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- Evolutionary genetics (2)
- Life -- Origin (2)
- Bacteria -- Identification (1)
- Bacterial diversity -- Genetic aspects (1)
- Catalytic RNA (1)
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- Comparative genomics (1)
- Cooperation (1)
- Developmental genetics (1)
- Diapause (1)
- Drug resistance in microorganisms -- Genetic aspects (1)
- Environmental Sciences (1)
- Extreme environments -- Microbiology (1)
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- Genomics (1)
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- Hot springs (1)
- Killifishes -- Embryos -- Development (1)
- Metagenomics (1)
- Microbiology (1)
- Molecular biology -- Technique (1)
- Molecular evolution (1)
- Polymerase chain reaction (1)
- Proteins -- Evolution (1)
- RNA -- Evolution (1)
- Ribozymes (1)
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- Thermophilic microorganisms (1)
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Articles 1 - 7 of 7
Full-Text Articles in Genetics and Genomics
Transcriptomic Regulation Of Alternative Phenotypic Trajectories In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Amie L. Romney
Transcriptomic Regulation Of Alternative Phenotypic Trajectories In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Amie L. Romney
Dissertations and Theses
The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype …
Prebiotic Rna Network Formation: A Taxonomy Of Molecular Cooperation, Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker, Niles Lehman
Prebiotic Rna Network Formation: A Taxonomy Of Molecular Cooperation, Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker, Niles Lehman
Chemistry Faculty Publications and Presentations
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcusribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other …
Life’S Late Digital Revolution And Why It Matters For The Study Of The Origins Of Life, David A. Baum, Niles Lehman
Life’S Late Digital Revolution And Why It Matters For The Study Of The Origins Of Life, David A. Baum, Niles Lehman
Chemistry Faculty Publications and Presentations
The information contained in life exists in two forms, analog and digital. Analog information is manifest mainly in the differing concentrations of chemicals that get passed from generation to generation and can vary from cell to cell. Digital information is encoded in linear polymers such as DNA and RNA, whose side chains come in discrete chemical forms. Here, we argue that the analog form of information preceded the digital. Acceptance of this dichotomy, and this progression, can help direct future studies on how life originated and initially complexified on the primordial Earth, as well as expected trajectories for other, independent …
Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan
Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan
Biology Faculty Publications and Presentations
We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also …
Pcr-Activated Cell Sorting As A General, Cultivation-Free Method For High-Throughput Identification And Enrichment Of Virus Hosts, Shaun W. Lim, Shea T. Lance, Kenneth M. Stedman, Adam R. Abate
Pcr-Activated Cell Sorting As A General, Cultivation-Free Method For High-Throughput Identification And Enrichment Of Virus Hosts, Shaun W. Lim, Shea T. Lance, Kenneth M. Stedman, Adam R. Abate
Biology Faculty Publications and Presentations
Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages …
Editorial: Genetics, Genomics And –Omics Of Thermophiles, Kian Mau Goh, Kok-Gan Chan, Rajesh Kumar Sani, Edgardo Ruben Donati, Anna-Louise Reysenbach
Editorial: Genetics, Genomics And –Omics Of Thermophiles, Kian Mau Goh, Kok-Gan Chan, Rajesh Kumar Sani, Edgardo Ruben Donati, Anna-Louise Reysenbach
Biology Faculty Publications and Presentations
Thermophilic Archaea and Bacteria occupy heated environments. Advancement of next-generation sequencing (NGS), single-cell analyses, and combinations of –omics and microscopic technologies have resulted in the discovery of new thermophiles. This e-book consists of a review, and 10 original articles authored by 94 authors. The main aim of this Research Topic of Frontiers in Microbiology was to provide a platform for researchers to describe recent findings on the ecology of thermophiles using NGS, functional genomics, comparative genomics, gene evolution, and extremozyme discovery.
Topological And Thermodynamic Factors That Influence The Evolution Of Small Networks Of Catalytic Rna Species, Jessica Anne Mellor Yeates, Philippe Nghe, Niles Lehman
Topological And Thermodynamic Factors That Influence The Evolution Of Small Networks Of Catalytic Rna Species, Jessica Anne Mellor Yeates, Philippe Nghe, Niles Lehman
Chemistry Faculty Publications and Presentations
An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative …