Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

Report of the PRA carried out at Ihale Beach, Tanzania, April 11-14, 2000

Ihale is a large landing site lying approximately 65 km. from Mwanza along the main Mwanza-Musoma highway. Ihale Beach was selected as a potential candidate for the 3-beaches study because of its proximity to Mwanza, and hence suitability for frequent monitoring; and because it is served by a road accessible during the rainy seasons. As with the first training Participatory Rural Appraisal (PRA) on Kiumba Beach on Kenya's Rusinga Island, the objectives with this PRA were as follows: (a) To identify and understand Ihale's community-based organizations and institutions which have a role in the lake's fishery. (b) To consider the key issues which arise from this study for the involvement of communities and community-based organizations and/or institutions such as those at Ihale Beach, in the co-management of Lake Victoria's fishery.

Report of the PRA carried out at Lwalalo Beach, Uganda, June 5-14, 2000

This document contains the findings of the second Participatory Rural Appraisal (PRA) carried out under the LVFRP. Its principal objectives were to develop base-line information on a Ugandan beach for the 3-beaches survey of the LVFRP.

Report of the PRA carried out at Obenge Beach, Kenya, June 23-26, 2000

This document contains the findings of the third Participatory Rural Appraisal (PRA) carried out on Obenge Beach in Kenya, from the 23rd to the 26th of June 2000, under the LVFRP. Its principal objectives were to develop base-line information on a Kenyan beach for the 3-beaches survey of the LVFRP.

Report of the PRA carried out at Nkombe Beach, Uganda, September 2-10, 2000

This document contains the findings of the fourth Participatory Rural Appraisal (PRA) carried out under the LVFRP. Its principal objectives were to develop base-line information on a Ugandan beach for the 3-beaches survey of the LVFRP.

Report of the PRA carried out at Mwasonge Beach, Tanzania, October 23rd - November 3rd, 2000

This paper comprises part of the so-called "3-beaches Survey" of the LVFRP. In Tanzania, this study has developed to examine two landing sites (Mwasonge and Ihale), and to chart the progress of the newly established Beach Management Units (BMU) at each beach, comparing one BMU against the other. The over-arching objective of this survey was to develop an understanding of the context in which Mwasonge's fishery exists. The study does so by examining the community's history, culture and beliefs, various other socio-cultural factors, their resources, society and economy, wealth and the community's perceptions of wealth. Importantly, the survey examines the community's institutions and its perceptions of fishing rules and changes within the fishery. All of these facets of community life are examined with the use of participatory Rural Appraisal tools, and the images that the study generated are reproduced herein.

Some engineering issues of an FBG sensor with the dual gratings parallel matched interrogation method

The key issues of engineering application of the dual gratings parallel matched interrogation method are expanding the measurable range, improving the usability, and lowering the cost by adopting a compact and simple setup based on existing conditions and improving the precision of the data-processing scheme. A credible and effective data-processing scheme based on a novel divisional look-up table is proposed based on the advantages of other schemes. Any undetermined data is belonged to a certain section, which can be confirmed at first, then it can be looked up in the table to correspond to microstrain by the scheme. It not only solves inherent problems of the traditional one (double value and small measurable range) but also enhances the precision, which improves the performance of the system. From the experimental results, the measurable range of the system is 525 mu epsilon, and the precision is +/- 1 mu epsilon based on normal matched gratings. The system works in real time, which is competent for most engineering measurement requirements. (C) 2007 Elsevier GmbH. All rights reserved.

Fish production, catches and the carrying capacity of the world oceans

A brief review of the status of the world fisheries is presented with emphasis on the differences between catches (= landings + bycatch), biological production of fish, and predation (= production - catches). The ECOPATH II approach implemented as a new, Windows-based software is then shown to allow construction of a stratified world model accoutinng for global catches, production of and predation on fishes, and thus improved estimates of global potentials. A newly initiated, cooperative project is described through which the foundation for such a global model could be constructed, based on a stratified database with more than 100 trophic models. Collaborators are invited to join in this, and will be assisted in constructing models covering their areas of interest.

A preliminary report on Chanos fry surveys carried out in the brackish water areas of Mannar, Puttalam and Negombo

This paper records the results of the Chanos fry surveys carried out in Mannar, Puttalam and Negombo lagoon areas since 1967, and gives a summary of the earlier surveys. The maximum amount of Chanos fry was obtained from Mannar area during April and May. All three areas have their main commercial fry season in April and May with a second commercially negligible season in October–November. The quantity of fry collected has been utilized to evaluate the potential fry production figures. Mannar 400,000,000 fry/annum. Puttalam 200,000,000 fry/annum. It would be extremely difficult to estimate the number of eggs laid, the larvae hatched and the fry available each year along the coastal areas of Ceylon. It is necessary to obtain biological, meteorological and oceanographical data so as to provide a basis for the prediction and estimation of fry populations in the coastal waters of Ceylon. The suggested ideal season for commercial catches of Chanos fry is April–May with operations to be carried out simultaneously all along the west coast.

Multiple maternal origins of chickens: Out of the Asian jungles

Domestic chickens have long been important to human societies for food, religion, entertainment, and decorative uses, yet the origins and phylogeography of chickens through Eurasia remain uncertain. Here, we assessed their origins and phylogeographic hist

TEMPERATURE-DEPENDENCE OF THE LOW-FIELD MOBILITY OF MINIBAND CONDUCTION IN SUPERLATTICES

The existing interpretation of the T-1 temperature dependence of the low-field miniband conduction is derived from certain concepts of conventional band theory for band structures resulting from spatial periodicities commensurable with the dimensionalities of the system. It is pointed out that such concepts do not apply to the case of miniband conduction, where we are dealing with band structures resulting from a one-dimensional periodicity in a three-dimensional system. It is shown that in the case of miniband conduction, the current carriers are distributed continuously over all energies in a sub-band, but only those with energies within the width of the miniband contribute to the current. The T-1 temperature dependence of the low-field mobility is due to the depletion of these current-carrying carriers with the rise of temperature.

The neutron/proton ratio of squeezed-out nucleons and the high density behavior of the nuclear symmetry energy

Within a transport model it is shown that the neutron/proton ratio of squeezed-out nucleons perpendicular to the reaction plane, especially at high transverse momenta, in heavy-ion reactions induced by high energy neutron-rich nuclei can be a useful tool for studying the high density behavior of the nuclear symmetry energy.