Identifying the molecular components that matter: a statistical modelling approach to linking functional genomics data to cell physiology

Functional genomics technologies, in which thousands of mRNAs, proteins, or metabolites can be measured in single experiments, have contributed to reshape biological investigations. One of the most important issues in the analysis of the generated large datasets is the selection of relatively small sub-sets of variables that are predictive of the physiological state of a cell or tissue. In this thesis, a truly multivariate variable selection framework using diverse functional genomics data has been developed, characterized, and tested. This framework has also been used to prove that it is possible to predict the physiological state of the tumour from the molecular state of adjacent normal cells. This allows us to identify novel genes involved in cell to cell communication. Then, using a network inference technique networks representing cell-cell communication in prostate cancer have been inferred. The analysis of these networks has revealed interesting properties that suggests a crucial role of directional signals in controlling the interplay between normal and tumour cell to cell communication. Experimental verification performed in our laboratory has provided evidence that one of the identified genes could be a novel tumour suppressor gene. In conclusion, the findings and methods reported in this thesis have contributed to further understanding of cell to cell interaction and multivariate variable selection not only by applying and extending previous work, but also by proposing novel approaches that can be applied to any functional genomics data

Identification of Leptographium species by oligonucleotide discrimination on a DNA microarray

Leptographium is an anamorph genus within the Ophiostomatoid group of fungi and represents a unique case for molecular applications. The genus has a near complete sequence data available for three genes across all known species. This characteristic makes it a perfect test group for investigating applications of new diagnostic techniques within ascomycetes. Probes and primers, for microarrays, are designed from phylogenetically useful gene regions and are fabricated onto a solid substrate using printing technology. The sample is prepared using PCR and is hybridised to the probes under stringent conditions. The resulting fluorescent pattern is rigorously analysed to distinguish species from each other. Diagnostic PCR uses primers that are designed in similar way to the way probes are designed for microarrays and indicate the presence of a species through positive amplification. This research methodology will be applied to Leptographium to evaluate the efficacy of microarray technology for discriminating species within that genus. The data gained from this research study will be used in applications for other genera using microarray technology.Dissertation (MSc)--University of Pretoria, 2009.GeneticsUnrestricte

Development of a sensitive diagnostic multiplex platform based on digitally encoded microcarriers

In answer to the ever-increasing need in biomolecular research and clinical diagnostics to carry out many assays simultaneously in on tube, several microcarrier-based multiplex technologies (suspension arrays) have arisen in the past few years. Simultaneous detection of different target molecules that are present in one sample is possible by incubating the sample with a mixture of differently encoded microcarriers, each carrying another probe which can specifically interact with one of the targets. This means that each target will bind to a differently encoded microcarrier. When the targets are caught, several methods exist to label those 'positive' microcarriers. By means of this label, and by means of the code, it becomes possible to verify whether a target was caught at its surface, and which target was caught, respectively. Those multiplex measurements work quantitatively, because the more a target is present in the sample, the more targets will bind to their corresponding microcarrier. Five years ago, our research group proposed the use of spatial selective photobleaching, as an alternative method for the development of digitally encoded microcarriers, which were called 'memobeads'. It was suggested that this method could overcome the multiplexing limitations of existing technologies. The present study aimed to optimize the surface characteristics of t hose memobeads, and to verify whether they could then be applied to multiplex protein tests and nucleic acid tests. Furthermore, it was investigated in which way these memobead assays (and in general the assays performed with every kind of suspension arrays) could be improved to make them more efficient and sensitive

Brain tumor microarray data analyzed using clustering and novel consensus clustering techniques

Brain Tumor MA Data is analyzed with different clustering methods obtaining heterogenous results. Application of consensus clustering produces a robust unique solution.Results are validated with internal and external techniques. Feature extraction and Domain Knowledge confirm discovery of subclasses

Biometrics

Biometrics uses methods for unique recognition of humans based upon one or more intrinsic physical or behavioral traits. In computer science, particularly, biometrics is used as a form of identity access management and access control. It is also used to identify individuals in groups that are under surveillance. The book consists of 13 chapters, each focusing on a certain aspect of the problem. The book chapters are divided into three sections: physical biometrics, behavioral biometrics and medical biometrics. The key objective of the book is to provide comprehensive reference and text on human authentication and people identity verification from both physiological, behavioural and other points of view. It aims to publish new insights into current innovations in computer systems and technology for biometrics development and its applications. The book was reviewed by the editor Dr. Jucheng Yang, and many of the guest editors, such as Dr. Girija Chetty, Dr. Norman Poh, Dr. Loris Nanni, Dr. Jianjiang Feng, Dr. Dongsun Park, Dr. Sook Yoon and so on, who also made a significant contribution to the book

Human Papillomavirus and Related Diseases

Cervical cancer is the second most prevalent cancer among women worldwide, and infection with Human Papilloma Virus (HPV) has been identified as the causal agent for this condition. The natural history of cervical cancer is characterized by slow disease progression, rendering the condition in essence preventable and even treatable when diagnosed in early stages. Pap smear and the recently introduced prophylactic vaccines are the most prominent prevention options, but despite the availability of these primary and secondary screening tools, the global burden of disease is unfortunately still very high This book will focus on the clinical and diagnostic aspects of HPV and related disease, highlighting the latest developments in this field

Induse jõe oru inimeste, parside, India juutide ja Tharu hõimu geneetilise põlvnemise piiritlemine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKäesolev on viies Tartu Ülikoolis valminud väitekiri Lõuna-Aasia rahvaste geneetilisest ajaloost. Asustatud kaasaegse inimese poolt märksa enne viimase jääaja maksimumi, elab tänapäeval selles regioonis üle 1.8 miljardi inimese – pea veerand inimkonnast. Seega ei ole võimalik süvitsi mõista kaasaegse inimese geneetise varieeruvuse kujunemist, sh eriti väljapool Sahara-alust Aafrikat, omamata detailsemat teadmist Lõuna-Aasia rahvaste geneetikast Väitekiri põhineb neljal ilmunud artiklil. Neist esimeses uurisime Kirde-Indiat asustavaid rahvaid seoses võimaliku pärinevusega Induse oru kultuurist ja järgnenud vedade ajastust. Teine ja kolmas artikkel on pühendatud migratsioonidele, mis tõid Indiasse religioosses mõttes uusi rahvagruppe: parsid Iraanist alates 7. sajandi lõpupoolelt ja juudid, kelle saabumine Indiasse on toimunud mitme lainena. Neljandas artiklis on vaatluse all Nepaalis, kuid ka India põhjapoolsetes osariikides elutsev rahvarohke tharu hõim. Esimes artikli huvitavamaks leiuks on usutavasti juba vedade ajastust tuntud Rori populatsiooni genoomis väljenduv suurem geneetiline afiinsus põhjapoolse stepivööndi rahvastega, samuti ka lääne-eurooplastega, mis räägib põhja-lõunasuunalistest migratsiooni(de)st eelajaloolisel ajal. Parside saabumist Lõuna-Aasiasse seostatakse Iraani islamiseerumisega 7. sajandil. Võrreldes parside genoome nende ajaloolises kontekstis leidsime ulatusliku segunemise Lõuna-Aasia rahvastega, sealjuures asümeetriliselt isa ja emaliinides. Sama saab väita ka Indias judaistliku traditsiooni elemente säilitanud erinevate kogukondade kohta, kelle genoomis on siiski selgelt säilunud Lähis- ja Kesk-Ida pärandit. Puudutavalt aga geneetiliselt ulatuslikult varieeruvat tharu hõimu, kelle hulgas on selgesti eristatav ka Ida-Aasia komponent, segunenuna Lõuna-Aasia pärandiga, paistab õigustatud olevat neid vaadelda esmajoones mitte sedavõrd deemilise, kuivõrd just kultuurilise konstruktsioonina.Presented hereby is the 5th in a series of PhD theses prepared in Tartu University, addressing genetics of population history of the South Asian peoples. Inhabited considerably before the Last Glacial Maximum, the region harbors by now about 1.8 billion humans – almost a quarter of the global population. Therefore, understanding of present-day variation of the latter, in particular outside sub-Saharan Africa, is not possible without deeper knowledge about genetics of South Asian populations. This thesis is based on four published papers. The first one is focused on selected populations inhabiting northeastern Indus Valley, bearing, in particular, in mind ancient Indus Valley civilization and following it Vedic period. The second and the third paper address historically somewhat better known migrations, bringing to India religiously distinct Parsi and Jewish peoples. The fourth paper analyses the genetic variation of a populous Tharu tribe, living predominantly in Nepal, but also in northern provinces of India. Perhaps the most interesting finding of the first paper is that the presumably identified already in Vedic texts, Ror population exhibits significant genetic affinity with northern Steppe and West European peoples, testifying about prehistoric north to south migration(s). The arrival of Parsis to South Asia in 7th century was a consequence of the Islamization of Iran. Comparing Parsi genomes in their historic contexts, we observed their extensive admixture with South Asians, in particular, asymmetrically in paternal and maternal lineages. Nearly the same can be said about different Indian communities that preserved Judaist traditions: their genomes show affinities to peoples living in the Near and Middle East. As far as the genetically highly diverse Tharu tribe is concerned, a clearly distinct East Asian contribution can be seen, admixed with South Asian genetic heritage. It seems justified to identify the Tharu as cultural, rather than demic phenomenon.https://www.ester.ee/record=b542949

Selected Works in Bioinformatics

This book consists of nine chapters covering a variety of bioinformatics subjects, ranging from database resources for protein allergens, unravelling genetic determinants of complex disorders, characterization and prediction of regulatory motifs, computational methods for identifying the best classifiers and key disease genes in large-scale transcriptomic and proteomic experiments, functional characterization of inherently unfolded proteins/regions, protein interaction networks and flexible protein-protein docking. The computational algorithms are in general presented in a way that is accessible to advanced undergraduate students, graduate students and researchers in molecular biology and genetics. The book should also serve as stepping stones for mathematicians, biostatisticians, and computational scientists to cross their academic boundaries into the dynamic and ever-expanding field of bioinformatics

The genetic and molecular analysis of primary ciliary dyskinesia.

Primary Ciliary Dyskinesia (PCD) is a recessively inherited disorder caused by cilia and sperm flagella dysmotility associated with axoneme ultrastructural defects. Symptoms include recurrent respiratory tract infections, sinusitis, bronchiectasis, subfertility, and laterality defects due to defective embryonic nodal cilia. PCD is genetically heterogeneous and two genes, DNAI1 and DNAH5, account for 38% of cases. To identify new PCD genes, genome wide linkage screens were undertaken in consanguineous PCD families using homozygosity mapping: (1) five Pakistani families with missing inner and outer dynein arms (2) two Arabic families with central pair agenesis and no dextrocardia. Three disease loci were mapped on chromosome llq23.3-24.3 and 17q21.31-22 (Pakistani), and chromosome 6p21.31-21.1 (Arabic), with peak multipoint LOD scores of 3.6, 6.0 and 6.7, respectively. Comparative bioinformatic analysis identified 7 positional candidate genes which were subjected to mutational analysis. A 3 bp deletion in C6ORF206 at 6p21.31-21.1 was revealed in affected Arabic PCD individuals, resulting in a predicted in-frame loss of a C-terminal lysine residue, K268. The protein encoded by C6ORF206 was identified as homologous to the Chlamydomonas reinhardtii radial spoke head protein, RSP9. Functional work was undertaken to determine if the K268del mutation was pathogenic. RSP9 is mutated in the paralysed flagella Chlamydomonas mutant, pfl 7, and transformation of pfl 7 with wild-type RSP9 rescued motility. However transformation of pfl 7 with RSP9 R261del (equivalent to human K268del) rescued motility to a lower level, resulting in an ineffective swimming stroke. Expression of RSP9 was investigated by in situ hybridisation, and zebrafish RSP9 knock-down morphants were created to investigate its role in vertebrate ciliary function. Although expressed at the vertebrate embryonic node, knockdown of RSP9 function did not affect laterality in zebrafish, however it did cause dysfunction of the nasal cilia. This data suggests that C6ORF206/RSP9 functions as a ciliary protein in ciliated organisms and that the K268del mutation likely causes PCD without situs inversus

Urological Cancer 2020

This Urological Cancer 2020 collection contains a set of multidisciplinary contributions to the extraordinary heterogeneity of tumor mechanisms, diagnostic approaches, and therapies of the renal, urinary tract, and prostate cancers, with the intention of offering to interested readers a representative snapshot of the status of urological research