BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

<p>Abstract</p> <p>Background</p> <p>Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes.</p> <p>Results</p> <p>The enzymes in the UniprotKB are identified and their sequences compared against each other with BLAST. The enzymes are then clustered into a number of trees, where each tree node is associated with a set of EC-numbers. The enzyme sequences in the tree nodes are aligned with ClustalW. The conserved columns of the resulting multiple alignments are used to construct sequence patterns. In the last step, we verify the quality of the patterns by computing their specificity. Patterns with low specificity are omitted and recomputed further down in the tree. The final high-quality patterns can be used for functional annotation. We ran our protocol on a recent Swiss-Prot release and show statistics, as well as a comparison to PRIAM, a probabilistic method that is also specialized on the functional annotation of enzymes. We determine the amount of true positive annotations for five common microorganisms with data from BRENDA and AMENDA serving as standard of truth. BrEPS is almost on par with PRIAM, a fact which we discuss in the context of five manually investigated cases.</p> <p>Conclusions</p> <p>Our protocol computes highly specific sequence patterns that can be used to support the functional annotation of enzymes. The main advantages of our method are that it is automatic and unsupervised, and quite fast once the patterns are evaluated. The results show that BrEPS can be a valuable addition to the reconstruction of metabolic networks.</p

A Framework for Exploring the Impact of Tutor Practices on Learner Self-regulation in Online Environments

There is increasing interest in the conceptualization of Self-Regulated learning (SRL) as a dynamic process which unfolds over the course of a learning activity. This is partly because this conceptualization could potentially be operationalized and used as the basis for AI and analytics tools which monitor and scaffold SRL in real-time. However, while there is an abundance of research on theories of SRL, little research explicitly reviews and operationalizes such theoretical considerations. Work is needed to develop frameworks for the practical applications of fundamental SRL theories, helping researchers move from conceptual considerations to operationalization in real world settings. In this paper, we propose a theoretically grounded framework for investigating SRL in the context of online tutoring for upper primary school learners. SRL is interpreted as a social learning construct, and the framework proposed is designed to investigate the influence of tutor practices on the development of learners’ SRL. We present the results of a pilot study that explored the applicability of the framework

Nucleotide Frequencies in Human Genome and Fibonacci Numbers

This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on two assumptions. First, Chargaff's second parity rule should be valid, and, second, the nucleotide frequencies should approach limit values when the number of bases is sufficiently large. Under these two hypotheses, it is possible to predict the human nucleotide frequencies with accuracy. It is noteworthy, that the predicted values are solutions of an optimization problem, which is commonplace in many nature's phenomena.Comment: 12 pages, 2 figure

Cord Blood Derived CD4+CD25high T Cells Become Functional Regulatory T Cells upon Antigen Encounter

Background: Upon antigen exposure, cord blood derived T cells respond to ubiquitous environmental antigens by high proliferation. To date it remains unclear whether these “excessive” responses relate to different regulatory properties of the putative T regulatory cell (Treg) compartment or even expansion of the Treg compartment itself

Geo-Biological Investigations on Azooxanthellate Cold-Water Coral Reefs on the Carbonate Mounds Along the Celtic Continental Slope

Northeast Atlantic 2004 Cruise No. 61, Leg 1 April 19 to May 4, 2004, Lisbon – Cor

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline

The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline