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4 results on '"Gehrmann, Thies"'

1. Phyllosticta citricarpa and sister species of global importance to Citrus

Author

Guarnaccia, Vladimiro, Gehrmann, Thies, Silva‐Junior, Geraldo J, Fourie, Paul H, Haridas, Sajeet, Vu, Duong, Spatafora, Joseph, Martin, Francis M, Robert, Vincent, Grigoriev, Igor V, Groenewald, Johannes Z, and Crous, Pedro W

Subjects
Plant Biology, Biological Sciences, Human Genome, Genetics, Ascomycota, Citrus, Genes, Mating Type, Fungal, Genome, Fungal, Phylogeography, Plant Diseases, Guignardia, mating type, systematics, Citrus, Guignardia, Microbiology, Crop and Pasture Production, Plant Biology & Botany, Evolutionary biology, Plant biology
Abstract

Several Phyllosticta species are known as pathogens of Citrus spp., and are responsible for various disease symptoms including leaf and fruit spots. One of the most important species is P. citricarpa, which causes a foliar and fruit disease called citrus black spot. The Phyllosticta species occurring on citrus can most effectively be distinguished from P. citricarpa by means of multilocus DNA sequence data. Recent studies also demonstrated P. citricarpa to be heterothallic, and reported successful mating in the laboratory. Since the domestication of citrus, different clones of P. citricarpa have escaped Asia to other continents via trade routes, with obvious disease management consequences. This pathogen profile represents a comprehensive literature review of this pathogen and allied taxa associated with citrus, focusing on identification, distribution, genomics, epidemiology and disease management. This review also considers the knowledge emerging from seven genomes of Phyllosticta spp., demonstrating unknown aspects of these species, including their mating behaviour.TaxonomyPhyllosticta citricarpa (McAlpine) Aa, 1973. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Phyllostictaceae, Genus Phyllosticta, Species citricarpa.Host rangeConfirmed on more than 12 Citrus species, Phyllosticta citricarpa has only been found on plant species in the Rutaceae.Disease symptomsP. citricarpa causes diverse symptoms such as hard spot, virulent spot, false melanose and freckle spot on fruit, and necrotic lesions on leaves and twigs.Useful websitesDOE Joint Genome Institute MycoCosm portals for the Phyllosticta capitalensis (https://genome.jgi.doe.gov/Phycap1), P. citriasiana (https://genome.jgi.doe.gov/Phycit1), P. citribraziliensis (https://genome.jgi.doe.gov/Phcit1), P. citrichinaensis (https://genome.jgi.doe.gov/Phcitr1), P. citricarpa (https://genome.jgi.doe.gov/Phycitr1, https://genome.jgi.doe.gov/Phycpc1), P. paracitricarpa (https://genome.jgi.doe.gov/Phy27169) genomes. All available Phyllosticta genomes on MycoCosm can be viewed at https://genome.jgi.doe.gov/Phyllosticta.

Published
2019

2. Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Author

Manson, Abigail L, Abeel, Thomas, Galagan, James E, Sundaramurthi, Jagadish Chandrabose, Salazar, Alex, Gehrmann, Thies, Shanmugam, Siva Kumar, Palaniyandi, Kannan, Narayanan, Sujatha, Swaminathan, Soumya, and Earl, Ashlee M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Human Genome, Rare Diseases, Biotechnology, Genetics, Tuberculosis, Antimicrobial Resistance, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Adult, Antitubercular Agents, Base Sequence, Drug Resistance, Multiple, Bacterial, Female, Genetic Variation, Genome, Bacterial, Humans, India, Male, Mutation, Mycobacterium tuberculosis, Phylogeny, Polymerase Chain Reaction, Indo-Oceanic lineage, EAI lineage, CAS lineage, drug resistance., Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

Background.India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3.Methods.We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance.Results.Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance.Conclusions.In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.

Published
2017

3. PLIS: A metabolomic response monitor to a lifestyle intervention study in older adults

Author

Bogaards, Fatih A., Gehrmann, Thies, Beekman, Marian, van den Akker, Erik Ben, van de Rest, Ondine, Hangelbroek, Roland W. J., Noordam, Raymond, Mooijaart, Simon P., de Groot, Lisette C. P. G. M., Reinders, Marcel J. T., and Slagboom, P. Eline

Subjects
Male, Nutrition and Disease, Biochemistry, Voeding, Metabolisme en Genomica, Voeding, Voeding en Ziekte, OT BVG/MNH/MDS, Genetics, Humans, Insulin, Life Science, Obesity, Life Style, Molecular Biology, Aged, Nutrition, VLAG, Cholesterol, HDL, lifestyle intervention, bioinformatics, response monitor, metabolomics, Metabolism and Genomics, Nutritional Biology, machine learning, Metabolisme en Genomica, Female, Nutrition, Metabolism and Genomics, healthy ageing, Biomarkers, Biotechnology
Abstract

The response to lifestyle intervention studies is often heterogeneous, especially in older adults. Subtle responses that may represent a health gain for individuals are not always detected by classical health variables, stressing the need for novel biomarkers that detect intermediate changes in metabolic, inflammatory, and immunity-related health. Here, our aim was to develop and validate a molecular multivariate biomarker maximally sensitive to the individual effect of a lifestyle intervention; the Personalized Lifestyle Intervention Status (PLIS). We used 1 H-NMR fasting blood metabolite measurements from before and after the 13-week combined physical and nutritional Growing Old TOgether (GOTO) lifestyle intervention study in combination with a fivefold cross-validation and a bootstrapping method to train a separate PLIS score for men and women. The PLIS scores consisted of 14 and four metabolites for females and males, respectively. Performance of the PLIS score in tracking health gain was illustrated by association of the sex-specific PLIS scores with several classical metabolic health markers, such as BMI, trunk fat%, fasting HDL cholesterol, and fasting insulin, the primary outcome of the GOTO study. We also showed that the baseline PLIS score indicated which participants respond positively to the intervention. Finally, we explored PLIS in an independent physical activity lifestyle intervention study, showing similar, albeit remarkably weaker, associations of PLIS with classical metabolic health markers. To conclude, we found that the sex-specific PLIS score was able to track the individual short-term metabolic health gain of the GOTO lifestyle intervention study. The methodology used to train the PLIS score potentially provides a useful instrument to track personal responses and predict the participant's health benefit in lifestyle interventions similar to the GOTO study.

Published
2022

4. Schizophyllum commune has an extensive and functional alternative splicing repertoire

Author

Gehrmann, Thies, Pelkmans, J.F., Lugones, L.G., Wösten, HAB, Abeel, Thomas, Reinders, Marcel J, Molecular Microbiology, and Sub Molecular Microbiology

Subjects
0106 biological sciences, 0301 basic medicine, Genetics, Multidisciplinary, biology, Alternative splicing, Schizophyllum commune, Exonic splicing enhancer, Intron, biology.organism_classification, 01 natural sciences, Exon skipping, Article, 03 medical and health sciences, Exon, 030104 developmental biology, RNA splicing, Gene, 010606 plant biology & botany
Abstract

Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically.

Published
2016

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