Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

Report on Special Investigation of the City of Pleasant Plain, For the period January 1, 2004 through May 3, 2006

City Audit Report - Special Investigation

Phylogenetic structures of the Holarctic Sorex araneus group and its relationships with S-samniticus, as inferred from mtDNA sequences

The shrews of the Sorex araneus group, characterized by the sexual chromosome complex XY1, Y2 have been intensively studied by morphological, karyotypical, and biochemical analyses. Nevertheless, the phylogenetic relationships among the species belonging to the araneus complex are still under debate, as different approaches gave often contradictory results. In this paper, partial nucleotide sequences of the mitochondrial DNA cytochrome b gene (1011 bp) were determined for 6 species of the araneus group from Eurasia and North America. We also included in the data set the sequences of Sorex samniticus, whose relationships with the araneus group remain controversial. Three other species representing two major karyological groups were also examined. Both parsimony and distance trees strongly support the monophyly of the araneus group. Sorex sumniticus is significantly more closely related to the araneus complex than to the other species included in the analysis. Based on the branching pattern within the araneus group, an attempt has been made to reconstruct the colonization history of the Holarctic region.

On prediction of individual sequences

Sequential randomized prediction of an arbitrary binary sequence isinvestigated. No assumption is made on the mechanism of generating the bit sequence. The goal of the predictor is to minimize its relative loss, i.e., to make (almost) as few mistakes as the best ``expert'' in a fixed, possibly infinite, set of experts. We point out a surprising connection between this prediction problem and empirical process theory. First, in the special case of static (memoryless) experts, we completely characterize the minimax relative loss in terms of the maximum of an associated Rademacher process. Then we show general upper and lower bounds on the minimaxrelative loss in terms of the geometry of the class of experts. As main examples, we determine the exact order of magnitude of the minimax relative loss for the class of autoregressive linear predictors and for the class of Markov experts.

MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

Structure of bee-flower system in the coastal sand dune of Abaeté, northeastern Brazil

For twelve months (from January to December of 1996) we investigated bee-flower interactions in a sea coastal ecosystem in Bahia, Brazil. Samples were taken three times each month. 3983 individuals belonging to 49 bee species, grouped in 13 morph-functional categories, visited 66 plant species belonging to 39 botanic families. It was observed 310 interactions between bees and plants at species level. The use of floral resources by bees was not homogeneous; most of the plant species received a low number of visitors. No restricted plant-bee species relationship in resource use concerning the subset of analyzed interactions was detected. In Abaeté the generalist relationships predominated.

Gall midge attack intensity and host-plant response in a Neotropical coastal ecosystem

The gall inducer Clusiamyia nitida Maia, 1996 (Diptera, Cecidomyiidae) often infests the shrub Clusia lanceolata (Camb.) (Clusiaceae) in the Neotropical vegetation of restinga of Rio de Janeiro State, Brazil. Leaves of Clusia lanceolata host up to 20 spheroid galls and show variation in their shape. We aimed to evaluate the effect of gall's intensity on leaves of Clusia lanceolata, and the extension of gall's impact on adjacent non-galled leaves. We analyzed the effect of the number of galls on leaf area, biomass, specific area and leaf appearance from 509 leaves of 14 individual plants. The results showed that differences of individual plants, pairs of leaves, and gall presence were responsible for more then 90% of variation on infested leaves. Variation on parasitic intensity level created differences in leaf response. Under moderate gall attack characterized by scattered galls on a leaf, the increase of the number of galls caused an increase of leaf biomass and area, and a decrease of specific area. The specific area was smaller also under high attack intensity, characterized by coalescent galls on a leaf. In those cases of extremely high parasitic intensity, galled leaves became deformed and the surface area was severely reduced. Leaf deformation due to gall attack led to early leaf abscission, indicated by the 90% of deformed leaves found in the youngest leaf pair of the branch. There was insufficient evidence that the impact of galls on leaf morpho-physiological parameters extended beyond the attacked leaves, because ungalled leaves did not change significantly when their opposite leaf had been galled.

Reconstruction of metal pollution and recent sedimentation processes in Havana Bay (Cuba): A tool for coastal ecosystem management.

Since 1998 the highly polluted Havana Bay ecosystem has been the subject of a mitigation program. In order to determine whether pollution-reduction strategies were effective, we have evaluated the historical trends of pollution recorded in sediments of the Bay. A sediment core was dated radiometrically using natural and artificial fallout radionuclides. An irregularity in the (210)Pb record was caused by an episode of accelerated sedimentation. This episode was dated to occur in 1982, a year coincident with the heaviest rains reported in Havana over the XX century. Peaks of mass accumulation rates (MAR) were associated with hurricanes and intensive rains. In the past 60 years, these maxima are related to strong El Niño periods, which are known to increase rainfall in the north Caribbean region. We observed a steady increase of pollution (mainly Pb, Zn, Sn, and Hg) since the beginning of the century to the mid 90s, with enrichment factors as high as 6. MAR and pollution decreased rapidly after the mid 90s, although some trace metal levels remain high. This reduction was due to the integrated coastal zone management program introduced in the late 90s, which dismissed catchment erosion and pollution.

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil. A list with 538 species of butterflies recorded in the Baixada Santista, São Paulo ( SE Brazil) is presented. Standard sampling protocols (i.e. with entomological nets) were followed. Baited traps were installed for fruit feeding species. Data from the literature and entomological collections were also considered in the total estimated species richness. The species richness recorded in the Baixada Santista region represents about 16% of the Brazilian butterfly fauna, and 34% of the known butterfly fauna for the state of São Paulo. The present list contains an appreciably higher number of species in comparison to other lists from similar biomes farther south, such as Blumenau in Santa Catarina, and Maquiné in Rio Grande do Sul.

A new species of Eccopsis Zeller (Lepidoptera, Tortricidae) from the coastal valleys of northern Chile, with the first continental record of E. galapagana Razowski & Landry

A new species of Eccopsis Zeller (Lepidoptera, Tortricidae) from the coastal valleys of northern Chile, with the first continental record of E. galapagana Razowski & Landry. Eccopsis Zeller, 1852 is reported for the first time from Chile. Eccopsis razowskii Vargas, n. sp. is described and illustrated based on specimens reared from larvae collected on native Acacia macracantha Willd. (Fabaceae) in the coastal valleys of the northern Chilean desert. Eccopsis galapagana Razowski & Landry, 2008, previously known only from the Galapagos Islands, Ecuador, is recorded for the first time from continental South America. Larvae of the latter were collected in northern Chile feeding on Prosopis alba Griseb (Fabaceae).

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.

The analysis of conservation between the human and mouse genomes resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic conservation remains unknown, however. The availability of the sequence of a third mammalian genome, the dog, allows for a large-scale analysis of evolutionary attributes of CNGs in mammals. We have aligned 1638 previously identified CNGs and 976 conserved exons (CODs) from human chromosome 21 (Hsa21) with their orthologous sequences in mouse and dog. Attributes of selective constraint, such as sequence conservation, clustering, and direction of substitutions were compared between CNGs and CODs, showing a clear distinction between the two classes. We subsequently performed a chromosome-wide analysis of CNGs by correlating selective constraint metrics with their position on the chromosome and relative to their distance from genes. We found that CNGs appear to be randomly arranged in intergenic regions, with no bias to be closer or farther from genes. Moreover, conservation and clustering of substitutions of CNGs appear to be completely independent of their distance from genes. These results suggest that the majority of CNGs are not typical of previously described regulatory elements in terms of their location. We propose models for a global role of CNGs in genome function and regulation, through long-distance cis or trans chromosomal interactions.

A zero-delay sequential scheme for lossy coding of individual sequences

We consider adaptive sequential lossy coding of bounded individual sequences when the performance is measured by the sequentially accumulated mean squared distortion. Theencoder and the decoder are connected via a noiseless channel of capacity $R$ and both are assumed to have zero delay. No probabilistic assumptions are made on how the sequence to be encoded is generated. For any bounded sequence of length $n$, the distortion redundancy is defined as the normalized cumulative distortion of the sequential scheme minus the normalized cumulative distortion of the best scalarquantizer of rate $R$ which is matched to this particular sequence. We demonstrate the existence of a zero-delay sequential scheme which uses common randomization in the encoder and the decoder such that the normalized maximum distortion redundancy converges to zero at a rate $n^{-1/5}\log n$ as the length of the encoded sequence $n$ increases without bound.