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Rolshausen G, Dal Grande F, Otte J, Schmitt I. Lichen holobionts show compositional structure along elevation. Mol Ecol 2023; 32:6619-6630. [PMID: 35398946 DOI: 10.1111/mec.16471] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/25/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.
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Affiliation(s)
- Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Center for Wildlife Genetics, Senckenberg Research Institute, Gelnhausen, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Departement of Biological Sciences, Goethe University, Frankfurt am Main, Germany
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. Microbiologyopen 2023; 12:e1386. [PMID: 37877655 PMCID: PMC10582450 DOI: 10.1002/mbo3.1386] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.
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Affiliation(s)
- Nadim Ahmad
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Manfred Ritz
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe University FrankfurtFrankfurt am MainGermany
| | - Thomas Brueck
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Norbert Mehlmer
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways. J Fungi (Basel) 2023; 9:jof9050546. [PMID: 37233257 DOI: 10.3390/jof9050546] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.
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Affiliation(s)
- Nadim Ahmad
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Manfred Ritz
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
| | - Thomas Brueck
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
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Hofmann B, Dreyling L, Dal Grande F, Otte J, Schmitt I. Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests. Front Microbiol 2023; 14:1067906. [PMID: 36950169 PMCID: PMC10025312 DOI: 10.3389/fmicb.2023.1067906] [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: 10/12/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests. Methods Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany. Results ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks. Discussion Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.
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Affiliation(s)
- Benjamin Hofmann
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Lukas Dreyling
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Department of Biology, University of Padova, Padua, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- *Correspondence: Imke Schmitt,
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Valim HF, Dal Grande F, Otte J, Singh G, Merges D, Schmitt I. Identification and expression of functionally conserved circadian clock genes in lichen-forming fungi. Sci Rep 2022; 12:15884. [PMID: 36151124 PMCID: PMC9508176 DOI: 10.1038/s41598-022-19646-y] [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] [Received: 03/28/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Lichen-forming fungi establish stable symbioses with green algae or cyanobacteria. Many species have broad distributions, both in geographic and ecological space, making them ideal subjects to study organism-environment interactions. However, little is known about the specific mechanisms that contribute to environmental adaptation in lichen-forming fungi. The circadian clock provides a well-described mechanism that contributes to regional adaptation across a variety of species, including fungi. Here, we identify the putative circadian clock components in phylogenetically divergent lichen-forming fungi. The core circadian genes (frq, wc-1, wc-2, frh) are present across the Fungi, including 31 lichen-forming species, and their evolutionary trajectories mirror overall fungal evolution. Comparative analyses of the clock genes indicate conserved domain architecture among lichen- and non-lichen-forming taxa. We used RT-qPCR to examine the core circadian loop of two unrelated lichen-forming fungi, Umbilicaria pustulata (Lecanoromycetes) and Dermatocarpon miniatum (Eurotiomycetes), to determine that the putative frq gene is activated in a light-dependent manner similar to the model fungus Neurospora crassa. Together, these results demonstrate that lichen-forming fungi retain functional light-responsive mechanisms, including a functioning circadian clock. Our findings provide a stepping stone into investigating the circadian clock in the lichen symbiosis, e.g. its role in adaptation, and in synchronizing the symbiotic interaction.
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Affiliation(s)
- Henrique F Valim
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Biology, University of Padua, Via U. Bassi 58/B, Padua, Italy
| | - Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7070, 750 07, Uppsala, Sweden
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
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6
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Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021; 23:6637-6650. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.
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Affiliation(s)
- Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
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7
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Rolshausen G, Hallman U, Grande FD, Otte J, Knudsen K, Schmitt I. Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients. Proc Biol Sci 2020; 287:20192311. [PMID: 32228406 DOI: 10.1098/rspb.2019.2311] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Keystone mutualisms, such as corals, lichens or mycorrhizae, sustain fundamental ecosystem functions. Range dynamics of these symbioses are, however, inherently difficult to predict because host species may switch between different symbiont partners in different environments, thereby altering the range of the mutualism as a functional unit. Biogeographic models of mutualisms thus have to consider both the ecological amplitudes of various symbiont partners and the abiotic conditions that trigger symbiont replacement. To address this challenge, we here investigate 'symbiont turnover zones'--defined as demarcated regions where symbiont replacement is most likely to occur, as indicated by overlapping abundances of symbiont ecotypes. Mapping the distribution of algal symbionts from two species of lichen-forming fungi along four independent altitudinal gradients, we detected an abrupt and consistent β-diversity turnover suggesting parallel niche partitioning. Modelling contrasting environmental response functions obtained from latitudinal distributions of algal ecotypes consistently predicted a confined altitudinal turnover zone. In all gradients this symbiont turnover zone is characterized by approximately 12°C average annual temperature and approximately 5°C mean temperature of the coldest quarter, marking the transition from Mediterranean to cool temperate bioregions. Integrating the conditions of symbiont turnover into biogeographic models of mutualisms is an important step towards a comprehensive understanding of biodiversity dynamics under ongoing environmental change.
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Affiliation(s)
- Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Uwe Hallman
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Kerry Knudsen
- Department of Ecology, Czech University of Life Sciences Prague
- CULS, Prague, Czech Republic
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Departement of Biological Sciences, Goethe University, Frankfurt am Main, Germany
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Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I. What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen. Genome Biol Evol 2020; 12:309-324. [PMID: 32163141 PMCID: PMC7186782 DOI: 10.1093/gbe/evaa049] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Accepted: 03/09/2020] [Indexed: 12/29/2022] Open
Abstract
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
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Affiliation(s)
- Bastian Greshake Tzovaras
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- Lawrence Berkeley National Laboratory, Berkeley, California
- Center for Research & Interdisciplinarity, Université de Paris, France
| | - Francisca H I D Segers
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
| | - Anne Bicker
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Francesco Dal Grande
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Imke Schmitt
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Molecular Evolutionary Biology Group, Institute of Ecology, Diversity, and Evolution, Goethe University Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
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9
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Manso MA, Cattaneo TM, Barzaghi S, Olieman C, López-Fandiño R, Leaver J, Otte J, S�nchez A, Svenning C, Tirelli A, Vegarud G. Determination of Vegetal Proteins in Milk Powder by Sodium Dodecyl Sulfate–Capillary Gel Electrophoresis: Interlaboratory Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/85.5.1090] [Citation(s) in RCA: 16] [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] [Indexed: 11/13/2022]
Abstract
Abstract
An interlaboratory study, with the participation of 8 laboratories, was conducted to evaluate a sodium dodecyl sulfate–capillary gel electrophoresis method for determination of adulteration of milk powder with soy and pea proteins. Calibration standards (0–8%, w/w, soy and pea protein in total protein) and adulterated skim milk powders (0–5%, w/w, soy and pea proteins in total protein) were produced. Vegetal proteins were determined after removal of milk proteins by pretreatment of the samples with tetraborate–EDTA buffer, pH 8.3. Repeatability standard deviations ranged from 9 to 15% and reproducibility standard deviations ranged from 25 to 30% in the samples containing 5% vegetal protein in total protein.
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Affiliation(s)
- María A Manso
- Instituto de Fermentaciones Industriales (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Stefania Barzaghi
- Istituto Sperimentale Lattiero-Caseario, Via A. Lombardo 11, 26900 Lodi, Italy
| | | | - Rosina López-Fandiño
- Instituto de Fermentaciones Industriales (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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10
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Affiliation(s)
- S. Mack
- Senior Officer, Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00100 Rome, Italy
| | - D. Hoffmann
- Senior Officer, Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00100 Rome, Italy
| | - J. Otte
- Senior Officer, Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00100 Rome, Italy
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11
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Singh G, Kukwa M, Dal Grande F, Łubek A, Otte J, Schmitt I. A Glimpse into Genetic Diversity and Symbiont Interaction Patterns in Lichen Communities from Areas with Different Disturbance Histories in Białowieża Forest, Poland. Microorganisms 2019; 7:E335. [PMID: 31505790 PMCID: PMC6780458 DOI: 10.3390/microorganisms7090335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022] Open
Abstract
Anthropogenic disturbances can have strong impacts on lichen communities, as well as on individual species of lichenized fungi. Traditionally, lichen monitoring studies are based on the presence and abundance of fungal morphospecies. However, the photobionts, as well photobiont mycobiont interactions also contribute to the structure, composition, and resilience of lichen communities. Here we assess the genetic diversity and interaction patterns of algal and fungal partners in lichen communities along an anthropogenic disturbance gradient in Białowieża Forest (Poland). We sampled a total of 224 lichen thalli in a protected, a managed, and a disturbed area of the forest, and sequenced internal transcribed spacer (ITS) ribosomal DNA (rDNA) of both, fungal and algal partners. Sequence clustering using a 97% similarity threshold resulted in 46 fungal and 23 green algal operational taxonomic units (OTUs). Most of the recovered photobiont OTUs (14 out of 23) had no similar hit in the NCBI-BLAST search, suggesting that even in well studied regions, such as central Europe, a lot of photobiont diversity is yet undiscovered. If a mycobiont was present at more than one site, it was typically associated with the same photobiont OTU(s). Generalist species, i.e., taxa that associate with multiple symbiont partners, occurred in all three disturbance regimes, suggesting that such taxa have few limitations in colonizing or persisting in disturbed areas. Trebouxia jamesii associated with 53% of the fungal OTUs, and was generally the most common photobiont OTU in all areas, implying that lichens that associate with this symbiont are not limited by the availability of compatible photobionts in Central European forests, regardless of land use intensity.
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Affiliation(s)
- Garima Singh
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany.
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany
| | - Anna Łubek
- Jan Kochanowski University in Kielce, Institute of Biology, 25-406 Kielce, Poland
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany.
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, 60325 Frankfurt am Main, Germany.
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Surowy HM, Giesen AK, Otte J, Büttner R, Falkenstein D, Friedl H, Meier F, Petzsch P, Wachtmeister T, Westphal D, Wieczorek D, Wruck W, Adjaye J, Rütten A, Redler S. Gene expression profiling in aggressive digital papillary adenocarcinoma sheds light on the architecture of a rare sweat gland carcinoma. Br J Dermatol 2019; 180:1150-1160. [PMID: 30472730 DOI: 10.1111/bjd.17446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Sweat gland carcinomas are rare cutaneous adnexal malignancies. Aggressive digital papillary adenocarcinoma (ADPA) represents a very rare subentity, thought to arise almost exclusively from the sweat glands of the fingers and toes. The aetiology of sweat gland carcinomas and ADPA is largely unknown. ADPAs are most likely driven by somatic mutations. However, somatic mutation patterns are largely unexplored, creating barriers to the development of effective therapeutic approaches to the treatment of ADPA. OBJECTIVES To investigate the transcriptome profile of ADPA using a sample of eight formalin-fixed, paraffin-embedded tissue samples of ADPA and healthy control tissue. METHODS Transcriptome profiling was performed using the Affymetrix PrimeView Human Gene Expression Microarray and findings were validated via reverse transcription of RNA and real-time quantitative polymerase chain reaction. RESULTS Transcriptome analyses showed increased tumour expression of 2266 genes, with significant involvement of cell cycle, ribosomal and crucial cancer pathways. Our results point to tumour overexpression of FGFR2 (P = 0·001). CONCLUSIONS The results indicate the involvement of crucial oncogenic driver pathways, highlighting cell cycle and ribosomal pathways in the aetiology of ADPA. Suggested tumour overexpression of FGFR2 raises the hope that targeting the fibroblast growth factor (FGF)/FGF receptor axis might be a promising treatment for ADPA and probably for the overall group of sweat gland carcinomas.
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Affiliation(s)
- H M Surowy
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - A K Giesen
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - J Otte
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - R Büttner
- Pathology, Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - D Falkenstein
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - H Friedl
- Klinikum Darmstadt, Department of Dermatology, Darmstadt, Germany
| | - F Meier
- Department of Dermatology, Carl Gustav Carus Medical Center, TU Dresden, Dresden, Germany.,National Center for Tumour Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - P Petzsch
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - T Wachtmeister
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - D Westphal
- Department of Dermatology, Carl Gustav Carus Medical Center, TU Dresden, Dresden, Germany.,National Center for Tumour Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - D Wieczorek
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - W Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - J Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - A Rütten
- Dermatopathology, Bodensee, Siemensstrasse 6/1, 88048, Friedrichshafen, Germany
| | - S Redler
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
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13
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Paul F, Otte J, Schmitt I, Dal Grande F. Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens. Sci Rep 2018; 8:8624. [PMID: 29872090 PMCID: PMC5988838 DOI: 10.1038/s41598-018-26947-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/22/2018] [Indexed: 11/26/2022] Open
Abstract
The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.
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Affiliation(s)
- Fiona Paul
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Departamento de Farmacología, Farmacognosia y Botánica, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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Schmidt PA, Schmitt I, Otte J, Bandow C, Römbke J, Bálint M, Rolshausen G. Season-Long Experimental Drought Alters Fungal Community Composition but Not Diversity in a Grassland Soil. Microb Ecol 2018; 75:468-478. [PMID: 28785816 DOI: 10.1007/s00248-017-1047-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 03/16/2017] [Accepted: 07/20/2017] [Indexed: 05/23/2023]
Abstract
Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.
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Affiliation(s)
- Philipp-André Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
| | - Cornelia Bandow
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- Goethe Universität Frankfurt, Institut für Ökologie, Evolution und Diversität, Max-von-Laue-Str. 13, 60438, Frankfurt/Main, Germany
- ECT Oekotoxikologie GmbH, 65439, Flörsheim/Main, Germany
| | - Jörg Römbke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany
- ECT Oekotoxikologie GmbH, 65439, Flörsheim/Main, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany.
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt/Main, Germany.
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15
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Dal Grande F, Rolshausen G, Divakar PK, Crespo A, Otte J, Schleuning M, Schmitt I. Environment and host identity structure communities of green algal symbionts in lichens. New Phytol 2018; 217:277-289. [PMID: 28892165 DOI: 10.1111/nph.14770] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 05/11/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
An understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Pradeep K Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
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16
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Meiser A, Otte J, Schmitt I, Grande FD. Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 2017; 7:14881. [PMID: 29097759 PMCID: PMC5668418 DOI: 10.1038/s41598-017-14576-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 01/07/2023] Open
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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Affiliation(s)
- Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany.
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
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17
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Wei X, Schmitt I, Hodkinson B, Flakus A, Kukwa M, Divakar PK, Kirika PM, Otte J, Meiser A, Lumbsch HT. Circumscription of the genus Lepra, a recently resurrected genus to accommodate the "Variolaria"-group of Pertusaria sensu lato (Pertusariales, Ascomycota). PLoS One 2017; 12:e0180284. [PMID: 28700682 PMCID: PMC5507398 DOI: 10.1371/journal.pone.0180284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/12/2017] [Indexed: 12/02/2022] Open
Abstract
Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as “Pertusaria amara-group”, “Monomurata-group”, or “Variolaria-group”, which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.
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Affiliation(s)
- Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany
| | | | - Adam Flakus
- Laboratory of Lichenology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, Kraków, Poland
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, WitaStwosza 59, Gdańsk, Poland
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, Madrid, Spain
| | - Paul M. Kirika
- Botany Department, NationalMuseums of Kenya, Nairobi, Kenya
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
| | - Anjuli Meiser
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
| | - H. Thorsten Lumbsch
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
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18
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Singh G, Dal Grande F, Divakar PK, Otte J, Crespo A, Schmitt I. Fungal-algal association patterns in lichen symbiosis linked to macroclimate. New Phytol 2017; 214:317-329. [PMID: 27918622 DOI: 10.1111/nph.14366] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 09/07/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Both macroclimate and evolutionary events may influence symbiont association and diversity patterns. Here we assess how climatic factors and evolutionary events shape fungal-algal association patterns in the widely distributed lichen-forming fungal genus Protoparmelia. Multilocus phylogenies of fungal and algal partners were generated using 174 specimens. Coalescent-based species delimitation analysis suggested that 23 fungal hosts are associating with 20 algal species. Principal component analysis (PCA) was performed to infer how fungal-algal association patterns varied with climate. Fungi associated with one to three algal partners whereas algae accepted one to five fungal partners. Both fungi and algae were more specific, associating with fewer partners, in the warmer climates. Interaction with more than one partner was more frequent in cooler climates for both the partners. Cophylogenetic analyses suggest congruent fungal-algal phylogenies. Host switch was a more common event in warm climates, whereas failure of the photobiont to diverge with its fungal host was more frequent in cooler climates. We conclude that both environmental factors and evolutionary events drive fungal and algal evolution in Protoparmelia. The processes leading to phylogenetic congruence of fungi and algae are different in different macrohabitats in our study system. Hence, closely related species inhabiting diverse habitats may follow different evolutionary pathways.
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Affiliation(s)
- Garima Singh
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Pradeep K Divakar
- Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal, s/n, Ciudad Universitaria, E-28040, Madrid, Spain
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Ana Crespo
- Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal, s/n, Ciudad Universitaria, E-28040, Madrid, Spain
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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19
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Dal Grande F, Sharma R, Meiser A, Rolshausen G, Büdel B, Mishra B, Thines M, Otte J, Pfenninger M, Schmitt I. Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus. BMC Evol Biol 2017; 17:93. [PMID: 28359299 PMCID: PMC5374679 DOI: 10.1186/s12862-017-0929-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 01/12/2017] [Accepted: 03/01/2017] [Indexed: 12/12/2022] Open
Abstract
Background Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments. Results We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction. Conclusions Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0929-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| | - Rahul Sharma
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Anjuli Meiser
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Department, University of Kaiserslautern, 67653, Kaiserslautern, Germany
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
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Kaminski R, Bella R, Yin C, Otte J, Ferrante P, Gendelman HE, Li H, Booze R, Gordon J, Hu W, Khalili K. Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther 2016; 23:696. [PMID: 27488023 DOI: 10.1038/gt.2016.45] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kaminski R, Bella R, Yin C, Otte J, Ferrante P, Gendelman HE, Li H, Booze R, Gordon J, Hu W, Khalili K. Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther 2016; 23:690-5. [PMID: 27194423 DOI: 10.1038/gt.2016.41] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 12/20/2022]
Abstract
A CRISPR/Cas9 gene editing strategy has been remarkable in excising segments of integrated HIV-1 DNA sequences from the genome of latently infected human cell lines and by introducing InDel mutations, suppressing HIV-1 replication in patient-derived CD4+ T-cells, ex vivo. Here, we employed a short version of the Cas9 endonuclease, saCas9, together with a multiplex of guide RNAs (gRNAs) for targeting the viral DNA sequences within the 5'-LTR and the Gag gene for removing critically important segments of the viral DNA in transgenic mice and rats encompassing the HIV-1 genome. Tail-vein injection of transgenic mice with a recombinant Adeno-associated virus 9 (rAAV9) vector expressing saCas9 and the gRNAs, rAAV:saCas9/gRNA, resulted in the cleavage of integrated HIV-1 DNA and excision of a 978 bp DNA fragment spanning between the LTR and Gag gene in the spleen, liver, heart, lung and kidney as well as in the circulating lymphocytes. Retro-orbital inoculation of rAAV9:saCas9/gRNA in transgenic rats eliminated a targeted segment of viral DNA and substantially decreased the level of viral gene expression in circulating blood lymphocytes. The results from the proof-of-concept studies, for the first time, demonstrate the in vivo eradication of HIV-1 DNA by CRISPR/Cas9 on delivery by an rAAV9 vector in a range of cells and tissues that harbor integrated copies of viral DNA.
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Affiliation(s)
- R Kaminski
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - R Bella
- Microbiology and Clinical Microbiology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - C Yin
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - J Otte
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - P Ferrante
- Microbiology and Clinical Microbiology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - H E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Durham Research Center, Omaha, NE, USA
| | - H Li
- Behavioral Neuroscience, Department of Psychology, University of South Carolina, Columbia, SC, USA
| | - R Booze
- Behavioral Neuroscience, Department of Psychology, University of South Carolina, Columbia, SC, USA
| | - J Gordon
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - W Hu
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - K Khalili
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
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Madeira S, Manteigas A, Ribeiro R, Otte J, Fonseca AP, Caetano P, Abernethy D, Boinas F. Factors that Influence Mycobacterium bovis Infection in Red Deer and Wild Boar in an Epidemiological Risk Area for Tuberculosis of Game Species in Portugal. Transbound Emerg Dis 2015; 64:793-804. [PMID: 26519121 DOI: 10.1111/tbed.12439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 08/04/2015] [Indexed: 11/27/2022]
Abstract
Bovine tuberculosis (bTB) is a worldwide zoonotic disease of domestic and wild animals. Eradication has proved elusive in those countries with intensive national programmes but with ongoing transmission between wildlife and cattle. In Portugal, a high-risk area for bTB was defined and specific measures implemented to assess and minimize the risk from wildlife. Data from the 2011 to 2014 hunting seasons for red deer (Cervus elaphus) and wild boar (Sus scrofa) were analysed with bovine demographic and bTB information to assess factors that determined the occurrence and distribution of bTB in both species. The likelihood of bTB-like lesions in wild boar was positively associated with density of red deer, wild boar and cattle, while for red deer, only their density and age were significant factors. The likelihood of Mycobacterium bovis isolation in wild boar was associated with density of cattle and red deer and also with the anatomical location of lesions, while for red deer, none of the variables tested were statistically significant. Our results suggest that, in the study area, the role of red deer and wild boar may be different from the one previously suggested by other authors for the Iberian Peninsula, as red deer may be the driving force behind M. bovis transmission to wild boar. These findings may assist the official services and game managing bodies for the management of hunting zones, what could also impact the success of the bTB eradication programme.
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Affiliation(s)
- S Madeira
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - A Manteigas
- Direção Geral de Alimentação e Veterinária, DSAVRC-DAVCB, Castelo Branco, Portugal
| | - R Ribeiro
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - J Otte
- Berkeley Economic Advising and Research, Rome, Italy
| | - A Pina Fonseca
- Direção Geral de Alimentação e Veterinária, DSAVRC-DAVG, Guarda, Portugal
| | - P Caetano
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - D Abernethy
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - F Boinas
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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Singh G, Dal Grande F, Divakar PK, Otte J, Leavitt SD, Szczepanska K, Crespo A, Rico VJ, Aptroot A, Cáceres MEDS, Lumbsch HT, Schmitt I. Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota). PLoS One 2015; 10:e0124625. [PMID: 25932996 PMCID: PMC4416777 DOI: 10.1371/journal.pone.0124625] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
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Affiliation(s)
- Garima Singh
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Steven D. Leavitt
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Katarzyna Szczepanska
- Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24a, 50-363, Wroclaw, Poland
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Víctor J. Rico
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - André Aptroot
- Advice Bureau for Bryology and Lichenology Herbarium, Soest, The Netherlands
| | | | - H. Thorsten Lumbsch
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
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Bálint M, Bartha L, O'Hara RB, Olson MS, Otte J, Pfenninger M, Robertson AL, Tiffin P, Schmitt I. Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Mol Ecol 2014; 24:235-48. [DOI: 10.1111/mec.13018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/19/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Miklós Bálint
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - László Bartha
- Laboratory of Molecular Environmental Biology; Institute for Interdisciplinary Research in Bio-Nano Sciences; Babe-Bolyai University; Treboniu Laurian 42 400271 Cluj Romania
| | - Robert B. O'Hara
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - Matthew S. Olson
- Department of Biological Sciences; Texas Tech University; P.O. Box 43131 Lubbock TX 79409-3131 USA
- Institute of Arctic Biology; University of Alaska Fairbanks; P.O. Box 757000 Fairbanks AK 99775 USA
| | - Jürgen Otte
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
| | - Markus Pfenninger
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
- Institut für Ökologie, Evolution und Diversität; Goethe Universität; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Amanda L. Robertson
- Institute of Arctic Biology; University of Alaska Fairbanks; P.O. Box 757000 Fairbanks AK 99775 USA
- Science Applications; U.S. Fish & Wildlife Service; 101 12th Avenue Fairbanks AK 99701 USA
| | - Peter Tiffin
- Department of Plant Biology; University of Minnesota; 1445 Gortner Avenue St. Paul MN 55108 USA
| | - Imke Schmitt
- Biodiversity and Climate Research Centre; Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt Germany
- Institut für Ökologie, Evolution und Diversität; Goethe Universität; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
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Sadowska-Deś AD, Dal Grande F, Lumbsch HT, Beck A, Otte J, Hur JS, Kim JA, Schmitt I. Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia. Mol Phylogenet Evol 2014; 76:202-10. [PMID: 24685499 DOI: 10.1016/j.ympev.2014.03.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 10/07/2013] [Revised: 03/04/2014] [Accepted: 03/17/2014] [Indexed: 02/05/2023]
Abstract
The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.
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Affiliation(s)
- Anna D Sadowska-Deś
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, Menzinger Straße 67, D-80638 München, Germany; GeoBio-Center, Ludwig-Maximilians Universität München, Richard-Wagner-Str. 10, D-80333 München, Germany
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Jung A Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 540-742, South Korea
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt, Germany.
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Sadowska-Deś AD, Bálint M, Otte J, Schmitt I. Corrigendum to “Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers” [Fungal Ecology (2012) 141–151]. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2013.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Petrón M, Broncano J, Otte J, Martín L, Timón M. Effect of commercial proteases on shelf-life extension of Iberian dry-cured sausage. Lebensm Wiss Technol 2013. [DOI: 10.1016/j.lwt.2013.02.014] [Citation(s) in RCA: 5] [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: 11/17/2022]
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Sadowska-Deś AD, Bálint M, Otte J, Schmitt I. Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Métras R, Magalhaes RJS, Dinh QH, Fournié G, Gilbert J, Huu DD, Roland-Holst D, Otte J, Pfeiffer DU. An assessment of the feasibility of a poultry tracing scheme for smallholders in Vietnam. REV SCI TECH OIE 2013; 30:703-14. [PMID: 22435183 DOI: 10.20506/rst.30.3.2072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Tracing movements could assist the implementation of bio-containment measures during a disease outbreak. To evaluate the potential for implementing a tracing system for a poultry supply chain in northern Vietnam, a four-month longitudinal study was conducted to identify marketing practices associated with poultry traceability. Poultry sold in batches were traced between farms and markets, and their traceability was assessed upon market arrival. A total of 315 batches were released from the farms; 37% arrived at a market, from which 57.3% were 'traceable'. The results of the multivariable analysis showed that traceability was associated with farms operating through no more than two traders (Odds ratio [OR] = 5.97, 95% CI 1.15-30.92) and batches brought to the market on the day of purchase (OR = 4.05, 95% CI 1.23-13.27). No specific incentives were provided to farmers or traders. Results suggest that there is potential for implementing a poultry traceability scheme, although the tracing methodology should be refined.
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Affiliation(s)
- R Métras
- Veterinary Epidemiology and Public Health Group, Department of Veterinary Clinical Sciences, The Royal Veterinary College, North Mymms, Hatfield, United Kingdom
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Azevedo M, Rombaldi A, Marques A, Fortes M, Otte J, Spohr C, Mattea C. Physical Education+: Practicing health at school–A physical activity intervention proposal. J Sci Med Sport 2012. [DOI: 10.1016/j.jsams.2012.11.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vogel JU, Otte J, Koch F, Gümbel H, Doerr HW, Cinatl J. Role of human cytomegalovirus genotype polymorphisms in AIDS patients with cytomegalovirus retinitis. Med Microbiol Immunol 2012; 202:37-47. [PMID: 22669631 DOI: 10.1007/s00430-012-0244-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/08/2012] [Indexed: 12/20/2022]
Abstract
Although several host factors have been identified to influence the course of HCMV infection, it still remains unclear why in AIDS patients without highly active antiretroviral therapy human cytomegalovirus (HCMV) retinitis is one of the most common opportunistic infections, whereas in other immunosuppressed individuals it has a low incidence. It was suggested that HCMV glycoprotein B strains may be suitable as marker for virulence and HCMV retinitis. Moreover, UL144 ORF, a member of the TNF-α receptor superfamily, may play a crucial role in innate defences and adaptive immune response of HCMV infection. Furthermore, sequence analyses of HCMV genes UL128, UL130, and UL131A as major determinants of virus entry and replication in epithelial and other cell types were performed. To evaluate the association of sequence variability of depicted viral genes with HCMV retinitis and in vitro growth properties in retinal pigment epithelial cells (RPE) and human foreskin fibroblasts (HFF), we compared 14 HCMV isolates obtained from vitreous fluid and urine of AIDS patients with clinically proven HCMV retinitis. Isolates were analyzed by PCR cycle sequencing and phylogenetic analysis. In addition, sequences of HCMV strains AF1, U8, U11, VR1814, and its cell culture adapted derivates were included. Sequence analysis of gB yielded three genetic subtypes (gB type 1 (5 isolates), gB type 2 (12 isolates), and gB type 3 (5 Isolates)), whereas sequence analysis of UL144 showed a greater diversity (7 isolates type 1A, 2 isolates type 1C, 7 isolates type 2, and 3 isolates type 3). In contrast, the UL128, UL130, and UL131A genes of all low-passage isolates were highly conserved and showed no preferential clustering. Moreover, in HFF and RPE cells, all of our HCMV isolates replicated efficiently independently of their genetic subtype. In conclusion, beside a possible link between the gB subtype 2 and HCMV retinitis, our study found no direct evidence for a connection between UL144/UL128/UL130/UL131A genotypes and the incidence of HCMV retinitis in AIDS patients.
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Affiliation(s)
- Jens-Uwe Vogel
- Institute of Medical Virology, Goethe University Hospital, Frankfurt am Main, Germany.
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Farrokh A, Wojcinski S, Bösing T, Otte J, Degenhardt F. Fetomaternale Makrotransfusion – Ein Fallbericht. Z Geburtshilfe Neonatol 2011. [DOI: 10.1055/s-0031-1293350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Preuss E, Muik A, Weber K, Otte J, von Laer D, Fehse B. Cancer suicide gene therapy with TK.007: superior killing efficiency and bystander effect. J Mol Med (Berl) 2011; 89:1113-24. [PMID: 21698427 DOI: 10.1007/s00109-011-0777-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/20/2011] [Accepted: 06/07/2011] [Indexed: 01/14/2023]
Abstract
Suicide gene therapy is a promising concept in oncology. We have recently introduced a novel suicide gene, TK.007, which was shown to excel established herpes simplex virus thymidine kinase (HSVtk) variants when used for donor-lymphocyte modification in adoptive immunotherapy models. Here, the potential of TK.007 in killing cancer cells was studied. Initially, we transduced tumour cell lines derived from different neoplasias (glioblastoma, melanoma, lung cancer, colon cancer) with lentiviral LeGO vectors encoding TK.007 or the splice-corrected (sc)HSVtk together with an eGFP/Neo-marker. Based on direct in vitro comparison, we found that TK.007 facilitates more efficient tumour cell killing at significantly lower ganciclovir doses in all tumour cell lines tested. Also, using different readout systems, we found a significantly stronger bystander effect of TK.007 as compared to scHSVtk. Importantly, in vitro data were confirmed in vivo using a subcutaneous G62 glioblastoma model in NOD/SCID mice. In mice transplanted with scHSVtk-positive tumours, treatment with low (10 mg/kg) or standard (50 mg/kg) ganciclovir doses resulted only in short-term growth inhibition or transient tumour remission, respectively. In striking contrast, in the TK.007 group, all animals achieved continuous complete remission after both standard and low-dose ganciclovir. Finally, a substantial bystander effect for TK.007 was also confirmed with the G62 model in vivo, where significantly prolonged survival for mice bearing tumours containing only 10% or 50% TK.007-expressing cells was observed. In summary, our data indicate strongly improved anti-tumour activity of TK.007 as compared to conventional HSVtk. We therefore suppose that TK.007 is an excellent candidate for cancer suicide gene therapy.
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Affiliation(s)
- Ellen Preuss
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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Schulte M, Jacobsen F, Otte J, Hirsch T, Al-Benna S, Steinau H, Steinstraesser L. Signal transduction in adenoviral induced immune reaction of the skin. Burns 2009. [DOI: 10.1016/j.burns.2009.06.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Abstract
This paper reviews the (predominantly grey) literature on impacts of highly pathogenic avian influenza (HPAI) strain H5N1 and control responses on the livestock sector and associated industries in developing countries. The authors distinguish between impacts that arise directly through HPAI-related morbidity and mortality, those that are a consequence of public intervention to control or eradicate HPAI, and impacts that are mediated through market reactions. The paper further considers how these impacts propagate up- and downstream through related supply and distribution networks, how short-term reactions are followed by longer-term adjustments, how impacts include direct cost elements and foregone income, and why losses to the poultry sector will, at least to some extent, be 'passed on' on the one hand, for example through compensation, and, on the other hand, be compensated for by gains in other livestock subsectors. Differences in methodology applied in the reviewed reports result in a lack of comparability of estimates for HPAI 'costs/impacts' across countries and even within countries and are compounded by information deficits. Despite these shortcomings, the literature permits some significant conclusions to be drawn on the relative importance of direct and indirect impacts and on their distribution across different types of poultry producers. The paper ends by outlining directions of future research that combine epidemiology and economics to provide a framework for disease control decision-making.
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Ardö Y, Lilbæk H, Kristiansen K, Zakora M, Otte J. Identification of large phosphopeptides from β-casein that characteristically accumulate during ripening of the semi-hard cheese Herrgård. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2006.06.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Dambacher J, Beigel F, Zitzmann K, Eichhorst ST, Otte J, Seiderer J, Diepolder H, Auernhammer CJ, Ochsenkühn T, Goeke B, Brand S. The novel IL-10 related cytokine IL-26 is increased in active inflammatory bowel disease and intestinal epithelial cells express the functional IL-26 receptor complex. Z Gastroenterol 2006. [DOI: 10.1055/s-2006-955514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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39
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Darbinian-Sarkissian N, Darbinyan A, Otte J, Radhakrishnan S, Sawaya BE, Arzumanyan A, Chipitsyna G, Popov Y, Rappaport J, Amini S, Khalili K. p27(SJ), a novel protein in St John's Wort, that suppresses expression of HIV-1 genome. Gene Ther 2006; 13:288-95. [PMID: 16251997 DOI: 10.1038/sj.gt.3302649] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [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: 11/09/2022]
Abstract
Transcription of the HIV-1 genome is controlled by the cooperation of viral regulatory proteins and several host factors which bind to specific DNA sequences within the viral promoter spanning the long terminal repeat, (LTR). Here, we describe the identification of a novel protein, p27(SJ), present in a laboratory callus culture of Hypericum perforatum (St John's Wort) that suppresses transcription of the HIV-1 genome in several human cell types including primary culture of microglia and astrocytes. p27(SJ) associates with C/EBPbeta, a transcription factor that regulates expression of the HIV-1 genome in macrophages and monocytic cells, and the viral transactivator, Tat. The association of p27(SJ) with C/EBPbeta and Tat alters their subcellular localization, causing their accumulation in the perinuclear cytoplasmic compartment of the cells. Fusion of a nuclear localization signal to p27(SJ) forces its entry into the nucleus and diminishes the capacity of p27(SJ) to suppress Tat activity, but does not alter its ability to suppress C/EBPbeta activation of the LTR. Results from binding assays showed the inhibitory effect of p27(SJ) on C/EBPbeta interaction with DNA. Finally, our results demonstrate that expression of p27(SJ) decreases the level of viral replication in HIV-1-infected cells. These observations suggest the potential for the development of a therapeutic advance based on p27(SJ) protein to control HIV-1 transcription and replication in cells associated with HIV-1 infection in the brain.
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Affiliation(s)
- N Darbinian-Sarkissian
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, PA, USA
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40
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41
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Otte J, Madlener K, Jung O, Lange U, Poetzsch B. Anti-endothelial cell antibodies (AECA): cDNA-based antigen screening. J Thromb Haemost 2003. [DOI: 10.1111/j.1538-7836.2003.tb05320.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Aigner L, Uyanik G, Couillard-Despres S, Ploetz S, Wolff G, Morris-Rosendahl D, Martin P, Eckel U, Spranger S, Otte J, Woerle H, Holthausen H, Apheshiotis N, Fluegel D, Winkler J. Somatic mosaicism and variable penetrance in doublecortin-associated migration disorders. Neurology 2003; 60:329-32. [PMID: 12552055 DOI: 10.1212/01.wnl.0000042091.90361.d2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [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: 11/15/2022] Open
Abstract
X-linked isolated lissencephaly sequence (XLIS) and subcortical band heterotopia (SBH) are allelic disorders caused by mutations in the doublecortin (DCX) gene. This genetic analysis of seven families revealed four novel mutations in the DCX gene. The authors detected a high rate of somatic mosaicism in male and female patients with variable penetrance of bilateral SBH including nonpenetrance in a heterozygous woman. In addition, the authors implemented prenatal diagnosis in a family with SBH/XLIS.
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Affiliation(s)
- L Aigner
- Department of Neurology, University of Regensburg, Universitätsstr. 84, D-93053 Regensburg, Germany
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43
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Sterner-Kock A, Thorey IS, Koli K, Wempe F, Otte J, Bangsow T, Kuhlmeier K, Kirchner T, Jin S, Keski-Oja J, von Melchner H. Disruption of the gene encoding the latent transforming growth factor-beta binding protein 4 (LTBP-4) causes abnormal lung development, cardiomyopathy, and colorectal cancer. Genes Dev 2002; 16:2264-73. [PMID: 12208849 PMCID: PMC186672 DOI: 10.1101/gad.229102] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transforming growth factor-betas (TGF-betas) are multifunctional growth factors that are secreted as inactive (latent) precursors in large protein complexes. These complexes include the latency-associated propeptide (LAP) and a latent transforming growth factor-beta binding protein (LTBP). Four isoforms of LTBPs (LTBP-1-LTBP-4) have been cloned and are believed to be structural components of connective tissue microfibrils and local regulators of TGF-beta tissue deposition and signaling. By using a gene trap strategy that selects for integrations into genes induced transiently during early mouse development, we have disrupted the mouse homolog of the human LTBP-4 gene. Mice homozygous for the disrupted allele develop severe pulmonary emphysema, cardiomyopathy, and colorectal cancer. These highly tissue-specific abnormalities are associated with profound defects in the elastic fiber structure and with a reduced deposition of TGF-beta in the extracellular space. As a consequence, epithelial cells have reduced levels of phosphorylated Smad2 proteins, overexpress c-myc, and undergo uncontrolled proliferation. This phenotype supports the predicted dual role of LTBP-4 as a structural component of the extracellular matrix and as a local regulator of TGF-beta tissue deposition and signaling.
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Affiliation(s)
- Anja Sterner-Kock
- Laboratory for Molecular Hematology, University of Frankfurt Medical School, 60596 Frankfurt am Main, Germany
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Knudsen J, Otte J, Olsen K, Skibsted L. Effect of high hydrostatic pressure on the conformation of β-lactoglobulin A as assessed by proteolytic peptide profiling. Int Dairy J 2002. [DOI: 10.1016/s0958-6946(02)00078-x] [Citation(s) in RCA: 65] [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] [Indexed: 11/25/2022]
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45
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Schmitz F, Schrader H, Otte J, Schmitz H, Stüber E, Herzig K, Schmidt WE. Identification of CCK-B/gastrin receptor splice variants in human peripheral blood mononuclear cells. Regul Pept 2001; 101:25-33. [PMID: 11495676 DOI: 10.1016/s0167-0115(01)00281-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is increasing evidence for a direct interaction of the enteric nervous and immune system. Receptors for neuropeptides such as VIP, somatostatin, and substance P have been characterised in human immuno-haematopoietic cells but little is known about the functional significance and expression of receptors for cholecystokinin (CCK) on cells of the immune system. There are only few studies that describe the expression of CCK receptors on human leukaemia-derived cell lines but the receptor structure and function in normal leukocytes have not been clearly established. We therefore sought to determine CCK receptor expression, structure, and function in nontransformed human peripheral blood mononuclear cells.Full-length cDNA clones encoding the human CCK-A and CCK-B/gastrin receptor are expressed in peripheral blood mononuclear cells from healthy volunteers without haematopoietic malignancy. In addition to wild-type CCK-B/gastrin receptor cDNAs, we isolated a splice variant with an in frame insertion of 69 amino acids within its putative third intracellular receptor loop. Dideoxy sequence analysis revealed that the cDNA of this splice variant comprises exons 1-4 but retains intron 4 (207 bp) in the absence of mutations within the splice donor sites. Transient expression of this splice variant in COS-7 cells reveals wild-type affinity for CCK-8, Gastrin-17, and antagonist L-365,260. Affinity for glycine-extended gastrin-17 was not increased when compared to the wild-type CCK-B/gastrin receptor. In vitro, gastrin decreased 3H-thymidine labelling in phytohaemagglutinin-pretreated mononuclear cells at a half-maximally effective concentration of 1.5 nM. We also isolated a cDNA encoding another splice variant of the CCK-B/gastrin receptor with a 158 bp deletion of the entire exon 4 sequence. We conclude that wild-type transcripts of both CCK receptor subtypes and splice variants of the CCK-B/gastrin receptor are expressed in nontransformed human mononuclear cells and that gastrin exhibits antiproliferative effects.
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Affiliation(s)
- F Schmitz
- Laboratory for Experimental Gastroenterology, Department of Medicine I at St. Josef-Hospital, Ruhr-University Bochum, Gudrunstr. 56, D-44791, Bochum, Germany.
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46
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Ipsen R, Otte J, Sharma R, Nielsen A, Gram Hansen L, Bruun Qvist K. Effect of limited hydrolysis on the interfacial rheology and foaming properties of β-lactoglobulin A. Colloids Surf B Biointerfaces 2001; 21:173-178. [PMID: 11377946 DOI: 10.1016/s0927-7765(01)00170-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [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]
Abstract
Hydrolysis of beta-lactoglobulin (beta-Lg), genetic variant A, using a serine protease specific for glutamic and aspartic acid residues from Bacillus licheniformis (BLP), resulted in improved foam overrun and foam stability. Limited hydrolysis (19-26% hydrolysed beta-Lg) led to a more rapid increase in the viscoelastic properties of air/water interfacial films and a concomitant increase in foam overrun compared with intact beta-Lg, presumably due to increased exposure of hydrophobic areas. The increased exposure did not, however, cause formation of an interfacial layer with increased viscoelastic properties. More extended hydrolysis (86% hydrolysed beta-Lg) resulted in a higher initial overrun than the unhydrolysed sample and the best foam stability. The interfacial elasticity and viscosity, though, was the lowest observed. Thus, high maximum values of these interfacial properties are not necessary prerequisites for formation of a voluminous and stable foam.
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Affiliation(s)
- R Ipsen
- Department of Dairy and Food Science, The Royal Veterinary and Agricultural University, Rolighedsvej 30, DK-1958 C, Frederiksberg, Denmark
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Abstract
Gelation of alpha-lactalbumin (alpha-la) incubated with a protease from Bacillus licheniformis (BLP) at 50 degrees C for 4 h was monitored using small oscillatory shear and the large deformation properties of final gels were characterized by uniaxial compression. Transmission electron microscopy was used to visualize the microstructure. Gels made from alpha-la (10 g/l) using BLP were almost transparent, although somewhat whitish, and they were more than 20 times stiffer (measured as complex modulus) than equivalent gels made from beta-lactoglobulin (beta-lg) at the same concentration. The microstructure of the gels consisted of non-branching, apparently hollow strands with a uniform diameter close to 20 nm, similar in overall structure to microtubules. Adding Ca2+ in amounts of 50 or 100 mM changed the spatial distribution of the strands and resulted in a reduction in the failure stress recorded in uniaxial compression. Apart from affecting the microstructure, Ca2+ was shown to be essential for the formation of the gels. It is proposed. that the mechanism behind the self-assembly of the partially hydrolysed alpha-la into long tubes is a spatially restricted creation of ionic bonds between Ca2+ and carboxyl acid groups on peptide fragments resulting from the action of BLP on alpha-la. Proteolysis of alpha-la with BLP in the presence of Ca2+ thus results in formation of a strong gel with a microstructure not previously observed in food protein systems.
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Affiliation(s)
- R Ipsen
- Department of Dairy and Food Science, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark.
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Otte J, Lomholt SB, Ipsen R, Qvist KB. Effect of partial hydrolysis with an immobilized proteinase on thermal gelation properties of beta-lactoglobulin B. J DAIRY RES 2000; 67:597-608. [PMID: 11131072 DOI: 10.1017/s0022029900004520] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [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: 11/07/2022]
Abstract
We have investigated the influence of partial hydrolysis with an immobilized proteinase from Bacillus licheniformis on the thermal gelation of isolated beta-lactoglobulin B. Gelation behaviour was determined by dynamic rheological measurements (small deformation) and the gels were characterized with respect to microstructure and water-holding properties. A fine-stranded gel with a complex modulus of approximately 2000 Pa was formed from beta-lactoglobulin (50 g/l in 75 mM-Tris-HCl, pH 7.5). Limited hydrolysis prior to thermal gelation resulted in coarser gels with thicker protein strands and larger pores. Gel structure correlated with its permeability, proton mobility and water-holding capacity. Total stiffness gel increased with low degrees of hydrolysis, but decreased after prolonged hydrolysis. Maximal gel stiffness was 1.5-fold that gels made from of unhydrolysed beta-lactoglobulin. This was much lower than the stiffening effect obtained after partial hydrolysis of whey protein isolate, showing that the gel strengthening effect of partial hydrolysis was depedent on the protein composition and/or the hydrolysis and gelatin conditions. A mechanism to explain the observed effects of hydrolysis on gelation and gel properties is presented.
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Affiliation(s)
- J Otte
- Department of Dairy and Food Science, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.
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49
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Gordon J, Del Valle L, Otte J, Khalili K. Pituitary neoplasia induced by expression of human neurotropic polyomavirus, JCV, early genome in transgenic mice. Oncogene 2000; 19:4840-6. [PMID: 11039901 DOI: 10.1038/sj.onc.1203849] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [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: 01/12/2023]
Abstract
In recent years, there has been mounting evidence pointing to the association of polyomaviruses with a wide range of human cancers. The human neurotropic polyomavirus, JCV, infecting greater than 75% of the human population produces a regulatory protein named T-antigen which is expressed at the early phase of viral lytic infection and plays a critical role in completion of the viral life cycle. Furthermore, this protein has the ability to transform neural cells in vitro and its expression has been detected in several human neural-origin tumors. To further investigate the oncogenic potential of the JCV early protein in vivo, transgenic mice expressing JCV T-antigen under the control of its own promoter were generated. Nearly 50% of the animals developed large, solid masses within the base of the skull by 1 year of age. Evaluation of the location as well as histological and immunohistochemical data suggest that the tumors arise from the pituitary gland. As T-antigen is known to interact with several cell cycle regulators, the neoplasms were analysed for the presence of the tumor suppressor protein, p53. Immunoprecipitation/Western blot analysis demonstrated overexpression of wild-type, but not mutant p53 within tumor tissue. In addition, co-immunoprecipitation established an interaction between p53 and T-antigen and overexpression of p53 downstream target protein, p21/WAF1. This report describes the analysis of inheritable pituitary adenomas induced by expression of the human polyomavirus, JCV T-antigen in transgenic mice where T-antigen disrupts the p53 pathway by binding to and sequestering wild-type p53. This animal model may serve as a useful tool to further evaluate mechanisms of tumorigenesis by JCV T-antigen.
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MESH Headings
- Adenoma/chemistry
- Adenoma/genetics
- Adenoma/pathology
- Adenoma/virology
- Animals
- Animals, Outbred Strains
- Antigens, Polyomavirus Transforming/analysis
- Antigens, Polyomavirus Transforming/genetics
- Antigens, Polyomavirus Transforming/physiology
- Cell Transformation, Viral/genetics
- Cyclin-Dependent Kinase Inhibitor p21
- Cyclins/biosynthesis
- Cyclins/genetics
- Female
- Gene Expression Regulation, Viral
- Genes, p53
- Genome, Viral
- Intestinal Neoplasms/genetics
- Intestinal Neoplasms/virology
- JC Virus/genetics
- JC Virus/immunology
- JC Virus/pathogenicity
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Neoplasm Proteins/analysis
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Pituitary Neoplasms/chemistry
- Pituitary Neoplasms/genetics
- Pituitary Neoplasms/pathology
- Pituitary Neoplasms/virology
- Promoter Regions, Genetic
- Recombinant Proteins/metabolism
- Tumor Suppressor Protein p53/antagonists & inhibitors
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- J Gordon
- Center for Neurovirology and Cancer Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
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50
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Abstract
Medulloblastoma, a malignant invasive tumor of the cerebellum, is one of the most common neoplasms of the nervous system in children. Utilization of the human neurotropic virus JC virus (JCV) early gene T-antigen allowed the development of a transgenic animal that models human medulloblastoma. Here we describe the characterization of two distinct populations of cells derived from the JCV-induced mouse medulloblastoma. Results from immunohistochemical and biochemical studies revealed the expression of T-antigen in some but not all tumor cells. In T-antigen-producing cells, T-antigen was found in association with wild-type p53 and pRb, two tumor suppressors that control cell growth and differentiation. In cells that lack expression of T-antigen, a novel mutant p53 with a deletion between residues 35 and 123 was detected. Morphological differences were observed between the two populations of cells, though there was no significant difference in their growth rates. However, subcutaneous transplantation of the T-antigen-positive, but not T-antigen-negative, cells resulted in the development of massive tumors in experimental animals. In light of earlier reports on the association of JCV with human medulloblastoma, the mouse cell lines described in this study may provide a valuable tool for deciphering the pathways involved in the formation and progression of medulloblastoma.
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Affiliation(s)
- B Krynska
- Center for Neurovirology and Cancer Biology, Laboratory of Brain Tumor Biology, College of Science and Technology, Temple University, 1900 North 12th Street, 015-96, Biology Life Sciences Building, Room 203, Philadelphia, Pennsylvania 19122, USA
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