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44
Models, algorithms and programs for phylogeny reconciliation
- Brief. Bioinform
, 2011
"... Gene sequences contain a goldmine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Amo ..."
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Gene sequences contain a goldmine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions.We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages.
Predictive microbiology: Theory and application.
, 1993
"... a b s t r a c t We review early work on the microbial growth curve and the concept of balanced growth followed by commentary on the stringent response and persister cells. There is a voluminous literature on the effect of antibiotics on resistance and persistence and we call for a greater focus in ..."
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a b s t r a c t We review early work on the microbial growth curve and the concept of balanced growth followed by commentary on the stringent response and persister cells. There is a voluminous literature on the effect of antibiotics on resistance and persistence and we call for a greater focus in food microbiology on the effect of biocides in the same context. We also raise potential issues in development of resistance arising from "sourceesink" dynamics and from horizontal gene transfer. Redox potential is identified as crucial in determining microbial survival or death, and the recently postulated role for reactive oxygen species in signalling also considered. "Traditional" predictive microbiology is revisited with emphasis on temperature dependence. We interpret the temperature vs growth rate curve as comprising 11 regions, some well-recognised but others leading to new insights into physiological responses. In particular we are intrigued by a major disruption in the monotonic rate of inactivation at a temperature, slightly below the actual maximum temperature for growth. This non-intuitive behaviour was earlier reported by other research groups and here we propose that it results from a rapid metabolic switch from the relaxed growth state to the stringent survival state. Finally, we envision the future of predictive microbiology in which models morph from empirical to mechanistic underpinned by microbial physiology and bioinformatics to grow into Systems Biology.
Caetano-Anollés, Global patterns of protein domain gain and loss in superkingdoms
- PLOS Comput. Biol
, 2014
"... Domains are modules within proteins that can fold and function independently and are evolutionarily conserved. Here we compared the usage and distribution of protein domain families in the free-living proteomes of Archaea, Bacteria and Eukarya and reconstructed species phylogenies while tracing the ..."
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Domains are modules within proteins that can fold and function independently and are evolutionarily conserved. Here we compared the usage and distribution of protein domain families in the free-living proteomes of Archaea, Bacteria and Eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. We show that both gains and losses of domains occurred frequently during proteome evolution. The rate of domain discovery increased approximately linearly in evolutionary time. Remarkably, gains generally outnumbered losses and the gain-to-loss ratios were much higher in akaryotes compared to eukaryotes. Functional annotations of domain families revealed that both Archaea and Bacteria gained and lost metabolic capabilities during the course of evolution while Eukarya acquired a number of diverse molecular functions including those involved in extracellular processes, immunological mechanisms, and cell regulation. Results also highlighted significant contemporary sharing of informational enzymes between Archaea and Eukarya and metabolic enzymes between Bacteria and Eukarya. Finally, the analysis provided useful insights into the evolution of species. The archaeal superkingdom appeared first in evolution by gradual loss of ancestral domains, bacterial lineages were the first to gain superkingdom-specific domains, and eukaryotes (likely) originated when an expanding proto-eukaryotic stem lineage gained organelles through endosymbiosis of already diversified bacterial lineages. The evolutionary dynamics of domain families in proteomes and the increasing number of domain gains is predicted to redefine the
A bayesian method for analyzing lateral gene transfer
- Syst. Biol
, 2014
"... Abstract.—Lateral gene transfer (LGT)—which transfers DNA between two non-vertically related individuals belonging to the same or different species—is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much p ..."
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Abstract.—Lateral gene transfer (LGT)—which transfers DNA between two non-vertically related individuals belonging to the same or different species—is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools.
Joint scaling laws in functional and evolutionary
, 2011
"... categories in prokaryotic genomes ..."
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Ecological and temporal constraints in the evolution of bacterial genomes
- Genes
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Summary
"... After 10 years of screening for breast cancer by mammography in Nijmegen, the predictive value of positive screening results (PV+) was evaluated. The percentage of women with breast cancer in the group of referred women (PV+) for women under age 50 was 16-26%, regardless of the number of screening e ..."
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After 10 years of screening for breast cancer by mammography in Nijmegen, the predictive value of positive screening results (PV+) was evaluated. The percentage of women with breast cancer in the group of referred women (PV+) for women under age 50 was 16-26%, regardless of the number of screening examinations they had. The percentage of women with breast cancer in the group of women who were biopsied was 25-40%, regardless of the number of examinations. For women aged 50 and over the predictive value was 34-57 % and 58-90 % respectively. It was further evaluated whether characteristics such as age, Quetelet index, parity, and Wolfe-classification could be used to increase the PV+ in women who were identified as positive by mammography. A logistic regression model analysis showed that true-positive and false-positive cases differ significantly only in terms of age and breast complaints. Although the model had a it could not be used to distinguish false-positive from true-positive test results. good fit, Since 1975 five screening rounds have been carried out in a non-randomised screening project with biennial mammography in the city of Nijmegen. The results of breast cancer screening projects such as the HIP-trial in the United States
Locating a tree in a phylogenetic network in quadratic time
- In: Przytycka T., editor. Research in Computational Molecular Biology, LectureNotes inComputer Science
, 2015
"... Abstract. A fundamental problem in the study of phylogenetic net-works is to determine whether or not a given phylogenetic network con-tains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number ..."
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Abstract. A fundamental problem in the study of phylogenetic net-works is to determine whether or not a given phylogenetic network con-tains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in the number of taxa. 1
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
, 2014
"... The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene trans-fer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few stud-ies have precisely addressed the distribution of these systems in light of HGT, its mechanisms ..."
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The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene trans-fer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few stud-ies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vec-tors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural trans-formation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Sur-prisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more fre-quently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
DISCOVERY AND APPLICATIONS OF NOVEL PROTEIN BASED MOLECULAR MARKERS FOR BACTERIAL CLASSIFICATION AND IDENTIFICATION By
"... TITLE: Discovery and applications of novel protein based molecular markers for bacterial classification and identification ..."
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TITLE: Discovery and applications of novel protein based molecular markers for bacterial classification and identification
