1
|
Pacha TO, Mommsen P, Brauckmann V, Aktas G, Krempec M, Wilhelmi B, Clausen JD, März V, Krezdorn N, Vogt PM, Sehmisch S, Hinrichs JB, Ernst J. [Interdisciplinary extremity board in the treatment of complex injuries]. Unfallchirurgie (Heidelb) 2023; 126:175-183. [PMID: 36746799 DOI: 10.1007/s00113-023-01290-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 02/08/2023]
Abstract
BACKGROUND Interdisciplinary case conferences are well-established in the field of oncology in order to provide the best possible treatment for patients with complex disease patterns which overlap several disciplines. METHODS After studying the available literature the aims, indications, frequency, patient enrolment and documentation modalities, disciplines necessary to create the reconstruction plan and evaluation parameters of the board, were agreed in an interdisciplinary discussion among colleagues. The utilization of the extremity board and demographic features of the cases presented in the extremity board within the first 6 months were subsequently descriptively analyzed. RESULTS The agreed primary aim of an extremity board is the timely and transparent preparation of a high-quality holistic reconstruction plan for optimized treatment of a challenging patient collective with complex injuries of the extremities. Decisive interfaces of an extremity board are the participation of interdisciplinary disciplines, established enrolment and documentation modalities and a longitudinal analysis of parameters of the acute medical treatment, the long-term function and quality of life of those affected. The patient collective so far mostly includes men under 40 years old with traumatic soft tissue defects and combined injuries. On average, reconstruction plans for 1-2 patients were approved in an interdisciplinary team per session. CONCLUSION The extremity board serves as a platform for coordinated planning of treatment for patients with complex injuries. The limited personnel and time resources represent the greatest challenge for the successful implementation. The extremity board enables a high degree of interdisciplinary networking. The digital registration and documentation modality within the internal hospital documentation system is of utmost relevance. The preparation of the reconstruction plan is of decisive importance for the qualitative success of treatment and the restoration of function. The longitudinal analysis of appropriate parameters is imperative to measure the quality of treatment.
Collapse
Affiliation(s)
- T Omar Pacha
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland.
| | - P Mommsen
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - V Brauckmann
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - G Aktas
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - M Krempec
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - B Wilhelmi
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - J-D Clausen
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - V März
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - N Krezdorn
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - P M Vogt
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - S Sehmisch
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| | - J B Hinrichs
- Klinik für Diagnostische und Interventionelle Radiologie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - J Ernst
- Klinik für Unfallchirurgie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625, Hannover, Deutschland
| |
Collapse
|
2
|
Fondevilla S, Krezdorn N, Rubiales D, Rotter B, Winter P. Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes. Sci Rep 2022; 12:18159. [PMID: 36307494 PMCID: PMC9616913 DOI: 10.1038/s41598-022-22621-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 12/31/2022] Open
Abstract
Peyronellaea pinodes is a devastating pathogen of pea crop. Quantitative trait loci (QTL) associated with resistance have been identified, as well as genes differentially expressed between resistant and susceptible pea lines. The key question is which of these many genes located into these QTLs, or differentially expressed, are the key genes that distinguish resistant from susceptible plants and could be used as markers. To identify these key genes, in the present study we applied MACE (Massive Analysis of cDNA Ends) -Seq to a whole Recombinant Inbred Line population segregating for resistance to this disease and their parental lines and identified those genes which expression was more correlated with the level of resistance. We also compared gene expression profiles between the most resistant and the most susceptible families of the RIL population. A total of 6780 transcripts were differentially expressed between the parental lines after inoculation. Of them, 803 showed the same expression pattern in the bulks formed by the most resistant and most susceptible RIL families. These genes, showing a consistent expression pattern, could be used as expression markers to distinguish resistant from susceptible plants. The analysis of these genes also discovered the crucial mechanisms acting against P. pinodes.
Collapse
Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain.
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | | | | |
Collapse
|
3
|
Jokuszies A, Martyniak L, Dastagir K, Weyand B, Vogt PM, Krezdorn N. [Reconstruction in polytraumatized burn patients]. Unfallchirurg 2021; 124:817-822. [PMID: 34283263 DOI: 10.1007/s00113-021-01053-z] [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] [Accepted: 06/22/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Polytraumatized burn patients represent a rare patient collective and necessitate an individualized treatment concept due to the particular combination of injuries. OBJECTIVE Against the background of this special injury pattern, especially with deep burns overlying the fracture zone, the question of a specific and interdisciplinary treatment algorithm arises. MATERIAL AND METHODS This article is based on a PubMed database search and experiences of a trauma center for severely injured burn patients at a university hospital, with presentation of the special therapeutic requirements and goals exemplified by a case report. RESULTS The evaluation of the literature search and own treatment results comes to the conclusion that the rate and extent of amputations and infections can be reduced by an early and interdisciplinary involvement of the plastic surgeon by early combined fracture stabilization, excision of necrotic tissue and immediate skin grafting. Furthermore, plastic reconstructive procedures enable a functional and esthetic reconstruction with optimized prosthesis fitting. CONCLUSION Polytraumatized severely burned patients necessitate an interdisciplinary treatment approach, whereby preservation of length, functionality and esthetic appearance of the affected extremities and concurrent avoidance of bone and soft tissue infections have utmost priority.
Collapse
Affiliation(s)
- Andreas Jokuszies
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.
| | - L Martyniak
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - K Dastagir
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - B Weyand
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - P M Vogt
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - N Krezdorn
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Replantationszentrum, Schwerbrandverletztenzentrum, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
| |
Collapse
|
4
|
Mahmood S, Sima R, Urbanova V, Trentelman JJA, Krezdorn N, Winter P, Kopacek P, Hovius JW, Hajdusek O. Identification of Tick Ixodes ricinus Midgut Genes Differentially Expressed During the Transmission of Borrelia afzelii Spirochetes Using a Transcriptomic Approach. Front Immunol 2021; 11:612412. [PMID: 33613535 PMCID: PMC7890033 DOI: 10.3389/fimmu.2020.612412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Lyme borreliosis is an emerging tick-borne disease caused by spirochetes Borrelia burgdorferi sensu lato. In Europe, Lyme borreliosis is predominantly caused by Borrelia afzelii and transmitted by Ixodes ricinus. Although Borrelia behavior throughout tick development is quite well documented, specific molecular interactions between Borrelia and the tick have not been satisfactorily examined. Here, we present the first transcriptomic study focused on the expression of tick midgut genes regulated by Borrelia. By using massive analysis of cDNA ends (MACE), we searched for tick transcripts expressed differentially in the midgut of unfed, 24h-fed, and fully fed I. ricinus nymphs infected with B. afzelii. In total, we identified 553 upregulated and 530 downregulated tick genes and demonstrated that B. afzelii interacts intensively with the tick. Technical and biological validations confirmed the accuracy of the transcriptome. The expression of five validated tick genes was silenced by RNA interference. Silencing of the uncharacterized protein (GXP_Contig_30818) delayed the infection progress and decreased infection prevalence in the target mice tissues. Silencing of other genes did not significantly affect tick feeding nor the transmission of B. afzelii, suggesting a possible role of these genes rather in Borrelia acquisition or persistence in ticks. Identification of genes and proteins exploited by Borrelia during transmission and establishment in a tick could help the development of novel preventive strategies for Lyme borreliosis.
Collapse
Affiliation(s)
- Sazzad Mahmood
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Radek Sima
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Veronika Urbanova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Jos J A Trentelman
- Center for Experimental and Molecular Medicine, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Nicolas Krezdorn
- GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Frankfurt am Main, Germany
| | - Peter Winter
- GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Frankfurt am Main, Germany
| | - Petr Kopacek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Joppe W Hovius
- Center for Experimental and Molecular Medicine, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Ondrej Hajdusek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| |
Collapse
|
5
|
Zhang L, Hofer TP, Zawada AM, Rotter B, Krezdorn N, Noessner E, Devaux Y, Heine G, Ziegler-Heitbrock L. Epigenetics in non-classical monocytes support their pro-inflammatory gene expression. Immunobiology 2020; 225:151958. [PMID: 32517883 DOI: 10.1016/j.imbio.2020.151958] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 01/12/2023]
Abstract
Non-classical human monocytes are characterized by high-level expression of cytokines like TNF, but the mechanisms involved are elusive. We have identified miRNAs and CpG-methylation sites that are unique to non-classical monocytes, defined via CD14 and CD16 expression levels. For down-regulated miRNAs that are linked to up-regulated mRNAs the dominant gene ontology term was intracellular signal transduction. This included down-regulated miRNA-20a-5p and miRNA-106b-5p, which both are linked to increased mRNA for the TRIM8 signaling molecule. Methylation analysis revealed 16 hypo-methylated CpG sites upstream of 14 differentially increased mRNAs including 2 sites upstream of TRIM8. Consistent with a positive role in signal transduction, high TRIM8 levels went along with high basal TNF mRNA levels in non-classical monocytes. Since cytokine expression levels in monocytes strongly increase after stimulation with toll-like-receptor ligands, we have analyzed non-classical monocytes (defined via slan expression) after stimulation with lipopolysaccharide (LPS). LPS-stimulated cells continued to have low miRNA-20a and miRNA-106b and high TRIM8 mRNA levels and they showed a 10-fold increase in TNF mRNA. These data suggest that decreased miRNAs and CpG hypo-methylation is linked to enhanced expression of TRIM8 and that this can contribute to the increased TNF levels in non-classical human monocytes.
Collapse
Affiliation(s)
- Lu Zhang
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Thomas P Hofer
- Immunoanalytics Research Group Tissue Control of Immunocytes, Helmholtz Center Munich, Munich, Germany
| | - Adam M Zawada
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | | | | | - Elfriede Noessner
- Immunoanalytics Research Group Tissue Control of Immunocytes, Helmholtz Center Munich, Munich, Germany
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Gunnar Heine
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | | |
Collapse
|
6
|
Lee BH, Cole S, Badel-Berchoux S, Guillier L, Felix B, Krezdorn N, Hébraud M, Bernardi T, Sultan I, Piveteau P. Biofilm Formation of Listeria monocytogenes Strains Under Food Processing Environments and Pan-Genome-Wide Association Study. Front Microbiol 2019; 10:2698. [PMID: 31824466 PMCID: PMC6882377 DOI: 10.3389/fmicb.2019.02698] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [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: 05/20/2019] [Accepted: 11/06/2019] [Indexed: 01/24/2023] Open
Abstract
Concerns about food contamination by Listeria monocytogenes are on the rise with increasing consumption of ready-to-eat foods. Biofilm production of L. monocytogenes is presumed to be one of the ways that confer its increased resistance and persistence in the food chain. In this study, a collection of isolates from foods and food processing environments (FPEs) representing persistent, prevalent, and rarely detected genotypes was evaluated for biofilm forming capacities including adhesion and sessile biomass production under diverse environmental conditions. The quantity of sessile biomass varied according to growth conditions, lineage, serotype as well as genotype but association of clonal complex (CC) 26 genotype with biofilm production was evidenced under cold temperature. In general, relative biofilm productivity of each strain varied inconsistently across growth conditions. Under our experimental conditions, there were no clear associations between biofilm formation efficiency and persistent or prevalent genotypes. Distinct extrinsic factors affected specific steps of biofilm formation. Sudden nutrient deprivation enhanced cellular adhesion while a prolonged nutrient deficiency impeded biofilm maturation. Salt addition increased biofilm production, moreover, nutrient limitation supplemented by salt significantly stimulated biofilm formation. Pan-genome-wide association study (Pan-GWAS) assessed genetic composition with regard to biofilm phenotypes for the first time. The number of reported genes differed depending on the growth conditions and the number of common genes was low. However, a broad overview of the ontology contents revealed similar patterns regardless of the conditions. Functional analysis showed that functions related to transformation/competence and surface proteins including Internalins were highly enriched.
Collapse
Affiliation(s)
- Bo-Hyung Lee
- École Doctorale des Sciences de la Vie, Santé, Agronomie, Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
- GenXPro GmbH, Frankfurt am Main, Germany
| | - Sophie Cole
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
| | | | - Laurent Guillier
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Benjamin Felix
- Maisons-Alfort Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | | | - Michel Hébraud
- UMR MEDiS, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thierry Bernardi
- BioFilm Control SAS, Biopôle Clermont Limagne, Saint-Beauzire, France
| | - Ibrahim Sultan
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| |
Collapse
|
7
|
Braun EM, Tsvetkova N, Rotter B, Siekmann D, Schwefel K, Krezdorn N, Plieske J, Winter P, Melz G, Voylokov AV, Hackauf B. Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye ( Secale cereale L.). Front Plant Sci 2019; 10:857. [PMID: 31333700 PMCID: PMC6616298 DOI: 10.3389/fpls.2019.00857] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/14/2019] [Indexed: 06/03/2023]
Abstract
The gibberellin (GA)-sensitive dwarfing gene Ddw1 provides an opportunity to genetically reduce plant height in rye. Genetic analysis in a population of recombinant inbred lines confirmed a monogenetic dominant inheritance of Ddw1. Significant phenotypic differences in PH between homo- and heterozygotic genotypes indicate an incomplete dominance of Ddw1. De novo transcriptome sequencing of Ddw1 mutant as well as tall genotypes resulted in 113,547 contigs with an average length of 318 bp covering 36.18 Mbp rye DNA. A hierarchical cluster analysis based on individual groups of rye homologs of functionally characterized rice genes controlling morphological or physiological traits including plant height, flowering time, and source activity identified the gene expression profile of stems at the begin of heading to most comprehensively mirror effects of Ddw1. Genome-wide expression profiling identified 186 transcripts differentially expressed between semi-dwarf and tall genotypes in stems. In total, 29 novel markers have been established and mapped to a 27.2 cM segment in the distal part of the long arm of chromosome 5R. Ddw1 could be mapped within a 0.4 cM interval co-segregating with a marker representing the C20-GA2-oxidase gene ScGA2ox12, that is up-regulated in stems of Ddw1 genotypes. The increased expression of ScGA2ox12 observed in semi-dwarf rye as well as structural alterations in transcript sequences associated with the ScGA2ox12 gene implicate, that Ddw1 is a dominant gain-of-function mutant. Integration of the target interval in the wheat reference genome sequence indicated perfect micro-colinearity between the Ddw1 locus and a 831 kb segment on chromosome 5A, which resides inside of a 11.21 Mb interval carrying the GA-sensitive dwarfing gene Rht12 in wheat. The potential of Ddw1 as a breeder's option to improve lodging tolerance in rye is discussed.
Collapse
Affiliation(s)
- Eva-Maria Braun
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| | - Natalia Tsvetkova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Dörthe Siekmann
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Konrad Schwefel
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| | | | | | | | | | - Anatoly V. Voylokov
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Bernd Hackauf
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Quedlinburg, Germany
| |
Collapse
|
8
|
Haslinger D, Waltes R, Yousaf A, Lindlar S, Schneider I, Lim CK, Tsai MM, Garvalov BK, Acker-Palmer A, Krezdorn N, Rotter B, Acker T, Guillemin GJ, Fulda S, Freitag CM, Chiocchetti AG. Loss of the Chr16p11.2 ASD candidate gene QPRT leads to aberrant neuronal differentiation in the SH-SY5Y neuronal cell model. Mol Autism 2018; 9:56. [PMID: 30443311 PMCID: PMC6220561 DOI: 10.1186/s13229-018-0239-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 05/02/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Background Altered neuronal development is discussed as the underlying pathogenic mechanism of autism spectrum disorders (ASD). Copy number variations of 16p11.2 have recurrently been identified in individuals with ASD. Of the 29 genes within this region, quinolinate phosphoribosyltransferase (QPRT) showed the strongest regulation during neuronal differentiation of SH-SY5Y neuroblastoma cells. We hypothesized a causal relation between this tryptophan metabolism-related enzyme and neuronal differentiation. We thus analyzed the effect of QPRT on the differentiation of SH-SY5Y and specifically focused on neuronal morphology, metabolites of the tryptophan pathway, and the neurodevelopmental transcriptome. Methods The gene dosage-dependent change of QPRT expression following Chr16p11.2 deletion was investigated in a lymphoblastoid cell line (LCL) of a deletion carrier and compared to his non-carrier parents. Expression of QPRT was tested for correlation with neuromorphology in SH-SY5Y cells. QPRT function was inhibited in SH-SY5Y neuroblastoma cells using (i) siRNA knockdown (KD), (ii) chemical mimicking of loss of QPRT, and (iii) complete CRISPR/Cas9-mediated knock out (KO). QPRT-KD cells underwent morphological analysis. Chemically inhibited and QPRT-KO cells were characterized using viability assays. Additionally, QPRT-KO cells underwent metabolite and whole transcriptome analyses. Genes differentially expressed upon KO of QPRT were tested for enrichment in biological processes and co-regulated gene-networks of the human brain. Results QPRT expression was reduced in the LCL of the deletion carrier and significantly correlated with the neuritic complexity of SH-SY5Y. The reduction of QPRT altered neuronal morphology of differentiated SH-SY5Y cells. Chemical inhibition as well as complete KO of the gene were lethal upon induction of neuronal differentiation, but not proliferation. The QPRT-associated tryptophan pathway was not affected by KO. At the transcriptome level, genes linked to neurodevelopmental processes and synaptic structures were affected. Differentially regulated genes were enriched for ASD candidates, and co-regulated gene networks were implicated in the development of the dorsolateral prefrontal cortex, the hippocampus, and the amygdala. Conclusions In this study, QPRT was causally related to in vitro neuronal differentiation of SH-SY5Y cells and affected the regulation of genes and gene networks previously implicated in ASD. Thus, our data suggest that QPRT may play an important role in the pathogenesis of ASD in Chr16p11.2 deletion carriers.
Collapse
Affiliation(s)
- Denise Haslinger
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Regina Waltes
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Afsheen Yousaf
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Silvia Lindlar
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ines Schneider
- Institute of Experimental Cancer Research in Pediatrics, Frankfurt am Main, Germany
| | - Chai K Lim
- 3Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales Australia
| | - Meng-Miao Tsai
- 4Neuropathology, University of Giessen, Giessen, Germany
| | - Boyan K Garvalov
- 4Neuropathology, University of Giessen, Giessen, Germany.,5Department of Microvascular Biology and Pathobiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Amparo Acker-Palmer
- 6Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences (BMLS), JW Goethe University of Frankfurt, Frankfurt am Main, Germany
| | | | | | - Till Acker
- 4Neuropathology, University of Giessen, Giessen, Germany
| | - Gilles J Guillemin
- 3Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales Australia
| | - Simone Fulda
- Institute of Experimental Cancer Research in Pediatrics, Frankfurt am Main, Germany
| | - Christine M Freitag
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- 1Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
9
|
Barth MB, Buchwalder K, Kawahara AY, Zhou X, Liu S, Krezdorn N, Rotter B, Horres R, Hundsdoerfer AK. Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes. Front Zool 2018; 15:20. [PMID: 29743927 PMCID: PMC5930835 DOI: 10.1186/s12983-018-0252-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
Background The European spurge hawkmoth, Hyles euphorbiae (Lepidoptera, Sphingidae), has been intensively studied as a model organism for insect chemical ecology, cold hardiness and evolution of species delineation. To understand species isolation mechanisms at a molecular level, this study aims at determining genetic factors underlying two adaptive ecological trait candidates, phorbol ester (TPA) detoxification and seasonal cold acclimation. Method A draft transcriptome of H. euphorbiae was generated using Illumina sequencing, providing the first genomic resource for the hawkmoth subfamily Macroglossinae. RNA expression levels in tissues of experimental TPA feeding larvae and cooled pupae was compared to levels in control larvae and pupae using 26 bp RNA sequence tag libraries (DeepSuperSAGE). Differential gene expression was assessed by homology searches of the tags in the transcriptome. Results In total, 389 and 605 differentially expressed transcripts for detoxification and cold hardiness, respectively, could be identified and annotated with proteins. The majority (22 of 28) of differentially expressed detox transcripts of the four 'drug metabolism' enzyme groups (cytochrome P450 (CYP), carboxylesterases (CES), glutathione S-transferases (GST) and lipases) are up-regulated. Triacylglycerol lipase was significantly over proportionally annotated among up-regulated detox transcripts. We record several up-regulated lipases, GSTe2, two CESs, CYP9A21, CYP6BD6 and CYP9A17 as candidate genes for further H. euphorbiae TPA detoxification analyses. Differential gene expression of the cold acclimation treatment is marked by metabolic depression with enriched Gene Ontology terms among down-regulated transcripts almost exclusively comprising metabolism, aerobic respiration and dissimilative functions. Down-regulated transcripts include energy expensive respiratory proteins like NADH dehydrogenase, cytochrome oxidase and ATP synthase. Gene expression patterns show shifts in carbohydrate metabolism towards cryoprotectant production. The Glycolysis enzymes, G1Pase, A1e, Gpi and an Akr isoform are up-regulated. Glycerol, an osmolyte which lowers the body liquid supercooling point, appears to be the predominant polyol cryoprotectant in H. euphorbiae diapause pupae. Several protein candidates involved in glucose, glycerol, myo-inositol and potentially sorbitol and trehalose synthesis were identified. Conclusions A majority of differently expressed transcripts unique for either detoxification or cold hardiness indicates highly specialized functional adaptation which may have evolved from general cell metabolism and stress response.The transcriptome and extracted candidate biomarkers provide a basis for further gene expression studies of physiological processes and adaptive traits in H. euphorbiae.
Collapse
Affiliation(s)
- M Benjamin Barth
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| | - Katja Buchwalder
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| | - Akito Y Kawahara
- 2Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Xin Zhou
- 3Department of Entomology, China Agricultural University, Bejing, 100193 China
| | - Shanlin Liu
- 3Department of Entomology, China Agricultural University, Bejing, 100193 China.,4China National Gene Bank, Beijing Genomics Institute, Shenzhen, 518083 China
| | - Nicolas Krezdorn
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Björn Rotter
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Ralf Horres
- 5GenXPro GmbH, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Anna K Hundsdoerfer
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Koenigsbruecker Landstrasse 159, D-01109 Dresden, Germany
| |
Collapse
|
10
|
Santos C, Almeida NF, Alves ML, Horres R, Krezdorn N, Leitão ST, Aznar-Fernández T, Rotter B, Winter P, Rubiales D, Vaz Patto MC. First genetic linkage map of Lathyrus cicera based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance. Hortic Res 2018; 5:45. [PMID: 30181885 PMCID: PMC6119197 DOI: 10.1038/s41438-018-0047-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/05/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
The Lathyrus cicera transcriptome was analysed in response to rust (Uromyces pisi) infection to develop novel molecular breeding tools with potential for genetic mapping of resistance in this robust orphan legume species. One RNA-seq library each was generated from control and rust-inoculated leaves from two L. cicera genotypes with contrasting quantitative resistance, de novo assembled into contigs and sequence polymorphisms were identified. In toto, 19,224 SNPs differentiate the susceptible from the partially resistant genotype's transcriptome. In addition, we developed and tested 341 expressed E-SSR markers from the contigs, of which 60.7% varied between the two L. cicera genotypes. A first L. cicera linkage map was created using part of the developed markers in a RIL population from the cross of the two genotypes. This map contains 307 markers, covered 724.2 cM and is organised in 7 major and 2 minor linkage groups, with an average mapping interval of 2.4 cM. The genic markers also enabled us to compare their position in L. cicera map with the physical position of the same markers mapped on Medicago truncatula genome, highlighting a high macrosyntenic conservation between both species. This study provides a large new set of genic polymorphic molecular markers with potential for mapping rust resistances. It represents the first step towards genomics-assisted precision breeding in L. cicera.
Collapse
Affiliation(s)
- Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | - Nuno Felipe Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | - Mara Lisa Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | - Ralf Horres
- GenXPro GmbH, Frankfurt am Main, D-60438 Germany
| | | | - Susana Trindade Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| | | | - Björn Rotter
- GenXPro GmbH, Frankfurt am Main, D-60438 Germany
| | - Peter Winter
- GenXPro GmbH, Frankfurt am Main, D-60438 Germany
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004 Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157 Portugal
| |
Collapse
|
11
|
Krezdorn N, Pomahac B. Chronic Allograft Deterioration: A Clinical Reality in Vascularized Composite Allotransplantation. Am J Transplant 2017; 17:1703-1704. [PMID: 28371193 DOI: 10.1111/ajt.14291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/02/2017] [Accepted: 03/18/2017] [Indexed: 01/25/2023]
Affiliation(s)
- N Krezdorn
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA.,Plastic, Aesthetic, Hand and Reconstructive Surgery, Hannover Medical School, Hannover, Germany
| | - B Pomahac
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA
| |
Collapse
|
12
|
Barrios A, Caminero C, García P, Krezdorn N, Hoffmeier K, Winter P, Pérez de la Vega M. Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.). BMC Plant Biol 2017; 17:111. [PMID: 28666411 PMCID: PMC5493078 DOI: 10.1186/s12870-017-1057-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/14/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation. RESULTS To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between -3 to -15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the acclimated tolerant lines. CONCLUSIONS This set of candidate genes implicated in the response to frost in lentil represents an useful base for deeper and more detailed investigations into this important agronomic trait in future.
Collapse
Affiliation(s)
- Abel Barrios
- Instituto Tecnológico Agrario de Castilla y León, Consejería de Agricultura y Ganadería, Junta de Castilla y León, Finca Zamadueñas, Ctra. Burgos km, 119, 47071 Valladolid, Spain
- Present Address: Escuela Universitaria de Ingeniería Agrícola I.N.E.A, Con. Viejo de Simancas, Km. 4.5, 47008 Valladolid, Spain
| | - Constantino Caminero
- Instituto Tecnológico Agrario de Castilla y León, Consejería de Agricultura y Ganadería, Junta de Castilla y León, Finca Zamadueñas, Ctra. Burgos km, 119, 47071 Valladolid, Spain
| | - Pedro García
- Area de Genética, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
| | | | - Klaus Hoffmeier
- GenXPro, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | - Peter Winter
- GenXPro, Altenhöferallee 3, D-60438 Frankfurt am Main, Germany
| | | |
Collapse
|
13
|
Zawada AM, Zhang L, Emrich IE, Rogacev KS, Krezdorn N, Rotter B, Fliser D, Devaux Y, Ziegler-Heitbrock L, Heine GH. Reprint of: MicroRNA profiling of human intermediate monocytes. Immunobiology 2017; 222:831-840. [PMID: 28578934 DOI: 10.1016/j.imbio.2017.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 04/29/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 01/23/2023]
Abstract
Among the three human monocyte subsets, intermediate CD14++CD16+ monocytes have been characterized as particularly proinflammatory cells in experimental studies and as potential biomarkers of cardiovascular risk in clinical cohorts. To further substantiate the distinct role of intermediate monocytes within human monocyte heterogeneity, we assessed subset-specific expression of miRNAs as central epigenetic regulators of gene expression. We hypothesized that intermediate monocytes have a distinct miRNA profile compared to classical and non-classical monocytes. By using small RNA-seq we analyzed 662 miRNAs in the three monocyte subsets. We identified 38 miRNAs that are differentially expressed in intermediate monocytes compared to both classical and non-classical monocytes with a p value of <10-10, of which two miRNAs - miR-6087 (upregulated) and miR-150-5p (downregulated) - differed in their expression more than ten-fold. Pathway analysis of the 38 differentially expressed miRNAs linked intermediate monocytes to distinct biological processes such as gene regulation, cell differentiation, toll-like receptor signaling as well as antigen processing and presentation. Moreover, differentially expressed miRNAs were connected to those genes that we previously identified as markers of intermediate monocytes. In aggregation, we provide first genome-wide miRNA data in the context of monocyte heterogeneity, which substantiate the concept of monocyte trichotomy in human immunity. The identification of miRNAs that are specific for intermediate monocytes may allow to develop strategies, which particularly target this cell population while sparing the other two subsets.
Collapse
Affiliation(s)
- Adam M Zawada
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Lu Zhang
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Insa E Emrich
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Kyrill S Rogacev
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany; University Heart Center Luebeck, Medical Clinic II (Cardiology/Angiology/Intensive Care Medicine), University Hospital Schleswig-Holstein, Luebeck, Germany
| | | | | | - Danilo Fliser
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Loems Ziegler-Heitbrock
- EvA Study Center, Comprehensive Pneumology Center Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Gauting, Germany
| | - Gunnar H Heine
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany.
| |
Collapse
|
14
|
Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P. A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea ( Pisum sp.). Front Plant Sci 2017; 8:542. [PMID: 28487704 PMCID: PMC5404241 DOI: 10.3389/fpls.2017.00542] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.
Collapse
Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
| | - Oldřich Trněný
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
- Agricultural Research, Ltd.Troubsko, Czechia
| | - Markéta Válková
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Monika Cechová
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Anna Janská
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Lenka Prokešová
- Department of Crop Science, Breeding and Plant Medicine, Mendel University in BrnoBrno, Czechia
| | - Khan Aamir
- Research Program-Genetic Gains, ICRISATHyderabad, India
| | | | | | | | | | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czechia
| | - Petr Bednář
- Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University in OlomoucOlomouc, Czechia
- Faculty of Science, Palacký University in OlomoucOlomouc, Czechia
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in BrnoBrno, Czechia
| | - Petr Smýkal
- Department of Botany, Palacký University in OlomoucOlomouc, Czechia
- *Correspondence: Petr Smýkal
| |
Collapse
|
15
|
Zawada AM, Zhang L, Emrich IE, Rogacev KS, Krezdorn N, Rotter B, Fliser D, Devaux Y, Ziegler-Heitbrock L, Heine GH. MicroRNA profiling of human intermediate monocytes. Immunobiology 2016; 222:587-596. [PMID: 27876379 DOI: 10.1016/j.imbio.2016.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 01/09/2023]
Abstract
Among the three human monocyte subsets, intermediate CD14++CD16+ monocytes have been characterized as particularly proinflammatory cells in experimental studies and as potential biomarkers of cardiovascular risk in clinical cohorts. To further substantiate the distinct role of intermediate monocytes within human monocyte heterogeneity, we assessed subset-specific expression of miRNAs as central epigenetic regulators of gene expression. We hypothesized that intermediate monocytes have a distinct miRNA profile compared to classical and non-classical monocytes. By using small RNA-seq we analyzed 662 miRNAs in the three monocyte subsets. We identified 38 miRNAs that are differentially expressed in intermediate monocytes compared to both classical and non-classical monocytes with a p value of <10-10, of which two miRNAs - miR-6087 (upregulated) and miR-150-5p (downregulated) - differed in their expression more than ten-fold. Pathway analysis of the 38 differentially expressed miRNAs linked intermediate monocytes to distinct biological processes such as gene regulation, cell differentiation, toll-like receptor signaling as well as antigen processing and presentation. Moreover, differentially expressed miRNAs were connected to those genes that we previously identified as markers of intermediate monocytes. In aggregation, we provide first genome-wide miRNA data in the context of monocyte heterogeneity, which substantiate the concept of monocyte trichotomy in human immunity. The identification of miRNAs that are specific for intermediate monocytes may allow to develop strategies, which particularly target this cell population while sparing the other two subsets.
Collapse
Affiliation(s)
- Adam M Zawada
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Lu Zhang
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Insa E Emrich
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Kyrill S Rogacev
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany; University Heart Center Luebeck, Medical Clinic II (Cardiology/Angiology/Intensive Care Medicine), University Hospital Schleswig-Holstein, Luebeck, Germany
| | | | | | - Danilo Fliser
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Loems Ziegler-Heitbrock
- EvA Study Center, Comprehensive Pneumology Center Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Gauting, Germany
| | - Gunnar H Heine
- Department of Internal Medicine IV, Saarland University Medical Center, Homburg, Germany.
| |
Collapse
|
16
|
Bojahr J, Nhengiwa O, Krezdorn N, Rotter B, Saal B, Ruge-Wehling B, Struck C, Winter P. Massive analysis of cDNA ends (MACE) reveals a co-segregating candidate gene for LpPg1 stem rust resistance in perennial ryegrass (Lolium perenne). Theor Appl Genet 2016; 129:1915-1932. [PMID: 27435735 DOI: 10.1007/s00122-016-2749-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/25/2016] [Indexed: 06/06/2023]
Abstract
Molecular markers including a potential resistance gene co-segregating with the LpPg1 stem rust resistance locus in perennial ryegrass were identified by massive analysis of cDNA ends (MACE) transcriptome profiling. Stem rust caused by Puccinia graminis subsp. graminicola is a severe fungal disease in the forage crop perennial ryegrass and other grasses. The previously identified LpPg1 locus confers efficient resistance against the pathogen. The aim of this study was to identify candidate genes involved in rust resistance and to use them as a resource for the development of molecular markers for LpPg1. To identify such candidates, bulked segregant analysis was combined with NGS-based massive analysis of cDNA ends (MACE) transcriptome profiling. Total RNA was isolated from bulks of infected and non-infected leaf segments from susceptible and resistant genotypes of a full-sibling mapping population and their respective parental lines and MACE was performed. Bioinformatic analysis detected 330 resistance-specific SNPs in 178 transcripts and 341 transcripts that were exclusively expressed in the resistant bulk. The sequences of many of these transcripts were homologous to genes in distinct regions of chromosomes one and four of the model grass Brachypodium distachyon. Of these, 30 were genetically mapped to a 50.8 cM spanning region surrounding the LpPg1 locus. One candidate NBS-LRR gene co-segregated with the resistance locus. Quantitative analysis of gene expression suggests that LpPg1 mediates an efficient resistance mechanism characterized by early recognition of the pathogen, fast defense signaling and rapid induction of antifungal proteins. We demonstrate here that MACE is a cost-efficient, fast and reliable tool that detects polymorphisms for genetic mapping of candidate resistance genes and simultaneously reveals deep insight into the molecular and genetic base of resistance.
Collapse
Affiliation(s)
- Jens Bojahr
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059, Rostock, Germany.
| | - Ottilia Nhengiwa
- Saatzucht Steinach GmbH & Co KG, Wittelsbacherstrasse 15, 94377, Steinach, Germany
| | - Nicolas Krezdorn
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Bernhard Saal
- Saatzucht Steinach GmbH & Co KG, Wittelsbacherstrasse 15, 94377, Steinach, Germany
| | - Brigitte Ruge-Wehling
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
| | - Christine Struck
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059, Rostock, Germany
| | - Peter Winter
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| |
Collapse
|
17
|
Könneker S, Krezdorn N, Vogt PM, Altintas MA, Hiller MT, Ipaktchi R, Radtke C. [Pest control in your garden - a case series of severe hand injuries caused by privately used explosives and shot traps]. Unfallchirurg 2016; 119:854-8. [PMID: 27444998 DOI: 10.1007/s00113-016-0212-2] [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] [Indexed: 11/30/2022]
Abstract
Booby traps and gun-like devices for vole control can lead to complex trauma requiring emergency medical care. We present a case series of patients who suffered severe hand and facial trauma through detonation of booby traps and paraphernalia (n = 9, Ø 60 years of age). All patients were admitted to the emergency department of Hannover Medical School for primary care. Between 2011 and 2015 we treated six patients with hand trauma due to gun-like devices, two patients with hand trauma due to booby traps, and one patient with injury to the face including eyes due to a gas cartridge explosion. All hand trauma patients (n = 8) showed injuries of the soft tissue. Six of these patients also presented fractures or lesions of capsular or tendon structures. Therapies included debridement as well as skin grafts or flaps for tissue defect coverage. We informed the Department for Commercial Safety (Gewerbeaufsicht Hannover) in 2014 because we believe that these traps pose a serious safety hazard.
Collapse
Affiliation(s)
- S Könneker
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland.
| | - N Krezdorn
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - P M Vogt
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - M A Altintas
- Klinik für Plastische und Ästhetische Chirurgie/Handchirurgie, Bergmannsheil und Kinderklinik Buer GmbH, Schernerweg 4, 45894, Gelsenkirchen, Deutschland
| | - M T Hiller
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - R Ipaktchi
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland
| | - C Radtke
- Klinik für Plastische, Ästhetische, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl- Neuberg-Str. 1, 30625, Hannover, Deutschland
| |
Collapse
|
18
|
Krezdorn N, Ipaktchi R, Vogt P. Injured fingertip remodeling through percutaneous collagen induction. Journal of Dermatology & Dermatologic Surgery 2016. [DOI: 10.1016/j.jdds.2016.02.004] [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: 10/22/2022] Open
|
19
|
Win T, Teague J, Lowry E, Kiwanuka H, Krezdorn N, Hamm D, Bueno E, Pomahac B, Clark R. 236 The role of skin resident donor T cells in face transplant rejection. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.02.265] [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: 11/17/2022]
|
20
|
Paprottka F, Krezdorn N, Young K, Ipaktchi R, Hebebrand D, Vogt P. German, European or American burn guidelines - Is one superior to another? Ann Burns Fire Disasters 2016; 29:30-36. [PMID: 27857648 PMCID: PMC5108224] [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] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/17/2015] [Indexed: 06/06/2023]
Abstract
Adequate medical care of severe burn injuries requires special organizational infrastructure and high educational standards, with an appropriate number of health care professionals. Guidelines were written by the German Society for Burn Treatment (DGV), the European Burns Association (EBA) and the American Burn Association (ABA) to assist with the delivery of such care. Current DGV (2010), EBA (2013) and ABA (2001/2006/2008) guidelines are compared, focusing on similarities, differences, conciseness and completeness. This publication presents advantages and disadvantages of each of them. DGV guidelines outline understandable treatment recommendations for first aid measures, clinical procedures and wound care. Extensive rehabilitation guidelines with clearly defined indications and precise infrastructure requirements for a Burn Centre are stated. Negative aspects are the presence of multiple documents containing redundant and confusing information. EBA guidelines offer the most comprehensive treatment recommendations with multidisciplinary approaches. Overall, infrastructural requirements are weighted much higher than staff qualification demands - in contrast to ABA guidelines. However, lack of conciseness and complicated criteria regarding transfer of patients to a Burn Center - including imprecise indications for rehabilitation treatment - have to be mentioned as disadvantages. ABA guidelines have a clear focus on staff qualifications and easy-to-understand transfer criteria. Another focus is on detailed clinical procedures. However, these guidelines lack burn definition and precise treatment recommendations for rehabilitation. The reviewed guidelines provide standardized treatment recommendations for burn patients. Despite their usefulness, they all have weaknesses and discrepancies. Findings should be used to improve each of them.
Collapse
Affiliation(s)
- F.J. Paprottka
- Department of Plastic and Reconstructive Surgery, Hand Surgery, Agaplesion Diakonieklinikum Rotenburg, Germany
| | - N. Krezdorn
- Department of Plastic and Reconstructive Surgery, Hand Surgery, Burn Center, Medizinische Hochschule Hannover, Germany
| | - K. Young
- Department of Hand and Plastic Surgery, Queen Elizabeth Hospital, Edgbaston, Birmingham, United Kingdom
| | - R. Ipaktchi
- Department of Plastic and Reconstructive Surgery, Hand Surgery, Burn Center, Medizinische Hochschule Hannover, Germany
| | - D. Hebebrand
- Department of Plastic and Reconstructive Surgery, Hand Surgery, Agaplesion Diakonieklinikum Rotenburg, Germany
| | - P.M. Vogt
- Department of Plastic and Reconstructive Surgery, Hand Surgery, Burn Center, Medizinische Hochschule Hannover, Germany
| |
Collapse
|
21
|
Zawada AM, Schneider JS, Michel AI, Rogacev KS, Hummel B, Krezdorn N, Müller S, Rotter B, Winter P, Obeid R, Geisel J, Fliser D, Heine GH. DNA methylation profiling reveals differences in the 3 human monocyte subsets and identifies uremia to induce DNA methylation changes during differentiation. Epigenetics 2016; 11:259-72. [PMID: 27018948 DOI: 10.1080/15592294.2016.1158363] [Citation(s) in RCA: 22] [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] [Indexed: 10/22/2022] Open
Abstract
Human monocytes are a heterogeneous cell population consisting of 3 subsets: classical CD14++CD16-, intermediate CD14++CD16+ and nonclassical CD14+CD16++ monocytes. Via poorly characterized mechanisms, intermediate monocyte counts rise in chronic inflammatory diseases, among which chronic kidney disease is of particular epidemiologic importance. DNA methylation is a central epigenetic feature that controls hematopoiesis. By applying next-generation Methyl-Sequencing we now tested how far the 3 monocyte subsets differ in their DNA methylome and whether uremia induces DNA methylation changes in differentiating monocytes. We found that each monocyte subset displays a unique phenotype with regards to DNA methylation. Genes with differentially methylated promoter regions in intermediate monocytes were linked to distinct immunological processes, which is in line with results from recent gene expression analyses. In vitro, uremia induced dysregulation of DNA methylation in differentiating monocytes, which affected several transcription regulators important for monocyte differentiation (e.g., FLT3, HDAC1, MNT) and led to enhanced generation of intermediate monocytes. As potential mediator, the uremic toxin and methylation inhibitor S-adenosylhomocysteine induced shifts in monocyte subsets in vitro, and associated with monocyte subset counts in vivo. Our data support the concept of monocyte trichotomy and the distinct role of intermediate monocytes in human immunity. The shift in monocyte subsets that occurs in chronic kidney disease, a proinflammatory condition of substantial epidemiological impact, may be induced by accumulation of uremic toxins that mediate epigenetic dysregulation.
Collapse
Affiliation(s)
- Adam M Zawada
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany
| | - Jenny S Schneider
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany
| | - Anne I Michel
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany
| | - Kyrill S Rogacev
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany.,b University Heart Center Luebeck, Medical Clinic II (Cardiology/Angiology/Intensive Care Medicine), University Hospital Schleswig-Holstein , Luebeck , Germany
| | - Björn Hummel
- c Department of Clinical Hemostaseology and Transfusion Medicine , Saarland University Medical Center , Homburg , Germany.,d Clinical Chemistry and Laboratory Medicine/Central Laboratory, Saarland University Medical Center , Homburg , Germany
| | | | - Soeren Müller
- e GenXPro GmbH , Frankfurt/Main , Germany.,f Department of Neurological Surgery , University of California, San Francisco , San Francisco , CA , USA
| | | | | | - Rima Obeid
- d Clinical Chemistry and Laboratory Medicine/Central Laboratory, Saarland University Medical Center , Homburg , Germany
| | - Jürgen Geisel
- d Clinical Chemistry and Laboratory Medicine/Central Laboratory, Saarland University Medical Center , Homburg , Germany
| | - Danilo Fliser
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany
| | - Gunnar H Heine
- a Department of Internal Medicine IV , Saarland University Medical Center , Homburg , Germany
| |
Collapse
|
22
|
Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P. In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends. Front Microbiol 2015; 6:1329. [PMID: 26648917 PMCID: PMC4664620 DOI: 10.3389/fmicb.2015.01329] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 09/10/2015] [Accepted: 11/12/2015] [Indexed: 11/21/2022] Open
Abstract
The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.
Collapse
Affiliation(s)
- Sara Fondevilla
- Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of FrankfurtFrankfurt am Main, Germany
| | | | | | - Guenter Kahl
- Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of FrankfurtFrankfurt am Main, Germany
| | | |
Collapse
|
23
|
Fischer K, Dieterich R, Nelson MN, Kamphuis LG, Singh KB, Rotter B, Krezdorn N, Winter P, Wehling P, Ruge-Wehling B. Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 2015; 128:2121-30. [PMID: 26169875 DOI: 10.1007/s00122-015-2572-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/23/2015] [Indexed: 05/15/2023]
Abstract
A novel and highly effective source of anthracnose resistance in narrow-leafed lupin was identified. Resistance was shown to be governed by a single dominant locus. Molecular markers have been developed, which can be used for selecting resistant genotypes in lupin breeding. A screening for anthracnose resistance of a set of plant genetic resources of narrow-leafed lupin (Lupinus angustifolius L.) identified the breeding line Bo7212 as being highly resistant to anthracnose (Colletotrichum lupini). Segregation analysis indicated that the resistance of Bo7212 is inherited by a single dominant locus. The corresponding resistance gene was given the designation LanrBo. Previously published molecular anchor markers allowed us to locate LanrBo on linkage group NLL-11 of narrow-leafed lupin. Using information from RNAseq data obtained with inoculated resistant vs. susceptible lupin entries as well as EST-sequence information from the model genome Lotus japonicus, additional SNP and EST markers linked to LanrBo were derived. A bracket of two LanrBo-flanking markers allows for precise marker-assisted selection of the novel resistance gene in narrow-leafed lupin breeding programs.
Collapse
Affiliation(s)
- Kristin Fischer
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany.
| | | | - Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Lars G Kamphuis
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- CSIRO, Agriculture Flagship, Wembley, Australia
| | - Karam B Singh
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- CSIRO, Agriculture Flagship, Wembley, Australia
| | | | | | | | - Peter Wehling
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany
| | - Brigitte Ruge-Wehling
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany
| |
Collapse
|
24
|
Bokszczanin KL, Krezdorn N, Fragkostefanakis S, Müller S, Rycak L, Chen Y, Hoffmeier K, Kreutz J, Paupière MJ, Chaturvedi P, Iannacone R, Müller F, Bostan H, Chiusano ML, Scharf KD, Rotter B, Schleiff E, Winter P. Identification of novel small ncRNAs in pollen of tomato. BMC Genomics 2015; 16:714. [PMID: 26385469 PMCID: PMC4575465 DOI: 10.1186/s12864-015-1901-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 02/16/2015] [Accepted: 09/09/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The unprecedented role of sncRNAs in the regulation of pollen biogenesis on both transcriptional and epigenetic levels has been experimentally proven. However, little is known about their global regulation, especially under stress conditions. We used tomato pollen in order to identify pollen stage-specific sncRNAs and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing as well as Massive Analysis of cDNA Ends (MACE) were performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions. RESULTS Using the omiRas analysis pipeline we identified known and predicted novel miRNAs as well as sncRNAs from other classes, responsive or not to heat. Differential expression analysis revealed that post-meiotic and mature pollen react most strongly by regulation of the expression of coding and non-coding genomic regions in response to heat. To gain insight to the function of these miRNAs, we predicted targets and annotated them to Gene Ontology terms. This approach revealed that most of them belong to protein binding, transcription, and Serine/Threonine kinase activity GO categories. Beside miRNAs, we observed differential expression of both tRNAs and snoRNAs in tetrad, post-meiotic, and mature pollen when comparing normal and heat stress conditions. CONCLUSIONS Thus, we describe a global spectrum of sncRNAs expressed in pollen as well as unveiled those which are regulated at specific time-points during pollen biogenesis. We integrated the small RNAs into the regulatory network of tomato heat stress response in pollen.
Collapse
Affiliation(s)
| | | | - Sotirios Fragkostefanakis
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | | | | | | | | | - Marine J Paupière
- Department of Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Palak Chaturvedi
- Department for Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Rina Iannacone
- ALSIA Research Center Metapontum Agrobios Metaponto (MT), Metaponto, Italy
| | - Florian Müller
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Klaus-Dieter Scharf
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Enrico Schleiff
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | | |
Collapse
|
25
|
Almeida NF, Krezdorn N, Rotter B, Winter P, Rubiales D, Vaz Patto MC. Lathyrus sativus transcriptome resistance response to Ascochyta lathyri investigated by deepSuperSAGE analysis. Front Plant Sci 2015; 6:178. [PMID: 25852725 PMCID: PMC4367168 DOI: 10.3389/fpls.2015.00178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/05/2015] [Indexed: 05/07/2023]
Abstract
Lathyrus sativus (grass pea) is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. It is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. Nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. To elucidate the pathways differentially regulated during ascochyta-grass pea interaction and to identify resistance candidate genes, we compared the early response of the leaf gene expression profile of a resistant L. sativus genotype to Ascochyta lathyri infection with a non-inoculated control sample from the same genotype employing deepSuperSAGE. This analysis generated 14.387 UniTags of which 95.7% mapped to a reference grass pea/rust interaction transcriptome. From the total mapped UniTags, 738 were significantly differentially expressed between control and inoculated leaves. The results indicate that several gene classes acting in different phases of the plant/pathogen interaction are involved in the L. sativus response to A. lathyri infection. Most notably a clear up-regulation of defense-related genes involved in and/or regulated by the ethylene pathway was observed. There was also evidence of alterations in cell wall metabolism indicated by overexpression of cellulose synthase and lignin biosynthesis genes. This first genome-wide overview of the gene expression profile of the L. sativus response to ascochyta infection delivered a valuable set of candidate resistance genes for future use in precision breeding.
Collapse
Affiliation(s)
- Nuno F. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB, Universidade Nova de LisboaOeiras, Portugal
| | | | | | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Maria C. Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB, Universidade Nova de LisboaOeiras, Portugal
| |
Collapse
|
26
|
Almeida NF, Leitão ST, Krezdorn N, Rotter B, Winter P, Rubiales D, Vaz Patto MC. Allelic diversity in the transcriptomes of contrasting rust-infected genotypes of Lathyrus sativus, a lasting resource for smart breeding. BMC Plant Biol 2014; 14:376. [PMID: 25522779 PMCID: PMC4331309 DOI: 10.1186/s12870-014-0376-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 05/19/2014] [Accepted: 12/09/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grass pea (Lathyrus sativus L.) is a valuable resource for potentially durable partial resistance to rust. To gain insight into the resistance mechanism and identify potential resistance genes, we generated the first comprehensive transcriptome assemblies from control and Uromyces pisi inoculated leafs of a susceptible and a partially rust-resistant grass pea genotype by RNA-seq. RESULTS 134,914 contigs, shared by both libraries, were used to analyse their differential expression in response to rust infection. Functional annotation grouped 60.4% of the contigs present in plant databases (37.8% of total) to 33 main functional categories, being "protein", "RNA", "signalling", "transport" and "stress" the most represented. Transcription profiles revealed considerable differences in regulation of major phytohormone signalling pathways: whereas Salicylic and Abscisic Acid pathways were up-regulated in the resistant genotype, Jasmonate and Ethylene pathways were down-regulated in the susceptible one. As potential Resistance-genes we identified a mildew resistance locus O (MLO)-like gene, and MLO-related transcripts. Also, several pathogenesis-related genes were up-regulated in the resistant and exclusively down regulated in the susceptible genotype. Pathogen effectors identified in both inoculated libraries, as e.g. the rust Rtp1 transcript, may be responsible for the down-regulation of defence-related transcripts. The two genotypes contained 4,892 polymorphic contigs with SNPs unevenly distributed between different functional categories. Protein degradation (29.7%) and signalling receptor kinases (8.2%) were the most diverged, illustrating evolutionary adaptation of grass pea to the host/pathogens arms race. CONCLUSIONS The vast array of novel, resistance-related genomic information we present here provides a highly valuable resource for future smart breeding approaches in this hitherto under-researched, valuable legume crop.
Collapse
Affiliation(s)
- Nuno Felipe Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Susana Trindade Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | | | - Björn Rotter
- GenXPro GmbH, D-60438, Frankfurt am Main, Germany.
| | - Peter Winter
- GenXPro GmbH, D-60438, Frankfurt am Main, Germany.
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, E-14080, Córdoba, Spain.
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| |
Collapse
|
27
|
Reister M, Hoffmeier K, Krezdorn N, Rotter B, Liang C, Rund S, Dandekar T, Sonnenborn U, Oelschlaeger TA. Complete genome sequence of the gram-negative probiotic Escherichia coli strain Nissle 1917. J Biotechnol 2014; 187:106-7. [PMID: 25093936 DOI: 10.1016/j.jbiotec.2014.07.442] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/24/2014] [Indexed: 11/29/2022]
Abstract
Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (trade name Mutaflor(®)) used for the treatment of patients with intestinal diseases such as ulcerative colitis and diarrhea. It has GRAS (generally recognized as save) status and has been shown to be a therapeutically effective drug (Sonnenborn and Schulze, 2009). The complete genomic DNA sequence will help in identifying genes and their products which are essential for the strains probiotic nature. Genbank/EMBL/DDBJ accession number: CP007799 (chromosome).
Collapse
Affiliation(s)
- Marten Reister
- GenXPro GmbH, Altenhoeferallee 3, 60438 Frankfurt/Main, Germany.
| | - Klaus Hoffmeier
- GenXPro GmbH, Altenhoeferallee 3, 60438 Frankfurt/Main, Germany.
| | - Nicolas Krezdorn
- GenXPro GmbH, Altenhoeferallee 3, 60438 Frankfurt/Main, Germany.
| | - Bjoern Rotter
- GenXPro GmbH, Altenhoeferallee 3, 60438 Frankfurt/Main, Germany.
| | - Chunguang Liang
- Bioinformatik, Biozentrum, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Stefan Rund
- Institut für Molekulare Infektionsbiologie, University of Wuerzburg, Josef-Schneider-Str. 2/D15, 97080 Wuerzburg, Germany.
| | - Thomas Dandekar
- Bioinformatik, Biozentrum, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Ulrich Sonnenborn
- Department of Biological Research, Ardeypharm GmbH, Loerfeldstr. 20, 58313 Herdecke, Germany.
| | - Tobias A Oelschlaeger
- Institut für Molekulare Infektionsbiologie, University of Wuerzburg, Josef-Schneider-Str. 2/D15, 97080 Wuerzburg, Germany.
| |
Collapse
|
28
|
Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C. Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. Front Plant Sci 2013; 4:423. [PMID: 24294214 PMCID: PMC3827546 DOI: 10.3389/fpls.2013.00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/05/2013] [Indexed: 05/23/2023]
Abstract
Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore, important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis, and degradation play a role in MCR.
Collapse
Affiliation(s)
- Astrid M. Draffehn
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Li Li
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Jia Ding
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KGWindeby, Germany
| | | | - Meki S. Muktar
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Birgit Walkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Christiane Gebhardt
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| |
Collapse
|
29
|
Leclerc M, Dupont S, Ortega-Martinez O, Hernroth B, Krezdorn N, Rotter B. Evidence of Kappa genes in the sea-star Asterias rubens (Echinoderma). Immunol Lett 2011; 138:197-8. [DOI: 10.1016/j.imlet.2011.01.016] [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] [Received: 12/23/2010] [Accepted: 01/24/2011] [Indexed: 10/18/2022]
|
30
|
Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 2011; 12:317. [PMID: 21679424 PMCID: PMC3128070 DOI: 10.1186/1471-2164-12-317] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [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: 10/27/2010] [Accepted: 06/16/2011] [Indexed: 11/22/2022] Open
Abstract
Background Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology.
Collapse
Affiliation(s)
- Barbara Feldmeyer
- Biodiversity and Climate Research Center (BiK-F), Molecular Ecology Group, Biocampus Siesmayerstraße, Goethe-Universität, Frankfurt am Main, Germany.
| | | | | | | | | |
Collapse
|