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Gomez-Polo P, Ballinger MJ, Lalzar M, Malik A, Ben-Dov Y, Mozes-Daube N, Perlman SJ, Iasur-Kruh L, Chiel E. An exceptional family: Ophiocordyceps-allied fungus dominates the microbiome of soft scale insects (Hemiptera: Sternorrhyncha: Coccidae). Mol Ecol 2017; 26:5855-5868. [PMID: 28833928 DOI: 10.1111/mec.14332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022]
Abstract
Hemipteran insects of the suborder Sternorrhyncha are plant sap feeders, where each family is obligately associated with a specific bacterial endosymbiont that produces essential nutrients lacking in the sap. Coccidae (soft scale insects) is the only major sternorrhynchan family in which obligate symbiont(s) have not been identified. We studied the microbiota in seven species from this family from Israel, Spain and Cyprus, by high-throughput sequencing of ribosomal genes, and found that no specific bacterium was prevalent and abundant in all the tested species. In contrast, an Ophiocordyceps-allied fungus sp.-a lineage widely known as entomopathogenic-was highly prevalent. All individuals of all the tested species carried this fungus. Phylogenetic analyses showed that the Ophiocordyceps-allied fungus from the coccids is closely related to fungi described from other hemipterans, and they appear to be monophyletic, although the phylogenies of the Ophiocordyceps-allied fungi and their hosts do not appear to be congruent. Microscopic observations show that the fungal cells are lemon-shaped, are distributed throughout the host's body and are present in the eggs, suggesting vertical transmission. Taken together, the results suggest that the Ophiocordyceps-allied fungus may be a primary symbiont of Coccidae-a major evolutionary shift from bacteria to fungi in the Sternorrhyncha, and an important example of fungal evolutionary lifestyle switch.
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Affiliation(s)
- Priscila Gomez-Polo
- Department of Biology and Environment, University of Haifa - Oranim, Tivon, Israel
| | | | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Bioinformatics Service Unit, University of Haifa, Haifa, Israel
| | - Yair Ben-Dov
- Department of Entomology, The Volcani Center, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Neta Mozes-Daube
- Newe-Ya'ar Research Center, Agricultural Research Organization (ARO), Ramat-Yishai, Israel
| | - Steve J Perlman
- Department of Biology, University of Victoria, Victoria, Canada
| | - Lilach Iasur-Kruh
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel, Israel
| | - Elad Chiel
- Department of Biology and Environment, University of Haifa - Oranim, Tivon, Israel
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102
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Fructose diet alleviates acetaminophen-induced hepatotoxicity in mice. PLoS One 2017; 12:e0182977. [PMID: 28832650 PMCID: PMC5568217 DOI: 10.1371/journal.pone.0182977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/27/2017] [Indexed: 12/02/2022] Open
Abstract
Acetaminophen (APAP) is a commonly used analgesic and antipyretic that can cause hepatotoxicity due to production of toxic metabolites via cytochrome P450 (Cyp) 1a2 and Cyp2e1. Previous studies have shown conflicting effects of fructose (the major component in Western diet) on the susceptibility to APAP-induced hepatotoxicity. To evaluate the role of fructose-supplemented diet in modulating the extent of APAP-induced liver injury, male C57BL/6J mice were given 30% (w/v) fructose in water (or regular water) for 8 weeks, followed by oral administration of APAP. APAP-induced liver injury (determined by serum levels of liver enzymes) was decreased by two-fold in mice pretreated with fructose. Fructose-treated mice exhibited (~1.5 fold) higher basal glutathione levels and (~2 fold) lower basal (mRNA and activity) levels of Cyp1a2 and Cyp2e1, suggesting decreased bioactivation of APAP and increased detoxification of toxic metabolite in fructose-fed mice. Hepatic mRNA expression of heat shock protein 70 was also found increased in fructose-fed mice. Analysis of bacterial 16S rRNA gene amplicons from the cecal samples of vehicle groups showed that the fructose diet altered gut bacterial community, leading to increased α-diversity. The abundance of several bacterial taxa including the genus Anaerostipes was found to be significantly correlated with the levels of hepatic Cyp2e1, Cyp1a2 mRNA, and glutathione. Together, these results suggest that the fructose-supplemented diet decreases APAP-induced liver injury in mice, in part by reducing metabolic activation of APAP and inducing detoxification of toxic metabolites, potentially through altered composition of gut microbiota.
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103
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Ben-Yosef M, Zaada DSY, Dudaniec RY, Pasternak Z, Jurkevitch E, Smith RJ, Causton CE, Lincango MP, Tobe SS, Mitchell JG, Kleindorfer S, Yuval B. Host-specific associations affect the microbiome ofPhilornis downsi, an introduced parasite to the Galápagos Islands. Mol Ecol 2017; 26:4644-4656. [DOI: 10.1111/mec.14219] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 05/25/2017] [Accepted: 06/13/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Michael Ben-Yosef
- Department of Entomology; Faculty of Agriculture Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
| | - Doron S. Y. Zaada
- Department of Entomology; Faculty of Agriculture Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
| | - Rachael Y. Dudaniec
- Department of Biological Sciences; Macquarie University; Sydney NSW Australia
| | - Zohar Pasternak
- Department of Microbiology and Plant Pathology; Faculty of Agriculture Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
| | - Edouard Jurkevitch
- Department of Microbiology and Plant Pathology; Faculty of Agriculture Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
| | - Renee J. Smith
- School of Biological Sciences; Flinders University; Adelaide SA Australia
| | - Charlotte E. Causton
- Charles Darwin Foundation; Puerto Ayora Santa Cruz Island Galápagos Islands Ecuador
| | - Maria Piedad Lincango
- Charles Darwin Foundation; Puerto Ayora Santa Cruz Island Galápagos Islands Ecuador
- Facultad De Ciencias Agrícolas; Universidad Central Del Ecuador; Quito Pichincha Ecuador
| | - Shanan S. Tobe
- School of Biological Sciences; Flinders University; Adelaide SA Australia
- Department of Chemistry and Physics; Arcadia University; Glenside PA USA
| | - James G. Mitchell
- School of Biological Sciences; Flinders University; Adelaide SA Australia
| | - Sonia Kleindorfer
- School of Biological Sciences; Flinders University; Adelaide SA Australia
| | - Boaz Yuval
- Department of Entomology; Faculty of Agriculture Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
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104
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Rago L, Cristiani P, Villa F, Zecchin S, Colombo A, Cavalca L, Schievano A. Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells. Bioelectrochemistry 2017; 116:39-51. [DOI: 10.1016/j.bioelechem.2017.04.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/01/2017] [Accepted: 04/05/2017] [Indexed: 01/06/2023]
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105
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Detection and Characterization of Histamine-Producing Strains of Photobacterium damselae subsp. damselae Isolated from Mullets. Vet Sci 2017; 4:vetsci4020031. [PMID: 29056690 PMCID: PMC5606600 DOI: 10.3390/vetsci4020031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 11/16/2022] Open
Abstract
Photobacterium damselae subsp. damselae (Pdd) is considered to be an emerging pathogen of marine fish and has also been implicated in cases of histamine food poisoning. In this study, eight strains isolated from mullets of the genera Mugil and Liza captured in the Ligurian Sea were characterized, and a method to detect histamine-producing Pdd from fish samples was developed. The histamine-producing potential of the strains was evaluated in culture media (TSB+) using a histamine biosensor. Subsequently, two strains were used to contaminate mackerel fillets (4 or 40 CFU/g), simulating a cross-contamination on the selling fish stalls. Sample homogenates were enriched in TSB+. The cultures were then inoculated on thiosulfate-citrate-bile salts-sucrose agar (TCBS) and the dark green colonies were cultured on Niven agar. The violet isolates were characterized using specific biochemical and PCR based tests. All Pdd strains were histamine producers, yielding concentration varying from 167 and 8977 µg/mL in TSB+ cultures incubated at 30 °C for 24 h. Pdd colonies were detected from the inoculated mackerel samples and their histidine decarboxylase gene was amplified using species-specific primer pairs designed for this study. The results indicate that mullets can be source of Pdd and the fish retailers needs to evaluate the risk posed by cross-contamination on the selling fish stalls.
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106
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Price JT, Paladino FV, Lamont MM, Witherington BE, Bates ST, Soule T. Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats. PLoS One 2017; 12:e0177642. [PMID: 28493980 PMCID: PMC5426784 DOI: 10.1371/journal.pone.0177642] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/01/2017] [Indexed: 02/01/2023] Open
Abstract
The gut microbiome of herbivorous animals consists of organisms that efficiently digest the structural carbohydrates of ingested plant material. Green turtles (Chelonia mydas) provide an interesting model of change in these microbial communities because they undergo a pronounced shift from a surface-pelagic distribution and omnivorous diet to a neritic distribution and herbivorous diet. As an alternative to direct sampling of the gut, we investigated the cloacal microbiomes of juvenile green turtles before and after recruitment to neritic waters to observe any changes in their microbial community structure. Cloacal swabs were taken from individual turtles for analysis of the 16S rRNA gene sequences using Illumina sequencing. One fecal sample was also obtained, allowing for a preliminary comparison with the bacterial community of the cloaca. We found significant variation in the juvenile green turtle bacterial communities between pelagic and neritic habitats, suggesting that environmental and dietary factors support different bacterial communities in green turtles from these habitats. This is the first study to characterize the cloacal microbiome of green turtles in the context of their ontogenetic shifts, which could provide valuable insight into the origins of their gut bacteria and how the microbial community supports their shift to herbivory.
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Affiliation(s)
- James T. Price
- Department of Biology, Indiana University-Purdue University, Fort Wayne, Indiana, United States of America
| | - Frank V. Paladino
- Department of Biology, Indiana University-Purdue University, Fort Wayne, Indiana, United States of America
| | | | - Blair E. Witherington
- Disney’s Animals, Science, and Environment, Lake Buena Vista, Florida, United States of America
| | - Scott T. Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, Indiana, United States of America
| | - Tanya Soule
- Department of Biology, Indiana University-Purdue University, Fort Wayne, Indiana, United States of America
- * E-mail:
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107
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Lee W, Syed Atif A, Tan SC, Leow CH. Insights into the chicken IgY with emphasis on the generation and applications of chicken recombinant monoclonal antibodies. J Immunol Methods 2017; 447:71-85. [PMID: 28502720 DOI: 10.1016/j.jim.2017.05.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 03/02/2017] [Accepted: 05/04/2017] [Indexed: 12/16/2022]
Abstract
The advantages of chicken (Gallus gallus domesticus) antibodies as immunodiagnostic and immunotherapeutic biomolecules has only been recently recognized. Even so, chicken antibodies remain less-well characterized than their mammalian counterparts. This review aims at providing a current overview of the structure, function, development and generation of chicken antibodies. Additionally, brief but comprehensive insights into current knowledge pertaining to the immunogenetic framework and diversity-generation of the chicken immunoglobulin repertoire which have contributed to the establishment of recombinant chicken mAb-generating methods are discussed. Focus is provided on the current methods used to generate antibodies from chickens with added emphasis on the generation of recombinant chicken mAbs and its derivative formats. The advantages and limitations of established protocols for the generation of chicken mAbs are highlighted. The various applications of recombinant chicken mAbs and its derivative formats in immunodiagnostics and immunotherapy are further detailed.
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Affiliation(s)
- Warren Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Minden, Penang, Malaysia
| | - Ali Syed Atif
- New Iberia Research Center, University of Louisiana at Lafayette4401 W Admiral Doyle Dr, New Iberia, LA 70560, United States
| | - Soo Choon Tan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Minden, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Minden, Penang, Malaysia.
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108
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Te SH, Tan BF, Thompson JR, Gin KYH. Relationship of Microbiota and Cyanobacterial Secondary Metabolites in Planktothricoides-Dominated Bloom. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4199-4209. [PMID: 28345890 DOI: 10.1021/acs.est.6b05767] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The identification of phytoplankton species and microbial biodiversity is necessary to assess water ecosystem health and the quality of water resources. We investigated the short-term (2 days) vertical and diel variations in bacterial community structure and microbially derived secondary metabolites during a cyanobacterial bloom that emerged in a highly urbanized tropical reservoir. The waterbody was largely dominated by the cyanobacteria Planktothricoides spp., together with the Synechococcus, Pseudanabaena, Prochlorothrix, and Limnothrix. Spatial differences (i.e., water depth) rather than temporal differences (i.e., day versus night) better-explained the short-term variability in water quality parameters and bacterial community composition. Difference in bacterial structure suggested a resource-driven distribution pattern for the community. We found that the freshwater bacterial community associated with cyanobacterial blooms is largely conserved at the phylum level, with Proteobacteria (β-proteobateria), Bacteroidetes, and Actinobacteria as the main taxa despite the cyanobacterial species present and geographical (Asia, Europe, Australia, and North America) or climatic distinctions. Through multivariate statistical analyses of the bacterial community, environmental parameters, and secondary metabolite concentrations, we observed positive relationships between the occurrences of cyanobacterial groups and off-flavor compounds (2-methyisoborneol and β-ionone), suggesting a cyanobacterial origin. This study demonstrates the potential of 16S rRNA gene amplicon sequencing as a supporting tool in algal bloom monitoring or water-resource management.
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Affiliation(s)
- Shu Harn Te
- NUS Environmental Research Institute, National University of Singapore , 5A Engineering Drive 1, No. 02-01 T-Lab Building, Singapore 117411
| | - Boon Fei Tan
- Centre for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology Centre , 1 CREATE Way, #09-03 CREATE Tower, Singapore 138602
| | - Janelle R Thompson
- Centre for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology Centre , 1 CREATE Way, #09-03 CREATE Tower, Singapore 138602
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore , 5A Engineering Drive 1, No. 02-01 T-Lab Building, Singapore 117411
- Department of Civil and Environmental Engineering, National University of Singapore , 1 Engineering Drive 2, E1A 07-03, Singapore 117576
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109
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Turk-Kubo KA, Farnelid HM, Shilova IN, Henke B, Zehr JP. Distinct ecological niches of marine symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa sublineages. JOURNAL OF PHYCOLOGY 2017; 53:451-461. [PMID: 27992651 DOI: 10.1111/jpy.12505] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
A recently described symbiosis between the metabolically streamlined nitrogen-fixing cyanobacterium UCYN-A and a single-celled eukaryote prymnesiophyte alga is widely distributed throughout tropical and subtropical marine waters, and is thought to contribute significantly to nitrogen fixation in these regions. Several UCYN-A sublineages have been defined based on UCYN-A nitrogenase (nifH) sequences. Due to the low abundances of UCYN-A in the global oceans, currently existing molecular techniques are limited for detecting and quantifying these organisms. A targeted approach is needed to adequately characterize the diversity of this important marine cyanobacterium, and to advance understanding of its ecological importance. We present findings on the distribution of UCYN-A sublineages based on high throughput sequencing of UCYN-A nifH PCR amplicons from 78 samples distributed throughout many major oceanic provinces. These UCYN-A nifH fragments were used to define oligotypes, alternative taxonomic units defined by nucleotide positions with high variability. The data set was dominated by a single oligotype associated with the UCYN-A1 sublineage, consistent with previous observations of relatively high abundances in tropical and subtropical regions. However, this analysis also revealed for the first time the widespread distribution of the UCYN-A3 sublineage in oligotrophic waters. Furthermore, distinct assemblages of UCYN-A oligotypes were found in oligotrophic and coastally influenced waters. This unique data set provides a framework for determining the environmental controls on UCYN-A distributions and the ecological importance of the different sublineages.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Hanna M Farnelid
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 34, Kalmar, Sweden
| | - Irina N Shilova
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Britt Henke
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California, 95064, USA
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110
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McFadden VC, Shalaby RE, Iram S, Oropeza CE, Landolfi JA, Lyubimov AV, Maienschein-Cline M, Green SJ, Kaestner KH, McLachlan A. Hepatic deficiency of the pioneer transcription factor FoxA restricts hepatitis B virus biosynthesis by the developmental regulation of viral DNA methylation. PLoS Pathog 2017; 13:e1006239. [PMID: 28235042 PMCID: PMC5342274 DOI: 10.1371/journal.ppat.1006239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/08/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
The FoxA family of pioneer transcription factors regulates hepatitis B virus (HBV) transcription, and hence viral replication. Hepatocyte-specific FoxA-deficiency in the HBV transgenic mouse model of chronic infection prevents the transcription of the viral DNA genome as a result of the failure of the developmentally controlled conversion of 5-methylcytosine residues to cytosine during postnatal hepatic maturation. These observations suggest that pioneer transcription factors such as FoxA, which mark genes for expression at subsequent developmental steps in the cellular differentiation program, mediate their effects by reversing the DNA methylation status of their target genes to permit their ensuing expression when the appropriate tissue-specific transcription factor combinations arise during development. Furthermore, as the FoxA-deficient HBV transgenic mice are viable, the specific developmental timing, abundance and isoform type of pioneer factor expression must permit all essential liver gene expression to occur at a level sufficient to support adequate liver function. This implies that pioneer transcription factors can recognize and mark their target genes in distinct developmental manners dependent upon, at least in part, the concentration and affinity of FoxA for its binding sites within enhancer and promoter regulatory sequence elements. This selective marking of cellular genes for expression by the FoxA pioneer factor compared to HBV may offer the opportunity for the specific silencing of HBV gene expression and hence the resolution of chronic HBV infections which are responsible for approximately one million deaths worldwide annually due to liver cirrhosis and hepatocellular carcinoma. This study demonstrates the connection between FoxA expression and gene silencing by DNA methylation in vivo during liver maturation. Insufficient FoxA expression results in selective developmentally regulated hepatitis B virus (HBV) silencing by DNA methylation. To our knowledge, this is the first in vivo demonstration that pioneer factors such as FoxA function by mediating the developmental demethylation of their target genes, leading to their tissue specific gene expression. Furthermore, our results strongly imply that the marking of cellular target genes for subsequent transcription later in development is dependent upon the level and timing of FoxA expression plus its affinity for its target sequences within enhancer and promoter regions. Consequently, these findings suggest that the appropriate control of FoxA activity during development could lead to the transcriptional inactivation of nuclear HBV covalently closed circular DNA by methylation and hence resolution of chronic HBV infection. This represents a clinical goal that current therapies are unable to attain, and hence suggests a potential route to a cure for this chronic infection which kills approximately 1 million individuals annually.
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Affiliation(s)
- Vanessa C. McFadden
- Department of Microbiology and Immunology College of Medicine University of Illinois at Chicago 909 South Wolcott Avenue Chicago, IL, United States of America
| | - Rasha E. Shalaby
- Department of Microbiology and Immunology College of Medicine University of Illinois at Chicago 909 South Wolcott Avenue Chicago, IL, United States of America
| | - Saira Iram
- Department of Microbiology and Immunology College of Medicine University of Illinois at Chicago 909 South Wolcott Avenue Chicago, IL, United States of America
| | - Claudia E. Oropeza
- Department of Microbiology and Immunology College of Medicine University of Illinois at Chicago 909 South Wolcott Avenue Chicago, IL, United States of America
| | - Jennifer A. Landolfi
- Toxicology Research Laboratory Department of Pharmacology College of Medicine University of Illinois at Chicago Chicago, IL, United States of America
| | - Alexander V. Lyubimov
- Toxicology Research Laboratory Department of Pharmacology College of Medicine University of Illinois at Chicago Chicago, IL, United States of America
| | - Mark Maienschein-Cline
- Research Resources Center College of Medicine University of Illinois at Chicago 835 South Wolcott Avenue Chicago, IL, United States of America
| | - Stefan J. Green
- Research Resources Center College of Medicine University of Illinois at Chicago 835 South Wolcott Avenue Chicago, IL, United States of America
| | - Klaus H. Kaestner
- Department of Genetics University of Pennsylvania School of Medicine Philadelphia, PA, United States of America
| | - Alan McLachlan
- Department of Microbiology and Immunology College of Medicine University of Illinois at Chicago 909 South Wolcott Avenue Chicago, IL, United States of America
- * E-mail:
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111
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Gong H, Liu M, Klomp J, Merrill BJ, Rehman J, Malik AB. Method for Dual Viral Vector Mediated CRISPR-Cas9 Gene Disruption in Primary Human Endothelial Cells. Sci Rep 2017; 7:42127. [PMID: 28198371 PMCID: PMC5309830 DOI: 10.1038/srep42127] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
Human endothelial cells (ECs) are widely used to study mechanisms of angiogenesis, inflammation, and endothelial permeability. Targeted gene disruption induced by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-Associated Protein 9 (Cas9) nuclease gene editing is potentially an important tool for definitively establishing the functional roles of individual genes in ECs. We showed that co-delivery of adenovirus encoding EGFP-tagged Cas9 and lentivirus encoding a single guide RNA (sgRNA) in primary human lung microvascular ECs (HLMVECs) disrupted the expression of the Tie2 gene and protein. Tie2 disruption increased basal endothelial permeability and prevented permeability recovery following injury induced by the inflammatory stimulus thrombin. Thus, gene deletion via viral co-delivery of CRISPR-Cas9 in primary human ECs provides a novel platform to investigate signaling mechanisms of normal and perturbed EC function without the need for clonal expansion.
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Affiliation(s)
- Haixia Gong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Menglin Liu
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jeff Klomp
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Bradley J. Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Genome Editing Core, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jalees Rehman
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Asrar B. Malik
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
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112
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Habtom H, Demanèche S, Dawson L, Azulay C, Matan O, Robe P, Gafny R, Simonet P, Jurkevitch E, Pasternak Z. Soil characterisation by bacterial community analysis for forensic applications: A quantitative comparison of environmental technologies. Forensic Sci Int Genet 2017; 26:21-29. [DOI: 10.1016/j.fsigen.2016.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/20/2016] [Accepted: 10/06/2016] [Indexed: 12/01/2022]
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113
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Bishehsari F, Saadalla A, Khazaie K, Engen PA, Voigt RM, Shetuni BB, Forsyth C, Shaikh M, Vitaterna MH, Turek F, Keshavarzian A. Light/Dark Shifting Promotes Alcohol-Induced Colon Carcinogenesis: Possible Role of Intestinal Inflammatory Milieu and Microbiota. Int J Mol Sci 2016; 17:ijms17122017. [PMID: 27918452 PMCID: PMC5187817 DOI: 10.3390/ijms17122017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Background: Colorectal cancer (CRC) is associated with the modern lifestyle. Chronic alcohol consumption—a frequent habit of majority of modern societies—increases the risk of CRC. Our group showed that chronic alcohol consumption increases polyposis in a mouse mode of CRC. Here we assess the effect of circadian disruption—another modern life style habit—in promoting alcohol-associated CRC. Method: TS4Cre × adenomatous polyposis coli (APC)lox468 mice underwent (a) an alcohol-containing diet while maintained on a normal 12 h light:12 h dark cycle; or (b) an alcohol-containing diet in conjunction with circadian disruption by once-weekly 12 h phase reversals of the light:dark (LD) cycle. Mice were sacrificed after eight weeks of full alcohol and/or LD shift to collect intestine samples. Tumor number, size, and histologic grades were compared between animal groups. Mast cell protease 2 (MCP2) and 6 (MCP6) histology score were analyzed and compared. Stool collected at baseline and after four weeks of experimental manipulations was used for microbiota analysis. Results: The combination of alcohol and LD shifting accelerated intestinal polyposis, with a significant increase in polyp size, and caused advanced neoplasia. Consistent with a pathogenic role of stromal tryptase-positive mast cells in colon carcinogenesis, the ratio of mMCP6 (stromal)/mMCP2 (intraepithelial) mast cells increased upon LD shifting. Baseline microbiota was similar between groups, and experimental manipulations resulted in a significant difference in the microbiota composition between groups. Conclusions: Circadian disruption by Light:dark shifting exacerbates alcohol-induced polyposis and CRC. Effect of circadian disruption could, at least partly, be mediated by promoting a pro-tumorigenic inflammatory milieu via changes in microbiota.
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Affiliation(s)
- Faraz Bishehsari
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Abdulrahman Saadalla
- Department of Immunology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Khashayarsha Khazaie
- Department of Immunology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| | - Phillip A Engen
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Robin M Voigt
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Brandon B Shetuni
- Northwestern Medicine, Central DuPage Hospital, Winfield, IL 60190, USA.
| | - Christopher Forsyth
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Maliha Shaikh
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
| | - Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL 60208, USA.
| | - Fred Turek
- Center for Sleep and Circadian Biology, Northwestern University, Evanston, IL 60208, USA.
| | - Ali Keshavarzian
- Department of Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA.
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114
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Vandenbussche F, Mathijs E, Lefebvre D, De Clercq K, Van Borm S. A Tale of Tails: Dissecting the Enhancing Effect of Tailed Primers in Real-Time PCR. PLoS One 2016; 11:e0164463. [PMID: 27723800 PMCID: PMC5056738 DOI: 10.1371/journal.pone.0164463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/26/2016] [Indexed: 11/29/2022] Open
Abstract
Non-specific tail sequences are often added to the 5’-terminus of primers to improve the robustness and overall performance of diagnostic assays. Despite the widespread use of tailed primers, the underlying working mechanism is not well understood. To address this problem, we conducted a detailed in vitro and in silico analysis of the enhancing effect of primer tailing on 2 well-established foot-and-mouth disease virus (FMDV) RT-qPCR assays using an FMDV reference panel. Tailing of the panFMDV-5UTR primers mainly affected the shape of the amplification curves. Modelling of the raw fluorescence data suggested a reduction of the amplification efficiency due to the accumulation of inhibitors. In depth analysis of PCR products indeed revealed the rapid accumulation of forward-primer derived artefacts. More importantly, tailing of the forward primer delayed artefacts formation and concomitantly restored the sigmoidal shape of the amplification curves. Our analysis also showed that primer tailing can alter utilisation patterns of degenerate primers and increase the number of primer variants that are able to participate in the reaction. The impact of tailed primers was less pronounced in the panFMDV-3D assay with only 5 out of 50 isolates showing a clear shift in Cq values. Sequence analysis of the target region of these 5 isolates revealed several mutations in the inter-primer region that extend an existing hairpin structure immediately downstream of the forward primer binding site. Stabilisation of the forward primer with either a tail sequence or cationic spermine units restored the sensitivity of the assay, which suggests that the enhancing effect in the panFMDV-3D assay is due to a more efficient extension of the forward primer. ur results show that primer tailing can alter amplification through various mechanisms that are determined by both the assay and target region. These findings expand our understanding of primer tailing and should enable a more targeted and efficient use of tailed primers.
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Affiliation(s)
- Frank Vandenbussche
- Molecular Platform, Operational Directorate of Viral Diseases, CODA-CERVA, Brussels, Belgium
- * E-mail:
| | - Elisabeth Mathijs
- Molecular Platform, Operational Directorate of Viral Diseases, CODA-CERVA, Brussels, Belgium
| | - David Lefebvre
- Vesicular and Exotic Diseases, Operational Directorate of Viral Diseases, CODA-CERVA, Brussels, Belgium
| | - Kris De Clercq
- Vesicular and Exotic Diseases, Operational Directorate of Viral Diseases, CODA-CERVA, Brussels, Belgium
| | - Steven Van Borm
- Molecular Platform, Operational Directorate of Viral Diseases, CODA-CERVA, Brussels, Belgium
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115
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Acrolein increases macrophage atherogenicity in association with gut microbiota remodeling in atherosclerotic mice: protective role for the polyphenol-rich pomegranate juice. Arch Toxicol 2016; 91:1709-1725. [PMID: 27696135 DOI: 10.1007/s00204-016-1859-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/22/2016] [Indexed: 01/13/2023]
Abstract
The unsaturated aldehyde acrolein is pro-atherogenic, and the polyphenol-rich pomegranate juice (PJ), known for its anti-oxidative/anti-atherogenic properties, inhibits macrophage foam cell formation, the hallmark feature of early atherosclerosis. This study aimed to investigate two unexplored areas of acrolein atherogenicity: macrophage lipid metabolism and the gut microbiota composition. The protective effects of PJ against acrolein atherogenicity were also evaluated. Atherosclerotic apolipoprotein E-deficient (apoE-/-) mice that were fed acrolein (3 mg/kg/day) for 1 month showed significant increases in serum and aortic cholesterol, triglycerides, and lipid peroxides. In peritoneal macrophages isolated from the mice and in J774A.1 cultured macrophages, acrolein exposure increased intracellular oxidative stress and stimulated cholesterol and triglyceride accumulation via enhanced rates of their biosynthesis and over-expression of key regulators of cellular lipid biosynthesis: sterol regulatory element-binding proteins (SREBPs), 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR), and diacylglycerol acyltransferase1 (DGAT1). Acrolein-fed mice demonstrated a major shift in the gut microbiota composition, including a significant phylum-level change in increased Firmicutes and decreased Bacteroidetes. At the family level, acrolein significantly increased the prevalence of Ruminococcaceae and Lachnospiraceae of which the Coprococcus genus was significantly and positively correlated with serum, aortic and macrophage lipid levels and peroxidation. The pro-atherogenic effects of acrolein on serum, aortas, macrophages, and the gut microbiota were substantially abolished by PJ. In conclusion, these findings provide novel mechanisms by which acrolein increases macrophage lipid accumulation and alters the gut microbiota composition in association with enhanced atherogenesis. Moreover, PJ was found as an effective strategy against acrolein atherogenicity.
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116
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Marmesat E, Soriano L, Mazzoni CJ, Sommer S, Godoy JA. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches. PLoS One 2016; 11:e0157402. [PMID: 27294261 PMCID: PMC4905633 DOI: 10.1371/journal.pone.0157402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications.
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Affiliation(s)
- Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - José A. Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
- * E-mail:
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117
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McDonald JE, Larsen N, Pennington A, Connolly J, Wallis C, Rooks DJ, Hall N, McCarthy AJ, Allison HE. Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules. PLoS One 2016; 11:e0157046. [PMID: 27276347 PMCID: PMC4898712 DOI: 10.1371/journal.pone.0157046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 05/24/2016] [Indexed: 11/18/2022] Open
Abstract
PCR amplification and sequencing of phylogenetic markers, primarily Small Sub-Unit ribosomal RNA (SSU rRNA) genes, has been the paradigm for defining the taxonomic composition of microbiomes. However, ‘universal’ SSU rRNA gene PCR primer sets are likely to miss much of the diversity therein. We sequenced a library comprising purified and reverse-transcribed SSU rRNA (RT-SSU rRNA) molecules from the canine oral microbiome and compared it to a general bacterial 16S rRNA gene PCR amplicon library generated from the same biological sample. In addition, we have developed BIONmeta, a novel, open-source, computer package for the processing and taxonomic classification of the randomly fragmented RT-SSU rRNA reads produced. Direct RT-SSU rRNA sequencing revealed that 16S rRNA molecules belonging to the bacterial phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Spirochaetes, were most abundant in the canine oral microbiome (92.5% of total bacterial SSU rRNA). The direct rRNA sequencing approach detected greater taxonomic diversity (1 additional phylum, 2 classes, 1 order, 10 families and 61 genera) when compared with general bacterial 16S rRNA amplicons from the same sample, simultaneously provided SSU rRNA gene inventories of Bacteria, Archaea and Eukarya, and detected significant numbers of sequences not recognised by ‘universal’ primer sets. Proteobacteria and Spirochaetes were found to be under-represented by PCR-based analysis of the microbiome, and this was due to primer mismatches and taxon-specific variations in amplification efficiency, validated by qPCR analysis of 16S rRNA amplicons from a mock community. This demonstrated the veracity of direct RT-SSU rRNA sequencing for molecular microbial ecology.
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Affiliation(s)
- James E. McDonald
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, United Kingdom
- * E-mail: (JM); (HA)
| | - Niels Larsen
- Danish Genome Institute, Skt. Lucas Kirkeplads 8, 8000, Aarhus C, Denmark
| | - Andrea Pennington
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - John Connolly
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Corrin Wallis
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, LE14 4RT, United Kingdom
| | - David J. Rooks
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Alan J. McCarthy
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Heather E. Allison
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
- * E-mail: (JM); (HA)
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118
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Farnelid HM, Turk-Kubo KA, Zehr JP. Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters. Front Microbiol 2016; 7:339. [PMID: 27148165 PMCID: PMC4834442 DOI: 10.3389/fmicb.2016.00339] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/03/2016] [Indexed: 01/10/2023] Open
Abstract
Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.
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Affiliation(s)
- Hanna M Farnelid
- Ocean Sciences Department, University of California at Santa CruzSanta Cruz, CA, USA; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmar, Sweden
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz Santa Cruz, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz Santa Cruz, CA, USA
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119
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A New Comparative-Genomics Approach for Defining Phenotype-Specific Indicators Reveals Specific Genetic Markers in Predatory Bacteria. PLoS One 2015; 10:e0142933. [PMID: 26569499 PMCID: PMC4646340 DOI: 10.1371/journal.pone.0142933] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/28/2015] [Indexed: 01/23/2023] Open
Abstract
Predatory bacteria seek and consume other live bacteria. Although belonging to taxonomically diverse groups, relatively few bacterial predator species are known. Consequently, it is difficult to assess the impact of predation within the bacterial realm. As no genetic signatures distinguishing them from non-predatory bacteria are known, genomic resources cannot be exploited to uncover novel predators. In order to identify genes specific to predatory bacteria, we developed a bioinformatic tool called DiffGene. This tool automatically identifies marker genes that are specific to phenotypic or taxonomic groups, by mapping the complete gene content of all available fully-sequenced genomes for the presence/absence of each gene in each genome. A putative ‘predator region’ of ~60 amino acids in the tryptophan 2,3-dioxygenase (TDO) protein was found to probably be a predator-specific marker. This region is found in all known obligate predator and a few facultative predator genomes, and is absent from most facultative predators and all non-predatory bacteria. We designed PCR primers that uniquely amplify a ~180bp-long sequence within the predators’ TDO gene, and validated them in monocultures as well as in metagenetic analysis of environmental wastewater samples. This marker, in addition to its usage in predator identification and phylogenetics, may finally permit reliable enumeration and cataloguing of predatory bacteria from environmental samples, as well as uncovering novel predators.
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120
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FitzGerald JA, Allen E, Wall DM, Jackson SA, Murphy JD, Dobson ADW. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities. PLoS One 2015; 10:e0142603. [PMID: 26555136 PMCID: PMC4640829 DOI: 10.1371/journal.pone.0142603] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/24/2015] [Indexed: 01/22/2023] Open
Abstract
Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.
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Affiliation(s)
- Jamie A. FitzGerald
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Science Foundation Ireland, Marine Renewable Energy Ireland (MaREI) Centre, University College Cork, Cork, Ireland
| | - Eoin Allen
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Engineering, University College Cork, Cork, Ireland
- Science Foundation Ireland, Marine Renewable Energy Ireland (MaREI) Centre, University College Cork, Cork, Ireland
| | - David M. Wall
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Engineering, University College Cork, Cork, Ireland
- Science Foundation Ireland, Marine Renewable Energy Ireland (MaREI) Centre, University College Cork, Cork, Ireland
| | - Stephen A. Jackson
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jerry D. Murphy
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Engineering, University College Cork, Cork, Ireland
- Science Foundation Ireland, Marine Renewable Energy Ireland (MaREI) Centre, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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