TY - JOUR A1 - Bayerl, Helmut A1 - Kraus, Robert H. S. A1 - Nowak, Carsten A1 - Foerster, Daniel W. A1 - Fickel, Jörns A1 - Kühn, Ralph T1 - Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq) JF - Molecular ecology resources N2 - Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies. KW - high-throughput sequencing KW - Lutra lutra KW - nonmodel species KW - RAMseq KW - RAPD KW - variant detection Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12717 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 1 SP - 107 EP - 117 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Förster, Daniel W. A1 - Bull, James K. A1 - Lenz, Dorina A1 - Autenrieth, Marijke A1 - Paijmans, Johanna L. A. A1 - Kraus, Robert H. S. A1 - Nowak, Carsten A1 - Bayerl, Helmut A1 - Kühn, Ralph A1 - Saveljev, Alexander P. A1 - Sindicic, Magda A1 - Hofreiter, Michael A1 - Schmidt, Krzysztof A1 - Fickel, Jörns T1 - Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species JF - Molecular ecology resources N2 - Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. KW - CDS KW - conservation genetics KW - Eurasian lynx KW - genetic monitoring KW - hybridization capture KW - single nucleotide polymorphism Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12924 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1356 EP - 1373 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Wuertz-Kozak, Karin A1 - Roszkowski, Martin A1 - Cambria, Elena A1 - Block, Andrea A1 - Kuhn, Gisela A. A1 - Abele, Thea A1 - Hitzl, Wolfgang A1 - Drießlein, David A1 - Müller, Ralph A1 - Rapp, Michael A. A1 - Mansuy, Isabelle M. A1 - Peters, Eva M. J. A1 - Wippert, Pia-Maria T1 - Effects of Early Life Stress on Bone Homeostasis in Mice and Humans T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - Bone pathology is frequent in stressed individuals. A comprehensive examination of mechanisms linking life stress, depression and disturbed bone homeostasis is missing. In this translational study, mice exposed to early life stress (MSUS) were examined for bone microarchitecture (μCT), metabolism (qPCR/ELISA), and neuronal stress mediator expression (qPCR) and compared with a sample of depressive patients with or without early life stress by analyzing bone mineral density (BMD) (DXA) and metabolic changes in serum (osteocalcin, PINP, CTX-I). MSUS mice showed a significant decrease in NGF, NPYR1, VIPR1 and TACR1 expression, higher innervation density in bone, and increased serum levels of CTX-I, suggesting a milieu in favor of catabolic bone turnover. MSUS mice had a significantly lower body weight compared to control mice, and this caused minor effects on bone microarchitecture. Depressive patients with experiences of childhood neglect also showed a catabolic pattern. A significant reduction in BMD was observed in depressive patients with childhood abuse and stressful life events during childhood. Therefore, future studies on prevention and treatment strategies for both mental and bone disease should consider early life stress as a risk factor for bone pathologies. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 670 KW - psychosocial stress KW - bone pathologies KW - osteoporosis KW - bone mineral density KW - childhood KW - neuroendocrine Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-485324 SN - 1866-8364 IS - 670 ER - TY - JOUR A1 - Wuertz-Kozak, Karin A1 - Roszkowski, Martin A1 - Cambria, Elena A1 - Block, Andrea A1 - Kuhn, Gisela A. A1 - Abele, Thea A1 - Hitzl, Wolfgang A1 - Drießlein, David A1 - Müller, Ralph A1 - Rapp, Michael A. A1 - Mansuy, Isabelle M. A1 - Peters, Eva M. J. A1 - Wippert, Pia-Maria T1 - Effects of Early Life Stress on Bone Homeostasis in Mice and Humans JF - International Journal of Molecular Sciences N2 - Bone pathology is frequent in stressed individuals. A comprehensive examination of mechanisms linking life stress, depression and disturbed bone homeostasis is missing. In this translational study, mice exposed to early life stress (MSUS) were examined for bone microarchitecture (μCT), metabolism (qPCR/ELISA), and neuronal stress mediator expression (qPCR) and compared with a sample of depressive patients with or without early life stress by analyzing bone mineral density (BMD) (DXA) and metabolic changes in serum (osteocalcin, PINP, CTX-I). MSUS mice showed a significant decrease in NGF, NPYR1, VIPR1 and TACR1 expression, higher innervation density in bone, and increased serum levels of CTX-I, suggesting a milieu in favor of catabolic bone turnover. MSUS mice had a significantly lower body weight compared to control mice, and this caused minor effects on bone microarchitecture. Depressive patients with experiences of childhood neglect also showed a catabolic pattern. A significant reduction in BMD was observed in depressive patients with childhood abuse and stressful life events during childhood. Therefore, future studies on prevention and treatment strategies for both mental and bone disease should consider early life stress as a risk factor for bone pathologies. KW - psychosocial stress KW - bone pathologies KW - osteoporosis KW - bone mineral density KW - childhood KW - neuroendocrine Y1 - 2020 U6 - https://doi.org/10.3390/ijms21186634 SN - 1422-0067 VL - 21 IS - 18 PB - Molecular Diversity Preservation International CY - Basel ER -