Differential prioritization of intramaze cue and boundary information during spatial navigation across the human lifespan

Spatial learning can be based on intramaze cues and environmental boundaries. These processes are predominantly subserved by striatal- and hippocampal-dependent circuitries, respectively. Maturation and aging processes in these brain regions may affect lifespan differences in their contributions to spatial learning. We independently manipulated an intramaze cue or the environment’s boundary in a navigation task in 27 younger children (6–8 years), 30 older children (10–13 years), 29 adolescents (15–17 years), 29 younger adults (20–35 years) and 26 older adults (65–80 years) to investigate lifespan age differences in the relative prioritization of either information. Whereas learning based on an intramaze cue showed earlier maturation during the progression from younger to later childhood and remained relatively stable across adulthood, maturation of boundary-based learning was more protracted towards peri-adolescence and showed strong aging-related decline. Furthermore, individual differences in prioritizing intramaze cue- over computationally more demanding boundary-based learning was positively associated with cognitive processing fluctuations and this association was partially mediated by spatial working memory capacity during adult, but not during child development. This evidence reveals different age gradients of two modes of spatial learning across the lifespan, which seem further influenced by individual differences in cognitive processing fluctuations and working memory, particularly during aging

Understanding Marine Microbes, the Driving Engines of the Ocean

When you hear the word microbes, what comes to your mind? Something much too small to see and that makes you fall ill? Just because some microbes cause diseases that does not mean they are all evil. For example, in the marine (ocean) environment, the vast majority of microbes are good ones. They are the “driving engines” of the ocean and are essential for the health of our whole planet. Unfortunately, most of the marine microbes and their interactions with the marine environment are poorly understood. So, it is important to get an idea of which microbes are helping us and how they are doing this. These data will provide scientists with the knowledge to fight against big global challenges, such as climate change and environmental pollution. Unfortunately, it is very hard to study marine microbes due to their microscopic size, huge diversity, and their big home – the ocean. Therefore, we would like to engage “citizen scientists” in this project to help us to sample marine microbes so that we can identify them

Ten steps toward a better personality science - How quality may be rewarded more in research evaluation

This target article is part of a theme bundle including open peer commentaries (https://doi.org/10.5964/ps.9227) and a rejoinder by the authors (https://doi.org/10.5964/ps.7961). We point out ten steps that we think will go a long way in improving personality science. The first five steps focus on fostering consensus regarding (1) research goals, (2) terminology, (3) measurement practices, (4) data handling, and (5) the current state of theory and evidence. The other five steps focus on improving the credibility of empirical research, through (6) formal modelling, (7) mandatory pre-registration for confirmatory claims, (8) replication as a routine practice, (9) planning for informative studies (e.g., in terms of statistical power), and (10) making data, analysis scripts, and materials openly available. The current, quantity-based incentive structure in academia clearly stands in the way of implementing many of these practices, resulting in a research literature with sometimes questionable utility and/or integrity. As a solution, we propose a more quality-based reward scheme that explicitly weights published research by its Good Science merits. Scientists need to be increasingly rewarded for doing good work, not just lots of work

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences

Background: Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. Findings: FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. Conclusions: The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data

Weak Poisson structures on infinite dimensional manifolds and hamiltonian actions

We introduce a notion of a weak Poisson structure on a manifold $M$ modeled on a locally convex space. This is done by specifying a Poisson bracket on a subalgebra \cA \subeq C^\infty(M) which has to satisfy a non-degeneracy condition (the differentials of elements of \cA separate tangent vectors) and we postulate the existence of smooth Hamiltonian vector fields. Motivated by applications to Hamiltonian actions, we focus on affine Poisson spaces which include in particular the linear and affine Poisson structures on duals of locally convex Lie algebras. As an interesting byproduct of our approach, we can associate to an invariant symmetric bilinear form $\kappa$ on a Lie algebra \g and a $\kappa$-skew-symmetric derivation $D$ a weak affine Poisson structure on \g itself. This leads naturally to a concept of a Hamiltonian $G$-action on a weak Poisson manifold with a \g-valued momentum map and hence to a generalization of quasi-hamiltonian group actions

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

Background: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

Background: The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings: We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious "guilty-by-association'' approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance: Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing

A recent investigation of bacterioplankton communities in the German Bight towards the end of a diatomdominated spring phytoplankton bloom revealed pronounced successions of distinct bacterial clades. A combination of metagenomics and metaproteomics indicated that these clades had distinct substrate spectra and consumed different algal substrates. In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing. This complementary approach provided new insights into the community composition and expressed genes as well as the assessment of metabolic activity levels of distinct clades. Flavobacteria (genera Ulvibacter, Formosa, and Polaribacter), Alphaproteobacteria (SARI 1 clade and Rhodobacteraceae) and Gammaproteobacteria (genus Reinekea and SAR92 dade) were the most abundant taxa. Mapping of the metatranscriptome data on assembled and taxonomically classified metagenome data of the same samples substantiated that Formosa and Polaribacter acted as major algal polymer degraders, whereas Rhodobacteraceae and Reinekea spp. exhibited less specialized substrate spectra. In addition, we found that members of the Rhodobacteraceae and SAR92 clade showed high metabolic activity levels, which suggests that these clades played a more important role during the bloom event as indicated by their in situ abundances. (c) 2014 The Authors. Published by Elsevier B.V