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Cerebral cavernous malformations (CCMs) are prevalent slow-flow vascular lesions which harbour the risk to develop intracranial haemorrhages, focal neurological deficits, and epileptic seizures. Autosomal dominantly inherited CCMs were found to be associated with heterozygous inactivating mutations in 3 genes, CCM1(KRIT1), CCM2(MGC4607), and CCM3(PDCD10) in 1999, 2003 and 2005, respectively. Despite the availability of high-throughput sequencing techniques, no further CCM gene has been published since. Here, we report on the identification of an autosomal dominantly inherited frameshift mutation in a gene of thus far unknown function, FAM222B(C17orf63), through exome sequencing of CCM patients mutation-negative for CCM1-3. A yeast 2-hybrid screen revealed interactions of FAM222B with the tubulin cytoskeleton and STAMBP which is known to be associated with microcephaly-capillary malformation syndrome. However, a phenotype similar to existing models was not found, neither in fam222bb/fam222ba double mutant zebrafish generated by transcription activator-like effector nucleases nor in an in vitro sprouting assay using human umbilical vein endothelial cells transfected with siRNA against FAM222B. These observations led to the assumption that aberrant FAM222B is not involved in the formation of CCMs.
Background: Newborns are prone to infections, which are independent predictors of neonatal mortality and morbidity. Neutrophil extracellular traps (NETs) are structures composed of chromatin and antimicrobial molecules that capture and kill pathogens. NETs may play an important role in the innate immune system and, thus, might be associated with impaired neonatal immune function. Objectives: This study aimed to compare NET formation between term neonates and healthy adults. We additionally investigated the effects of gestational age, birth weight, mode of delivery, gender, and perinatal infections. Methods: We collected cord blood from 57 term infants (mean gestational age, 39.1 weeks) and 9 late preterm infants (35 weeks), and peripheral blood from 18 healthy adult donors. Neutrophils were isolated, and then NET formation was induced using three different stimulants: N-formylmethionine-leucyl-phenylalanine, phorbol 12-myristate 13-acetate (PMA), or lipopolysaccharide. NETs were immunohistochemically stained and analyzed with regard to NET percentage and NET area. Results: With all three stimuli, healthy term infants showed a lower NET percentage than the adult control group (p < 0.0001 each). The groups also differed in NET area, but the significance level was lower. Following PMA stimulation, we observed greater reductions in NET percentage and NET area in preterm than term infants. Conclusions: The lower NET formation observed in term infants compared to adults likely contributes to the reduced neonatal immune response. NET formation appeared to be even further decreased in late preterm neonates. There remains a need for further investigations of NET formation in more immature preterm infants.
Glucocorticoid Receptor Gene Variants and Neonatal Outcome in Very-Low-Birth-Weight Preterm Infants
(2016)
Background: Induction of lung maturation by prenatal steroid treatment has become the standard of care for pregnant women at risk for preterm birth. In addition to the beneficial effects on lung maturation, prenatal steroids have been shown to reduce the incidence of neonatal death, necrotizing enterocolitis, sepsis, and intraventricular hemorrhage. However, little is known about the role of interindividual differences in corticoid sensitivity arising from polymorphisms in the glucocorticoid receptor (GR) gene. Objectives: To assess the impact of GR polymorphisms N363S (rs56149945), R23K (rs6190), and BclI (rs41423247) on neonatal outcome. Methods: The GR polymorphisms N363S, R23K, and BclI were examined in 10,490 very-low-birth-weight (VLBW) preterm infants from 49 German tertiary level neonatal units (German Neonatal Network, GNN) with respect to neonatal outcome. Results: Infants carrying the BclI genotype were at higher risk to develop bronchopulmonary dysplasia (BPD) (OR 1.12 per BclI allele, 95% CI: 1.02-1.23, p = 0.013) in a logistic regression model adjusted for gestational age, mechanical ventilation, and small for gestational age status. A similar relative risk was seen in the children (89.4%) who received antenatal betamethasone treatment (OR 1.16, 95% CI: 1.05-1.27, p = 0.003), whereas no such effect was detectable in infants without antenatal steroids. N363S and R23K did not show any stable association with neonatal outcome parameters. Conclusion: Except for a slightly higher risk of BPD in carriers of the GRBclI variant, the GR gene polymorphisms BclI, N363S, and R23K did not affect neonatal outcome parameters in this large multicenter cohort of VLBW preterm infants.
Introduction: Inhibition of androgen synthesis by abiraterone acetate (AA) entails enhanced overall survival rates and clinical benefit for patients with locally advanced and metastasized prostate cancer (PC). The expression of heat shock protein 27 (HSP27) is generally associated with cytoprotection and was demonstrated to mediate chemoresistance under cytostatic therapy, for instance, docetaxel treatment. In this study, we investigated the impact of AA treatment on HSP27 expression and PC cell growth. Materials and Methods: HSP27 expression levels in docetaxel and AA-treated PC cell lines LNCaP and PC-3 were determined by SDS PAGE and Western blot analysis. Proliferation assays were performed using a CASY Cell Counter and Analyzer Model TT (Roche Applied Science). Results: Despite significantly increased HSP27 expression in PC cells incubated with docetaxel, Western blot analysis implicated a significant reduction of the cytoprotective HSP27 in AA-treated PC cells. Notably, HSP27 stably overexpressed in PC-3-HSP27 cells did not appear as an HSP27-mediated proliferation benefit in the presence of AA as shown in docetaxel incubation studies. Conclusion: In contrast to repeatedly demonstrated HSP27-driven chemoresistance related to chemotherapeutics, our results may constitute a broader molecular mode of action of AA chemotherapy. AA efficacy may exert an HSP27 suppressive role that goes beyond the primarily assumed inhibition of androgen biosynthesis.
Urological Complications and BK Virus-Associated Diseases Under Allogenic Stem Cell Transplantation
(2016)
Every year 50,000 patients receive a stem cell transplantation worldwide, but there is lack of data pertaining to urological complications. Methods: We performed a retrospective analysis of all adult patients undergoing their first allogenic stem cell transplantation from January 2011 to June 2013 in our institution. Statistical tests performed were Pearson's correlation, chi-square testing and logistic regression using SPSS 22.0. Results: We identified 39 patients (22 males, 17 females). Twenty four patients (61.5%) had a urological complication. Most frequent urologic complications were bacterial urinary tract infection (n = 13; 33.3%), acute renal failure (n = 6; 15.4%) and BK virus-associated haemorrhagic cystitis (n = 5; 12.8%). BK viruria was detected in 12 patients (30.8%). We observed an association of creatinine increase (about 20 µmol/l at time of onset of BK viruria) with BK viruria (Pearson's correlation 0.64; p = 0.01), and BK viruria is significantly linked to acute renal failure (Pearson's correlation 0.35; p = 0.029). In univariate regression, BK viruria is significantly linked to urological complication (p = 0.025). Conclusions: We suggest that BK virus infection during stem cell transplantation can lead to BK virus associated nephropathy, which is so far only known from patients after kidney transplantation.
Introduction: Recently, FOLFIRINOX and gemcitabine + nab-paclitaxel have been introduced as a novel intensified chemotherapy regimen for patients with metastasized pancreatic cancer. This study aims to analyze the real-world clinical practice with FOLFIRINOX and gemcitabine + nab-paclitaxel across Europe. Methods: Invitations to participate in an anonymous web-based questionnaire were sent via e-mail to 5,420 doctors in 19 European countries through the network of national gastroenterological, oncological, surgical and pancreatic societies as well as the European Pancreatic Club. The questionnaire consisted of 20 questions, 14 regarding the use of intensified chemotherapy, 4 regarding demographics of the participants, and 1 to verify the active involvement in the management of metastatic pancreatic cancer. Results: Two hundred and thirteen responses were received and 153 entries were valid for analysis. Of those, 63.4% came from an academic institution, 51% were oncologists, and 52% treated more than 25 cases per year. A majority of responses (71%) were from Italy (40%), Germany (23%), and Spain (8%). As first-line therapy, 11% used gemcitabine +/- erlotinib, 42% used FOLFIRINOX, and 47% used gemcitabine + nab-paclitaxel. Of the intensified regimens, both were applied to equal parts, but the likelihood of protocol deviation was higher when using FOLFIRINOX (p < 0.01). FOLFIRINOX was considered more toxic than gemcitabine + nab-paclitaxel (neutropenia 88 vs. 68%; polyneuropathy 42 vs. 41%; rapid deterioration 42 vs. 31%). FOLFIRINOX was rated to achieve longer survival with an acceptable quality of life (52 vs. 44%). Moreover, 57% of participants thought that gemcitabine + nab-paclitaxel should be the backbone for further clinical trials in pancreatic cancer. Conclusion: Intensified chemotherapy is widely used in pancreatic cancer patients in Europe following its recent clinical approval. Interestingly, nab-paclitaxel and FOLFIRINOX were used at comparable frequency although the latter had to be de-escalated more often.
This paper reviews the first part of the outcomes of the ORCA Saturday Afternoon Symposium 2014 dealing with ‘caries epidemiology and community dentistry: chances for future improvements in caries risk groups'. After the caries decline in many countries, there are remaining pockets of higher caries levels, mostly in the primary dentition and/or linked to a low socio-economic status (SES). The review into the evidence of caries-preventive measures clearly points to the use of fluorides, especially toothbrushing with fluoridated toothpaste and collective measures such as water fluoridation. In contrast to several unsuccessful high-risk approaches, community and public health programmes seem to be able to ensure a population-wide access and compliance in risk groups. Their simple and evidence-based measures mostly combine regular plaque removal and fluoride applications via toothbrushing, at least for children and adolescents. For the future, the common risk factor approach which addresses associations between oral health, social deprivation, diet, hygiene, smoking, alcohol use and stress should lead to combined efforts with other community health and education specialists. Further engagement with public policy, community leaders and administration is needed in order to strengthen healthy choices and behaviour, e.g. in ‘healthy' schools and kindergartens. It seems advisable that these population programmes also aim at improving upstream factors.
Background: Stereotactic electroencephalography (SEEG) is an invasive diagnostic tool for localizing the epileptic zone in patients with medically refractory focal epilepsy. Despite technical and imaging advances in guiding the electrode placement, vascular injury is still one of its most serious complications. Object: To investigate the usefulness of intraoperative cerebral C-arm CT angiogram (CCTA) in avoiding intracranial hemorrhagic complications during SEEG electrode implantation. Methods: Trajectory data from 12 patients who underwent SEEG electrode implantation were studied in detail. This included an analysis of the implantation of 146 SEEG electrodes, which were guided by intraoperative CCTA, as well as the standard planning based on preoperative contrast-enhanced MRI. In addition, a prospective analysis of SEEG hemorrhagic complications using the studied methodology was performed in a total of 87 patients receiving 1,310 electrodes. Results: There was no complication related to the CCTA itself. Intraoperative CCTA entailed modification of the original trajectory based on the preoperative MRI in 27 of 146 electrode implantations (18.5%). In 10 of them, a severe vascular complication was adverted by intraoperative CCTA. The safety of this new approach was also confirmed by the analysis of postinterventional CT, which revealed a symptomatic hematoma caused by 1 single electrode out of the 1,310 implanted. Conclusions: This study showed that intraoperative CCTA in addition to preoperative MRI is useful in guiding a safer SEEG electrode implantation. The combination of both imaging modalities essentially minimizes the risk of serious hemorrhagic complications.
Background: Strategies to improve the life of patients suffering from recurrent major depression have a high relevance. This study examined the efficacy of 2 Internet-delivered augmentation strategies that aim to prolong symptom-free intervals. Methods: Efficacy was tested in a 3-arm, multicenter, open-label, evaluator-blind, randomized controlled trial. Upon discharge from inpatient mental health care, 232 adults with 3 or more major depressive episodes were randomized to 1 of 2 intervention groups (SUMMIT or SUMMIT-PERSON) or to treatment as usual (TAU) alone. Over 12 months, participants in both intervention arms received, in addition to TAU, intense monitoring via e-mail or a smartphone, including signaling of upcoming crises, assistance with personal crisis management, and facilitation of early intervention. SUMMIT-PERSON additionally offered regular expert chats. The primary outcome was ‘well weeks', i.e. weeks with at most mild symptoms assessed by the Longitudinal Interval Follow-Up Evaluation, during 24 months after the index treatment. Results: SUMMIT compared to TAU reduced the time with an unwell status (OR 0.48; 95% CI 0.23-0.98) through faster transitions from unwell to well (OR 1.44; 95% CI 0.83-2.50) and slower transitions from well to unwell (OR 0.69; 95% CI 0.44-1.09). Contrary to the hypothesis, SUMMIT-PERSON was not superior to either SUMMIT (OR 0.77; 95% CI 0.38-1.56) or TAU (OR 0.62; 95% CI 0.31-1.24). The efficacy of SUMMIT was strongest 8 months after the intervention. Conclusions: The fully automated Internet-delivered augmentation strategy SUMMIT has the potential to improve TAU by reducing the lifelong burden of patients with recurrent depression. The fact that the effects wear off suggests a time-unlimited extension.
Ausbildung des Charakters
(2016)
Bacterial infections represent an increasing threat in human health and hospital- acquired infections meanwhile account for 99,000 deaths every year in the United States (Ventola, 2015). Live-threating bacterial infections will certainly emerge to an even more serious concern in future, essentially by accelerated development of antibiotic resistance. Only recently, the discovery of plasmid-encoded mcr-1, that confers resistance against colistin, marks the point where this highly transmissible resistance mechanism is now reported for every so far developed antibiotic (Liu et al., 2016). Staphylococcus aureus is a Gram-positive bacterium and well-known for its ability to quickly acquire resistance toward antibiotics either by chromosomal mutations and/or horizontal gene transfer (Pantosti et al., 2007). Although approximately 30% of the population is colonized with S. aureus (Kluytmans et al., 1997), it can transform to an invasive pathogen that causes a wide range of severe infections including pneumonia. The success of S. aureus as opportunistic pathogen can be attributed to combinations of several beneficial properties and capabilities including the expression of an arsenal of virulence factors (Archer, 1998), intracellular persistence (Garzoni & Kelley, 2009) and subversion of host cell defense mechanisms (Schnaith et al., 2007). The airway epithelium is the first line of defense against bacterial pathogens by forming a relative impermeable physical barrier composed of epithelial cells that are linked by tight junctions, desmosomes and adherence junctions (Davies & Garrod, 1997). Additionally, the airway epithelium mediates the detection of bacterial pathogens via toll-like receptors (TLRs) that recognize a variety of bacterial molecular patterns such as lipopolysaccharide (LPS), peptidoglycan and flaggelin (Sha et al., 2012). This interaction is transduced via protein phosphorylations into the cell in order to promote adaptation to the infection by initiation of the adaptive and innate immune defense. Although few insights where obtained of the signaling host responses towards staphylococcal infections (Agerer et al., 2003; 2005; Ellington et al., 2001), a comprehensive description of the host signaling network is largely missing. Thus, this dissertation thesis focuses on the decipherment of phosphorylation-mediated signaling responses towards S. aureus infections in non- professional and professional phagocytes by mass spectrometry-based phosphoproteomic techniques. The results of this thesis are summarized in the four chapters. Chapter I introduces to recent advances in the development of methodologies applied in the field of phosphoproteomics, including quantification strategies, peptide fractionation techniques and phosphopeptide enrichment methods applied for the system-wide characterization of protein phosphorylations by mass spectrometry. Additionally, publications reporting phosphorylation-based host signaling responses towards bacterial pathogens or their molecular patterns that applied mass spectrometry-based phosphoproteomics are discussed. In chapter II, the responses of the human bronchial epithelial cell lines 16HBE14o- and S9 following challenge with staphylococcal alpha- toxin at the level of proteome and phosphoproteome are summarized. General and cell type-specific signaling events are highlighted and evidences linking the activity of the epidermal growth factor receptor (EGFR) with differences in tolerance toward alpha-toxin are provided. Chapter III describes the modulation of the host signaling network of 16HBE14o- airway epithelial cells triggered by infection with S. aureus including temporal dissection of signaling events. Several protein kinases were identified as important signaling hubs mediating the host response. Targeted pharmaceutical inhibition of these kinases was probed and resulted in reduction of intracellular bacterial load. Chapter IV describes the rearrangement of the kinome by the differentiation of THP-1 monocytes to macrophage-like cells by application of quantitative kinomics. This approach identified the kinase MAP3K7 (TAK1) as key mediator of bacterial clearance, chemokine secretion and the differentiation process itself.
The role of uptake and efflux transporters in the pharmacokinetics of ß1-receptor blocker talinolol
(2016)
Introduction: The β1-adrenergic receptor antagonist talinolol is a probe drug for P-glycoprotein (P-gp). It is absorbed erratically and incompletely from the gastrointestinal tract. However, its pharmacokinetics might also be influenced by further uptake and efflux transporters as concluded from interaction studies with naringin and verapamil in human. Additionally, the transcellular transport through the different tissues, including enterocytes, hepatocytes and kidney tubular cells, is not completely understood so far. Therefore, we aimed to measure the affinity of talinolol to drug transporting proteins (OCT1-3, PEPT1, OCTN2, ASBT, NTCP, MRP 1-3 and P-gp as well as OATP 1B1, 1B3, 2B1 and 1A2) and some of their genetic variants known to be of pharmacokinetic relevance (OATP1A2 *2 and*3 as well as OATP2B1 V201M, R312Q and S486F). In a further step, we retrospectively evaluated the impact of clinically relevant genetic polymorphisms of transporters on the pharmacokinetics of talinolol in healthy subjects. Materials and Methods: Time and concentration-dependent uptake assays with [3H]-talinolol were performed either in stable transfected HEK293 or MDCKII cells expressing OATP1A2 *1, *2 and *3, OATP1B1, OATP1B3, OATP2B1 (and its genetic variants p.V201M, p.R312Q and p.S486F), NTCP, ASBT, PEPT1, OCTN2, OCT 1-3 and the respective vector control or in inside-out lipovesicles expressing the efflux transporters MRP1-3 and P-gp. Talinolol was quantified by liquid scintillation counting. The transport rates were then corrected by the transporter proteomics measured in the cellular membrane. Regarding the pharmacogenomic evaluation, it was carried out retrospectively in 39 healthy subjects who had participated in former pharmacokinetic studies with talinolol. This evaluation included a variety of transporter related genetic variants, known to be of a clinical meaning for their substrates. Results: Among the uptake transporters, talinolol was shown to be a substrate of OATP1B3 (Km= 153 ± 137 μmol/l; Vmax= 168 ± 30.3 μmol/mgxmin), OATP1B1 (Km= 301 ± 133 μmol/l; Vmax= 1135 ± 348 μmol/mgxmin), OATP2B1 (Km= 459 ± 260 μmol/l; Vmax= 4.32 ± 1.33 μmol/mgxmin), OATP1A2 (Km= 477 ± 158 μmol/l; Vmax= 0.61 ± 0.1 μmol/mgxmin) and NTCP (Km= 2560 ± 781 μmol/l; Vmax= 15944 ± 3741 μmol/mgxmin) but not a substrate of OCT1-3, OCTN2, PEPT1 or ASBT. When it comes to the efflux transporters, talinolol was transported by both P-gp (Km = 175 ± 206 mol/l; Vmax = 14 ± 10.8 nmol/mgxmin) and MRP3 (Km= 86.8 ± 62.8 μmol/l; Vmax= 133 ± 51.5 μmol/mgxmin) but not by MRP2. The pharmacogenomic analysis supported the in-vitro results, as it showed a significant decrease in talinolol absorption (AUC and Cmax) in subjects with the loss of function variant MRP3 211C>T and in those with a decreased P-gp function due to having less than 5 T-allels in the haplotype P-gp 1236-2677-3435-TTT. No significant changes were found associated with other transporters’ genetic variants. Conclusion: Our in-vitro results suggested the vectorial transport of talinolol through the enterocytes to consist mainly of apical OATP2B1 and P-gp and basolateral MRP3. Additionally in the hepatocytes, apical OATP1B1, OATP1B3 and NTCP seem to be involved as well. This vectorial transport was demonstrated in-vivo for the first time by our pharmacogenomic analysis, where talinolol absorption was significantly influenced by both P-gp and MRP3 genetic variants.
This thesis is devoted to experiments on three-dimensional dust clouds which are confined in low temperature plasmas. Such ensembles of highly electrically charged micrometer-sized particles reveal fascinating physics, such as self-excited density waves and vortices. At the same time, these systems are challenging for experimental approaches due to their three-dimensional character. In this thesis, new optical diagnostics for dusty plasmas have been developed and, in combination with existing techniques, have been used to study these 3D dusty plasmas on different size and time scales.
Myxomycetes are fungus-like protists of the supergroup Amoebozoa found to be abundant in all terrestrial ecosystems. Mainly based on its macroscopically visible fruit bodies, our knowledge on ecology and diversity of myxomycetes is better than for most other protistean groups, but there is still a lacking knowledge about global diversity patterns since tropical regions, especially the old world tropics, are still understudied. In this thesis a combination of classical ecological analyses and modern molecular methods were used to expand the current knowledge on myxomycete diversity and biogeography in the Paleotropics. A number of surveys in the Philippine archipelago are conducted to provide and to add information about the distribution of myxomycetes in the Southeast Asian region. A combination of field collecting and ca. 2500 moist chamber cultures from four unexplored areas in the Philippines, namely, the Bicol Peninsula (746 records, 57 taxa), Puerto Galera (926 records, 42 taxa), Quezon National Park (205 records, 35 taxa), and Negros Province (193 records, 28 taxa), now brings the number of species recorded for Philippines to 150; with one record, Stemonaria fuscoides, noted as new for the Asian Paleotropics. Collecting localities that have more diverse plant communities showed as well higher species diversity of myxomycetes. In congruence with studies from the Neotropical forests, it seems also that anthropogenic disturbances and the type of forest structure affect the occurrence of myxomycetes for the Philippines. Another survey carried out in another paleotropical region, the highlands of Ethiopia, revealed a total of 151 records, with all 39 species found as new for the country. Three records of Diderma cf. miniatum with a strong bright red peridium and one record of Didymium cf. flexuosum with a conspicuous broad reticulation in the spore ornamentation were described and barcoded, since both may represent morphospecies new to science. A number of rarely recorded species, like Didymium saturnus, Metatrichia floripara, Perichaena areolata, and Physarina echinospora showed that resembling to its unique flora, the east African mountain ranges harbor a diverse and distinctive myxomycete assemblage. One incentive of this study was to compile a solid large dataset for the Paleotropical region that is comparable to data obtained from comprehensive studies performed in the Neotropical areas a decade ago. A total of eight surveys (with four comprehensive regional surveys, two from lowland and two from highland, for each region, the Neo- and the Paleotropics) were used, to compare the myxomycete assemblages of both regions. Each survey comes from a region with fairly homogenous vegetation, and includes specimens from both field and moist chamber cultures component. A statistical analysis of species accumulation curves revealed that only between 70 and 95% of all species to be expected have been found. Even for >1000 specimens per survey these figures seem hardly to increase with increasing collection effort, since a high proportion of species is always represented by a single or a few records only. Both ordination and cluster analysis suggests that geographical separation explains differences in species composition of the myxomycete assemblages much better than elevational differences. 5 The molecular component of this thesis is a phylogeographic study of the widely distributed tropical myxomycete Hemitrichia serpula. It is a morphologically distinct species with golden-yellow fructifications forming a reticulum. However, subtle variation in spore ornamentation points to cryptic speciation within this myxomycete. Using two independent molecular markers, 135 partial sequences of the small subunit (SSU) rRNA (a nuclear but extrachromosomal gene) and 30 partial sequences of the elongation factor 1 alpha gene (EF1A) (a nuclear gene), a study of 135 Hemitrichia serpula specimens collected worldwide revealed the existence of four clades that are likely to represent reproductively isolated biospecies, since each clade shows a unique combination of SSU and EF1A genotypes. A Mantel test with the partial SSU sequences indicated geographical differentiation, giving a correlation coefficient of 0.467 between the pairwise computed geographic and genetic distances, compared with the 95% confidence interval from 999 permutations (-0.013 to 0.021). Biogeographical analysis of the 40 SSU ribotypes showed clear intraspecific variation and geographic differentiation demonstrating a limited gene flow among the world population. We argue that the distribution of cryptic species in the different clade can be explained by ongoing, but still incomplete speciation. An event-based ancestral area reconstruction using the software S-DIVA employed in RASP showed that the probable origin of the ribotypes was a global dispersal event in the Neotropics. Additional species distribution models that were implemented for the three most prominent clades show different putative ranges. As such H. serpula supports the moderate endemicity hypothesis for protists. In summary, myxomycete assemblages in the Paleotropics (1) displayed a higher diversity than for Neotropical forests, (2) harbor unique taxa that differentiates those assemblages in spite of the expected similar macroecological all over the Tropics, (3) are affected by geographical barriers that likely causes speciation both at a morphospecies and biospecies level, and (4) follow the ubiquitous model in the sense that gene flow mediated by long-distance dispersal of spores is high enough that a species can fill out its entire putative range, but (5) the gene flow is not high enough to prevent variation in regional gene pools, which may lead to speciation and is better explained by the moderate endemicity model. Our data are still too limited to draw a comprehensive picture of the diversity of tropical myxomycetes, but the baseline information compiled with the aid of both classical ecology and molecular approaches from this study are first major steps towards this goal.
Myxomycetes (Amoebozoa, plasmodial slime molds) are one of the last larger groups of organisms where the biodiversity is not yet investigated by molecular methods, except for a very few cultivable model species. Based on the first phylogenies for the group produced in 2012 and 2013, this thesis work explores the genetic diversity of wild populations of myxomycetes, addressing two questions: 1. Does diversity and phylogenetic trees found with barcode markers fit the current morphological species concept, and do barcode markers reveal a lower or higher diversity than found by morphological characters? In the first case, morphological characters seen as decisive for species differentiation would be plastic (shaped by the environment), in the second case we must assume the existence of cryptic species. 2. Can genetic markers be used to see if natural populations of myxomycetes reproduce mainly sexual or asexual? Sexuality is proven to occur in the Amoebozoa, but asexual reproduction should be advantageous for habitat colonization. Experiments with cultivable species have shown that both reproductive modes occur in the myxomycetes. Two species complexes were chosen for an in-depth investigation. The first species is the common wood-inhabiting myxomycete Trichia varia (Pers. ex J.F. Gmel.) Pers., one of the first myxomycetes to be described and always seen as a variable, yet single, species. The second example involves a snowbank species so far known as Lamproderma atrosporum Meyl., which was recently transferred to a genus on its own, Meriderma Mar. Mey. & Poulain, and a morphological species concept, including several taxa, was proposed. Trichia varia belongs to the bright-spored myxomycetes. Partial sequences of three independent markers (nuclear small-subunit ribosomal RNA gene, SSU, extrachromosomal; protein elongation factor 1 alpha gene, EF1A, chromosomal; cytochrome oxidase subunit 1 gene, COI, mitochondrial) from 198 specimens resulted in a three-gene phylogeny containing three groups, within each group combinations of the single-marker genotypes occurred exclusively. Complete SSU sequences were generated for 66 specimens, which revealed six positions that can carry group I introns and putatively functional or degenerated homing endonuclease genes in two groups. All observations (genotypic combinations of the three markers, signs of recombination, intron patterns) fit well into a pattern of three cryptic biological species that reproduce predominantly sexual but are reproductively isolated. The pattern of group I introns and inserted homing endonuclease genes mounts evidence that the Goddard-Burt intron life cycle model applies to naturally occurring myxomycete populations. A total of 89 specimens of the dark-spored myxomycete genus Meriderma from five European mountain ranges were sequenced for partial genes of SSU and EF1A. The latter gene includes an extremely variable spliceosomal intron. Three clades, the two morphologically recognizable taxa M. fuscatum, M. aggregatum, and the morphologically complicated complex species M. atrosporum agg., were recovered. The EF1A-based phylogeny of the 81 specimens of M. atrosporum agg. resulted in seven subclades, with the two EF1A-haplotypes of a sequence sharing always one subclade for each of the 50 heterozygous specimens, a pattern consistent with the existence of several independent but sexually reproducing biospecies. Identical EF1A genotypes occurred more often within a regional population than in between. A simulation assuming panmixis within a biospecies but not in between, and isolation between mountain ranges suggested that similar numbers of shared genotypes can be created by chance through sexual reproduction alone. Numbers of haplotypes shared between mountain ranges correlate with geographical distance, suggesting occasional long-distance dispersal by spores. An enlarged data set containing 227 partial SSU sequences of Meriderma spp. identified 53 ribotypes, with a ribotype accumulation curve indicating 68.4±14.5 ribotypes to expect according to the Chao2 estimator. The topology of the SSU phylogeny generally confirms results from the partial SSU and EF1A data set of 89 specimens, where several putative biospecies could be recognized. A novel method for automated analyses of SEM images allows to derive quantitative descriptors for spore ornamentation, which were subjected to multivariate analyses. Spore ornamentation provided traits with the highest explanatory power in a multivariate statistics, whereas spore size and stalk length were much less significant. For some but not all putative biospecies a unique combination of morphological characters was found, which is in accordance with the hypothesis of instant sympatric 8 speciation via mutations creating incompatible strains splitting from existing biospecies. The morphologically recognizable taxa of the genus are described and a key for the genus Meriderma is given. To compare morphological and molecular diversity in lignicolous myxomycetes, all specimens found in a study covering the late-autumn aspect were sequenced, using partial SSU gene as a barcode marker. A total of 161 logs in the old-growth forest Eldena, northeastern Germany, was surveyed, resulting in 530 collections representing 27 taxa from 14 genera. Bright-spores species were far more abundant than dark-spored taxa. A phylogeny based on partial SSU sequences for bright-spored myxomycetes revealed morphospecies to be largely consistent with phylogenetic groups. Most but not all morphospecies may contain multiple ribotypes that cannot be differentiated by light microscopy. This first study backing up a traditional morphology-based survey by a full molecular component demonstrates that partial SSU sequences can function as reliable barcode markers for myxomycetes, but reveals as well a significant, yet not infinite, amount of hidden diversity. The main conclusions of this work, set up in the frame of a project funded by the German Research Council (DFG), are the following: 1. Sexual reproduction seems to be an important, if not the dominating mode (apart from clonal myxamoebal populations built up by binary fission) of reproduction in naturally occurring populations of myxomycetes. 2. From the two investigated species complexes we can expect many, if not most, morphopecies to be composed of reproductively isolated, sexually reproducing, biospecies. 3. Partial SSU sequences, as most widely used in this study, seem to represent suitable barcode markers for the group and can be used to distinguish the (usually cryptic) biospecies, although they alone do not allow any conclusions about reproductive isolation and speciation processes. 4. We have to expect a significant amount of hidden diversity in myxomycetes, which will increase the number of taxa from ca. 1000 recognized morphologically by a factor between two and ten.
Nanoengineering and laser optics allow for the fabrication of a wide range of systems that subject fermionic particles to geometric restrictions. In addition to strong correlations, the fermions may couple to internal or external bosonic fields, such as quantized lattice vibrations or light fields. This thesis considers the theoretical description of two such systems. One is a molecular junction, i.e., a small organic molecule contacted by metallic electrodes or leads. Itinerant electrons induce molecular vibrations and deformations, corresponding to phonon modes of considerable energy. The thesis investigates the effects of this local electron-phonon interaction on the electric and thermoelectric transport through the junction. Starting with an Anderson-Holstein quantum dot model, our ansatz is based on the application of a variational Lang-Firsov transformation that accounts for the polaronic character of the dot state. We solve the steady-state Kadanoff-Baym equations and derive a self-consistent approximation to the polaronic self-energy that accounts for finite densities and multi-phonon scattering processes. The optimal variational parameter is determined numerically by minimizing the thermodynamical potential. This allows a detailed study of the electronic dot spectral function for all interaction strengths and adiabaticity regimes. For instance, we discuss how a voltage dependent polaronic renormalization of the dot-lead coupling and the dot level causes negative differential conductance and novel conductance features. The investigation of the second system is motivated by recent experiments on the Bose-Einstein condensation of excitons in small semiconducting cuprous oxide crystals. At ultra cold temperatures three species of para- and orthoexcitons are caught in stress induced potential traps. Their decay luminescence is the primary method of detection. This thesis considers the thermodynamics of this system in terms of a multicomponent gas of weakly interacting bosons in external potentials. The coupled equations of motion are solved within a Hartree-Fock-Bogoliubov-Popov approximation. For typical experimental parameters the density distributions of the interacting species are calculated numerically. Based on the luminescence formula by Shi and Verechaka we discuss, e.g., how the spectrum of the direct decay of thermal paraexcitons may reveal the formation of a nonluminescent paraexciton condensate as well as the spatial separation of strongly repulsive orthocondensates. First results for an extended luminescence theory are presented, which takes into account the polariton effect.
Comprehensive study of the discharge mode transition in inductively coupled radio frequency plasmas
(2016)
In this contribution, the mode transition of an inductively coupled radio frequency plasma at low pressure is investigated. Therefore, a comprehensive set of plasma diagnostics were applied to determine plasma and processing parameters. Therewith, the plasma kinetics and especially the important elementary processes were studied. Hence, the reason for the mode transition was identified.
Because of the vital role of the liquid as interface in plasma medicine, this work is focused on the elucidation of the interaction of plasmas with biologically relevant liquids. The results of this thesis are an important step in the direction of the applications to real biological liquids such as blood and wound secretion ex vivo as well as in vivo. In this thesis the following questions are investigated and answered with the special focus on the free radicals as highly reactive and, therefore, hard to detect relevant group of chemical species: What is the impact of the atmospheric-pressure argon plasma jet on biologically relevant solutions? Which species are generated due to the plasma treatment of liquids? What is an appropriate detection procedure for the qualification and quantification of the short-lived species? Does the surrounding conditions influence the formation of liquid-phase reactive species and can this influence be used to tailor a desired liquid composition? What is the influence of the plasma surroundings? What is the influence of feed gas manipulation regarding the reactive species generation? Can these impacts be used for a selected reactive species composition generation? Does the treated liquid medium affect the plasma-generated reactive species output and in what way? Which are the underlying mechanisms and origins of the plasma-caused chemical changes in the solutions? Do reactive species exist, which origin is located in the gaseous phase? What is the impact of the plasma jet radiation?
Protamine (PRT) is a positively charged protein, which is widely used in medicine as an adjunct to certain preparations of insulin and as a rapidly-acting antidote for heparin, particularly to neutralize the effects of high heparin concentrations needed for anticoagulation during cardiac surgical procedures using cardiopulmonary bypass. It has been demonstrated that PRT and heparin form multimolecular complexes and that these complexes have high immunogenicity in a mouse model. Studies in this thesis provide new insights into the pathophysiology of anti-PRT/heparin antibodies. The results of study I showed that the administration of PRT combined with heparin is responsible for high immunoglobulin G (IgG) immunization after cardiac surgery. A subset of these antibodies was able to induce platelet activation in a way similar to that observed by heparin-induced thrombocytopenia (HIT). Using an animal model, we demonstrated that anti-PRT/heparin antibodies are capable of platelet destruction in the presence of PRT and heparin. Moreover, our data suggests that platelet-activating anti-PRT/heparin antibodies at surgery are potentially associated with postoperative thrombocytopenia and an increased risk for thromboembolic events. In study II, the immune response against PRT/heparin complexes was investigated. This study showed a relatively fast development of IgG with no general preceding IgM formation. In addition, patients undergoing liver transplantation developed anti-PRT/heparin antibodies without previous exposure to PRT. These results suggest that a previous contact with the antigen(s) itself or other antigens with molecular mimicry induced this immune response. In fact, we were able to identify Neutral Protamine Hagedorn (NPH) insulin and core histones (DNA-binding proteins) as potentially antigenic candidates for a previous immunization. Furthermore, the findings of study III demonstrate the ability of anti-PRT/heparin antibodies to activate platelets in the presence of NPH insulin in a heparin-dependent way suggesting that diabetic patients may have an enhanced risk for thromboembolic complications if treated with NPH insulin and possibly while receiving prophylactic heparin. These observations justify further clinical investigations to assess the impact of the interaction between anti-PRT/heparin antibodies and PRT-mimicking antigens, such as NPH insulin or histones.
Achieving commercial production of electricity by magnetic confinement fusion requires improvements in energy and particle confinement. In order to better understand and optimise confinement, numerical simulations of plasma phenomena are useful. One particularly challenging regime is that in which long wavelength MHD phenomena interact with kinetic phenomena. In such a regime, global electromagnetic gyrokinetic simulations are necessary. In this regime, computational requirements have been excessive for Eulerian methods, while Particle-in-Cell (PIC) methods have been particularly badly affected by the "cancellation problem", a numerical problem resulting from the structure of the electromagnetic gyrokinetic equations. A number of researchers have been working on mitigating this problem with some significant successes. Another alternative to mitigating the problem is to move to a hybrid system of fluid and gyrokinetic equations. At the expense of reducing the physical content of the numerical model, particularly electron kinetic physics, it is possible in this way to perform global electromagnetic PIC simulations retaining ion gyrokinetic effects but eliminating the cancellation problem. The focus of this work has been the implementation of two such hybrid models into the gyrokinetic code EUTERPE. The two models treat electrons and the entire bulk plasma respectively as a fluid. Both models are additionally capable of considering the self-consistent interaction of an energetic ion species, described gyrokinetically, with the perturbed fields. These two models have been successfully benchmarked in linear growth rate and frequency against other codes for a Toroidal Alfvén Eigenmode (TAE) case. The m=1 internal kink mode, which is particularly challenging in terms of the fully gyrokinetic cancellation problem, has also been successfully benchmarked using the hybrid models with the MHD eigenvalue code CKA. Non-linear simulations in this TAE case have been performed confirming the analytical prediction of a quadratic relationship between the linear growth rate of the TAE and the saturated amplitude of the TAE for a range of moderate values of the linear growth rate. At higher linear growth rate, a slower scaling of saturated amplitude with linear growth rate is observed. This analysis has been extended to include the non-linear wave-wave coupling between multiple TAE modes. It has been shown that wave-wave coupling results in a significant reduction in the saturated amplitude. It has been demonstrated that both plasma elongation and ion kinetic effects can exert a stabilising influence on the internal kink mode. A population of energetic particles can also exert a stabilising influence at low normalised pressure. At high normalised fast particle pressure the stabilised kink mode has been shown to give way to the m=1 EPM, which has been simulated both linearly and non-linearly (the "fishbone" mode). The first self-consistent simulations of global modes in the magnetic geometry of the optimised stellarator Wendelstein 7-X have been performed both linearly and non-linearly. Limitations have been encountered in performing simulations in 3D geometry. A hypothesis for the cause of these problems is outlined and ideas for mitigation are briefly described. In addition to the hybrid model simulations, some of the first utilisations of a new scheme for mitigating the cancellation problem in the fully gyrokinetic regime have been carried out in the framework of this thesis. This scheme, which was developed separately, is concisely described in this work. The new scheme has been benchmarked with existing gyrokinetic and hybrid results. The linear Wendelstein 7-X simulations and linear and single mode non-linear TAE simulations have been repeated with the new model. It is shown that bulk plasma kinetics can suppress the growth rate of global modes in Wendelstein 7-X. The results of fully gyrokinetic TAE simulations, the first to have been performed to our knowledge, are shown to be in close agreement with those results obtained using hybrid models. In the TAE case, the hybrid models are an order of magnitude less computationally demanding than the new gyrokinetic scheme, which is in turn at least an order of magnitude less computationally demanding than the previous gyrokinetic scheme.