572 Biochemie
Refine
Has Fulltext
- yes (94)
Is part of the Bibliography
- yes (94)
Year of publication
Document Type
- Doctoral Thesis (51)
- Journal article (38)
- Master Thesis (2)
- Preprint (2)
- Book article / Book chapter (1)
Keywords
- Transkriptionsfaktor (5)
- DNS-Reparatur (4)
- Ubiquitin (4)
- Regulation (3)
- SMN (3)
- Saccharomyces cerevisiae (3)
- TFIIH (3)
- Thrombozyt (3)
- gene expression (3)
- mass spectrometry (3)
Institute
- Graduate School of Life Sciences (35)
- Lehrstuhl für Biochemie (32)
- Theodor-Boveri-Institut für Biowissenschaften (22)
- Rudolf-Virchow-Zentrum (12)
- Institut für Molekulare Infektionsbiologie (7)
- Institut für Experimentelle Biomedizin (4)
- Fakultät für Chemie und Pharmazie (3)
- Institut für Pharmazie und Lebensmittelchemie (3)
- Medizinische Klinik und Poliklinik II (3)
- Fakultät für Biologie (2)
Schriftenreihe
Sonstige beteiligte Institutionen
ResearcherID
No abstract available.
Rekonstitution des Chromophors und der Funktion von Bakteriorhodopsin aus Halobacterium halobium
(1976)
Ein Modell der lichtgetriebenen Protonenpumpe Bakteriorhodopsin postulierte die direkte Beteiligung der Wasserstoffe in der 4-Stellung des Cyclohexenringes des Retinalchromophors an dem Vorgang der Protonenverschiebung. Mittels Blockaden der Retroform-Bildung von Retinal durch chemische Modifizierungen des Cyclohexenringes (4-Hydroxy-Retinal, 5,6-Epoxy-Retinal) konnten nach Einbau der modifizierten Moleküle in die isolierte Purpurmembran und nach Zugabe zu Halobakterien mit unterdrückter Retinalsynthese die direkte Beteiligung des Cyclohexenringes an der Protonenpumpe mit großer Wahrscheinlichkeit ausgeschlossen werden.
Background:
The SWI/SNF chromatin remodeling factors have the ability to remodel nucleosomes and play essential roles in key developmental processes. SWI/SNF complexes contain one subunit with ATPase activity, which in Drosophila melanogaster is called Brahma (Brm). The regulatory activities of SWI/SNF have been attributed to its influence on chromatin structure and transcription regulation, but recent observations have revealed that the levels of Brm affect the relative abundances of transcripts that are formed by alternative splicing and/or polyadenylation of the same pre-mRNA.
Results:
We have investigated whether the function of Brm in pre-mRNA processing in Drosophila melanogaster is mediated by Brm alone or by the SWI/SNF complex. We have analyzed the effects of depleting individual SWI/SNF subunits on pre-mRNA processing throughout the genome, and we have identified a subset of transcripts that are affected by depletion of the SWI/SNF core subunits Brm, Snr1 or Mor. The fact that depletion of different subunits targets a subset of common transcripts suggests that the SWI/SNF complex is responsible for the effects observed on pre-mRNA processing when knocking down Brm. We have also depleted Brm in larvae and we have shown that the levels of SWI/SNF affect the pre-mRNA processing outcome in vivo.
Conclusions:
We have shown that SWI/SNF can modulate alternative pre-mRNA processing, not only in cultured cells but also in vivo. The effect is restricted to and specific for a subset of transcripts. Our results provide novel insights into the mechanisms by which SWI/SNF regulates transcript diversity and proteomic diversity in higher eukaryotes.
Background:
Retinitis pigmentosa (RP) is an inherited eye disease characterized by the progressive degeneration of rod photoreceptor cells. Mutations in pre-mRNA splicing factors including PRPF31 have been identified as cause for RP, raising the question how mutations in general factors lead to tissue specific defects.
Results:
We have recently shown that the zebrafish serves as an excellent model allowing the recapitulation of key events of RP. Here we use this model to investigate two pathogenic mutations in PRPF31, SP117 and AD5, causing the autosomal dominant form of RP. We show that SP117 leads to an unstable protein that is mislocalized to the rod cytoplasm. Importantly, its overexpression does not result in photoreceptor degeneration suggesting haploinsufficiency as the underlying cause in human RP patients carrying SP117. In contrast, overexpression of AD5 results in embryonic lethality, which can be rescued by wild-type Prpf31. Transgenic retina-specific expression of AD5 reveals that stable AD5 protein is initially localized in the nucleus but later found in the cytoplasm concurrent with progressing rod outer segment degeneration and apoptosis. Importantly, we show for the first time in vivo that retinal transcripts are wrongly spliced in adult transgenic retinas expressing AD5 and exhibiting increased apoptosis in rod photoreceptors.
Conclusion:
Our data suggest that distinct mutations in Prpf31 can lead to photoreceptor degeneration through different mechanisms, by haploinsufficiency or dominant-negative effects. Analyzing the AD5 effects in our animal model in vivo, our data imply that aberrant splicing of distinct retinal transcripts contributes to the observed retina defects.
Introduction:
Oncolytic viruses show promise for treating cancer. However, to assess therapeutic efficacy and potential toxicity, a noninvasive imaging modality is needed. This study aimed to determine if insertion of the human sodium iodide symporter (hNIS) cDNA as a marker for non-invasive imaging of virotherapy alters the replication and oncolytic capability of a novel vaccinia virus, GLV-1h153.
Methods:
GLV-1h153 was modified from parental vaccinia virus GLV-1h68 to carry hNIS via homologous recombination. GLV-1h153 was tested against human pancreatic cancer cell line PANC-1 for replication via viral plaque assays and flow cytometry. Expression and transportation of hNIS in infected cells was evaluated using Westernblot and immunofluorescence. Intracellular uptake of radioiodide was assessed using radiouptake assays. Viral cytotoxicity and tumor regression of treated PANC-1tumor xenografts in nude mice was also determined. Finally, tumor radiouptake in xenografts was assessed via positron emission tomography (PET) utilizing carrier-free (124)I radiotracer.
Results:
GLV-1h153 infected, replicated within, and killed PANC-1 cells as efficiently as GLV-1h68. GLV-1h153 provided dose-dependent levels of hNIS expression in infected cells. Immunofluorescence detected transport of the protein to the cell membrane prior to cell lysis, enhancing hNIS-specific radiouptake (P < 0.001). In vivo, GLV-1h153 was as safe and effective as GLV-1h68 in regressing pancreatic cancer xenografts (P < 0.001). Finally, intratumoral injection of GLV-1h153 facilitated imaging of virus replication in tumors via (124)I-PET.
Conclusion:
Insertion of the hNIS gene does not hinder replication or oncolytic capability of GLV-1h153, rendering this novel virus a promising new candidate for the noninvasive imaging and tracking of oncolytic viral therapy.
Background:
Over 90% of low risk (LR) neuroblastoma patients survive whereas less than 30% of high risk (HR) patients are long term survivors. Age (children younger than 18 months old) is associated with LR disease. Considering that adaptive immune system is well developed in older children, and that T cells were shown to be involved in tumor escape and progression of cancers, we sought to determine whether HR patients may tend to show a signature of adaptive immune responses compared to LR patients who tend to have diminished T-cell responses but an intact innate immune response.
Methods:
We performed microarray analysis of RNA extracted from the tumor specimens of HR and LR patients. Flow cytometry was performed to determine the cellular constituents in the blood while multiplex cytokine array was used to detect the cytokine profile in patients' sera. A HR tumor cell line, SK-N-SH, was also used for detecting the response to IL-1 beta, a cytokines which is involved in the innate immune responses.
Results:
Distinct patterns of gene expression were detected in HR and LR patients indicating an active T-cell response and a diminished adaptive immune response, respectively. A diminished adaptive immune response in LR patients was evident by higher levels of IL-10 in the sera. In addition, HR patients had lower levels of circulating myeloid derived suppressor cells (MDSC) compared with a control LR patient. LR patients showed slightly higher levels of cytokines of the innate immune responses. Treatment of the HR tumor line with IL-1b induced expression of cytokines of the innate immune responses.
Conclusions:
This data suggests that adaptive immune responses may play an important role in the progression of HR disease whereas innate immune responses may be active in LR patients.
Multiple fluorescence in situ hybridization is the method of choice for studies aimed at determining simultaneous production of signal transduction molecules and neuromodulators in neurons. In our analyses of the monoamine receptor mRNA expression of peptidergic neurons in the rat telencephalon, double tyramide-signal-amplified fluorescence in situ hybridization delivered satisfactory results for coexpression analysis of neuropeptide Y (NPY) and serotonin receptor 2C (5-HT2C) mRNA, a receptor subtype expressed at high-to-moderate abundance in the regions analyzed. However, expression of 5-HT1A mRNA, which is expressed at comparatively low abundance in many telencephalic areas, could not be unequivocally identified in NPY mRNA-reactive neurons due to high background and poor signal-to-noise ratio in fluorescent receptor mRNA detections. Parallel chromogenic in situ hybridization provided clear labeling for 5-HT1A mRNA and additionally offered the possibility to monitor the chromogen deposition at regular time intervals to determine the optimal signal-to-noise ratio. We first developed a double labeling protocol combining fluorescence and chromogenic in situ hybridization and subsequently expanded this variation to combine double fluorescence and chromogenic in situ hybridization for triple labelings. With this method, we documented expression of 5-HT2C and/or 5-HT1A in subpopulations of telencephalic NPY-producing neurons. The method developed in the present study appears suitable for conventional light and fluorescence microscopy, combines advantages of fluorescence and chromogenic in situ hybridization protocols and thus provides a reliable non-radioactive alternative to previously published multiple labeling methods for coexpression analyses in which one mRNA species requires highly sensitive detection.
Agrobacterium species are capable of interkingdom gene transfer between bacteria and plants. The genome of Agrobacterium tumefaciens consists of a circular and a linear chromosome, the At-plasmid and the Ti-plasmid, which harbors bacterial virulence genes required for tumor formation in plants. Little is known about promoter sequences and the small RNA (sRNA) repertoire of this and other α-proteobacteria. We used a differential RNA sequencing (dRNA-seq) approach to map transcriptional start sites of 388 annotated genes and operons. In addition, a total number of 228 sRNAs was revealed from all four Agrobacterium replicons. Twenty-two of these were confirmed by independent RNA gel blot analysis and several sRNAs were differentially expressed in response to growth media, growth phase, temperature or pH. One sRNA from the Ti-plasmid was massively induced under virulence conditions. The presence of 76 cis-antisense sRNAs, two of them on the reverse strand of virulence genes, suggests considerable antisense transcription in Agrobacterium. The information gained from this study provides a valuable reservoir for an in-depth understanding of sRNA-mediated regulation of the complex physiology and infection process of Agrobacterium.
Background: The weight that gene copy number plays in transcription remains controversial; although in specific cases gene expression correlates with copy number, the relationship cannot be inferred at the global level. We hypothesized that genes steadily expressed by 15 melanoma cell lines (CMs) and their parental tissues (TMs) should be critical for oncogenesis and their expression most frequently influenced by their respective copy number.
Results: Functional interpretation of 3,030 transcripts concordantly expressed (Pearson's correlation coefficient p-value < 0.05) by CMs and TMs confirmed an enrichment of functions crucial to oncogenesis. Among them, 968 were expressed according to the transcriptional efficiency predicted by copy number analysis (Pearson's correlation coefficient p-value < 0.05). We named these genes, "genomic delegates" as they represent at the transcriptional level the genetic footprint of individual cancers. We then tested whether the genes could categorize 112 melanoma metastases. Two divergent phenotypes were observed: one with prevalent expression of cancer testis antigens, enhanced cyclin activity, WNT signaling, and a Th17 immune phenotype (Class A). This phenotype expressed, therefore, transcripts previously associated to more aggressive cancer. The second class (B) prevalently expressed genes associated with melanoma signaling including MITF, melanoma differentiation antigens, and displayed a Th1 immune phenotype associated with better prognosis and likelihood to respond to immunotherapy. An intermediate third class (C) was further identified. The three phenotypes were confirmed by unsupervised principal component analysis.
Conclusions: This study suggests that clinically relevant phenotypes of melanoma can be retraced to stable oncogenic properties of cancer cells linked to their genetic back bone, and offers a roadmap for uncovering novel targets for tailored anti-cancer therapy.
The Epstein-Barr Virus (EBV) -encoded EBNA2 protein, which is essential for the in vitro transformation of B-lymphocytes, interferes with cellular processes by binding to proteins via conserved sequence motifs. Its Arginine-Glycine (RG) repeat element contains either symmetrically or asymmetrically di-methylated arginine residues (SDMA and ADMA, respectively). EBNA2 binds via its SDMA-modified RG-repeat to the survival motor neurons protein (SMN) and via the ADMA-RG-repeat to the NP9 protein of the human endogenous retrovirus K (HERV-K (HML-2) Type 1). The hypothesis of this work was that the methylated RG-repeat mimics an epitope shared with cellular proteins that is used for interaction with target structures. With monoclonal antibodies against the modified RG-repeat, we indeed identified cellular homologues that apparently have the same surface structure as methylated EBNA2. With the SDMA-specific antibodies, we precipitated the Sm protein D3 (SmD3) which, like EBNA2, binds via its SDMA-modified RG-repeat to SMN. With the ADMA-specific antibodies, we precipitated the heterogeneous ribonucleoprotein K (hnRNP K). Specific binding of the ADMA-antibody to hnRNP K was demonstrated using E. coli expressed/ADMA-methylated hnRNP K. In addition, we show that EBNA2 and hnRNP K form a complex in EBV-infected B-cells. Finally, hnRNP K, when co-expressed with EBNA2, strongly enhances viral latent membrane protein 2A (LMP2A) expression by an unknown mechanism as we did not detect a direct association of hnRNP K with DNA-bound EBNA2 in gel shift experiments. Our data support the notion that the methylated surface of EBNA2 mimics the surface structure of cellular proteins to interfere with or co-opt their functional properties.
RNase P processes the 5'-end of tRNAs. An essential catalytic RNA has been demonstrated in Bacteria, Archaea and the nuclei of most eukaryotes; an organism-specific number of proteins complement the holoenzyme. Nuclear RNase P from yeast and humans is well understood and contains an RNA, similar to the sister enzyme RNase MRP. In contrast, no protein subunits have yet been identified in the plant enzymes, and the presence of a nucleic acid in RNase P is still enigmatic. We have thus set out to identify and characterize the subunits of these enzymes in two plant model systems. Expression of the two known Arabidopsis MRP RNA genes in vivo was verified. The first wheat MRP RNA sequences are presented, leading to improved structure models for plant MRP RNAs. A novel mRNA encoding the central RNase P/MRP protein Pop1p was identified in Arabidopsis, suggesting the expression of distinct protein variants from this gene in vivo. Pop1p-specific antibodies precipitate RNase P activity and MRP RNAs from wheat extracts. Our results provide evidence that in plants, Pop1p is associated with MRP RNAs and with the catalytic subunit of RNase P, either separately or in a single large complex.
Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in \(tRNA^{Asp(GUC)}\) in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified \(tRNA^{Glu(CUC/UUC)}\) and \(tRNA^{Gly(GCC)}\) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation.
Integrative "Omics"-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses
(2013)
Bacteria constantly face stress conditions and therefore mount specific responses to ensure adaptation and survival. Stress responses were believed to be predominantly regulated at the transcriptional level. In the phototrophic bacterium Rhodobacter sphaeroides the response to singlet oxygen is initiated by alternative sigma factors. Further adaptive mechanisms include post-transcriptional and post-translational events, which have to be considered to gain a deeper understanding of how sophisticated regulation networks operate. To address this issue, we integrated three layers of regulation: (1) total mRNA levels at different time-points revealed dynamics of the transcriptome, (2) mRNAs in polysome fractions reported on translational regulation (translatome), and (3) SILAC-based mass spectrometry was used to quantify protein abundances (proteome). The singlet oxygen stress response exhibited highly dynamic features regarding short-term effects and late adaptation, which could in part be assigned to the sigma factors RpoE and RpoH2 generating distinct expression kinetics of corresponding regulons. The occurrence of polar expression patterns of genes within stress-inducible operons pointed to an alternative of dynamic fine-tuning upon stress. In addition to transcriptional activation, we observed significant induction of genes at the post-transcriptional level (translatome), which identified new putative regulators and assigned genes of quorum sensing to the singlet oxygen stress response. Intriguingly, the SILAC approach explored the stress-dependent decline of photosynthetic proteins, but also identified 19 new open reading frames, which were partly validated by RNA-seq. We propose that comparative approaches as presented here will help to create multi-layered expression maps on the system level ("expressome"). Finally, intense mass spectrometry combined with RNA-seq might be the future tool of choice to re-annotate genomes in various organisms and will help to understand how they adapt to alternating conditions.
Pigment cells and neuronal cells both are derived from the neural crest. Here, we describe the Pit-Oct-Unc (POU) domain transcription factor Brn3a, normally involved in neuronal development, to be frequently expressed in melanoma, but not in melanocytes and nevi. RNAi-mediated silencing of Brn3a strongly reduced the viability of melanoma cell lines and decreased tumour growth in vivo. In melanoma cell lines, inhibition of Brn3a caused DNA double-strand breaks as evidenced by Mre11/Rad50-containing nuclear foci. Activated DNA damage signalling caused stabilization of the tumour suppressor p53, which resulted in cell cycle arrest and apoptosis. When Brn3a was ectopically expressed in primary melanocytes and fibroblasts, anchorage-independent growth was increased. In tumourigenic melanocytes and fibroblasts, Brn3a accelerated tumour growth in vivo. Furthermore, Brn3a cooperated with proliferation pathways such as oncogenic BRAF, by reducing oncogene-induced senescence in non-malignant melanocytes. Together, these results identify Brn3a as a new factor in melanoma that is essential for melanoma cell survival and that promotes melanocytic transformation and tumourigenesis.
Background
Oncolytic virotherapy of tumors is an up-coming, promising therapeutic modality of cancer therapy. Unfortunately, non-invasive techniques to evaluate the inflammatory host response to treatment are rare. Here, we evaluate \(^{19}\)F magnetic resonance imaging (MRI) which enables the non-invasive visualization of inflammatory processes in pathological conditions by the use of perfluorocarbon nanoemulsions (PFC) for monitoring of oncolytic virotherapy.
Methodology/Principal Findings
The Vaccinia virus strain GLV-1h68 was used as an oncolytic agent for the treatment of different tumor models. Systemic application of PFC emulsions followed by \(^1H\)/\(^{19}\)F MRI of mock-infected and GLV-1h68-infected tumor-bearing mice revealed a significant accumulation of the \(^{19}\)F signal in the tumor rim of virus-treated mice. Histological examination of tumors confirmed a similar spatial distribution of the \(^{19}\)F signal hot spots and \(CD68^+\)-macrophages. Thereby, the \(CD68^+\)-macrophages encapsulate the GFP-positive viral infection foci. In multiple tumor models, we specifically visualized early inflammatory cell recruitment in Vaccinia virus colonized tumors. Furthermore, we documented that the \(^{19}\)F signal correlated with the extent of viral spreading within tumors.
Conclusions/Significance
These results suggest \(^{19}\)F MRI as a non-invasive methodology to document the tumor-associated host immune response as well as the extent of intratumoral viral replication. Thus, \(^{19}\)F MRI represents a new platform to non-invasively investigate the role of the host immune response for therapeutic outcome of oncolytic virotherapy and individual patient response.
Metastatic tumor cells in body fluids are important targets for treatment, and critical surrogate markers for evaluating cancer prognosis and therapeutic response. Here we report, for the first time, that live metastatic tumor cells in blood samples from mice bearing human tumor xenografts and in blood and cerebrospinal fluid samples from patients with cancer were successfully detected using a tumor cell-specific recombinant vaccinia virus (VACV). In contrast to the FDA-approved CellSearch system, VACV detects circulating tumor cells (CTCs) in a cancer biomarker-independent manner, thus, free of any bias related to the use of antibodies, and can be potentially a universal system for detection of live CTCs of any tumor type, not limited to CTCs of epithelial origin. Furthermore, we demonstrate for the first time that VACV was effective in preventing and reducing circulating tumor cells in mice bearing human tumor xenografts. Importantly, a single intra-peritoneal delivery of VACV resulted in a dramatic decline in the number of tumor cells in the ascitic fluid from a patient with gastric cancer. Taken together, these results suggest VACV to be a useful tool for quantitative detection of live tumor cells in liquid biopsies as well as a potentially effective treatment for reducing or eliminating live tumor cells in body fluids of patients with metastatic disease.
Using viruses to treat cancer is a novel approach to an age-old disease. Oncolytic viruses are native or recombinant viruses that have the innate or enhanced capability to infect tumour cells, replicate within the tumour microenvironment and subsequently lyse those cells. One representative, the vaccinia virus (VACV), belongs to the orthopoxvirus genus of the Poxviridae family. GLV-1h68, a recombinant and attenuated vaccinia virus devel- oped by the Genelux Corporation, is a member of this family currently being tested in various phase I/II clinical trials under the name GL-ONC1. It has been shown to specif- ically replicate in tumour cells while sparing healthy tissue and to metabolise prodrug at or transport immunological payloads to the site of affliction. Since imaging modalities offer little insight into viral replication deep within the body, and because oncolytic virotherapy is dependent on replication within the target tissue, the need for a monitoring system is evident. Pharmacokinetic analysis of this oncolytic agent was to give insight into the dynamics present in tumours during treatment. This, in turn, would give clinicians the opportunity to monitor the efficacy as early as possible after the onset of treatment, to observe treatment progression and possibly to gauge prognosis, without resorting to invasive procedures, e.g. biopsies. A criteria for viable biomarkers was that it had to be directly dependent on viral replica- tion. Ideally, a marker for treatment efficacy would be specific to the treatment modality, not necessarily the treatment type. Such a marker would be highly detectable (high sen- sitivity), specific for the treatment (high specificity), and present in an easily obtained specimen (blood). Taking this into consideration, the biomarkers were chosen for their potential to be indicators of viral replication. Thus, the biomarkers analysed in this thesis are: the native proteins expressed by the viral genes A27L and B5R, the virally encoded recombinant proteins β-galactosidase, β-glucuronidase, green fluorescent protein (GFP), carboxypeptidase G2 (CPG2) and carcinoembryonic antigen (CEA). Each marker is under the control of one of five different promoters present. All recombinant viruses used in this thesis express A27L, B5R, GFP and β-glucuronidase and all are derived from the parental virus GLV-1h68. In addition to these markers, GLV-1h68 expresses β-galactosidase; GLV-1h181 expresses CPG2. [...]
GAS2L3 was identified recently as a target gene of the DREAM complex (Reichert et al., 2010; Wolter et al., 2012). It was shown that GAS2L3 is expressed in a cell cycle specific manner and that depletion of the protein leads to defects in cytokinesis and genomic instability (Wolter et al., 2012).
Major aim of this thesis was, to further characterize the biochemical properties and physiological function of GAS2L3.
By in vitro co-sedimentation and bundling assays, GAS2L3 was identified as a cytoskeleton associated protein which bundles, binds and crosslinks F-actin and MTs. GST pulldown assays and co-immunoprecipitation experiments revealed that GAS2L3 interacts in vitro and in vivo with the chromosomal passenger complex (CPC), a very important regulator of mitosis and cytokinesis, and that the interaction is mediated by the GAR domain of GAS2L3 and the C-terminal part of Borealin and the N-terminal part of Survivin. Kinase assays showed that GAS2L3 is not a substrate of the CPC but is strongly phosphorylated by CDK1 in vitro. Depletion of GAS2L3 by shRNA influenced protein stability and activity of the CPC. However pharmacological studies showed that the decreased CPC activity is not responsible for the observed cytokinesis defects upon GAS2L3 depletion. Immunofluorescence experiments revealed that GAS2L3 is localized to the constriction zone by the CPC in a GAR dependent manner and that the GAR domain is important for proper protein function.
New interacting proteins of GAS2L3 were identified by stable isotope labelling by amino acids in cell culture (SILAC) in combination with tandem affinity purification and subsequent mass spectrometrical analysis. Co-immunoprecipitation experiments further confirmed the obtained mass spectrometrical data.
To address the physiological function of GAS2L3 in vivo, a conditional and a non-conditional knockout mouse strain was established. The non-conditional mouse strain showed a highly increased mortality rate before weaning age probably due to heart failure. The physiological function of GAS2L3 in vivo as well as the exact reason for the observed heart phenotype is not known at the moment.
The aim of this work was to synthesize and functionalize different bio-relevant nanomaterials like silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) as contrast agents for T2 magnetic resonance imaging (MRI) and detonation nanodiamond (DND) with the neurohormone peptide allatostatin 1 (ALST1) and a fluorescent dye. Analytical techniques for the determination and quantification of surface functional groups like amines, azides, and peptides were also developed and established.
Thus, in the first part of the work, a TGF-1 binding peptide and allatostatin 1 (ALST1), both supposed to act as active tumour targeting vectors, were synthesized by solid-phase peptide synthesis (SPPS) and characterized by high pressure liquid chromatography (HPLC) and mass spectrometry. Then, azide-functionalized silica nanoparticles were synthesized by the Stöber process and characterized by transmission electron microscopy (TEM) and infrared spectroscopy (IR). The surface loading of amine and azide groups was determined by a new protocol. The azide groups were reduced with sodium boronhydride to amine and then functionalized with Fmoc-Rink Amide linker according to a standard SPPS protocol. Upon cleavage of Fmoc by piperidine, the resulting dibenzofulvene and its piperidine adduct were quantified by UV/Vis spectroscopy and used to determine the amount of amine groups on the nanoparticle surface. Then, ALST1 and related tyrosine- and phenylalanine substituted model peptides were conjugated to the azide-functionalized silica nanoparticles by copper(I)-catalyzed azide-alkyne dipolar cycloaddition (CuAAC). The successful peptide conjugation was demonstrated by the Pauly reaction, which however is only sensitive to histidine- and tyrosine-containing peptides. As a more general alternative, the acid hydrolysis of the peptides to their individual amino acid building blocks followed by derivatization with phenyl isothiocyanate (PITC) allowed the separation, determination, and quantification of the constituent amino acids by HPLC.
In the second part of the work, amine- and azide-functionalized silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) were synthesized by co-precipitation and subsequent silica-coated based on the Stöber process and characterized by TEM and IR. The amine surface loading was determined by the method already established for the pure silica systems. The azide surface loading could also be quantified by reduction with sodium boronhydride to amine groups and then conjugation to Fmoc-Rink amide linker. Upon cleavage of Fmoc with piperidine, the total amine surface loading was obtained. The amount of azide surface groups was then determined from the difference of the total amine surface loading and the amine surface loading. Thus, it was possible to quantify both amine and azide surface groups on a single nanoparticle system. Superparamagnetic iron oxide nanoparticles (SPIONs) are potent T2 contrast agents for magnetic resonance imaging (MRI). Due to their natural metabolism after injection into the blood stream, SPIONs mostly end up inside macrophages, liver, spleen or kidneys. To generate a potential target-specific SPION-based T2 contrast agent for MRI, the neurohormone peptide ALST1 was conjugated by CuAAC to the azide- and amine functionalized superparamagnetic iron oxide nanoparticles, since ALST1 is supposed to target difficult-to-treat neuroendocrinic tumours due to its analogy to galanin and somastatin receptor ligands. The organic fluorescent dye cyanine 5 (Cy5) was also conjugated to the silica-coated superparamagnetic iron oxide nanoparticles (SPIONs) via a NHS-ester to the amines to enable cell uptake studies by fluorescence microscopy. These constructs were characterized by TEM, dynamic light scattering (DLS), and IR. The amino acids of the conjugated ALST1 were determined by the HPLC method as described before for peptide-modified silica nanoparticle surfaces. Then, the relaxivity r2 was measured at 7 T. However, a r2 value of 27 L/mmolFe·s for the dual ALST1-/Cy5-functionalized silica-coated SPIONs was not comparable to T2 contrast agents in clinical use, since their relaxivity is commonly determined at 1.5 T, and no such instrument was available. However, it can be assumed that the synthesized dual
ALST1-/Cy5-functionalized silica-coated SPION would show a lower r2 at 1.5 T than at 7T. Commercial T2 MRI contrast agents like VSOP-C184 from Ferropharm show at r2 values of about 30 L/mmolFe·s at 1.5 T. Still, the relaxivity of the new material has some potential for application as a T2 contrast agent. Then, the material was used in cell uptake studies by fluorescence microscopy with the conjugated Cy5 dye as a probe. The dual
ALST1-/Cy5-functionalized silica-coated SPION showed a high degree of agglomeration with no cellular uptake unlike described for ALST1-functionalized nanoparticles in literature. It is assumed that upon agglomeration of the particles, constructs form which are unable to be internalized by the cellular endocytotic pathways anymore. As a future perspective, the tendency of the particle to agglomerate should be reduced by changing the coating material to polyethylene glycol (PEG) or chitosan, which are known to be bio-compatible, bio-degradable and prevent agglomeration.
In the third part of the work, the rhenium compound [ReBr(CO)3(L)] with L = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline and its manganese analogue were synthesized by heating the ligand and rhenium pentacarbonyl bromide or and manganese pentacarbonyl bromide respectively, in toluene. However, [MnBr(CO)3(L)] was unstable upon illumination by UV light at 365 nm. Thus, it was dismissed for further application. The photophysical properties of [ReBr(CO)3(L)] were explored, by determination of the excited-state life time by the time-correlated single-photon counting (TCSPC) method and the quantum yield by a fluorescence spectrometer equipped with an integration sphere. A value of = 455 ns, a Stokes shift of 197 nm and a rather low quantum yield =were found. Metal complexes are supposed to have superior properties compared to organic dyes due to their large Stokes shifts, long excited-state life times, and high quantum yields. Thus, amine- and azide-functionalized detonation nanodiamond (DND) as an alternative biological inert carrier system was functionalized with ALST1 to enhance its cell uptake properties. A luminescent probe for cell uptake studies using fluorescence microscopy was also attached, either based on the new rhenium complex or the commercially available organic dye Cy5, respectively. The aldehyde-functionalized rhenium complex was conjugated to the DND via oxime ligation, which is known to be a mild and catalyst-free conjugation method. The amount of peptide ALST1 on the DND was analyzed and quantified after acid hydrolysis and PITC derivatization by HPLC as described before. Then, the ALST1-/luminescent probe-functionalized DND was investigated for its photophysical properties by fluorescence spectroscopy. The Cy5-functionalized material showed a slightly lower fluorescence performance in aqueous solution than reported in literature and commercial suppliers with a life time < 0.4 ns and quantum yields not determinable by integration sphere due to the week signal intensity. The rhenium complex-functionalized material had a very low signal intensity in only aqueous medium, and thus determination of life times and quantum yield by fluorescence spectroscopy was not possible. After incubation with MDA-MB 231 cells, the Cy5-functionalized DND could easily be detected due to its red fluorescence. However, it was not possible to visualize the rhenium complex-functionalized DND with fluorescence microscopy due to the low fluorescence intensity of the complex in aqueous medium and the lack of proper filters for the fluorescence microscope. Cy5-functionalized DND did not show any cellular uptake in fluorescence microscopy after conjugation with ALST1. Since the nanodiamond surface is known to strongly adsorb peptides and proteins, it is assumed that the peptide chain is oriented perpendicular to the nanoparticle surface and thus not able to interact with cell membrane receptors to promote cell uptake of the particles. As a future perspective, the ALST1-promoted cellular uptake of the DND should be improved by using different linker systems for peptide conjugation to prevent adsorption of the peptide chain on the particle surface.
The new analytical methods for amino-, azide-, and peptide-functionalized nanoparticles have great potential to assist in the quantification of nanoparticle surface modifications by UV/Vis spectroscopy and HPLC. The determination of surface amine and azide groups based on the cleavage of conjugated Fmoc-Rink amide linker and detected by UV/Vis spectroscopy is applicable to all amine-/azide-functionalized nanomaterials. However, particles which form very stable suspension with the cleavage mixture can cause quantification problems due to scattering, making an accurate quantification of dibenzofulvene and its piperidine adduct impossible. The detection of tyrosine- and histidine-containing peptides based on the Pauly reaction is well-suited as a fast and easy-to-perform qualitative demonstration of successful peptide surface conjugation. However, its major drawback as a colourimetric approach is that coloured particles cannot be evaluated by this method. The amino acid analysis based on HPLC after acid hydrolysis of peptides conjugated to nanoparticle surfaces to its individual building blocks and subsequent derivatization with PITC, can be used on all nanomaterials with peptide or protein surface modification. It allows detection of amino acids down to picomolar concentrations and even enables analysis of very small peptide surface loadings. However, the resulting HPLC traces are difficult to analyze.
Three new analytical methods based on UV/Vis and HPLC techniques have been developed and established. They assisted in the characterization of the synthesized DND and SPIONs with dual functionalization by ALST1 and Cy5 or [ReBr(CO)3(L)], respectively. However, the nanomaterials showed no cellular uptake due to a high tendency to agglomerate. The cellular uptake should be improved and the tendency to agglomerate of the SPIONs should be reduced by changing the surface coating from silica to either PEG or chitosan. Furthermore, different linker systems for connecting peptides to DND surfaces should be synthesized and evaluated to reduce potential peptide chain adsorption.
Plant hormones involving salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and auxin, gibberellins, and abscisic acid (ABA) are known to regulate host immune responses. However, plant hormone cytokinin has the potential to modulate defense signaling including SA and JA. It promotes plant pathogen and herbivore resistance; underlying mechanisms are still unknown. Using systems biology approaches, we unravel hub points of immune interaction mediated by cytokinin signaling in Arabidopsis. High-confidence Arabidopsis protein-protein interactions (PPI) are coupled to changes in cytokinin-mediated gene expression. Nodes of the cellular interactome that are enriched in immune functions also reconstitute sub-networks. Topological analyses and their specific immunological relevance lead to the identification of functional hubs in cellular interactome. We discuss our identified immune hubs in light of an emerging model of cytokinin-mediated immune defense against pathogen infection in plants.