Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, 01/2010, Volume 54, Issue 1, pp. 24 - 38
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CARBAPENEM-HYDROLYZING OXACILLINASE | SITE-SPECIFIC RECOMBINATION | EXTENDED-SPECTRUM VARIANT | MULTIRESISTANCE TRANSPOSON TN1331 | PSEUDOMONAS-AERUGINOSA | RESISTANT ACINETOBACTER-BAUMANNII | BIOCHEMICAL-CHARACTERIZATION | MOLECULAR EPIDEMIOLOGY | MICROBIOLOGY | PHARMACOLOGY & PHARMACY | INTERNATIONAL CLONAL COMPLEX | KLEBSIELLA-PNEUMONIAE | Amino Acid Sequence | Bacterial Infections - genetics | Animals | beta-Lactamases - genetics | Molecular Epidemiology | Humans | Bacterial Infections - epidemiology | Drug Resistance, Bacterial | Molecular Sequence Data | Bacteria - enzymology | beta-Lactamases - metabolism | Bacteria - genetics | Minireview
CARBAPENEM-HYDROLYZING OXACILLINASE | SITE-SPECIFIC RECOMBINATION | EXTENDED-SPECTRUM VARIANT | MULTIRESISTANCE TRANSPOSON TN1331 | PSEUDOMONAS-AERUGINOSA | RESISTANT ACINETOBACTER-BAUMANNII | BIOCHEMICAL-CHARACTERIZATION | MOLECULAR EPIDEMIOLOGY | MICROBIOLOGY | PHARMACOLOGY & PHARMACY | INTERNATIONAL CLONAL COMPLEX | KLEBSIELLA-PNEUMONIAE | Amino Acid Sequence | Bacterial Infections - genetics | Animals | beta-Lactamases - genetics | Molecular Epidemiology | Humans | Bacterial Infections - epidemiology | Drug Resistance, Bacterial | Molecular Sequence Data | Bacteria - enzymology | beta-Lactamases - metabolism | Bacteria - genetics | Minireview
Journal Article
Philosophical Transactions of the Royal Society B: Biological Sciences, ISSN 0962-8436, 09/2015, Volume 370, Issue 1676, pp. 20140243 - 20140243
We quantify the VDJ recombination and somatic hypermutation processes in human B cells using probabilistic inference methods on high-throughput DNA sequence...
B cell | Somatic hypermutations | IgH | Statistical inference | VDJ recombination | Immune repertoire | HUMAN IGV(H) GENES | NUCLEOTIDE-REPLACEMENT SPECTRUM | SOMATIC HYPERMUTATION | SEQUENCES | MUTATION | LENGTH | BIOLOGY | RECEPTOR | INFERENCE | COMPLEMENTARITY | ANTIGEN SELECTION | Antibody Diversity | Models, Immunological | Algorithms | B-Lymphocytes - immunology | Clonal Selection, Antigen-Mediated | Somatic Hypermutation, Immunoglobulin | Humans | V(D)J Recombination | Receptors, Antigen, B-Cell - genetics | Models, Genetic | 199 | somatic hypermutations | immune repertoire | 1001 | statistical inference
B cell | Somatic hypermutations | IgH | Statistical inference | VDJ recombination | Immune repertoire | HUMAN IGV(H) GENES | NUCLEOTIDE-REPLACEMENT SPECTRUM | SOMATIC HYPERMUTATION | SEQUENCES | MUTATION | LENGTH | BIOLOGY | RECEPTOR | INFERENCE | COMPLEMENTARITY | ANTIGEN SELECTION | Antibody Diversity | Models, Immunological | Algorithms | B-Lymphocytes - immunology | Clonal Selection, Antigen-Mediated | Somatic Hypermutation, Immunoglobulin | Humans | V(D)J Recombination | Receptors, Antigen, B-Cell - genetics | Models, Genetic | 199 | somatic hypermutations | immune repertoire | 1001 | statistical inference
Journal Article
Nature Reviews Microbiology, ISSN 1740-1526, 2014, Volume 12, Issue 4, pp. 263 - 273
Comparisons of closely related microorganisms have shown that individual genomes can be highly diverse in terms of gene content. In this Review, we discuss...
RECOMBINATION | CLONAL INTERFERENCE | POPULATION GENOMICS | GENOTYPIC DIVERSITY | FREQUENCY-DEPENDENT SELECTION | MICROBIOLOGY | BACTERIAL | DIFFERENTIATION | POLYMORPHISM | COOPERATION | HORIZONTAL GENE-TRANSFER | Archaea - physiology | Biological Evolution | Genetic Variation | Archaea - metabolism | Bacteria - growth & development | Bacteria - metabolism | Ecosystem | Selection, Genetic | Bacterial Physiological Phenomena | Biodiversity | Microbial Interactions | Archaea - growth & development | Environmental aspects | Research | Microbial colonies | Biological diversity
RECOMBINATION | CLONAL INTERFERENCE | POPULATION GENOMICS | GENOTYPIC DIVERSITY | FREQUENCY-DEPENDENT SELECTION | MICROBIOLOGY | BACTERIAL | DIFFERENTIATION | POLYMORPHISM | COOPERATION | HORIZONTAL GENE-TRANSFER | Archaea - physiology | Biological Evolution | Genetic Variation | Archaea - metabolism | Bacteria - growth & development | Bacteria - metabolism | Ecosystem | Selection, Genetic | Bacterial Physiological Phenomena | Biodiversity | Microbial Interactions | Archaea - growth & development | Environmental aspects | Research | Microbial colonies | Biological diversity
Journal Article
Arteriosclerosis, Thrombosis, and Vascular Biology, ISSN 1079-5642, 09/2019, Volume 39, Issue 9, pp. 1715 - 1723
Vascular smooth muscle cells (SMC) play a critical role in controlling blood pressure and blood distribution, as well as maintaining the structural integrity...
atherosclerosis | blood pressure | MACROPHAGE | cell division | INJURY | PROLIFERATION | vascular remodeling | SITE-SPECIFIC RECOMBINASE | ADULT | HETEROGENEITY | ORIGIN | CLONAL HEMATOPOIESIS | GENE-EXPRESSION | PERIPHERAL VASCULAR DISEASE | DIFFERENTIATION | cell plasticity | HEMATOLOGY
atherosclerosis | blood pressure | MACROPHAGE | cell division | INJURY | PROLIFERATION | vascular remodeling | SITE-SPECIFIC RECOMBINASE | ADULT | HETEROGENEITY | ORIGIN | CLONAL HEMATOPOIESIS | GENE-EXPRESSION | PERIPHERAL VASCULAR DISEASE | DIFFERENTIATION | cell plasticity | HEMATOLOGY
Journal Article
Global Ecology and Biogeography, ISSN 1466-822X, 3/2009, Volume 18, Issue 2, pp. 223 - 239
Aim: Climate change may cause loss of genetic diversity. Here we explore how a multidisciplinary approach can be used to infer effects of past climate change...
Climate change | Population ecology | Ecological genetics | Biogeography | Population structure | Genetic diversity | Climate models | Population genetics | Alpine glaciers | Fossils | glacial refugia | range shifts | Amphi‐Atlantic | colonization | ice age | arctic‐alpine | climate change | conservation genetics | phylogeography | Phylogeography | Amphi-Atlantic | Glacial refugia | Range shifts | Colonization | Conservation genetics | Arctic-alpine | Ice age | EUROPEAN ALPS | ALPINE PLANTS | COMPARATIVE PHYLOGEOGRAPHY | arctic-alpine | SPECIES DISTRIBUTIONS | CLIMATE-CHANGE | GEOGRAPHY, PHYSICAL | CLONAL DIVERSITY | ICE-AGES | POPULATION-STRUCTURE | ECOLOGY | MOLECULAR PHYLOGEOGRAPHY | Last Glacial Maximum | Global temperature changes | Analysis | Genetics | Models | Museums | Universities and colleges | Natural history
Climate change | Population ecology | Ecological genetics | Biogeography | Population structure | Genetic diversity | Climate models | Population genetics | Alpine glaciers | Fossils | glacial refugia | range shifts | Amphi‐Atlantic | colonization | ice age | arctic‐alpine | climate change | conservation genetics | phylogeography | Phylogeography | Amphi-Atlantic | Glacial refugia | Range shifts | Colonization | Conservation genetics | Arctic-alpine | Ice age | EUROPEAN ALPS | ALPINE PLANTS | COMPARATIVE PHYLOGEOGRAPHY | arctic-alpine | SPECIES DISTRIBUTIONS | CLIMATE-CHANGE | GEOGRAPHY, PHYSICAL | CLONAL DIVERSITY | ICE-AGES | POPULATION-STRUCTURE | ECOLOGY | MOLECULAR PHYLOGEOGRAPHY | Last Glacial Maximum | Global temperature changes | Analysis | Genetics | Models | Museums | Universities and colleges | Natural history
Journal Article
PLoS Pathogens, ISSN 1553-7366, 02/2012, Volume 8, Issue 2, p. e1002544
The elderly are particularly susceptible to influenza A virus infections, with increased occurrence, disease severity and reduced vaccine efficacy attributed...
RECALL RESPONSES | MICROBIOLOGY | EFFECTOR | VIROLOGY | MEMORY | REPERTOIRE DIVERSITY | CLONAL EXPANSIONS | INFECTION | MICE | VIRUS NUCLEOPROTEIN EPITOPE | INFLUENZA-VIRUS | RECEPTOR REPERTOIRE | PARASITOLOGY | CD8-Positive T-Lymphocytes - cytology | Precursor Cells, T-Lymphoid - physiology | Age Factors | Mice, Inbred C57BL | Cells, Cultured | Antigen Presentation - immunology | CD8-Positive T-Lymphocytes - physiology | Immunologic Memory - physiology | Aging - immunology | Animals | Validation Studies as Topic | CD8-Positive T-Lymphocytes - metabolism | Female | Receptors, Antigen, T-Cell - immunology | Mice | Epitopes, T-Lymphocyte - immunology | CD8-Positive T-Lymphocytes - immunology | Precursor Cells, T-Lymphoid - immunology | Antigen Presentation - physiology | Lymphocytes | Influenza | Older people | Colleges & universities | Viruses | Amino acids | T cell receptors | Vaccines | Grants | Age
RECALL RESPONSES | MICROBIOLOGY | EFFECTOR | VIROLOGY | MEMORY | REPERTOIRE DIVERSITY | CLONAL EXPANSIONS | INFECTION | MICE | VIRUS NUCLEOPROTEIN EPITOPE | INFLUENZA-VIRUS | RECEPTOR REPERTOIRE | PARASITOLOGY | CD8-Positive T-Lymphocytes - cytology | Precursor Cells, T-Lymphoid - physiology | Age Factors | Mice, Inbred C57BL | Cells, Cultured | Antigen Presentation - immunology | CD8-Positive T-Lymphocytes - physiology | Immunologic Memory - physiology | Aging - immunology | Animals | Validation Studies as Topic | CD8-Positive T-Lymphocytes - metabolism | Female | Receptors, Antigen, T-Cell - immunology | Mice | Epitopes, T-Lymphocyte - immunology | CD8-Positive T-Lymphocytes - immunology | Precursor Cells, T-Lymphoid - immunology | Antigen Presentation - physiology | Lymphocytes | Influenza | Older people | Colleges & universities | Viruses | Amino acids | T cell receptors | Vaccines | Grants | Age
Journal Article
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 6, p. e20968
Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring > 14%(w/v)...
HALOBACTERIUM-SALINARUM | SEQUENCE-ANALYSIS | GENOME SEQUENCE | MULTIDISCIPLINARY SCIENCES | SQUARE HALOARCHAEON | TRANSPOSABLE ELEMENTS | PATHOGENICITY ISLAND | HALOFERAX-VOLCANII | HALOPHILIC ARCHAEA | MULTIPLE REPLICATION ORIGINS | DNA-REPLICATION | Molecular Sequence Data | RNA, Ribosomal, 16S - genetics | Halobacteriaceae - genetics | Phylogeny | Genome, Archaeal - genetics | Halobacteriaceae - classification | Genomes | Transposons | Genes | Genomics | Geographical isolation | Salts | Divergence | Ecosystems | Homology | Biochemistry | Information management | Gene deletion | Molecular weight | Gene sequencing | Microorganisms | Conserved sequence | Clonal deletion | Dispersal | Deletion | Population | Chromosomes | Bioinformatics | Deoxyribonucleic acid--DNA | CRISPR | Data analysis | Wildlife conservation | Gene clusters | Prokaryotes | Dispersion | Flora | Use statistics | Plasmids | Spacer | Fitness | Deoxyribonucleic acid | DNA
HALOBACTERIUM-SALINARUM | SEQUENCE-ANALYSIS | GENOME SEQUENCE | MULTIDISCIPLINARY SCIENCES | SQUARE HALOARCHAEON | TRANSPOSABLE ELEMENTS | PATHOGENICITY ISLAND | HALOFERAX-VOLCANII | HALOPHILIC ARCHAEA | MULTIPLE REPLICATION ORIGINS | DNA-REPLICATION | Molecular Sequence Data | RNA, Ribosomal, 16S - genetics | Halobacteriaceae - genetics | Phylogeny | Genome, Archaeal - genetics | Halobacteriaceae - classification | Genomes | Transposons | Genes | Genomics | Geographical isolation | Salts | Divergence | Ecosystems | Homology | Biochemistry | Information management | Gene deletion | Molecular weight | Gene sequencing | Microorganisms | Conserved sequence | Clonal deletion | Dispersal | Deletion | Population | Chromosomes | Bioinformatics | Deoxyribonucleic acid--DNA | CRISPR | Data analysis | Wildlife conservation | Gene clusters | Prokaryotes | Dispersion | Flora | Use statistics | Plasmids | Spacer | Fitness | Deoxyribonucleic acid | DNA
Journal Article
Immunity, ISSN 1074-7613, 2009, Volume 31, Issue 6, pp. 859 - 871
The adaptive immune response meets the needs of the organism to generate effector cells capable of controlling pathogens but also leads to production of memory...
LUNG AIRWAYS | SECONDARY EXPANSION | DENDRITIC CELLS | CD8(+) MEMORY | PROMOTES DIFFERENTIATION | CLONAL EXPANSIONS | BONE-MARROW | IL-7 RECEPTOR-ALPHA | IMMUNOLOGY | HOMEOSTATIC PROLIFERATION | CUTTING EDGE | Adaptive Immunity | T-Lymphocyte Subsets - immunology | Cytokines - metabolism | Infection - immunology | Humans | Homeostasis - immunology | Inflammation - immunology | Immunity, Innate | Cell Differentiation - immunology | Inflammation - metabolism | Animals | Apoptosis - immunology | T-Lymphocyte Subsets - metabolism | Immunologic Memory | Cytokines - immunology | T cells | Cell division | Genotype & phenotype | Population | T cell receptors | Gene expression | Immune system
LUNG AIRWAYS | SECONDARY EXPANSION | DENDRITIC CELLS | CD8(+) MEMORY | PROMOTES DIFFERENTIATION | CLONAL EXPANSIONS | BONE-MARROW | IL-7 RECEPTOR-ALPHA | IMMUNOLOGY | HOMEOSTATIC PROLIFERATION | CUTTING EDGE | Adaptive Immunity | T-Lymphocyte Subsets - immunology | Cytokines - metabolism | Infection - immunology | Humans | Homeostasis - immunology | Inflammation - immunology | Immunity, Innate | Cell Differentiation - immunology | Inflammation - metabolism | Animals | Apoptosis - immunology | T-Lymphocyte Subsets - metabolism | Immunologic Memory | Cytokines - immunology | T cells | Cell division | Genotype & phenotype | Population | T cell receptors | Gene expression | Immune system
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2015, Volume 112, Issue 47, pp. E6496 - E6505
The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects...
Genetic diversity | Intratumor heterogeneity | Neutral evolution | Cancer evolution | Natural selection | genetic diversity | intratumor heterogeneity | natural selection | LANDSCAPE | MULTIDISCIPLINARY SCIENCES | MOLECULAR EVOLUTION | CLONAL EVOLUTION | cancer evolution | MODEL | IDENTIFICATION | CANCER | neutral evolution | MUTATIONS | NEUTRAL THEORY | PROGRESSION | Reproducibility of Results | Gene Library | Microdissection | Cell Count | Genes, Neoplasm | Humans | Selection, Genetic | Molecular Sequence Data | Genotype | Male | Mutation Rate | Sequence Analysis, DNA | Biological Evolution | Genetic Variation | Neoplasms - genetics | Base Sequence | Computer Simulation | Cell Line, Tumor | Polymorphism, Single Nucleotide - genetics | Aged | Clone Cells | Models, Genetic | Mutation | Neoplasms - pathology | Oncology, Experimental | Exome sequencing | Genetic research | Development and progression | Genetic aspects | Hepatoma | Research | Methods | Cancer | Biological Sciences | PNAS Plus
Genetic diversity | Intratumor heterogeneity | Neutral evolution | Cancer evolution | Natural selection | genetic diversity | intratumor heterogeneity | natural selection | LANDSCAPE | MULTIDISCIPLINARY SCIENCES | MOLECULAR EVOLUTION | CLONAL EVOLUTION | cancer evolution | MODEL | IDENTIFICATION | CANCER | neutral evolution | MUTATIONS | NEUTRAL THEORY | PROGRESSION | Reproducibility of Results | Gene Library | Microdissection | Cell Count | Genes, Neoplasm | Humans | Selection, Genetic | Molecular Sequence Data | Genotype | Male | Mutation Rate | Sequence Analysis, DNA | Biological Evolution | Genetic Variation | Neoplasms - genetics | Base Sequence | Computer Simulation | Cell Line, Tumor | Polymorphism, Single Nucleotide - genetics | Aged | Clone Cells | Models, Genetic | Mutation | Neoplasms - pathology | Oncology, Experimental | Exome sequencing | Genetic research | Development and progression | Genetic aspects | Hepatoma | Research | Methods | Cancer | Biological Sciences | PNAS Plus
Journal Article
Cancer, ISSN 0008-543X, 03/2017, Volume 123, Issue 6, pp. 917 - 927
The authors review and discuss the implications of genomic analyses documenting the diversity of tumors, both among patients and within individual tumors....
driver mutations | targeted therapy | intratumor heterogeneity | next‐generation sequencing | immunotherapy | next-generation sequencing | TARGETED CANCER-THERAPY | PD-1 BLOCKADE | LUNG-CANCER | ONCOLOGY | DNA | SQUAMOUS-CELL CARCINOMA | RESISTANCE | GENOMIC ALTERATIONS | MUTATIONS | INHIBITORS | Genetic Predisposition to Disease | Prognosis | Humans | Neoplasms - mortality | Molecular Targeted Therapy | Biomarkers, Tumor | Genetic Heterogeneity | Genetic Variation | Neoplasms - therapy | Animals | Neoplasms - genetics | Mutation | Neoplasms - pathology | Clonal Evolution | Precision Medicine | Cancer patients | Oncology | Genetic aspects | Research | Health aspects | Biological diversity | Tumors | Training | Heterogeneity | Panels | Therapy | Pathways | Genetic diversity | Solid tumors | Patients | Cancer | Gene sequencing | intra-tumor heterogeneity
driver mutations | targeted therapy | intratumor heterogeneity | next‐generation sequencing | immunotherapy | next-generation sequencing | TARGETED CANCER-THERAPY | PD-1 BLOCKADE | LUNG-CANCER | ONCOLOGY | DNA | SQUAMOUS-CELL CARCINOMA | RESISTANCE | GENOMIC ALTERATIONS | MUTATIONS | INHIBITORS | Genetic Predisposition to Disease | Prognosis | Humans | Neoplasms - mortality | Molecular Targeted Therapy | Biomarkers, Tumor | Genetic Heterogeneity | Genetic Variation | Neoplasms - therapy | Animals | Neoplasms - genetics | Mutation | Neoplasms - pathology | Clonal Evolution | Precision Medicine | Cancer patients | Oncology | Genetic aspects | Research | Health aspects | Biological diversity | Tumors | Training | Heterogeneity | Panels | Therapy | Pathways | Genetic diversity | Solid tumors | Patients | Cancer | Gene sequencing | intra-tumor heterogeneity
Journal Article
PLoS Genetics, ISSN 1553-7390, 2014, Volume 10, Issue 3, p. e1004222
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected...
BACKGROUND SELECTION | ASEXUAL POPULATIONS | COALESCENT PROCESS | RAPIDLY ADAPTING POPULATIONS | CLONAL INTERFERENCE | DROSOPHILA-MELANOGASTER |
BACKGROUND SELECTION | ASEXUAL POPULATIONS | COALESCENT PROCESS | RAPIDLY ADAPTING POPULATIONS | CLONAL INTERFERENCE | DROSOPHILA-MELANOGASTER |