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

The Relationship between Physical Growth and Infant Behavioral Development in Rural Guatemala

The present study investigated the relationship between a number of anthropometric indices and behavioral development during the first 2 years of life in rural Guatemala. Length and weight were the indices most strongly correlated with behavioral development. If the effect of the infant\u27s length and weight was statistically controlled for, none of the other anthropometric variables explained a significant proportion of the variance in behavioral development. Con- trolling for length (or weight) assessed at the same age as the behavioral assessment, length (or weight) for younger ages was not significantly correlated with behavioral development. Changes in length or weight over time were correlated with changes in behavioral performance. We were unable to explain the association between physical growth and behavioral development by a number of variables including gestational age, nutrient intake, prevalence of disease, and familial characteristics

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific ‘service provision units’ is introduced together with the factors influencing them and the main underlying assumptions for these ‘value influencing factors’. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared

Учет и контроль расчетов с дебиторами и кредиторами в ООО «Вектор»

Рассмотрены теоретические аспекты учета и контроля расчетов с дебиторами и кредиторами организации, основные определения, цели, задачи. Представлена краткая характеристика о предприятии ООО "Вектор", его видах деятельности, организационной структуре. Представлен подробный анализ предприятия ООО "Вектор" выявлены все слабые и сильные стороны. Представлены результаты проведенного исследования, а именно: предложения по совершенствованию учета и контроля расчетов с дебиторами и кредиторами.The theoretical aspects of accounting and control of settlements with debtors and creditors of the organization, the main definitions, goals, objectives are presented. A brief description of the enterprise “Vector”, its types of activities, organizational structure is presented. A detailed analysis of the enterprise “Vector” is presented. All weak and strong parties. The results of the study are presented, namely: proposals for improving the accounting and control of settlements with debtors and creditors

Framing or Gaming? Constructing a Study to Explore the Impact of Option Presentation on Consumers

The manner in which choice is framed influences individuals’ decision-making. This research examines the impact of different decision constructs on decision-making by focusing on the more problematic decision constructs: the un-selected and pre-selected optout. The study employs eye-tracking with cued retrospective think-aloud (RTA) to combine quantitative and qualitative data. Eye-tracking will determine how long a user focuses on a decision construct before taking action. Cued RTA where the user will be shown a playback of their interaction will be used to explore their attitudes towards a decision construct and identify problematic designs. This pilot begins the second of a three phase study, which ultimately aims to develop a research model containing the theoretical constructs along with hypothesized causal associations between the constructs to reveal the impact of measures such as decision construct type, default value type and question framing have on the perceived value of the website and loyalty intentions

Improved annotation with <i>de novo</i> transcriptome assembly in four social amoeba species

Background: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species. Results: An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum. Conclusions: In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects

Properties of field functionals and characterization of local functionals

Functionals (i.e. functions of functions) are widely used in quantum field theory and solid-state physics. In this paper, functionals are given a rigorous mathematical framework and their main properties are described. The choice of the proper space of test functions (smooth functions) and of the relevant concept of differential (Bastiani differential) are discussed. The relation between the multiple derivatives of a functional and the corresponding distributions is described in detail. It is proved that, in a neighborhood of every test function, the support of a smooth functional is uniformly compactly supported and the order of the corresponding distribution is uniformly bounded. Relying on a recent work by Yoann Dabrowski, several spaces of functionals are furnished with a complete and nuclear topology. In view of physical applications, it is shown that most formal manipulations can be given a rigorous meaning. A new concept of local functionals is proposed and two characterizations of them are given: the first one uses the additivity (or Hammerstein) property, the second one is a variant of Peetre's theorem. Finally, the first step of a cohomological approach to quantum field theory is carried out by proving a global Poincar\'e lemma and defining multi-vector fields and graded functionals within our framework.Comment: 32 pages, no figur

Geographic distribution at subspecies resolution level: closely related Rhodopirellula species in European coastal sediments.

Members of the marine genus Rhodopirellula are attached living bacteria and studies based on cultured Rhodopirellula strains suggested that three closely related species R. baltica, 'R. europaea' and 'R. islandica' have a limited geographic distribution in Europe. To address this hypothesis, we developed a nested PCR for a single gene copy detection of a partial acetyl CoA synthetase (acsA) from intertidal sediments collected all around Europe. Furthermore, we performed growth experiments in a range of temperature, salinity and light conditions. A combination of Basic Local Alignment Search Tool (BLAST) and Minimum Entropy Decomposition (MED) was used to analyze the sequences with the aim to explore the geographical distribution of the species and subspecies. MED has been mainly used for the analysis of the 16S rRNA gene and here we propose a protocol for the analysis of protein-coding genes taking into account the degeneracy of the codons and a possible overestimation of functional diversity. The high-resolution analysis revealed differences in the intraspecies community structure in different geographic regions. However, we found all three species present in all regions sampled and in agreement with growth experiments we demonstrated that Rhodopirellula species do not have a limited geographic distribution in Europe