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Evans JR, Vis ML. Relative expression analysis of light-harvesting genes in the freshwater alga Lympha mucosa (Batrachospermales, Rhodophyta). J Phycol 2020; 56:540-548. [PMID: 31930498 PMCID: PMC9290634 DOI: 10.1111/jpy.12967] [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] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
Members of the freshwater red algal order Batrachospermales are often described as shade-adapted. Nevertheless, recent ecophysiological studies have demonstrated species-level differences in acclimation to a range of irradiances. Lympha mucosa occurs in open and shaded portions of temperate streams and is abundant during summer months, suggesting it tolerates high and low irradiances. Specimens of L. mucosa were collected from open (sun-acclimated) or shaded (shade-acclimated) sites and exposed to low (<20 μmol photons · m-2 · s-1 ) or high (220 μmol photon · m-2 · s-1 ) light for 72 h to examine mechanisms of photoacclimation at the transcriptional level. High-throughput sequence data were used to design specific primers for genes involved with light harvesting and these were quantified with qPCR. The greatest significant difference in transcript abundances was observed in the psaA gene (Photosystem I P700 apoprotein), and site-type had an effect on these responses. Shade-acclimated thalli were 22-fold down-regulated at high light, whereas sun-acclimated thalli were only 5-fold down-regulated. Another gene involved with Photosystem I (petF ferredoxin) was down-regulated at high light, but only individuals from the shaded site were significantly different (4-fold). In thalli from both sites, cpeA (Phycoerythrin alpha chain) was down-regulated at high light. Although not statistically significant, patterns consistent with previous physiological and transcriptomic studies were uncovered, namely the inverse response of transcriptional activity in genes that encode phycobiliproteins. In support of previous ecophysiological studies of freshwater red algae, these data indicate significant transcriptional changes involving Photosystem I and phycobiliprotein synthesis are required to tolerate and grow at various irradiances.
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Affiliation(s)
- Joshua R. Evans
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
| | - Morgan L. Vis
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
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2
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Manzello DP, Matz MV, Enochs IC, Valentino L, Carlton RD, Kolodziej G, Serrano X, Towle EK, Jankulak M. Role of host genetics and heat-tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming. Glob Chang Biol 2019; 25:1016-1031. [PMID: 30552831 DOI: 10.1111/gcb.14545] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 09/28/2018] [Accepted: 11/30/2018] [Indexed: 05/28/2023]
Abstract
Identifying which factors lead to coral bleaching resistance is a priority given the global decline of coral reefs with ocean warming. During the second year of back-to-back bleaching events in the Florida Keys in 2014 and 2015, we characterized key environmental and biological factors associated with bleaching resilience in the threatened reef-building coral Orbicella faveolata. Ten reefs (five inshore, five offshore, 179 corals total) were sampled during bleaching (September 2015) and recovery (May 2016). Corals were genotyped with 2bRAD and profiled for algal symbiont abundance and type. O. faveolata at the inshore sites, despite higher temperatures, demonstrated significantly higher bleaching resistance and better recovery compared to offshore. The thermotolerant Durusdinium trenchii (formerly Symbiondinium trenchii) was the dominant endosymbiont type region-wide during initial (78.0% of corals sampled) and final (77.2%) sampling; >90% of the nonbleached corals were dominated by D. trenchii. 2bRAD host genotyping found no genetic structure among reefs, but inshore sites showed a high level of clonality. While none of the measured environmental parameters were correlated with bleaching, 71% of variation in bleaching resistance and 73% of variation in the proportion of D. trenchii was attributable to differences between genets, highlighting the leading role of genetics in shaping natural bleaching patterns. Notably, D. trenchii was rarely dominant in O. faveolata from the Florida Keys in previous studies, even during bleaching. The region-wide high abundance of D. trenchii was likely driven by repeated bleaching associated with the two warmest years on record for the Florida Keys (2014 and 2015). On inshore reefs in the Upper Florida Keys, O. faveolata was most abundant, had the highest bleaching resistance, and contained the most corals dominated by D. trenchii, illustrating a causal link between heat tolerance and ecosystem resilience with global change.
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Affiliation(s)
- Derek P Manzello
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas
| | - Ian C Enochs
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
| | - Lauren Valentino
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Renee D Carlton
- Khaled bin Sultan Living Oceans Foundation, Landover, Maryland
| | - Graham Kolodziej
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Xaymara Serrano
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Erica K Towle
- Office of the NOAA Administrator, Silver Spring, Maryland
| | - Mike Jankulak
- Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, Miami, Florida
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
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Hou Y, Ji N, Zhang H, Shi X, Han H, Lin S. Genome size-dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism. J Phycol 2019; 55:37-46. [PMID: 30468510 DOI: 10.1111/jpy.12815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/22/2018] [Indexed: 06/09/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) plays critical roles in eukaryotic DNA replication and replication-associated processes. It is typically encoded by one or two gene copies (pcna) in eukaryotic genomes. Recently reported higher copy numbers of pcna in some dinoflagellates raised a question of how this gene has uniquely evolved in this phylum. Through real-time PCR quantification, we found a wide range of pcna copy number (2-287 copies) in 11 dinoflagellate species (n = 38), and a strong positive correlation between pcna copy number and genome size (log10 -log10 transformed). Intraspecific pcna diverged up to 21% and are dominated by nonsynonymous substitutions, indicating strong purifying selection pressure on and hence functional necessity of this gene. By surveying pcna copy numbers in eukaryotes, we observed a genome size threshold at 4 pg DNA, above which more than two pcna copies are found. To examine whether retrotransposition is a mechanism of pcna duplication, we measured the copy number of retroposed pcna, taking advantage of the 22-nt dinoflagellate-specific spliced leader (DinoSL) capping the 5' end of dinoflagellate nuclear-encoded mRNAs, which would exist in the upstream region of a retroposed gene copy. We found that retroposed pcna copy number increased with total pcna copy number and genome size. These results indicate co-evolution of dinoflagellate pcna copy number with genome size, and retroposition as a major mechanism of pcna duplication in dinoflagellates. Furthermore, we posit that the demand of faithful replication and maintenance of the large dinoflagellate genomes might have favored the preservation of the retroposed pcna as functional genes.
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Affiliation(s)
- Yubo Hou
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Department of Biology, Skidmore College, Saratoga Springs, New York, 12866, USA
| | - Nanjing Ji
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, Fujian, 361102, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, Fujian, 361102, China
| | - Hansen Han
- Department of Biology, Skidmore College, Saratoga Springs, New York, 12866, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
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Jarau M, Di Natale A, Huber PE, MacInnes JI, Lumsden JS. Virulence of Flavobacterium psychrophilum isolates in rainbow trout Oncorhynchus mykiss (Walbaum). J Fish Dis 2018; 41:1505-1514. [PMID: 30074253 DOI: 10.1111/jfd.12861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease (BCWD) in freshwater-reared salmonids, is also a common commensal organism of healthy fish. The virulence potential of F. psychrophilum isolates obtained from BCWD cases in Ontario between 1994 and 2009 was evaluated. In preliminary infection trials of rainbow trout juveniles, significant differences (0% to 63% mortality) in the virulence of the 22 isolates tested were noted following intraperitoneal injection with 108 cfu/fish. A highly virulent strain, FPG 101, was selected for further study. When fish were injected intraperitoneally with a 106 , 107 or 108 cfu/fish of F. psychrophilum FPG 101, the 108 cfu/fish dose produced significantly greater mortality (p < 0.05). The bacterial load in spleen samples collected from fish every 3 days after infection was determined using rpoC quantitative polymerase chain reaction amplification and by plate counting. Bacterial culture and rpoC qPCR were highly correlated (R2 = 0.92); however, culture was more sensitive than the qPCR assay for the detection of F. psychrophilum in spleen tissue. Ninety-seven per cent of the asymptomatic and the morbid fish had splenic bacterial loads of <2.8 log10 gene/copies and >3.0 log10 gene copies/reaction, respectively, following infection with 108 cfu/fish.
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Affiliation(s)
- Maureen Jarau
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Adrian Di Natale
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Paul E Huber
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Janet I MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - John S Lumsden
- Fish Pathology Laboratory, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- Adjunct Faculty, St. George's University, True Blue, Grenada
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Farlora R, Valdebenito-Aguayo F, Valenzuela-Muñoz V, Gallardo-Escárate C. Hydrogen peroxide treatment modulates the transcription of sex-related genes in the sea lice Caligus rogercresseyi. J Fish Dis 2018; 41:921-926. [PMID: 28984365 DOI: 10.1111/jfd.12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Affiliation(s)
- R Farlora
- Laboratorio de Biotecnología Acuática y Genómica Reproductiva/Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - F Valdebenito-Aguayo
- Laboratory of Biotechnology and Aquatic Genomics, Universidad de Concepción, Concepción, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - V Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Universidad de Concepción, Concepción, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - C Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Universidad de Concepción, Concepción, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
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Bustin S, Nolan T. Talking the talk, but not walking the walk: RT- qPCR as a paradigm for the lack of reproducibility in molecular research. Eur J Clin Invest 2017; 47:756-774. [PMID: 28796277 DOI: 10.1111/eci.12801] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022]
Abstract
Poorly executed and inadequately reported molecular measurement methods are amongst the causes underlying the lack of reproducibility of much biomedical research. Although several high impact factor journals have acknowledged their past failure to scrutinise adequately the technical soundness of manuscripts, there is a perplexing reluctance to implement basic corrective measures. The reverse transcription real-time quantitative PCR (RT-qPCR) is probably the most straightforward measurement technique available for RNA quantification and is widely used in research, diagnostic, forensic and biotechnology applications. Despite the impact of the minimum information for the publication of quantitative PCR experiments (MIQE) guidelines, which aim to improve the robustness and the transparency of reporting of RT-qPCR data, we demonstrate that elementary protocol errors, inappropriate data analysis and inadequate reporting continue to be rife and conclude that the majority of published RT-qPCR data are likely to represent technical noise.
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Affiliation(s)
- Stephen Bustin
- Postgraduate Medical Institute, Faculty of Medical Science, Anglia Ruskin University, Chelmsford, Essex, UK
| | - Tania Nolan
- Institute of Population Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
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Emerson JB, Keady PB, Clements N, Morgan EE, Awerbuch J, Miller SL, Fierer N. High temporal variability in airborne bacterial diversity and abundance inside single-family residences. Indoor Air 2017; 27:576-586. [PMID: 27743387 DOI: 10.1111/ina.12347] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/10/2016] [Indexed: 05/14/2023]
Abstract
Our homes are microbial habitats, and although the amounts and types of bacteria in indoor air have been shown to vary substantially across residences, temporal variability within homes has rarely been characterized. Here, we sought to quantify the temporal variability in the amounts and types of airborne bacteria in homes, and what factors drive this variability. We collected filter samples of indoor and outdoor air in 15 homes over 1 year (approximately eight time points per home, two per season), and we used culture-independent DNA sequencing approaches to characterize bacterial community composition. Significant differences in indoor air community composition were observed both between homes and within each home over time. Indoor and outdoor air community compositions were not significantly correlated, suggesting that indoor and outdoor air communities are decoupled. Indoor air communities from the same home were often just as different at adjacent time points as they were across larger temporal distances, and temporal variation correlated with changes in environmental conditions, including temperature and relative humidity. Although all homes had highly variable indoor air communities, homes with the most temporally variable communities had more stable, lower average microbial loads than homes with less variable communities.
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Affiliation(s)
- J B Emerson
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO, USA
| | - P B Keady
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - N Clements
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - E E Morgan
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, CO, USA
| | - J Awerbuch
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - S L Miller
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO, USA
| | - N Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA
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Scherer PI, Raeder U, Geist J, Zwirglmaier K. Influence of temperature, mixing, and addition of microcystin-LR on microcystin gene expression in Microcystis aeruginosa. Microbiologyopen 2017; 6:e00393. [PMID: 27411372 PMCID: PMC5300888 DOI: 10.1002/mbo3.393] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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] [Received: 02/27/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Cyanobacteria, such as the toxin producer Microcystis aeruginosa, are predicted to be favored by global warming both directly, through elevated water temperatures, and indirectly, through factors such as prolonged stratification of waterbodies. M. aeruginosa is able to produce the hepatotoxin microcystin, which causes great concern in freshwater management worldwide. However, little is known about the expression of microcystin synthesis genes in response to climate change-related factors. In this study, a new RT-qPCR assay employing four reference genes (GAPDH, gltA, rpoC1, and rpoD) was developed to assess the expression of two target genes (the microcystin synthesis genes mcyB and mcyD). This assay was used to investigate changes in mcyB and mcyD expression in response to selected environmental factors associated with global warming. A 10°C rise in temperature significantly increased mcyB expression, but not mcyD expression. Neither mixing nor the addition of microcystin-LR (10 μg L-1 or 60 μg L-1 ) significantly altered mcyB and mcyD expression. The expression levels of mcyB and mcyD were correlated but not identical.
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Affiliation(s)
- Pia I. Scherer
- Aquatic Systems Biology UnitLimnological Research Station IffeldorfDepartment of Ecology and Ecosystem ManagementTechnical University of MunichMunichGermany
| | - Uta Raeder
- Aquatic Systems Biology UnitLimnological Research Station IffeldorfDepartment of Ecology and Ecosystem ManagementTechnical University of MunichMunichGermany
| | - Juergen Geist
- Aquatic Systems Biology UnitLimnological Research Station IffeldorfDepartment of Ecology and Ecosystem ManagementTechnical University of MunichMunichGermany
| | - Katrin Zwirglmaier
- Aquatic Systems Biology UnitLimnological Research Station IffeldorfDepartment of Ecology and Ecosystem ManagementTechnical University of MunichMunichGermany
- Present address: Bundeswehr Institute of MicrobiologyMunichGermany
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