Ab initio RNA folding

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure

Integrating multi-type aberrations from DNA and RNA through dynamic mapping gene space for subtype-specific breast cancer driver discovery

Driver event discovery is a crucial demand for breast cancer diagnosis and therapy. Especially, discovering subtype-specificity of drivers can prompt the personalized biomarker discovery and precision treatment of cancer patients. still, most of the existing computational driver discovery studies mainly exploit the information from DNA aberrations and gene interactions. Notably, cancer driver events would occur due to not only DNA aberrations but also RNA alternations, but integrating multi-type aberrations from both DNA and RNA is still a challenging task for breast cancer drivers. On the one hand, the data formats of different aberration types also differ from each other, known as data format incompatibility. One the other hand, different types of aberrations demonstrate distinct patterns across samples, known as aberration type heterogeneity. To promote the integrated analysis of subtype-specific breast cancer drivers, we design a "splicing-and-fusing" framework to address the issues of data format incompatibility and aberration type heterogeneity respectively. To overcome the data format incompatibility, the "splicing-step" employs a knowledge graph structure to connect multi-type aberrations from the DNA and RNA data into a unified formation. To tackle the aberration type heterogeneity, the "fusing-step" adopts a dynamic mapping gene space integration approach to represent the multi-type information by vectorized profiles. The experiments also demonstrate the advantages of our approach in both the integration of multi-type aberrations from DNA and RNA and the discovery of subtype-specific breast cancer drivers. In summary, our "splicing-and-fusing" framework with knowledge graph connection and dynamic mapping gene space fusion of multi-type aberrations data from DNA and RNA can successfully discover potential breast cancer drivers with subtype-specificity indication.Comment: 14 pages, 5 figures, 1 tabl

Numerical characterization of protein sequences based on the generalized Chou\u27s pseudo amino acid composition

The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical-chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a (21+λ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins

Immuno Magnetic Thermosensitive Liposomes For Cancer Therapy

The present work describes the encapsulation of the drug doxorubicin (DOX) in immuno paramagnetic thermosensitive liposomes. DOX is the most common chemotherapeutic agent for the treatment of a variety of carcinomas. However, the pure drug has high cytotoxicity and therefore requires a targeted and biocompatible delivery system. The introduction includes concepts, modalities, and functionalities of the project. First, a detailed description of the cell type (triple-negative breast cancer) is given. Furthermore, the importance of liposomal doxorubicin is explained and the current state of research is shown. The importance of modification to achieve thermosensitive properties and the procedure for co-encapsulation with Gd chelate to achieve paramagnetic properties is also discussed. In addition, the first part describes the surface modification with ADAM8 antibodies, which leads to improved targeting. The second part of the thesis covers the different materials and methods used in this paper. The production of the liposomes LipTS, LipTS-GD, LipTS-GD-CY, LipTS-GD-CY-MAB and the loading of DOX using an ammonium sulfate gradient method were described in detail. The results part deals with the physicochemical characterization using dynamic light scattering and laser Doppler velocimetry, which confirmed a uniform monodisperse distribution of the liposomes. These properties facilitate the approach of liposomes to target cancer cells. The influence of lipid composition of liposomes, co-encapsulation with Gd chelate and surface modification of liposomes was evaluated and described accordingly. The size and structure of the individual liposomal formulations were determined by atomic force microscopy and transmission electron microscopy. Morphological examination of the liposomes confirmed agreement with the sizes obtained by dynamic light scattering. Temperature-dependent AFM images showed an intact liposome structure at 37 °C, whereas heating by UHF-MRI led to a lipid film indicating the destruction of the lipid bilayer. Furthermore, TEM images showed the morphological properties of the liposomes and gave a more precise indication of how Gd-chelate accumulates within the liposomes. Liposomes with Gd-chelate showed well-separated vesicles, suggesting that Gd- chelate is deposited in the lipid bilayer of the liposomes. Gd was encapsulated in the hydrophilic core whereas chelate was extended into the lipid bilayer. By differential scanning calorimetry and drug release, the heat-sensitive functionality of the liposomes could be determined. Liposomes showed a beginning of phase transition temperature at about 38 °C, which can be achieved by UHF-MRI exposure. The maximum phase transition temperature in the case of LipTS-GD and LipTS-GD-CY-MAB was 42 °C and 40 °C, respectively. A proof of concept study for the thermosensitive properties of liposomes and a time-dependent DOX release profile in hyperthermia was performed. Gd-chelate is encapsulated in both LipTS-GD and LipTS-GD-CY-MAB and led to paramagnetic properties of the liposomes. This facilitates imaging mediated DOX delivery and diagnosis of the solid tumor and metastatic cells. The change in relaxation rate R1 of liposomes was quantified before and after heating above Tm (T> Tm). The relaxivity of the liposomes was obtained from the adapted slope of the relaxation rate against the Gd concentration. Remarkably, the relaxation rate and relaxivity increased after heating the liposomes above Tm (T> Tm), suggesting that the liposomes opened, released Gd chelate, and the exchange of water molecules became faster and more practicable. Toxicity studies describe the different mechanisms for induced DOX toxicity. The increased cytotoxic effect at elevated temperatures showed that the induced toxicity is thermally dependent, i.e. DOX was released from the liposomes. The high viability of the cells at 37 °C indicates that the liposomes were intact at normal physiological temperatures. Under UHF-MRI treatment, cell toxicity due to elevated temperature was observed. The cellular uptake of liposomes under UHF-MRI was followed by a confocal laser scanning microscope. An increase in fluorescence intensity was observed after UHF-MRI exposure. The study of the uptake pathway showed that the majority of liposomes were mainly uptake by clathrin-mediated endocytosis. In addition, the liposomes were modified with anti-ADAM8 antibodies (MAB 1031) to allow targeted delivery. The cellular binding capabilities of surface-modified and non-modified liposomes were tested on cells that had ADAM8 overexpression and on ADAM8 knockdown cells. Surface-modified liposomes showed a significant increase in binding ability, indicating significant targeting against cells that overexpress ADAM8 on their surface. In addition, cells with knockdown ADAM8 could not bind a significant amount of modified liposomes. The biocompatibility of liposomes was assessed using a hemolysis test, which showed neglected hemolytic potential and an activated thromboplastin time (aPTT), where liposomes showed minimal interference with blood clotting. Hemocompatibility studies may help to understand the correlation between in vitro and in vivo. The chorioallantois model was used in ovo to evaluate systematic biocompatibility in an alternative animal model. In the toxicity test, liposomes were injected intravenously into the chicken embryo. The liposomes showed a neglectable harmful effect on embryo survival. While free DOX has a detrimental effect on the survival of chicken embryos, this confirms the safety profile of liposomes compared to free DOX. LipTS-GD-CY-MAB were injected into the vascular system of the chicken embryo on egg development day 11 and scanned under UHF-MRI to evaluate the magnetic properties of the liposomes in a biological system with T2-weighted images (3D). The liposomal formulation had distinct magnetic properties under UHF MRI and the chick survived the scan. In summary, immunomagnetic heat-sensitive liposomes are a novel drug for the treatment of TNBC. It is used both for the diagnosis and therapy of solid and metastasizing tumors without side effects on the neighboring tissue. Furthermore, a tumor in the CAM model will be established. Thereafter, the selective targeting of the liposomes will be visualized and quantitated using fluorescence and UHF-MRI. Liposomes are yet to be tested on mice as a xenograft triple-negative breast cancer model, in which further investigation on the effect of DOX-LipTS-GD-CY-MAB is evaluated. On one hand, the liposomes will be evaluated regarding their targetability and their selective binding. On the other hand, the triggered release of DOX from the liposomes after UHF-MRI exposure will be quantitated, as well as evaluate the DOX-Liposomes therapeutic effect on the tumor

Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis

Tachyzoite to bradyzoite development in Toxoplasma is marked by major changes in gene expression resulting in a parasite that expresses a new repertoire of surface antigens hidden inside a modified parasitophorous vacuole called the tissue cyst. The factors that control this important life cycle transition are not well understood. Here we describe an important transcriptional repressor mechanism controlling bradyzoite differentiation that operates in the tachyzoite stage. The ApiAP2 factor, AP2IV-4, is a nuclear factor dynamically expressed in late S phase through mitosis/cytokinesis of the tachyzoite cell cycle. Remarkably, deletion of the AP2IV-4 locus resulted in the expression of a subset of bradyzoite-specific proteins in replicating tachyzoites that included tissue cyst wall components BPK1, MCP4, CST1 and the surface antigen SRS9. In the murine animal model, the mis-timing of bradyzoite antigens in tachyzoites lacking AP2IV-4 caused a potent inflammatory monocyte immune response that effectively eliminated this parasite and prevented tissue cyst formation in mouse brain tissue. Altogether, these results indicate that suppression of bradyzoite antigens by AP2IV-4 during acute infection is required for Toxoplasma to successfully establish a chronic infection in the immune-competent host

DEVELOPMENT OF BIOINFORMATICS TOOLS AND ALGORITHMS FOR IDENTIFYING PATHWAY REGULATORS, INFERRING GENE REGULATORY RELATIONSHIPS AND VISUALIZING GENE EXPRESSION DATA

In the era of genetics and genomics, the advent of big data is transforming the field of biology into a data-intensive discipline. Novel computational algorithms and software tools are in demand to address the data analysis challenges in this growing field. This dissertation comprises the development of a novel algorithm, web-based data analysis tools, and a data visualization platform. Triple Gene Mutual Interaction (TGMI) algorithm, presented in Chapter 2 is an innovative approach to identify key regulatory transcription factors (TFs) that govern a particular biological pathway or a process through interaction among three genes in a triple gene block, which consists of a pair of pathway genes and a TF. The identification of key TFs controlling a biological pathway or a process allows biologists to understand the complex regulatory mechanisms in living organisms. TF-Miner, presented in Chapter 3, is a high-throughput gene expression data analysis web application that was developed by integrating two highly efficient algorithms; TF-cluster and TF-Finder. TF-Cluster can be used to obtain collaborative TFs that coordinately control a biological pathway or a process using genome-wide expression data. On the other hand, TF-Finder can identify regulatory TFs involved in or associated with a specific biological pathway or a process using Adaptive Sparse Canonical Correlation Analysis (ASCCA). Chapter 4 presents ExactSearch; a suffix tree based motif search algorithm, implemented in a web-based tool. This tool can identify the locations of a set of motif sequences in a set of target promoter sequences. ExactSearch also provides the functionality to search for a set of motif sequences in flanking regions from 50 plant genomes, which we have incorporated into the web tool. Chapter 5 presents STTM JBrowse; a web-based RNA-Seq data visualization system built using the JBrowse open source platform. STTM JBrowse is a unified repository to share/produce visualizations created from large RNA-Seq datasets generated from a variety of model and crop plants in which miRNAs were destroyed using Short Tandem Target Mimic (STTM) Technology

Structural studies of 5´ UTR of Hepatitis C viral RNA by NMR-based structural biology

RNA is a single-stranded biopolymer that plays a myriad of roles in physiological and pathological processes and is the carrier of genetic information in many human pathogens. Hepatitis C virus (HCV) is one of the most impactful representatives of RNA viruses. Liver-abundant human microRNA-122 (miR-122) binds to two tandem sites within domain I of the 5´ untranslated region (5´ UTR) of HCV, ultimately resulting in upregulation of viral propagation. Despite many studies of the interaction between HCV and miR-122, the exact mechanism by which this recognition event leads to increased viral propagation is unknown. In this thesis, I have studied the 5´ UTR HCV–miR-122 interaction at different levels of structural complexity (domain I, domains I-II and the full 5´ UTR) using an integrative NMR-based structural biology approach. First, I have performed the near-complete assignment of domain I resonances and determined its secondary structure. Isolated domain I binds two copies of miR-122 with different affinities, and the binding kinetics fall into the slow-to-intermediate exchange-regime on the NMR chemical-shift timescale. Magnesium ions promote structural rearrangement of domain I, which in turn changes its interaction pattern with miR-122. Next, I have determined the secondary structures of the isolated domain II and a domain I-II construct, both in their apo (without miR-122) and holo (bound to miR-122) states. The data demonstrates that, in the domain I-II construct, domains I and II maintain independent folds; furthermore, the secondary structure of domain II remains intact upon domain I binding two copies of miR-122. However, the binding of miR-122 to the domain I-II construct does lead to a structural rearrangement that changes the relative orientation of the two domains, resulting in more open and extended conformation. Finally, I have investigated the interaction of miR-122 with the full 5´UTR. Since the differences between the low-resolution scattering data of the 5´ UTR in the apo and holo states were minimal, no major structural changes in the 5´ UTR upon miR-122 binding appear to occur. To study the local structural details of the 5´ UTR, I have explored the use of solid-state NMR. While there were clear changes in chemical shifts of the 5´ UTR upon miR-122 binding, indicating conformational changes in the 5´ UTR, acquisition of solid-state NMR data on segmentally labeled samples and isolated domain I was challenging and could not provide definitive answers at this stage. Overall, using an NMR-based integrative structural biology approach, I could show that miR-122 binding to domain I causes both widespread local rearrangements within domain I and a significant reorientation of domain I relative to domain II, while the effect of miR-122 binding on the overall structure of the full 5’ UTR was found to be minimal