Hummel, Susanne

[["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","BioTechniques"],["dc.bibliographiccitation.volume","72"],["dc.contributor.author","Wittmeier, Patrick"],["dc.contributor.author","Hummel, Susanne"],["dc.date.accessioned","2022-04-01T10:01:30Z"],["dc.date.available","2022-04-01T10:01:30Z"],["dc.date.issued","2022"],["dc.description.abstract","Agarose gel electrophoresis is a relatively easy to use method, commonly applied to evaluate PCR reaction success. Intercalating agents or dyes are used to visualize the amplified fragments. However, it is uncertain to what extent the brightness of bands is informative about the concentration of the amplicons. To more closely examine the suitability of agarose gel electrophoresis to assess PCR product yield, we quantified the brightness of bands on a gel and compared these data with the results from spectrophotometry, fluorometry and qPCR. Evaluation of the results suggests that assessment of the relative quantity of amplicons by band brightness is precise enough even for post-PCR analysis steps requiring PCR product concentrations within a certain range to function properly."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2022"],["dc.identifier.doi","10.2144/btn-2021-0094"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105680"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.eissn","1940-9818"],["dc.relation.issn","0736-6205"],["dc.rights","CC BY-NC-ND 4.0"],["dc.title","Agarose gel electrophoresis to assess PCR product yield: comparison with spectrophotometry, fluorometry and qPCR"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","137"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Entomological Science"],["dc.bibliographiccitation.lastpage","141"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Buesse, Sebastian"],["dc.contributor.author","von Grumbkow, Philipp"],["dc.contributor.author","Mazanec, Janine"],["dc.contributor.author","Troester, Gert"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Hoernschemeyer, Thomas"],["dc.date.accessioned","2018-11-07T10:28:52Z"],["dc.date.available","2018-11-07T10:28:52Z"],["dc.date.issued","2017"],["dc.description.abstract","A protocol using insect specimens or parts thereof allows for sequencing of sections of nuclear 28S rDNA. In the present note it is demonstrated that this protocol can readily be applied to strongly degraded DNA (ancient, fixed or contaminated). Primers that are specifically designed to discriminate against humanDNAbut also other non-arthropod species are tested on a range of species covering all insect groups (59 insect species from all 33 orders). Additionally, the samples represent a selection of various, mostly DNA-degrading, preservation methods, including the most common fixatives used for morphological investigations and for long-term storage in collections. Successful amplification was possible for all tested samples including ca. 200 year-old dried museum specimens as well as for over 4000 year-old fossil insects embedded in copal. When the NCBI database contained information on the tested species an unambiguous taxonomic discrimination was possible. This approach is based on a standardized protocol that guarantees easy application. This note presents primer pairs for 28S rDNA that can be a useful tool for ancient DNA (aDNA) research."],["dc.identifier.doi","10.1111/ens.12242"],["dc.identifier.isi","000396406800017"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/43520"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Wiley"],["dc.relation.issn","1479-8298"],["dc.relation.issn","1343-8786"],["dc.title","Note on using nuclear 28S rDNA for sequencing ancient and strongly degraded insect DNA"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3224"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of Archaeological Science"],["dc.bibliographiccitation.lastpage","3229"],["dc.bibliographiccitation.volume","39"],["dc.contributor.author","Seidenberg, Verena"],["dc.contributor.author","Schilz, Felix"],["dc.contributor.author","Pfister, Daniela"],["dc.contributor.author","Georges, Lea E."],["dc.contributor.author","Fehren-Schmitz, Lars"],["dc.contributor.author","Hummel, Susanne"],["dc.date.accessioned","2018-11-07T09:05:33Z"],["dc.date.available","2018-11-07T09:05:33Z"],["dc.date.issued","2012"],["dc.description.abstract","The analysis of short tandem repeats (STRs) is a useful tool in various contexts of ancient DNA research. Main applications are the reconstruction of kinship, identification, and authentication. Here we describe a short amplicon autosomal short tandem repeat (miniSTR) heptaplex system for the amplification of D13S317, D21S11, D18S51, TH01, D5S818, FGA and Amelogenin from highly degraded DNA as an inexpensive alternative to commercially available kits. All primers were newly designed and the amplicon length of all systems is less than 200 bp, with the exception of some rare alleles in the FGA and D21S11 systems. To validate the suitability of this system for typing STRs from human specimens with low DNA preservation we systematically tested it on 20 skeletal samples from four archaeological sites representing different burial environments and time spans since death. Finally, to test the sensitivity of the heptaplex system, we analyzed serial dilutions of control DNA and ancient DNA extracts. Using the system we were able to reproducibly obtain full STR profiles, down to a concentration of 0.06 ng DNA. Even with 0.004 ng DNA partial profiles could be amplified. The accumulated power of discrimination for the six selected STR loci is 0.99999984, plus the option of genetic sex determination through Amelogenin. The tests conducted prove that the system presented is efficient and especially suited for cases where STRs have to be typed and sex has to be assessed from human specimens with highly degraded DNA. (C) 2012 Elsevier Ltd. All rights reserved."],["dc.identifier.doi","10.1016/j.jas.2012.05.019"],["dc.identifier.isi","000308452600016"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/25349"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Academic Press Ltd- Elsevier Science Ltd"],["dc.relation.issn","0305-4403"],["dc.title","A new miniSTR heptaplex system for genetic fingerprinting of ancient DNA from archaeological human bone"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","7"],["dc.bibliographiccitation.journal","Mobile DNA"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Kothe, Maximilian"],["dc.contributor.author","Seidenberg, Verena"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Piskurek, Oliver"],["dc.date.accessioned","2018-11-07T10:15:29Z"],["dc.date.available","2018-11-07T10:15:29Z"],["dc.date.issued","2016"],["dc.description.abstract","Background: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. Results: For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. Conclusions: Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome."],["dc.identifier.doi","10.1186/s13100-016-0063-y"],["dc.identifier.isi","000374742800001"],["dc.identifier.pmid","27096009"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13219"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/40820"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Biomed Central Ltd"],["dc.relation.issn","1759-8753"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","266"],["dc.bibliographiccitation.journal","Annals of Human Genetics"],["dc.bibliographiccitation.lastpage","283"],["dc.bibliographiccitation.volume","75"],["dc.contributor.author","Fehren-Schmitz, Lars"],["dc.contributor.author","Warnberg, Ole"],["dc.contributor.author","Reindel, Markus"],["dc.contributor.author","Seidenberg, Verena"],["dc.contributor.author","Tomasto-Cagigao, Elsa"],["dc.contributor.author","Isla-Cuadrado, Johny"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Herrmann, Bernd"],["dc.date.accessioned","2018-11-07T08:58:54Z"],["dc.date.available","2018-11-07T08:58:54Z"],["dc.date.issued","2011"],["dc.description.abstract","P>This study examines the reciprocal effects of cultural evolution, and population dynamics in pre-Columbian southern Peru by the analysis of DNA from pre-Columbian populations that lived in the fringe area between the Andean highlands and the Pacific coast. The main objective is to reveal whether the transition from the Middle Horizon (MH: 650-1000 AD) to the Late Intermediate Period (LIP: 1000-1400 AD) was accompanied or influenced by population dynamic processes. Tooth samples from 90 individuals from several archaeological sites, dating to the MH and LIP, in the research area were collected to analyse mitochodrial, and Y-chromosomal genetic markers. Coding region polymorphisms were successfully analysed and replicated for 72 individuals, as were control region sequences for 65 individuals and Y-chromosomal single nucleotide polymorphisms (SNPs) for 19 individuals, and these were compared to a large set of ancient and modern indigenous South American populations. The diachronic comparison of the upper valley samples from both time periods reveals no genetic discontinuities accompanying the cultural dynamic processes. A high genetic affinity for other ancient and modern highland populations can be observed, suggesting genetic continuity in the Andean highlands at the latest from the MH. A significant matrilineal differentiation to ancient Peruvian coastal populations can be observed suggesting a differential population history."],["dc.description.sponsorship","German Federal Ministry of Education and Research [01UA0804B]"],["dc.identifier.doi","10.1111/j.1469-1809.2010.00620.x"],["dc.identifier.isi","000287247100008"],["dc.identifier.pmid","21091452"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/23756"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0003-4800"],["dc.title","Diachronic Investigations of Mitochondrial and Y-Chromosomal Genetic Markers in Pre-Columbian Andean Highlanders from South Peru"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","99"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","American Journal of Physical Anthropology"],["dc.bibliographiccitation.lastpage","109"],["dc.bibliographiccitation.volume","172"],["dc.contributor.author","Schmidt, Nicole"],["dc.contributor.author","Schücker, Katharina"],["dc.contributor.author","Krause, Ina"],["dc.contributor.author","Dörk, Thilo"],["dc.contributor.author","Klintschar, Michael"],["dc.contributor.author","Hummel, Susanne"],["dc.date.accessioned","2021-04-14T08:27:44Z"],["dc.date.available","2021-04-14T08:27:44Z"],["dc.date.issued","2020"],["dc.description.abstract","Abstract Objective A genome‐wide high‐throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini‐sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. Material and methods The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm®. Results Thirty‐eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified. Discussion The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable."],["dc.identifier.doi","10.1002/ajpa.23996"],["dc.identifier.eissn","1096-8644"],["dc.identifier.issn","0002-9483"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82386"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.publisher","John Wiley \\u0026 Sons, Inc."],["dc.relation.eissn","1096-8644"],["dc.relation.issn","0002-9483"],["dc.rights","This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited."],["dc.title","Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","208"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","American Journal of Physical Anthropology"],["dc.bibliographiccitation.lastpage","221"],["dc.bibliographiccitation.volume","141"],["dc.contributor.author","Fehren-Schmitz, Lars"],["dc.contributor.author","Reindel, Markus"],["dc.contributor.author","Cagigao, Elsa Tomasto"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Herrmann, Bernd"],["dc.date.accessioned","2018-11-07T08:45:58Z"],["dc.date.available","2018-11-07T08:45:58Z"],["dc.date.issued","2010"],["dc.description.abstract","Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. Am J Phys Anthropol 141:208-221, 2010. (C) 2009 Wiley-Liss, Inc."],["dc.description.sponsorship","German Federal Ministry of Education and Research (BMBF) [03HEX1VP]"],["dc.identifier.doi","10.1002/ajpa.21135"],["dc.identifier.isi","000273749100004"],["dc.identifier.pmid","19639639"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/20578"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0002-9483"],["dc.title","Pre-Columbian Population Dynamics in Coastal Southern Peru: A Diachronic Investigation of mtDNA Patterns in the Palpa Region by Ancient DNA Analysis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","242"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","American Journal of Physical Anthropology"],["dc.bibliographiccitation.lastpage","249"],["dc.bibliographiccitation.volume","149"],["dc.contributor.author","Georges, Lea E."],["dc.contributor.author","Seidenberg, Verena"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Fehren-Schmitz, Lars"],["dc.date.accessioned","2018-11-07T09:05:19Z"],["dc.date.available","2018-11-07T09:05:19Z"],["dc.date.issued","2012"],["dc.description.abstract","The majority of Native Americans nearly exclusively belong to group O of the ABO blood group system. Several hypotheses have been formulated to explain this observation, primarily differing by the presumption that the observed patterns of ABO diversity are due to the processes of the initial peopling of the Americas or due to subsequent events, especially the demographic consequences in the wake of European contact. A promising strategy to reveal possible diachronic ABO frequency changes is the molecular genetic analysis of relevant genetic markers in precontact populations. A previous study by Halverson and Bolnick [Am J Phys Anthropol 137 (2008) 342-347] already accomplished this for indigenous North American populations. Here we present the first study to analyze ABO blood types from pre-Columbian individuals from South America using molecular genetic methods and comparing them to several extant South American, North American, and Siberian populations. We tried to determine ABO blood types for 59 individuals from the southern Peruvian highlands dating to similar to 650 to 1250 AD using a newly developed multiplex PCR/SBE assay coamplifying the fragments relevant for blood type determination and three highly discriminating autosomal STRs. Analysis was successful for 31 individuals and revealed that all are exclusively in the O group, predominantly carrying the O02 (01v) allele. No significant difference could be observed between the ancient and modern Native American populations, while all significantly differed from the extant Siberian populations, supporting the suggestion that low ABO diversity results from founder effects during the initial peopling of the Americas. Am J Phys Anthropol 149:242249, 2012. (c) 2012 Wiley Periodicals, Inc."],["dc.description.sponsorship","German Research Foundation (DFG) [FE1161/1-1]"],["dc.identifier.doi","10.1002/ajpa.22115"],["dc.identifier.isi","000308879100009"],["dc.identifier.pmid","22806956"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/25288"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0002-9483"],["dc.title","Molecular characterization of ABO blood group frequencies in pre-Columbian Peruvian highlanders"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","141"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Anthropologischer Anzeiger"],["dc.bibliographiccitation.lastpage","153"],["dc.bibliographiccitation.volume","75"],["dc.contributor.author","Jugert, Friederike"],["dc.contributor.author","Hummel, Susanne"],["dc.contributor.author","Grosskopf, Birgit"],["dc.date.accessioned","2020-12-10T18:36:47Z"],["dc.date.available","2020-12-10T18:36:47Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1127/anthranz/2018/0778"],["dc.identifier.issn","0003-5548"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/76738"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Investigations of the relation between birth trauma and pelvic size in females from a medieval gravesite from Lübeck"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","43"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Diversity"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Flux, Anna Lena"],["dc.contributor.author","Mazanec, Janine"],["dc.contributor.author","Strommenger, Birgit"],["dc.contributor.author","Hummel, Susanne"],["dc.date.accessioned","2019-07-09T11:44:36Z"],["dc.date.available","2019-07-09T11:44:36Z"],["dc.date.issued","2017"],["dc.description.abstract","Staphylococcus aureus is a major pathogen causing osteomyelitis, amongst other diseases, and its methicillin-resistant form (MRSA) in particular poses a huge threat to public health. To increase our knowledge of the origin and evolution of S. aureus, genetic studies of historical microorganisms may be beneficial. Thus, the aim of this study was to investigate whether osteomyelitic skeletal material (autopsy specimens collected from the mid 19th century until the 1920s) is suitable for detecting historical S. aureus DNA sequences. We established a PCR-based analysis system targeting two specific genes of S. aureus (nuc and fib). We successfully amplified the historical S. aureus nuc and fib sequences for six and seven pre-antibiotic, osteomyelitic bone specimens, respectively. These results encourage further investigations of historical S. aureus genomes that may increase our understanding of pathogen evolution in relation to anthropogenically introduced antibiotics."],["dc.identifier.doi","10.3390/d9040043"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14836"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59047"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1424-2818"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","570"],["dc.title","Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]