Feeding repellence of Antarctic and sub-Antarctic benthic invertebrates against the omnivorous sea star Odontaster validus

Antarctic and sub-Antarctic benthic invertebrates are subjected to intense predation by mobile macroinvertebrates. Accordingly, chemical protection as well as other defensive mechanisms are expected to be common in organisms inhabiting these ecosystems. In order to evaluate anti-predation activities and allocation of chemical defenses within the anatomy of marine benthic Antarctic and sub-Antarctic invertebrates, 55 species were tested for feeding repellence against the sea star Odontaster validus, a common eurybathic sympatric predator. The invertebrates tested were collected from the deep waters of two poorly surveyed areas in terms of chemical ecology studies: the eastern Weddell Sea (Antarctica) and the vicinities of Bouvet Island (sub-Antarctica). Experiments were conducted at the Spanish Antarctic Base in Deception Island. In the feeding deterrence experiments, shrimp pieces were treated with crude lipophilic fractions obtained from each species, and were offered to the sea stars. A total of 29 species (53 %) from 7 different phyla (Porifera, Cnidaria, Chordata, Bryozoa, Echinodermata, Mollusca, and Annelida) showed feeding repellence against O. validus, and are therefore chemically protected against this keystone predator. Furthermore, 25 species were dissected into parts to investigate the possible allocation of defensive compounds. Some of the results obtained from these analyses support the prediction that the most exposed/vulnerable tissues concentrate chemical defenses to avoid predation against the sea stars. In summary, the results obtained in our survey support the hypothesis that deep-water Antarctic and sub-Antarctic benthic invertebrates are well protected chemically against sympatric predators, similarly to what has been reported in previous studies investigating shallow-water Antarctic species.     

Polymerization of coniferyl alcohol by Mn3+‐mediated (enzymatic) oxidation: Effects of H2O2 concentration,aqueous organic solvents,and pH

The objective of this study was to evaluate the ability of one versatile peroxidase and the biocatalytically generated complex Mn(III)‐malonate to polymerize coniferyl alcohol (CA) to obtain dehydrogenation polymers (DHPs) and to characterize how closely the structures of the formed DHPs resemble native lignin. Hydrogen peroxide was used as oxidant and Mn²⁺ as mediator. Based on the yields of the polymerized product, it was concluded that the enzymatic reaction should be performed in aqueous solution without organic solvents at 4.5 ≤ pH ≤ 6.0 and with 0.75 ≤ H₂O₂:CA ratio ≤ 1. The results obtained from the Mn³⁺‐malonate‐mediated polymerization showed that the yield was almost 100%. Reaction conditions had, however, effect on the structures of the formed DHPs, as detected by size exclusion chromatography and pyrolysis‐GC/MS. It can be concluded that from the structural point of view, the optimal pH for DHP formation using the presently studied system was 3 or 4.5. Low H₂O₂/CA ratio was beneficial to avoid oxidative side reactions. However, the high frequency of β–β linkages in all cases points to dimer formation between monomeric CA rather than endwise polymerization. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:81–90, 2018     

Genetic Characterization and Pathogenicity of Rhizoctonia solani Associated with Common Bean Web Blight in the Main Bean Growing area of Argentina

Common bean web blight (WB), caused by the fungus Rhizoctonia solani (teleomorph Thanatephorus cucumeris), is among the endemic fungal diseases of major impact in north‐western Argentina (NWA). This study aimed to analyse the genetic and pathogenic diversity of R. solani in Salta, NWA, where 97 isolates were recovered from commercial bean cultivars and wild beans showing WB symptoms in a major bean production area. The isolates were characterized on the basis of specific primers, rDNA‐ITS sequences and morphological characteristics. All the isolates were identified as R. solani AG 2‐2WB, and they exhibited considerable intragroup variation. The phylogenetic tree generated with the ITS sequences confirmed the isolates identification. Aggressiveness of the isolates towards bean seedlings was assessed in the greenhouse. A great variability in virulence was observed among the isolates analysed. On the basis of the disease reaction on foliar tissues, the isolates were grouped into three virulence categories as follows: weakly virulent (30%), moderately virulent (38%) and highly virulent (32%). However, no correlation between virulence and geographical origin was detected. The information generated in this study provides initial data on the population variability of the WB pathogen in north‐western Argentina and represents a valuable contribution to regional breeding programmes aimed to obtain cultivars with durable resistance.     

Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes

A DNA-based microarray designed to detect somatic (O) and flagellar (H) antigens present in the five most commonly isolated Salmonella serovars within Canada was developed as an alternative to the traditional Kauffmann-White serotyping scheme currently used to serotype salmonellae. Short oligonucleotide probes were designed based on publicly available sequence data of selected genes responsible for O and H antigen biosynthesis. These targets included: antigen-specific sequences within the flagella (H) antigen phase 1 (fliC) and phase 2 (fljB) genes and somatic (O) antigen biosynthesis genes within the rfb cluster (Groups B--rfbJ, C1--wbaA, C2--rfbJ, D1--rfbS). A prototype microarray with 117 O and H antigen-specific probes and controls was used to assess probe performance against two pools of gene target PCR amplicons. A set of 31 of these antigen-specific probes (8 O and 23 H) with high specific signal and low non-specific signal were selected based on t-test (p-value <0.01) and log(2) ratio distribution analysis to create a prototype microarray. The microarray was tested against 16 Salmonella strains of known serotype. Based on the strains tested in this study, these probes successfully identified and differentiated 11 of the 12 antigens targeted. The prototype DNA-based typing microarray described here has the potential to be an automated alternative to the traditional antigen-antibody serotyping scheme currently used for Salmonella.     

Energetics and conformational changes upon complexation of a phenothiazine drug with human serum albumin

The interactions and complexation process of the amphiphilic phenothiazine fluphenazine hydrochloride with human serum albumin in aqueous buffered solutions of pH 3.0 and 7.4 have been examined by zeta-potential, isothermal titration calorimetry (ITC), UV-vis spectroscopy, and dynamic light scattering (DLS) techniques with the aim of analyzing the effect of hydrophobic and electrostatic forces on the complexation process and the alteration of protein conformation upon binding. Thus, the energetics and stoichiometry of the binding process were derived from ITC data. The enthalpies of binding obtained are small and exothermic, so the Gibbs energies of binding are dominated by large increases in entropy, consistent with hydrophobic interactions at a acidic pH. However, at physiological pH, binding to the first class of binding sites is dominated by an enthalpic contribution due to the existence of electrostatic interactions and probably some hydrogen bonding. Binding isotherms were obtained from microcalorimetric data by using a theoretical model based on the Langmuir isotherm. zeta-Potential data showed a reversal in the sign of the protein charge at pH 7.4, as a consequence of the binding of the drug to the protein. Gibbs energies of drug binding per mole of drug were also derived from zeta-potential data. On the other hand, binding of the phenothiazine that causes a conformational transition on the protein structure was followed as a function of drug concentration using UV-vis spectroscopy, and the data were analyzed to obtain the Gibbs energy of the transition in water (deltaG(degree)w) and in a hydrophobic environment (deltaG(degree)hc). Finally, the population distribution of the different species in solution and the size of the complexes were analyzed through dynamic light scattering. The existence of an aggregation process of drug/protein complexes, as a consequence of the expanded structure of the protein induced by the drug and subsequent further binding, is in agreement with ITC data. In addition, detection of drug aggregates at concentrations below the drug critical micelle concentration was also detected by this technique.     

Effects of melatonin in an experimental model of ventilator-induced lung injury

Melatonin is a free radical scavenger and a broad-spectrum antioxidant and has well-documented immunomodulatory effects. We studied the effects of this hormone on lung damage, oxidative stress, and inflammation in a model of ventilator-induced lung injury (VILI), using 8- to 12-wk-old Swiss mice (n = 48). Animals were randomized into three experimental groups: control (not ventilated); low-pressure ventilation [peak inspiratory pressure 15 cmH(2)O, positive end-expiratory pressure (PEEP) 2 cmH(2)O], and high-pressure ventilation (peak inspiratory pressure 25 cmH(2)O, PEEP 0 cmH(2)O). Each group was divided into two subgroups: eight animals were treated with melatonin (10 mg/kg ip, 30 min before the onset of ventilation) and the remaining eight with vehicle. After 2 h of ventilation, lung injury was evaluated by gas exchange, wet-to-dry weight ratio, and histological analysis. Levels of malondialdehyde, glutathione peroxidase, interleukins IL-1beta, IL-6, TNF-alpha, and IL-10, and matrix metalloproteinases 2 and 9 in lung tissue were measured as indicators of oxidation status, pro-/anti-inflammatory cytokines, and matrix turnover, respectively. Ventilation with high pressures induced severe lung damage and release of TNF-alpha, IL-6, and matrix metalloproteinase-9. Treatment with melatonin improved oxygenation and decreased histological lung injury but significantly increased oxidative stress quantified by malondialdehyde levels. There were no differences in TNF-alpha, IL-1beta, IL-6, or matrix metalloproteinases caused by melatonin treatment, but IL-10 levels were significantly higher in treated animals. These results suggest that melatonin decreases VILI by increasing the anti-inflammatory response despite an unexpected increase in oxidative stress.     

Rapid Determination of Escherichia coli O157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting

In this study, variably absent or present (VAP) regions discovered through comparative genomics experiments were targeted for the development of a rapid, PCR-based method to subtype and fingerprint Escherichia coli O157:H7. Forty-four VAP loci were analyzed for discriminatory power among 79 E. coli O157:H7 strains of 13 phage types (PT). Twenty-three loci were found to maximize resolution among strains, generating 54 separate fingerprints, each of which contained strains of unique PT. Strains from the three previously identified major E. coli O157:H7 lineages, LSPA6-LI, LSPA6-LI/II, and LSPA6-LII, formed distinct branches on a dendrogram obtained by hierarchical clustering of comparative genomic fingerprinting (CGF) data. By contrast, pulsed-field gel electrophoresis (PFGE) typing generated 52 XbaI digestion profiles that were not unique to PT and did not cluster according to O157:H7 lineage. Our analysis identified a subpopulation comprised of 25 strains from a closed herd of cattle, all of which were of PT87 and formed a cluster distinct from all other E. coli O157:H7 strains examined. CGF found five related but unique fingerprints among the highly clonal herd strains, with two dominant subtypes characterized by a shift from the presence of locus fprn33 to its absence. CGF had equal resolution to PFGE typing but with greater specificity, generating fingerprints that were unique among phenotypically related E. coli O157:H7 lineages and PT. As a comparative genomics typing method that is amenable for use in high-throughput platforms, CGF may be a valuable tool in outbreak investigations and strain characterization.     

The genetic bases for the variation in the lipo-oligosaccharide of the mucosal pathogen, Campylobacter jejuni. Biosynthesis of sialylated ganglioside mimics in the core oligosaccharide.

We have compared the lipo-oligosaccharide (LOS) biosynthesis loci from 11 Campylobacter jejuni strains expressing a total of 8 different ganglioside mimics in their LOS outer cores. Based on the organization of the genes, the 11 corresponding loci could be classified into three classes, with one of them being clearly an intermediate evolutionary step between the other two. Comparative genomics and expression of specific glycosyltransferases combined with in vitro activity assays allowed us to identify at least five distinct mechanisms that allow C. jejuni to vary the structure of the LOS outer core as follows: 1) different gene complements; 2) phase variation because of homopolymeric tracts; 3) gene inactivation by the deletion or insertion of a single base (without phase variation); 4) single mutation leading to the inactivation of a glycosyltransferase; and 5) single or multiple mutations leading to "allelic" glycosyltransferases with different acceptor specificities. The differences in the LOS outer core structures expressed by the 11 C. jejuni strains examined can be explained by one or more of the five mechanisms described in this work.     

Seasonality of North Atlantic phytoplankton from space: impact of environmental forcing on a changing phenology (1998–2012)

Seasonal pulses of phytoplankton drive seasonal cycles of carbon fixation and particle sedimentation, and might condition recruitment success in many exploited species. Taking advantage of long‐term series of remotely sensed chlorophyll a (1998–2012), we analyzed changes in phytoplankton seasonality in the North Atlantic Ocean. Phytoplankton phenology was analyzed based on a probabilistic characterization of bloom incidence. This approach allowed us to detect changes in the prevalence of different seasonal cycles and, at the same time, to estimate bloom timing and magnitude taking into account uncertainty in bloom detection. Deviations between different sensors stressed the importance of a prolonged overlap between successive missions to ensure a correct assessment of phenological changes, as well as the advantage of semi‐analytical chlorophyll algorithms over empirical ones to reduce biases. Earlier and more intense blooms were detected in the subpolar Atlantic, while advanced blooms of less magnitude were common in the Subtropical gyre. In the temperate North Atlantic, spring blooms advanced their timing and decreased in magnitude, whereas fall blooms delayed and increased their intensity. At the same time, the prevalence of locations with a single autumn/winter bloom or with a bimodal seasonal cycle increased, in consonance with a poleward expansion of subtropical conditions. Changes in bloom timing and magnitude presented a clear signature of environmental factors, especially wind forcing, although changes on incident photosynthetically active radiation and sea surface temperature were also important depending on latitude. Trends in bloom magnitude matched changes in mean chlorophyll a during the study period, suggesting that seasonal peaks drive long‐term trends in chlorophyll a concentration. Our results link changes in North Atlantic climate with recent trends in the phenology of phytoplankton, suggesting an intensification of these impacts in the near future.     

FastMPJ: a scalable and efficient Java message-passing library

The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, multithreading) of Java for parallel programming, its poor communications support has hindered its adoption in the HPC community. This paper presents FastMPJ, an efficient message-passing in Java (MPJ) library, boosting Java for HPC by: (1) providing high-performance shared memory communications using Java threads; (2) taking full advantage of high-speed cluster networks (e.g., InfiniBand) to provide low-latency and high bandwidth communications; (3) including a scalable collective library with topology aware primitives, automatically selected at runtime; (4) avoiding Java data buffering overheads through zero-copy protocols; and (5) implementing the most widely extended MPI-like Java bindings for a highly productive development. The comprehensive performance evaluation on representative testbeds (InfiniBand, 10 Gigabit Ethernet, Myrinet, and shared memory systems) has shown that FastMPJ communication primitives rival native MPI implementations, significantly improving the efficiency and scalability of Java HPC parallel applications.