Small RNA-guided processes in the hyperthermophilic methanogen Methanopyrus kandleri

In this thesis, a combination of RNAseq, computational and biochemical methods was applied to analyze processes that use small RNAs (sRNAs) as guide molecules at extreme temperatures. Here, the hyperthermophilic archaeon Methanopyrus kandleri, which grows at temperatures of up to 110°C, was used as a model organism. The genome of M. kandleri harbors two CRISPR-Cas systems that use CRISPR RNA (crRNA) as guide molecules to target foreign nucleic acids. RNAseq analysis revealed a high abundance and processing of crRNAs in M. kandleri that indicated that CRISPR-Cas systems are highly active at extreme temperatures. Furthermore, the crystal structure of the CRISPR-associated protein Csm3 was solved in collaboration with Prof. Dr. Elena Conti (MPI Martinsried). Csm3 was found to bind crRNAs and was shown to function as the crRNA-binding backbone protein in type III-A CRISPR-Cas interference complexes. A recently discovered nucleic acid-guided mechanism uses prokaryotic Argonaute (pAgo) proteins. In M. kandleri, a pAgo protein was found to be encoded within a potential operon of CRISPR-associated genes and the analysis of recombinant pAgo protein production revealed a high toxicity in Escherichia coli that might correlate with its potential defense function against plasmid DNA. Methylation of rRNA is regulated by a different sRNA-guided mechanism that utilizes C/D box sRNAs to target a ribonucleoprotein complex to the rRNA methylation site. In M. kandleri, a record number of 126 C/D box sRNAs were detected by RNAseq analysis and indicate an increased potential for rRNA methylation reactions. Furthermore, most of the C/D box sRNAs were detected as circular molecules. Taken together, the circularization of C/D box sRNAs and the high requirement for rRNA methylation are suggested to be adaptations to the hyperthermophilic lifestyle of M. kandleri. Finally, RNAseq analyses were used to identify tRNA precursors in M. kandleri that feature a unique C-to-U editing reaction of base 8. The occurrence of this editing event was used to deduce the order of tRNA processing steps in a non-compartmentalized cell, indicating that termini truncation precedes intron removal and editing

Shape analysis on homogeneous spaces: a generalised SRVT framework

Shape analysis is ubiquitous in problems of pattern and object recognition and has developed considerably in the last decade. The use of shapes is natural in applications where one wants to compare curves independently of their parametrisation. One computationally efficient approach to shape analysis is based on the Square Root Velocity Transform (SRVT). In this paper we propose a generalised SRVT framework for shapes on homogeneous manifolds. The method opens up for a variety of possibilities based on different choices of Lie group action and giving rise to different Riemannian metrics.Comment: 28 pages; 4 figures, 30 subfigures; notes for proceedings of the Abel Symposium 2016: "Computation and Combinatorics in Dynamics, Stochastics and Control". v3: amended the text to improve readability and clarify some points; updated and added some references; added pseudocode for the dynamic programming algorithm used. The main results remain unchange

IFNAR1-Signalling Obstructs ICOS-mediated Humoral Immunity during Non-lethal Blood-Stage Plasmodium Infection

Funding: This work was funded by a Career Development Fellowship (1028634) and a project grant (GRNT1028641) awarded to AHa by the Australian National Health & Medical Research Council (NHMRC). IS was supported by The University of Queensland Centennial and IPRS Scholarships. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Direct Visualization of Dislocation Dynamics in Grain Boundary Scars

Mesoscale objects with unusual structural features may serve as the analogues of atoms in the design of larger-scale materials with novel optical, electronic or mechanical behaviour. In this paper we investigate the structural features and the equilibrium dynamics of micron-scale spherical crystals formed by polystyrene particles adsorbed on the surface of a spherical water droplet. The ground state of sufficiently large crystals possesses finite-length grain boundaries (scars). We determine the elastic response of the crystal by measuring single-particle diffusion and quantify the fluctuations of individual dislocations about their equilibrium positions within a scar determining the dislocation spring constants. We observe rapid dislocation glide with fluctuations over the barriers separating one local Peierls minimum from the next and rather weak binding of dislocations to their associated scars. The long-distance (renormalised) dislocation diffusion glide constant is extracted directly from the experimental data and is found to be moderately faster than single particle diffusion. We are also able to determine the parameters of the Peierls potential induced by the underlying crystalline lattice.Comment: 11 pages, 4 figures, pdf forma

Rare Z-decay into light CP-odd Higgs bosons: a comparative study in different new physics models

Various new physics models predict a light CP-odd Higgs boson (labeled as $a$) and open up new decay modes for Z-boson, such as $Z \to \bar{f} f a$, $Z\to a\gamma$ and $Z\to aaa$, which could be explored at the GigaZ option of the ILC. In this work we investigate these rare decays in several new physics models, namely the type-II two Higgs doublet model (type-II 2HDM), the lepton-specific two Higgs doublet model (L2HDM), the nearly minimal supersymetric standard model (nMSSM) and the next-to-minimal supersymmetric standard model (NMSSM). We find that in the parameter space allowed by current experiments, the branching ratios can reach $10^{-4}$ for $Z \to \bar{f} f a$ ($f=b,\tau$), $10^{-9}$ for $Z\to a\gamma$ and $10^{-3}$ for $Z\to aaa$, which implies that the decays $Z \to \bar{f} f a$ and $Z \to a a a$ may be accessible at the GigaZ option. Moreover, since different models predict different patterns of the branching ratios, the measurement of these rare decays at the GigaZ may be utilized to distinguish the models.Comment: Version in JHEP (discussions added, errors corrected

Polypeptide-grafted macroporous polyHIPE by surface-initiated N-Carboxyanhydride (NCA) polymerization as a platform for bioconjugation

A new class of functional macroporous monoliths from polymerized high internal phase emulsion (polyHIPE) with tunable surface functional groups was developed by direct polypeptide surface grafting. In the first step, amino-functional polyHIPEs were obtained by the addition of 4-vinylbenzyl or 4-vinylbenzylphthalimide to the styrenic emulsion and thermal radical polymerization. The obtained monoliths present the expected open-cell morphology and a high surface area. The incorporated amino group was successfully utilized to initiate the ring-opening polymer- ization of benzyl-L-glutamate N-carboxyanhydride (BLG NCA) and benzyloxycarbonyl-L-lysine (Lys(Z)) NCA, which resulted in a dense homogeneous coating of polypeptides throughout the internal polyHIPE surfaces as confirmed by SEM and FTIR analysis. The amount of polypeptide grafted to the polyHIPE surfaces could be modulated by varying the initial ratio of amino acid NCA to amino-functional polyHIPE. Subsequent removal of the polypeptide protecting groups yielded highly functional polyHIPE-g-poly(glutamic acid) and polyHIPE-g- poly(lysine). Both types of polypeptide-grafted monoliths responded to pH by changes in their hydrohilicity. The possibility to use the high density of function (−COOH or −NH2) for secondary reaction was demonstrated by the successful bioconjugation of enhanced green fluorescent protein (eGFP) and fluorescein isocyanate (FITC) on the polymer 3D-scaffold surface. The amount of eGFP and FITC conjugated to the polypeptide-grafted polyHIPE was significantly higher than to the amino- functional polyHIPE, signifying the advantage of polypeptide grafting to achieve highly functional polyHIPEs

Dendritic Cell Based Tumor Vaccination in Prostate and Renal Cell Cancer: A Systematic Review and Meta-Analysis

BACKGROUND: More than 200 clinical trials have been performed using dendritic cells (DC) as cellular adjuvants in cancer. Yet the key question whether there is a link between immune and clinical response remains unanswered. Prostate and renal cell cancer (RCC) have been extensively studied for DC-based immunotherapeutic interventions and were therefore chosen to address the above question by means of a systematic review and meta-analysis. METHODOLOGY/PRINCIPAL FINDINGS: Data was obtained after a systematic literature search from clinical trials that enrolled at least 6 patients. Individual patient data meta-analysis was performed by means of conditional logistic regression grouped by study. Twenty nine trials involving a total of 906 patients were identified in prostate cancer (17) and RCC (12). Objective response rates were 7.7% in prostate cancer and 12.7% in RCC. The combined percentages of objective responses and stable diseases (SD) amounted to a clinical benefit rate (CBR) of 54% in prostate cancer and 48% in RCC. Meta-analysis of individual patient data (n = 403) revealed the cellular immune response to have a significant influence on CBR, both in prostate cancer (OR 10.6, 95% CI 2.5-44.1) and in RCC (OR 8.4, 95% CI 1.3-53.0). Furthermore, DC dose was found to have a significant influence on CBR in both entities. Finally, for the larger cohort of prostate cancer patients, an influence of DC maturity and DC subtype (density enriched versus monocyte derived DC) as well as access to draining lymph nodes on clinical outcome could be demonstrated. CONCLUSIONS/SIGNIFICANCE: As a 'proof of principle' a statistically significant effect of DC-mediated cellular immune response and of DC dose on CBR could be demonstrated. Further findings concerning vaccine composition, quality control, and the effect of DC maturation status are relevant for the immunological development of DC-based vaccines

Controlling Spin Qubits in Quantum Dots

We review progress on the spintronics proposal for quantum computing where the quantum bits (qubits) are implemented with electron spins. We calculate the exchange interaction of coupled quantum dots and present experiments, where the exchange coupling is measured via transport. Then, experiments on single spins on dots are described, where long spin relaxation times, on the order of a millisecond, are observed. We consider spin-orbit interaction as sources of spin decoherence and find theoretically that also long decoherence times are expected. Further, we describe the concept of spin filtering using quantum dots and show data of successful experiments. We also show an implementation of a read out scheme for spin qubits and define how qubits can be measured with high precision. Then, we propose new experiments, where the spin decoherence time and the Rabi oscillations of single electrons can be measured via charge transport through quantum dots. Finally, all these achievements have promising applications both in conventional and quantum information processing.Comment: 18 pages, 6 figure

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin