Computational Biology and Chemistry

The use of computers and software tools in biochemistry (biology) has led to a deep revolution in basic sciences and medicine. Bioinformatics and systems biology are the direct results of this revolution. With the involvement of computers, software tools, and internet services in scientific disciplines comprising biology and chemistry, new terms, technologies, and methodologies appeared and established. Bioinformatic software tools, versatile databases, and easy internet access resulted in the occurrence of computational biology and chemistry. Today, we have new types of surveys and laboratories including “in silico studies” and “dry labs” in which bioinformaticians conduct their investigations to gain invaluable outcomes. These features have led to 3-dimensioned illustrations of different molecules and complexes to get a better understanding of nature

Characterizing freshwater macroinvertebrates of Bangladesh using metagenetic techniques

The degradation of freshwater ecosystems has become a global concern, in particular, the critical conditions of rivers in Bangladesh demand a monitoring programme through the assessment of bioindicator organisms. Macroinvertebrates as prominent bioindicators are widely used for assessing the health of aquatic ecosystems. Recent technological advances have enabled routine assessment with the genomic characterization of macroinvertebrates using different metagenetic techniques such as DNA barcoding for individual specimen identification, metabarcoding for multi-species identification of bulk samples and mitochondrial metagenomics for extraction of mitogenomes from mixed samples. In this thesis, I commence by generating Cytochrome Oxidase subunit (COI) barcodes for Bangladeshi freshwater macroinvertebrates belonging to the Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, Hemiptera, Odonata, Diptera, Gastropoda and Bivalvia. These barcodes can be used as a DNA reference library for species identification in metabarcoding of macroinvertebrates. I also aim for exploring complete mitogenomes from selected macroinvertebrates using a mitochondrial metagenomic pipeline. I carry out phylogenetic analysis with protein-coding genes that reveals the evolutionary relationship of Bangladeshi macroinvertebrate lineages and also support deeper level identification of barcodes placing them into the phylogenetic tree (chapter 2). In chapter 3, I assess some methodological aspects of the metabarcoding pipeline required for diversity estimation from complex bulk samples of macroinvertebrates in large-scale biomonitoring programmes. These include preparation of bulk macroinvertebrate samples, optimization of the procedure of homogenization of samples required for DNA extraction, strategies for DNA pooling from these extracts, choice of robust universal primers, and viable OTU clustering for reliable diversity estimation. The results have implications for the optimization and standardization of these steps in metabarcoding of freshwater macroinvertebrates. In chapter 4, I apply the metabarcoding technique to establish the macroinvertebrate diversity and impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in highland and lowland rivers. The results document high diversity, local endemicity and pronounced responses to disturbance in largely unexplored but threatened habitats of Bangladesh. My investigations manifest the viability of metagenetic techniques for applied conservation management as a step towards building a biomonitoring system in freshwater ecosystems globally.Open Acces

ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)

The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe

Phylogeny, Phylogeography and Population Connectivity of Lessonia (Phaeophyceae)

The brown algal genus Lessonia is distributed in the Southern Hemisphere where it can form dominant kelp beds on the exposed rocky shores of New Zealand, South America and Tasmania. Its disjunct distribution within the West Wind Drift contrasts with the view that it is a poor disperser. Apart from studies in Chile, where it is an economically important genus, little is known about Lessonia and in some areas even the number of species is unknown. Using different genetic markers I examined the phylogeny, phylogeography, and the connectivity of populations in Lessonia. Using the literature, species affiliations and nomenclatural problems have been investigated. Combining the sequences of three mitochondrial, one chloroplast and two nuclear markers, a supermatrix approach was used to investigate the phylogenetic relationship and the timing of speciation for all known Lessonia species. The Australasian Lessonia species form a clade within a paraphyletic grouping of South American species. Radiation in Lessonia occurred about 5 Mya at the beginning of the Pliocene and rapid radiation took place in Australasia 3.5 Mya. The data also revealed cryptic species within a L. variegata species complex. Further analysis within the Australasian clade, using mitochondrial (atp8-sp) and chloroplast (rbc-sp) markers and wider sampling (469 individuals from 57 sample sites) supported four cryptic species and revealed localized distribution for all Australasian lineages. Genetic breaks between Lessonia lineages corresponded well to known biogeographic regions and could be correlated to the geographic structure of New Zealand at the end of the Pliocene. The Cook Strait region was analysed more closely with newly developed microsatellite markers to test the influence of geographic breaks (Cook Strait and Palliser Bay) on the connectivity of populations. The results suggested that connectivity depends on the width of unsuitable habitat, and within inner Cook Strait it is facilitated by sometimes strong tidal flows that create turbulences and unique current patterns. The results implied that rafting is an important mean of dispersal. The study of the early literature on Lessonia supported the new lectotypification of L. flavicans but revealed that L. frutescens and possibly L. ovata (supported by images of rediscovered herbarium material) are synonymous to L. searlesiana and as the older epithets they should have priority. Suggestions have been made for the lectotypification of L. fuscescens and L. ovata. In general Lessonia shows non-overlapping distribution in Australasia but overlapping distribution in South America. Despite being a poor disperser, indicated by fine scale genetic structure, Lessonia is also able to connect populations over wide areas of unsuitable habitats

Phylogenetics of Begonia section Gireoudia

Begonia is one of the most species-rich angiosperm genera with c. 1500 species currently identified and a pantropical distribution. Although Begonia are predominantly found in ever wet rain forests, they can also be found in other habitats including dry, desert scrub, and at altitudes from sea level to over 3000 meters. Begonia can also exhibit huge morphological variation between closely related species thus making them an ideal system for the study of the ecology, biogeography and developmental evolution of tropical plants. Previous work carried out at the Royal Botanic Gardens, Edinburgh focused on the phylogenetic framework and biogeographic history of African and Asian Begonias. This work on the Neotropical Begonia Section Gireoudia, aims to complement those studies and to provide a framework for determining how macro- and micro-evolutionary processes have contributed to the high level of diversity in Begonia worldwide. Traditionally used nuclear and chloroplast markers for phylogenetics failed to resolve species level relationships within sect. Gireoudia, therefore an alternative approach using next-generation sequencing technology was developed. A multiplexed, massively parallel sequencing approach was developed to sequence sixteen Begonia chloroplast genomes on the Illumina GAIIx genome analyser in order to identify chloroplast regions with sufficient phylogenetic information to resolve a species-level phylogeny. The lack of a reference chloroplast genome sequence for Begonia led to the development of a new method combining sequence from conserved angiosperm chloroplast genome sequences together with long-range PCR to generate the samples. Eighteen, overlapping long-range PCR amplicons for each Begonia species were used in a multiplexed sequencing reaction on an Illumina GAIIx and the chloroplast sequence reads were assembled using a de novo approach. A selection of potentially, phylogenetically informative regions, determined from the large-scale chloroplast alignment generated during this study, were assessed. Two of these regions were chosen for further phylogenetic analysis and resulted in improved resolution of American Begonia, sect. Gireoudia. This study successfully demonstrates a new innovative approach to that normally taken in traditional molecular systematics. The research presented provides a framework for the development of new molecular markers that are suitable for low-level phylogenetic studies, especially where recent radiations make resolution of species groups difficult, such as Begonia. New sequencing technologies such as those used here will provide powerful new tools for students of molecular evolution, phylogenetics and taxonom

A modular, open-source information extraction framework for identifying clinical concepts and processes of care in clinical narratives

In this thesis, a synthesis is presented of the knowledge models required by clinical informa- tion systems that provide decision support for longitudinal processes of care. Qualitative research techniques and thematic analysis are novelly applied to a systematic review of the literature on the challenges in implementing such systems, leading to the development of an original conceptual framework. The thesis demonstrates how these process-oriented systems make use of a knowledge base derived from workflow models and clinical guidelines, and argues that one of the major barriers to implementation is the need to extract explicit and implicit information from diverse resources in order to construct the knowledge base. Moreover, concepts in both the knowledge base and in the electronic health record (EHR) must be mapped to a common ontological model. However, the majority of clinical guideline information remains in text form, and much of the useful clinical information residing in the EHR resides in the free text fields of progress notes and laboratory reports. In this thesis, it is shown how natural language processing and information extraction techniques provide a means to identify and formalise the knowledge components required by the knowledge base. Original contributions are made in the development of lexico-syntactic patterns and the use of external domain knowledge resources to tackle a variety of information extraction tasks in the clinical domain, such as recognition of clinical concepts, events, temporal relations, term disambiguation and abbreviation expansion. Methods are developed for adapting existing tools and resources in the biomedical domain to the processing of clinical texts, and approaches to improving the scalability of these tools are proposed and evalu- ated. These tools and techniques are then combined in the creation of a novel approach to identifying processes of care in the clinical narrative. It is demonstrated that resolution of coreferential and anaphoric relations as narratively and temporally ordered chains provides a means to extract linked narrative events and processes of care from clinical notes. Coreference performance in discharge summaries and progress notes is largely dependent on correct identification of protagonist chains (patient, clinician, family relation), pronominal resolution, and string matching that takes account of experiencer, temporal, spatial, and anatomical context; whereas for laboratory reports additional, external domain knowledge is required. The types of external knowledge and their effects on system performance are identified and evaluated. Results are compared against existing systems for solving these tasks and are found to improve on them, or to approach the performance of recently reported, state-of-the- art systems. Software artefacts developed in this research have been made available as open-source components within the General Architecture for Text Engineering framework