TY - THES A1 - Gonzalez Duran, Enrique T1 - Genetic control of intracellular gene transfer by DNA repair in N. tabacum N2 - Mitochondria and plastids are organelles with an endosymbiotic origin. During evolution, many genes are lost from the organellar genomes and get integrated in the nuclear genome, in what is known as intracellular/endosymbiotic gene transfer (IGT/EGT). IGT has been reproduced experimentally in Nicotiana tabacum at a gene transfer rate (GTR) of 1 event in 5 million cells, but, despite its centrality to eukaryotic evolution, there are no genetic factors known to influence the frequency of IGT in higher eukaryotes. The focus of this work was to determine the role of different DNA repair pathways of double strand break repair (DSBR) in the integration step of organellar DNA in the nuclear genome during IGT. Here, a CRISPR/Cas9 mutagenesis strategy was implemented in N. tabacum, with the aim of generating mutants in nuclear genes without expected visible phenotypes. This strategy led to the generation of a collection of independent mutants in the LIG4 (necessary for non-homologous end joining, NHEJ) and POLQ genes (necessary for microhomology mediated end joining, MMEJ). Targeting of other DSBR genes (KU70, KU80, RPA1C) generated mutants with unexpectedly strong developmental phenotypes.. These factors have telomeric roles, hinting towards a possible relationship between telomere length, and strength of developmental disruption upon loss of telomere structure in plants. The mutants were made in a genetic background encoding a plastid-encoded IGT reporter, that confers kanamycin resistance upon transfer to the nucleus. Through large scale independent experiments, increased IGT from the chloroplast to the nucleus was observed in lig4 mutants, as well as lines encoding a POLQ gene with a defective polymerase domain (polqΔPol). This shows that NHEJ or MMEJ have a double-sided relationship with IGT: while transferred genes may integrate using either pathway, the presence of both pathways suppresses IGT in wild-type somatic cells, thus demonstrating for the first time the extent on which nuclear genes control IGT frequency in plants. The IGT frequency increases in the mutants are likely mediated by increased availability of double strand breaks for integration. Additionally, kinetic analysis reveals that gene transfer (GT) events accumulate linearly as a function of time spent under antibiotic selection in the experiment, demonstrating that, contrary to what was previously thought, there is no such thing as a single GTR in somatic IGT experiments. Furthermore, IGT in tissue culture experiments appears to be the result of a "race against the clock" for integration in the nuclear genome, that starts when the organellar DNA arrives to the nucleus granting transient antibiotic resistance. GT events and escapes of kanamycin selection may be two possible outcomes from this race: those instances where the organellar DNA gets to integrate are recovered as GT events, and in those cases where timely integration fails, antibiotic resistance cannot be sustained, and end up considered as escapes. In the mutants, increased opportunities for integration in the nuclear genome change the overall ratio between IGT and escape events. The resources generated here are promising starting points for future research: (1) the mutant collection, for the further study of processes that depend on DNA repair in plants (2) the collection of GT lines obtained from these experiments, for the study of the effect of DSBR pathways over integration patterns and stability of transferred genes and (3) the developed CRISPR/Cas9 workflow for mutant generation, to make N. tabacum meet its potential as an attractive model for answering complex biological questions. N2 - Mitochondrien und Plastiden sind beides Organellen endosymbiotischen Ursprungs. Im Laufe der Evolution gehen viele Gene aus den Organellengenomen verloren und werden in das Kerngenom integriert, was als intrazellulärer/endosymbiotischer Gentransfer (IGT/EGT) bezeichnet wird. IGT konnte experimentell in Nicotiana tabacum mit einer Gentransferrate (GTR) von einem Ereignis in fünf Millionen Zellen nachgestellt werden, aber trotz seiner zentralen Bedeutung für die eukaryotische Evolution sind keine genetischen Faktoren bekannt, die die Häufigkeit von IGT in höheren Eukaryoten beeinflussen. Der Schwerpunkt dieser Arbeit lag auf der Bestimmung der Rolle verschiedener DNA-Reparaturwege der Doppelstrangbruchreparatur (DSBR) bei der Integration von Organellen-DNA in das Kerngenom während des IGT. Dazu wurde in N. tabacum eine CRISPR/Cas9-basierte Mutagenesestrategie angewandt, mit dem Ziel, Mutanten in Kerngenen zu erzeugen, für die keine sichtbaren Phänotypen zu erwarten sind. Diese Strategie führte zur Erzeugung einer Reihe unabhängiger Mutanten im LIG4-Gen (notwendig für „non-homologous end joining“, die nicht-homologe Verbindung von Enden, NHEJ) und POLQ (notwendig für „microhomology mediated end joining“, die Mikrohomologie-vermittelte Verbindung von Enden, MMEJ). Die gezielte Beeinflussung anderer DSBR-Gene (KU70, KU80, RPA1C) führte zu Mutanten mit unerwartet starken Entwicklungsphänotypen. Diese Gene spielen eine Rolle beim Erhalt der Telomere, was auf einen möglichen Zusammenhang zwischen der Telomerlänge und der Stärke der Entwicklungsstörung bei Verlust der Telomerstruktur in Pflanzen hindeutet. Die Mutanten wurden in einem genetischen Hintergrund erzeugt, der über einen in den Plastiden lokalisierten IGT-Reporter verfügt, der nach Übertragung in den Zellkern Kanamycin-Resistenz vermittelt. In groß angelegten unabhängigen Experimenten wurde in lig4-Mutanten sowie in Linien, die für ein POLQ-Gen mit einer defekten Polymerase-Domäne (polqΔPol) kodieren, eine erhöhte GTR vom Chloroplasten zum Zellkern beobachtet. Dies zeigt, dass NHEJ oder MMEJ eine zweischneidige Beziehung zum IGT haben: Während übertragene Gene folglich über jeden der beiden Mechanismen integriert werden können, unterdrückt das gleichzeitige Vorhandensein beider Wege IGT in somatischen Wildtyp-Zellen, wodurch zum ersten Mal gezeigt wird, in welchem Ausmaß Kerngene die IGT-Häufigkeit in Pflanzen kontrollieren. Die erhöhte Verfügbarkeit von Doppelstrangbrüchen für die Integration könnte für die erhöhte IGT-Häufigkeit in den Mutanten verantwortlich sein. Darüber hinaus zeigt die Analyse des Zeitverlaufs, dass Gentransferereignisse (GT) in Abhängigkeit von der Zeit, die im Experiment unter Antibiotikaselektion verbracht wurde, linear akkumulieren, was beweist, dass es, anders als bisher angenommen, in somatischen IGT-Experimenten keine statische GTR gibt. Darüber hinaus scheint IGT in Gewebekulturexperimenten das Ergebnis eines Wettlaufs mit der Zeit um die Integration in das Kerngenom zu sein, der beginnt, wenn die Organellen-DNA in den Zellkern gelangt und eine vorübergehende Antibiotikaresistenz gewährt. Echte GT-Ereignisse und „Escapes“ (scheinbare Resistenz, ein vorläufiges Ausweichen vor der Kanamycin-Selektion) können zwei mögliche Ergebnisse dieses Wettlaufs sein: Die Fälle, in denen die Organellen-DNA integriert wird, werden als GT-Ereignisse gewertet, und in den Fällen, in denen die rechtzeitige Integration scheitert, kann die Antibiotikaresistenz nicht aufrechterhalten werden und sie werden als „Escape“ betrachtet. In den Mutanten verändern sich die Möglichkeiten zur Integration in das Kerngenom, wodurch sich das Gesamtverhältnis zwischen IGT- und „Escape“-Ereignissen ändert. Die hier erzeugten Ressourcen sind vielversprechende Ausgangspunkte für künftige Forschungen: (1) die Mutantensammlung, für die Untersuchung von weiteren Prozessen, die von der DNA-Reparatur in Pflanzen abhängen, (2) die Sammlung von GT-Linien, die aus den hier beschriebenen Experimenten gewonnen wurden, für die Untersuchung der Auswirkungen von DSBR-Mechanismen auf Integrationsmuster und Stabilität übertragener Gene und (3) der hier entwickelte Arbeitsablauf für die Mutantenerzeugung mittels CRISPR/Cas9, damit N. tabacum sein Potenzial als attraktives Modell für die Beantwortung komplexer biologischer Fragestellungen erfüllen kann. T2 - Genetische Kontrolle des intrazellulären Gentransfers durch DNA-Reparatur in N. tabacum KW - endosymbiosis KW - organelles KW - gene KW - transfer KW - DNA KW - repair KW - genome KW - editing KW - evolution KW - plant Y1 - 2023 ER - TY - JOUR A1 - Van Hout, Cristopher V. A1 - Tachmazidou, Ioanna A1 - Backman, Joshua D. A1 - Hoffman, Joshua D. A1 - Liu, Daren A1 - Pandey, Ashutosh K. A1 - Gonzaga-Jauregui, Claudia A1 - Khalid, Shareef A1 - Ye, Bin A1 - Banerjee, Nilanjana A1 - Li, Alexander H. A1 - O'Dushlaine, Colm A1 - Marcketta, Anthony A1 - Staples, Jeffrey A1 - Schurmann, Claudia A1 - Hawes, Alicia A1 - Maxwell, Evan A1 - Barnard, Leland A1 - Lopez, Alexander A1 - Penn, John A1 - Habegger, Lukas A1 - Blumenfeld, Andrew L. A1 - Bai, Xiaodong A1 - O'Keeffe, Sean A1 - Yadav, Ashish A1 - Praveen, Kavita A1 - Jones, Marcus A1 - Salerno, William J. A1 - Chung, Wendy K. A1 - Surakka, Ida A1 - Willer, Cristen J. A1 - Hveem, Kristian A1 - Leader, Joseph B. A1 - Carey, David J. A1 - Ledbetter, David H. A1 - Cardon, Lon A1 - Yancopoulos, George D. A1 - Economides, Aris A1 - Coppola, Giovanni A1 - Shuldiner, Alan R. A1 - Balasubramanian, Suganthi A1 - Cantor, Michael A1 - Nelson, Matthew R. A1 - Whittaker, John A1 - Reid, Jeffrey G. A1 - Marchini, Jonathan A1 - Overton, John D. A1 - Scott, Robert A. A1 - Abecasis, Goncalo R. A1 - Yerges-Armstrong, Laura M. A1 - Baras, Aris T1 - Exome sequencing and characterization of 49,960 individuals in the UK Biobank JF - Nature : the international weekly journal of science N2 - The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world(1). Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, includingPIEZO1on varicose veins,COL6A1on corneal resistance,MEPEon bone density, andIQGAP2andGMPRon blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenicBRCA1andBRCA2variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
Exome sequences from the first 49,960 participants in the UK Biobank highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community. KW - clinical exome KW - breast-cancer KW - mutations KW - recommendations KW - gene KW - metaanalysis KW - variants, KW - BRCA1 KW - risk KW - susceptibility Y1 - 2020 U6 - https://doi.org/10.1038/s41586-020-2853-0 SN - 0028-0836 SN - 1476-4687 VL - 586 IS - 7831 SP - 749 EP - 756 PB - Macmillan Publishers Limited CY - London ER - TY - JOUR A1 - Perscheid, Cindy T1 - Integrative biomarker detection on high-dimensional gene expression data sets BT - a survey on prior knowledge approaches JF - Briefings in bioinformatics N2 - Gene expression data provide the expression levels of tens of thousands of genes from several hundred samples. These data are analyzed to detect biomarkers that can be of prognostic or diagnostic use. Traditionally, biomarker detection for gene expression data is the task of gene selection. The vast number of genes is reduced to a few relevant ones that achieve the best performance for the respective use case. Traditional approaches select genes based on their statistical significance in the data set. This results in issues of robustness, redundancy and true biological relevance of the selected genes. Integrative analyses typically address these shortcomings by integrating multiple data artifacts from the same objects, e.g. gene expression and methylation data. When only gene expression data are available, integrative analyses instead use curated information on biological processes from public knowledge bases. With knowledge bases providing an ever-increasing amount of curated biological knowledge, such prior knowledge approaches become more powerful. This paper provides a thorough overview on the status quo of biomarker detection on gene expression data with prior biological knowledge. We discuss current shortcomings of traditional approaches, review recent external knowledge bases, provide a classification and qualitative comparison of existing prior knowledge approaches and discuss open challenges for this kind of gene selection. KW - gene selection KW - external knowledge bases KW - biomarker detection KW - gene KW - expression KW - prior knowledge Y1 - 2021 U6 - https://doi.org/10.1093/bib/bbaa151 SN - 1467-5463 SN - 1477-4054 VL - 22 IS - 3 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Hasnat, Muhammad Abrar T1 - A-Type Carrier Proteins are involved in [4Fe-4S] Cluster insertion into the Radical S-adenosylmethionine (SAM) Protein MoaA and other molybdoenzymes N2 - Iron-sulfur clusters are essential enzyme cofactors. The most common and stable clusters are [2Fe-2S] and [4Fe-4S] that are found in nature. They are involved in crucial biological processes like respiration, gene regulation, protein translation, replication and DNA repair in prokaryotes and eukaryotes. In Escherichia coli, Fe-S clusters are essential for molybdenum cofactor (Moco) biosynthesis, which is a ubiquitous and highly conserved pathway. The first step of Moco biosynthesis is catalyzed by the MoaA protein to produce cyclic pyranopterin monophosphate (cPMP) from 5’GTP. MoaA is a [4Fe-4S] cluster containing radical S-adenosyl-L-methionine (SAM) enzyme. The focus of this study was to investigate Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions using E. coli as a model organism. Nitrate and TMAO respiration usually occur under anaerobic conditions, where oxygen is depleted. Under these conditions, E. coli uses nitrate and TMAO as terminal electron. Previous studies revealed that Fe-S cluster insertion is performed by Fe-S cluster carrier proteins. In E. coli, these proteins are known as A-type carrier proteins (ATC) by phylogenomic and genetic studies. So far, three of them have been characterized in detail in E. coli, namely IscA, SufA, and ErpA. This study shows that ErpA and IscA are involved in Fe-S cluster insertion into MoaA under nitrate and TMAO respiratory conditions. ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. SufA is not able to replace the functions of IscA or ErpA under nitrate respiratory conditions. Nitrate reductase is a molybdoenzyme that coordinates Moco and Fe-S clusters. Under nitrate respiratory conditions, the expression of nitrate reductase is significantly increased in E. coli. Nitrate reductase is encoded in narGHJI genes, the expression of which is regulated by the transcriptional regulator, fumarate and nitrate reduction (FNR). The activation of FNR under conditions of nitrate respiration requires one [4Fe-4S] cluster. In this part of the study, we analyzed the insertion of Fe-S cluster into FNR for the expression of narGHJI genes in E. coli. The results indicate that ErpA is essential for the FNR-dependent expression of the narGHJI genes, a role that can be replaced partially by IscA and SufA when they are produced sufficiently under the conditions tested. This observation suggests that ErpA is indirectly regulating nitrate reductase expression via inserting Fe-S clusters into FNR. Most molybdoenzymes are complex multi-subunit and multi-cofactor-containing enzymes that coordinate Fe-S clusters, which are functioning as electron transfer chains for catalysis. In E. coli, periplasmic aldehyde oxidoreductase (PaoAC) is a heterotrimeric molybdoenzyme that consists of flavin, two [2Fe-2S], one [4Fe-4S] cluster and Moco. In the last part of this study, we investigated the insertion of Fe-S clusters into E. coli periplasmic aldehyde oxidoreductase (PaoAC). The results show that SufA and ErpA are involved in inserting [4Fe-4S] and [2Fe-2S] clusters into PaoABC, respectively under aerobic respiratory conditions. KW - enzyme KW - gene KW - iron sulfur clusters KW - Enzyme KW - Gen KW - Eisen-Schwefel-Cluster Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-530791 ER - TY - GEN A1 - Igual Gil, Carla A1 - Ost, Mario A1 - Kasch, Juliane A1 - Schumann, Sara A1 - Heider, Sarah A1 - Klaus, Susanne T1 - Role of GDF15 in active lifestyle induced metabolic adaptations and acute exercise response in mice T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Physical activity is an important contributor to muscle adaptation and metabolic health. Growth differentiation factor 15 (GDF15) is established as cellular and nutritional stress-induced cytokine but its physiological role in response to active lifestyle or acute exercise is unknown. Here, we investigated the metabolic phenotype and circulating GDF15 levels in lean and obese male C57BI/6J mice with long-term voluntary wheel running (VWR) intervention. Additionally, treadmill running capacity and exercise-induced muscle gene expression was examined in GDF15-ablated mice. Active lifestyle mimic via VWR improved treadmill running performance and, in obese mice, also metabolic phenotype. The post-exercise induction of skeletal muscle transcriptional stress markers was reduced by VWR. Skeletal muscle GDF15 gene expression was very low and only transiently increased post-exercise in sedentary but not in active mice. Plasma GDF15 levels were only marginally affected by chronic or acute exercise. In obese mice, VWR reduced GDF15 gene expression in different tissues but did not reverse elevated plasma GDF15. Genetic ablation of GDF15 had no effect on exercise performance but augmented the post exercise expression of transcriptional exercise stress markers (Atf3, Atf6, and Xbp1s) in skeletal muscle. We conclude that skeletal muscle does not contribute to circulating GDF15 in mice, but muscle GDF15 might play a protective role in the exercise stress response. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1090 KW - skeletal-muscle KW - growth KW - induction KW - insulin KW - activation KW - increases KW - glucagon KW - health KW - gene KW - diet Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460541 SN - 1866-8372 IS - 1090 ER - TY - GEN A1 - Nakamura, Moritaka A1 - Claes, Andrea R. A1 - Grebe, Tobias A1 - Hermkes, Rebecca A1 - Viotti, Corrado A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Auxin and ROP GTPase signaling of polar nuclear migration in root epidermal hair cells T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 992 KW - Arabidopsis-thaliana KW - planar polarity KW - tip growth KW - morphogenesis KW - gene KW - proteins KW - dynamics KW - transformation KW - activation KW - initiation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441278 SN - 1866-8372 IS - 992 SP - 378 EP - 391 ER - TY - GEN A1 - Merks, Anne Margarete A1 - Swinarski, Marie A1 - Meyer, Alexander Matthias A1 - Müller, Nicola Victoria A1 - Özcan, Ismail A1 - Donat, Stefan A1 - Burger, Alexa A1 - Gilbert, Stephen A1 - Mosimann, Christian A1 - Abdelilah-Seyfried, Salim A1 - Panáková, Daniela T1 - Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Development of a multiple-chambered heart from the linear heart tube is inherently linked to cardiac looping. Although many molecular factors regulating the process of cardiac chamber ballooning have been identified, the cellular mechanisms underlying the chamber formation remain unclear. Here, we demonstrate that cardiac chambers remodel by cell neighbour exchange of cardiomyocytes guided by the planar cell polarity (PCP) pathway triggered by two non-canonical Wnt ligands, Wnt5b and Wnt11. We find that PCP signalling coordinates the localisation of actomyosin activity, and thus the efficiency of cell neighbour exchange. On a tissue-scale, PCP signalling planar-polarises tissue tension by restricting the actomyosin contractility to the apical membranes of outflow tract cells. The tissue-scale polarisation of actomyosin contractility is required for cardiac looping that occurs concurrently with chamber ballooning. Taken together, our data reveal that instructive PCP signals couple cardiac chamber expansion with cardiac looping through the organ-scale polarisation of actomyosin-based tissue tension. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 849 KW - convergent extension KW - branching morphogenesis KW - actin cytoskeleton KW - zebrafish heart KW - mouse heart KW - drosophila KW - cadherin KW - gene KW - differentiation KW - proliferation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427026 SN - 1866-8372 IS - 849 ER - TY - GEN A1 - Siska, Veronika A1 - Jones, Eppie Ruth A1 - Jeon, Sungwon A1 - Bhak, Youngjune A1 - Kim, Hak-Min A1 - Cho, Yun Sung A1 - Kim, Hyunho A1 - Lee, Kyusang A1 - Veselovskaya, Elizaveta A1 - Balueva, Tatiana A1 - Gallego-Llorente, Marcos A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Eriksson, Anders A1 - Pinhasi, Ron A1 - Bhak, Jong A1 - Manica, Andrea T1 - Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 791 KW - Mitochondrial-DNA analysis KW - positive selection KW - jomon skeletons KW - ancient DNA KW - pigmentation KW - population KW - admixture KW - edar KW - gene KW - polymorohism Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439977 SN - 1866-8372 IS - 791 ER - TY - GEN A1 - Choi, Youngeun A1 - Schmidt, Carsten A1 - Tinnefeld, Philip A1 - Bald, Ilko A1 - Rödiger, Stefan T1 - A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads T2 - Postprints der Universität Potsdam : Mathematisch-naturwissenschaftliche Reihe N2 - The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 705 KW - nucleic-acids KW - hybridization KW - microrna KW - flourescence KW - biomarkers KW - platform KW - particle KW - binding KW - array KW - gene Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428271 SN - 1866-8372 IS - 705 ER - TY - JOUR A1 - Choi, Youngeun A1 - Schmidt, Carsten A1 - Tinnefeld, Philip A1 - Bald, Ilko A1 - Rödiger, Stefan T1 - A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads JF - Scientific Reports N2 - The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters. KW - nucleic-acids KW - hybridization KW - microrna KW - flourescence KW - biomarkers KW - platform KW - particle KW - binding KW - array KW - gene Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-41136-x SN - 2045-2322 IS - 9 PB - Macmillan Publishers Limited CY - London ER -