Microscopic eukaryotes living in a dying lake (Lake Koronia, Greece)

The morphological and phylogenetic diversity of the microscopic eukaryotes of the Lake Koronia water column was investigated during a mass kill of birds and fish in August–September 2004. The dominant morphospecies corresponded to the known toxin-producing species Prymnesium parvum , followed by Amoebidium sp., a taxon belonging to the group of parasitic Mesomycetozoea , and the common chlorophyte Pediastrum boryanum. Prymnesium exhibited heteromorphic life-cycle stages (flagellate and nonmotile coccoid cells). Phylogenetic analysis with 18S rRNA gene suggested that these heteromorphic stages belonged to the Platychrysis – Prymnesium monophyletic group. The most abundant phylotype was almost identical to P. boryanum . The fungal phylotypes were related to the Chytridiomycota , and the ciliate-like ones were closely related to Enchelys polynucleata and Pattersoniella vitiphila . Two phylotypes representing novel members belonging to the Jakobida and the Apicomplexa were also found. The microscopic eukaryotes of Lake Koronia include several organisms that are related to parasitic life modes.     

Resveratrol metabolites in urine as a biomarker of wine intake in free-living subjects: The PREDIMED Study

Several clinical and epidemiological studies have shown that moderate wine consumption may exert a protective effect against oxidative stress involved in several diseases, such as cardiovascular and neurodegenerative disorders. However, the epidemiological assessment of wine consumption has usually been obtained using self-reported questionnaires containing less reliable information for assessing total intake than nutritional biomarkers. A reliable biomarker for wine consumption is, therefore, needed. To validate urinary resveratrol metabolites (RMs) as a biomarker of wine consumption in a large cohort of free-living subjects, 1000 consecutive subjects entering a substudy of the PREDIMED trial (Prevención con Dieta Mediterránea) were evaluated. Data were collected in a validated semiquantitative food frequency questionnaire. RMs were measured in morning urine by LC-MS/MS. Urinary RM values correlated directly with reported daily amounts of wine consumed (r = 0.895; p < 0.001). One drink of wine per week can be detected. Using a cut-off of 411.4 nmol/g creatinine, the measurement of urinary RMs could discriminate wine consumers from non-wine consumers with a sensitivity of 93.3% (95% confidence interval (CI) 91.5–94.7%) and a specificity of 92.1% (CI 90.2–93.7%). Urinary RMs fulfill the criteria to be considered as a nutritional biomarker of wine consumption in a large sample of free-living subjects. This biomarker would provide an additional tool for investigating more precisely the relationship between wine consumption and health benefits.     

Modelling dynamic plant cells

A major challenge in plant biology is to understand how functions in plant cells emerge from interactions between molecular components. Computational and mathematical modelling can encapsulate the relationships between molecular components and reveal how biological functions emerge. We review recent progress in modelling in metabolism, growth, signalling and circadian rhythms in plant cells. We discuss challenges and opportunities for future directions.     

The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses

Background  

Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra of metabolites in the tissues. In pathological situations, the MRS profile changes and this has been particularly described for brain tumours. However, radiologists are frequently not familiar to the interpretation of MRS data and for this reason, the usefulness of decision-support systems (DSS) in MRS data analysis has been explored.     

SpectraClassifier 1.0: a user friendly,automated MRS-based classifier-development system

Background  

SpectraClassifier (SC) is a Java solution for designing and implementing Magnetic Resonance Spectroscopy (MRS)-based classifiers. The main goal of SC is to allow users with minimum background knowledge of multivariate statistics to perform a fully automated pattern recognition analysis. SC incorporates feature selection (greedy stepwise approach, either forward or backward), and feature extraction (PCA). Fisher Linear Discriminant Analysis is the method of choice for classification. Classifier evaluation is performed through various methods: display of the confusion matrix of the training and testing datasets; K-fold cross-validation, leave-one-out and bootstrapping as well as Receiver Operating Characteristic (ROC) curves.     

Notch and NGF/p75NTR control dendrite morphology and the balance of excitatory/inhibitory synaptic input to hippocampal neurones through Neurogenin 3

We have previously shown that dendrite morphology of cultured hippocampal neurones is controlled by Notch receptor activation or binding of nerve growth factor (NGF) to its low affinity receptor p75NTR, i.e. processes that up-regulate the expression of the Homologue of enhancer of split 1 and 5. Thus, the increased expression of these genes decreases the number of dendrites, whereas abrogation of Homologue of enhancer of split 1/5 activity stimulates the outgrowth of new dendrites. Here, we show that Neurogenin 3 is a proneural gene that is negatively regulated by Homologue of enhancer of split 1/5. It also influences dendrite morphology. Hence, a deficit of Notch or NGF/p75NTR activation can lead to the production of high levels of Neurogenin 3, which stimulates the outgrowth of new dendrites. Conversely, activation of either Notch or p75NTR depressed Neurogenin 3 expression, which not only decreased the number of dendrites but also favoured inhibitory (GABAergic) synaptogenesis, thereby diminishing the ratios of excitatory/inhibitory inputs. NGF also augmented the levels of mRNA encoding the vesicular inhibitory amino acid transporter, but it did not affect the fraction of GAD65/67-positive neurones. Conversely, overexpression of Neurogenin 3 largely reduced the number of inhibitory synaptic contacts and, consequently, produced a strong increase in the ratios of excitatory/inhibitory synaptic terminals. Our results reveal a hitherto unknown contribution of NGF/p75NTR to dendritic and synaptic plasticity through Neurogenin 3 signalling.     

Aphid orientation and performance in glasshouses under different UV‐A/UV‐B radiation regimes

Visual cues leading to host selection and landing are of major importance for aphids and evidence suggests that flight activity is very dependent on ultraviolet (UV)‐A radiation in the environment. At the same time research on insect plant hosts suggest that the UV‐B component can deter some pests via changes in secondary metabolite chemistry. Here, we examine the potential of UV (UV‐A/UV‐B) radiation to control insect pests in the glasshouse environment. We first examined artificial exposure to UV‐B and the potential to trigger morphological and biochemical modifications in pepper (Capsicum annuum L., Solanaceae) with implications for the fitness of green peach aphid, Myzus persicae Sulzer (Hemiptera: Aphididae). UV‐B caused accumulation of leaf secondary metabolites and soluble carbohydrates, and stimulated photosynthetic pigments. However, UV‐B did not impact on foliar protein content and aphid performance was unaffected. Next, we studied how altering the UV‐A/UV‐B ratio environment affected aphid orientation and spatial distribution over time, either directly or by exposing plants to supplemental UV before insect introduction. Aphids directly settled and dispersed on their host pepper plants more readily in the presence of supplemental UV‐A and UV‐B. In the control treatment with ambient glasshouse UV‐A and UV‐B, insects remained more aggregated. Furthermore, insects were less attracted to peppers pre‐exposed to supplemental UV‐A and UV‐B radiation. Our results suggest that suppression of UV‐A and UV‐B inside the protected environment reduces aphid colonization and dispersal. Furthermore, application of moderate exposure of young pepper plants to supplemental UV‐B radiation could aid in protection from the colonization by phytophagous insects.     

Whole-genome QTL analysis for MAGIC

Key message

An efficient whole genome method of QTL analysis is presented for Multi-parent advanced generation integrated crosses.

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations have been developed for mice and several plant species and are useful for the genetic dissection of complex traits. The analysis of quantitative trait loci (QTL) in these populations presents some additional challenges compared with traditional mapping approaches. In particular, pedigree and marker information need to be integrated and founder genetic data needs to be incorporated into the analysis. Here, we present a method for QTL analysis that utilizes the probability of inheriting founder alleles across the whole genome simultaneously, either for intervals or markers. The probabilities can be found using three-point or Hidden Markov Model (HMM) methods. This whole-genome approach is evaluated in a simulation study and it is shown to be a powerful method of analysis. The HMM probabilities lead to low rates of false positives and low bias of estimated QTL effect sizes. An implementation of the approach is available as an R package. In addition, we illustrate the approach using a bread wheat MAGIC population.     

Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano

We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon–Wiener diversity index H was higher for Bacteria (1.92–4.03) than for Archaea (0.99–1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.