Genetic Diversity of Staphylocoagulase Genes (coa): Insight into the Evolution of Variable Chromosomal Virulence Factors in Staphylococcus aureus

. Although SCs have been classified into 10 serotypes based on the differences in the antigenicity, genetic bases for their diversities and relatedness to chromosome types are poorly understood. type except for the cases of CC1 and CC8, which contained two and three different SC types, respectively. loci, resulting in the carriage of the combinations of allotypically different important virulence determinants in staphylococcal chromosome

Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dubia and Tetraselmis sp. CCMP 881

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction

Exploiting natural selection to study adaptive behavior

The research presented in this dissertation explores different computational and modeling techniques that combined with predictions from evolution by natural selection leads to the analysis of the adaptive behavior of populations under selective pressure. For this thesis three computational methods were developed: EXPLoRA, EVORhA and SSA-ME. EXPLoRA finds genomic regions associated with a trait of interests (QTL) by explicitly modeling the expected linkage disequilibrium of a population of sergeants under selection. Data from BSA experiments was analyzed to find genomic loci associated with ethanol tolerance. EVORhA explores the interplay between driving and hitchhiking mutations during evolution to reconstruct the subpopulation structure of clonal bacterial populations based on deep sequencing data. Data from mixed infections and evolution experiments of E. Coli was used and their population structure reconstructed. SSA-ME uses mutual exclusivity in cancer to prioritize cancer driver genes. TCGA data of breast cancer tumor samples were analyzed.status: publishe

Functional identification of a Ligase in the Red Sea Atlantis II deepest Layer

Red sea, described as one of the unique marine ecosystems, incorporates up to 25 deep-sea brine pools. These pools posses multiple extreme conditions influencing the evolution and survival of their inhabiting microbial community. The combination of maximum depth (2194 m), high temperature (68C), anoxia, high salinity (26%), high pressure and high concentrations of heavy metals in the lower convective layer (LCL) of the Atlantis II brine pool makes it an ideal environment for identification of novel enzymes with unique characteristics and potential biotechnological applications. Here we describe the identification and the preliminary in vivo functional investigation of the ligase domain of an ATP-dependent DNA ligase from the DNA of the prokaryotic community extracted from water samples of the LCL of Atlantis II brine pool. Previously, these water samples were serially filtered on different membranes and the DNA isolated from the 0.1­m filter was subjected to 454 pyrosequencing. A metagenomic dataset was initiated and used in this study to mine for genes encoding DNA ligases through Pfam search of conserved domains. The search and subsequent bioinformatic analysis resulted in the identification of a contig harboring an ORF of 915 bp (305 amino acids) that encodes a putative DNA ligase (LigATII). Homology search of the putative DNA ligase showed highest similarity to Erysiopelotrichaceae Bacterium (39% identity, 54% positive). LigATII displays modular architecture that is similar to two distinct domains-(the adenylation domain of LigD and the oligonucleotide binding (OB) fold domain)-that are conserved in ATP-dependent DNA ligases. Functional annotation of the LigATII ORF, identification of the functional conserved amino acids by the Consurf tool, 3D modeling and comprehensive phylogenetic analysis were conducted. These analyses have revealed the relatedness of LigATII to the family of ATP-dependent DNA ligases that has been recently identified through computational studies to exist in prokaryotes. This family is expected to be involved in the specialized form of genomic DNA repair through the non-homologous end joining pathway which acts to join double-stranded breaks (DSBs) or to promote genetic diversity under conditions of selection pressures. Accordingly, the putative LigATII was amplified from the whole genome DNA amplification of LCL. Sanger sequencing confirmed the sequence of the gene before cloning into pET100 Topo directional expression vector. The cloned LigATII was transformed into a temperature sensitive mutant strain of Escherichia coli; strain GR501, with mutation in the DNA ligase gene. LigATII complemented the temperature sensitive strain at the non-permissive temperature (43â—¦C) verifying the in vivo functional activity. The biochemical characteristics of the novel LigATII protein will be described

Morphological plasticity in Cladosporium sphaerospermum

A morphologically distinct isolate of Cladosporium sphaerospermum from a North American patent collection, referenced as Cladosporium lignicola in the patent, was examined. Generic affinity was confirmed by scanning electron microscopic examination of conidiogenous loci and conidial hila. Species identity as C. sphaerospermum was indicated by DNA sequence data derived from actin and translation elongation factor 1-α genes, and the internal transcribed spacer region. The isolate broadens the morphological limits of C. sphaerospermum by production of obclavate, occasionally transversely septate conidia with subrostrate conidiogenous apices (‘alternarioid’ conidia), and by production of conidia larger than those in prior standard descriptions. Type material of C. lignicola was re-examined and compared with the North American fungus, from which it is morphologically distinct. The decision to reduce C. lignicola to synonymy under C. herbarum was confirmed

On the Representation of Objects in the Visual System

There is evidence in the psychological literature for representations of objects (Pylyshyn's visual indexes) that refer to and track, not properties, but what in our sort of world typically turn out to be individual physical objects. I am concerned with how such representations acquire their content. Two strategies for accounting for the content of representations are a) representations of particulars refer to the entity that caused them; and b) representations of particulars refer to the entity whose properties are represented by the visual system. The first strategy faces the "which link" problem: since any one of the links in the causal chain leading to the token representation counts as a cause of the token representation, no particular link is individuated as the referent. I examine a recent proposed solution to this problem (Fodor's counterfactual triangulation) and conclude that it fails to determine whether the referent of a visual index is an object, as opposed to a state of affairs, or an event. The problems with the first strategy are a reason to explore the second strategy: representations of objects refer to the entity whose properties are represented by the visual system. I adopt Fodor's asymmetric dependency account (ADA) of intentionality to account for how representations of properties get their content. Fodor's account is chosen not because it is free of problems, but because it has the structure of a theory that promises to deal with many of the classic problems that befall informational semantics (e.g. the disjunction problem). Since ADA is designed to work for causal relations between properties and not for causal relations between particulars, it cannot, by itself, account for how representations of particulars get their content. So I suggest that ADA be supplemented with conceptual role semantics to account for the logico-syntactic roles of representations of particulars. In particular, I suggest that to represent objects the visual system requires the capacity to form and store in memory definite descriptions containing: a) predicates referring to spatio-temporal relations; and b) temporal indexicals

Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

<p>Abstract</p> <p>Background</p> <p>Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (<it>Spadella cephaloptera</it>) and to use them in phylogenetic studies.</p> <p>Results</p> <p>This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.</p> <p>Conclusion</p> <p>These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.</p

Sequencing fragments of cryptophyte plastomes from 16S rRNA to rbcL genes and phylogenetic analyses based on the protein-encoding genes located in these fragments

In recent phylogenetic analyses combining nuclear and nucleomorph RNA genes of the ribosomal operons, three different colourless lineages were found in the genus Cryptomonas. This raised questions about the evolutionary history of these interesting objects and their relatives as well as the role of plastid genomes such as whether these three lineages resulted from similar or from different evolutionary events or what are the mutual relationship or/and roles of photosynthetic genes in the absence of photosynthetic activities, etc. To answer the interesting questions, the biological information has to been collected systematically from their plastid genomes. At the first stage of the thesis, the cryptophyte plastid rbcL gene (1,5- biphosphate carboxylase/oxygenase [RuBisCO] large subunit) was chosen to amplify by BioTherm� Taq DNA Polymerase and read their DNA compositions by SequiTherm EXCEL� II DNA Sequencing Kit-LC and Li-Cor 4200L bidirectional sequencer. Eighteen newly rbcL sequences of Cryptomonas strains were obtained. Of these, five sequences were from heterotrophic (colorless) strains and the remaining was from photosynthetic (pigmented) strains. The results of rbcL phylogeny analyses showed that the colorless C. paramecium and their closely relative photosynthetic Cryptomonas had increased their evolutionary rates significantly. These were congruent with those of nuclear rDNA (concatenated SSU rDNA, ITS2 and partial LSU rDNA) and nucleomorph SSU rDNA that had been examined in previously. They were combined with other result done by Dr. Kerstin Hoef-Emden such as analyzing the shift from NNC to NNU in two-fold degenerate NNY codon in rbcL gene in Cryptomonas to discuss some hypotheses of the loss of photosynthetic activities in the colorless C. paramaecium strains. Detail results and discussion were published in BMC Evolutionary Biology 2005; 5:56. In the second part of the thesis, the goals were to amplify the cryptophyte plastome 16S rRNA-rbcL fragments by MasterAmpTM Extra-long PCR kit and read their DNA sequences by BigDye Terminator v1.1 Cycle sequencing kit and automated ABI3730 sequencer, then exploited the sequencing information for further understanding the evolutionary history of cryptophyte plastomes. The task also attempted to find new evidence to explain the relationship between the changing from autotrophic to heterotrophic lifestyle in colorless Cryptomonas lineages and the elevation of evolutionary rates of photosynthetic genes that were located in the plastome 16S rRNA-rbcL fragment. Twenty-two cryptophyte strains (four of them were colorless) were participated in this part. Most of the fragments (15) were read completely as planned while several fragments (7) were not, due to lack of time. The colorless strains possessed the smallest fragments; their plastomes, thus, were predicted to be the smallest among those of Cryptomonas. Strain C. erosa CCAC 0018 and C. obovoidea CCAC 0031 seemed to have the largest plastomes as their 16S-rbcL fragments contained an additional gene � ycf26 � that was not found in other Cryptomonas strains. Advantages and disadvantages of long-range PCR and primer-walking sequencing combination were discussed. Based on the conserved domain analyses, all ycf26 from secondary plastids seems to be inactive and on the way to become pseudogene than alter its function. Another additional gene � ORF403 encoding Tic22 protein � also was examined the conserved domains and done a phylogenetic analysis. Some specific characteristics of ORF403 in rhodoplasts and cryptophyte plastome were found. Three protein-coding genes � chlI, rps4 and rbcL � were used as separated phylogenetic markers or in combined. The results confirmed that one colorless lineage (presented by CCAC 0056, CCAP 977/2a, M2452, M2180) had accelerated evolutionary rates in all gene or/and protein trees. The observations also suggested that chlI gene increased its substitution rate earlier than rps4 and rbcL genes as well as the elevated evolutionary rates could be ordered by chlI > rps4 > rbcL. Although having moderate size (609 bp), rps4 had an evolution rate neither as high as in chlI gene nor as low as in rbcL gene, producing acceptable phylogenetic trees for both nucleotide and protein levels. Therefore, rps4 gene seems to be more suitable protein-enoding plastid gene maker for phylogenies than its sisters, chlI and rbcL genes. The ratio of NNC to NNU in two-fold degenerate NNY codons was calculated for each gene and discussed. It is possible that the shift in codon usage from NNC to NNU did not correlate to the relaxation of functional constraints and/or reduction of gene expression levels. Furthermore, the usage of NNU codons over the NNC in two-fold degenerate NNY codon seemed to be controlled by neutral mutation pressure rather than by selection followed by the gradually acceleration of evolutionary rate. A hypothetical scenario for the relations among the loss of photosynthesis, increasing of substitution rate of interring genes and time of diverging in colorless lineages was discussed