POC ratios, high growth rates, and significant ammonium recycling (lower f ratios) as biomass built up. In contrast, downstream polar frontal waters with a similar or higher iron supply were dominated by smaller diatoms (20–50 μm) and exhibited greater ammonium recycling. Stations in a deep-water bathymetrically trapped recirculation south of the polar front with lower iron levels showed the large-cell dominance observed on the plateau but much less biomass. Comparison of these communities to surface water nitrate (and silicate) depletions as a proxy for export shows that the low-biomass recirculation feature had exported similar amounts of nitrogen to the high-biomass blooms over the plateau and north of the polar front. This suggests that early spring trophodynamic and export responses differed between regions with persistent low levels vs. intermittent high levels of iron fertilisation