Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction

Since Gleason and Clements, our understanding of community dynamics has been influenced by theories emphasising either dispersal or niche assembly as central to community structuring. Determining the relative importance of these processes in structuring real‐world communities remains a challenge. We tracked reef fish community reassembly after a catastrophic coral mortality in a relatively unfished archipelago. We revisited the stochastic model underlying MacArthur and Wilson's Island Biogeography Theory, with a simple extension to account for trophic identity. Colonisation and extinction rates calculated from decadal presence‐absence data based on (1) species neutrality, (2) trophic identity and (3) site‐specificity were used to model post‐disturbance reassembly, and compared with empirical observations. Results indicate that species neutrality holds within trophic guilds, and trophic identity significantly increases overall model performance. Strikingly, extinction rates increased clearly with trophic position, indicating that fish communities may be inherently susceptible to trophic downgrading even without targeted fishing of top predators.     

iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration

The short storage life of harvested cassava roots is an important constraint that limits the full potential of cassava as a commercial food crop in developing countries. We investigated the molecular changes during physiological deterioration of cassava root after harvesting using isobaric tags for relative and absolute quantification (iTRAQ) of proteins in soluble and non‐soluble fractions prepared during a 96 h post‐harvest time course. Combining bioinformatic approaches to reduce information redundancy for unsequenced or partially sequenced plant species, we established a comprehensive proteome map of the cassava root and identified quantitatively regulated proteins. Up‐regulation of several key proteins confirmed that physiological deterioration of cassava root after harvesting is an active process, with 67 and 170 proteins, respectively, being up‐regulated early and later after harvesting. This included regulated proteins that had not previously been associated with physiological deterioration after harvesting, such as linamarase, glutamic acid‐rich protein, hydroxycinnamoyl transferase, glycine‐rich RNA binding protein, β‐1,3‐glucanase, pectin methylesterase, maturase K, dehydroascorbate reductase, allene oxide cyclase, and proteins involved in signal pathways. To confirm the regulation of these proteins, activity assays were performed for selected enzymes. Together, our results show that physiological deterioration after harvesting is a highly regulated complex process involving proteins that are potential candidates for biotechnology approaches to reduce such deterioration.     

The implications of mitochondrial DNA copy number regulation during embryogenesis

Mutations of mitochondrial DNA (mtDNA) cause a wide array of multisystem disorders, particularly affecting organs with high energy demands. Typically only a proportion of the total mtDNA content is mutated (heteroplasmy), and high percentage levels of mutant mtDNA are associated with a more severe clinical phenotype. MtDNA is inherited maternally and the heteroplasmy level in each one of the offspring is often very different to that found in the mother. The mitochondrial genetic bottleneck hypothesis was first proposed as the explanation for these observations over 20 years ago. Although the precise bottleneck mechanism is still hotly debated, the regulation of cellular mtDNA content is a key issue. Here we review current understanding of the factors regulating the amount of mtDNA within cells and discuss the relevance of these findings to our understanding of the inheritance of mtDNA heteroplasmy.     

New protein isoforms identified within Arabidopsis thaliana seed oil bodies combining chymotrypsin/trypsin digestion and peptide fragmentation analysis

Plant seed oil bodies, subcellular lipoprotein inclusions providing storage reserves, are composed of a neutral lipid core surrounded by a phospholipid monolayer with several integrated proteins that play a significant role in stabilization of the particles and probably also in lipid mobilization. Oil bodies' proteins are generally very hydrophobic, due to the long uncharged sequences anchoring them into the lipid core, which makes them extremely difficult to handle and to digest successfully. Although oil bodies have been intensively studied during last decades, not all their proteins have been identified yet. To overcome the problems connected with their identification, a method based on SDS-PAGE, in-gel digestion and LC-MS/MS analysis was used. Digestion was carried out with trypsin and chymotrypsin, single or in combination, which increased significantly the number of identified peptides, namely the hydrophobic ones. Thanks to this methodology it was possible to achieve an extensive coverage of proteins studied, to analyze their N-terminal modifications and moreover, to detect four new oil bodies' protein isoforms, which demonstrates the complexity of oil bodies' protein composition.     

In vivo post-translational modifications of recombinant mussel adhesive protein in insect cells

Mussel adhesive proteins (MAPs) have been suggested as promising bioadhesives for diverse application fields, including medical uses. Previously, we successfully constructed and produced a new type of functional recombinant MAP, fp-151, in a prokaryotic Escherichia coli expression system. Even though the E. coli-derived MAP showed several excellent features, such as high production yield and efficient purification, in vitro enzymatic modification is required to convert tyrosine residues to l-3,4-dihydroxyphenyl alanine (dopa) molecules for its adhesive ability, due to the intrinsic inability of E. coli to undergo post-translational modification. In this work, we produced a soluble recombinant MAP in insect Sf9 cells, which are widely used as an effective and convenient eukaryotic expression system for eukaryotic foreign proteins. Importantly, we found that insect-derived MAP contained converted dopa residues by in vivo post-translational modification. In addition, insect-derived MAP also had other post-translational modifications including phosphorylation of serine and hydroxylation of proline that originally occurred in some natural MAPs. To our knowledge, this is the first report on in vivo post-translational modifications of MAP containing dopa and other modified amino acid residues.     

Method of Isolated Ex Vivo Lung Perfusion in a Rat Model: Lessons Learned from Developing a Rat EVLP Program

The number of acceptable donor lungs available for lung transplantation is severely limited due to poor quality. Ex-Vivo Lung Perfusion (EVLP) has allowed lung transplantation in humans to become more readily available by enabling the ability to assess organs and expand the donor pool. As this technology expands and improves, the ability to potentially evaluate and improve the quality of substandard lungs prior to transplant is a critical need. In order to more rigorously evaluate these approaches, a reproducible animal model needs to be established that would allow for testing of improved techniques and management of the donated lungs as well as to the lung-transplant recipient. In addition, an EVLP animal model of associated pathologies, e.g., ventilation induced lung injury (VILI), would provide a novel method to evaluate treatments for these pathologies. Here, we describe the development of a rat EVLP lung program and refinements to this method that allow for a reproducible model for future expansion. We also describe the application of this EVLP system to model VILI in rat lungs. The goal is to provide the research community with key information and “pearls of wisdom”/techniques that arose from trial and error and are critical to establishing an EVLP system that is robust and reproducible.     

Germination response of common annual and perennial forbs to heat shock and smoke treatments in the Chaco Serrano,central Argentina

Fire is a key ecological factor affecting plant dynamics. In the last few decades, fire occurrence in the Chaco region has increased noticeably, challenging the adaptive capacity of plants to regenerate after a fire. Broad‐leaved forb species have been much less studied than woody and graminoids, although they are an important component of fire dynamics. Here we analysed the germination response to heat shock of 70 and 110°C, smoke and their combination in 10 broad‐leaved herbaceous species frequently occurring in the Chaco Serrano of Córdoba province, central Argentina, including five annual (Bidens subalternans, Conyza bonariensis, Schkuhria pinnata, Tagetes minuta and Zinnia peruviana) and five perennial species (Borreria eryngioides, Sida rhombifolia, Solidago chilensis, Taraxacum officinale and Verbena litoralis). We also compared the response of annual versus perennial species. Six species had highest germination when treated with heat and smoke combined, whereas two had lowest germination under this treatment, indicating synergistic and antagonistic interaction of these factors respectively. Most of the species tolerated heat shock (i.e. germination was similar to that in control treatment), whereas others had higher germination in response to heat shock, especially under the moderate 70°C treatment. Germination was higher than control (i.e. no heat and no smoke) after smoke treatment in four species. Perennial species showed higher average germination than annuals in both heat treatments and in the control. Annual species had higher average germination for all treatments involving smoke. The high variability observed at the species level, and the limited number of species studied calls for precaution in interpreting and extrapolating results. Nevertheless, our study shows a general positive response of both perennial and annual species to fire cues, suggesting an advantage of these species for colonizing post‐fire environments, and being favoured under scenarios of increasingly frequent low‐to‐medium intensity fires.     

Chemiluminescence behaviour of alkaline earth metal ions in the potassium permanganate–fluorescein reaction

A chemiluminescence (CL) signal was observed when alkaline earth metal ion solution, Mg²⁺ or Ca²⁺ or Ba²⁺, was injected into a reaction mixture of fluorescein and potassium permanganate. A possible CL mechanism is proposed based upon the CL, fluorescence and UV‐visible spectra. Furthermore, the feasibility of the application of these reactions to the analysis of these alkaline earth metal ions was evaluated and the analytical parameters of the methods were determined. Copyright © 2003 John Wiley & Sons, Ltd.