The impact of sequence database choice on metaproteomic results in gut microbiota studies

Background: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Results: Here, we present a systematic investigation of variables concerning database construction and annotation and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. In particular, the contribution of experimental metagenomic databases was revealed to be mandatory when dealing with mouse samples. Moreover, the use of a "merged" database, containing all metagenomic sequences from the population under study, was found to be generally preferable over the use of sample-matched databases. We also observed that taxonomic and functional results are strongly database-dependent, in particular when analyzing the mouse gut microbiota. As a striking example, the Firmicutes/Bacteroidetes ratio varied up to tenfold depending on the database used. Finally, assembling reads into longer contigs provided significant advantages in terms of functional annotation yields. Conclusions: This study contributes to identify host- and database-specific biases which need to be taken into account in a metaproteomic experiment, providing meaningful insights on how to design gut microbiota studies and to perform metaproteomic data analysis. In particular, the use of multiple databases and annotation tools has to be encouraged, even though this requires appropriate bioinformatic resources

The Butcher-Oemler Effect in Abell 2317

This paper presents deep narrow band photometry of the cluster A2317 (z=0.211) carried out using KPNO 4 m and Steward 2.3 m telescopes. Using rest frame Stromgren photometry, it is determined that A2317 has an unusually high fraction of blue galaxies (the Butcher-Oemler effect) for its redshift (f_B=0.35). We demonstrate that the ratio of blue to red galaxies has a strong dependence on absolute magnitude such that blue galaxies dominate the top of the luminosity function. Spectrophotometric classification shows that a majority of the red galaxies are E/S0's, with a small number of reddened starburst galaxies. Butcher-Oemler galaxies are shown to be galaxies with star formation rates typical of late-type spirals and irregular. Starburst systems were typically found to be on the lower end of the cluster luminosity function. In addition, blue galaxies are preferentially found in the outer edges of the cluster, whereas the red galaxies are concentrated in the cluster core.Comment: 23 pages including 1 table and 6 figures, AASTeX v4.0. Accepted by Ap.J. Data, referee report and response are avaliable from http://zebu.uoregon.edu/~j

Elliptical Galaxies with Emission Lines from the Sloan Digital Sky Survey

We present the results of 11 elliptical galaxies with strong nebular emission lines during our study of star formation history along the Hubble sequence. After removing the dilution from the underlying old stellar populations by use of stellar population synthesis model, we derive the accurate fluxes of all emission lines for these objects, which are later classified with emission line ratios into one Seyfert 2, six LINERs and four HII galaxies. We also identify one HII galaxy (A1216+04) as a hitherto unknown Wolf-Rayet galaxy from the presence of the Wolf-Rayet broad bump at 4650 \AA. We propose that the star-forming activities in elliptical galaxies are triggered by either galaxy-galaxy interaction or the merging of a small satellite/a massive star cluster, as already suggested by recent numerical simulations

Generation of file processing programs based on JSP

This paper describes the generation of file processing programmes within the TUBA environment. Program structures are derived from data structures according to the JSP method. Expressions describing output data are specified in user-system dialogues. The program specifications are stored in the dictionary. Complete executable programs can be generated from these specifications

Learning Concise Models from Long Execution Traces

Abstract models of system-level behaviour have applications in design exploration, analysis, testing and verification. We describe a new algorithm for automatically extracting useful models, as automata, from execution traces of a HW/SW system driven by software exercising a use-case of interest. Our algorithm leverages modern program synthesis techniques to generate predicates on automaton edges, succinctly describing system behaviour. It employs trace segmentation to tackle complexity for long traces. We learn concise models capturing transaction-level, system-wide behaviour--experimentally demonstrating the approach using traces from a variety of sources, including the x86 QEMU virtual platform and the Real-Time Linux kernel

Modeling functional requirements using tacit knowledge: a design science research methodology informed approach

The research in this paper adds to the discussion linked to the challenge of capturing and modeling tacit knowledge throughout software development projects. The issue emerged when modeling functional requirements during a project for a client. However, using the design science research methodology at a particular point in the project helped to create an artifact, a functional requirements modeling technique, that resolved the issue with tacit knowledge. Accordingly, this paper includes research based upon the stages of the design science research methodology to design and test the artifact in an observable situation, empirically grounding the research undertaken. An integral component of the design science research methodology, the knowledge base, assimilated structuration and semiotic theories so that other researchers can test the validity of the artifact created. First, structuration theory helped to identify how tacit knowledge is communicated and can be understood when modeling functional requirements for new software. Second, structuration theory prescribed the application of semiotics which facilitated the development of the artifact. Additionally, following the stages of the design science research methodology and associated tasks allows the research to be reproduced in other software development contexts. As a positive outcome, using the functional requirements modeling technique created, specifically for obtaining tacit knowledge on the software development project, indicates that using such knowledge increases the likelihood of deploying software successfully

Searching edges in the overlap of two plane graphs

Consider a pair of plane straight-line graphs, whose edges are colored red and blue, respectively, and let n be the total complexity of both graphs. We present a O(n log n)-time O(n)-space technique to preprocess such pair of graphs, that enables efficient searches among the red-blue intersections along edges of one of the graphs. Our technique has a number of applications to geometric problems. This includes: (1) a solution to the batched red-blue search problem [Dehne et al. 2006] in O(n log n) queries to the oracle; (2) an algorithm to compute the maximum vertical distance between a pair of 3D polyhedral terrains one of which is convex in O(n log n) time, where n is the total complexity of both terrains; (3) an algorithm to construct the Hausdorff Voronoi diagram of a family of point clusters in the plane in O((n+m) log^3 n) time and O(n+m) space, where n is the total number of points in all clusters and m is the number of crossings between all clusters; (4) an algorithm to construct the farthest-color Voronoi diagram of the corners of n axis-aligned rectangles in O(n log^2 n) time; (5) an algorithm to solve the stabbing circle problem for n parallel line segments in the plane in optimal O(n log n) time. All these results are new or improve on the best known algorithms.Comment: 22 pages, 6 figure