Occurrence of false killer whales (Pseudorca crassidens) and their association with common bottlenose dolphins (Tursiops truncatus) off northeastern New Zealand

On a global scale, false killer whales (Pseudorca crassidens) remain one of the lesser‐known delphinids. The occurrence, site fidelity, association patterns, and presence/absence of foraging in waters off northeastern New Zealand are examined from records collected between 1995 and 2012. The species was rarely encountered; however, of the 61 distinctive, photo‐identified individuals, 88.5% were resighted, with resightings up to 7 yr after initial identification, and movements as far as 650 km documented. Group sizes ranged from 20 to ca. 150. Results indicate that all individuals are linked in a single social network. Most observations were recorded in shallow (<100 m) nearshore waters. Occurrence in these continental shelf waters is likely seasonal, coinciding with the shoreward flooding of a warm current. During 91.5% of encounters, close interspecific associations with common bottlenose dolphins (Tursiops truncatus) were observed. Photo‐identification reveals repeat inter‐ and intraspecific associations among individuals with 34.2% of common bottlenose dolphins resighted together with false killer whales over 1,832 d. While foraging was observed during 39.5% of mixed‐species encounters, results suggest that social and antipredatory factors may also play a role in the formation of these mixed‐species groups.     

Fatty acid contents and profiles of 16 macroalgae collected from the Irish Coast at two seasons

Due to the established health benefits of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA), there is a globally increasing demand for alternative natural resources with appropriate fatty acid profiles. To assess the suitability of macroalgae as a source, 16 species (nine Phaeophyceae, five Rhodophyta and two Chlorophyta) were collected at two seasons (June and November) from the Irish west Coast, and total fatty acid contents and specific profiles were determined. Total fatty acid contents, expressed per percentage of dry weight, ranged from 6.4 %?±?0.3 (Pelvetia canaliculata, Phaeophyceae) to 0.8 %?±?0.2 (Porphyra dioica, Rhodophyta). Most common fatty acids were palmitic (16:0), oleic (OLE, 18:1 n-9), α-linolenic (ALA, 18:3 n-3), arachidonic (ARA, 20:4 n-6) and eicosapentaenoic (EPA, 20:5 n-3) acids. Fatty acid profiles were highly variable between and within algal groups; red and brown seaweeds were generally richer in LC-PUFA (e.g. 20:4 n-6 and 20:5 n-3), while high levels of saturated fatty acids such as palmitic acid (16:0) were observed in green species. Most omega-3 PUFA-rich species investigated had a omega-6/omega-3 fatty acid ratio close to 1, which is favourable for human health. The two seasonal sampling times revealed significant differences in total fatty acid and 20:5 n-3 (EPA) contents, with changes depending on species, thus implying varying suitability as potential target species for EPA production. At both times of the year, Palmaria palmata was identified as most promising species as a source of 20:5 n-3 (EPA) amongst all species investigated, with levels ranging from 0.44 to 0.58 % of dry weight in June and November, respectively.     

Mitochondrial leucine tRNA level and PTCD1 are regulated in response to leucine starvation

Pentatricopeptide repeat domain protein 1 (PTCD1) is a novel human protein that was recently shown to decrease the levels of mitochondrial leucine tRNAs. The physiological role of this regulation, however, remains unclear. Here we show that amino acid starvation by leucine deprivation significantly increased the mRNA steady-state levels of PTCD1 in human hepatocarcinoma (HepG2) cells. Amino acid starvation also increased the mitochondrially encoded leucine tRNA (tRNA^Leu(CUN)) and the mRNA for the mitochondrial leucyl-tRNA synthetase (LARS2). Despite increased PTCD1 mRNA steady-state levels, amino acid starvation decreased PTCD1 on the protein level. Decreasing PTCD1 protein concentration increases the stability of the mitochondrial leucine tRNAs, tRNA^Leu(CUN) and tRNA^Leu(UUR) as could be shown by RNAi experiments against PTCD1. Therefore, it is likely that decreased PTCD1 protein contributes to the increased tRNA^Leu(CUN) levels in amino acid-starved cells. The stabilisation of the mitochondrial leucine tRNAs and the upregulation of the mitochondrial leucyl-tRNA synthetase LARS2 might play a role in adaptation of mitochondria to amino acid starvation.     

Genome-wide association mapping of tan spot resistance (Pyrenophora tritici-repentis) in European winter wheat

The effect of low temperature on the physiology of maize has been well studied, but the genetics behind cold tolerance is poorly understood. To better understand the genetics of cold tolerance we conducted a quantitative trait locus (QTL) analysis on a segregating population from the cross of a cold-tolerant (EP42) and a cold-susceptible (A661) inbred line. The experiments were carried under cold (15 °C) and control (25 °C) conditions in a phytotron. Cold temperature reduced the shoot dry weight, number of survival plants and quantum yield of electron transport at photosystem II (ΦPSII) and increased the anthocyanin content in maize seedlings. Low correlations were found between characteristics under low and optimum temperature. Ten QTLs were identified, six of them at control temperatures and four under cold temperatures. Through a meta-QTL analysis we identified three genomic regions in chromosomes 2, 4 and 8 that regulate the development of maize seedlings under cold conditions and are the most promising regions to be the target of future marker-assisted selection breeding programs or to perform fine mapping to identify genes involved in cold tolerance in maize.     

The Spatiotemporal Dynamics and Membranous Features of the Plasmodium Liver Stage Tubovesicular Network

For membrane‐bound intracellular pathogens, the surrounding vacuole is the portal of communication with the host cell. The parasitophorous vacuole (PV) harboring intrahepatocytic Plasmodium parasites satisfies the parasites' needs of nutrition and protection from host defenses to allow the rapid parasite growth that occurs during the liver stage of infection. In this study, we visualized the PV membrane (PVM) and the associated tubovesicular network (TVN) through fluorescent tagging of two PVM‐resident Plasmodium berghei proteins, UIS4 and IBIS1. This strategy revealed previously unrecognized dynamics with which these membranes extend throughout the host cell. We observed dynamic vesicles, elongated clusters of membranes and long tubules that rapidly extend and contract from the PVM in a microtubule‐dependent manner. Live microscopy, correlative light‐electron microscopy and fluorescent recovery after photobleaching enabled a detailed characterization of these membranous features, including velocities, the distribution of UIS4 and IBIS1, and the connectivity of PVM and TVN. Labeling of host cell compartments revealed association of late endosomes and lysosomes with the elongated membrane clusters. Moreover, the signature host autophagosome protein LC3 was recruited to the PVM and TVN and colocalized with UIS4. Together, our data demonstrate that the membranes surrounding intrahepatic Plasmodium are involved in active remodeling of host cells.      

Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mould disease establishment

Sclerotinia sclerotiorum is a serious pathogen of numerous crops around the world. The major virulence factor of this pathogen is oxalic acid (OA). Mutants that cannot produce OA do not cause disease, and plants that express enzymes that degrade OA, such as oxalate oxidase (OxO), are very resistant to S. sclerotiorum. To examine the effect of OA on plants, we infiltrated soybean leaves with 5 mm OA and examined the gene expression changes at 2 h post‐infiltration. By comparing the gene expression levels between leaves of a transgenic soybean carrying an OxO gene (OxO) and its parent AC Colibri (AC) infiltrated with OA (pH 2.4) or water (pH 2.4 or 5.5), we were able to compare the effects of OA dependent or independent of its pH. Gene expression by microarray analysis identified 2390 genes that showed changes in expression, as determined using an overall F‐test P‐value cut‐off of 0.001. The additional requirement that at least one pairwise t‐test false discovery rate (FDR)‐corrected P value should be less than 0.001 reduced the list of the most highly significant differentially expressed genes to 1054. Independent of pH, OA altered the expression levels of 78 genes, with ferritin showing the strongest induction by OA. The combination of OA plus its low pH caused 1045 genes (99% of all significant genes) to be differentially expressed, with many of the up‐regulated genes being related to basal defence, such as genes of the phenylpropanoid pathway and various cytochrome P450s. RNA‐seq was also conducted on four samples: OxO and AC genotypes infiltrated with either OA pH 2.4 or water pH 2.4. The RNA‐seq analysis also identified ferritin paralogues as being strongly induced by OA. As the expression of ferritin, a gene that encodes for an iron storage protein, is induced by free iron, these results suggest that S. sclerotiorum benefits from the ability of OA to free iron from plant proteins, as this induces host cell death, and also allows the uptake and assimilation of the iron for its own metabolic needs.     

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.     

The impact of increased soil risk elements on carotenoid contents

A pot experiment was conducted to compare the responses of a non-transgenic tobacco plant (WT) and plants with genetically prolonged life-span (SAG) to risk elements of As, Cd and Zn. Plants were grown in control soil and in soil with higher levels of risk elements. The pigment contents were established by HPLC and chlorophyll fluorescence parameters were measured from slow kinetics after a 15 min dark period with the PAM fluorometer. Top (i.e. young) leaves of both WT and SAG plants were more sensitive to photoinhibition caused by these risk elements but plants showed acclimation to such elements in the bottom leaves. Plants differed in the participation of individual pigments of xanthophyll cycle: increased levels of risk elements seem to stimulate especially first (violaxanthin to antheraxanthin) and second (anhtheraxanthin to zeaxanthin) steps of the cycle in WT plants. In SAG plants, toxic elements caused an increase in the content, particularly of the initial compound of the cycle — violaxanthin.