affyPara—a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data

Microarray data repositories as well as large clinical applications of gene expression allow to analyse several hundreds of microarrays at one time. The preprocessing of large amounts of microarrays is still a challenge. The algorithms are limited by the available computer hardware. For example, building classification or prognostic rules from large microarray sets will be very time consuming. Here, preprocessing has to be a part of the cross-validation and resampling strategy which is necessary to estimate the rule’s prediction quality honestly

Highlights from the ISCB Student Council Symposium 2013

This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) / European Conference on Computational Biology (ECCB) conference in Berlin, Germany, on July 19, 2013

Homology-based inference sets the bar high for protein function prediction

Background: Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference. Methods: Here, we describe a few methods that predict protein function exclusively through homology. Together, they set the bar or lower limit for future improvements. Results and conclusions: During the development of these methods, we faced two surprises. Firstly, our most successful implementation for the baseline ranked very high at CAFA1. In fact, our best combination of homology-based methods fared only slightly worse than the top-of-the-line prediction method from the Jones group. Secondly, although the concept of homology-based inference is simple, this work revealed that the precise details of the implementation are crucial: not only did the methods span from top to bottom performers at CAFA, but also the reasons for these differences were unexpected. In this work, we also propose a new rigorous measure to compare predicted and experimental annotations. It puts more emphasis on the details of protein function than the other measures employed by CAFA and may best reflect the expectations of users. Clearly, the definition of proper goals remains one major objective for CAFA

Late Cretaceous alveolinaceans (larger foraminifera) of the Caribbean palaeobioprovince and their stratigraphic distribution

Architectural analysis of the Late Cretaceous alveolinaceans of the Caribbean palaeobioprovince has made it possible to separate four genera: Praechubbina, Chubbinella gen. nov., Chubbina and Caribalveolina. The first three genera belong to the family Rhapydioninidae, while the fourth is placed in the family Alveolinidae. Two species, Praechubbina breviclaustra and P. oxchucensis sp. nov., represent the primitive genus Praechubbina, while the species cardenasensis and obesa, previously ascribed to this genus, must be reassigned respectively to Chubbinella gen. nov. and Caribalveolina. The species Chubbina jamaicensis, C. macgillavryi and C. fourcadei sp. nov. complete the inventory of Chubbina. The alveolinid genus Caribalveolina comprises two species, C. obesa and C. michaudi. Caribbean alveolinaceans include two successive assemblages. The lower assemblage is characterized by Praechubbina oxchucensis, P. brevisclaustra, Chubbinella cardenasensis and Caribalveolina obesa. The upper assemblage is represented by the genus Chubbina, with C. fourcadei, C. jamaicensis and C. macgillavryi, and Caribalveolina michaudi. The age of the lower assemblage is uncertain (probably Late Campanian-Early Maastrichtian), while the upper assemblage has been dated by strontium isotope stratigraphy as Late Maastrichtian. © 2013 Natural History Museum

Canalispina iapygia gen. et sp. nov.: The last Siderolitidae (Foraminiferida) from the upper Maastrichtian of southern Italy

Siderolitid larger benthic foraminifera are widespread and abundant microfossils in high-energy shallow-water Tethyan carbonate platform facies of Campanian – Maastrichtian age. The more evolved representatives of this group, placed in the genus Siderolites, are characterized by a complex canal system and by canaliculate spines. For these characters they have been often compared to recent calcarinids. The specific name Siderolites calcitrapoides has been almost invariantly used for all Maastrichtian siderolitids with spines. In this paper we give the first accurate description of the siderolitids occurring in the Maastrichtian carbonate platform facies of the Salento Peninsula (southeastern Apulia) and of the Pachino area (southeastern Sicily). The architecture of the test of these siderolitids differs considerably from that of true S. calcitrapoides. For these morphotypes we erect the new taxon Canalispina iapygia gen. et sp. nov. The new taxon developed longer and more robust spines by changing the architecture of the canal system and by embodying the base of the spines within the chambers. Biostratigraphy and strontium isotope stratigraphy support a late Maastrichtian age for the studied material, indicating that Canalispina iapygia gen. et sp. nov., represents the last step in the evolution of siderolitids before the extinction of the group at the Cretaceous-Paleocene boundary. Keywords SiderolitidaeLarger benthic foraminiferaTaxonomyMaastrichtiansouthern Ital

A new siderolitid from the late Maastrichian of Italy

During the latest Cretaceous, many representatives of the larger benthic foraminifera (LBF) community reached a high level of “maturation”, developing large-sized shells with complex architectures. Increasing size and complexity in a relatively short period of time can be interpreted as a rapid response to biologic competition for space and resources with other LBF (like for instance fabularids, lacazinids, alveolinids, rotaliids, orbitoidids) in the shallow carbonate to mixed carbonate-clastic platforms. A paradigm of this type of fast evolution is the group of the Siderolitidae, lamellar-perforate LBF with a complex canal system that were abundant in shallow-water platforms during the late Cretaceous (Campanian-Maastrichtian). Five genera have been described up to now that represent five different steps of evolution in terms of complexity: Arnaudiella, Praesiderolites, Pseudosiderolites, Wannierina and Siderolites. In broad terms, the species ascribed to these genera replace each other in time, offering a good tool for high resolution biostratigraphy. Recent studies on material from the late Maastrichtian of Italy have yielded a siderolitid with a singular architectural pattern that differs from its relatives. The new morphotype has a very large test with large canaliferous spines and a very complex enveloping canal system. This new morphotype is the youngest siderolitid known so far. Strontium isotope stratigraphy indicates a late Maastrichtian age of 66.4 ±1.5 Ma, very close to the K-Pg boundary. The large size and very high complexity shown by the new morphotype are in accordance with the general evolutionary trends of LBF

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

<div><p>Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by <i>Deinococcus radiodurans</i>. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.</p></div

Protein disorder linked to habitat more than to phylogeny.

<p>The fractions of proteins with long disordered regions are predicted by two disorder predictor methods (MD in green bars and IUPred in red bars). Eukaryotes are predicted with substantially more disorder than prokaryotes. Within the kingdoms predictions vary greatly: organisms in similar habitats tend to resemble each other in terms of disorder more than they resemble their closest phylogenetic relatives. (A) Hyperthermophilic archaea (dark red) are more ordered than their phylogenetic neighbors; halophilic archaea are more disordered (green). (B) Halophilic bacteria also appear more disordered than their relatives. (C) The bacterial thermophile (red) also has less disorder than its relatives. Other extreme organisms included: psychrophile (blue), psychrotolerant (light blue), radiation resistant (purple) and alkalophile (pink). We could also find organisms with relative high/low disorder content explainable separately.</p

Distribution of disorder content in different organisms.

<p>Fractions of proteins with long regions of disorder (here ≥30 consecutive residues) were predicted by three prediction methods (MD, NORSnet and IUPred). <b>(A)</b> The raw values are standardized using the Z-scores (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133990#pone.0133990.e001" target="_blank">Eq 1</a>; mean and standard deviation σ from a 1613 prokaryotes calculated for each method; positive: higher than the mean; negative: below the mean; integers +/- N imply N*σ above/below the mean). The top panel shows the extremophiles; the lower panel shows the closest phylogenetic relative for each extremophile in the top panel (for relatives discussed in the text and left out for clarity from the figure, for all studied organisms <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133990#pone.0133990.s003" target="_blank">S3 Fig</a>). The archaeal halophiles <i>Haloarcula marismortui ATCC 43049</i> and <i>Halobacterium sp</i>. <i>NRC-1</i> were predicted with the highest content of proteins with long disorder. Conversely, the archaeal thermophile <i>Aeropyrum pernix K1</i> was one of the organisms predicted with the lowest disorder. The taxonomic neighbors section compares the disorder predicted for the closest relatives of the extremophiles. <b>(B-D)</b> Mapping of disorder protein content predictions for all organisms for each prediction method (B: MD [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133990#pone.0133990.ref042" target="_blank">42</a>], C: NORSnet [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133990#pone.0133990.ref006" target="_blank">6</a>], and D: IUPred Clearly, all three methods put the thermophiles on the left (less disorder), while the halophiles appear on the right (high disorder). The blue curves are Gaussian fits based on the mean and σ of our data.</p