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Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas rnaltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the Li and L2 beta-lactamases in response to beta-lactam treatment. Here we report that the patient isolate S. rnaltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bleu and bla(L2) were transcriptionally the most strongly upregulated genes. Promoter fusions of b/a(L1) and b/a(L2) genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla(L2) expressing cells as identified by RNA(seq) analysis. Overexpression of cornE in S. maltophilia K279a reduced the level of cells that were in a bla(L2)-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including b/a(L1), b/a(L2), and comE.
Virotherapy on the basis of oncolytic vaccinia virus (VACV) strains is a novel approach for canine cancer therapy. Here we describe, for the first time, the characterization and the use of VACV strain GLV-5b451 expressing the anti-vascular endothelial growth factor (VEGF) single-chain antibody (scAb) GLAF-2 as therapeutic agent against different canine cancers. Cell culture data demonstrated that GLV-5b451 efficiently infected and destroyed all four tested canine cancer cell lines including: mammary carcinoma (MTH52c), mammary adenoma (ZMTH3), prostate carcinoma (CT1258), and soft tissue sarcoma (STSA-1). The GLV-5b451 virus-mediated production of GLAF-2 antibody was observed in all four cancer cell lines. In addition, this antibody specifically recognized canine VEGF. Finally, in canine soft tissue sarcoma (CSTS) xenografted mice, a single systemic administration of GLV-5b451 was found to be safe and led to anti-tumor effects resulting in the significant reduction and substantial long-term inhibition of tumor growth. A CD31-based immuno-staining showed significantly decreased neo-angiogenesis in GLV-5b451-treated tumors compared to the controls. In summary, these findings indicate that GLV-5b451 has potential for use as a therapeutic agent in the treatment of CSTS.
Background
The dmrt1 and sox9 genes have a well conserved function related to testis formation in vertebrates, and the group of fish presents a great diversity of species and reproductive mechanisms. The lambari fish (Astyanax altiparanae) is an important Neotropical species, where studies on molecular level of sex determination and gonad maturation are scarce.
Methods
Here, we employed molecular cloning techniques to analyze the cDNA sequences of the dmrt1 and sox9 genes, and describe the expression pattern of those genes during development and the male reproductive cycle by qRT-PCR, and related to histology of the gonad.
Results
Phylogenetic analyses of predicted amino acid sequences of dmrt1 and sox9 clustered A. altiparanae in the Ostariophysi group, which is consistent with the morphological phylogeny of this species. Studies of the gonad development revealed that ovary formation occurred at 58 days after hatching (dah), 2 weeks earlier than testis formation. Expression studies of sox9 and dmrt1 in different tissues of adult males and females and during development revealed specific expression in the testis, indicating that both genes also have a male-specific role in the adult. During the period of gonad sex differentiation, dmrt1 seems to have a more significant role than sox9. During the male reproductive cycle dmrt1 and sox9 are down-regulated after spermiation, indicating a role of these genes in spermatogenesis.
Conclusions
For the first time the dmrt1 and sox9 were cloned in a Characiformes species. We show that both genes have a conserved structure and expression, evidencing their role in sex determination, sex differentiation and the male reproductive cycle in A. altiparanae. These findings contribute to a better understanding of the molecular mechanisms of sex determination and differentiation in fish.
Background:
The interaction of eukaryotic host and prokaryotic pathogen cells is linked to specific changes in the cellular proteome, and consequently to infection-related gene expression patterns of the involved cells. To simultaneously assess the transcriptomes of both organisms during their interaction we developed dual 3'Seq, a tag-based sequencing protocol that allows for exact quantification of differentially expressed transcripts in interacting pro-and eukaryotic cells without prior fixation or physical disruption of the interaction.
Results:
Human epithelial cells were infected with Salmonella enterica Typhimurium as a model system for invasion of the intestinal epithelium, and the transcriptional response of the infected host cells together with the differential expression of invading and intracellular pathogen cells was determined by dual 3'Seq coupled with the next-generation sequencing-based transcriptome profiling technique deepSuperSAGE (deep Serial Analysis of Gene Expression). Annotation to reference transcriptomes comprising the operon structure of the employed S. enterica Typhimurium strain allowed for in silico separation of the interacting cells including quantification of polycistronic RNAs. Eighty-nine percent of the known loci are found to be transcribed in prokaryotic cells prior or subsequent to infection of the host, while 75% of all protein-coding loci are represented in the polyadenylated transcriptomes of human host cells.
Conclusions:
Dual 3'Seq was alternatively coupled to MACE (Massive Analysis of cDNA ends) to assess the advantages and drawbacks of a library preparation procedure that allows for sequencing of longer fragments. Additionally, the identified expression patterns of both organisms were validated by qRT-PCR using three independent biological replicates, which confirmed that RELB along with NFKB1 and NFKB2 are involved in the initial immune response of epithelial cells after infection with S. enterica Typhimurium.
The Urban Heat Island (UHI) is the phenomenon of altered increased temperatures in urban areas compared to their rural surroundings. UHIs grow and intensify under extreme hot periods, such as during heat waves, which can affect human health and also increase the demand for energy for cooling. This study applies remote sensing and land use/land cover (LULC) data to assess the cooling effect of varying urban vegetation cover, especially during extreme warm periods, in the city of Munich, Germany. To compute the relationship between Land Surface Temperature (LST) and Land Use Land Cover (LULC), MODIS eight-day interval LST data for the months of June, July and August from 2002 to 2012 and the Corine Land Cover (CLC) database were used. Due to similarities in the behavior of surface temperature of different CLCs, some classes were reclassified and combined to form two major, rather simplified, homogenized classes: one of built-up area and one of urban vegetation. The homogenized map was merged with the MODIS eight-day interval LST data to compute the relationship between them. The results revealed that (i) the cooling effect accrued from urban vegetation tended to be non-linear; and (ii) a remarkable and stronger cooling effect in terms of LST was identified in regions where the proportion of vegetation cover was between seventy and almost eighty percent per square kilometer. The results also demonstrated that LST within urban vegetation was affected by the temperature of the surrounding built-up and that during the well-known European 2003 heat wave, suburb areas were cooler from the core of the urbanized region. This study concluded that the optimum green space for obtaining the lowest temperature is a non-linear trend. This could support urban planning strategies to facilitate appropriate applications to mitigate heat-stress in urban area.
A simple test setup has been developed at Institute of Aerospace Information Technology, University of Würzburg, Germany to realize basic functionalities for formation flight of quadrocopters. The test environment is planned to be utilized for developing and validating the algorithms for formation flying capability in real environment as well as for education purpose. An already existing test bed for single quadrocopter was extended with necessary inter-communication and distributed control mechanism to test the algorithms for formation flights in 2 degrees of freedom (roll / pitch). This study encompasses the domain of communication, control engineering and embedded systems programming. Bluetooth protocol has been used for inter-communication between two quadrocopters. A simple approach of PID control in combination with Kalman filter has been exploited. MATLAB Instrument Control Toolbox has been used for data display, plotting and analysis. Plots can be drawn in real-time and received information can also be stored in the form of files for later use and analysis. The test setup has been developed indigenously and at considerably low cost. Emphasis has been placed on simplicity to facilitate students learning process. Several lessons have been learnt during the course of development of this setup. Proposed setup is quite flexible that can be modified as per changing requirements.
The flagellate Trypanosoma brucei, which causes the sleeping sickness when infecting a mammalian host, goes through an intricate life cycle. It has a rather complex propulsion mechanism and swims in diverse microenvironments. These continuously exert selective pressure, to which the trypanosome adjusts with its architecture and behavior. As a result, the trypanosome assumes a diversity of complex morphotypes during its life cycle. However, although cell biology has detailed form and function of most of them, experimental data on the dynamic behavior and development of most morphotypes is lacking. Here we show that simulation science can predict intermediate cell designs by conducting specific and controlled modifications of an accurate, nature-inspired cell model, which we developed using information from live cell analyses. The cell models account for several important characteristics of the real trypanosomal morphotypes, such as the geometry and elastic properties of the cell body, and their swimming mechanism using an eukaryotic flagellum. We introduce an elastic network model for the cell body, including bending rigidity and simulate swimming in a fluid environment, using the mesoscale simulation technique called multi-particle collision dynamics. The in silico trypanosome of the bloodstream form displays the characteristic in vivo rotational and translational motility pattern that is crucial for survival and virulence in the vertebrate host. Moreover, our model accurately simulates the trypanosome's tumbling and backward motion. We show that the distinctive course of the attached flagellum around the cell body is one important aspect to produce the observed swimming behavior in a viscous fluid, and also required to reach the maximal swimming velocity. Changing details of the flagellar attachment generates less efficient swimmers. We also simulate different morphotypes that occur during the parasite's development in the tsetse fly, and predict a flagellar course we have not been able to measure in experiments so far.
In the present thesis the MBE growth and sample characterization of HgTe structures is investigated
and discussed. Due to the first experimental discovery of the quantum Spin Hall effect
(QSHE) in HgTe quantum wells, this material system attains a huge interest in the spintronics
society. Because of the long history of growing Hg-based heterostructures here at the Experimentelle
Physik III in Würzburg, there are very good requirements to analyze this material
system more precisely and in new directions. Since in former days only doped HgTe quantum
wells were grown, this thesis deals with the MBE growth in the (001) direction of undoped
HgTe quantum wells, surface located quantum wells and three dimensional bulk layers. All
Hg-based layers were grown on CdTe substrates which generate strain in the layer stack and
provide therefore new physical effects. In the same time, the (001) CdTe growth was investigated
on n-doped (001) GaAs:Si because the Japanese supplier of CdTe substrates had a
supply bottleneck due to the Tohoku earthquake and its aftermath in 2011.
After a short introduction of the material system, the experimental techniques were demonstrated
and explained explicitly. After that, the experimental part of this thesis is displayed.
So, the investigation of the (001) CdTe growth on (001) GaAs:Si is discussed in chapter 4.
Firstly, the surface preparation of GaAs:Si by oxide desorption is explored and analyzed.
Here, rapid thermal desorption of the GaAs oxide with following cool down in Zn atmosphere
provides the best results for the CdTe due to small holes at the surface, while e.g. an atomic
flat GaAs buffer deteriorates the CdTe growth quality. The following ZnTe layer supplies the
(001) growth direction of the CdTe and exhibits best end results of the CdTe for 30 seconds
growth time at a flux ratio of Zn/Te ~ 1/1.2. Without this ZnTe layer, CdTe will grow in the
(111) direction. However, the main investigation is here the optimization of the MBE growth
of CdTe. The substrate temperature, Cd/Te flux ratio and the growth time has to be adjusted
systematically. Therefore, a complex growth process is developed and established. This optimized
CdTe growth process results in a RMS roughness of around 2.5 nm and a FWHM value
of the HRXRD w-scan of 150 arcsec. Compared to the literature, there is no lower FWHM
value traceable for this growth direction. Furthermore, etch pit density measurements show
that the surface crystallinity is matchable with the commercial CdTe substrates (around 1x10^4
cm^(-2)). However, this whole process is not completely perfect and offers still room for improvements.
The growth of undoped HgTe quantum wells was also a new direction in research in contrast
to the previous n-doped grown HgTe quantum wells. Here in chapter 5, the goal of very low
carrier densities was achieved and therefore it is now possible to do transport experiments in
the n - and p - region by tuning the gate voltage. To achieve this high sample quality, very precise
growth of symmetric HgTe QWs and their HRXRD characterization is examined. Here,
the quantum well thickness can now determined accurate to under 0.3 nm. Furthermore, the transport analysis of different quantum well thicknesses shows that the carrier density and
mobility increase with rising HgTe layer thickness. However, it is found out that the band
gap of the HgTe QW closes indirectly at a thickness of 11.6 nm. This is caused by the tensile
strained growth on CdTe substrates. Moreover, surface quantum wells are studied. These
quantum wells exhibit no or a very thin HgCdTe cap. Though, oxidization and contamination
of the surface reduces here the carrier mobility immensely and a HgCdTe layer of around 5 nm
provides the pleasing results for transport experiments with superconductors connected to the
topological insulator [119]. A completely new achievement is the realization of MBE growth
of HgTe quantum wells on CdTe/GaAs:Si substrates. This is attended by the optimization of
the CdTe growth on GaAs:Si. It exposes that HgTe quantum wells grown in-situ on optimized
CdTe/GaAs:Si show very nice transport data with clear Hall plateaus, SdH oscillations, low
carrier densities and carrier mobilities up to 500 000 cm^2/Vs. Furthermore, a new oxide etching
process is developed and analyzed which should serve as an alternative to the standard
HCl process which generates volcano defects at some time. However, during the testing time
the result does not differ in Nomarski, HRXRD, AFM and transport measurements. Here,
long-time tests or etching and mounting in nitrogen atmosphere may provide new elaborate
results.
The main focus of this thesis is on the MBE growth and standard characterization of HgTe bulk
layers and is discussed in chapter 6. Due to the tensile strained growth on lattice mismatched
CdTe, HgTe bulk opens up a band gap of around 22 meV at the G-point and exhibits therefore
its topological surface states. The analysis of surface condition, roughness, crystalline quality,
carrier density and mobility via Nomarski, AFM, XPS, HRXRD and transport measurements
is therefore included in this work. Layer thickness dependence of carrier density and mobility
is identified for bulk layer grown directly on CdTe substrates. So, there is no clear correlation
visible between HgTe layer thickness and carrier density or mobility. So, the carrier density is
almost constant around 1x10^11 cm^(-2) at 0 V gate voltage. The carrier mobility of these bulk
samples however scatters between 5 000 and 60 000 cm^2/Vs almost randomly. Further experiments
should be made for a clearer understanding and therefore the avoidance of unusable
bad samples.But, other topological insulator materials show much higher carrier densities and
lower mobility values. For example, Bi2Se3 exhibits just density values around 1019 cm^(-2)
and mobility values clearly below 5000 cm2/Vs. The carrier density however depends much
on lithography and surface treatment after growth. Furthermore, the relaxation behavior and
critical thickness of HgTe grown on CdTe is determined and is in very good agreement with
theoretical prediction (d_c = 155 nm). The embedding of the HgTe bulk layer between HgCdTe
layers created a further huge improvement. Similar to the quantum well structures the carrier
mobility increases immensely while the carrier density levels at around 1x10^11 cm^(-2) at 0
V gate voltage as well. Additionally, the relaxation behavior and critical thickness of these
barrier layers has to be determined. HgCdTe grown on commercial CdTe shows a behavior as
predicted except the critical thickness which is slightly higher than expected (d_c = 850 nm).
Otherwise, the relaxation of HgCdTe grown on CdTe/GaAs:Si occurs in two parts. The layer
is fully strained up to 250 nm. Between 250 nm and 725 nm the HgCdTe film starts to relax
randomly up to 10 %. The relaxation behavior for thicknesses larger than 725 nm occurs than
linearly to the inverse layer thickness. A explanation is given due to rough interface conditions
and crystalline defects of the CdTe/GaAs:Si compared to the commercial CdTe substrate. HRXRD and AFM data support this statement. Another point is that the HgCdTe barriers protect the active HgTe layer and because of the high carrier mobilities the Hall measurements provide new transport data which have to be interpreted more in detail in the future. In addition, HgTe bulk samples show very interesting transport data by gating the sample from the top and the back. It is now possible to manipulate the carrier densities of the top and bottom surface states almost separately. The back gate consisting of the n-doped GaAs substrate and the thick insulating CdTe buffer can tune the carrier density for Delta(n) ~ 3x10^11 cm^(-2). This is sufficient to tune the Fermi energy from the p-type into the n-type region [138].
In this thesis it is shown that strained HgTe bulk layers exhibit superior transport data by embedding between HgCdTe barrier layers. The n-doped GaAs can here serve as a back gate.
Furthermore, MBE growth of high crystalline, undoped HgTe quantum wells shows also new
and extended transport output. Finally, it is notable that due to the investigated CdTe growth
on GaAs the Hg-based heterostructure MBE growth is partially independent from commercial
suppliers.
The brain-derived neurotrophic factor BDNF plays a critical role in neuronal development and the induction of L-LTP at glutamatergic synapses in several brain regions. However, the cellular and molecular mechanisms underlying these BDNF effects have not been firmly established. Using in vitro cultures of cortical neurons from knockout mice for Pld1 and Rsk2, BDNF was observed to induce a rapid RSK2-dependent activation of PLD and to stimulate BDNF ERK1/2-CREB and mTor-S6K signalling pathways, but these effects were greatly reduced in Pld1\(^{-/-}\) neurons. Furthermore, phospho-CREB did not accumulate in the nucleus, whereas overexpression of PLD1 amplified the BDNF-dependent nuclear recruitment of phospho-ERK1/2 and phospho-CREB. This BDNF retrograde signalling was prevented in cells silenced for the scaffolding protein PEA15, a protein which complexes with PLD1, ERK1/2, and RSK2 after BDNF treatment. Finally PLD1, ERK1/2, and RSK2 partially colocalized on endosomal structures, suggesting that these proteins are part of the molecular module responsible for BDNF signalling in cortical neurons.
Background
International collaborative research is a mechanism for improving the development of disease-specific therapies and for improving health at the population level. However, limited data are available to assess the trends in research output related to orphan diseases.
Methods and Findings
We used bibliometric mapping and clustering methods to illustrate the level of fragmentation in myeloma research and the development of collaborative efforts. Publication data from Thomson Reuters Web of Science were retrieved for 2005-2009 and followed until 2013. We created a database of multiple myeloma publications, and we analysed impact and co-authorship density to identify scientific collaborations, developments, and international key players over time. The global annual publication volume for studies on multiple myeloma increased from 1,144 in 2005 to 1,628 in 2009, which represents a 43% increase. This increase is high compared to the 24% and 14% increases observed for lymphoma and leukaemia. The major proportion (> 90% of publications) was from the US and EU over the study period. The output and impact in terms of citations, identified several successful groups with a large number of intra-cluster collaborations in the US and EU. The US-based myeloma clusters clearly stand out as the most productive and highly cited, and the European Myeloma Network members exhibited a doubling of collaborative publications from 2005 to 2009, still increasing up to 2013.
Conclusion and Perspective
Multiple myeloma research output has increased substantially in the past decade. The fragmented European myeloma research activities based on national or regional groups are progressing, but they require a broad range of targeted research investments to improve multiple myeloma health care.
In classical conditioning, an initially neutral stimulus (conditioned stimulus, CS) becomes associated with a biologically salient event (unconditioned stimulus, US), which might be pain (aversive conditioning) or food (appetitive conditioning). After a few associations, the CS is able to initiate either defensive or consummatory responses, respectively. Contrary to aversive conditioning, appetitive conditioning is rarely investigated in humans, although its importance for normal and pathological behaviors (e.g., obesity, addiction) is undeniable. The present study intents to translate animal findings on appetitive conditioning to humans using food as an US. Thirty-three participants were investigated between 8 and 10 am without breakfast in order to assure that they felt hungry. During two acquisition phases, one geometrical shape (avCS+) predicted an aversive US (painful electric shock), another shape (appCS+) predicted an appetitive US (chocolate or salty pretzel according to the participants' preference), and a third shape (CS) predicted neither US. In a extinction phase, these three shapes plus a novel shape (NEW) were presented again without US delivery. Valence and arousal ratings as well as startle and skin conductance (SCR) responses were collected as learning indices. We found successful aversive and appetitive conditioning. On the one hand, the avCS+ was rated as more negative and more arousing than the CS and induced startle potentiation and enhanced SCR. On the other hand, the appCS+ was rated more positive than the CS and induced startle attenuation and larger SCR. In summary, we successfully confirmed animal findings in (hungry) humans by demonstrating appetitive learning and normal aversive learning.
Swelling-activated pathways for myo-inositol, one of the most abundant organic osmolytes in mammalian cells, have not yet been identified. The present study explores the SLC5A3 protein as a possible transporter of myo-inositol in hyponically swollen HEK293 cells. To address this issue, we examined the relationship between the hypotonicity-induced changes in plasma membrane permeability to myo-inositol Pino [m/s] and expression/localization of SLC5A3. Pino values were determined by cell volumetry over a wide tonicity range (100–275 mOsm) in myo-inositol-substituted solutions. While being negligible under mild hypotonicity (200–275 mOsm), Pino grew rapidly at osmolalities below 200 mOsm to reach a maximum of ∼3 nm/s at 100–125 mOsm, as indicated by fast cell swelling due to myo-inositol influx. The increase in Pino resulted most likely from the hypotonicity-mediated incorporation of cytosolic SLC5A3 into the plasma membrane, as revealed by confocal fluorescence microscopy of cells expressing EGFP-tagged SLC5A3 and super-resolution imaging of immunostained SLC5A3 by direct stochastic optical reconstruction microscopy (dSTORM). dSTORM in hypotonic cells revealed a surface density of membrane-associated SLC5A3 proteins of 200–2000 localizations/μm2. Assuming SLC5A3 to be the major path for myo-inositol, a turnover rate of 80–800 myo-inositol molecules per second for a single transporter protein was estimated from combined volumetric and dSTORM data. Hypotonic stress also caused a significant upregulation of SLC5A3 gene expression as detected by semiquantitative RT-PCR and Western blot analysis. In summary, our data provide first evidence for swelling-mediated activation of SLC5A3 thus suggesting a functional role of this transporter in hypotonic volume regulation of mammalian cells.
LIM and SH3 protein 1 (LASP1) is a nucleocytoplasmic scaffolding protein. LASP1 interacts with various cytoskeletal proteins via its domain structure and is known to participate in physiological processes of cells. In the present study, a detailed investigation of the expression pattern of LASP1 protein in normal skin, melanocytic nevi and melanoma was carried out and the melanocyte–specific function of LASP1 was analyzed. LASP1 protein was identified in stratum basale of skin epidermis and a very high level was detected in nevi, the benign tumor of melanocyte. In the highly proliferative basal cells, an additional distinct nuclear localization of the protein was noted. In different tumor entities, an elevated LASP1 expression and nuclear localization, correlated positively with malignancy and tumor grade. However, LASP1 level was determined to be very low in melanoma and even reduced in metastases. Melanoma is distinguished as the first tumor tested to date – that displayed an absence of elevated LASP1 expression. In addition no significant relation was observed between LASP1 protein expression and clinicopathological parameters in melanoma.
The epidermal melanin unit of skin comprises of melanocytes and keratinocytes. Melanocytes are specialized cells that synthesize the photo protective coloring pigment, melanin inside unique organelles called melanosomes. The presence of LASP1 in melanocytes is reported for the first time through this study and the existence was confirmed by immunoblotting analysis in cultured normal human epidermal melanocyte (NHEM) and in melanoma cell lines, along with the immunohistostaining imaging in normal skin and in melanocytic nevi. LASP1 depletion in MaMel2 cells revealed a moderate increase in the intracellular melanin level independently of de novo melanogenesis, pointing to a partial hindrance in melanin release. Immunofluorescence images of NHEM and MaMel2 cells visualized co-localization of LASP1 with dynamin and tyrosinase concomitant with melanosomes at the dendrite tips of the cells. Melanosome isolation experiments by sucrose density gradient centrifugation clearly demonstrated the presence of LASP1 and the melanosome specific markers tyrosinase and TRP1 in late stage melanosomes.
The study identified LASP1 and dynamin as novel binding partners in melanocytes and provides first evidence for the existence of LASP1 and dynamin (a protein well–known for its involvement in vesicle formation and budding) in melanosomes. Co-localization of LASP1 and dynamin along the dendrites and at the tips of the melanocytes indicates a potential participation of the two proteins in the membrane vesicle fission at the plasma membrane.
In summary, a possible involvement of LASP1 in the actin–dynamin mediated membrane fission and exocytosis of melanin laden melanosome vesicles into the extracellular matrix is suggested.
Part 1 of this work describes the development of accurate physically grounded force fields for
intermolecular Cation-π interactions based on SAPT energy decomposition analysis.
The presented results demonstrate the benefits of the used DFT-SAPT method to describe non-bonding
interactions. First of all, this method is able to reproduce the high level CCSD(T) energy values
but using much less computational time. Second it provides the possibility to separate the total
intermolecular interaction energy into several physically meaningful contributions. The relative
contributions of the dimers investigated can be seen in Fig. 6.16. In Tab. 6.3 the percentage
contribution of the attractive energy parts to the stabilization energy is shown. The polarization
energy is important for the NH+...C6H6 interaction, whereas it becomes less crucial
considering other dimers. The dispersion energy contribution is large in the case of
the C6H6...H2O dimers, whereas it is relatively less important for the NH+...C6H6
interaction. The electrostatic energy contributes a large amount of stabilizing energy
in all considered dimer interactions. ...
Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.
In unserem Alltag kommen wir heute ständig mit Systemen der Informations- und Kommunikationstechnik in Kontakt. Diese bestehen häufig aus mehreren interagierenden und kommunizierenden Komponenten, wie zum Beispiel nebenläufige Software zur effizienten Nutzung von Mehrkernprozessoren oder Sensornetzwerke. Systeme, die aus mehreren interagierenden und kommunizierenden Komponenten bestehen sind häufig komplex und dadurch sehr fehleranfällig. Daher ist es wichtig zuverlässige Methoden, die helfen die korrekte Funktionsweise solcher Systeme sicherzustellen, zu besitzen.
Im Rahmen dieser Doktorarbeit wurden neue Methoden zur Verbesserung der Verifizierbarkeit von asynchronen nebenläufigen Systemen durch Anwendung der symbolischen Modellprüfung mit binären Entscheidungsdiagrammen (BDDs) entwickelt. Ein asynchrones nebenläufiges System besteht aus mehreren Komponenten, von denen zu einem Zeitpunkt jeweils nur eine Komponente Transitionen ausführen kann. Die Modellprüfung ist eine Technik zur formalen Verifikation, bei der die Gültigkeit einer Menge von zu prüfenden Eigenschaften für eine gegebene Systembeschreibung automatisch durch Softwarewerkzeuge, die Modellprüfer genannt werden, entschieden wird. Das Hauptproblem der symbolischen Modellprüfung ist das Problem der Zustandsraumexplosion und es sind weitere Verbesserungen notwendig, um die symbolische Modellprüfung häufiger erfolgreich durchführen zu können.
Bei der BDD-basierten symbolischen Modellprüfung werden Mengen von Systemzuständen und Mengen von Transitionen jeweils durch BDDs repräsentiert. Zentrale Operationen bei ihr sind die Berechnung von Nachfolger- und Vorgängerzuständen von gegebenen Zustandsmengen, welche Bildberechnungen genannt werden. Um die Gültigkeit von Eigenschaften für eine gegebene Systembeschreibung zu überprüfen, werden wiederholt Bildberechnungen durchgeführt. Daher ist ihre effiziente Berechnung entscheidend für eine geringe Laufzeit und einen niedrigen Speicherbedarf der Modellprüfung. In einer Bildberechnung werden ein BDD zur Repräsentation einer Menge von Transitionen und ein BDD für eine Menge von Zuständen kombiniert, um eine Menge von Nachfolger- oder Vorgängerzuständen zu berechnen. Oft ist auch die Größe von BDDs zur Repräsentation der Transitionsrelation von Systemen entscheidend für die erfolgreiche Anwendbarkeit der Modellprüfung.
In der vorliegenden Arbeit werden neue Datenstrukturen zur Repräsentation der Transitionsrelation von asynchronen nebenläufigen Systemen bei der BDD-basierten symbolischen Modellprüfung vorgestellt. Zusätzlich werden neue Algorithmen zur Durchführung von Bildberechnungen präsentiert. Beides kann zu großen Reduktionen der Laufzeit und des Speicherbedarfs führen. Asynchrone nebenläufige Systeme besitzen häufig Symmetrien. Eine Technik zur Reduktion des Problems der Zustandsraumexplosion ist die Symmetriereduktion. In dieser Arbeit wird ebenfalls ein neuer effizienter Algorithmus zur Symmetriereduktion bei der symbolischen Modellprüfung mit BDDs aufgeführt.
Background
To use combinatorial epitope mapping ("fingerprinting") of the antibody response to identify targets of the humoral immune response in patients with transitional cell carcinoma (TCC) of the bladder.
Methods
A combinatorial random peptide library was screened on the circulating pool of immunoglobulins purified from an index patient with a high risk TCC (pTa high grade plus carcinoma in situ) to identify corresponding target antigens. A patient cohort was investigated for antibody titers against ubiquitin.
Results
We selected, isolated, and validated an immunogenic peptide motif from ubiquitin as a dominant epitope of the humoral response. Patients with TCC had significantly higher antibody titers against ubiquitin than healthy donors (p<0.007), prostate cancer patients (p<0.0007), and all patients without TCC taken together (p<0.0001). Titers from superficial tumors were not significantly different from muscle invasive tumors (p = 0.0929). For antibody response against ubiquitin, sensitivity for detection of TCC was 0.44, specificity 0.96, positive predictive value 0.96 and negative predictive value 0.41. No significant titer changes were observed during the standard BCG induction immunotherapy.
Conclusions
This is the first report to demonstrate an anti-ubiquitin antibody response in patients with TCC. Although sensitivity of antibody production was low, a high specificity and positive predictive value make ubiquitin an interesting candidate for further diagnostic and possibly immune modulating studies.
Merocyanine Dyes as Organic Semiconductors for Vacuum-processed Solar Cell and Transistor Devices
(2015)
The present thesis comprises the synthesis of new functional merocyanine dyes, the study of their electro-optical properties as well as solid state packing and their application as p-type semiconductor materials in transistor and solar cell devices. The absorption properties of the obtained compounds could be modified by variation of the donor unit, the introduction of electron-withdrawing substituents in the acceptor unit or elongation of the polymethine chain. For a particular dye, the absorption band could be shifted by more than 160 nm by increasing the solvent polarity due to a conformational switch between a merocyanine-like and a cyanine-like structure. Single crystal analyses revealed that the studied dyes tend to pack either in an antiparallel fashion forming dimers with no overall dipole moment or in a staircase-like pattern where the dipole moments point to the same direction and are only balanced by another staircase oriented in the opposite direction (stair dimer). With respect to application as semiconductor materials, the latter packing arrangement resulted most favorable for charge carrier mobility. We concluded that this packing motif is preserved in the solar cell devices, where the selenium-containing dye afforded the highest performance of this series for an optimized planar-mixed heterojunction solar cell (6.2 %).
Im Rahmen der vorliegenden Arbeit wurden Dihydroborane (H2BR) sowie Dihalogenborane (X2BR) mit Übergangsmetall-Lewis-Basen umgesetzt und die Reaktivität der auf diese Weise erhaltenen Übergangsmetall–Bor-Komplexe eingehend untersucht. So wurde eine Serie neuer Borylkomplexe des Typs trans-[Pt{B(Br)R‘}Br(PR3)2] dargestellt und mit Salzen schwach-koordinierender Anionen umgesetzt. Diese Studien sollten die Triebkraft für die Bildung kationischer Borylenkomplexe näher beleuchten. Die experimentellen Ergebnisse zeigen, dass eine Substitution in ortho-Position des borgebundenen Arylliganden für den notwendigen [1,2]-Halogenshift vom Bor- zum Platinzentrum und somit zur Realisierung einer Pt=B-Mehrfachbindung unabdingbar ist. Demnach reagieren Komplexe mit para-substituierten Arylliganden bei Halogenidabstraktion aus Borylkomplexen zu T-förmigen, kationischen Borylplatinkomplexen, während die Duryl-substituierten Analoga unter [1,2]-Halogenwanderung in kationische Borylenplatinkomplexe überführt werden. Neben dem Substitutionsmuster des borgebundenen Arylliganden wurde auch der Einfluss des Phosphanliganden untersucht.
Die Molekülstrukturen der Borylkomplexe 2 und 4 im Festkörper zeigen grundlegende Unterschiede im strukturellen Aufbau. Der Durylsubstituent ist in 2 im Vergleich zur (Ph-4-tBu)-Einheit in 4 deutlich aus der {Br2–Pt–B–Br1}-Ebene herausgedreht (2: Pt–B–C1–C2: 31.4(1); 4: 4.3(7)°), was vermutlich einen [1,2]-Halogenshift in 2 begünstigt. Die Pt–B-Bindungen der kationischen Borylenkomplexe 6 (1.861(5) Å) und 7 (1.863(5) Å) sind deutlich kürzer als im neutralen Borylkomplex 2 (2.004(4) Å), was ein eindeutiger Beleg für den Mehrfachbindungscharakter der Pt–B-Bindungen in 6 und 7 ist. Demzufolge scheint der sterische Anspruch des borgebundene Arylsubstituenten entscheidend für den Reaktionspfad bei Halogenidabstraktionen und somit für die Bildung kationischer Borylenplatinkomplexe zu sein, während diesen Studien zu Folge der Einfluss der Ligandensphäre am Platinzentrum eher eine untergeordnete Rolle spielt.
Des Weiteren gelang die Synthese der neuartigen heteroleptischen Platinkomplexe [Pt(cAACMe)(PiPr3)] (13) und [Pt(cAACMe)(PCy3)] (14) durch Umsetzung von [Pt(PCy3)2] und [Pt(PiPr3)2] mit dem cyclischen (Alkyl)(Amino)Carben cAACMe (Schema 34, A), bzw. durch Umsetzung von [Pt(nbe)2(PCy3)] (Schema 34, B) mit cAACMe. Die Darstellung des literaturbekannten homoleptischen Komplexes [Pt(cAACMe)2] (11) konnte durch Reaktion von [Pt(nbe)3] mit cAACMe deutlich vereinfacht werden bei gleichzeitiger Steigerung der Ausbeute (96%, Literatur: 79%). Die ungewöhnlich intensiv orangene Farbe dieser Verbindungsklasse geht laut DFT-Rechnungen auf die elektronische Anregung aus dem HOMO in das LUMO zurück, wobei hauptsächlich die π-Wechselwirkungen zwischen den Platin- und Carbenkohlenstoffatomen des cAACMe-Liganden beteiligt sind (DFT-Rechnungen von Dr. Mehmet Ali Celik). Auch in ihren strukturellen Eigenschaften sind sich 11 - 14 sehr ähnlich, wohingegen deutliche Unterschiede in deren Elektrochemie und Reaktivität beobachtet wurden. So konnte für 11 eine quasi-reversible Oxidationswelle (E1/2 = –0.30 V gegen [Cp2Fe]/[Cp2Fe]+ in THF) bestimmt werden, während die heteroleptischen Komplexe 13 und 14 (Epa = –0.09 V; –0.11 V) sowie deren Vorläufer [Pt(PCy3)2] und [Pt(PiPr3)2] (Epa = 0.00 V; +0.12 V) irreversible Oxidationswellen zeigen. Demnach kann 13 und 14 im Vergleich zu [Pt(PCy3)2] und [Pt(PiPr3)2] ein größeres Reduktionsvermögen zugeordnet werden. Reaktivitätsstudien zeigen, dass der homoleptische Komplex 11 inert gegenüber vielen Substraten wie z.B. Boranen, Diboranen(4) und Lewis-Säuren ist. Im Gegensatz dazu haben sich die heteroleptischen Komplexe 13 und 14 als deutlich reaktiver erwiesen, womit diese eine Mittelstellung zwischen 11 und der Spezies [Pt(PR3)2] einnimmt.
Die Umsetzung von [Pt(cAACMe)(PiPr3)] (13) mit BBr3 und Br2BPh lieferte die Borylkomplexe 18 und 19, welche vollständig charakterisiert wurden. Die Reaktivität von 13 und 14 gegenüber den Lewis-Säuren GaCl3 und HgCl2 zeigt ebenfalls Analogien zu der von Bis(phosphan)platinkomplexen. Reaktion mit GaCl3 führte hierbei zur Bildung der MOLP-Komplexe [(cAACMe)(PiPr3)Pt→GaCl3] (21) und [(cAACMe)(PCy3)Pt→GaCl3] (22), während die oxidative Addition der Hg–Cl-Bindung an das Platinzentrum von 14 im Komplex [PtCl(HgCl)(cAACMe)(PiPr3)] (23) resultierte. Die Synthese von 23 gelang auch durch Umsetzung mit Kalomel unter Abscheidung eines Äquivalentes elementaren Quecksilbers.
Ein weiterer Schwerpunkt dieser Arbeit lag auf der Übergangsmetall-vermittelten Dehydrokupplung von Dihydroboranen. Die Umsetzung von [Pt(cAACMe)(PiPr3)] (13) mit BBr3 und Br2BPh lieferte die Borylkomplexe 18 und 19, welche vollständig charakterisiert wurden. Die Reaktivität von 13 und 14 gegenüber den Lewis-Säuren GaCl3 und HgCl2 zeigt ebenfalls Analogien zu der von Bis(phosphan)platinkomplexen. Reaktion mit GaCl3 führte hierbei zur Bildung der MOLP-Komplexe [(cAACMe)(PiPr3)Pt→GaCl3] (21) und [(cAACMe)(PCy3)Pt→GaCl3] (22), während die oxidative Addition der Hg–Cl-Bindung an das Platinzentrum von 14 im Komplex [PtCl(HgCl)(cAACMe)(PiPr3)] (23) resultierte. Die Synthese von 23 gelang auch durch Umsetzung mit Kalomel unter Abscheidung eines Äquivalentes elementaren Quecksilbers.
Ein weiterer Schwerpunkt dieser Arbeit lag auf der Übergangsmetall-vermittelten Dehydrokupplung von Dihydroboranen. Vor Beginn dieser Reaktivitätsstudien wurde zunächst eine vereinfachte Syntheseroute für Dihydroborane entwickelt. Durch Umsetzung von Cl2BDur mit HSiEt3 konnte auf diese Weise der Syntheseaufwand deutlich verringert und die Ausbeute an H2BDur von 74% auf 98% deutlich gesteigert werden. Zur Dehydrokupplung wurden neben Gold-, Rhodium- und Iridiumkomplexen auch Platinkomplexe mit H2BDur umgesetzt. Die Untersuchungen mit Gold- und Rhodiumverbindungen erwiesen sich hierbei als erfolglos und die Umsetzung der Iridiumpincerkomplexe [(PCP)IrH2] 26 und 27 (tBuPCP, AdPCP) mit H2BDur lieferte die Boratkomplexe 28 und 29 mit κ2-koordinierten {H2BHDur}-Liganden. Analog konnte bei Umsetzung von 26 mit H2BThx der Boratkomplex 30 spektroskopisch beobachtet, jedoch nicht isoliert werden. Bei den Komplexen 28 - 30 handelt es sich um die ersten κ2-σ:σ-Dihydroboratkomplexe mit sterisch anspruchsvollen Arylsubstituenten. Neben den Iridiumpincerkomplexen wurde auch der Komplex [Cp*IrCl2]2 mit H2BDur umgesetzt. Die Bildung des Boratkomplexes 34 ist mit einem [1,2]-Shift eines Chloratoms von Iridium auf das Borzentrum verbunden.
Die Reaktivität von H2BDur gegenüber [Pt(PCy3)2] zeigte eine starke Abhängigkeit hängt von der Stöchiometrie. Bei der 1:1-Umsetzung konnten sowohl die farblosen Verbindungen trans-[(PCy3)2PtH2] und Cy3P→BH2Dur (48) isoliert werden, als auch die beiden dunkelroten Verbindungen [(Cy3P)3Pt3(2-B2Dur2)] (36) und [{(PCy3)Pt}4(2-BDur)2(4-BDur)] (37), kristallographisch untersucht werden.
Der B–B-Abstand im π-Diborenkomplex 36 (1.614(6) Å) deutet eindeutig auf die Gegenwart einer B=B-Doppelbindung hin, wobei das Diboren side-on gebunden an zwei der drei Platinatome des Pt3-Gerüsts koordiniert ist. Die Zusammensetzung von 36 und 37 konnte auch durch Elementaranalysen bestätigt werden.
Die Bildung von 36 und 37 deuten auch darauf hin, dass bei dieser Art der Dehydrokupplung multimetallische Wechselwirkungen eine wichtige Rolle für die Stabilisierung der borzentrierten Liganden spielen. So konnten bei der Reaktion von [Pt(PCy3)2] mit zwei Äquivalenten H2BDur neben Cy3P→BH2Dur (48) auch zwei weitere zweikernige Platinverbindungen isoliert und vollständig charakterisiert werden. Erhitzen der Reaktionslösung auf 68°C für 170 Minuten führte hierbei zur Bildung von [{(Cy3P)Pt}2(μ-BDur)(ƞ2:(μ-B)-HB(H)Dur)] (38) mit zwei verbrückenden borzentrierten Liganden, einem Borylen- (BDur) und einem Boranliganden (BH2Dur), welche im 11B{1H}-NMR Spektrum bei δ = 101.3 und δ = 32.8 ppm detektiert wurden. Die Röntgenstrukturanalyse von 38 lässt einen signifikanten σ-BH-Hinbindungsanteil des Boranliganden zu einem der Platinzentren vermuten, was einen anteiligen Pt2→B-Bindungscharakter andeutet. Dieser Befund konnte auch durch DFT-Rechnungen von Dr. William Ewing bestätigt werden.
Die Studien haben auch gezeigt, dass die Bildung von 38 über eine Zwischenstufe verläuft, den hypercloso-Cluster [{(Cy3P)HPt}2(μ-H){μ:ƞ2-B2Dur2(μ-H)}] (39) mit einer tetraedrischen {Pt2B2}-Einheit, zwei terminalen Pt–H-Bindungen sowie je einen die Pt–Pt- bzw. B–B-Bindung verbrückenden Hydridliganden. 39 erwies sich als anfällig gegenüber H2-Eliminierung und lagert bei Raumtemperatur innerhalb von Tagen, bzw. bei 68°C innerhalb einer Stunde unter B–B-Bindungsbruch quantitativ in 38 um, welche selbst keinen direkten Bor–Bor-Kontakt mehr aufweist.
Auf Grundlage der beschriebenen Resultate wurde zudem ein einfacher Zugang zu zweikernigen Platinkomplexen entwickelt. Demnach gelang es, den literaturbekannten zweikernigen Komplex [Pt2(μ:ƞ2-dppm)3] (50) (dppm = Ph2PCH2PPh2) durch Umsetzung von [Pt(nbe)3] mit dppm in guten Ausbeuten zu synthetisieren. Des Weiteren wurde die Reaktivität von 50 gegenüber verschiedenen Lewis-Säuren untersucht. Ein Großteil dieser Umsetzungen war mit der Bildung von schwer löslichen Feststoffen verbunden, weshalb lediglich bei der Reaktion mit Br2BPh und Br2BMes geringe Mengen an definiertem Produkt isoliert und durch Röntgenstrukturanalyse charakterisiert werden konnten. Demnach führte die Umsetzung von 50 mit Br2BPh oder Br2BMes zur oxidativen Addition beider B–Br-Bindungen an je eines der Platinzentren und der Bildung der verbrückenden Borylenplatinkomplexe 51 und 52. NMR-spektroskopische Studien deuteten eine analoge Reaktivität von Br2BDur und Br2BFc an, wobei die Komplexe 53 und 54 noch nicht vollständig charakterisiert werden konnten.