Jelly-falls historic and recent observations: a review to drive future research directions

The biological pump describes the transport of particulate matter from the sea surface to the ocean’s interior including the seabed. The contribution by gelatinous zooplankton bodies as particulate organic matter (POM) vectors (“jelly-falls”) has been neglected owing to technical and spatiotemporal sampling limitations. Here, we assess the existing evidence on jelly-falls from early ocean observations to present times. The seasonality of jelly-falls indicates that they mostly occur after periods of strong upwelling and/or spring blooms in temperate/subpolar zones and during late spring/early summer. A conceptual model helps to define a jelly-fall based on empirical and field observations of biogeochemical and ecological processes. We then compile and discuss existing strategic and observational oceanographic techniques that could be implemented to further jelly-falls research. Seabed video- and photography-based studies deliver the best results, and the correct use of fishing techniques, such as trawling, could provide comprehensive regional datasets. We conclude by considering the possibility of increased gelatinous biomasses in the future ocean induced by upper ocean processes favouring their populations, thus increasing jelly-POM downward transport. We suggest that this could provide a “natural compensation” for predicted losses in pelagic POM with respect to fuelling benthic ecosystems.     

Dispersed oil disrupts microbial pathways in pelagic food webs

Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf.     

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.     

An improved, simple nest-box trap

ABSTRACT.   The success of ornithological studies often hinges on a researcher's ability to capture individuals quickly and efficiently. Sometimes it is necessary to capture the same individual multiple times, as is the case in many metabolic, ecotoxicological, and immunocompetence studies. Several methods of capturing cavity-nesting birds at their nest boxes have been described. However, these methods proved inefficient when attempting to catch wary individuals that had already been captured previously. Here we describe a simple and inexpensive method for capturing cavity-nesting birds using a square plate of sheet metal (5.8 × 5.8 × 0.2 cm), a drinking straw, a piece of duct tape, and a monofilament line. This method has the advantages of allowing selective capture of one, but not both members of a pair and being nearly invisible to trap-shy birds.     

Cell culture mutants as aminoacyl-tRNA synthetase complex probes

A number of Chinese hamster ovary cell culture mutants have been characterized by us for their high-molecular-weight aminoacyl-tRNA synthetase (aaRS) complexes. The results all support a model of aaRS complex function wherein the high-molecular-weight complexes form aminoacyl-tRNA by utilizing extracellular amino acids immediately on their transport and before they have equilibrated with the internal pool. The low-molecular-weight aaRS forms exclusively utilize amino acids from only the intracellular pool.     

Adsorption of ethylenediaminetetraacetic dianhydride modified oxalate decarboxylase on calcium oxalate

We used ethylenediaminetetraacetic acid dianhydride (EDTAD) to modify oxalate decarboxylase (OXDC) to improve its adsorption on calcium oxalate stones. The modified sites were identified by Ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and the adsorption mechanism of the EDTAD-modified OXDC on calcium oxalate (CaOx) was investigated. We investigated adsorption time, initial enzyme concentration, temperature and solution pH on the adsorption process. Data were analyzed using kinetics, thermodynamics and isotherm adsorption models. UPLC-MS showed that EDTAD was attached to OXDC covalently and suggested that the chemical modification occurred at both the free amino of the side chain and the α-NH₂ of the peptide. The adsorption capacity of the EDTAD-OXDC on calcium oxalate was 53.37% greater than that of OXDC at the initial enzyme concentration of 5 mg/ml, pH = 7.0, at 37° C. The modified enzyme (EDTAD-OXDC) demonstrated improved oxalate degradation activity at pH 4.5?6.0. Kinetic data fitting analysis suggested a pseudo second order kinetic model. Estimates of the thermodynamic parameters including ΔG⁰, ΔH⁰ and ΔS⁰ of the adsorption process showed it to be feasible, spontaneous and endothermic. Isotherm data fitting analysis indicated that the adsorption process is reduced to monolayer adsorption at a low enzyme concentration and to multilayer adsorption at a high enzyme concentration. It may be possible to apply OXDC to degradation of calcium oxalate stones.     

Occurrence of a Highly Heat-Sensitive Spore Subpopulation of Bacillus coagulans STCC 4522 and Its Conversion to a More Heat-Stable Form

The profile of the survival curves, at different heating temperatures, of B. coagulans STCC 4522 sporulated at 52(deg)C has been studied, focusing on the early moments of treatment. A highly heat-sensitive spore subpopulation that includes more than 90% of the total spore population has been found. This heat-sensitive spore fraction was inactivated after 2 s of treatment at 111(deg)C. Its heat resistance was as much as 200-fold lower than that of the heat-resistant spore fraction (D(inf111(deg)C) of 0.01 min for the heat-sensitive spore fraction compared with D(inf111(deg)C) of 2 min for the heat-resistant fraction). The shape of the survival curve at 108.5(deg)C was modified after a sublethal heat shock at 80(deg)C for 3.5 h, resulting in a straight-line survival curve. The temperature of treatment also influenced the shape of the survival curves. The conversion of the highly heat-sensitive spore subpopulation to a more heat-stable form is discussed.