Yersinia pestis, the causative agent of plague, is estimated to have claimed the lives of 30-50% of the European population in five years. Although it can now be controlled through antibiotics, there are still lurking dangers of outbreaks from biowarfare and bioterrorism; therefore, ongoing research to further our understanding of its strong virulence factors is necessary for development of new vaccines. Many Gram-negative bacteria, including Y. pseudotuberculosis, the evolutionary ancestor of Y. pestis, produce a hexa-acylated lipid A/LPS which can strongly trigger innate immune responses via activation of Toll-like receptor 4 (TLR4)-MD2. In contrast, Y. pestis grown at 37ºC generates a tetra-acylated lipid A/LPS that poorly induces TLR4-mediated immune activation. We have reported that expression of E. coli lpxL in Y. pestis, which lacks a homologue of this gene, forces the biosynthesis of a hexa-acylated LPS, and that this single modification dramatically reduces virulence in wild type mice, but not in mice lacking a functional TLR4. This emphasizes that avoiding activation of innate immunity is important for Y. pestis virulence. It also provides a model in which survival is strongly dependent on innate immune defenses, presenting a unique opportunity for evaluating the relative importance of innate immunity in protection against bacterial infection. TLR signaling is critical for the sensing of pathogens, and one implication of TLR4 engagement is the induction of the pro-forms of the potent inflammatory cytokines IL-1β and IL-18. Therefore Y. pestis is able to suppress production of these which are generated through caspase-1-activating nucleotide-binding domain and leucine-rich repeat (NLR)-containing inflammasomes. For my thesis, I sought to elucidate the role of NLRs and IL-18/IL-1β during bubonic and pneumonic plague infection. Mice lacking IL-18 signaling led to increased susceptibility to wild type Y. pestis, and an attenuated strain producing a Y. pseudotuberculosis-like hexa-acylated lipid A. I found that the NLRP12, NLRP3 and NLRC4 inflammasomes were important protein complexes in maturing IL-18 and IL-1β during Y. pestis infection, and mice deficient in each of these NLRs were more susceptible to bacterial challenge. NLRC4 and NLRP12 also directed interferongamma production via induction of IL-18 against plague, and minimizing inflammasome activation may have been a central factor in evolution of the high virulence of Y. pestis. This is also the first study that elucidated a pro-inflammatory role for NLRP12 during bacterial infection.

Die humane Yersiniose wird durch Lebensmittel tierischen Ursprungs übertragen und stellt aufgrund der jährlich gleichbleibend hohen Zahl übermittelter Krankheitsfälle sowie der wahrscheinlich weitaus höheren Dunkelziffer ein Problem des gesundheitlichen Verbraucherschutzes dar. Die intermittierende Ausscheidung des Erregers Yersinia enterocolitica beim klinisch unauffälligen Reservoirtier Schwein und die aufwändige Kultivierung erschweren den direkten Erregernachweis. Hier könnte der serologische Nachweis, in der Humanmedizin bereits seit langem etabliert, eine wertvolle diagnostische Hilfe sein. Die Erkennung serologisch positiver Bestände ähnlich dem Salmonellen-Monitoring und daran anschließende Hygienemaßnahmen, vor allem vor und während der Schlachtung, können den Eintrag des Erregers in die Lebensmittelkette vermindern. So wurde im Rahmen dieser Arbeit ein hochspezifisches serologisches Nachweissystem entwickelt, das durch die Verwendung rekombinanter und ausschließlich bei pathogenen Yersinien vorkommender Antigene eine hohe Sensitivität und Spezifität garantiert. Neun ausgewählte Yersinia Outer Proteins (Yops) wurden kloniert und mit spezifisch auf jedes Protein abgestimmten Bedingungen zur optimalen Expression gebracht. Durch die Evaluierung verschiedener Aufreinigungssysteme konnten schließlich reproduzierbare hochreine Antigene auch in großen Mengen hergestellt werden. Mit Blick auf eine sichere Auswertbarkeit bei der Verwendung des Testsystems in Laboratorien wurden die Antigene nicht elektrophoretisch aufgebracht, sondern mittels Sprühverfahren auf eine Nitrozellulosemembran aufliniert. Das gebrauchsfertige Testsystem, Blotstreifen von 2,5 mm Breite mit neun auflinierten, rekombinant hergestellten und Virulenzplasmid-basierenden Yersinia-Antigenen, eignet sich zur Diagnostik serologisch positiver Schweine. Mit Hilfe dieses Testsystems wurde die isotypspezifische Antikörperantwort von Schweinen im Infektionsmodell gegen den Erreger Y. enterocolitica ausgewertet. Nach zwei Vorversuchen mit jeweils zwei Schweinen wurden im Hauptversuch neun Ferkel experimentell mit einer Infektionsdosis von 5x1011 KBE per Magenschlundsonde infiziert, wobei die Tiere nach leichtem und kurzfristigem Durchfallgeschehen den Erreger symptomlos mit dem Kot ausschieden. Weitere neun Ferkel stellten eine Kontrollgruppe nicht infizierter Tiere dar. Vom Tag der Infektion bis zum Tag der Tötung (Tag 33) wurde regelmäßig bei den achtzehn Schweinen Blut, Speichel und Tränenflüssigkeit gewonnen, am letzten Tag zusätzlich Gelenkflüssigkeit und Darmsekrete. Die Auswertung der Seren im zeitlichen Verlauf zeigte deutlich die Immunogenität der Yops. Bei dominierenden Yops wie YopO, YopH, LcrV, YopD und YopE ließ sich das Einsetzen der Antikörperbildung (IgG und IgA) mit nachfolgendem Anstieg bei allen infizierten Tieren feststellen. Die früheste Bildung von Immunglobulin G konnte am Tag 10 gegen YopD verzeichnet werden, Immunglobulin A wurde gegen YopD bereits am Tag 7 gebildet. Die nicht infizierten Kontrolltiere waren im Immunoblot durchgehend negativ. In den Darmsekreten, der Gelenk- und Tränenflüssigkeit und vor allem im Speichel liessen sich mit dem entwickelten Test ebenfalls spezifische Yop- Antikörper detektieren. Der Test kann somit zur Diagnostik von Beständen mit Yersinia-Problematik herangezogen werden; er eignet sich als kompletter Kit sowohl für Labore als auch für veterinärmedizinische Praxen.

Yersinia enterocolitica es un patógeno Gram-negativo que provoca diversos síndromes gastrointestinales y expresa una panoplia de factores de virulencia, la mayoría regulados por la temperatura. El lipopolisacatido (LPS) es uno de los principales factores de virulencia de las bacterias Gram-negativas patógenas. Además, es una de las moléculas reconocidas por el sistema inmune innato y diana de los péptidos antimicrobianos. Por consiguiente, no es de extrañar que las bacterias modifiquen la estructura de su LPS con el fin de resistir a la defensa del sistema inmune. En esta Tesis Doctoral se han identificado los loci responsables de las modificaciones del lípido A de Y. enterocolitica O:8 (YeO8) y se ha demostrado que están reguladas por la temperatura. Se ha definido un circuito regulatorio complejo en el que intervienen los sistemas PhoP/PhoQ y PmrA/PmrB y en el que RovA y H-NS son piezas centrales. Además se demuestra que el lípido A tiene un papel en la virulencia de YeO8. Por último , se han identificado por primera vez en YeO8 la enzima PmrC, encargada de la adición de fosfoetanolamina al lípido A y la enzima LpxR encargada de la deacilación del lípido A.

<p>Over the past decade, the development of macromolecular drugs based on peptides, proteins and nucleic acids has increased the interest in microparticulate drug delivery, i.e., the delivery of drug systems in the nanometer and micrometer ranges. However, little is known so far about the effect that microparticulate systems have on various tissues after administration. Additionally, the knowledge of mechanisms responsible for the uptake and transport of microparticles across the human intestine is incomplete and requires further investigation to improve both the safety profiles and the efficiency of these drug delivery systems.</p><p>This thesis is comprised of two parts. The first one investigates gene expression responses obtained from DNA arrays in local and distal tissues after microparticulate drug delivery. The second part focuses on the mechanisms responsible for the transport of microparticles across epithelial cells lining the intestine.</p><p>The results presented in the first part demonstrated that gene expression analysis offers a detailed picture of the tissue responses after intramuscular or pulmonary administration of microparticulate drug delivery systems compared to the traditional techniques used for such evaluations. In addition, DNA arrays provided a useful and sensitive tool for the initial characterization and evaluation of both local and distal tissue responses, making it possible to distinguish between gene expression patterns related to each studied delivery system.</p><p>The results presented in the second part demonstrated that the surface properties of the microparticle were important for the extent of transport across an <i>in vitro</i> model of the follicle-associated epithelium (FAE), comprised of intestinal epithelial cells specialized in particle transport (M cells). Another important finding was that the enteropathogen bacterium, <i>Yersinia pseudotuberculosis</i>, induced microparticle transport across the normal intestinal epithelium, represented by Caco-2 cells and excised human ileal tissue. This transport was most probably mediated by an increased capacity for macropinocytosis in the epithelial cells.</p>

Over the past decade, the development of macromolecular drugs based on peptides, proteins and nucleic acids has increased the interest in microparticulate drug delivery, i.e., the delivery of drug systems in the nanometer and micrometer ranges. However, little is known so far about the effect that microparticulate systems have on various tissues after administration. Additionally, the knowledge of mechanisms responsible for the uptake and transport of microparticles across the human intestine is incomplete and requires further investigation to improve both the safety profiles and the efficiency of these drug delivery systems. This thesis is comprised of two parts. The first one investigates gene expression responses obtained from DNA arrays in local and distal tissues after microparticulate drug delivery. The second part focuses on the mechanisms responsible for the transport of microparticles across epithelial cells lining the intestine. The results presented in the first part demonstrated that gene expression analysis offers a detailed picture of the tissue responses after intramuscular or pulmonary administration of microparticulate drug delivery systems compared to the traditional techniques used for such evaluations. In addition, DNA arrays provided a useful and sensitive tool for the initial characterization and evaluation of both local and distal tissue responses, making it possible to distinguish between gene expression patterns related to each studied delivery system. The results presented in the second part demonstrated that the surface properties of the microparticle were important for the extent of transport across an in vitro model of the follicle-associated epithelium (FAE), comprised of intestinal epithelial cells specialized in particle transport (M cells). Another important finding was that the enteropathogen bacterium, Yersinia pseudotuberculosis, induced microparticle transport across the normal intestinal epithelium, represented by Caco-2 cells and excised human ileal tissue. This transport was most probably mediated by an increased capacity for macropinocytosis in the epithelial cells.

In the first part of the thesis, protein-ligand interactions were investigated using the chaperone LcrH, from Yersinia as target protein. The structure of a peptide encompassing the amphipathic domain (residue 278-300) of the protein YopD from Yersinia was determined by NMR in 40% TFE. The structure of YopD278-300 is a well defined α-helix with a β-turn at the C-terminus of the helix capping the structure. This turn is crucial for the structure as peptides lacking the residues involved in the turn are unstructured. NMR relaxation indicates that the peptide is not monomeric. This is supported by intermolecular NOEs found from residue Phe280 to Ile288 and Val292 indicative of a multimeric structure with the helical structures oriented in an antiparallel manner with hydrophobic residues forming the oligomer. The interaction with the chaperone LcrH was confirmed by 1H relaxation experiments and induced chemical shift changes in the peptide Protein-ligand interactions were investigated further in the second paper using a different approach. A wide range of substances were used in screening for affinity against the chaperones PapD and FimC from uropathogenic Escherichia coli using 1H relaxation NMR experiments, surface plasmon resonance and 19F NMR. Fluorine NMR proved to be advantageous as compared to proton NMR as it is straight forward to identify binding ligands due to the well resolved 19F NMR spectra. Several compounds were found to interact with PapD and FimC through induced line-broadening and chemical shift changes for the ligands. Data corroborate well with surface plasmon resonance and proton NMR experiments. However, our results indicate the substances used in this study to have poor specificity for PapD and FimC as the induced chemical shift is minor and hardly no competitive binding is observed. Paper III and IV is an investigation of the structural features of the allergenic 2S albumin Ber e 1 from Brazil nut. Ber e 1 is a 2S albumin previously identified as the major allergen of Brazil nut. Recent studies have demonstrated that endogenous Brazil nut lipids are required for an immune response to occur in vivo. The structure was obtained from 3D heteronuclear NMR experiments followed by simulated annealing using the software ARIA. Interestingly, the common fold of the 2S albumin family, described as a right-handed super helix with the core composed of a helix bundle, is not found in Ber e 1. Instead the C-terminal region is participating in the formation of the core between helix 3, 4 and 5. The dynamic properties of Ber e 1 were investigated using 15N relaxation experiments and data was analyzed using the model-free approach. The analysis showed that a few residues in the loop between helix 2 and 3 experience decreased mobility, compared to the rest of the loop. This is consistent with NOE data as long range NOEs were found from the loop to the core region of the protein. The anchoring of this loop is a unique feature of Ber e 1, as it is not found in any other structures of 2S albumins. Chemical shift mapping of Ber e 1 upon the addition of lipid extract from Brazil nut identified 4 regions in the protein where chemical shift perturbations were detected. Interestingly, all four structural clusters align along a cleft in the structure formed by helix 1-3 on one side and helix 4-5 on the other. This cleft is big enough to encompass a lipid molecule. It is therefore tempting to speculate whether this cleft is the lipid binding epitope in Ber e 1.

Die Infektion mit Salmonella und Yersinia (Y.) enterocolitica über Produkte tierischen Ursprungs stellt nach wie vor ein ungelöstes Problem des gesundheitlichen Verbraucherschutzes dar. Will man diese Zoonoseerreger aus der Lebensmittelkette fernhalten, sind moderne und gut validierte Nachweissysteme erforderlich. Eine Infektion von Schweinen erfolgt überwiegend im Mastbetrieb mit Infektionsdosen, die nur zu einer milden klinischen Symptomatik führen. In den meisten Fällen überstehen die Tiere die Infektion mit Salmonella und Y. enterocolitica und werden zu klinisch inapparenten Keimträgern. Solche Schweine stellen ein Reservoir für die Infektion anderer Tiere und für den Eintrag in die Lebensmittelkette dar. Im Rahmen dieser Arbeit wurden zwei PCR-Methoden zum spezifischen Nachweis von Salmonella und Y. enterocolitica im Schlachtschwein entwickelt und anhand von Probenmaterial aus eigens dafür durchgeführten Infektionsversuchen mit S. Typhimuirum und Y. enterocolitica evaluiert. Beide Methoden mussten sich am diagnostischen Goldstandard für den jeweiligen Erreger messen lassen. Für Salmonella Typhimurium wurde die ISO-Norm 6579 und für Y. enterocolitica die ISO-Norm 10273 zum kulturellen Nachweis ausgewählt. Es konnte eine neue PCR-Methodik zum Salmonella-Nachweis in 14 verschiedenen Gewebeproben etabliert werden, die im Vergleich zum kulturellen Nachweis nach ISO 6579 eine Sensitivität von 100 % und eine Spezifität von 96 % aufweist und die Zeitspanne bis zum spezifischen Nachweis des Erregers um mindestens 24 Stunden reduziert. Die Untersuchungen erfolgten anhand von 420 Gewebeproben aus persistent infizierten Schweinen aus Infektionsversuchen mit S. Typhimurium DT104. Dieses neu entwickelte und validierte PCR-Verfahren wurde mit einem bereits etablierten PCR-Nachweissystem nach RAHN et al. (1992) - wie in der DIN 10135 angegeben - verglichen. Beide PCR-Methoden basieren auf dem invA-Virulenzgen von S. Typhimurium. Im Infektionsversuch konnten zwei Gewebeproben (Caecum und Lnn. Ileocolici) bestimmt werden, durch deren Kombination man mit beiden Nachweismethoden 96 % (23 von 24 Tieren) aller im Versuch infizierten Schweine als Salmonella positiv identifizieren konnte. Erstmals gelang in dieser Arbeit der Nachweis des yopT-Gens bei plasmidtragenden Y. pseudotuberculosis-Stämmen sowie die Bestimmung der Sequenz (European Bioinformatics Institute, Accession-Number: AJ304833). Das yopT-Gen kodiert für ein 35,5 kDa großes Effektor-Protein, das einen zytotoxischen Effekt auf HELA-Zellen und Makrophagen besitzt. Durch den Nachweis des yopT-Gens bei Y. pseudotuberculosis-Stämmen war es erstmals möglich, eine für Y. enterocolitica spezifische, auf dem yopT-Gen des Virulenzplasmids basierende PCR-Methode zu etablieren, die auch die Diskriminierung von Y. pseudotuberculosis-Isolaten gestattet. In einem weiteren Infektionsversuch konnte gezeigt werden, dass es die auf dem yopT-Gen von Y. enterocolitica basierende PCR-Methode erlaubt, Carrier-Tiere mit hoher Sensitivität (100 %) und Spezifität (87 %) innerhalb von 56 Stunden in lymphatischen Geweben zu identifizieren. Besonders geeignet für den Nachweis mit der ISO 10273 und dem neu etablierten yopT PCR-Verfahren waren das Ileum und die Lnn. ileocolici. In dieser Arbeit ist der Versuch gelungen, die Diagnostik für zwei der drei wichtigsten beim Schwein vorkommenden humanen Enteritiserreger zu standardisieren, indem Kombinationen aus Gewebeproben bestimmt wurden, die sowohl für den Nachweis mit der jeweiligen Goldstandard-Methode als auch mit den schnelleren und sensitiveren PCR-Methoden geeignet sind. Die Ergebnisse dieser Arbeit tragen zu einer deutlichen Verbesserung der Diagnostik von Salmonella und Y. enterocolitica beim Schlachtschwein bei. Es bleibt zu hoffen, dass somit der Eintrag dieser Zoonoseerreger in die Lebensmittelkette reduziert und der Verbraucherschutz auf diesem Gebiet beträchtlich verbessert werden kann. / The infection with Salmonella and Yersinia (Y.) enterocolitica through foodstuff from slaughter pigs is one of the major problems of hygienic consumer protection. To avoid the contamination of products from pig industry modern and well validated bacteriological identification systems are necessary. An infection predominantly occurs in the fattening pens, showing mild clinical symtoms only. The majority of infected pigs overcome the infection with Salmonella and Y. enterocolitica and become clinically inapparent carrier pigs. Those pigs are a reservoir for the contamination of other animals and pork products. In the context of this work two PCR-assays for the specific detection of Salmonella and Y. enterocolitica have been developed and validated on the basis of tissue samples from experimentally infected pigs. Both methods have been compared with the classical bacterial culture. Two international standards were used for bacterial detection: ISO 6579 for S. Typhimurium and ISO 10273 for pathogenic Y. enterocolitica. It was possible to establish a new PCR-assay for the specific detection of Salmonella in 14 different tissues of experimentally infected pigs. In comparison to the standard ISO 6579 a sensitivity of 100 % and a specificity of 96 % were calculated for the PCR-assay. The investigations were carried out with 420 tissue samples of persistently infected pigs that have been experimentally infected with S. Typhimurium. By using the PCR-method for the detection of Salmonella in positive tissue samples, the detection-time could be reduced around 24 hours. The new PCR-assay developed and validated in this work, was compared with the PCR-method described in DIN 10135, which is based on the studies of RAHN et al. (1992). Both methods were based on the invA-virulence gene of S. Typhimurium. A combination of samples from ileocolic lymph node and caecum was particularly suitable for the detection of 96 % of the experimentally infected pigs (23 off 24 animals) with the PCR-assay and the culture method. In this study, the yopT-gene was proved for the first time to be present in plasmid bearing Y. pseudotuberculosis-Isolates, and the nucleotid sequence was determined (European Bioinformatics Institute, Accession-Number: AJ304833). YopT encodes a 35.5 kDa effector protein (YopT), which induces a cytotoxic effect in HeLa cells and macrophages. This finding was used to develop a specific PCR-assay for the detection of pathogenic Y. enterocolicica strains and the discrimination from pathogenic Y. pseudotuberculosis strains. Embedded in an experimental Y. enterocolitica-infection-model in swine, it was shown that the yopT PCR-assay is suitable for the detection of pathogenic Y. enterocolitica in lymphatic tissue of persistently infected pigs. The yopT PCR-method shows a sensitivity of 100 % and a specificity of 87 % in lymphatic tissue. By the use of the PCR-assay, the detection of Y. enterocolitica was possible within 56 hours. A combination of specimens from the ileum and ileocolic lymph nodes was most suitable for the detection of pathogenic Y. enterocolitica in slaughter pigs with the ISO-Standard 10273 and the yopT PCR. This investigation succeeded in standardizing the identification of two of the three most important zoonotic agents for human enteric disease. The standardization was achived by the use of a combination of samples suitable for the identification with both, the “Goldstandard” and the specific and rapid PCR-method. The results of this work offer a better identification of Salmonella and Y. enterocolitica in slaughter pigs in the future. Based on these facts it is possible to avoid contamination of food products from slaughter pigs and to improve the hygienic consumer protection considerably.

Innate immunity is the first line of defense against invading pathogens. Vertebrate innate immunity provides both initial protection, and activates adaptive immune responses, including memory. As a result, the study of innate immune signaling is crucial for understanding the interactions between host and pathogen. Unlike mammals, the insect Drosophila melanogasterlack classical adaptive immunity, relying on innate immune signaling via the Toll and IMD pathways to detect and respond to invading pathogens. Once activated these pathways lead to the rapid and robust production of a variety of antimicrobial peptides. These peptides are secreted directly into the hemolymph and assist in clearance of the infection. The genetic and molecular tools available in the Drosophila system make it an excellent model system for studying immunity. Furthermore, the innate immune signaling pathways used by Drosophilashow strong homology to those of vertebrates making them ideal for the study of activation, regulation and mechanism. Currently a number of questions remain regarding the activation and regulation of both vertebrate and insect innate immune signaling. Over the past years many proteins have been implicated in mammalian and insect innate immune signaling pathways, however the mechanisms by which these proteins function remain largely undetermined. My work has focused on understanding the molecular mechanisms of innate immune activation in Drosophila. In these studies I have identified a number of novel protein/protein interactions which are vital for the activation and regulation of innate immune induction. This work shows that upon stimulation the Drosophila protein IMD is cleaved by the caspase-8 homologue DREDD. Cleaved IMD then binds the E3 ligase DIAP2 and promotes the K63-polyubiquitination of IMD and activation of downstream signaling. Furthermore the Yersinia pestis effector protein YopJ is able to inhibit the critical IMD pathway MAP3 kinase TAK1 by serine/threonine-acetylation of its activation loop. Lastly TAK1 signaling to the downstream Relish/NF-κB and JNK signaling pathways can be regulated by two isoforms of the TAB2 protein. This work elucidates the molecular mechanism of the IMD signaling pathway and suggests possible mechanisms of homologous mammalian systems, of which the molecular details remain unclear.

Yersinia pestis, the causative agent of plague, specializes in causing dense bacteremia following intradermal deposition of a small number of bacteria by the bite of an infected flea. This robust invasiveness requires the ability to evade containment by the innate immune system. Of the various mechanisms employed by Y. pestis to subvert the innate immune response and to proliferate rapidly in mammalian tissue, only a few are well-characterized. Here, I present two complementary genetic analyses of Y. pestis adaptations to the mammalian environment. In the first, genome-wide fitness profiling for Y. pestis by Tn-seq demonstrates that the bacterium has adapted to overcome limitation of diverse nutrients during mammalian infection. In the second, a series of combinatorial targeted mutations disentangles apparent functional redundancy among the effectors of the Y. pestis type III secretion system, and we report that YpkA, YopT, and YopJ contribute to virulence in mice. We have also begun to investigate a novel relationship between Y. pestis and mammalian platelets, a highly abundant cell type in plasma. I present evidence that Y. pestis has evolved specific mechanisms to interfere with platelet activation, likely in order to evade immune responses and promote maintenance of bacteremia by undermining platelet thrombotic and innate immune functions. The principles guiding this work – systematic genetic analysis of complex systems, coupled with rational modification of in vitro assays to more closely mimic the in vivo environment – are a generalizable approach for increasing the efficiency of discovering new virulence determinants in bacterial pathogens.

<p>This dissertation discusses molecular analyses of dental and skeletal material from victims of the Black Death with the goal of both identifying and describing the evolutionary history of the causative agent of the pandemic. Through this work, <em>Yersinia pestis</em> DNA was successfully identified in skeletal material from a well-documented Black Death burial ground, the East Smithfield cemetery of London, England (1348 -1350). The thesis presents two major methodological advancements in the field of ancient pathogen research: 1) it describes a protocol to confirm the authenticity of ancient pathogen DNA, thus circumventing tenuous issues relating to modern contaminants, and 2) it demonstrates the applicability of DNA capture methods to isolate ancient pathogen DNA from its complex metagenomic background common to ancient DNA extracts. The dissertation is comprised of three publications. The first, submitted to the journal BMC Systems Biology, describes a computational software program for oligo design that has applications to PCR, and capture techniques such as primer extension capture (PEC) and array-based capture. The second manuscript, published in the Proceedings of the National Academy of Sciences, presents a novel capture technique for retrieval of the <em>pestis</em>-specific pPCP (9.6kb) plasmid which can be used as a simple screening tool for the presence of <em>Y. pestis</em> DNA in ancient remains, and describes a method for authenticating ancient pathogen DNA. The third paper, published in the journal Nature, presents a draft genome of <em>Yersinia pestis </em>isolated from the individuals of the East Smithfield collection, thus presenting the first ancient pathogen genome in published literature. Evolutionary changes as they relate to phylogenetic placement and the evolution of virulence are discussed within an anthropological framework.</p> / Doctor of Philosophy (PhD)