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Rob DeSalle

Publications and source records attributed to Rob DeSalle.

29 records · Page 2Linked to original sources
PubMed2003

The Widespread Colonization Island of Actinobacillus actinomycetemcomitans.

Genomic islands, such as pathogenicity islands, contribute to the evolution and diversification of microbial life. Here we report on the Widespread Colonization Island, which encompasses the tad (tight adherence) locus for colonization of surfaces and biofilm formation by the human pathogen Actinobacillus actinomycetemcomitans. At least 12 of the 14 genes at the tad locus are required for tenacious biofilm formation and synthesis of bundled Flp pili (fibrils) that mediate adherence. The pilin subunit, Flp1, remains inside the cell in tad-locus mutants, indicating that these genes encode a secretion system for export and assembly of fibrils. We found tad-related regions in a wide variety of Bacterial and Archaeal species, and their sequence characteristics indicate possible horizontal transfer. To test the hypothesis of horizontal transfer, we compared the phylogeny of the tad locus to a robust organismal phylogeny using statistical tests of congruence and tree reconciliation techniques. Our analysis strongly supports a complex history of gene shuffling by recombination and multiple horizontal transfers, duplications and losses. We present evidence for a specific horizontal transfer event leading to the establishment of this region as a determinant of disease.

Aggregatibacter actinomycetemcomitans↗
PubMed2003

Combined support for wholesale taxic atavism in gavialine crocodylians.

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed.

Adaptation, Biological↗
PubMed2002

'Pluralism' and the aims of phylogenetic research.

In science, and particularly in the field of phylogenetic systematics, investigators may choose among different methods to analyze their data. These methods include neighbor-joining (or other genetic distance approaches), maximum-likelihood, and cladistic parsimony, among others. These distinct methods of analysis differ considerably in how they process information from the observed data. However, many published molecular analyses utilize trees generated under more than one of these methods, which we will call a 'pluralistic' approach. Here, we explore the statistical, philosophical and operational aspects of the pluralistic approach. We suggest that the pluralistic approach is misguided from all three perspectives and we propose an alternative, logically consistent, strategy as an aim of phylogenetic research.

Animals↗
PubMed2002

Development, homology and systematics.

The basic issue of recognizing and delimiting characters derived from different levels of biological organization, including molecular, cellular, morphological and behavioral levels, has been addressed previously in the cladistic literature. But when considering new sources of information (such as the proliferating Evo-Devo data), it is critical to review traditional theoretical and methodological approaches to their interpretation. This is especially important because the conclusions of a phylogenetic analysis are dependent upon the initial recognition and definition of the characters, the basic units of comparison in phylogeny reconstruction. This chapter explores the role of recent Evo-Devo studies in systematics and attempts to place the Evo-Devo literature into a systematics context.

Animals↗
PubMed2002

Is the evolution of Cnox-2 Hox/ParaHox genes "multicolored" and "polygenealogical?".

Understanding the evolution of metazoan bauplans is linked to understanding the evolution of Hox and ParaHox genes. At the base of metazoan radiation we see in both cases a quite confusing picture yet. Here Cnox-2 is one of the best studied diploblast Hox genes. Homologs of this gene are known from Placozoa and several Cnidaria. In those cases where full length gene sequences, or at least full length homeobox sequences, are available the relationship to Hox genes from triploblastic animals as well as the classification to Hox or ParaHox genes can be controversially discussed. The existing data on possible gene functions also reveal a quite heterogeneous picture. It seems conceivable that part of the "multicolored" picture relates to a "polygenealogical" origin of the Cnox-2 gene.

Animals↗
PubMed2002

An automated phylogenetic key for classifying homeoboxes.

When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.

Algorithms↗
PubMed2002

Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana.

The ionotropic glutamate receptor (iGluR) gene family has been widely studied in animals and is determined to be important in excitatory neurotransmission and other neuronal processes. We have previously identified ionotropic glutamate receptor-like genes (GLRs) in Arabidopsis thaliana, an organism that lacks a nervous system. Upon the completion of the Arabidopsis genome sequencing project, a large family of GLR genes has been uncovered. A preliminary phylogenetic analysis divides the AtGLR gene family into three clades and is used as the basis for the recently established nomenclature for the AtGLR gene family. We performed a phylogenetic analysis with extensive annotations of the iGluR gene family, which includes all 20 Arabidopsis GLR genes, the entire iGluR family from rat (except NR3), and two prokaryotic iGluRs, Synechocystis GluR0 and Anabaena GluR. Our analysis supports the division of the AtGLR gene family into three clades and identifies potential functionally important amino acid residues that are conserved in both prokaryotic and eukaryotic iGluRs as well as those that are only conserved in AtGLRs. To begin to investigate whether the three AtGLR clades represent different functional classes, we performed the first comprehensive mRNA expression analysis of the entire AtGLR gene family. On the basis of RT-PCR, all AtGLRs are expressed genes. The three AtGLR clades do not show distinct clade-specific organ expression patterns. All 20 AtGLR genes are expressed in the root. Among them, five of the nine clade-II genes are root-specific in 8-week-old Arabidopsis plants.

Animals↗
PubMed2002

The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion.

Identification of regulatory molecules that determine the extent and direction of expansion is necessary to understand how cell morphogenesis is controlled in plants. We recently identified COB (COBRA) as a key regulator of the orientation of cell expansion in the root. Analysis of the Arabidopsis genome sequence indicated that COB belongs to a multigene family consisting of 12 members, all predicted to encode glycosylphosphatidylinositol-anchored proteins. All but two of the COBL (COB-like) genes are expressed in most organs examined, suggesting possible redundancy. Sequence comparisons, phylogenetic analyses, and exon-intron positions revealed that the COB family is composed of two main subgroups sharing a common architecture, one subgroup being characterized by an additional N-terminal domain. Identification of expressed sequence tags corresponding to potential orthologs in other plant species suggested that COB-related functions are required in all vascular plants. Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface.

Amino Acid Sequence↗
PubMed2002

Lack of canonical E6 and E7 open reading frames in bird papillomaviruses: Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus.

Determination and analyses of the complete sequence of Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus indicate that they represent a distinct and distant lineage of papillomaviruses. The lack of canonical E6-E7 open reading frames suggests that they serve adaptive functions during papillomavirus evolution.

Amino Acid Sequence↗
PubMed2002

In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migration.

Eosinophil migration from circulation is controlled, in part, by chemokines through a family of G-protein-coupled chemokine receptors (CCR). Studies of human eosinophils have demonstrated that signaling through CCR3 receptors is a prominent pathway leading to chemotaxis, although several other receptor-ligand interactions also appear to mediate eosinophil recruitment. The availability of genetically unique strains of mice permits a reductionist approach to assess the signaling pathways in experimental models of human disease. However, despite similarities in these pathways between mice and humans, significant species differences exist, complicating the translation of results from animal models to humans. Purified mouse eosinophils were used in this study to investigate the chemokine receptor expression and the activities of 18 chemokines. Mouse eosinophils isolated from IL-5 transgenic mice expressed transcripts encoding the chemokine receptors CCR1, CCR2, CCR3, CCR5, CCR8, CXCR2, and CXCR4, but not CCR4. Mouse eosinophils also migrated in response to human and mouse eotaxin-1 and -2, but not human eotaxin-3. In addition, the induced migration of mouse eosinophils by TARC, MIP-1beta, and KC suggests that unidentified receptor-ligand interactions contribute to eosinophil recruitment. It is interesting that the potent chemoattractant of human eosinophils, RANTES, was unable to mediate mouse eosinophil migration. Furthermore, despite the ability of MIP-1alpha to bind receptors on purified mouse eosinophils, it was only able to induce significant eosinophil migration in a mixed splenocyte population and was unable to induce migration of highly purified eosinophils. Collectively, these observations reveal physiologically relevant distinctions in mechanisms mediating human and mouse eosinophil migration that potentially reflect evolutionary disparities between these species.

Amino Acid Sequence↗