Electron Detachment Dissociation for Top-Down Mass Spectrometry of Acidic Proteins

Electron detachment dissociation (EDD) is an emerging mass spectrometry (MS) technique for the primary structure analysis of peptides, carbohydrates, and oligonucleotides. Herein, we explore the potential of EDD for sequencing of proteins of up to 147 amino acid residues by using top-down MS. Sequence coverage ranged from 72 % for Melittin, which lacks carboxylic acid functionalities, to 19 % for an acidic 147-residue protein, to 12 % for Ferredoxin, which showed unusual backbone fragmentation next to cysteine residues. A limiting factor for protein sequencing by EDD is the facile loss of small molecules from amino acid side chains, in particular CO2. Based on the types of fragments observed and fragmentation patterns found, we propose detailed mechanisms for protein backbone cleavage and side chain dissociation in EDD. The insights from this study should further the development of EDD for top-down MS of acidic proteins

Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products

Collisionally activated dissociation of RNA gives base loss diagnostic for uridine, and nucleoside loss diagnostic for pseudouridine residues

Spring phenological responses of marine and freshwater plankton to changing temperature and light conditions

Shifts in the timing and magnitude of the spring plankton bloom in response to climate change have been observed across a wide range of aquatic systems. We used meta-analysis to investigate phenological responses of marine and freshwater plankton communities in mesocosms subjected to experimental manipulations of temperature and light intensity. Systems differed with respect to the dominant mesozooplankton (copepods in seawater and daphnids in freshwater). Higher water temperatures advanced the bloom timing of most functional plankton groups in both marine and freshwater systems. In contrast to timing, responses of bloom magnitudes were more variable among taxa and systems and were influenced by light intensity and trophic interactions. Increased light levels increased the magnitude of the spring peaks of most phytoplankton taxa and of total phytoplankton biomass. Intensified size-selective grazing of copepods in warming scenarios affected phytoplankton size structure and lowered intermediate (20–200 lm)-sized phytoplankton in marine systems. In contrast, plankton peak magnitudes in freshwater systems were unaffected by temperature, but decreased at lower light intensities, suggesting that filter feeding daphnids are sensitive to changes in algal carrying capacity as mediated by light supply. Our analysis confirms the general shift toward earlier blooms at increased temperature in both marine and freshwater systems and supports predictions that effects of climate change on plankton production will vary among sites, depending on resource limitation and species composition

Report on the Marine Imaging Workshop 2022

Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public

Report on the Marine Imaging Workshop 2022

Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4 th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging. This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public

Phytoplankton response to a changing climate

Phytoplankton are at the base of aquatic food webs and of global importance for ecosystem functioning and services. The dynamics of these photosynthetic cells are linked to annual fluctuations of temperature, water column mixing, resource availability, and consumption. Climate can modify these environmental factors and alter phytoplankton structure, seasonal dynamics, and taxonomic composition. Here, we review mechanistic links between climate alterations and factors limiting primary production, and highlight studies where climate change has had a clear impact on phytoplankton processes. Climate affects phytoplankton both directly through physiology and indirectly by changing water column stratification and resource availability, mainly nutrients and light, or intensified grazing by heterotrophs. These modifications affect various phytoplankton processes, and a widespread advance in phytoplankton spring bloom timing and changing bloom magnitudes have both been observed. Climate warming also affects phytoplankton species composition and size structure, and favors species traits best adapted to changing conditions associated with climate change. Shifts in phytoplankton can have far-reaching consequences for ecosystem structure and functioning. An improved understanding of the mechanistic links between climate and phytoplankton dynamics is important for predicting climate change impacts on aquatic ecosystem