Suite aux séismes et au tsunami qui ont frappé les côtes japonaises le 11 mars 2011, d’importantes quantités de radionucléides ont été émises par la centrale de Fukushima Dai-Ichi. Une part non négligeable (20%) du radiocésium rejeté s’est ensuite déposée sur les sols de la Préfecture de Fukushima. Cette étude vise à développer des méthodes de traçage sédimentaire originales afin de comprendre la dispersion des particules contaminées. L’étude se concentre sur 3 bassins versants côtiers situés au nord de la centrale (bassins de la Mano – 175 km², Niida – 270 km² et Ota – 75 km²) et drainant la partie la plus contaminée du panache de pollution radioactive. Cette région connaît un climat particulièrement érosif, avec des crues printanières et le passage de typhons entre juin et octobre. Pour étudier la dispersion de la contamination radioactive initiale, des sols et des laisses de crues ont été collectés au cours de 6 campagnes de terrain (organisées tous les 6 mois entre novembre 2011 et mai 2014 après les crues printanières et les typhons estivaux). L’activité des principaux radionucléides a été mesurée par spectrométrie gamma et une sélection d’échantillons a également été analysée par activation neutronique afin de déterminer leur teneur en une vingtaine d’éléments. L’analyse de l’activité en 137Cs dans 10 carottes de sols collectées dans des rizières a confirmé la faible migration du césium en profondeur dans les sols de la région. Plus de 90 % de la contamination étaient concentrés dans les 2 cm superficiels des sols en novembre 2013. Cette contamination située à la surface du sol reste donc potentiellement mobilisable par l’érosion. Par ailleurs, la détection d’argent-110 métastable (110mAg) et le fait que ce radioisotope ait un comportement similaire à celui du césium, ont permis de l’utiliser pour tracer la dispersion de la contamination dans le bassin versant de la Niida. En effet, le rapport d’activités 110mAg/137Cs dans les sols de ce bassin est significativement différent à l’amont et à l’aval de celui-ci. L’utilisation de ce rapport et d’un modèle de mélange binaire a permis d’identifier l’occurrence de cycles d’érosion et de dispersion saisonniers de la contamination. Cependant, 110mAg ayant une demi-vie de 250 jours, il a rapidement décru et l’activité est devenue inférieure aux limites de détection à compter de mai 2013. Pour pallier sa disparition, la contribution des sols des plateaux montagneux aux sédiments transitant dans la plaine côtière a été quantifiée à partir de leur signature en 137Cs. En utilisant un modèle de mélange binaire basé sur les distributions du 137Cs à l’amont (> 20 kBq/m²) et à l’aval (< 20 kBq/m²) des bassins versants, les résultats montrent que la contribution de la zone amont diffère en fonction du bassin versant. Elle fournit une part non négligeable (≈46%) des sédiments à la rivière Niida, qui est dépourvue de barrage, à la différence de la rivière Mano (≈20 %) qui en est équipée. Ces résultats montrent donc l’impact de ce type d’ouvrage qui génère une dysconnectivité sédimentaire. Afin de préciser l’origine spatiale des sédiments contaminés transportés par ces rivières, la carte des sols des bassins versants a été utilisée. Les principaux types de sols (Andosols, Cambisols et Fluvisols) ont été caractérisés par leurs teneurs en éléments chimiques, et Sc et Yb se sont révélés être le couple d’éléments le plus discriminant. Les distributions de ces deux éléments dans les trois sources ont ensuite été utilisées dans un modèle de mélange. Les résultats montrent une contribution majoritaire (> 70 %) des Fluvisols dans les sédiments. La forte contribution de ce type de sol, que l’on trouve principalement dans les rizières, confirme donc l’érodabilité accrue de ces zones agricoles. Pour poursuivre ces travaux, l’ensemble des données acquises pourrait être utilisé pour améliorer les modèles d’érosion des sols opérant à l’échelle des bassins versants. / Large quantities of radionuclides were released into the atmosphere by the Fukushima Dai-Ichi Nuclear Power Plant (FDNPP) after the earthquake-triggered tsunami devastated the eastern coast of Japan on March 11, 2011. Many of these radionuclides (20%) were deposited on soils of the Fukushima Prefecture. This PhD thesis develops original fingerprinting methods to track the dispersion of contaminated particles following this accident. The study focuses on 3 coastal catchments north of the FDNPP (Mano — 175km², Niida — 270km² and Ota — 75km²) draining heavily contaminated areas of the radioactive plume. The Fukushima Prefecture is characterized by an erosive climate, with the occurrence of spring floods and summer typhoons. To study the dispersion of the radioactive contamination, soil samples and sediment drape deposits were collected during 6 sampling campaigns (every six months between November 2011 and May 2014; i.e., after the major flood events). Each sample was analyzed by gamma spectrometry to determine radionuclide activities, and several soil and sediment samples were also analyzed by neutron activation analysis to determine their geochemistry. First, the analysis of 137Cs activity in 10 soil cores collected in paddy fields confirmed the limited migration of radiocesium with depth in the soils of the coastal catchments. More than 90% of the contamination was still concentrated in the uppermost 2cm of the soils by November 2013. Particles contaminated were therefore available for mobilization and transport downstream by processes that govern soil erosion. Second, metastable silver-110 (110mAg) was detected in most of the samples collected between November 2011 and November 2012, and our investigation showed that this radionuclide has a similar behavior as 137Cs in soil and sediment. Consequently, we used 110mAg to track the dispersion of the contamination as the 110mAg/137Cs activity ratio in soils of the Niida catchment showed significant differences between upstream and downstream locations. The use of a binary mixing model allowed the identification of a seasonal cycle of erosion and dispersion of particles. However, as 110mAg has a short half-life (250 days), it rapidly decayed and could not be detected anymore by May 2013. To overcome its disappearance, the contribution of soils located on the mountainous plateaus to the sediment transiting the river in the coastal plains was quantified based on their 137Cs signature. Binary mixing models were used, based on the distributions of 137Cs in mountainous areas (> 20 kBq/m²) and in coastal plains (< 20 kBq/m²). The results demonstrated that the contribution of the mountainous area varied in the different catchments. In the Niida catchment where no dam has been built, the mountainous area supplies more sediment to the river (≈46%) than in the Mano catchment that has a dam (≈20%). These results show the impact of dams generating a sediment disconnectivity. Finally, the soil map of the region was used in order to identify the soil types that may supply sediment to the rivers. The main soil types (Andosols, Cambisols and Fluvisols) were characterized by their geochemical composition, and Sc and Yb were identified as the most discriminant elements. The distributions of these elements in the three sources were used in a mixing model. Results show that Fluvisols are the main source supplying >70% of sediment to the rivers in both catchments. This soil type is mainly found in paddy fields, which confirms the enhanced erodibility of these cultivated areas. In the future, the dataset compiled could be used to improve soil erosion model operating at the catchment scale. Moreover, the impact of the ongoing decontamination works on the dispersion of contaminated sediments should be investigated.

Ha Wai-Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 166-180). / Abstracts in English and Chinese. / Acknowledgements --- p.ii / Abstract --- p.iii / Abbreviations --- p.vi / Table of Contents --- p.vii / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter 1.1 --- "Hstory, cultivation and trade" --- p.2 / Chapter 1.2 --- Botany --- p.4 / Chapter 1.3 --- Chemical Constituents and Pharmacological effects --- p.8 / Chapter 1.4 --- Authentication of Chinese herbal materials --- p.13 / Chapter 1.4.1 --- Morphological marker --- p.15 / Chapter 1.4.2 --- Histological marker --- p.18 / Chapter 1.4.3 --- Chemical marker --- p.20 / Chapter 1.4.4 --- Molecular markers --- p.24 / Chapter 1.4.4.1 --- Protein marker --- p.24 / Chapter 1.4.4.2 --- DNA-based markers --- p.26 / Chapter 1.4.4.2.1 --- PCR-based markers --- p.27 / Chapter 1.4.4.2.1.1 --- Random-primed PCR --- p.28 / Chapter 1.4.4.2.1.2 --- Simple Sequence Repeats (SSR) --- p.30 / Chapter 1.4.4.2.1.3 --- Polymerase Chain Reaction Fragment Length Polymorphism (PCR-RFLP) --- p.31 / Chapter 1.4.4.2.2 --- Hybridization-based markers --- p.33 / Chapter 1.4.4.2.3 --- Sequencing-based markers --- p.35 / Chapter 1.5 --- Objectives and Strategies of the studies --- p.39 / Chapter Chapter 2 --- General Materials and Methods --- p.40 / Chapter 2.1 --- Reagents and Buffers --- p.41 / Chapter 2.1.1 --- Media for bacterial culture --- p.41 / Chapter 2.1.2 --- Reagents for preparation of competent cells --- p.42 / Chapter 2.1.3 --- Reagents for plasmid DNA preparation --- p.42 / Chapter 2.1.4 --- Reagents for agarose gel electrophoresis --- p.43 / Chapter 2.1.5 --- Reagents for polyacrylamide gel electrophoresis --- p.43 / Chapter 2.1.6 --- Reagents for Southern hybridization --- p.44 / Chapter 2.2 --- Agarose Gel electrophoresis of DNA --- p.46 / Chapter 2.3 --- Purification of PCR products --- p.46 / Chapter 2.3.1 --- From agarose gel using Geneclean® II kit --- p.46 / Chapter 2.3.2 --- Using Microspin´ёØ Column --- p.47 / Chapter 2.4 --- End modification of PCR amplified DNA --- p.47 / Chapter 2.5 --- Preparation of Escherichia coli Competent Cells --- p.48 / Chapter 2.6 --- "Ligation and Transformation of E, coli" --- p.49 / Chapter 2.7 --- Plasmid Preparation --- p.50 / Chapter 2.7.1 --- Minipreparation of plasmid DNA --- p.50 / Chapter 2.7.2 --- Preparation of plasmid DNA using Wizard® Plus SV Minipreps DNA Purification Kit (Promega) --- p.50 / Chapter 2.8 --- Screening for the Presence of insert in plasmid --- p.51 / Chapter 2.8.1 --- Rapid alkaline lysis --- p.51 / Chapter 2.8.2 --- PCR screening --- p.52 / Chapter 2.8.3 --- Restriction digestion of plasmid DNA --- p.53 / Chapter 2.9 --- DNA sequencing --- p.53 / Chapter 2.9.1 --- Plasmid sequencing using T7 Sequencing Kit --- p.53 / Chapter 2.9.2 --- Cycle Sequencing from PCR products or plasmid --- p.54 / Chapter 2.10 --- DNA Sequencing electrophoresis --- p.55 / Chapter 2.10.1 --- Preparation of 6 % polyacrylamide gel solution --- p.55 / Chapter 2.10.2 --- Gel casting --- p.55 / Chapter 2.10.3 --- Electrophoresis of Sequencing Gel --- p.56 / Chapter 2.10.4 --- Autoradiography --- p.57 / Chapter 2.11 --- DNA elution from dried sequencing gel --- p.57 / Chapter 2.12 --- Southern blot analysis --- p.58 / Chapter 2.12.1 --- Restriction digestion of genomic DNA --- p.58 / Chapter 2.12.2 --- Purification of digested DNA and agarose gel electrophoresis --- p.58 / Chapter 2.12.3 --- Capillary transfer of DNA to a Hybond´ёØ N+ nylon membrane --- p.59 / Chapter 2.12.4 --- DNA radiolabeling by nick translation --- p.60 / Chapter 2.12.5 --- Purificaiton of radiolabeled probe by NICK® Spin Column --- p.60 / Chapter 2.12.6 --- Hybridization of DNA --- p.61 / Chapter Chapter 3 --- Plant DNA extraction --- p.62 / Chapter 3.1 --- Introduction --- p.63 / Chapter 3.2 --- Reagents and buffer for total DNA extraction --- p.66 / Chapter 3.3 --- Extraction methods --- p.70 / Chapter 3.3.1 --- Sample preparation --- p.70 / Chapter 3.3.2 --- CTAB extraction method --- p.70 / Chapter 3.3.3 --- Potassium acetate/ SDS extraction method --- p.71 / Chapter 3.3.4 --- GIBRO Plant DNAzol® reagent for genomic DNA isolation --- p.72 / Chapter 3.4 --- Qualitative and quantitative analysis of DNA --- p.74 / Chapter 3.5 --- Results --- p.75 / Chapter 3.6 --- Discussion --- p.78 / Chapter Chapter 4 --- Amplified Fragment Length Polymorphism (AFLP) analysis of P. ginseng and P. quinquefolius --- p.81 / Chapter 4.1 --- Introduction --- p.82 / Chapter 4.2 --- Materials and methods --- p.88 / Chapter 4.2.1 --- Plant materials --- p.88 / Chapter 4.2.2 --- Choice of Primers and radiolabeling --- p.89 / Chapter 4.2.3 --- AFLP assay --- p.90 / Chapter 4.2.4 --- Electrophoresis of AFLP fingerprint --- p.91 / Chapter 4.2.5 --- Similarity Index (S.I.) analysis of AFLP profile --- p.91 / Chapter 4.2.6 --- Re-amplification of polymorphic DNA fragments isolated from dried sequencing gel --- p.92 / Chapter 4.2.7 --- Cloning and Sequencing of the AFLP fragments --- p.93 / Chapter 4.2.8 --- Conversion of AFLP marker into Directed Amplification of Minisatellite-region DNA polymorphism (DAMD) marker --- p.93 / Chapter 4.3 --- Results --- p.95 / Chapter 4.4 --- Discussion --- p.102 / Chapter Chapter 5 --- Direct Amplification of Length Polymorphisms (DALP) analysis of P. ginseng and P. quinquefolius --- p.107 / Chapter 5.1 --- Introduction --- p.108 / Chapter 5.2 --- Materials and methods --- p.112 / Chapter 5.2.1 --- Plant materials --- p.112 / Chapter 5.2.2 --- Choice of Primers --- p.113 / Chapter 5.2.3 --- Alternative labelled Amplification reaction --- p.114 / Chapter 5.2.4 --- Electrophoresis of the multi-locus amplification products --- p.114 / Chapter 5.2.5 --- Isolation and Re-amplification of polymorphic DALP fragments from dried sequencing gel --- p.115 / Chapter 5.2.6 --- Cloning and Sequencing --- p.115 / Chapter 5.2.7 --- Conversion of DALP marker to Sequence Tagged Site (STS) marker --- p.116 / Chapter 5.3 --- Results --- p.117 / Chapter 5.4 --- Discussion --- p.135 / Chapter Chapter 6 --- Sequence-characterized amplified region (SCAR): the sequel of random amplified polymorphic DNA (RAPD) --- p.137 / Chapter 6.1 --- Introduction --- p.138 / Chapter 6.2 --- Materials and methods --- p.140 / Chapter 6.2.1 --- Plant materials --- p.140 / Chapter 6.2.2 --- PCR reaction --- p.141 / Chapter 6.2.3 --- Cloning and sequencing --- p.143 / Chapter 6.3 --- Results --- p.144 / Chapter 6.4 --- Discussion --- p.157 / Chapter Chapter 7 --- Outlook --- p.159 / Chapter 7.1 --- Molecular authentication of Chinese medicinal materials --- p.160 / Chapter 7.2 --- Development of molecular markers for Ginseng --- p.161 / Appendix I --- p.164 / Appendix II --- p.165 / References --- p.166

Poon Wing-sem. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 163-171). / Abstracts in English and Chinese. / ABSTRACT I-IV --- p.I-IV / ACKNOWLEDGMENTS V --- p.V / TABLE OF CONTENT --- p.VI-VIII / LIST OF FIGURES AND TABLES --- p.IX-XI / LIST OF ABBREVIATIONS --- p.XII / Chapter CHAPTER ONE --- LITERATURE REVIEW --- p.1 / Chapter 1.1 --- Rutaceae --- p.1 / Chapter 1.1.1 --- Introduction --- p.1 / Chapter 1.1.2 --- taxonomy of Rutaceae --- p.2 / Chapter 1.1.3 --- Controversial taxonomic issues --- p.4 / Chapter 1.1.3.1 --- Subfamilies Rutoideae and Toddalioideae --- p.4 / Chapter 1.1.3.2 --- "Euodia, Melicope and Tetradium" --- p.7 / Chapter 1.1.3.2.1 --- History --- p.7 / Chapter 1.1.3.2.2 --- Arguments based on morphology --- p.10 / Chapter 1.2 --- Molecular Approach --- p.12 / Chapter 1.2.1 --- Introduction to molecular systematics --- p.12 / Chapter 1.2.2 --- DNA sequence markers --- p.14 / Chapter 1.2.3 --- Applications --- p.18 / Chapter 1.3 --- Traditional Chinese Medicine (TCM) --- p.21 / Chapter 1.3.1 --- Introduction --- p.21 / Chapter 1.3.2 --- Fructus Evodiae --- p.22 / Chapter 1.3.3 --- Functional chemicals and pharmacological effects of Fructus Evodiae --- p.23 / Chapter 1.3.4 --- Problem in authentication --- p.25 / Chapter 1.4 --- Objectives --- p.27 / Chapter CHAPTER TWO --- METHODOLOGY AND MATERIALS --- p.29 / Chapter 2.1 --- Plant and Herb Materials --- p.29 / Chapter 2.2 --- DNA extraction --- p.44 / Chapter 2.2.1 --- Modified cetyltriethylammonium bromide (CTAB) extraction --- p.44 / Chapter 2.2.2 --- Kit extraction --- p.45 / Chapter 2.2.2.1 --- DNeasy® Plant MiniKit of Qiagen --- p.45 / Chapter 2.2.2.2 --- GenElute´ёØ Plant Genomic DNA Miniprep Kit of Sigma® --- p.46 / Chapter 2.3 --- Polymerase chain reaction (PCR) reaction --- p.47 / Chapter 2.4 --- DNA gel electrophoresis --- p.49 / Chapter 2.5 --- PCR product purification --- p.49 / Chapter 2.5.1 --- Rapid Gel Extraction System of Marligen Biosciences INC --- p.50 / Chapter 2.5.2 --- Gel-M´ёØ Gel Extraction System --- p.50 / Chapter 2.6 --- Ligation and transformation --- p.51 / Chapter 2.6.1 --- Ligation and transformation --- p.51 / Chapter 2.6.2 --- Cell culture --- p.52 / Chapter 2.6.3 --- Plasmid extraction --- p.52 / Chapter 2.7 --- Determination of DNA concentration --- p.54 / Chapter 2.8 --- Cycle Sequencing --- p.54 / Chapter 2.9 --- Sequence Analysis --- p.55 / Chapter 2.10 --- Materials --- p.56 / Chapter CHAPTER THREE --- MOLECULAR AUTHENTICATION OF FRUCTUSEVODIAE --- p.60 / Chapter 3.1 --- Results and data analysis --- p.60 / Chapter 3.1.1 --- Authentication based on ITS-1 region --- p.60 / Chapter 3.1.1.1 --- Phylogram study --- p.60 / Chapter 3.1.1.2 --- Sequence alignment --- p.65 / Chapter 3.1.1.3 --- ITS-1 region nucleotide differences significant in authentication of Fructus Evodiae --- p.71 / Chapter 3.1.1.4 --- Comparison of sequences --- p.74 / Chapter 3.1.2 --- Authentication based on ITS-2 region --- p.78 / Chapter 3.1.2.1 --- Phylogram study --- p.78 / Chapter 3.1.2.2 --- Sequence alignment --- p.82 / Chapter 3.1.2.3 --- ITS-2 region nucleotide differences significant inauthentication of Fructus Evodiae --- p.86 / Chapter 3.1.2.4 --- Comparison of sequences --- p.89 / Chapter 3.2 --- Discussion --- p.93 / Chapter 3.2.1 --- Molecular markers --- p.93 / Chapter CHAPTER FOUR --- PHYLOGENETIC STUDIES ON RUTACEAE --- p.96 / Chapter 4.1 --- Results and data analysis --- p.96 / Chapter 4.1.1 --- Chloroplast trnL intron region --- p.96 / Chapter 4.1.1.1 --- Sequence alignment --- p.96 / Chapter 4.1.1.2 --- Phylogenetic analysis --- p.107 / Chapter 4.1.2 --- Chloroplast trnL-F intergenic spacer region --- p.116 / Chapter 4.1.2.1 --- Sequence alignment --- p.116 / Chapter 4.1.2.2 --- Phylogenetic analysis --- p.126 / Chapter 4.1.3 --- Nuclear ITS-1 region --- p.132 / Chapter 4.1.3.1 --- Sequence alignment --- p.132 / Chapter 4.1.3.2 --- Phylogenetic analysis --- p.143 / Chapter 4.2 --- Discussion --- p.152 / Chapter 4.2.1 --- "Euodia, Melicope and Tetradium" --- p.152 / Chapter 4.2.2 --- Tetradium --- p.153 / Chapter 4.2.3 --- Tetradium and Phellodendron --- p.155 / Chapter 4.2.4 --- Zanthoxylum and Toddalia --- p.156 / Chapter 4.2.5 --- Rutoideae and Toddalioideae --- p.156 / Chapter 4.2.6 --- Tree constructing methods --- p.158 / Chapter CHAPTER FIVE --- CONCLUSION --- p.161 / REFERENCES --- p.163

Considérées comme des menaces pour les écosystèmes marins tropicaux et subtropicaux, les proliférations de macroalgues sont susceptibles de modifier le fonctionnement et la structure des récifs coralliens. Le genre Asparagopsis (Rhodophyta) est connu pour être largement distribué, introduit et parfois invasif dans certaines régions comme en Méditerranée occidentale. Le premier objectif était de corréler le métabolisme spécialisé et la bioactivité de l’algue à son génotype, et éventuellement à son caractère proliférant. Aucune corrélation génétique/métabolomique n’a été démontrée, ce qui laisse entendre que le métabolisme macroalgal serait principalement influencé par l'environnement et/ou sa flore microbienne associée. En milieu tempéré, A. taxiformis et A. armata présentent des signatures métabolomiques globalement similaires et associées à une bioactivité significativement plus importante qu'en milieu tropical. Cependant, même lorsqu’elle a été introduite, une même lignée génétique et un même phénotype chimique peuvent présenter des caractères proliférants opposés. En milieu tropical, les extraits de macroalgues testés in situ sur 4 espèces de coraux n'ont provoqué que de faibles blanchissements. En milieu tempéré, aucun effet biologique de l’algue n’a été enregistré sur le corail Astroides calycularis. Par contre des expériences en aquarium ont permis de montrer qu’A. taxiformis pouvait exprimer un métabolisme spécifique avec une bioactivité augmentée après 10 jours de contact avec ce corail. En conclusion, qu’elle soit indigène ou introduite, A. taxiformis exerce peu d’effets sur la santé des coraux, et le caractère invasif de cette algue reste une source de débat. / Considered as a major threat for sub–tropical and tropical ecosystems, macroalgal proliferations are susceptible to modify the structure and the functioning of coral reefs. The genus Asparagopsis (Rhodophyta) is known to be widespread, introduced and sometimes invasive in certain regions such as the Western Mediterranean Sea. The first objective of this thesis was to correlate the algal specialized metabolism and its bioactivity with its genotype, and eventually with its proliferation trait. No correlation between genetics and metabolomics has been demonstrated, which would suggest the main influence of environmental factors and/or the associated microbial diversity on the algal metabolism. In temperate regions, A. taxiformis and A. armata showed similar metabolomic fingerprints with bioactivities significantly higher than in tropical regions. However, even when it is introduced, a given genetic lineage and a given chemical phenotype can exhibit opposite proliferative traits. In tropical areas, algal extracts tested in situ on 4 coral species did not lead to any coral bleaching. In temperate areas, no biological effect of the alga was recorded on Astroides calycularis. However, some aquarium experiments allowed to show that A. taxiformis can express a specific metabolism, with an increased bioactivity after 10–days of contact with this coral. To conclude, either indigenous or introduced, A. taxiformis poorly affects corals’ health, and thus the invasiveness of this alga remains a matter of debate.

In this paper, we present a working research prototype codeid-elf for ELF binaries based on its Windows counterpart codeid, which can identify kernels through relocation entries extracted from the binaries. We show that relocation-based signatures are unique and distinct and thus, can be used to accurately determine Linux kernel versions and derandomize the base address of the kernel in memory (when kernel Address Space Layout Randomization is enabled). We evaluate the effectiveness of codeid-elf on a subset of Linux kernels and find that the relocations in kernel code have nearly 100\% code coverage and low similarity (uniqueness) across various kernels. Finally, we show that codeid-elf, which leverages relocations in kernel code, can detect all kernel versions in the test set with almost 100% page hit rate and nearly zero false negatives.

Because tuberculosis (TB) is a public health threat that continues to elude elimination in the United States, there is a need to identify contributing factors that may have implications for targeted control measures. Molecular studies of genetic clustering are crucial for pinpointing these contributing factors. It is for this reason this study was conducted. This was a non-experimental, cross-sectional population-based molecular epidemiological study of TB in SC from 2005 to 2011. Its purpose was to estimate the proportion of TB that may be due to recently acquired infection and to determine the risk factors associated with the genetic clustering of identical M. tuberculosis isolates from TB patients in South Carolina from 2005-2011. The analysis sample included 627 confirmed pulmonary and/or pleural cases of TB, for which complete data on all covariates and a valid genotype were available. The results strongly suggested that about 50% of TB in South Carolina is recently transmitted. The study also revealed that being born in the United States and Black race were independently and significantly associated with being part of a TB genotype cluster. The key messages of this study were as follows: a substantial portion of TB in South Carolina is due to recent transmission, not reactivation or importation, and transmission of TB in South Carolina occurs in groups often defined by American birth and Black race. These important findings indicate that most TB in South Carolina is preventable and that enhanced TB control efforts should be explored. The implication for positive social change is that employing targeted contact investigation informed by these findings could lead to decreased disease transmission. Future studies should explore pilot programs that investigate alternatives to the traditional TB contact investigation.

[Truncated abstract] Traditional medicines are used by millions of people throughout the world as their primary source of medical care. A range of materials are in used traditional medicines including plant and animal parts. Even though the traditional medicine trade is estimated to be worth sixty billion dollars annually the trade remains largely unregulated. Unscrupulous practices by vendors to increase their profit margins such as substituting and adulterating expensive material with cheaper varieties go unchecked. This can be dangerous to consumers because some substitutions involve poisonous material. Also, animal parts from endangered species can find their way into traditional medicines, therefore there needs to be a way to identify them in traditional medicines to prosecute poachers. The traditional techniques used for the identification of material used in Traditional Chinese Medicine (TCM) include, morphological, histological, chemical and immunological analysis. However, these techniques have their limitations. This makes applying multiple techniques essential to provide thorough authentication of the material. DNA profiling provides a technique well suited to analysing material used in TCM. DNA profiling is advantageous over other techniques used to authenticate material used in TCM because it requires only a small sample amount, can determine the cultivator, be used on all forms of TCM and potentially distinguish the components of mixtures. ... Therefore, profiles of different species/individual are different and species? can be distinguished. Commercially sold traditional medicines are processed which is likely to degrade the DNA of the sample making extraction and amplification difficult. Here an organic Phenol:Chloroform extraction technique extracted DNA from commercial dried root samples. The extracted DNA was amplifiable using RAPD primers. The RAPD primers used here produced enough polymorphic bands to distinguish different plant species. They were used to distinguish commercial samples that were sold as three different species within the Panax genus, Panax ginseng, Panax quinquefolium and Panax notoginseng and genetically unrelated plant material; Potato and Eleutherococcus senticosus. Liquid samples and mixtures were also profiled with the RAPD primers to determine whether the RAPD primers provide enough distinguishing ability to analyse these forms of TCM. DNA was extracted from the liquid samples, one a ginseng drink and the other an ginseng extractum. However, there was no reliability in the production of PCR products. The analysis of the mixture samples found that not enough polymorphic bands were produced by the RAPD primers used here to identify Panax species within mixtures of two Panax species. While when P. ginseng was mixed with a genetically unrelated sample there was enough polymorphism to differentiate the two samples in the mixture. The results of this research show that RAPD analysis provides a simple and inexpensive technique to begin analysis of materials used in TCM. Using RAPD analysis it is possible to distinguish Panax plant species from each other. However, the RAPD primers used here did not provide enough reproducibility or polymorphism to analyse liquid and mixtures of Panax species plants.

<p>With the development of the Internet, illegal copying of electronic documents has become a growing problem. There is an increasing need of prevention in the field of pirate copying. One method is to mark the document by changing some of the words to synonyms. In this way it is possible to construct legal copies which do not differ in content but still are unique. Since the copies of the documents are unique, it is possible to trace the owner of a document and accordingly call him or her to account for pirate copying if several exactly similar copies are reaching the market. </p><p>The aim of this study was to investigate the possibility of exchanging words for synonyms in a text from a work of fiction, examining both the literary qualities of the manipulated texts and the security aspect. The conclusion of the study is that it is possible to mark texts of imaginative literature by means of the use of synonyms.</p>

Carbon isotope analyses of gases extracted from drilling muds while drilling in the Western Canada Sedimentary Basin (WCSB) can be used to create carbon isotopic depth profiles. These profiles provide essentially continuous data through the stratigraphic section, offering a unique opportunity to study the in-situ gases in various rock matrices. Carbon isotope and molecular compositions of Jurassic - Cretaceous mud gases have been examined from ten depth profiles in the undisturbed WCSB. The isotopic profiles are surprisingly complex, showing numerous inflections and deviations towards increasing and decreasing carbon isotope values (13C) and wetness index with depth that suggest a correlation with the stratigraphic framework and can be explained in terms of the origin and alteration of the gases. However, the gas isotope geochemistry must be incorporated and applied in a multidisciplinary approach in order to gain a better understanding of causes of variations. The discernible degree of correlativity of carbon isotope trends between the WCSB wells are likely to be related to the presence of major gas compartments bounded by stratigraphic surfaces, compartmentalization of the gas being strongly influenced by stratigraphic variations. The majority of these boundaries act as effective barriers to gas migration. Mudgas geochemistry is best employed in conjunction with petrophysical analysis and conversion into mineralogy, for defining details of transition zones and reservoir compartments. Combined evidence suggests that isotopic variability of WCSB gases is only partly induced by source maturity at one single location. The main shifts of carbon isotope ratios are likely to be related to the physical properties of the rocks, differences between organic precursors (type II versus type III kerogen), total organic carbon (TOC) content, gas biodegradation and mixing. The present thesis demonstrates that the carbon isotopic mud gas profiles represent a powerful tool that provide information about the compartmentalization of the gas, the effectiveness of low permeability barriers, the origin, alteration and maturity of gases, and the regional gas dynamics. Mudgas geochemistry proves to be one part of the puzzle in the investigation of regional gas dynamics, and should be integrated with geological information, lithostratigraphic-, and sequence stratigraphic information, petrographic information and geophysical data.

This thesis describes bioanalytical methods for generating fingerprints of biological systems for extracting relevant information with (protein) drugs in focus. Similarities and differences between samples can reveal the hidden relevant information, which can be used to optimize the production and facilitate the quality control of such protein drugs during their development and manufacture. Metabolic fingerprinting and multivariate data analysis (MVDA) can also facilitate early diagnosis of diseases and the effects and toxicity of drugs. Currently, several protein drugs are available on the global market. Nevertheless, despite, the success of such biotherapeutics significant challenges remain to be overcome in maintaining their stability and efficacity throughout their production cycle and long-term storage. The native structure and functional activity of therapeutic proteins is affected by many variables from production to delivery, incl. variables assoc. with conditions in bioreactors, purification, storage and delivery. Thus, part of the work underlying this thesis focused on structural analysis of a protein drug using chemical labeling, peptide mapping, and evaluation of the charge state distributions of the whole protein generated by ESI. The other part focuses on non-targeted metabolomics with a view to optimizing the cell cultivation process and assessment of the drug’s toxicity. A combination of appropriate analytical methods and MVDA is needed to find markers that can facilitate optimization of the cultivation system and expression of the target proteins in early stages of process development. Rapid methods for characterizing the protein drugs in different stages of the process are also required for quality control. In order to obtain high quality fingerprints analytical separation techniques with high resolution (such as HPLC or UHPLC) and sensitive analytical detection techniques (such as ESI, quadrupole or TOF MS) have been used, singly or in combination. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript.