Report on IOCCG Workshop Phytoplankton Composition from Space: towards a validation\ud strategy for satellite algorithms

The IOCCG-supported workshop “Phytoplankton Composition from Space: towards a validation strategy for satellite algorithms” was organized as a follow-up to the Phytoplankton Functional Types from Space splinter session, held at the International Ocean Colour Science Meeting (Germany, 2013). The specific goals of the workshop were to: 1. Provide a summary of the status of activities from relevant IOCCG working groups, the 2nd PFT intercomparison working group, PFT validation data sets and other research developments. 2. Provide a PFT validation strategy that considers the different applications of PFT products: and seeks community consensus on datasets and analysis protocols. 3. Discuss possibilities for sustaining ongoing PFT algorithm validation and intercomparison activities. The workshop included 15 talks, breakout sessions and plenary discussions. Talks covered community algorithm intercomparison activity updates, review of established and novel methods for PFT validation, validation activities for specific applications and space-agency requirements for PFT products and validation. These were followed by general discussions on (a) major recommendations for global intercomparison initiative in respect to validation, intercomparison and user’s guide; (b) developing a community consensus on which data sets for validation are optimal and which measurement and analysis protocols should be followed to support sustained validation of PFT products considering different applications; (c) the status of different validation data bases and measurement protocols for different PFT applications, and (d) engagement of the various user communities for PFT algorithms in developing PFT product specifications. From these discussions, two breakout groups provided in depth discussion and recommendations on (1) validation of current algorithms and (2) work plan to prepare for validation of future missions. Breakout group 1 provided an action list for progressing the current international community validation and intercomparison activity. Breakout group 2 provided the following recommendations towards developing a future validation strategy for satellite PFT products: 1. Establish a number of validation sites that maintain measurements of a key set of variables. 2. This set of variables should include: • Phytoplankton pigments from HPLC, phycobilins from spectrofluorometry • Phytoplankton cell counts and ID, volume / carbon estimation and imaging (e.g. from flow cytometry, FlowCam, FlowCytobot type technologies) • Inherent optical properties (e.g. absorption, backscattering, VSF) • Hyperspectral radiometry (both above and in-water) • Particle size distribution • Size-fractionated measurements of pigments and absorption • Genetic / -omics data 3. Undertake an intercomparison of methods / instruments over several years at a few sites to understand our capabilities to fully characterize the phytoplankton community. 4. Organise workshops to address the following topics: • Techniques for particle analysis, characterization and classification • Engagement with modellers and understanding end-user requirements • Data storage and management, standards for data contributors, data challenges In conclusion, the workshop was assessed to have fulfilled its goals. A follow-on meeting will be organized during the International Ocean Colour Science Meeting 2015 in San Francisco. Specific follow-on actions are listed at the end of the report

Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

<p>Abstract</p> <p>Background</p> <p>Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs.</p> <p>Results</p> <p>Using a combination of <it>in silico </it>and experimental approaches, we identified and characterized novel <it>P</it>. <it>abyssi </it>ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in the late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel <it>P</it>. <it>abyssi </it>ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four <it>P</it>. <it>abyssi </it>CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized.</p> <p>Conclusions</p> <p>This work proposes a revised annotation of CRISPR loci in <it>P</it>. <it>abyssi </it>and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.</p

L’utilisation de mesures indirectes et directes du comportement dans l’évaluation des interventions ciblant les enfants agressifs

L’efficacité des interventions auxquelles sont exposés les enfants agressifs doit être évaluée avec rigueur. Pour ce faire, les chercheurs et praticiens doivent disposer de mesures fiables, valides, exemptes de biais et qui soient suffisamment sensibles pour permettre de détecter tout changement dans le comportement des enfants. Le premier objectif de cet article consiste à mettre en évidence les limites associées à l’utilisation de mesures indirectes pour évaluer le comportement des enfants exposés à une intervention. Le second objectif vise à illustrer les enjeux associés à l’utilisation de mesures directes basées sur l’observation du comportement. Une analyse des différentes possibilités qui s’offrent aux chercheurs et aux praticiens, notamment en ce qui a trait au choix des comportements ciblés par l’observation et au contexte où se déroule l’observation, est proposée.Behavioral outcomes of intervention targeting young aggressive children have to be carefully assessed. Researchers and practioners need reliable, valid, and bias-free instruments that are also sensitive enough to detect any change in children’s behavior. The first goal of this article is to highlight limitations imposed by indirect measures of behavioral assessment with children exposed to an intervention. The second goal is to illustrate issues related to direct behavioral assessment using observation procedure. The different options for researchers and practioners regarding the choice of behavioral targets and observation settings are discussed.A eficácia das intervenções às quais são expostas as crianças agressivas deve ser avaliada com rigor. Para tal, os investigadores e os práticos devem dispor de medições fiáveis, válidas, isentas de enviesamentos e que sejam suficientemente sensíveis para permitir detectar toda a mudança no comportamento das crianças. o primeiro objectivo deste artigo consiste em evidenciar os limites associados à utilização de medições indirectas para avaliar o comportamento das crianças expostas a uma intervenção. o segundo objectivo visa ilustrar os desafios associados à utilização de medições directas baseadas sobre a observação do comportamento. é proposta uma análise das diferentes possibilidades que se apresentam aos investigadores e aos práticos, nomeadamente no que se refere à escolha de comportamentos-alvo para a observação e ao contexto no qual se desenvolve a observação

EuGene: an eucaryotic gene finder that combines several sources of evidence

In this paper, we describe the basis of EuGne, a gene nder for eucaryotic organisms applied to Arabidopsis thaliana. The specicity of EuGne, compared to existing gene nding software, is that EuGne combines the output of several information sources, including output of other software, in a weighted directed acyclic graph (DAG) designed in such a way that a shortest path in this graph represents the most likely gene structure of the underlying ADN sequence. The usual simple Bellman linear time shortest path algorithm for DAG has been replaced by a shortest path with constraints algorithm. The constraints express minimum length of introns or intergenic regions. The specicity of the constraints leads to an algorithm which is still linear both in time and space. EuGne eectiveness has been assessed on Araset, a recent dataset of Arabidopsis thaliana sequences used to evaluate several existing gene nding software. It appears that, despite its simplicity, EuGne gives results..

EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences

EUGE`NE’HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. EUGE` NE’HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which allows EUGE`NE’HOM to handle sequences from a variety of organisms. The current target of EUGE`NE’HOM is plant sequences. The EUGE`NE’HOM web site is available at http://genopole. toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

Diversity of CRISPR systems in the euryarchaeal Pyrococcales

International audiencePyrococcales are members of the order Thermococcales, a group of hyperthermophilic euryarchaea that are frequently found in deep sea hydrothermal vents. Infectious genetic elements, such as plasmids and viruses, remain a threat even in this remote environment and these microorganisms have developed several ways to fight their genetic invaders. Among these are the recently discovered CRISPR systems. In this review, we have combined and condensed available information on genetic elements infecting the Thermococcales and on the multiple CRISPR systems found in the Pyrococcales to fight them. Their organization and mode of action will be presented with emphasis on the Type III-B system that is the only CRISPR system known to target RNA molecules in a process reminiscent of RNA interference. The intriguing case of Pyrococcus abyssi, which is among the rare strains to present a CRISPR system devoid of the universal cas1 and cas2 genes, is also discussed