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Institute
- Theodor-Boveri-Institut für Biowissenschaften (87)
- Physikalisches Institut (70)
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ResearcherID
- B-1911-2015 (1)
- C-2593-2016 (1)
- D-1221-2009 (1)
- N-2030-2015 (1)
- N-3741-2015 (1)
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.