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Martorell-Ribera J, Koczan D, Tindara Venuto M, Viergutz T, Brunner RM, Goldammer T, Gimsa U, Rebl A. Experimental Handling Challenges Result in Minor Changes in the Phagocytic Capacity and Transcriptome of Head-Kidney Cells of the Salmonid Fish Coregonus maraena. Front Vet Sci 2022; 9:889635. [PMID: 35591870 PMCID: PMC9111177 DOI: 10.3389/fvets.2022.889635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 12/05/2022] Open
Abstract
Aquaculture management involves regular handling procedures, but these can evoke stress responses in farmed fish. We compiled an extensive list of published parameters that indicate the most likely handling-induced physiological deviations from the norm. However, since these parameters are based almost exclusively on studies of rainbow trout and Atlantic salmon, we conducted a handling-challenge experiment with maraena whitefish (Coregonus maraena). This salmonid fish was sampled at either 3 or 24 h after a single 1-min handling or after 10 days of daily repeated 1-min handling. The cortisol levels were strongly elevated in some individuals at 3 h after the single handling challenge, but these elevations were not significantly different between the challenged and control cohorts. The phagocytic capacity of myeloid head-kidney cells stimulated with fluorophore-labeled, inactivated Aeromonas salmonicida was significantly decreased in maraena whitefish at 3 h after the handling challenge compared to control fish. Microarray analysis of head-kidney samples from the challenged and control fish revealed 12 differentially expressed genes at 3 h and 70 at 24 h after the single handling episode, but only 5 differentially expressed genes after 10 days of repeated daily handling. The identified genes were assigned to numerous stress- and immune-relevant functional pathways, including “glucocorticoid receptor signaling” (3 h post-challenge), “HIF1A signaling” (24 h post-challenge), or “complement system” (10 days of repeated challenge). Our data reveal the tight interconnection of immune and stress pathways in the head kidney of maraena whitefish and corroborate several parameters previously found regulated in other tissues of handling-stressed rainbow trout. These findings indicate that handling may compromise the health and welfare of maraena whitefish in aquaculture.
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Affiliation(s)
- Joan Martorell-Ribera
- Fish Genetics Unit, Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Psychophysiology Unit, Institute of Behavioural Physiology, FBN, Dummerstorf, Germany
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine and Health Sciences, Universitat de Barcelona – UB, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dirk Koczan
- Core Facility for Microarray Analysis, Institute of Immunology, University of Rostock, Rostock, Germany
| | | | - Torsten Viergutz
- Service Group Cytometry, Institute of Reproductive Biology, FBN, Dummerstorf, Germany
| | - Ronald M. Brunner
- Fish Genetics Unit, Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Tom Goldammer
- Fish Genetics Unit, Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Ulrike Gimsa
- Psychophysiology Unit, Institute of Behavioural Physiology, FBN, Dummerstorf, Germany
- *Correspondence: Ulrike Gimsa
| | - Alexander Rebl
- Fish Genetics Unit, Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Alexander Rebl
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Galow AM, Kussauer S, Wolfien M, Brunner RM, Goldammer T, David R, Hoeflich A. Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias. Cell Mol Life Sci 2021; 78:6585-6592. [PMID: 34427691 PMCID: PMC8558157 DOI: 10.1007/s00018-021-03916-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/20/2021] [Accepted: 08/08/2021] [Indexed: 10/30/2022]
Abstract
Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to "low quality" potentially leading to data misinterpretation. Common standard quality control parameters involve the number of detected genes, transcripts per cell, and the fraction of transcripts from mitochondrial genes. While cutoffs for transcripts and genes per cell are usually user-defined for each experiment or individually calculated, a fixed threshold of 5% mitochondrial transcripts is standard and often set as default in scRNA-seq software. However, this parameter is highly dependent on the tissue type. In the heart, mitochondrial transcripts comprise almost 30% of total mRNA due to high energy demands. Here, we demonstrate that a 5%-threshold not only causes an unacceptable exclusion of cardiomyocytes but also introduces a bias that particularly discriminates pacemaker cells. This effect is apparent for our in vitro generated induced-sinoatrial-bodies (iSABs; highly enriched physiologically functional pacemaker cells), and also evident in a public data set of cells isolated from embryonal murine sinoatrial node tissue (Goodyer William et al. in Circ Res 125:379-397, 2019). Taken together, we recommend omitting this filtering parameter for scRNA-seq in cardiovascular applications whenever possible.
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Affiliation(s)
- Anne-Marie Galow
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
| | - Sophie Kussauer
- Department of Cardiac Surgery, Rostock University Medical Center, 18057, Rostock, Germany
- Department of Life, Light, and Matter, Interdisciplinary Faculty, Rostock University, 18059, Rostock, Germany
| | - Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
- Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059, Rostock, Germany
| | - Robert David
- Department of Cardiac Surgery, Rostock University Medical Center, 18057, Rostock, Germany
- Department of Life, Light, and Matter, Interdisciplinary Faculty, Rostock University, 18059, Rostock, Germany
| | - Andreas Hoeflich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
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3
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Schäfer N, Matoušek J, Rebl A, Stejskal V, Brunner RM, Goldammer T, Verleih M, Korytář T. Effects of Chronic Hypoxia on the Immune Status of Pikeperch ( Sander lucioperca Linnaeus, 1758). Biology (Basel) 2021; 10:biology10070649. [PMID: 34356504 PMCID: PMC8301350 DOI: 10.3390/biology10070649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 01/16/2023]
Abstract
Simple Summary Inadequate oxygen saturation, or hypoxia, belongs to one of the critical stress factors in intensive aquaculture. Exposure of fish to low oxygen levels over prolonged periods substantially affects their well-being and immune competence, resulting in increased disease susceptibility and consequent economic losses. In this interdisciplinary research, we aimed to provide a deeper understanding of the effect of chronic low oxygen saturation on pikeperch farmed in recirculating aquaculture systems. The obtained data offer unprecedented insights into the changes in the immunocompetence of studied fish and suggest high robustness of this new aquaculture species to the stress factors of intensive aquaculture. Abstract Inadequate oxygen saturation can induce stress responses in fish and further affect their immunity. Pikeperch, recently introduced in intensive aquaculture, is suggested to be reared at nearly 100% DO (dissolved oxygen), yet this recommendation can be compromised by several factors including the water temperature, stocking densities or low circulation. Herein, we aimed to investigate the effect of low oxygen saturation of 40% DO (±3.2 mg/L) over 28 days on pikeperch farmed in recirculating aquaculture systems. The obtained data suggest that—although the standard blood and health parameters did not reveal any significant differences at any timepoint—the flow cytometric analysis identified a slightly decreased proportion of lymphocytes in the HK (head kidney) of fish exposed to hypoxia. This has been complemented by marginally downregulated expression of investigated immune and stress genes in HK and liver (including FTH1, HIF1A and NR3C1). Additionally, in the model of acute peritoneal inflammation induced with inactivated Aeromonas hydrophila, we observed a striking dichotomy in the sensitivity to the low DO between innate and adaptive immunity. Thus, while the mobilization of myeloid cells from HK to blood, spleen and peritoneal cavity, underlined by changes in the expression of key proinflammatory cytokines (including MPO, IL1B and TNF) was not influenced by the low DO, hypoxia impaired the influx of lymphocytes to the peritoneal niche in the later phases of the immune reaction. Taken together, our data suggest high robustness of pikeperch towards the low oxygen saturation and further encourage its introduction to the intensive aquaculture systems.
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Affiliation(s)
- Nadine Schäfer
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (N.S.); (A.R.); (R.M.B.); (T.G.)
| | - Jan Matoušek
- Institute of Aquaculture and Protection of Waters (IAPW), Faculty of Fisheries and Protection of Waters, University of South Bohemia, 370 05 České Budějovice, Czech Republic; (J.M.); (V.S.)
| | - Alexander Rebl
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (N.S.); (A.R.); (R.M.B.); (T.G.)
| | - Vlastimil Stejskal
- Institute of Aquaculture and Protection of Waters (IAPW), Faculty of Fisheries and Protection of Waters, University of South Bohemia, 370 05 České Budějovice, Czech Republic; (J.M.); (V.S.)
| | - Ronald M. Brunner
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (N.S.); (A.R.); (R.M.B.); (T.G.)
| | - Tom Goldammer
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (N.S.); (A.R.); (R.M.B.); (T.G.)
- Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Marieke Verleih
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (N.S.); (A.R.); (R.M.B.); (T.G.)
- Correspondence: (M.V.); (T.K.); Tel.: +49-38208-68-721 (M.V.); +420-387-775-471 (T.K.)
| | - Tomáš Korytář
- Institute of Aquaculture and Protection of Waters (IAPW), Faculty of Fisheries and Protection of Waters, University of South Bohemia, 370 05 České Budějovice, Czech Republic; (J.M.); (V.S.)
- Institute of Parasitology, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
- Correspondence: (M.V.); (T.K.); Tel.: +49-38208-68-721 (M.V.); +420-387-775-471 (T.K.)
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Schäfer N, Kaya Y, Rebl H, Stüeken M, Rebl A, Nguinkal JA, Franz GP, Brunner RM, Goldammer T, Grunow B, Verleih M. Insights into early ontogenesis: characterization of stress and development key genes of pikeperch (Sander lucioperca) in vivo and in vitro. Fish Physiol Biochem 2021; 47:515-532. [PMID: 33559015 PMCID: PMC8026417 DOI: 10.1007/s10695-021-00929-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/18/2021] [Indexed: 05/11/2023]
Abstract
There are still numerous difficulties in the successful farming of pikeperch in the anthropogenic environment of various aquaculture systems, especially during early developmental steps in the hatchery. To investigate the physiological processes involved on the molecular level, we determined the basal expression patterns of 21 genes involved in stress and immune responses and early ontogenesis of pikeperch between 0 and 175 days post hatch (dph). Their transcription patterns most likely reflect the challenges of growth and feed conversion. The gene coding for apolipoprotein A (APOE) was strongly expressed at 0 dph, indicating its importance for yolk sac utilization. Genes encoding bone morphogenetic proteins 4 and 7 (BMP4, BMP7), creatine kinase M (CKM), and SRY-box transcription factor 9 (SOX9) were highly abundant during the peak phases of morphological changes and acclimatization processes at 4-18 dph. The high expression of genes coding for peroxisome proliferator-activated receptors alpha and delta (PPARA, PPARD) at 121 and 175 dph, respectively, suggests their importance during this strong growth phase of juvenile stages. As an alternative experimental model to replace further in vivo investigations of ontogenetically important processes, we initiated the first approach towards a long-lasting primary cell culture from whole pikeperch embryos. The present study provides a set of possible biomarkers to support the monitoring of pikeperch farming and provides a first basis for the establishment of a suitable cell model of this emerging aquaculture species.
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Affiliation(s)
- Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Yagmur Kaya
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henrike Rebl
- Department of Cell Biology, Rostock University Medical Center, 18059, Rostock, Germany
| | - Marcus Stüeken
- Institute of Fisheries, Department of Aquaculture, Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries, 17194, Hohen Wangelin, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Julien A Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - George P Franz
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059, Rostock, Germany
| | - Bianka Grunow
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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5
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Wolfien M, Galow AM, Müller P, Bartsch M, Brunner RM, Goldammer T, Wolkenhauer O, Hoeflich A, David R. Single nuclei sequencing of entire mammalian hearts: strain-dependent cell-type composition and velocity. Cardiovasc Res 2021; 116:1249-1251. [PMID: 32243511 DOI: 10.1093/cvr/cvaa054] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/17/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Anne-Marie Galow
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Paula Müller
- Department of Cardiac Surgery, Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Rostock University Medical Center, 18057 Rostock, Germany.,Department of Life, Light, and Matter of the Interdisciplinary, Faculty at Rostock University, 18059 Rostock, Germany
| | - Madeleine Bartsch
- Department of Cardiac Surgery, Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Rostock University Medical Center, 18057 Rostock, Germany.,Department of Life, Light, and Matter of the Interdisciplinary, Faculty at Rostock University, 18059 Rostock, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.,Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.,Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, 7602 Stellenbosch, South Africa
| | - Andreas Hoeflich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Robert David
- Department of Cardiac Surgery, Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Rostock University Medical Center, 18057 Rostock, Germany.,Department of Life, Light, and Matter of the Interdisciplinary, Faculty at Rostock University, 18059 Rostock, Germany
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6
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Martorell-Ribera J, Venuto MT, Otten W, Brunner RM, Goldammer T, Rebl A, Gimsa U. Time-Dependent Effects of Acute Handling on the Brain Monoamine System of the Salmonid Coregonus maraena. Front Neurosci 2020; 14:591738. [PMID: 33343287 PMCID: PMC7746803 DOI: 10.3389/fnins.2020.591738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
The immediate stress response involves the activation of the monoaminergic neurotransmitter systems including serotonin, dopamine and noradrenaline in particular areas of the fish brain. We chose maraena whitefish as a stress-sensitive salmonid species to investigate the influence of acute and chronic handling on the neurochemistry of monoamines in the brain. Plasma cortisol was quantified to assess the activation of the stress axis. In addition, we analyzed the expression of 37 genes related to the monoamine system to identify genes that could be used as markers of neurophysiological stress effects. Brain neurochemistry responded to a single handling (1 min netting and chasing) with increased serotonergic activity 3 h post-challenge. This was accompanied by a modulated expression of monoaminergic receptor genes in the hindbrain and a significant increase of plasma cortisol. The initial response was compensated by an increased monoamine synthesis at 24 h post-challenge, combined with the modulated expression of serotonin-receptor genes and plasma cortisol concentrations returning to control levels. After 10 days of repeated handling (1 min per day), we detected a slightly increased noradrenaline synthesis and a down-regulated expression of dopamine-receptor genes without effect on plasma cortisol levels. In conclusion, the changes in serotonergic neurochemistry and selected gene-expression profiles, together with the initial plasma cortisol variation, indicate an acute response and a subsequent recovery phase with signs of habituation after 10 days of daily exposure to handling. Based on the basal expression patterns of particular genes and their significant regulation upon handling conditions, we suggest a group of genes as potential biomarkers that indicate handling stress on the brain monoamine systems.
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Affiliation(s)
- Joan Martorell-Ribera
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Marzia Tindara Venuto
- Glycobiology Group, Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Winfried Otten
- Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ronald M Brunner
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Tom Goldammer
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Alexander Rebl
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ulrike Gimsa
- Psychophysiology Unit, Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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7
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de Los Ríos-Pérez L, Nguinkal JA, Verleih M, Rebl A, Brunner RM, Klosa J, Schäfer N, Stüeken M, Goldammer T, Wittenburg D. An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale. Sci Rep 2020; 10:22335. [PMID: 33339898 PMCID: PMC7749136 DOI: 10.1038/s41598-020-79358-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.
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Affiliation(s)
- Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Julien A Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Jan Klosa
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Marcus Stüeken
- Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries, Malchower Chaussee 1, 17194, Hohen Wangelin, Germany
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059, Rostock, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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8
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Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls. Int J Mol Sci 2020; 21:ijms21093292. [PMID: 32384694 PMCID: PMC7247587 DOI: 10.3390/ijms21093292] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid β-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Harald M. Hammon
- Institute of Nutritional Physiology “Oskar Kellner”, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia 4067 QLD, Australia;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
- Correspondence:
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Galow AM, Wolfien M, Müller P, Bartsch M, Brunner RM, Hoeflich A, Wolkenhauer O, David R, Goldammer T. Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice. Cells 2020; 9:cells9051144. [PMID: 32384695 PMCID: PMC7291011 DOI: 10.3390/cells9051144] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 01/22/2023] Open
Abstract
The recent development and broad application of sequencing techniques at the single-cell level is generating an unprecedented amount of data. The different techniques have their individual limits, but the datasets also offer unexpected possibilities when utilized collectively. Here, we applied snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain to directly compare the data with the publicly available scRNA-seq data of the tabula muris project. Explicitly choosing a single-nucleus approach allowed us to pin down the typical heart tissue-specific technical bias, coming up with novel insights on the mammalian heart cell composition. For our integrated dataset, cardiomyocytes, fibroblasts, and endothelial cells constituted the three main cell populations accounting for about 75% of all cells. However, their numbers severely differed between the individual datasets, with cardiomyocyte proportions ranging from about 9% in the tabula muris data to around 23% for our BL6 data, representing the prime example for cell capture technique related bias when using a conventional single-cell approach for these large cells. Most strikingly in our comparison was the discovery of a minor population of cardiomyocytes characterized by proliferation markers that could not be identified by analyzing the datasets individually. It is now widely accepted that the heart has an, albeit very restricted, regenerative potential. However there is still an ongoing debate where new cardiomyocytes arise from. Our findings support the idea that the renewal of the cardiomyocyte pool is driven by cytokinesis of resident cardiomyocytes rather than differentiation of progenitor cells. We thus provide data that can contribute to an understanding of heart cell regeneration, which is a prerequisite for future applications to enhance the process of heart repair.
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Affiliation(s)
- Anne-Marie Galow
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (A.-M.G.); (R.M.B.); (A.H.)
| | - Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany;
| | - Paula Müller
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany; (P.M.); (M.B.)
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
| | - Madeleine Bartsch
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany; (P.M.); (M.B.)
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (A.-M.G.); (R.M.B.); (A.H.)
| | - Andreas Hoeflich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (A.-M.G.); (R.M.B.); (A.H.)
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany;
- Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, 7602 Stellenbosch, South Africa
- Correspondence: (O.W.); (R.D.); (T.G.)
| | - Robert David
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany; (P.M.); (M.B.)
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
- Correspondence: (O.W.); (R.D.); (T.G.)
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (A.-M.G.); (R.M.B.); (A.H.)
- Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
- Correspondence: (O.W.); (R.D.); (T.G.)
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10
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Martorell Ribera J, Nipkow M, Viergutz T, Brunner RM, Bochert R, Koll R, Goldammer T, Gimsa U, Rebl A. Early response of salmonid head-kidney cells to stress hormones and toll-like receptor ligands. Fish Shellfish Immunol 2020; 98:950-961. [PMID: 31770645 DOI: 10.1016/j.fsi.2019.11.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 05/25/2023]
Abstract
The functional spectrum of the teleostean head kidney covers haematopoietic, immune and endocrine signalling pathways with physiological effects that are likely to conflict if activated at the same time. An in vivo experiment on the salmonid fish maraena whitefish (Coregonus maraena) revealed that the head kidney shows a remarkably strong response after injection of Aeromonas salmonicida within 48 h. In order to investigate the potential influence of endocrine signalling on the initiation of immune responses, we established a primary culture of head-kidney cells of maraena whitefish. For the characterisation of this model system, we used flow cytometry complemented with an extensive panel of immunological/haematological and stress-physiological/neuroendocrinological qPCR assays. More than one third of the cells expressed the characteristic signature of myeloid cells, while more than half of the cells expressed those genes typical for lymphocytes and monocytes. In parallel, we quantified the expression of genes encoding endocrine receptors and identified ADRA2D as by far the most highly expressed adrenergic-receptor gene in head-kidney cells. The stimulation of the head-kidney cells with toll-like receptor ligands induced the expression of typical immune genes (IL1B, CXCL8, TNF, SAA) after only 1 h. The incubation with the stress hormones cortisol, adrenaline and noradrenaline also had an immune-activating effect, though less pronounced. However, cortisol had the strongest suppressive effect on the stimulation-induced immune response, while adrenaline exerted a comparably weaker effect and noradrenaline was almost ineffective. Moreover, we found that cortisol reduced the expression of genes coding for adrenergic and some glucocorticoid receptors, while noradrenaline increased it. In conclusion, the primary head-kidney cells of maraena whitefish reflect the immunological and neuroendocrinological diversity of the entire organ. This in vitro system allowed thus identifying the correlative changes between the activities of hormones and immune factors in salmonid fish in order to contribute to a better understanding of the regulation circuit between stress and immune defence.
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Affiliation(s)
- Joan Martorell Ribera
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany; FBN, Institute of Behavioural Physiology, Psychophysiology Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Mareen Nipkow
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Torsten Viergutz
- FBN, Institute of Reproductive Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ralf Bochert
- Research Station Aquaculture Born, Institute of Fisheries, Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries (LFA MV), Südstraße 8, 18375, Born/Darss, Germany
| | - Raphael Koll
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ulrike Gimsa
- FBN, Institute of Behavioural Physiology, Psychophysiology Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
| | - Alexander Rebl
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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11
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Wolfien M, Galow AM, Müller P, Bartsch M, Brunner RM, Goldammer T, Wolkenhauer O, Hoeflich A, David R. Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity. Cells 2020; 9:E318. [PMID: 32013057 PMCID: PMC7072447 DOI: 10.3390/cells9020318] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/24/2020] [Accepted: 01/25/2020] [Indexed: 12/21/2022] Open
Abstract
: Analyses on the cellular level are indispensable to expand our understanding of complex tissues like the mammalian heart. Single-nucleus sequencing (snRNA-seq) allows for the exploration of cellular composition and cell features without major hurdles of single-cell sequencing. We used snRNA-seq to investigate for the first time an entire adult mammalian heart. Single-nucleus quantification and clustering led to an accurate representation of cell types, revealing 24 distinct clusters with endothelial cells (28.8%), fibroblasts (25.3%), and cardiomyocytes (22.8%) constituting the major cell populations. An additional RNA velocity analysis allowed us to study transcription kinetics and was utilized to visualize the transitions between mature and nascent cellular states of the cell types. We identified subgroups of cardiomyocytes with distinct marker profiles. For example, the expression of Hand2os1 distinguished immature cardiomyocytes from differentiated cardiomyocyte populations. Moreover, we found a cell population that comprises endothelial markers as well as markers clearly related to cardiomyocyte function. Our velocity data support the idea that this population is in a trans-differentiation process from an endothelial cell-like phenotype towards a cardiomyocyte-like phenotype. In summary, we present the first report of sequencing an entire adult mammalian heart, providing realistic cell-type distributions combined with RNA velocity kinetics hinting at interrelations.
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Affiliation(s)
- Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Anne-Marie Galow
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany (R.M.B.)
| | - Paula Müller
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
| | - Madeleine Bartsch
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany (R.M.B.)
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany (R.M.B.)
- Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
- Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, 7602 Stellenbosch, South Africa
| | - Andreas Hoeflich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany (R.M.B.)
| | - Robert David
- Reference and Translation Center for Cardiac Stem Cell therapy (RTC), Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany
- Department of Life, Light, and Matter of the Interdisciplinary Faculty at Rostock University, 18059 Rostock, Germany
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Koll R, Martorell Ribera J, Brunner RM, Rebl A, Goldammer T. Gene Profiling in the Adipose Fin of Salmonid Fishes Supports its Function as a Flow Sensor. Genes (Basel) 2019; 11:genes11010021. [PMID: 31878086 PMCID: PMC7016824 DOI: 10.3390/genes11010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
In stock enhancement and sea-ranching procedures, the adipose fin of hundreds of millions of salmonids is removed for marking purposes annually. However, recent studies proved the significance of the adipose fin as a flow sensor and attraction feature. In the present study, we profiled the specific expression of 20 neuron- and glial cell-marker genes in the adipose fin and seven other tissues (including dorsal and pectoral fin, brain, skin, muscle, head kidney, and liver) of the salmonid species rainbow trout Oncorhynchus mykiss and maraena whitefish Coregonus maraena. Moreover, we measured the transcript abundance of genes coding for 15 mechanoreceptive channel proteins from a variety of mechanoreceptors known in vertebrates. The overall expression patterns indicate the presence of the entire repertoire of neurons, glial cells and receptor proteins on the RNA level. This quantification suggests that the adipose fin contains considerable amounts of small nerve fibers with unmyelinated or slightly myelinated axons and most likely mechanoreceptive potential. The findings are consistent for both rainbow trout and maraena whitefish and support a previous hypothesis about the innervation and potential flow sensory function of the adipose fin. Moreover, our data suggest that the resection of the adipose fin has a stronger impact on the welfare of salmonid fish than previously assumed.
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Affiliation(s)
- Raphael Koll
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (R.K.); (J.M.R.); (R.M.B.); (A.R.)
| | - Joan Martorell Ribera
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (R.K.); (J.M.R.); (R.M.B.); (A.R.)
| | - Ronald M. Brunner
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (R.K.); (J.M.R.); (R.M.B.); (A.R.)
| | - Alexander Rebl
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (R.K.); (J.M.R.); (R.M.B.); (A.R.)
| | - Tom Goldammer
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (R.K.); (J.M.R.); (R.M.B.); (A.R.)
- Professorship for Molecular Biology and Fish Genetics, Faculty of Agriculture and Environmental Sciences, University of Rostock, 18055 Rostock, Germany
- Correspondence: ; Tel.: +49-38208-68-708
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13
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Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle. Front Genet 2019; 10:1130. [PMID: 31824560 PMCID: PMC6883949 DOI: 10.3389/fgene.2019.01130] [Citation(s) in RCA: 21] [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: 06/25/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Genomic regions associated with divergent livestock feed efficiency have been found predominantly outside protein coding sequences. Long non-coding RNAs (lncRNA) can modulate chromatin accessibility, gene expression and act as important metabolic regulators in mammals. By integrating phenotypic, transcriptomic, and metabolomic data with quantitative trait locus data in prioritizing co-expression network analyses, we aimed to identify and functionally characterize lncRNAs with a potential key regulatory role in metabolic efficiency in cattle. Materials and Methods: Crossbred animals (n = 48) of a Charolais x Holstein F2-population were allocated to groups of high or low metabolic efficiency based on residual feed intake in bulls, energy corrected milk in cows and intramuscular fat content in both genders. Tissue samples from jejunum, liver, skeletal muscle and rumen were subjected to global transcriptomic analysis via stranded total RNA sequencing (RNAseq) and blood plasma samples were used for profiling of 640 metabolites. To identify lncRNAs within the indicated tissues, a project-specific transcriptome annotation was established. Subsequently, novel transcripts were categorized for potential lncRNA status, yielding a total of 7,646 predicted lncRNA transcripts belonging to 3,287 loci. A regulatory impact factor approach highlighted 92, 55, 35, and 73 lncRNAs in jejunum, liver, muscle, and rumen, respectively. Their ensuing high regulatory impact factor scores indicated a potential regulatory key function in a gene set comprising loci displaying differential expression, tissue specificity and loci overlapping with quantitative trait locus regions for residual feed intake or milk production. These were subjected to a partial correlation and information theory analysis with the prioritized gene set. Results and Conclusions: Independent, significant and group-specific correlations (|r| > 0.8) were used to build a network for the high and the low metabolic efficiency group resulting in 1,522 and 1,732 nodes, respectively. Eight lncRNAs displayed a particularly high connectivity (>100 nodes). Metabolites and genes from the partial correlation and information theory networks, which each correlated significantly with the respective lncRNA, were included in an enrichment analysis indicating distinct affected pathways for the eight lncRNAs. LncRNAs associated with metabolic efficiency were classified to be functionally involved in hepatic amino acid metabolism and protein synthesis and in calcium signaling and neuronal nitric oxide synthase signaling in skeletal muscle cells.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Institute of Nutritional Physiology "Oskar Kellner," Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
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14
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Affiliation(s)
- Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Roseworthy, SA, 5371, Australia.,Robinson Research Institute, The University of Adelaide, 55 King William St, North Adelaide, SA, 5006, Australia
| | - Cynthia D K Bottema
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Roseworthy, SA, 5371, Australia
| | - Ronald M Brunner
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, W.-Stahl-Allee 2, Dummerstorf, 18196, Germany
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15
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Kaiser B, Böttner M, Wedel T, Brunner RM, Goldammer T, Lesko S, Gäbel G, Gleich A, Pfannkuche H. Establishment and Characterization of an SV40 Large T Antigen-Transduced Porcine Colonic Epithelial Cell Line. Cells Tissues Organs 2017; 203:267-286. [DOI: 10.1159/000453394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2016] [Indexed: 11/19/2022] Open
Abstract
Continuous cell lines have become indispensable tools that have enabled investigations into cellular mechanisms by increasing experimental reproducibility and sample availability, and decreasing the use of experimental animals. To facilitate studies of epithelial barrier function of the porcine colon, we aimed to establish an epithelial cell line with an extended replicative capacity. Cells were isolated from the proximal colon of a 3-week-old piglet and transduced using a recombinant retroviral vector construct containing the simian virus 40 large T antigen (SV40 TAg). We established a clonal epithelial cell line, referred to as PoCo83-3, that stably expressed the SV40 TAg, verified at mRNA and protein levels. PoCo83-3 showed epithelial cell-specific features, such as cobblestone-like morphology, dome structure formation, the presence of apical microvilli, and the expression of keratin 18, E-cadherin and the tight junction-associated proteins zonula occludens-1, occludin, and claudin-1. To validate PoCo83-3 as an in vitro model in epithelial barrier research, proinflammatory cytokine-inducible alterations in barrier integrity were demonstrated by incubating the cells with TNF-α and IFN-γ for 48 h. These cytokine treatments promoted a decreased transepithelial electrical resistance. In summary, PoCo83-3 exhibited an extended life span and a differentiated phenotype while maintaining epithelial characteristics. Based on these results, we present this cell line as a valuable in vitro model for investigations of epithelial barrier function in the porcine colon.
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16
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Brietzke A, Borchel A, Altmann S, Nipkow M, Rebl A, Brunner RM, Goldammer T. Transcriptome sequencing of maraena whitefish (Coregonus maraena). Mar Genomics 2016; 29:27-29. [PMID: 27270125 DOI: 10.1016/j.margen.2016.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 04/01/2016] [Revised: 05/30/2016] [Accepted: 05/30/2016] [Indexed: 01/22/2023]
Abstract
Maraena whitefish (Coregonus maraena, Bloch, 1779) is a high-quality food fish belonging to the family Salmonidae with considerable economic relevance in the Baltic area. Aquaculture of this species is fundamental for its successful conservation and thus sustainable fisheries. Robust fishes obtained from breeding lines build the basis for effective aquaculture. Doubtless, the utilization of transcriptome sequencing and identification of genetic markers contribute to this aim. 454 FLX Titanium Sequencing provided 1.31 million sequence reads representing a first insight into the C. maraena transcriptome. The 454 Newbler Assembly arranged 29,094 contigs with an average length of 798bp. We found a whole series of transcripts highly probably resulting from ancient genome duplication and annotated 2887 different transcripts with an average length of 812bp. Functional annotation obtained a transcript composition predominantly comprising enzyme-coding genes.
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Affiliation(s)
- Andreas Brietzke
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Andreas Borchel
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany; SLRC - Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgata 55, 5008 Bergen, Norway
| | - Simone Altmann
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Mareen Nipkow
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Alexander Rebl
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Ronald M Brunner
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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17
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Zante MD, Borchel A, Brunner RM, Goldammer T, Rebl A. Cloning and characterization of the proximal promoter region of rainbow trout (Oncorhynchus mykiss) interleukin-6 gene. Fish Shellfish Immunol 2015; 43:249-256. [PMID: 25549935 DOI: 10.1016/j.fsi.2014.12.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/15/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
Interleukin-6 (IL6) is a pleiotropic cytokine with important immunoregulatory functions. Its expression is inducible in immune cells and tissues of several fish species. We also found that IL6 mRNA abundance was significantly increased in spleen, liver, and gill of rainbow trout after experimental infection with Aeromonas salmonicida. Genomic DNA sequences of IL6 orthologs from three salmonid species revealed a conserved exon/intron structure and a high overall nucleotide identity of >88%. To uncover key mechanisms regulating IL6 expression in salmonid fish, we amplified a fragment of the proximal IL6 promoter from rainbow trout and identified in-silico conserved binding sites for NF-κB and CEBP. The activity of this IL6 promoter fragment was analyzed in the established human embryonic kidney line HEK-293. Luciferase- and GFP-based reporter systems revealed that the proximal IL6 promoter is activated by Escherichia coli. Essentially, both reporter systems proved that NF-κB p50, but not NF-κB p65 or CEBP, activates the IL6 promoter fragment. Truncation of this fragment caused a significant decrease in IL6 promoter activation. This characterization of the proximal promoter of the IL6-encoding gene provides basic knowledge about the IL6 gene expression in rainbow trout.
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Affiliation(s)
- Merle D Zante
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Andreas Borchel
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Ronald M Brunner
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Alexander Rebl
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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18
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Rangkasenee N, Murani E, Brunner RM, Schellander K, Cinar MU, Luther H, Hofer A, Stoll M, Witten A, Ponsuksili S, Wimmers K. Genome-Wide Association Identifies TBX5 as Candidate Gene for Osteochondrosis Providing a Functional Link to Cartilage Perfusion as Initial Factor. Front Genet 2013; 4:78. [PMID: 23675383 PMCID: PMC3650520 DOI: 10.3389/fgene.2013.00078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/19/2013] [Indexed: 11/13/2022] Open
Abstract
Osteochondrosis (OC) is an orthopedic syndrome of the joints that occurs in children and adolescents and domestic animals, particularly pigs, horses, and dogs. OC is the most frequent cause of leg weakness in rapidly growing pigs causing animal welfare issues and economic losses. In this study, a genome-wide association study (GWAS) was performed using the Porcine 60k SNPChip in animals of the breed Large White (n = 298) to identify chromosome regions and candidate genes associated with OC lesion scores. A total of 19 SNPs on chromosomes (SSC) 3, 5, 8, 10, 14, and 18 were significantly associated with OC lesion scores (p-values ≤ 10(-5)). The SNPs MARC0098684, MARC00840086, MARC0093124, and ASGA0062794 at SSC14 36.1-38.2 Mb encompass a region of six linkage disequilibrium (LD) blocks. The most significant SNP ASGA0062794 is located in a LD block spanning 465 kb and covering the gene encoding T-box transcription factor 5 (TBX5). A SNP (c.54T > C) identified in TBX5 was significantly associated with OC lesion scores in a single-marker analysis. TBX5 c.54T > C showed highest LD with ASGA00627974 (r (2) = 0.96) and superior association with OC lesion scores over other SNPs when included in the genome scan, whereas its treatment as an additional fixed effect in the GWAS statistical model led to a drop of significance of nearby markers. Moreover, real-time PCR showed different transcript abundance of TBX5 in healthy and defect cartilage. The results imply that the association signal obtained on SCC14 is largely attributable to TBX5 c.54T > C likely to be in LD with a regulatory polymorphism of TBX5. The transcription factor TBX5 interacts with GJA5 and MEF2C both being involved in vascularization. This study provides evidence for epistatic interaction of TBX5 and MEF2C, thus supporting deficiency of blood supply to growth cartilage as being fundamental for the initiation of OC.
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Affiliation(s)
- Noppawan Rangkasenee
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology Dummerstorf, Germany
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Weikard R, Goldammer T, Brunner RM, Kuehn C. Tissue-specific mRNA expression patterns reveal a coordinated metabolic response associated with genetic selection for milk production in cows. Physiol Genomics 2012; 44:728-39. [PMID: 22669841 DOI: 10.1152/physiolgenomics.00007.2012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanisms regulating the physiological adaptation of tissues important for nutrient partitioning and metabolism in lactating cows are still not completely understood. The aim of our study was to identify tissue-specific regulatory mechanisms necessary to accommodate metabolic changes associated with different genetic potential for milk performance. For this purpose, we analyzed mRNA expression of genes involved in energy metabolism of segregating F(2) beef type cows with a combined genetic dairy and beef background (Charolais × German Holstein cross, CH×GH) in contrast to purebred German Holstein (GH) dairy cows. Three groups of cows differing in milk performance were examined using quantitative real-time PCR in liver, mammary gland, and skeletal muscle. Our results describe substantial tissue-specific differences in mRNA transcription profiles between cow groups in relation to their genetic potential for milk performance and highlight genes exhibiting specific, partially yet-unknown functions in dairy and beef type cows, e.g., upregulation of PCK2 transcripts in the mammary gland and FBP2 transcripts in skeletal muscle of dairy cows. Noticeably, PCCA and PPARGC1A mRNA abundance varied significantly across experimental groups in all three tissues, pointing to potential key gene functions in the metabolic adaptation relative to divergent milk production performance. Correlations of mRNA expression levels to milk performance traits indicate that gene transcriptional processes may play a regulatory role in liver, mammary gland, and skeletal muscle to enable cows with different genetic potential for milk performance to cope with metabolic lactation-associated challenges.
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Affiliation(s)
- R Weikard
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
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20
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Brunner RM, Srikanchai T, Murani E, Wimmers K, Ponsuksili S. Genes with expression levels correlating to drip loss prove association of their polymorphism with water holding capacity of pork. Mol Biol Rep 2011; 39:97-107. [PMID: 21556776 DOI: 10.1007/s11033-011-0714-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 04/23/2011] [Indexed: 01/03/2023]
Abstract
Six genes that were known to exhibit expression levels that are correlated to drip loss BVES, SLC3A2, ZDHHC5, CS, COQ9, and EGFR have been for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing, and used for genotyping. The SNPs were genotyped in about 1,800 animals from six pig populations including commercial herds of Pietrain (PI) and German Landrace (DL), different commercial herds of Pietrain×(German Large White×German Landrace) (PIF1(a/b/c)), and one experimental F2-population Duroc×Pietrain (DUPI). Comparative and genetic mapping established the location of BVES on SSC1, of SLC3A2 and ZDHHC5 on SSC2, of CS on SSC5, of COQ9 on SSC6 and of EGFR on SSC9, respectively, coinciding with QTL regions for carcass and meat quality traits. BVES, SLC3A2, and CS revealed association at least with drip loss and with several other measures of water holding capacity (WHC). Moreover, COQ9 and EGFR were associated with several meat quality traits such as meat color and/or thawing loss. This study reveals statistic evidence in addition to the functional relationship of these genes to WHC previously evidenced by expression analysis. This study reveals positional and genetic statistical evidence for a link of genetic variation at these loci or close to them and promotes those six candidate genes as functional and/or positional candidate genes for meat quality traits.
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Affiliation(s)
- R M Brunner
- Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
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21
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Eberlein A, Kalbe C, Goldammer T, Brunner RM, Kuehn C, Weikard R. Analysis of structure and gene expression of bovine CCDC3 gene indicates a function in fat metabolism. Comp Biochem Physiol B Biochem Mol Biol 2010; 156:19-25. [PMID: 20132904 DOI: 10.1016/j.cbpb.2010.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/22/2010] [Accepted: 01/22/2010] [Indexed: 01/19/2023]
Abstract
Our study reports the molecular analysis of the bovine gene encoding the coiled-coil domain-containing protein 3 (CCDC3). Based on comparative sequence analysis and in silico sequence merging of predicted gene models, a new full-length gene model for the bovine CCDC3 gene was predicted and confirmed experimentally. The CCDC3 gene was assigned to bovine chromosome 13. It consists of three exons comprising 2599bp encoding for a respective protein of 274 amino acids. The strong CCDC3 sequence homology on amino acid level between species suggests a conserved universal function of this protein. In mice, the CCDC3 gene had been found to be highly expressed in adipocytes and regulated by hormonal-nutritional alternations and in obesity. The tissue expression pattern of bovine CCDC3 mRNA indicates a ubiquitous physiological function of the gene. Significant differences in CCDC3 mRNA expression in skeletal muscle between individuals characterized by divergent intramuscular fat deposition support the potential function of the gene in fat or energy metabolism, which possibly could also be inferred for other mammalian species. This first report of structural analysis and molecular characterization of the CCDC3 gene in cattle will contribute to a better understanding of the yet unknown physiological role of the respective protein in mammals.
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Affiliation(s)
- Annett Eberlein
- Research Institute for the Biology of Farm Animals, Dummerstorf, Germany.
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22
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Goldammer T, Brunner RM, Rebl A, Wu CH, Nomura K, Hadfield T, Gill C, Dalrymple BP, Womack JE, Cockett NE. A high-resolution radiation hybrid map of sheep chromosome X and comparison with human and cattle. Cytogenet Genome Res 2009; 125:40-5. [PMID: 19617695 DOI: 10.1159/000207520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2009] [Indexed: 11/19/2022] Open
Abstract
A radiation hybrid (RH) map of sheep X chromosome (Ovisaries; OARX) containing 146 physically anchored loci was generated in this study, providing information for comparative X chromosome analysis between the maps of sheep, human, and cattle. Primers typed on the USUoRH5000 ovine whole-genome radiation hybrid panel were designed from sequences predicted to be on the ovine X chromosome, based on comparative mapping within the virtual sheep genome browser (v1.2). The resulting RH map for the ovine X chromosome consists of 4 linkage groups composed of 76 BAC end sequences (BES), 28 gene loci that were confirmed within ovine BAC clones in the CHORI-243 ovine BAC library, 28 additional gene loci from the ovine comparative map and 14 polymorphic sequence tagged sites (STS) from the OARX linkage map. This first-generation RH map of OARX contributes to the expansion of a comprehensive ovine genome map for sheep and provides evidence of rearrangements in loci order compared to the human and cattle orders.
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Affiliation(s)
- T Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Dummerstorf, Germany.
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23
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Goldammer T, Brunner RM, Rebl A, Wu CH, Nomura K, Hadfield T, Maddox JF, Cockett NE. Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human. Chromosome Res 2009; 17:497-506. [PMID: 19575301 DOI: 10.1007/s10577-009-9047-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 04/15/2009] [Accepted: 06/04/2009] [Indexed: 01/05/2023]
Abstract
A comprehensive physical map was generated for Ovis aries chromosome X (OARX) based on a cytogenomics approach. DNA probes were prepared from bacterial artificial chromosome (BAC) clones from the CHORI-243 sheep library and were assigned to G-banded metaphase spreads via fluorescence in-situ hybridization (FISH). A total of 22 BACs gave a single hybridization signal to the X chromosome and were assigned out of 32 tested. The positioned BACs contained 16 genes and a microsatellite marker which represent new cytogenetically mapped loci in the sheep genome. The gene and microsatellite loci serve to anchor between the existing radiation hybrid (RH) and virtual sheep genome (VSG) maps to the cytogenetic OARX map, whilst the BACs themselves also serve as anchors between the VSG and the cytogenetic maps. An additional 17 links between the RH and cytogenetic maps are provided by BAC end sequence (BES) derived markers that have also been positioned on the RH map. Comparison of the map orders for the cytogenetic, RH, and virtual maps reveals that the orders for the cytogenetic and RH maps are most similar, with only one locus, represented by BAC CH243-330E18, mapping to relatively different positions. Several discrepancies, including an inverted segment are found when comparing both the cytogenetic and RH maps with the virtual map. These discrepancies highlight the value of using physical mapping methods to inform the process of future in silico map construction. A detailed comparative analysis of sheep, human, and cattle mapping data allowed the construction of a comparative map that confirms and expands the knowledge about evolutionary conservation and break points between the X chromosomes of the three mammalian species.
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Affiliation(s)
- Tom Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere, Dummerstorf, Germany.
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24
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Amaral MEJ, Grant JR, Riggs PK, Stafuzza NB, Filho EAR, Goldammer T, Weikard R, Brunner RM, Kochan KJ, Greco AJ, Jeong J, Cai Z, Lin G, Prasad A, Kumar S, Saradhi GP, Mathew B, Kumar MA, Miziara MN, Mariani P, Caetano AR, Galvão SR, Tantia MS, Vijh RK, Mishra B, Kumar STB, Pelai VA, Santana AM, Fornitano LC, Jones BC, Tonhati H, Moore S, Stothard P, Womack JE. A first generation whole genome RH map of the river buffalo with comparison to domestic cattle. BMC Genomics 2008; 9:631. [PMID: 19108729 PMCID: PMC2625372 DOI: 10.1186/1471-2164-9-631] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [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: 10/10/2008] [Accepted: 12/24/2008] [Indexed: 01/28/2023] Open
Abstract
Background The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. Results A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). Conclusion We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
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Goldammer T, Weikard R, Miziara MN, Brunner RM, Agarwala R, Schaffer AA, Womack JE, Amaral MEJ. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes. Cytogenet Genome Res 2008; 119:235-41. [PMID: 18253035 DOI: 10.1159/000112067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2007] [Indexed: 12/16/2022] Open
Abstract
A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR(5,000). Comparative analysis of the BBU7 RH(5,000) map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH(5,000) map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence.
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Affiliation(s)
- T Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut fur die Biologie landwirtschaftlicher Nutztiere (FBN), Dummerstorf, Germany.
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26
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de Koning DJ, Jaffrézic F, Lund MS, Watson M, Channing C, Hulsegge I, Pool MH, Buitenhuis B, Hedegaard J, Hornshøj H, Jiang L, Sørensen P, Marot G, Delmas C, Cao KAL, San Cristobal M, Baron MD, Malinverni R, Stella A, Brunner RM, Seyfert HM, Jensen K, Mouzaki D, Waddington D, Jiménez-Marín Á, Pérez-Alegre M, Pérez-Reinado E, Closset R, Detilleux JC, Dovč P, Lavrič M, Nie H, Janss L. The EADGENE Microarray Data Analysis Workshop (open access publication). Genet Sel Evol 2007; 39:621-31. [PMID: 18053572 PMCID: PMC2682810 DOI: 10.1186/1297-9686-39-6-621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 07/03/2007] [Indexed: 02/02/2023] Open
Abstract
Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.
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Affiliation(s)
| | | | | | | | | | - Ina Hulsegge
- Animal Sciences Group Wageningen UR, Lelystad, The Netherlands
| | - Marco H Pool
- Animal Sciences Group Wageningen UR, Lelystad, The Netherlands
| | | | | | | | - Li Jiang
- University of Aarhus, Tjele, Denmark
| | | | | | | | - Kim-Anh Lê Cao
- INRA, UMR444, Castanet-Tolosan, France,Université Paul Sabatier, Toulouse, France
| | | | | | | | | | - Ronald M Brunner
- Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
| | | | | | | | | | | | | | | | | | | | - Peter Dovč
- University of Ljubljana, Ljubljana, Slovenia
| | - Miha Lavrič
- University of Ljubljana, Ljubljana, Slovenia
| | - Haisheng Nie
- Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Luc Janss
- University of Aarhus, Tjele, Denmark
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Eberhard M, Hennig U, Kuhla S, Brunner RM, Kleessen B, Metges CC. Effect of inulin supplementation on selected gastric, duodenal, and caecal microbiota and short chain fatty acid pattern in growing piglets. Arch Anim Nutr 2007; 61:235-46. [PMID: 17760302 DOI: 10.1080/17450390701431631] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We explored whether bifidobacteria and lactobacilli numbers and other selected bacteria in the upper intestine and the caecum of growing pigs were affected by diet and intake of inulin. Starting at two weeks after weaning (28 d) 72 pigs were fed two types of diets (wheat/barley (WB) or maize/gluten (MG)), without or with 3% inulin (WB + I, MG + I) for three and six weeks. Intestinal bacteria were quantified by fluorescence-in-situ-hybridization (n = 8/group). Duration of feeding had no effect on the variables tested, so data for both periods were pooled. Gastric total bacteria amounted to log(10) 7.4/g digesta. Bifidobacteria were detected in stomach and duodenum two weeks after weaning and disappeared thereafter. In jejunum and caecum bifidobacteria were present at a level of log(10) 7.0/g digesta. Inulin did not alter numbers of lactobacilli, bifidobacteria, enterococci, enterobacteria and bacteria of the Clostridium coccoides/Eubacterium rectale-group. Inulin disappearance in stomach plus jejunum was higher with the MG diet (73.7 vs. 60.7%, p = 0.013). Caecal acetate was lower in inulin-supplemented diets (p < 0.05) whereas propionate and butyrate were higher in pigs fed the WB diets (p < 0.05). With the WB diet total caecal short chain fatty acids concentration was higher which resulted in a lower pH value (p < 0.05).
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Affiliation(s)
- Markus Eberhard
- Research Units Nutritional Physiology and Molecular Biology, Research Institute for the Biology of Farm Animals (FBN), Dummerstorf, Germany
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28
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Goldammer T, Brunner RM, Weikard R, Kuehn C, Wimmers K. Generation of an improved cytogenetic and comparative map of Bos taurus chromosome BTA27. Chromosome Res 2007; 15:203-13. [PMID: 17205384 DOI: 10.1007/s10577-006-1113-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2006] [Revised: 11/21/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
Comparative genome analysis in cattle, human, and mouse identified various evolutionary breakpoints between Bos taurus 27 chromosome (BTA27) and corresponding segments in the Homo sapiens 4 and 8 chromosomes (HSA4, HSA8) and the Mus musculus 8 chromosome (MMU8). The fragmentary cytogenetic location of breaks is based on nine known loci and Zoo-FISH data on BTA27. A comparative mapping approach combining in-silico mapping and physical mapping by fluorescence in-situ hybridization (FISH) revealed an improved cytogenetic map of BTA27 based on 25 new and nine existing assignments of loci. Furthermore, hybrid cell mapping techniques identified and anchored three additional gene loci on BTA27. The BTA27 map was compared with available mapping and annotated sequence data for the chromosome and a generated comparative map displays conserved syntenic chromosome blocks between cattle, human, and mouse. The new anchor loci identify and narrow down evolutionary breakpoints on a cytogenetic level and can help to support the cattle genome assembly and annotation process.
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MESH Headings
- Animals
- Cattle/genetics
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 8
- Chromosomes, Mammalian
- Cytogenetics
- Electrophoresis, Agar Gel
- Gene Library
- Humans
- In Situ Hybridization, Fluorescence
- Mice
- Polymerase Chain Reaction
- Sequence Analysis, DNA
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Affiliation(s)
- Tom Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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29
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Uboldi C, Paulis M, Guidi E, Bertoni A, Meo GPD, Perucatti A, Iannuzzi L, Raimondi E, Brunner RM, Eggen A, Ferretti L. Cloning of the bovine prion-like Shadoo (SPRN) gene by comparative analysis of the predicted genomic locus. Mamm Genome 2006; 17:1130-9. [PMID: 17091316 DOI: 10.1007/s00335-006-0078-7] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 08/01/2006] [Indexed: 10/23/2022]
Abstract
SPRN is a new prion-like gene coding for Sho, a protein with significant similarity to PrP. SPRN was initially described in zebrafish; however, the strong evolutionary conservation led to the hypothesis that SPRN might be the ancestral prion-like gene. We mapped SPRN in Bos taurus by comparative analysis of the locus and of the predicted flanking genes. BACs, spanning the whole SPRN genomic locus, were assigned to BTA26q23 by radiation hybrid mapping and fluorescent in situ hybridization (FISH). Sequencing of five genes flanking SPRN, namely, ECHS1, PAOX, MTG1, SPRN, and CYP2E1, high-resolution FISH on mechanically stretched chromosomes, and combed BAC DNA allowed us to establish their order and reciprocal orientation. The results confirmed that BTA26q23 corresponds to HSA10q24.3-26.3, which is the site where the human SPRN is located. The gene order in Bos taurus is the same as in man, cen-ECHS1-PAOX-MTG1-SPRN-CYP2E1-tel, but PAOX has a different orientation in the two species. SPRN has the typical two-exon PRNP arrangement, with the CDS fully contained within exon 2; furthermore, it codes for a 143-amino-acid protein with 74.8% identity and 84.7% similarity with the human PRNP. RT-PCR and Northern blot analysis showed that SPRN is expressed at high levels in brain and less in testis and lung.
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Affiliation(s)
- Cristina Uboldi
- Department of Genetics and Microbiology A. Buzzati-Traverso, University of Pavia, Pavia, Italy
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30
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Loh G, Eberhard M, Brunner RM, Hennig U, Kuhla S, Kleessen B, Metges CC. Inulin alters the intestinal microbiota and short-chain fatty acid concentrations in growing pigs regardless of their basal diet. J Nutr 2006; 136:1198-202. [PMID: 16614404 DOI: 10.1093/jn/136.5.1198] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inulin stimulates intestinal bifidobacteria in humans and rodents but its effect in pigs is inconsistent. We assessed the effect of inulin on the intestinal microbiota by fluorescent in situ hybridization in growing pigs (age 9-12 wk). Pigs (n = 64) were assigned to 2 types of basal diets [wheat and barley (WB) or corn and wheat gluten (CG)] with or without 3% inulin (WBI or CGI) for 3 and 6 wk (n = 8/group) to test whether naturally occurring dietary fibers influence the inulin effect. Intestinal organic acids, pH values, and residual inulin were determined. The composition of the microbiota was highly individual. The duration of feeding did not affect any of the variables tested; therefore, data for the 2 periods were pooled. Bifidobacteria were detected in less than half of the pigs. Inulin did not stimulate lactobacilli and bifidobacteria numbers irrespective of the basal diet, although 20-50% of inulin was degraded in the jejunum. The number of pigs with colonic bifidobacteria was higher in those fed diets containing inulin (40 vs. 13%; P < 0.05). Total colonic short-chain fatty acid (SCFA) concentrations were lower in both inulin-fed groups due to reduced acetate (P < 0.05). Proportions of colonic butyrate were higher in pigs fed inulin-supplemented diets (P < 0.05). Colonic pH tended to be lower in the WB groups (WB; 6.6 +/- 0.6), and was higher due to inulin (CGI, 7.1 +/- 0.1; P < 0.05). In conclusion, inulin affected intestinal SCFA and the number of pigs harboring bifidobacteria; this effect was independent of the basal diet.
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Affiliation(s)
- Gunnar Loh
- Research Institute for the Biology of Farm Animals, Dummerstorf, Germany
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Goldammer T, Brunner RM, Kata SR, Womack JE. Assignment of the bovine receptor-interacting serine-threonine kinase 2 gene (RIPK2) to BTA14 with somatic and radiation cell hybrids. Cytogenet Genome Res 2006; 112:341C. [PMID: 16485369 DOI: 10.1159/000089893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- T Goldammer
- Research Unit Molecular Biology, Research Institute for the Biology of Farm Animals Dummerstorf, Dummerstorf, Germany
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Ponsuksili S, Brunner RM, Goldammer T, Kühn C, Walz C, Chomdej S, Tesfaye D, Schellander K, Wimmers K, Schwerin M. Bovine NALP5, NALP8, and NALP9 Genes: Assignment to a QTL Region and the Expression in Adult Tissues, Oocytes, and Preimplantation Embryos. Biol Reprod 2006; 74:577-84. [PMID: 16339045 DOI: 10.1095/biolreprod.105.045096] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A 3204-bp full-length cDNA of bovine NALP9 was cloned and its genomic organization was analyzed. The 2988-bp open reading frame covers 9 exons and encodes a deduced protein of 996 amino acids containing Pyrin, Nacht and leucine-rich repeat domains like the human NALP gene family members. Mapping with the WGRH5000 panel and fluorescence in situ hybridization assigned NALP9 in close vicinity to BM2078 (LOD score 25.71; distance 0.0 cR5000) on bovine chromosome 18, BTA18q25-q26, within a previously identified QTL region for reproductive traits flanked by the bovine marker BM2078 and TGLA227. BAC contig analysis revealed that NALP9, NALP8, and NALP5 map in this QTL region. Temporospatial expression of these members of the NALP gene family was monitored. Among the adult tissues examined, transcripts of NALP8 and NALP9 were detected exclusively in testis and ovary, whereas transcripts of the NALP5 gene are limited to the ovary. The transcripts of NALP9, NALP8, and NALP5 were detected in oocytes before and after in vitro maturation and with a gradual decline from 2-cell to 8-cell stage, suggesting no reactivation at the time of bovine maternal to embryonic transition. Assignment to a QTL region for reproductive traits and preferential expression of NALP9, NALP8, and NALP5 in oocyte, germinal lineage, and gonad cells may suggest their functional relevance to reproduction and possible contribution to phenotypic variation.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Group Functional Genomics, Research Institute for the Biology of Farm Animals (FBN), 18196 Dummerstorf, Germany
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Goldammer T, Brunner RM, Lyahyai J, Zaragoza P, Martín-Burriel I. Assignment of the bovine B-cell CLL/lymphoma 2 gene (BCL2) to BTA24q27 and the bovine BCL2-like 1 gene (BCL2L1) to BTA13q22 by in situ hybridization. Cytogenet Genome Res 2006; 112:341D. [PMID: 16484795 DOI: 10.1159/000089894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Accepted: 07/26/2005] [Indexed: 11/19/2022] Open
Affiliation(s)
- T Goldammer
- Research Unit Molecular Biology, Research Institute for the Biology of Farm Animals Dummerstorf (FBN), Dummerstorf, Germany
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Brunner RM, Kata SR, Womack JE, Goldammer T. Assignment of the bovine tumor protein D52 gene (TPD52) to the distal half of BTA14 with somatic and radiation cell hybrid panel mapping. Cytogenet Genome Res 2005; 111:96. [PMID: 16097081 DOI: 10.1159/000085676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- R M Brunner
- Research Institute for the Biology of Farm Animals Dummerstorf, Dummerstorf, Germany
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Martín-Burriel I, Lyahyai J, Zaragoza P, Brunner RM, Womack JE, Goldammer T. Assignment of the bovine BCL2-like 2 gene (BCL2L2) to BTA10q15-->q21 by in situ hybridization and with somatic cell hybrids. Cytogenet Genome Res 2005; 112:180A. [PMID: 16276654 DOI: 10.1159/000087533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- I Martín-Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria (INGEN, I3A), Universidad de Zaragoza, Zaragoza, Spain
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Rubes J, Kubickova S, Musilova P, Amaral ME, Brunner RM, Goldammer T. Assignment of chromosome rearrangements between X chromosomes of human and cattle by laser microdissection and Zoo-FISH. Chromosome Res 2005; 13:569-74. [PMID: 16170621 DOI: 10.1007/s10577-005-0982-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Cross-species fluorescence in-situ hybridization (Zoo-FISH) was performed on cattle metaphase spreads using Homo sapiens X chromosome (HSAX) painting probes specific for the p- and q-arms to identify the cytogenetic location of a chromosome breakpoint between HSAX and the Bos taurus X chromosome (BTAX). The existence of a breakpoint is strongly suggested by recent radiation hybrid and FISH mapping results. Hybridization probes were generated by microdissection of HSAX p- and q-arms using the contact-free technology of Laser Microdissection and Pressure Catapulting (LMPC), amplification of the isolated chromosome material by DOP-PCR, and labelling of the PCR products with digoxigenin in a secondary PCR. Independent Zoo-FISH of the two painting probes on bovine metaphase chromosomes (detected by antidigoxigenin-fluorescein) resulted in clear hybridization signals on BTAX. A breakpoint was identified between HSAXp and HSAXq on BTAX, and narrowed down between the G-bands BTAXq25 and BTAXq26. The assumed centromere transposition between HSAX and BTAX associated with the rearranged chromosome segments is supported by cytogenetic assignments of the genes BGN and G6PD to BTAX.
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Affiliation(s)
- Jiri Rubes
- Veterinary Research Institute, Hudcova 70, 621 32, Brno, Czech Republic
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Goldammer T, Kata SR, Brunner RM, Kühn C, Weikard R, Womack JE, Schwerin M. High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle. Genomics 2004; 84:696-706. [PMID: 15475247 DOI: 10.1016/j.ygeno.2003.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 12/10/2003] [Indexed: 11/30/2022]
Abstract
To get more information about the order of genes located in Bos taurus (BTA) chromosome 27 segments, supposed to harbor loci influencing clinical mastitis and somatic cell count, and to identify genes that serve as positional candidates for the mentioned traits, we constructed a high-resolution, comparative, and comprehensive gene map for BTA27. The map includes 57 loci in a 5000-rad cattle-hamster whole genome radiation hybrid panel supported by 50 syntenic assignments in a cattle-murine somatic hybrid cell panel. Thirty-eight new loci (36 genes, 2 microsatellites) together with repeated mappings of 5 genes and 7 microsatellites and integration of existing data from 7 microsatellites were used to generate a comprehensive RH5000 map. The RH map, constructed at lod score criterion 8 using the software RHMAP v.3.0, consisted of three linkage groups 23, 22, and 590 cR5000 in length. Gene assignments on BTA27 and the localization of 8 more genes on BTA8 and BTA14 previously predicted on BTA8/BTA27 and BTA14/BTA27 narrowed down significantly the chromosome break points between the three cattle chromosomes and segments on Homo sapiens chromosomes HSA4 and HSA8. Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27.
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Affiliation(s)
- Tom Goldammer
- Research Unit Molecular Biology, Research Institute for the Biology of Farm Animals (FBN), D-18196 Dummerstorf, Germany.
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Goldammer T, Zerbe H, Molenaar A, Schuberth HJ, Brunner RM, Kata SR, Seyfert HM. Mastitis increases mammary mRNA abundance of beta-defensin 5, toll-like-receptor 2 (TLR2), and TLR4 but not TLR9 in cattle. Clin Diagn Lab Immunol 2004; 11:174-85. [PMID: 14715566 PMCID: PMC321333 DOI: 10.1128/cdli.11.1.174-185.2004] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Coordination of the primary defense mechanisms against pathogens relies on the appropriate expression of pathogen recognition receptors (PRRs) triggering the early release of effector molecules of the innate immune system. To analyze the impact of this system on the counteraction of infections of the mammary gland (mastitis), we characterized the bovine gene encoding the key PRR Toll-like receptor 9 (TLR9) and mapped its precise position on chromosome BTA22. The sequence information was used to establish real-time PCR quantification assays to measure the mRNA abundances of TLR9, TLR2, and TLR4 together with those of beta-defensin 5 (BNBD5), an early bactericidal effector molecule of the innate system, in healthy and infected mammary glands. Mastitis strongly increased (4- to 13-fold) the mRNA abundances of all of these genes except TLR9. Slight subclinical infections already caused a substantial increase in the copy numbers, though they did so the least for TLR9. Induction was not systemic, since mRNA abundance was low in uninfected control quarters of the udder but high in the severely infected quarters of the same animal. The number of TLR2 copies correlated well with those of TLR4, indicating coordinated regulation of these two PRRs during infection of the udder. Their coordinated regulation explains our unexpected observation that pure Staphylococcus aureus infections caused a strong increase also in TLR4 mRNA abundance. In situ hybridizations revealed that BNBD5 is expressed predominantly in the mammary epithelial cells (MEC) of the infected gland. Our data therefore suggest a significant contribution of the innate immune system to counteract mastitis and attribute a prominent effector function to the MEC.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cattle
- Chromosome Mapping
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- Female
- Gene Expression
- Immunity, Innate
- Mammary Glands, Animal/immunology
- Mammary Glands, Animal/pathology
- Mastitis, Bovine/genetics
- Mastitis, Bovine/immunology
- Mastitis, Bovine/pathology
- Membrane Glycoproteins/genetics
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface/genetics
- Sequence Homology, Amino Acid
- Staphylococcus aureus/pathogenicity
- Toll-Like Receptor 2
- Toll-Like Receptor 4
- Toll-Like Receptor 9
- Toll-Like Receptors
- beta-Defensins/genetics
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Affiliation(s)
- T Goldammer
- Molecular Biology Research Division, Research Institute for the Biology of Farm Animals, 18196 Dummerstorf, Germany
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Goldammer T, Amaral MEJ, Brunner RM, Owens E, Kata SR, Schwerin M, Womack JE. Clarifications on breakpoints in HSAX and BTAX by comparative mapping of F9, HPRT, and XIST in cattle. Cytogenet Genome Res 2004; 101:39-42. [PMID: 14571135 DOI: 10.1159/000073416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2003] [Accepted: 04/16/2003] [Indexed: 11/19/2022] Open
Abstract
The coagulation factor IX gene (F9), the hypoxanthine phosphoribosyl transferase 1 gene (HPRT1), and the X-inactive specific transcript gene (XIST) were physically assigned in cattle to analyze chromosomal breakpoints on BTAX recently identified by radiation hybrid (RH) mapping experiments. Whereas the FISH assignment of XIST indicates a similar location on the q-arm of the human and cattle X chromosomes, the locus of HPRT1 supported the assumption of a chromosome rearrangement between the distal half of the q-arm of HSAX and the p-arm of BTAX identified by RH mapping. F9 previously located on the q-arm of BTAX was assigned to the p-arm of BTAX using RH mapping and FISH. The suggested new position of F9 close to HPRT1 supports the homology between HSAXq and BTAXp. The F9 locus corresponds with the gene order found in the homologous human chromosome segment. XIST was assigned on BTAXq23, HPRT1 and F9 were mapped to BTAXp22, and the verification of the location of F9 in a 5000 rad cattle-hamster whole genome radiation hybrid panel linked the gene to markers URB10 and HPRT1.
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Affiliation(s)
- T Goldammer
- Department of Molecular Biology, FBN-Research Institute for the Biology of Farm Animals, Dummerstorf, Germany.
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Goldammer T, Rottengatter K, Weikard R, Horstmann R, Gehlhaus A, Brunner RM, Hanotte O, Schwerin M. Targeted Generation of 16 Sequence-Tagged Sites for Bovine Chromosome Region 5q21-q25 by Microdissection. Chromosome Res 2004; 12:309-15. [PMID: 15241011 DOI: 10.1023/b:chro.0000034102.54635.b9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cattle chromosome region BTA5q21-q25 is associated with immune defense and is linked with several economically important traits for growth, ovulation, twinning and milk yield. Chromosome microdissection of the region was performed to generate fragment-specific DNA libraries and to provide new bovine-specific DNA sequences as starting material for physical fine-mapping approaches or linkage studies. A first library screening resulted in the identification of 16 region-specific sequence-tagged sites (STS). Fifteen STS represent new unique cattle DNA sequences, of which one identifies a new microsatellite. Homology with the gene CDK2 was found for the remaining STS.
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Affiliation(s)
- Tom Goldammer
- Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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Goldammer T, Owens E, Brunner RM, Kata SR, Womack JE, Schwerin M. Assignment of syndecan 2 (SDC2)gene to cattle chromosome band 14q22 and thymus high mobility group box protein TOX (TOX)(2) gene to cattle chromosome band 14q17-->q18 by in situ hybridization. Cytogenet Genome Res 2003; 98:311B. [PMID: 12826761 DOI: 10.1159/000071056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2003] [Accepted: 03/20/2003] [Indexed: 11/19/2022] Open
Affiliation(s)
- T Goldammer
- Department of Molecular Biology, FBN-Research Institute for the Biology of Farm Animals, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany.
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Schwerin M, Czernek-Schäfer D, Goldammer T, Kata SR, Womack JE, Pareek R, Pareek C, Walawski K, Brunner RM. Application of disease-associated differentially expressed genes--mining for functional candidate genes for mastitis resistance in cattle. Genet Sel Evol 2003; 35 Suppl 1:S19-34. [PMID: 12927078 PMCID: PMC3231760 DOI: 10.1186/1297-9686-35-s1-s19] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In this study the mRNA differential display method was applied to identify mastitis-associated expressed DNA sequences based on different expression patterns in mammary gland samples of non-infected and infected udder quarters of a cow. In total, 704 different cDNA bands were displayed in both udder samples. Five hundred-and-thirty two bands, (75.6%) were differentially displayed. Ninety prominent cDNA bands were isolated, re-amplified, cloned and sequenced resulting in 87 different sequences. Amongst the 19 expressed sequence tags showing a similarity with previously described genes, the majority of these sequences exhibited homology to protein kinase encoding genes (26.3%), to genes involved in the regulation of gene expression (26.3%), to growth and differentiation factor encoding genes (21.0%) and to immune response or inflammation marker encoding genes (21.0%). These sequences were shown to have mastitis-associated expression in the udder samples of animals with and without clinical mastitis by quantitative RT-PCR. They were mapped physically using a bovine-hamster somatic cell hybrid panel and a 5000 rad bovine whole genome radiation hybrid panel. According to their localization in QTL regions based on an established integrated marker/gene-map and their disease-associated expression, four genes (AHCY, PRKDC, HNRPU, OSTF1) were suggested as potentially involved in mastitis defense.
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Affiliation(s)
- Manfred Schwerin
- Research Unit for Molecular Biology, Research Institute for the Biology of Farm Animals, Dummerstorf, Germany.
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Brunner RM, Sanftleben H, Goldammer T, Kühn C, Weikard R, Kata SR, Womack JE, Schwerin M. The telomeric region of BTA18 containing a potential QTL region for health in cattle exhibits high similarity to the HSA19q region in humans. Genomics 2003; 81:270-8. [PMID: 12659811 DOI: 10.1016/s0888-7543(03)00019-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have applied a targeted physical mapping approach, based on the isolation of bovine region-specific large-insert clones using homologous human sequences and chromosome microdissection, to enhance the physical gene map of the telomeric region of BTA18 and to prove its evolutionary conservation. The latter is a prerequisite to exploit the dense human gene map for future positional cloning approaches. Partial sequencing and homology search were used to characterize 20 BACs targeted to the BTA18q2.4-q2.6 region. We used fluorescence in situ hybridization (FISH) to create physical maps of 11 BACs containing 15 gene loci; these BACs served as anchor loci. Using these approaches, 12 new gene loci (CKM, STK13, PSCD2, IRF3, VASP, ACTN4, ITPKC, CYP2B6, FOSB, DMPK, MIA, SIX5) were assigned on BTA18 in the bovine cytogenetic map. A resolved physical map of BTA18q2.4-q2.6 was developed, which encompasses 28 marker loci and a comparative cytogenetic map that contains 15 genes. The mapping results demonstrate the high evolutionary conservation between the telomeric region of BTA18q and HSA19q.
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Affiliation(s)
- Ronald M Brunner
- Research Unit for Molecular Biology, Research Institute for the Biology of Farm Animals Dummerstorf, D-18196 Dummerstorf, Germany
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Goldammer T, Dorroch U, Brunner RM, Kata SR, Womack JE, Schwerin M. Identification and chromosome assignment of 23 genes expressed in meat and dairy cattle. Chromosome Res 2002; 10:411-8. [PMID: 12296524 DOI: 10.1023/a:1016857820524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Hepatic and intestinal expressed sequence tags (ESTs) of lactating German Holstein and Charolais cows were used to identify and map genes potentially involved in the regulation of metabolic processes in cattle. Seventeen ESTs were homologous to human gene sequences and six ESTs identified unknown coding sequences in human genomic DNA clones. A cattle-hamster somatic hybrid cell panel and cattle-hamster 5000 rad whole genome radiation hybrid (WGRH) panel were used to assign the ESTs in the bovine genome. Fifteen of the mapped genes and the six ESTs represent new assignments in the established cattle WGRH5000 map. Calculation of the radiation hybrid (RH) mapping data was performed with the software RHMAPPER. The new loci contribute to the completion of the bovine transcript maps and their comparative assignments increase our knowledge about genome evolution between cattle and human.
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Affiliation(s)
- Tom Goldammer
- Department of Veterinary Pathobiology, Texas A&M University, College Station 77843, USA.
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Goldammer T, Kata SR, Brunner RM, Schwerin M, Womack JE. Comparative mapping of five coding DNA sequences on cattle chromosomes 7 and 25. Cytogenet Genome Res 2002; 95:192-5. [PMID: 12063399 DOI: 10.1159/000059345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Comparative mapping of four genes and one unknown coding DNA sequence in breakpoint positions of bovine chromosomes (BTA) 7 and 25 are presented. Performing a genome data base search five bovine expressed sequence tags from the MARC library matched with human genes coding for the general transcription factor IIIC polypeptide 1 (GTF3C1), the hypothetical protein KIAA0556, the interleukin 4 receptor (IL4R), the regulatory factor X-associated ankyrin-containing protein (RFXANK), and with an unknown human coding sequence partially homologous to the genomic cosmid clone R30923. Loci for these sequences were COMPASS predicted on BTA7 or BTA18 and to BTA18 or BTA25. Mapping was performed in a cattle-hamster somatic hybrid cell panel and a cattle-hamster 5000 rad whole genome radiation hybrid panel. GTF3C1, KIAA0556 and IL4R were assigned to the centromere region of BTA25 and RFXANK and R30923 close to the centromere of BTA7. The assignments contribute to the identification of evolutionary chromosome break points between human chromosomes 16 and 19 and BTA7, BTA18, and BTA25.
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Affiliation(s)
- T Goldammer
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA.
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Goldammer T, Kata SR, Brunner RM, Dorroch U, Sanftleben H, Schwerin M, Womack JE. A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice. Proc Natl Acad Sci U S A 2002; 99:2106-11. [PMID: 11854506 PMCID: PMC122326 DOI: 10.1073/pnas.042688699] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comprehensive radiation hybrid (RH) map and a high resolution comparative map of Bos taurus (BTA) chromosome 18 were constructed, composed of 103 markers and 76 markers, respectively, by using a cattle-hamster somatic hybrid cell panel and a 5,000 rad whole-genome radiation hybrid (WGRH) panel. These maps include 65 new assignments (56 genes, 3 expressed-sequence tags, 6 microsatellites) and integrate 38 markers from the first generation WGRH(5,000) map of BTA18. Fifty-nine assignments of coding sequences were supported by somatic hybrid cell mapping to markers on BTA18. The total length of the comprehensive map was 1666 cR(5,000). Break-point positions within the chromosome were refined and a new telomeric RH linkage group was established. Conserved synteny between cattle, human, and mouse was found for 76 genes of BTA18 and human chromosomes (HSA) 16 and 19 and for 34 cattle genes and mouse chromosomes (MMU) 7 and 8. The new RH map is potentially useful for the identification of candidate genes for economically important traits, contributes to the expansion of the existing BTA18 gene map, and provides new information about the chromosome evolution in cattle, humans, and mice.
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Affiliation(s)
- Tom Goldammer
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
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Weikard R, Kühn C, Brunner RM, Roschlau D, Pitra C, Laurent P, Schwerin M. Sex determination in cattle based on simultaneous amplification of a new male-specific DNA sequence and an autosomal locus using the same primers. Mol Reprod Dev 2001; 60:13-9. [PMID: 11550263 DOI: 10.1002/mrd.1056] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A PCR-based method for sex determination of bovine DNA samples and embryo biopsies is presented. Using only one primer pair both the male-specific sequence FBNY (127 bp) and a sex-independent control PCR-fragment, the microsatellite marker FBN17 (136-140 bp) are generated in the same PCR reaction. Synteny mapping assigned the male-specific sequence to bovine chromosome Y (BTA Y), whereas FBN17 was mapped to bovine chromosome 2. Localisation of FBNY on BTA Y was confirmed by fluorescence in hybridisation of two BAC clones containing the male-specific sequence. There was no amplification of the male-specific target sequence FBNY in sheep, pig, goat, mice, man, and several wild species of the tribe Bovini. The bovine male-specific fragment was detected in dilutions containing as little as 10 pg genomic DNA and in blastomeres from embryo biopsies. The PCR assay presented here does require neither restriction endonuclease digestion of the PCR product nor additional nested PCR steps. Owing to the advantage of parallel amplification of the autosomal locus FBN17 no additional control fragment is necessary to detect PCR failure. The results of sex determination in embryo biopsies using FBNY were in agreement with the outcome from a reference assay used in commercial breeding programs.
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Affiliation(s)
- R Weikard
- Forschungsinstitut für die Biologie Landwirtschaftlicher Nutztiere, Forschungsbereich Molekularbiologie, Dummerstorf, Germany.
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Abstract
OBJECTIVE To determine if orally delivered tizanidine will control spastic hypertonia due to acquired brain injury. DESIGN Randomized, double-blind, placebo-controlled, crossover design, with 2 8-week treatment arms separated by a 1-week washout period at baseline. Patients were randomly assigned to receive tizanidine or a matching placebo. SETTING Tertiary care outpatient and inpatient rehabilitation center attached to a university hospital. PARTICIPANTS Seventeen persons recruited in a consecutive manner, 9 of whom had suffered a stroke and 8 a traumatic brain injury, and had more than 6 months of intractable spastic hypertonia. INTERVENTION Over a 6-week period, subjects were slowly titrated up to their maximum tolerated dose (up to 36 mg/d). Following a 1-week drug taper and 1-week period in which no study drug was administered, patients were then crossed over to the other study medication following an identical titration regime. MAIN OUTCOME MEASURES Subjects were evaluated for dose and effect throughout the trial as well as for side effects. Data for Ashworth rigidity scores, spasm scores, deep tendon reflex scores, and motor strength were collected on the affected upper extremity (UE) and lower extremity (LE). Differences over time were assessed via descriptive statistics, Friedman's analysis, and Wilcoxon's signed-rank. Data are reported as the mean +/- 1 standard deviation. RESULTS Following 4 weeks of treatment when subjects reached their maximal tolerated dosage, the average LE Ashworth score on the affected side decreased from 2.3 +/- 1.4 to 1.7 +/- 1.1 (p <.0001). The spasm score decreased from 1.0 +/- 0.9 to 0.5 +/- 0.8 (p =.0464), while the reflex score was not statistically significant decreasing from 2.2 +/- 1.0 to 2.0 +/- 1.1 (p =.0883). The average UE Ashworth score on the affected side decreased from 1.9 +/- 1.1 to 1.5 +/- 0.9 (p <.0001). There was no significant change in the UE spasm and reflex scores. While there were positive placebo effects on motor tone, the active drug was still significantly better than placebo for decreasing LE tone (p =.0006) and UE tone (p =.0007). With a reduction in motor tone, there was an increase in motor strength (p =.0089). The average dosage at 4 weeks was 25.2mg/d. CONCLUSION Tizanidine is effective in decreasing the spastic hypertonia associated with acquired brain injury, which is dose-dependent. There are limitations on its use due to side effects related to drowsiness.
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Affiliation(s)
- J M Meythaler
- Department of Physical Medicine and Rehabilitation, University of Alabama School of Medicine, Birmingham, AL, USA.
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Dorroch U, Goldammer T, Brunner RM, Kata SR, Kühn C, Womack JE, Schwerin M. Isolation and characterization of hepatic and intestinal expressed sequence tags potentially involved in trait differentiation between cows of different metabolic type. Mamm Genome 2001; 12:528-37. [PMID: 11420616 DOI: 10.1007/s003350020031] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2000] [Accepted: 02/14/2001] [Indexed: 10/28/2022]
Abstract
mRNA differential display was applied to identify hepatic and intestinal expressed sequence tags (ESTs) in lactating cows of different metabolic types (milk type, meat/milk type, meat type) that are potentially associated with energy turnover and involved in the regulation of these processes. Altogether, 277 ESTs (liver: 161, intestine: 116) were identified. For 150 transcripts (liver: 99, intestine: 51), the sequences showed similarity to previously described genes and ESTs. Many of these homologous sequences are reported to be involved in hepatic metabolism. Ninety-four ESTs (liver: 43, intestine: 51) did not match with any database entries. Semi-quantitative RT-PCR revealed quantitative differences in transcript represented by randomly chosen ESTs in liver samples of animals of the Holstein and Charolais breeds. One hundred twenty-two ESTs were mapped physically by using a bovine-hamster somatic cell hybrid panel (SCP) and a 5000-rad bovine whole genome radiation hybrid panel (WGRH). These ESTs were assigned to the bovine syntenic groups and positioned in the recently established RH-based ordered comparative map of the cattle and human genomes. The mapped, differentially expressed sequence tags are a useful prerequisite for cloning of genetic variation underlying economic traits.
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Affiliation(s)
- U Dorroch
- Research Unit for Molecular Biology, Research Institute for the Biology of Farm Animals Dummerstorf, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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Brunner RM, Goldammer T, Fürbass R, Vanselow J, Schwerin M. Genomic organization of the bovine aromatase encoding gene and a homologous pseudogene as revealed by DNA fiber FISH. Cytogenet Cell Genet 2000; 82:37-40. [PMID: 9763656 DOI: 10.1159/000015060] [Citation(s) in RCA: 18] [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] [Indexed: 11/19/2022]
Abstract
In cattle, the CYP19 locus comprises the aromatase cytochrome P450-encoding gene (CYP19) and a homologous pseudogene (CYP19P1). It has been assigned to chromosome region 10q26. Cloning of genomic DNA revealed that the CYP19 gene covers more than 56 kb. Its precise extent is still unknown because the DNA spanning the untranslated first exon 1.1 and the coding region (exons 2 to 10) have not been isolated. Furthermore, the chromosome arrangement of closely linked CYP19 and CYP19P1 was also not clear. To establish a high resolution physical map of the entire CYP19 locus, fluorescence in situ hybridization to extended bovine genomic DNA fibers (fiber FISH) was performed. The results demonstrate (1) that the clone containing exon 1.1 is located about 19 kb upstream from the CYP19 coding region. (2) Within the chromosome region 10q26 CYP19 and CYP19P1 are arranged "tail-to-head", being separated by a distance of about 24 kb between the labeled clones. (3) The physical size of the bovine CYP19 locus amounts to a minimum of 130 kb.
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Affiliation(s)
- R M Brunner
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere Dummerstorf, Dummerstorf, Germany.
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