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Vasquez YM, Li Z, Xue AZ, Bennett GM. Chromosome-level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution. Mol Ecol Resour 2024; 24:e13919. [PMID: 38146900 DOI: 10.1111/1755-0998.13919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Leafhoppers comprise over 20,000 plant-sap feeding species, many of which are important agricultural pests. Most species rely on two ancestral bacterial symbionts, Sulcia and Nasuia, for essential nutrition lacking in their phloem and xylem plant sap diets. To understand how pest leafhopper genomes evolve and are shaped by microbial symbioses, we completed a chromosomal-level assembly of the aster leafhopper's genome (ALF; Macrosteles quadrilineatus). We compared ALF's genome to three other pest leafhoppers, Nephotettix cincticeps, Homalodisca vitripennis, and Empoasca onukii, which have distinct ecologies and symbiotic relationships. Despite diverging ~155 million years ago, leafhoppers have high levels of chromosomal synteny and gene family conservation. Conserved genes include those involved in plant chemical detoxification, resistance to various insecticides, and defence against environmental stress. Positive selection acting upon these genes further points to ongoing adaptive evolution in response to agricultural environments. In relation to leafhoppers' general dependence on symbionts, species that retain the ancestral symbiont, Sulcia, displayed gene enrichment of metabolic processes in their genomes. Leafhoppers with both Sulcia and its ancient partner, Nasuia, showed genomic enrichment in genes related to microbial population regulation and immune responses. Finally, horizontally transferred genes (HTGs) associated with symbiont support of Sulcia and Nasuia are only observed in leafhoppers that maintain symbionts. In contrast, HTGs involved in non-symbiotic functions are conserved across all species. The high-quality ALF genome provides deep insights into how host ecology and symbioses shape genome evolution and a wealth of genetic resources for pest control targets.
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Affiliation(s)
- Yumary M Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, Merced, California, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Allen Z Xue
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, Merced, California, USA
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Deng J, Bennett GM, Franco DC, Prus-Frankowska M, Stroiński A, Michalik A, Łukasik P. Genome comparison reveals inversions and alternative evolutionary history of nutritional endosymbionts in planthoppers (Hemiptera: Fulgoromorpha). Genome Biol Evol 2023:evad120. [PMID: 37392458 DOI: 10.1093/gbe/evad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/04/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
The evolutionary success of sap-feeding hemipteran insects in the suborder Auchenorrhyncha was enabled by nutritional contributions from their heritable endosymbiotic bacteria. However, the symbiont diversity, functions, and evolutionary origins in this large insect group have not been broadly characterized using genomic tools. In particular, the origins and relationships among ancient betaproteobacterial symbionts Vidania (in Fulgoromorpha) and Nasuia/Zinderia (in Cicadomorpha) are uncertain. Here, we characterized the genomes of Vidania and Sulcia from three Pyrops planthoppers (family Fulgoridae) to understand their metabolic functions and evolutionary histories. We find that, like in previously characterized planthoppers, these symbionts share nutritional responsibilities, with Vidania providing seven out of ten essential amino acids. Sulcia lineages across the Auchenorrhyncha have a highly conserved genome but with multiple independent rearrangements occurring in an early ancestor of Cicadomorpha or Fulgoromorpha and in a few succeeding lineages. Genomic synteny was also observed within each of the betaproteobacterial symbiont genera Nasuia, Zinderia, and Vidania, but not across them, which challenges the expectation of a shared ancestry for these symbionts. The further comparison of other biological traits strongly suggests an independent origin of Vidania early in the planthopper evolution and possibly of Nasuia and Zinderia in their respective host lineages. This hypothesis further links the potential acquisition of novel nutritional endosymbiont lineages with the emergence of auchenorrhynchan superfamilies.
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Affiliation(s)
- Junchen Deng
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Gordon M Bennett
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | | | | | - Adam Stroiński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Anna Michalik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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Gossett JM, Porter ML, Vasquez YM, Bennett GM, Chong RA. Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers. Genome Biol Evol 2023; 15:7067397. [PMID: 36864565 PMCID: PMC10030309 DOI: 10.1093/gbe/evad031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Planthoppers in the family Cixiidae (Hemiptera: Auchenorrhyncha: Fulgoromorpha) harbor a diverse set of obligate bacterial endosymbionts that provision essential amino acids and vitamins that are missing from their plant-sap diet. "Candidatus Sulcia muelleri" and "Ca. Vidania fulgoroidea" have been associated with cixiid planthoppers since their origin within the Auchenorrhyncha, whereas "Ca. Purcelliella pentastirinorum" is a more recent endosymbiotic acquisition. Hawaiian cixiid planthoppers occupy diverse habitats including lava tube caves and shrubby surface landscapes, which offer different nutritional resources and environmental constraints. Genomic studies have focused on understanding the nutritional provisioning roles of cixiid endosymbionts more broadly, yet it is still unclear how selection pressures on endosymbiont genes might differ between cixiid host species inhabiting such diverse landscapes, or how variation in selection might impact symbiont evolution. In this study, we sequenced the genomes of Sulcia, Vidania, and Purcelliella isolated from both surface and cave-adapted planthopper hosts from the genus Oliarus. We found that nutritional biosynthesis genes were conserved in Sulcia and Vidania genomes in inter- and intra-host species comparisons. In contrast, Purcelliella genomes retain different essential nutritional biosynthesis genes between surface- and cave-adapted planthopper species. Finally, we see the variation in selection pressures on symbiont genes both within and between host species, suggesting that strong coevolution between host and endosymbiont is associated with different patterns of molecular evolution on a fine scale that may be associated with the host diet.
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Vasquez YM, Bennett GM. Erratum: A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes. iScience 2022; 26:105810. [PMID: 36590156 PMCID: PMC9800188 DOI: 10.1016/j.isci.2022.105810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
[This corrects the article DOI: 10.1016/j.isci.2022.104786.].
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Vasquez YM, Bennett GM. A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes. iScience 2022; 25:104786. [PMID: 35982793 PMCID: PMC9379567 DOI: 10.1016/j.isci.2022.104786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023] Open
Abstract
Many insects depend on ancient associations with intracellular bacteria for essential nutrition. The genomes of these bacteria are often highly reduced. Although drift is a major driver of symbiont evolution, other evolutionary forces continue to influence them. To understand how ongoing molecular evolution and gene loss shape symbiont genomes, we sequenced two of the most ancient symbionts known, Sulcia and Nasuia, from 20 Hawaiian Nesophrosyne leafhoppers. We leveraged the parallel divergence of Nesophrosyne lineages throughout Hawaii as a natural experimental framework. Sulcia and Nasuia experience ongoing-but divergent-gene loss, often in a convergent fashion. Although some genes are under relaxed selection, purifying and positive selection are also important drivers of genome evolution, particularly in maintaining certain nutritional and cellular functions. Our results further demonstrate that symbionts experience dramatically different evolutionary environments, as evidenced by the finding that Sulcia and Nasuia have one of the slowest and fastest rates of molecular evolution known.
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Affiliation(s)
- Yumary M. Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA,Corresponding author
| | - Gordon M. Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA,Corresponding author
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Medina M, Baker DM, Baltrus DA, Bennett GM, Cardini U, Correa AMS, Degnan SM, Christa G, Kim E, Li J, Nash DR, Marzinelli E, Nishiguchi M, Prada C, Roth MS, Saha M, Smith CI, Theis KR, Zaneveld J. Grand Challenges in Coevolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.618251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Stever H, Eiben J, Bennett GM. Hawaiian Nysius Insects Rely on an Obligate Symbiont with a Reduced Genome That Retains a Discrete Nutritional Profile to Match Their Plant Seed Diet. Genome Biol Evol 2021; 13:6349176. [PMID: 34383896 PMCID: PMC8412300 DOI: 10.1093/gbe/evab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/19/2022] Open
Abstract
Seed-feeding Nysius insects (Hemiptera: Lygaeidae) have a symbiotic association with distinct intracellular bacteria, “Candidatus Schneideria nysicola” (Gammaproteobacteria). Although many other hemipteran insect groups generally rely on bacterial symbionts that synthesize all ten essential amino acids lacking in their plant sap diets, the nutritional role of Schneideria in Nysius hosts that specialize on a more nutritionally complete seed-based diet has remained unknown. To determine the nutritional and functional capabilities of Schneideria, we sequenced the complete Schneideria genomes from three distantly related endemic Hawaiian Nysius seed bug species. The complete Schneideria genomes are highly conserved and perfectly syntenic among Hawaiian Nysius host species. Each circular chromosome is ∼0.57 Mb in size and encodes 537 protein-coding genes. They further exhibit a strong A + T nucleotide substitution bias with an average G + C nucleotide content of 29%. The predicted nutritional contribution of Schneideria includes four B vitamins and five of the ten essential amino acids that likely match its hosts’ seed-based diet. Disrupted and degraded genes in Schneideria suggests that Hawaiian lineages are undergoing continued gene losses observed in the smaller genomes of the other more ancient hemipteran symbionts.
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Affiliation(s)
- Heather Stever
- Department of Life and Environmental Sciences, University of California, Merced, USA
| | - Jesse Eiben
- Department of Biology, Geology, and Environmental Sciences, California University of Pennsylvania, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, USA
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Waneka G, Vasquez YM, Bennett GM, Sloan DB. Mutational Pressure Drives Differential Genome Conservation in Two Bacterial Endosymbionts of Sap-Feeding Insects. Genome Biol Evol 2020; 13:6020258. [PMID: 33275136 PMCID: PMC7952229 DOI: 10.1093/gbe/evaa254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 11/16/2022] Open
Abstract
Compared with free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation versus selection. For example, the ancestor of Auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing ∼300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novode novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is potentially even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia versus BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Yumary M Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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Gillespie RG, Bennett GM, De Meester L, Feder JL, Fleischer RC, Harmon LJ, Hendry AP, Knope ML, Mallet J, Martin C, Parent CE, Patton AH, Pfennig KS, Rubinoff D, Schluter D, Seehausen O, Shaw KL, Stacy E, Stervander M, Stroud JT, Wagner C, Wogan GOU. Comparing Adaptive Radiations Across Space, Time, and Taxa. J Hered 2020; 111:1-20. [PMID: 31958131 PMCID: PMC7931853 DOI: 10.1093/jhered/esz064] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.
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Affiliation(s)
- Rosemary G Gillespie
- University of California, Berkeley, Essig Museum of Entomology & Department of Environmental Science, Policy, and Management, Berkeley, CA
| | - Gordon M Bennett
- University of California Merced, Life and Environmental Sciences Unit, Merced, CA
| | - Luc De Meester
- University of Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belguim
| | - Jeffrey L Feder
- University of Notre Dame, Dept. of Biological Sciences, Notre Dame, IN
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Luke J Harmon
- University of Idaho, Dept. of Biological Sciences, Moscow, ID
| | | | | | | | - Christopher Martin
- University of California Berkeley, Integrative Biology and Museum of Vertebrate Zoology, Berkeley, CA
| | | | - Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA
| | - Karin S Pfennig
- University of North Carolina at Chapel Hill, Department of Biology, Chapel Hill, NC
| | - Daniel Rubinoff
- University of Hawaiʻi at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu, HI
| | | | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, BE, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Eawag, Kastanienbaum, LU, Switzerland
| | - Kerry L Shaw
- Cornell University, Neurobiology and Behavior, Tower Road,, Ithaca, NY
| | - Elizabeth Stacy
- University of Nevada Las Vegas, School of Life Sciences, Las Vegas, NV
| | - Martin Stervander
- University of Oregon, Institute of Ecology and Evolution, Eugene, OR
| | - James T Stroud
- Washington University in Saint Louis, Biology, Saint Louis, MO
| | | | - Guinevere O U Wogan
- University of California Berkeley, Environmental Science Policy, and Management, Berkeley, CA
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Mao M, Yang X, Bennett GM. Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host. Proc Natl Acad Sci U S A 2018; 115:E11691-E11700. [PMID: 30463949 PMCID: PMC6294904 DOI: 10.1073/pnas.1811932115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system.
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Affiliation(s)
- Meng Mao
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343;
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Bennett GM, Mao M. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol 2018; 20:4461-4472. [PMID: 30047196 DOI: 10.1111/1462-2920.14367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/15/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Insects in the Auchenorrhyncha (Hemiptera: Suborder) established nutritional symbioses with bacteria approximately 300 million years ago (MYA). The suborder split early during its diversification (~ 250 MYA) into the Fulgoroidea (planthoppers) and Cicadomorpha (leafhoppers and cicadas). The two lineages share some symbionts, including Sulcia and possibly a Betaproteobacteria that collaboratively provide their hosts with 10 essential amino acids (EAA). Some hosts harbour three bacteria, as is common among planthoppers. However, genomic studies are currently restricted to the dual-bacterial symbioses found in Cicadomorpha, leaving the origins and functions of these more complex symbioses unclear. To address these questions, we sequenced the genomes and performed phylogenomic analyses of 'Candidatus Sulcia muelleri' (Bacteroidetes), 'Ca. Vidania fulgoroideae' (Betaproteobacteria) and 'Ca. Purcelliella pentastirinorum' (Gammaproteobacteria) from a planthopper (Cixiidae: Oliarus). In contrast to the Cicadomorpha, nutritional synthesis responsibilities are rearranged between the cixiid symbionts. Although Sulcia has a highly conserved genome across the Auchenorrhyncha, in the cixiids it is greatly reduced and provides only three EAAs. Vidania contributes the remaining seven EAAs. Phylogenomic results suggest that it represents an ancient symbiont lineage paired with Sulcia throughout the Auchenorrhyncha. Finally, Purcelliella was recently acquired from plant-insect associated bacteria (Pantoea-Erwinia) to provide B vitamins and metabolic support to its degenerate partners.
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Affiliation(s)
- Gordon M Bennett
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
| | - Meng Mao
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
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Bennett GM, McCutcheon JP, McDonald BR, Moran NA. Lineage-Specific Patterns of Genome Deterioration in Obligate Symbionts of Sharpshooter Leafhoppers. Genome Biol Evol 2015; 8:296-301. [PMID: 26260652 PMCID: PMC4758232 DOI: 10.1093/gbe/evv159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant sap-feeding insects (Hemiptera) rely on obligate bacterial symbionts that provision nutrients. Some of these symbionts are ancient and have evolved tiny genomes, whereas others are younger and retain larger, dynamic genomes. Baumannia cicadellinicola, an obligate symbiont of sharpshooter leafhoppers, is derived from a relatively recent symbiont replacement. To better understand evolutionary decay of genomes, we compared Baumannia from three host species. A newly sequenced genome for Baumannia from the green sharpshooter (B-GSS) was compared with genomes of Baumannia from the blue-green sharpshooter (B-BGSS, 759 kilobases [kb]) and from the glassy-winged sharpshooter (B-GWSS, 680 kb). B-GSS has the smallest Baumannia genome sequenced to date (633 kb), with only three unique genes, all involved in membrane function. It has lost nearly all pathways involved in vitamin and cofactor synthesis, as well as amino acid biosynthetic pathways that are redundant with pathways of the host or the symbiotic partner, Sulcia muelleri. The entire biosynthetic pathway for methionine is eliminated, suggesting that methionine has become a dietary requirement for hosts. B-GSS and B-BGSS share 33 genes involved in bacterial functions (e.g., cell division, membrane synthesis, metabolite transport, etc.) that are lost from the more distantly related B-GWSS and most other tiny genome symbionts. Finally, pairwise divergence estimates indicate that B-GSS has experienced a lineage-specific increase in substitution rates. This increase correlates with accelerated protein-level changes and widespread gene loss. Thus, the mode and tempo of genome reduction vary widely among symbiont lineages and result in wide variation in metabolic capabilities across hosts.
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Affiliation(s)
- Gordon M Bennett
- Department of Integrative Biology, University of Texas, Austin Department of Plant and Environmental Protection Sciences, University of Hawaii, Manoa
| | | | | | - Nancy A Moran
- Department of Integrative Biology, University of Texas, Austin Institute for Cellular and Molecular Biology, University of Texas, Austin
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Affiliation(s)
- Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Texas 78712; ,
| | - Gordon M. Bennett
- Department of Integrative Biology, University of Texas at Austin, Texas 78712; ,
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Abstract
Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola, of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia-ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia-ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia-ALF is most closely related to Zinderia, the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia/Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs >200 Ma, and possibly since the origin of the Auchenorrhyncha, >260 Ma.
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Affiliation(s)
- Gordon M Bennett
- Department of Ecology and Evolutionary Biology & Microbial Diversity Institute, Yale University
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Koga R, Bennett GM, Cryan JR, Moran NA. Evolutionary replacement of obligate symbionts in an ancient and diverse insect lineage. Environ Microbiol 2013; 15:2073-81. [PMID: 23574391 DOI: 10.1111/1462-2920.12121] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/11/2013] [Indexed: 11/27/2022]
Abstract
Many insect groups depend on ancient obligate symbioses with bacteria that undergo long-term genomic degradation due to inactivation and loss of ancestral genes. Sap-feeding insects in the hemipteran suborder Auchenorrhyncha show complex symbioses with at least two obligate bacterial symbionts, inhabiting specialized host cells (bacteriocytes). We explored the symbiotic relationships of the spittlebugs (Auchenorrhyncha: Cercopoidea) using phylogenetic and microscopy methods. Results show that most spittlebugs contain the symbionts Sulcia muelleri (Bacteroidetes) and Zinderia insecticola (Betaproteobacteria) with each restricted to its own bacteriocyte type. However, the ancestral Zinderia symbiont has been replaced with a novel symbiont closely related to Sodalis glossinidius (Enterobacteriaceae) in members of the ecologically successful spittlebug tribe Philaenini. At least one spittlebug species retains Sulcia and Zinderia, but also has acquired a Sodalis-like symbiont, possibly representing a transitional stage in the evolutionary succession of symbioses. Phylogenetic analyses including symbionts of other Auchenorrhyncha lineages suggest that Zinderia, like Sulcia, descends from an ancestral symbiont present in the common ancestor of Auchenorrhyncha. This betaproteobacterial symbiont has been repeatedly replaced by other symbionts, such as the Sodalis-like symbiont of spittlebugs. Symbiont replacement may offer a route for hosts to escape dependence on an ancient, degraded and potentially inefficient symbiont.
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Affiliation(s)
- Ryuichi Koga
- Department of Ecology and Evolutionary Biology & Microbial Diversity Institute, Yale University, New Haven, CT 06511, USA
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Abstract
The recovery and assembly of genome sequences from samples containing communities of organisms pose several challenges. Because it is rarely possible to disassociate the resident organisms prior to sequencing, a major obstacle is the assignment of sequences to a single genome that can be fully assembled. This chapter delineates many of the decisions, methodologies, and approaches that can lead to the generation of complete or nearly complete microbial genome sequences from heterogeneous samples-that is, the procedures that allow us to turn metagenomes into genomes.
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Affiliation(s)
- Daniel B Sloan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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Bennett GM, O’Grady PM. Host–plants shape insect diversity: Phylogeny, origin, and species diversity of native Hawaiian leafhoppers (Cicadellidae: Nesophrosyne). Mol Phylogenet Evol 2012; 65:705-17. [PMID: 22884527 DOI: 10.1016/j.ympev.2012.07.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/04/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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Yoon SY, Bennett GM. Effects of a stimulus-stimulus pairing procedure on conditioning vocal sounds as reinforcers. Anal Verbal Behav 2012; 17:75-88. [PMID: 22477215 DOI: 10.1007/bf03392957] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Two experiments were conducted to investigate the effects of stimulus-stimulus pairing on conditioning vocal sounds as reinforcers. Four preschoolers with severe language and communication delays participated. In Experiment 1, an attempt was made to condition vocal sounds as a reinforcer by pairing a specific vocal sound with a reinforcing event (e.g., physical interaction). Results indicated that presentation of a stimulus-stimulus pairing was effective in conditioning the target vocal sounds as reinforcers, which increased the occurrence of vocalizations of those sounds by the participants. Experiment 2 compared the effects of the pairing procedure with those of echoic training. The pairing procedure was identical to that in Experiment 1. In the echoic training condition, the experimenter produced the target vocal sound and gave the participant an opportunity to echo. The same reinforcing stimulus (e.g., physical interaction) was provided contingent upon the occurrence of the target vocal sound emitted by the participant. Results showed that the pairing procedure was more effective than the echoic training. Findings from this study suggest that for these participants, who had no vocal imitation skills, the stimulus-stimulus pairing was an effective procedure for conditioning vocal sounds as reinforcers and increased the probability of occurrence of the vocalization without a direct reinforcement contingency.
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Bennett GM, Pantoja NA, O'Grady PM. Diversity and phylogenetic relationships of Wolbachia in Drosophila and other native Hawaiian insects. Fly (Austin) 2012; 6:273-83. [PMID: 22878693 DOI: 10.4161/fly.21161] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Wolbachia is a genus of parasitic alphaproteobacteria found in arthropods and nematodes, and represents on of the most common, widespread endosymbionts known. Wolbachia affects a variety of reproductive functions in its host (e.g., male killing, cytoplasmic incompatibility, parthenogenesis), which have the potential to dramatically impact host evolution and species formation. Here, we present the first broad-scale study to screen natural populations of native Hawaiian insects for Wolbachia, focusing on the endemic Diptera. Results indicate that Wolbachia infects native Hawaiian taxa, with alleles spanning phylogenetic supergroups, A and B. The overall frequency of Wolbachia incidene in Hawaiian insects was 14%. The incidence of infection in native Hawaiian Diptera was 11% for individuals and 12% for all species screened. Wolbachia was not detected in two large, widespread Hawaiian dipteran families-Dolichopodidae (44 spp screened) and Limoniidae (12 spp screened). Incidence of infection within endemic Hawaiian lineages that carry Wolbachia was 18% in Drosophilidae species, 25% in Caliphoridae species, > 90% in Nesophrosyne species, 20% in Drosophila dasycnemia and 100% in Nesophrosyne craterigena. Twenty unique alleles were recovered in this study, of which 18 are newly recorded. Screening of endemic populations of D. dasycnemia across Hawaii Island revealed 4 unique alleles. Phylogenetic relationships and allele diversity provide evidence for horizontal transfer of Wolbachia among Hawaiian arthropod lineages.
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Affiliation(s)
- Gordon M Bennett
- Department of Environmental Science, Policy and Management; University of California, Berkeley, Berkeley, CA, USA.
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Abstract
Emerging diseases are increasing in incidence; therefore, understanding how pathogens are introduced into new regions and cause epidemics is of importance for the development of strategies that may hinder their spread. We used molecular data to study how a vector-borne banana virus, Banana bunchy top virus (BBTV), spread in Hawaii after it was first detected in 1989. Our analyses suggest that BBTV was introduced once into Hawaii, on the island of Oahu. All other islands were infected with isolates originating from Oahu, suggesting that movement of contaminated plant material was the main driving factor responsible for interisland spread of BBTV. The rate of mutation inferred by the phylogenetic analysis (1.4 x 10(-4) bp/year) was similar to that obtained in an experimental evolution study under greenhouse conditions (3.9 x 10(-4) bp/year). We used these values to estimate the number of infections occurring under field conditions per year. Our results suggest that strict and enforced regulations limiting the movement of banana plant material among Hawaiian islands could have reduced interisland spread of this pathogen.
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Affiliation(s)
- Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA.
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Abstract
Focal myositis is a rare, benign focal inflammation of muscle. The lesion often presents as a mass that may be mistaken for a soft tissue sarcoma. This report describes the MRI and histopathological features of a case and illustrates how the diagnosis may be suspected on the basis of the MR findings.
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Affiliation(s)
- H R Galloway
- Department of Medical Imaging, The University of Sydney, Canberra Clinical School, Garran, Australian Capital Territory 2605, Australia.
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Wallis RB, Seale L, Finney S, Sawyer RT, Bennett GM, Ross-Murphy SB. Reduction of plasma clot stability by a novel factor XIIIa inhibitor from the Giant Amazon Leech, Haementeria ghilianii. Blood Coagul Fibrinolysis 1997; 8:291-5. [PMID: 9282793 DOI: 10.1097/00001721-199707000-00005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The blood-sucking leech, Haementeria ghilianii, has evolved a number of agents that attenuate haemostasis. Recently we have isolated a potent inhibitor of factor XIIIa, tridegin, in the salivary glands which is almost certainly involved in feeding. Addition of purified natural tridegin to plasma, prior to clotting with thrombin, results in clots that deform more readily as adjudged by the greatly reduced development of the storage modulus on application of a shear force. The increase in the storage modulus in developing plasma clots is a slow process and continues for many hours. The effect of tridegin is particularly great when the clots are permitted to age in this way, demonstrating the role of factor XIIIa in the process. The IC50 for this inhibition is 138 ng/ml. Clots formed in the presence of tridegin are also lysed more rapidly in vitro by the leech's own fibrinolytic enzyme, hementin (time for 50% lysis, 16.0 +/- 0.8 h versus 22.3 +/- 2.0 h, P < 0.05). The synergy with which these agents act together may provide lessons for therapy of thrombosis in man.
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Abstract
Alterations in phenotype and function of intestinal macrophages occur in inflammatory bowel disease (IBD) but it is unclear whether these changes result from the recruitment of circulating monocytes to the intestine or from proliferation of resident intestinal macrophages. We sought to demonstrate the arrival of blood monocytes, the precursors of macrophages, in IBD mucosa. Peripheral blood mononuclear cells were isolated from 23 patients with clinically active intestinal inflammation (13 Crohn's disease, eight ulcerative colitis, two infective colitis), then radiolabelled with 99mtechnetium (Tc)-stannous colloid (n = 13) or 111indium (In)-oxine (n = 10) before re-injection and abdominal scanning. Four patients had demonstrable intestinal monocyte uptake using [99mTc]-stannous colloid, while six [111In]-oxine-labelled monocyte scans were positive. Uptake sites correlated with actively inflamed regions. Patients demonstrating monocyte uptake had been treated with corticosteroids for a significantly (P < 0.02) shorter duration (median 3 vs 20 days) than those with negative scans. There was no significant difference between positive and negative scans for disease category, clinical or histological disease, activity, or radioisotope used. Biopsies of inflamed mucosa from two patients suffering ulcerative colitis who had positive scans showed a high proportion of CD14-positive macrophages, 4-9% of which contained autoradiographic grains. These results demonstrate that blood monocytes are recruited to the mucosa of actively inflamed bowel, and suggest that this process may be inhibited by corticosteroids. Moreover, the phenotype of the recently-arrived monocytes indicates their susceptibility to stimulation by lipopolysaccharide, and suggests a mechanism for the continuing inflammation in the bacterial product-rich milieu of IBD.
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Affiliation(s)
- M C Grimm
- Division of Clinical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Scrutton MC, Ross-Murphy SB, Bennett GM, Stirling Y, Meade TW. Changes in clot deformability--a possible explanation for the epidemiological association between plasma fibrinogen concentration and myocardial infarction. Blood Coagul Fibrinolysis 1994; 5:719-23. [PMID: 7865677 DOI: 10.1097/00001721-199410000-00007] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This study examined the rheological properties of fibrin gels formed by adding thrombin to plasma samples from 99 subjects with fibrinogen concentrations ranging from 1.45 to 4.14 g/l. A highly significant (r = 0.757; P < 0.001) inverse correlation was observed between plasma fibrinogen concentration and the extent of clot deformability as estimated from the final value of the storage modulus (G') of the fibrin gel when obtained by rheological analysis. A similarly significant correlation (r = 0.844; P < 0.001) was obtained using samples from 47 subjects in which fibrin cross-linking was blocked by addition of 0.1 mM iodoacetamide to inactivate factor XIIIa. The characteristics of the relationship between G' and fibrinogen concentration in the plasma samples was comparable with that observed when the fibrin gel was formed by adding thrombin to purified fibrinogen. These results suggest that the increased risk of myocardial infarction associated with an elevated plasma fibrinogen concentration may, in part, be explained on the basis of a decreased deformability of the fibrin clot formed.
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Affiliation(s)
- M C Scrutton
- Division of Life Sciences, King's College, London
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Porter RR, Bailey C, Bennett GM, Catalfamo AT, Daniels KJ, Ehle JE, Gibbs S, Krout LS, Luers ES. Stress during the waiting period: a review of pretransplantation fears. Crit Care Nurs Q 1991; 13:25-31. [PMID: 1986804 DOI: 10.1097/00002727-199102000-00005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Bennett GM, Seaver A, Calcott PH. Effect of defined lipopolysaccharide core defects on resistance of Salmonella typhimurium to freezing and thawing and other stresses. Appl Environ Microbiol 1981; 42:843-9. [PMID: 6797349 PMCID: PMC244117 DOI: 10.1128/aem.42.5.843-849.1981] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A family of mutants of Salmonella typhimurium with altered lipopolysaccharide (LPS) core chain lengths were assessed for sensitivity to freeze-thaw and other stresses. Deep rough strains with decreased chain length in the LPS core were more susceptible to novobiocin, polymyxin B, bacitracin, and sodium lauryl sulfate during growth, to ethylenediaminetetraacetic acid and sodium lauryl sulfate in resting suspension, and to slow and rapid freeze-thaw in water and saline, and these strains exhibited more outer membrane damage than the wild type or less rough strains. Variations in the LPS chain length did not dramatically affect the sensitivity of the strains to tetracycline, neomycin, or NaCl in growth conditions or the degree of freeze-thaw-induced cytoplasmic membrane damage. The deeper rough isogenic strains incorporated larger quantities of less-stable LPS and less protein into the outer membrane than did the wild type or less rough mutants, indicating that the mutations affected outer membrane synthesis or organization or both. Nikaido's model of the role of LPS and protein in determining the resistance of gram-negative bacteria to low-molecular-weight hydrophobic antibiotics is discussed in relation to the stress of freeze-thaw.
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Bennett GM, Stanley TH. Cardiovascular effects of fentanyl during enflurane anesthesia in man. Anesth Analg 1979; 58:179-82. [PMID: 572155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cardiovascular effects of three doses of intravenous fentanyl (50, 100, and 200 microgram) were determined in 42 adult patients undergoing intraabdominal surgical procedures with enflurane (2--3%) and nitrous oxide (50%) in oxygen. Fentanyl was administered a minimum of 40 minutes after induction of anesthesia and 30 minutes after initiation of the surgical procedure. Stroke volume, heart rate, cardiac output, mean arterial and central venous blood pressures, and peripheral arterial resistance were determined by computer analysis of the central aortic pulse-pressure curve according to the method of Warner. Measurements were made before and 2, 4, 6, 8, and 10 minutes after fentanyl. Fentanyl (50 microgram) produced increases in stroke volume and cardiac output as well as a decrease in peripheral arterial resistance but did not alter heart rate or mean arterial blood pressure. Fentanyl (100 microgram) did not significantly change any variable at any time. Fentanyl (1l (200 microgram) produced sustained decreases in stroke volume, cardiac output and mean arterial blood pressure and increased central venous pressure but did not alter heart rate or peripheral arterial resistance. The data indicate that fentanyl (50--100 microgram) stimulates or has no effect on cardiovascular dynamics during enflurane-nitrous oxide anesthesia but fentanyl (200 microgram) produces significant cardiovascular depression. Our findings suggest that small doses of intravenous fentanyl may be of benefit during enflurane-nitrous oxide but larger doses should probably be avoided.
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Loeser EA, Machin R, Colley J, Orr D, Bennett GM, Stanley TH. Postoperative sore throat--importance of endotracheal tube conformity versus cuff design. Anesthesiology 1978; 49:430-2. [PMID: 727546 DOI: 10.1097/00000542-197812000-00010] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bennett GM, Loeser EA, Kawamura R, Stanley TH. Cardiovascular responses to nitrous oxide during enflurane and oxygen anesthesia. Anesthesiology 1977; 46:227-9. [PMID: 842878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bennett GM, Loeser EA, Stanley TH. Cardiovascular effects of scopolamine during morphine-oxygen and morphine-nitrous oxide-oxygen anesthesia in man. Anesthesiology 1977; 46:225-7. [PMID: 842877 DOI: 10.1097/00000542-197703000-00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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