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  • 1
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    Evolution. Climb every mountain? (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-12-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elena, Santiago F -- Sanjuan, Rafael -- New York, N.Y. -- Science. 2003 Dec 19;302(5653):2074-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-UPV, 46022 Valencia, Spain. sfelena@ibmcp.upv.es〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684807" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; *Biological Evolution ; Chlamydomonas/physiology ; Darkness ; *Ecosystem ; Environment ; *Genetic Variation ; Genotype ; Light ; Mutation ; Phenotype ; Pseudomonas fluorescens/genetics/*physiology ; RNA Viruses/physiology ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Clonal interference and the evolution of RNA viruses (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-11
    Description: In asexual populations, beneficial mutations that occur in different lineages compete with one another. This phenomenon, known as clonal interference, ensures that those beneficial mutations that do achieve fixation are of large effect. Clonal interference also increases the time between fixations, thereby slowing the adaptation of asexual populations. The effects of clonal interference were measured in the asexual RNA virus vesicular stomatitis virus; rates and average effects of beneficial mutations were quantified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miralles, R -- Gerrish, P J -- Moya, A -- Elena, S F -- New York, N.Y. -- Science. 1999 Sep 10;285(5434):1745-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genetica, Universitat de Valencia, Apartado 22085, 46071 Valencia, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10481012" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Biological Evolution ; Cell Line ; Confidence Intervals ; Cricetinae ; Gene Frequency ; Genes, Viral ; Likelihood Functions ; Models, Biological ; Models, Statistical ; *Mutation ; Vesicular stomatitis Indiana virus/genetics/*physiology ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Extremely high mutation rate of a hammerhead viroid (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-07
    Description: The mutation rates of viroids, plant pathogens with minimal non-protein-coding RNA genomes, are unknown. Their replication is mediated by host RNA polymerases and, in some cases, by hammerhead ribozymes, small self-cleaving motifs embedded in the viroid. By using the principle that the population frequency of nonviable genotypes equals the mutation rate, we screened for changes that inactivated the hammerheads of Chrysanthemum chlorotic mottle viroid. We obtained a mutation rate of 1/400 per site, the highest reported for any biological entity. Such error-prone replication can only be tolerated by extremely simple genomes such as those of viroids and, presumably, the primitive replicons of the RNA world. Our results suggest that the emergence of replication fidelity was critical for the evolution of complexity in the early history of life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gago, Selma -- Elena, Santiago F -- Flores, Ricardo -- Sanjuan, Rafael -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1308. doi: 10.1126/science.1169202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, 46022 Valencia, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19265013" target="_blank"〉PubMed〈/a〉
    Keywords: Genome, Viral ; Molecular Sequence Data ; *Mutation ; Nucleic Acid Conformation ; RNA, Catalytic/chemistry/*genetics ; RNA, Viral/chemistry/*genetics ; Replicon ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Viroids/*genetics/physiology ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Response: mechanisms of punctuated evolution (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elena, S F -- Cooper, V S -- Lenski, R E -- New York, N.Y. -- Science. 1996 Dec 6;274(5293):1749-50.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17842245" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Punctuated evolution caused by selection of rare beneficial mutations (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-06-21
    Description: For more than two decades there has been intense debate over the hypothesis that most morphological evolution occurs during relatively brief episodes of rapid change that punctuate much longer periods of stasis. A clear and unambiguous case of punctuated evolution is presented for cell size in a population of Escherichia coli evolving for 3000 generations in a constant environment. The punctuation is caused by natural selection as rare, beneficial mutations sweep successively through the population. This experiment shows that the most elementary processes in population genetics can give rise to punctuated evolution dynamics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Elena, S F -- Cooper, V S -- Lenski, R E -- New York, N.Y. -- Science. 1996 Jun 21;272(5269):1802-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Microbial Ecology, Michigan State University, East Lansing, 48824, USA. selena@ant.css.msu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8650581" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Analysis of Variance ; *Biological Evolution ; Culture Media ; Escherichia coli/cytology/*genetics/growth & development ; Models, Statistical ; *Mutation ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Biogeochemistry and microbiology of groundwater during acetate and bicarbonate amendment to an alluvial aquifer (2015)
    PANGAEA
    In:  Supplement to: Long, Philip E; Williams, Kenneth H; Davis, James A; Fox, Patricia M; Wilkins, Michael J; Yabusaki, Steven B; Fang, Yilin; Waichler, Scott R; Berman, Elena S F; Gupta, Manish; Chandler, Darrell P; Murray, Chris; Peacock, Aaron D; Giloteaux, Ludovic; Handley, Kim M; Lovley, Derek R; Banfield, Jillian F (2015): Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer. Geochimica et Cosmochimica Acta, 150, 106-124, https://doi.org/10.1016/j.gca.2014.11.013
    Details
    Publication Date: 2024-05-25
    Description: Field-scale biostimulation and desorption tracer experiments conducted in a uranium (U) contaminated, shallow alluvial aquifer have provided insight into the coupling of microbiology, biogeochemistry, and hydrogeology that control U mobility in the subsurface. Initial experiments successfully tested the concept that Fe-reducing bacteria such as Geobacter sp. could enzymatically reduce soluble U(VI) to insoluble U(IV) during in situ electron donor amendment (Anderson et al., 2003; Williams et al., 2011). In parallel, in situ desorption tracer tests using bicarbonate amendment demonstrated rate-limited U(VI) desorption (Fox et al., 2012). These results and prior laboratory studies underscored the importance of enzymatic U(VI)-reduction and suggested the ability to combine desorption and bioreduction of U(VI). Here we report the results of a new field experiment in which bicarbonate-promoted uranium desorption and acetate amendment were combined and compared to an acetate amendment-only experiment in the same experimental plot. Results confirm that bicarbonate amendment to alluvial aquifer sediments desorbs U(VI) and increases the abundance of Ca-uranyl-carbonato complexes. At the same time, the rate of acetate-promoted enzymatic U(VI) reduction was greater in the presence of added bicarbonate in spite of the increased dominance of Ca-uranyl-carbonato aqueous complexes. A model-simulated peak rate of U(VI) reduction was ~3.8 times higher during acetate-bicarbonate treatment than under acetate-only conditions. Lack of consistent differences in microbial community structure between acetate-bicarbonate and acetate-only treatments suggest that a significantly higher rate of U(VI) reduction in the bicarbonate-impacted sediment may be due to a higher intrinsic rate of microbial reduction induced by elevated concentrations of the bicarbonate oxyanion. The findings indicate that bicarbonate amendment may be useful in improving the engineered bioremediation of uranium in aquifers.
    Type: Dataset
    Format: application/zip, 3 datasets
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  • 7
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    (Tab 3) Signal to noise ratio (SNR) by genus for microarray probes in an alluvial aquifer along the Colorado River in Rifle, Colorado, USA (2015)
    PANGAEA
    Details
    Publication Date: 2024-05-25
    Keywords: Calculated; Colorado, U.S.A., North America; Date; DATE/TIME; Depth, relative; ELEVATION; Elevation 2; LATITUDE; LONGITUDE; Rilfe; Sample code/label; Sampling Well; Signal/noise ratio; WELL
    Type: Dataset
    Format: text/tab-separated-values, 2386 data points
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  • 8
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    (Tab 1) Biogeochemistry of groundwater during acetate and bicarbonate amendment to an alluvial aquifer along the Colorado River in Rifle, Colorado, USA (2015)
    PANGAEA
    Details
    Publication Date: 2024-05-25
    Keywords: Acetate; Aluminium; Aluminium, standard deviation; Arsenic; Arsenic, standard deviation; Barium, standard deviation; Barium 2+; Boron; Boron, standard deviation; Bromide; Bromine; Bromine, standard deviation; Calcium; Calcium, standard deviation; Carbon, inorganic, total; Chloride; Chromium; Chromium, standard deviation; Cobalt; Cobalt, standard deviation; Colorado, U.S.A., North America; Conductivity, electrolytic; Damage rate, standard deviation; DATE/TIME; Depth, logging; Depth, relative; ELEVATION; Elevation 2; Iron; Iron, standard deviation; Iron 2+; LATITUDE; Lithium; Lithium, standard deviation; LONGITUDE; Magnesium; Magnesium, standard deviation; Manganese; Manganese, standard deviation; Molybdenum; Molybdenum, standard deviation; pH; Potassium; Rilfe; Rubidium; Rubidium, standard deviation; Sample code/label; Sampling Well; Selenium; Selenium, standard deviation; Silicate; Silicate, standard deviation; Sodium; Sodium, standard deviation; Strontium, standard deviation; Strontium 2+; Sulfate; Sulfide; Thiosulfate; Titanium; Titanium, standard deviation; Uranium; Uranium, standard deviation; Vanadium; Vanadium, standard deviation; Water level; WELL; Zinc; Zinc, standard deviation; δ18O; δ18O, standard deviation; δ34S; δ34S, standard deviation; δ Deuterium; δ Deuterium, standard deviation
    Type: Dataset
    Format: text/tab-separated-values, 58204 data points
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  • 9
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    (Tab 2) Average signal to noise ratio (SNR) for individual microarray probes in an alluvial aquifer along the Colorado River in Rifle, Colorado, USA (2015)
    PANGAEA
    Details
    Publication Date: 2024-05-25
    Keywords: 20-mer oligonucleotide; Calculated; Colorado, U.S.A., North America; DATE/TIME; Depth, relative; ELEVATION; Elevation 2; Fluorescent dye, Cyanine 3; Hybridization marker; LATITUDE; LONGITUDE; Rilfe; Sample code/label; Sampling Well; Signal/noise ratio; WELL
    Type: Dataset
    Format: text/tab-separated-values, 8480 data points
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  • 10
    Electronic Resource
    Electronic Resource
    Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift (1996)
    Springer
    Molecular genetics and genomics 252 (1996), S. 733-738 
    Details
    ISSN: 1617-4623
    Keywords: Quasispecies ; Genetic bottleneck ; Vesicular stomatitis virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The population dynamics of RNA viruses have an important influence on fitness variation and, in consequence, on the adaptative potential and virulence of this ubiquitous group of pathogens. Earlier work with vesicular stomatitis virus showed that large population transfers were reproducibly associated with fitness increases, whereas repeated transfers from plaque to plaque (genetic bottlenecks) lead to losses in fitness. We demonstrate here that repeated five-plaque to five-plaque passage series yield long-term fitness stability, except for occasional stochastic fitness jumps. Repeated five-plaque passages regularly alternating with two consecutive large population transmissions did not cause fitness losses, but did limit the size of fitness gains that would otherwise have occurred. These results underscore the profound effects of bottleneck transmissions in virus evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02173980
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    Paper (German National Licenses)
    Fulltext
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