Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator .     

Cell Cycle Control in Arabidopsis

Although the basic mechanism of cell cycle control is conservedamong eukaryotes, its regulation differs in each type of organism.Plants have unique developmental features that distinguish themfrom other eukaryotes. These include the absence of cell migration,the formation of organs throughout the entire life-span fromspecialized regions called meristems, and the potency of non-dividingcells to re-enter the cell cycle. The study of plant cell cyclecontrol genes is expected to contribute to the understandingof these unique developmental phenomena. The principal regulatorsof the eukaryotic cell cycle, the cyclin-dependent kinases (CDKs)and cyclins, are conserved in plants. This review focuses oncell cycle regulation in the plant Arabidopsis thaliana . Whileexpression of one Arabidopsis CDK gene, Cdc2aAt, was positivelycorrelated with the competence of cells to divide, expressionof a mitotic-like cyclin, cyc1At, was almost exclusively confinedto dividing cells. The expression of the Arabidopsis -type cyclinsappears to be an early stage in the response of plant cellsto external and internal stimuli. Arabidopsis thaliana (L.) Heynh.; cell cycle; CDK; cyclin; plant development; plant hormone     

Membrane Skeletal Proteins and Their Integral Membrane Protein Anchors are Targets for Tyrosine and Threonine Kinases in Euglena

ABSTRACT. Proteins of the membrane skeleton of Euglena gracilis were extensively phosphorylated in vivo and in vitro after incubation with [³²P]-orthophosphate or γ-[³²P] ATP. Endogenous protein threonine/serine activity phosphorylated the major membrane skeletal proteins (articulins) and the putative integral membrane protein (IP39) anchor for articulins. The latter was also the major target for endogenous protein tyrosine kinase activity. A cytoplasmic domain of IP39 was specifically phosphorylated, and removal of this domain with papain eliminated the radiolabeled phosphoamino acids and eliminated or radically shifted the PI of the multiple isoforms of IP39. In gel kinase assays IP39 autophosphorylated and a 25 kDa protein which does not autophosphorylate was identified as a threonine/serine (casein) kinase. Plasma membranes from the membrane skeletal protein complex contained threonine/serine (casein) kinase activity, and cross-linking experiments suggested that IP39 was the likely source for this membrane activity. pH optima, cation requirements and heparin sensitivity of the detergent solubilized membrane activity were determined. Together these results suggest that protein kinases may be important modulators of protein assembly and function of the membrane skeleton of these protistan cells.     

Cold snaps,heatwaves, and arthropod growth

1. Arthropod performance is a non‐linear function of temperature, and thus global climate change may impact arthropods in a variety of non‐obvious ways. 2. In this paper, the well‐known thermal performance curve is reviewed briefly and attention is drawn to the importance of variance in temperature, particularly major weather events such as cold snaps and heatwaves. 3. A model is developed that considers the asymmetry between cold and heat stress and, particularly, the different timescales of recovery from these stressors: near‐instantaneous for cold and lagged effects from heat. 4. Growth rate is evaluated as a function of weather‐event intensity and length. Including the timescale asymmetry exacerbates both heat stress and, to a much lesser degree, cold stress.     

Evidence for mate‐encounter Allee effect in an invasive longhorn beetle (Coleoptera: Cerambycidae)

1. Limited empirical support is available for mate‐encounter Allee effects in invasive insects due to the logistical challenges of studying demographic trends in low‐density populations. 2. Traps baited with pheromone and spruce volatiles were used to monitor the abundance of female Tetropium fuscum F. (Coleoptera: Cerambycidae) at multiple sites in Nova Scotia in 2011 and 2012. Each female was dissected to determine the presence or absence of sperm in its spermatheca (mated or virgin female, respectively). 3. Both male and total T. fuscum abundance declined with increasing distance to the focal point of T. fuscum's invasion. Female mating probability declined with male abundance and with distance from the invasion focus, and mating probabilities were very low at the most peripheral sites. Difficulty in encountering mates may thus contribute to limiting the spread of T. fuscum. 4. The approach outlined here could be integrated into existing surveys of wood borers using traps baited with semiochemicals to improve our understanding of the role of the mate‐encounter Allee effect in invasion dynamics.     

Methanol Accumulation in Maturing Seeds

During in vitro growth and maturation of soybean seeds, cessationof embryo growth and dry weight accumulation occurred in thepresence of abundant C and N nutrients. Axis followed by cotyledontissues changed from green to yellow, and post-harvest germinationpotential declined if cultured after yellowing of axis tissues.A tissue specific accumulat;on of methanol occurred during thein vitro culture of immature seeds (i.e. initially 50 to 70mg fresh weight) to maturity in liquid medium. Methanol accumulatedto 3.0 g m^–3 or 50 µg seed^–1 in the medium,while methanol decreased from 37 to about 3.0 µg g^–1fresh weight in cotyledons. By contrast, axis tissues increased20-fold in methanol concentration to 90 µg g^–1 during20 d in culture. Ethanol was present only in trace amounts inaxis tissues and medium. Addition of exogenous methanol vapourto in situ grown seeds during precocious maturation decreasedsubsequent seedling vigour and germination with increasing levelsof exposure. Methanol accumulation in axis tissues during thegermination phase was not correlated with high temperature andtissue water content treatments which simulated pre-harvestdeterioration of seeds. However, the accumulation of methanolduring in vitro seed development and maturation in liquid culturemay contribute to reduced post-harvest germination performance. Key words: Soybean, Glycine max, seed maturation, in vitro, methanol     

Proceedings of the signature series symposium “cellular therapies for orthopaedics and musculoskeletal disease proven and unproven therapies—promise,facts and fantasy,” international society for cellular therapies,montreal, canada,may 2, 2018

The Signature Series Symposium “Cellular Therapies for Orthopaedics and Musculoskeletal Disease Proven and Unproven Therapies—Promise, Facts and Fantasy” was held as a pre-meeting of the 26^th International Society for Cellular Therapy (ISCT) annual congress in Montreal, Canada, May 2, 2018. This was the first ISCT program that was entirely dedicated to the advancement of cell-based therapies for musculoskeletal diseases. Cellular therapies in musculoskeletal medicine are a source of great promise and opportunity. They are also the source of public controversy, confusion and misinformation. Patients, clinicians, scientists, industry and government share a commitment to clear communication and responsible development of the field. Therefore, this symposium convened thought leaders from around the world in a forum designed to catalyze communication and collaboration to bring the greatest possible innovation and value to patients with musculoskeletal conditions.     

Oxygen Uptake and Antioxidant Responses of the Free-Living Diplomonad Hexamita sp.

ABSTRACT. The free-living anaerobic flagellate Hexamita sp. was observed to actively consume O₂ with a K_m O₂ of 13 μM. Oxygen consumption increased lineraly with O₂ tension up to a threshold level of 100 μM, above which it was inhibited. Oxygen uptake was supported by a number of substrates but probably not coupled to energy conservation as cytochromes could not be detected spectro-photometrically. In addition, inhibitors specific for respiratory chain components did not significantly affect O₂ uptake. Respiration was however, partially inhibited by flavoprotein and iron-sulfur protein inhibitors. NAD(P)H supported O₂ consumption was measured in both particulate and soluble fractions; this activity was partially inhibited by quinacrine. A chemosensory response was observed in cells exposed to air, however no response was observed in the presence of superoxide dismutase plus catalase. Catalase and nonspecific peroxidase activity could not be detected, but superoxide dismutase activity was present. Superoxide dismutase was sensitive to NaN₃ and H₂O₂ but not KCN, suggesting a Fe prosthetic group. Flow cytometric analysis revealed that thiol levels in live cells were depleted in the presence of t-butyl H₂O₂. The observed NADPH-driven glutathione reductase activity is believed to recycle oxidized thiols in order to re-establish reduced thiol levels in the cell. The corresponding thiol cycling enzyme glutathione peroxidase could not be detected. The ability to withstand high O₂ tensions (100 μM) would enable Hexamita to spend short periods in a wider range of habitats. Prologed exposure to O₂ tensions higher than 100 μM leads to irreversible damage and cell death.     

Simulated mechanisms of soil N feedback on the forest CO2 response

An improved understanding of the response of forest ecosystems to elevated levels of CO₂ in the atmosphere is crucial because atmospheric CO₂ concentration continues to increase at an accelerating rate and forests are an important sink in the global carbon cycle. Several CO₂‐enrichment experiments have now been running for more than 10 years, with highly variable short‐term results after the first decade. Responses to rising [CO₂] over the next few decades will depend on several plant and ecosystem feedbacks that are inadequately understood. In this study, we conduct a sensitivity analysis, within the context of the simulated CO₂ response, using a new version of the G'DAY ecosystem model, with an improved decomposition submodel, applied to a nitrogen‐limited Norway spruce forest site in the north of Sweden. The new decomposition model incorporates important modifications to soil processes, including some that constitute negative feedbacks on an ecosystem's growth response to elevated [CO₂]. The sensitivity analysis reveals key parameters and processes that are important for the simulated CO₂ response on the short term and others that are more important on the long term. A process that has a strong impact on the short‐term response is a change in decomposer composition, potentially in response to altered litter quality. Parameters that become increasingly important in the long term are carbon allocation to root exudates that are directly or indirectly associated with atmospheric N₂ fixation, and the rate of humification of soil organic matter. We identify factors intrinsic to species and site (microbes and resources) and ecosystem nutrient supply that determine the duration of the enhanced simulated growth response to elevated [CO₂].     

Correspondence analysis of shell morphology in the African freshwater snail Biomphalaria pfeifferi (Kraus 1848) (Pulmonata: Gastropoda)

A correspondence analysis of shell measurements taken from 521 widely dispersed specimens of the African aquatic pulmonate snail Biomphalaria pfeifferi suggests the existence of eight morphological groups. These groups appear to relate to either ecophysiological factors or to factors associated with the stability of the freshwater system rather than to aspects of geographic distribution and genetic isolation.