Species identification of archived fish bones collected from the Mediterranean Sea 100 years ago using molecular techniques

With the discovery that DNA can be successfully recovered from museum collections, a new source of genetic information has been provided to extend our comprehension of the evolutionary history of species. However, historical specimens are often mislabeled or report incorrect information of origin, thus accurate identification of specimens is essential. Due to the highly damaged nature of ancient DNA many pitfalls exist and particular precautions need to be considered in order to perform genetic analysis. In this study we analyze 208 historical remains of pelagic fishes collected in the beginning of the 20th century. Through the adaptation of existing protocols, usually applied to human remains, we manage to successfully retrieve valuable genetic material from almost all of the examined samples using a guanidine and silica column-based approach. The combined use of two mitochondrial markers cytochrome-oxidase-1(mtDNA COI) and Control Region (mtDNA CR), and the nuclear marker first internal transcriber space (ITS1) allowed us to identify the majority of the examined specimens using traditional PCR and Sanger sequencing techniques. The creation of primers capable of amplifying heavily degraded DNA have great potential for future uses, both in ancient and in modern investigation. The methodologies developed in this study can in fact be applied for other ancient fish specimens as well as cooked or canned samples.

Populationsgenetik eisenzeitlicher Reiternomaden der Eurasischen Steppe

Vorliegende Dissertation beschäftigt sich mit der Populationsgenetik eisenzeitlicher Bevölkerungen der Eurasischen Steppe, die mit der skythischen Kultur assoziiert werden. Für die Analysen wurden 30 Fragmente der kodierenden Region und die HVR1 (16040–16400) des mitochondrialen Genoms, sowie 20 phänotypische Marker untersucht. Die Marker wurden durch Multiplex-PCRs angereichert, mit einem probenspezifischen barcode versehen und einer parallelen Sequenzanalyse mit dem 454 GS FLX Sequenzierer unterzogen. 97 Individuen wurden erfolgreich analysiert, von denen 19 aus dem Westen der Eurasischen Steppe und 78 aus dem Bereich des Altai-Gebirges stammen. Die populationsgenetischen Analysen ergaben geringe genetische Distanzen zwischen den skythischen Populationen aus dem Bereich des Altai-Gebirges, die sich vom 9. bis zum 3. Jahrhundert vor Christus erstrecken, was für eine kontinuierliche Bevölkerungsentwicklung sprechen könnte. Weiterhin finden sich geringe genetische Distanzen zwischen den Gruppen im Osten und Westen der Eurasischen Steppe, was auf eine gemeinsame Ursprungspopulation, oder zumindest Genfluss hinweisen kann. Die Ergebnisse aus dem Vergleich mit neolithischen und bronzezeitlichen Referenzpopulationen aus Zentralasien und den angrenzenden Gebieten weisen auf die Möglichkeit eines gemeinsamen zentral-asiatischen Ursprungs hin, zeigen aber auch, dass die östlichen und westlichen Gruppen der Eisenzeit jeweils zusätzlich lokalem Genfluss ausgesetzt waren. Die Allelfrequenzen der phänotypischen Marker deuten auf einen größeren europäischen Einfluss auf das östliche Zentralasien in der Eisenzeit hin, oder ansteigenden Genfluss aus Ostasien nach der Eisenzeit.

A river runs through it - ancient DNA data on the neolithic populations of the Great Hungarian Plain

This thesis was part of a multidisciplinary research project funded by the German Research Foundation (“Bevölkerungsgeschichte des Karpatenbeckens in der Jungsteinzeit und ihr Einfluss auf die Besiedlung Mitteleuropas”, grant no. Al 287/10-1) aimed at elucidating the population history of the Carpathian Basin during the Neolithic. The Carpathian Basin was an important waypoint on the spread of the Neolithic from southeastern to central Europe. On the Great Hungarian Plain (Alföld), the first farming communities appeared around 6000 cal BC. They belonged to the Körös culture, which derived from the Starčevo-Körös-Criş complex in the northern Balkans. Around 5600 cal BC the Alföld-Linearbandkeramik (ALBK), so called due to its stylistic similarities with the Transdanubian and central European LBK, emerged in the northwestern Alföld. Following a short “classical phase”, the ALBK split into several regional subgroups during its later stages, but did not expand beyond the Great Hungarian Plain. Marking the beginning of the late Neolithic period, the Tisza culture first appeared in the southern Alföld around 5000 cal BC and subsequently spread into the central and northern Alföld. Together with the Herpály and Csőszhalom groups it was an integral part of the late Neolithic cultural landscape of the Alföld. Up until now, the Neolithic cultural succession on the Alföld has been almost exclusively studied from an archaeological point of view, while very little is known about the population genetic processes during this time period. The aim of this thesis was to perform ancient DNA (aDNA) analyses on human samples from the Alföld Neolithic and analyse the resulting mitochondrial population data to address the following questions: is there population continuity between the Central European Mesolithic hunter-gatherer metapopulation and the first farming communities on the Alföld? Is there genetic continuity from the early to the late Neolithic? Are there genetic as well as cultural differences between the regional groups of the ALBK? Additionally, the relationships between the Alföld and the neighbouring Transdanubian Neolithic as well as other European early farming communities were evaluated to gain insights into the genetic affinities of the Alföld Neolithic in a larger geographic context. 320 individuals were analysed for this study; reproducible mitochondrial haplogroup information (HVS-I and/or SNP data) could be obtained from 242 Neolithic individuals. According to the analyses, population continuity between hunter-gatherers and the Neolithic cultures of the Alföld can be excluded at any stage of the Neolithic. In contrast, there is strong evidence for population continuity from the early to the late Neolithic. All cultural groups on the Alföld were heavily shaped by the genetic substrate introduced into the Carpathian Basin during the early Neolithic by the Körös and Starčevo cultures. Accordingly, genetic differentiation between regional groups of the ALBK is not very pronounced. The Alföld cultures are furthermore genetically highly similar to the Transdanubian Neolithic cultures, probably due to common ancestry. In the wider European context, the Alföld Neolithic cultures also highly similar to the central European LBK, while they differ markedly from contemporaneous populations of the Iberian Peninsula and the Ukraine. Thus, the Körös culture, the ALBK and the Tisza culture can be regarded as part of a “genetic continuum” that links the Neolithic Carpathian Basin to central Europe and likely has its roots in the Starčevo -Körös-Criş complex of the northern Balkans.

The role of DNA damage in the pathogenesis of nitrate tolerance - nitrosative versus oxidative DNA damage

6. Summary Despite the lack of direct evidence from large clinical trials for mutagenic and genotoxic effects of GTN therapy, the present study show s the induction of pre-mutagenic lesions, such as 8- oxo - G and O 6 - me - G by GTN t reatment as well as increased formation of DNA strand breaks. These results were obtained in an in vitro (EA.hy 926 – human endothelial cell line) and in vivo (Wistar rats and C57BL/6 mice) setting. However, GTN - induced DNA damage had no effect on the degr ee of nitrate tolerance but only on other pathological side effects such as oxidative stress, as confirmed by studies in MGMT knockout mice. Of clinical importance , this study establishes potent apoptotic properties of organic nitrates, which has been demo nstrated by the levels of the novel apoptotic marker and caspase - 3 substrate, fractin, as well as levels of cleaved caspase - 3 , the activated form of this pro - apoptotic enzyme . The p rotein analy tical data ha ve been confirmed by an independent assay for the apoptosis , Cell death detection assay (TUNEL) . First, these GTN - mediated apoptotic effects may account for the previously reported anti - cancer effects of GTN therapy (probably based on induction of apoptosis in tumor cells). Second, these GTN - mediated apop totic effects may account for the increased mortality rates observed in the group of organic nitrate - treated patients as reported by two independent meta - analysis (probably due to induction of apoptosis in highly beneficial endothelial progenitor cells as well as in cardiomyocytes during wound healing and cardiac remodeling) . Summary of the current investigations can be seen in Figure 18.

First assessment on genetic structure and phylogeography of Mediterranean blue shark (prionace glauca, L. 1758) population using mitochondrial gene variation: a comparison with the Atlantic.

The blue shark, Prionace glauca, is one of the most vagile shark species worldwide distributed. The particular body shape allows blue sharks make transoceanic movements, leading to a circumglobal distribution. Due to its reproductive cycle, an extraordinarily high number of specimens is globally registered but, even if it is still a major bycatch of longline fishery rather than a commercial target, it is characterized by a high vulnerability. In this perspective it is important to increase the amount of informations regarding its population extent in the different worldwide areas, evaluating the possible phylogeographic patterns between different locations. This study, included in the "MedBlueSGen" European project, aims exactly at filling a gap in knowledges regarding the genetic population structure of the Mediterranean blue sharks, which has never been investigated before, with a comparison with the North-Eastern Atlantic blue shark population. To reach this objective, we used a dataset of samples from different Mediterranean areas implementing it with some samples from North-Eastern Atlantic. Analyzing the variability of the two mitochondrial markers control region and cytochrome b, with the design of new species-specific primer pairs, we assessed the mitochondrial genetic structure of Mediterranean and North-Eastern Atlantic samples, focusing on the analysis of their possible connectivity, and we tried to reconstruct their demographic history and population size. Data analyses highlighted the absence of a genetic structuring within the Mediterranean and among it and North-Eastern Atlantic, suggesting that the Strait of Gibraltar doesn't represent a phylogeographic barrier. These results are coherent to what has been found in similar investigations on other worldwide blue shark populations. Analysis of the historical demographic trend revealed a general stable pattern for the cytochrome-b and a slightly population expansion for the control region marker.

Cold ischemia contributes to the development of chronic rejection and mitochondrial injury after cardiac transplantation

Chronic rejection (CR) remains an unsolved hurdle for long-term heart transplant survival. The effect of cold ischemia (CI) on progression of CR and the mechanisms resulting in functional deficit were investigated by studying gene expression, mitochondrial function, and enzymatic activity. Allogeneic (Lew F344) and syngeneic (Lew Lew) heart transplantations were performed with or without 10 h of CI. After evaluation of myocardial contraction, hearts were excised at 2, 10, 40, and 60 days for investigation of vasculopathy, gene expression, enzymatic activities, and mitochondrial respiration. Gene expression studies identified a gene cluster coding for subunits of the mitochondrial electron transport chain regulated in response to CI and CR. Myocardial performance, mitochondrial function, and mitochondrial marker enzyme activities declined in all allografts with time after transplantation. These declines were more rapid and severe in CI allografts (CR-CI) and correlated well with progression of vasculopathy and fibrosis. Mitochondria related gene expression and mitochondrial function are substantially compromised with the progression of CR and show that CI impacts on progression, gene profile, and mitochondrial function of CR. Monitoring mitochondrial function and enzyme activity might allow for earlier detection of CR and cardiac allograft dysfunction.

Deficient CEBPA DNA binding function in normal karyotype AML patients is associated with favorable prognosis

CCAAT/enhancer binding protein-α (CEBPA) mutations in acute myeloid leukemia (AML) patients with a normal karyotype (NK) confer favorable prognosis, whereas NK-AML patients per se are of intermediate risk. This suggests that blocked CEBPA function characterizes NK-AML with favorable outcome. We determined the prognostic significance of CEBPA DNA binding function by enzyme-linked immunosorbent assay in 105 NK-AML patients. Suppressed CEBPA DNA binding was defined by 21 good-risk AML patients with inv(16) or t(8;21) (both abnormalities targeting CEBPA) and 8 NK-AML patients with dominant-negative CEBPA mutations. NK-AML patients with suppressed CEBPA function showed a better overall survival (P = .0231) and disease-free survival (P = .0069) than patients with conserved CEBPA function. Suppressed CEBPA DNA binding was an independent marker for better overall survival and disease-free survival in a multivariable analysis that included FLT3-ITD, NPM1 and CEBPA mutation status, white blood cell count, age and lactate dehydrogenase. These data indicate that suppressed CEBPA function is associated with favorable prognosis in NK-AML patients.

A pyrosequencing assay for the rapid discrimination of mitochondrial lineages in the Salmo trutta species complex

The European trout (Salmo trutta species complex) is genetically very diverse consisting of five distinct mitochondrial lineages that probably originated in the Pleistocene. Here, we describe a novel pyrosequencing protocol to generate two short sequence reads from the mitochondrial control region, which allow the unambiguous identification of all five lineages. The approach was found to be easily transferable between laboratories and should be a valuable tool for the assessment of genetic diversity in trout. Pyrosequencing-based assays for molecular species identification are expected to be generally useful whenever multiple positions in a short DNA sequence need to be assessed.

Intralesional bovine papillomavirus DNA loads reflect severity of equine sarcoid disease

REASONS FOR PERFORMING STUDY: Sarcoids are nonmetastasising, yet locally aggressive skin tumours that constitute the most frequent neoplasm in equids. Infection by bovine papillomaviruses types 1 and 2 (BPV-1, BPV-2) has been recognised as major causative factor in sarcoid pathogenesis, but a possible correlation of intralesional virus load with disease severity has not been established thus far. HYPOTHESIS: Given the pathogenic role of BPV-1 and BPV-2 in sarcoid disease, we suggest that intralesional viral DNA concentration may reflect the degree of affection. METHODS: Severity of disease was addressed by recording the tumour growth kinetics, lesion number and tumour type for 37 sarcoid-bearing horses and one donkey. Viral load was estimated via quantitative real-time PCR (qPCR) of the E2, E5, L1 and L2 genes from the BPV-1/-2 genome for one randomly selected lesion per horse and correlated with disease severity. RESULTS: Quantitative PCR against E2 identified viral DNA concentrations ranging from 0-556 copies/tumour cell. Of 16 horses affected by quiescent, slowly growing single tumours or multiple mild-type lesions, 15 showed a viral load up to 1.4 copies per cell. In stark contrast, all equids (22/22) bearing rapidly growing and/or multiple aggressive sarcoids had a viral load between 3 and 569 copies per cell. Consistent results were obtained with qPCR against E5, L1 and L2. CONCLUSIONS: While tumours of the same clinical type carried variable virus load, confirming that viral titre does not determine clinical appearance, we identified a highly significant correlation between intralesional viral load and disease severity. POTENTIAL RELEVANCE: The rapid determination of BPV viral load will give a reliable marker for disease severity and may also be considered when establishing a therapeutic strategy.

Effect of remifentanil on mitochondrial oxygen consumption of cultured human hepatocytes

During sepsis, liver dysfunction is common, and failure of mitochondria to effectively couple oxygen consumption with energy production has been described. In addition to sepsis, pharmacological agents used to treat septic patients may contribute to mitochondrial dysfunction. This study addressed the hypothesis that remifentanil interacts with hepatic mitochondrial oxygen consumption. The human hepatoma cell line HepG2 and their isolated mitochondria were exposed to remifentanil, with or without further exposure to tumor necrosis factor-α (TNF-α). Mitochondrial oxygen consumption was measured by high-resolution respirometry, Caspase-3 protein levels by Western blotting, and cytokine levels by ELISA. Inhibitory κBα (IκBα) phosphorylation, measurement of the cellular ATP content and mitochondrial membrane potential in intact cells were analysed using commercial ELISA kits. Maximal cellular respiration increased after one hour of incubation with remifentanil, and phosphorylation of IκBα occurred, denoting stimulation of nuclear factor κB (NF-κB). The effect on cellular respiration was not present at 2, 4, 8 or 16 hours of incubation. Remifentanil increased the isolated mitochondrial respiratory control ratio of complex-I-dependent respiration without interfering with maximal respiration. Preincubation with the opioid receptor antagonist naloxone prevented a remifentanil-induced increase in cellular respiration. Remifentanil at 10× higher concentrations than therapeutic reduced mitochondrial membrane potential and ATP content without uncoupling oxygen consumption and basal respiration levels. TNF-α exposure reduced respiration of complex-I, -II and -IV, an effect which was prevented by prior remifentanil incubation. Furthermore, prior remifentanil incubation prevented TNF-α-induced IL-6 release of HepG2 cells, and attenuated fragmentation of pro-caspase-3 into cleaved active caspase 3 (an early marker of apoptosis). Our data suggest that remifentanil increases cellular respiration of human hepatocytes and prevents TNF-α-induced mitochondrial dysfunction. The results were not explained by uncoupling of mitochondrial respiration.

Hyperbaric oxygen induces apoptosis via a mitochondrial mechanism

During therapeutic hyperbaric oxygenation lymphocytes are exposed to high partial pressures of oxygen. This study aimed to analyze the mechanism of apoptosis induction by hyperbaric oxygen. For intervals of 0.5-4 h Jurkat-T-cells were exposed to ambient air or oxygen atmospheres at 1-3 absolute atmospheres. Apoptosis was analyzed by phosphatidylserine externalization, caspase-3 activation and DNA-fragmentation using flow cytometry. Apoptosis was already induced after 30 min of hyperbaric oxygenation (HBO, P < 0.05). The death receptor Fas was downregulated. Inhibition of caspase-9 but not caspase-8 blocked apoptosis induction by HBO. Hyperbaric oxygen caused a loss of mitochondrial membrane potential and caspase-9 induction. The mitochondrial pro-survival protein Bcl-2 was upregulated, and antagonizing Bcl-2 function potentiated apoptosis induction by HBO. In conclusion, a single exposure to hyperbaric oxygenation induces lymphocyte apoptosis by a mitochondrial and not a Fas-related mechanism. Regulation of Fas and Bcl-2 may be regarded as protective measures of the cell in response to hyperbaric oxygen.

Is ITS-2 rDNA suitable marker for genetic characterization of Sarcoptes mites from different wild animals in different geographic areas?

The present study examined the relationship among individual Sarcoptes scabiei mites from 13 wild mammalian populations belonging to nine species in four European countries using the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) as genetic marker. The ITS-2 plus primer flanking 5.8S and 28S rDNA (ITS-2+) was amplified from individual mites by polymerase chain reaction (PCR) and the amplicons were sequenced directly. A total of 148 ITS-2+ sequences of 404bp in length were obtained and 67 variable sites were identified (16.59%). UPGMA analyses did not show any geographical or host-specific clustering, and a similar outcome was obtained using population pairwise Fst statistics. These results demonstrated that ITS-2 rDNA does not appear to be suitable for examining genetic diversity among mite populations.

Plasma DNA is Elevated in Patients with Deep Vein Thrombosis

OBJECTIVE To investigate if plasma DNA is elevated in patients with deep vein thrombosis (DVT) and to determine whether there is a correlation with other biomarkers of DVT. BACKGROUND Leukocytes release DNA to form extracellular traps (ETs), which have recently been linked to experimental DVT. In baboons and mice, extracellular DNA co-localized with von Willebrand factor (VWF) in the thrombus and DNA appeared in circulation at the time of thrombus formation. ETs have not been associated with clinical DVT. SETTING From December 2008 to August 2010, patients were screened through the University of Michigan Diagnostic Vascular Unit and were divided into three distinct groups: 1) the DVT positive group, consisting of patients who were symptomatic for DVT, which was confirmed by compression duplex ultrasound (n=47); 2) the DVT negative group, consisting of patients that present with swelling and leg pain but had a negative compression duplex ultrasound, (n=28); and 3) a control group of healthy non-pregnant volunteers without signs or symptoms of active or previous DVT (n=19). Patients were excluded if they were less than 18 years of age, unwillingness to consent, pregnant, on an anticoagulant therapy, or diagnosed with isolated calf vein thrombosis. METHODS Blood was collected for circulating DNA, CRP, D-dimer, VWF activity, myeloperoxidase (MPO), ADAMTS13 and VWF. The Wells score for a patient's risk of DVT was assessed. The Receiver Operating Characteristic (ROC) curve was generated to determine the strength of the relationship between circulating DNA levels and the presence of DVT. A Spearman correlation was performed to determine the relationship between the DNA levels and the biomarkers and the Wells score. Additionally the ratio of ADAMTS13/VWF was assessed. RESULTS Our results showed that circulating DNA (a surrogate marker for NETs) was significantly elevated in DVT patients, compared to both DVT negative patients (57.7±6.3 vs. 17.9±3.5ng/mL, P<.01) and controls (57.7±6.3 vs. 23.9±2.1ng/mL, P<.01). There was a strong positive correlation with CRP (P<.01), D-dimer (P<.01), VWF (P<.01), Wells score (P<.01) and myeloperoxidase (MPO) (P<.01), along with a strong negative correlation with ADAMTS13 (P<.01) and the ADAMTS13/VWF ratio. The logistic regression model showed a strong association between plasma DNA and the presence of DVT (ROC curve was determined to be 0.814). CONCLUSIONS Plasma DNA is elevated in patients with deep vein thrombosis and correlates with biomarkers of DVT. A strong correlation between circulating DNA and MPO suggests that neutrophils may be a source of plasma DNA in patients with DVT.

Chromosomal organization and evolutionary conservation of the human chromosome 19q linkage group containing three DNA repair genes

A series of human-rodent somatic cell hybrids were investigated by Southern blot analysis for the presence or absence of twenty-six molecular markers and three isozyme loci from human chromosome 19. Based on the co-retention of these markers in the various independent hybrid clones containing portions of human chromosome 19 and on pulsed field mapping, chromosome 19 is divided into twenty ordered regions. The most likely marker order for the chromosome is: (LDLR, C3)-(cen-MANNB)-D19S7-PEPD-D19S9-GPI-TGF$ \beta$-(CYP2A, NCA, CGM2, BCKAD)-PSG1a-(D19S8, XRCC1)-(D19S19, ATP1A3)-(D19S37, APOC2)-CKMM-ERCC2-ERCC1-(D19S62, D19S51)-D19S6-D19S50-D19S22-(CGB, FTL)-qter.^ The region of 19q between the proximal marker D19S7 and the distal gene coding for the beta subunit of chorionic gonadotropin (CGB) is about 37 Mb in size and covers about 37 cM genetic distance. The ration of genetic to physical distance on 19q is therefore very close to the genomic average OF 1 cM/Mb. Estimates of physical distances for intervals between chromosome 19 markers were calculated using a mapping function which estimates distances based on the number of breaks in hybrid clone panels. The consensus genetic distances between individual markers (established at HBM10) were compared to these estimates of physical distances. The close agreement between the two estimates suggested that spontaneously broken hybrids are as appropriate for this type of study as radiation hybrids.^ All three DNA repair genes located on chromosome 19 were found to have homologues on Chinese hamster chromosome 9, which is hemizygous in CHO cells, providing an explanation for the apparent ease with which mutations at these loci were identified in CHO cells. Homologues of CKMM and TGF$\beta$ (from human chromosome 19q) and a mini-satellite DNA specific to the distal region of human chromosome 19q were also mapped to Chinese hamster 9. Markers from 19p did not map to this hamster chromosome. Thus the q-arm of chromosome 19, at least between the genes PEPD and ERCC1, appears to be a linkage group which is conserved intact between humans and Chinese hamsters. ^

CHROMOSOMAL MAPPING, LINKAGE RELATIONSHIPS, AND EVOLUTIONARY STUDIES OF THE HUMAN ANONYMOUS DNA CLONE D1S1 (IN SITU HYBRIDIZATION, PRIMATES, GENE MAPPING, AUTOSOMAL DOMINANT RETINITIS PIGMENTOSA, GENE DUPLICATION)

D1S1, an anonymous human DNA clone originally called (lamda)Ch4-H3 or (lamda)H3, was the first single copy mapped to a human chromosome (1p36) by in situ hybridization. The chromosomal assignment has been confirmed in other laboratories by repeating the in situ hybridization but not by another method. In the present study, hybridization to a panel of hamster-human somatic cell hybrids revealed copies of D1S1 on both chromosomes 1 and 3. Subcloning D1S1 showed that the D1S1 clone itself is from chromosome 3, and the sequence detected by in situ hybridization is at least two copies of part of the chromosome 3 copy. This finding demonstrates the importance of verifying gene mapping with two methods and questions the accuracy of in situ hybridization mapping.^ Non-human mammals have only one copy of D1S1, and the non-human primate D1S1 map closely resembles the human chromosome 3 copy. Thus, the human chromosome 1 copies appear to be part of a very recent duplication that occurred after the divergence between humans and the other great apes.^ A moderately informative HindIII D1S1 RFLP was mapped to chromosome 3. This marker and 12 protein markers were applied to a linkage study of autosomal dominant retinitis pigmentosa (ADRP). None of the markers proved linkage, but adding the three families examined to previously published data raises the ADRP:Rh lod score to 1.92 at (THETA) = 0.30. ^