This thesis describes a series of three experiments designed to estimate the nutritional cost of the immune response to the gastrointestinal nematodes Trichostrongylus colubriformis and Teladorsagia circumcincta in sheep. For each experiment, animals were allocated hierarchically by liveweight into one of four groups that were either infected (group IF), similarly infected and concurrently immuno-suppressed with weekly intramuscular injections of 1.3mg kg liveweight (LW)⁻¹ of methylprednisolone acetate (group ISIF), immunosuppressed only (group IS) or remained as controls (group C). Body composition of all animals was estimated using x-ray computer tomography prior to infection and at the conclusion of each study with bodyweight and faecal nematode egg counts (FEC; eggs gram⁻¹ of fresh faeces (epg)) measured along with blood samples taken for the determination of levels of serum proteins, phosphate and antibodies. In the first trial (Chapter 3), the nutritional cost of both the acquisition and maintenance of immunity to gastro-intestinal nematodes was investigated using immunologically naive 5-month-old lambs and immunologically competent 17-month-old ewes during infection with 2,000 and 4,000 L3 infective T. colubriformis larvae d⁻¹, respectively (80 L3 T. colubriformis larvae kgLW⁻¹ d⁻¹). Profiles of FEC and comparative worm burdens at slaughter indicated an effective immune response was maintained in IF ewes and developed in IF lambs while successfully suppressed in both ISIF lambs and ISIF ewes and was confirmed by serum antibody titres. The typical reduction in voluntary feed intake as a consequence of infection was observed in IF lambs (0.30, p<0.001) but not in IF ewes, ISIF lambs or ISIF ewes, and appeared to be associated with L3 IgA. Gross efficiency of use of metabolizable energy (ME) for net energy (NE) deposition was reduced by 0.20 in lambs during acquisition of immunity and by 0.16 in ewes maintaining an established immunity. Infection in immuno-suppressed animals reduced efficiency by 0.05 and 0.15 for lambs and ewes. These findings allowed the hypothesis that the reduction in feed intake and nutrient utilization in young parasitized sheep is caused by physiological signalling associated with the acquisition phase of the host immune response to infection, rather than simply the damage caused by the parasite per se. The second trial (Chapter 4) investigated the influence of metabolizable protein (MP) supply on the metabolic disturbances associated with the acquisition phase of the immune response during infection with 2,000 L3 T. colubriformis d⁻¹. Groups of lambs were offered either a low protein (L; 62g MP kgDM⁻¹) or high protein diet (H; 95g MP kgDM⁻¹). Patterns of total daily egg excretion indicated that an effective immune response was developed in HIF, but not LIF, HISIF nor LISF and was confirmed by comparative worm burdens. The proportionate reduction in feed intake in immunologically normal animals was reduced through the provision of additional protein, being 0.12 in HIF and 0.23 in LIF. Regardless of diet, infection did not cause a reduction in feed intake in immuno-suppressed animals (p>0.05). Infection proportionately reduced the gross efficiency of ME utilization in immunologically normal animals by 0.23 in HIF (p=0.09) and by 0.51 in LIF (p=0.01), but not in immuno-suppressed animals. Immuno-suppression did not suppress serum L3 IgA levels in seven of the eight HISIF and four of the eight LISIF animals. Furthermore, only four out of the eight immunologically normal animals from both the HIF and LIF groups displayed an L3 IgA response. Consequently, regardless of immunosuppression treatment, animals were termed as IgA responders (HR or LR) or non-responders (HN or LN). Feed intake was proportionately reduced from day 22 by 0.15 in HR (p=0.03) and by 0.32 in LR (p=0.01), but was not significantly reduced in HN or LN. Gross efficiency of ME utilization was significantly reduced for LN animals only, being proportionately 0.59 (p<0.01). These findings allowed the conclusion that additional MP reduced the consequence of immunological signalling that was displayed in reduced feed intake and in nutrient utilization, both of which appeared to be associated with an IgA response. It is hypothesized that the lessening of nutritional disturbance observed in high protein and immuno-suppressed animals could be a consequence of altered physiological signalling during the immunological cascade. The third trial (Chapter 5) utilized lambs infected with the abomasal parasite T. circumcincta to explore the possibility that the reduction in feed intake and nutrient utilization is a universal phenomenon of the acquisition phase of the immune response to nematode parasites inhabiting different organs along the gastrointestinal tract. In addition, immunological changes at the site of parasite infestation in the abomasal mucosa were measured from serial biopsy tissue samples taken from a further twelve animals that were surgically fitted with an abomasal cannula and either infected (CIF) or concurrently infected and immuno-suppressed as described previously (CISIF). The development of immunity in IF animals was accompanied by a 0.17 proportional decrease in feed intake between days 15 to 28 of infection (p<0.05) and a 0.20 proportional reduction in nutrient utilization (p=0.07), none of which were observed in ISIF animals. While FEC and worm burdens indicated successful immunosuppression in ISIF animals, both serum IgA and total antibody production were not reduced. The development of immunity in CIF was reflected in an increase in both mast cells and globule leukocytes in serial abomasal tissue biopsies, both of which were reduced in CISIF (p<0.01 for both). In serial biopsy tissue, immuno-suppression did prevent a rise in tissue IgA that was apparent in CIF animals (p<0.01) although these changes were not reflected in serum IgA levels. It appears that the alleviation of the reduction in feed intake and nutrient utilization in young lambs through the use of corticosteroid induced immuno-suppression may be a universal phenomenon for both intestinal and abomasal parasites, but the association with and/or role of IgA during infection with T. circumcincta is unclear. In summary, the reduction in feed intake and nutrient utilization in sheep during infection with both the abomasal nematode T. circumcincta and the small intestine nematode T. colubriformis appears to be associated with a component(s) of the acquisition phase of the host immune response, rather than, as conventionally assumed, the direct mechanical damage of the parasite per se. It is hypothesised that the nutritional disturbance as a consequence of infection in young lambs may be the result of pro-inflammatory cytokines involved in immunological signalling that may also be associated with the production of IgA, the effects of which can be reduced through the provision of adequate MP. These studies provide evidence that the immune response to gastrointestinal parasites is nutritionally costly to the animal and have implications for application of manipulations that are intended to promote the development of a strong immune reaction in high producing animals.

This thesis describes a series of three experiments designed to estimate the nutritional cost of the immune response to the gastrointestinal nematodes Trichostrongylus colubriformis and Teladorsagia circumcincta in sheep. For each experiment, animals were allocated hierarchically by liveweight into one of four groups that were either infected (group IF), similarly infected and concurrently immuno-suppressed with weekly intramuscular injections of 1.3mg kg liveweight (LW)⁻¹ of methylprednisolone acetate (group ISIF), immunosuppressed only (group IS) or remained as controls (group C). Body composition of all animals was estimated using x-ray computer tomography prior to infection and at the conclusion of each study with bodyweight and faecal nematode egg counts (FEC; eggs gram⁻¹ of fresh faeces (epg)) measured along with blood samples taken for the determination of levels of serum proteins, phosphate and antibodies. In the first trial (Chapter 3), the nutritional cost of both the acquisition and maintenance of immunity to gastro-intestinal nematodes was investigated using immunologically naive 5-month-old lambs and immunologically competent 17-month-old ewes during infection with 2,000 and 4,000 L3 infective T. colubriformis larvae d⁻¹, respectively (80 L3 T. colubriformis larvae kgLW⁻¹ d⁻¹). Profiles of FEC and comparative worm burdens at slaughter indicated an effective immune response was maintained in IF ewes and developed in IF lambs while successfully suppressed in both ISIF lambs and ISIF ewes and was confirmed by serum antibody titres. The typical reduction in voluntary feed intake as a consequence of infection was observed in IF lambs (0.30, p<0.001) but not in IF ewes, ISIF lambs or ISIF ewes, and appeared to be associated with L3 IgA. Gross efficiency of use of metabolizable energy (ME) for net energy (NE) deposition was reduced by 0.20 in lambs during acquisition of immunity and by 0.16 in ewes maintaining an established immunity. Infection in immuno-suppressed animals reduced efficiency by 0.05 and 0.15 for lambs and ewes. These findings allowed the hypothesis that the reduction in feed intake and nutrient utilization in young parasitized sheep is caused by physiological signalling associated with the acquisition phase of the host immune response to infection, rather than simply the damage caused by the parasite per se. The second trial (Chapter 4) investigated the influence of metabolizable protein (MP) supply on the metabolic disturbances associated with the acquisition phase of the immune response during infection with 2,000 L3 T. colubriformis d⁻¹. Groups of lambs were offered either a low protein (L; 62g MP kgDM⁻¹) or high protein diet (H; 95g MP kgDM⁻¹). Patterns of total daily egg excretion indicated that an effective immune response was developed in HIF, but not LIF, HISIF nor LISF and was confirmed by comparative worm burdens. The proportionate reduction in feed intake in immunologically normal animals was reduced through the provision of additional protein, being 0.12 in HIF and 0.23 in LIF. Regardless of diet, infection did not cause a reduction in feed intake in immuno-suppressed animals (p>0.05). Infection proportionately reduced the gross efficiency of ME utilization in immunologically normal animals by 0.23 in HIF (p=0.09) and by 0.51 in LIF (p=0.01), but not in immuno-suppressed animals. Immuno-suppression did not suppress serum L3 IgA levels in seven of the eight HISIF and four of the eight LISIF animals. Furthermore, only four out of the eight immunologically normal animals from both the HIF and LIF groups displayed an L3 IgA response. Consequently, regardless of immunosuppression treatment, animals were termed as IgA responders (HR or LR) or non-responders (HN or LN). Feed intake was proportionately reduced from day 22 by 0.15 in HR (p=0.03) and by 0.32 in LR (p=0.01), but was not significantly reduced in HN or LN. Gross efficiency of ME utilization was significantly reduced for LN animals only, being proportionately 0.59 (p<0.01). These findings allowed the conclusion that additional MP reduced the consequence of immunological signalling that was displayed in reduced feed intake and in nutrient utilization, both of which appeared to be associated with an IgA response. It is hypothesized that the lessening of nutritional disturbance observed in high protein and immuno-suppressed animals could be a consequence of altered physiological signalling during the immunological cascade. The third trial (Chapter 5) utilized lambs infected with the abomasal parasite T. circumcincta to explore the possibility that the reduction in feed intake and nutrient utilization is a universal phenomenon of the acquisition phase of the immune response to nematode parasites inhabiting different organs along the gastrointestinal tract. In addition, immunological changes at the site of parasite infestation in the abomasal mucosa were measured from serial biopsy tissue samples taken from a further twelve animals that were surgically fitted with an abomasal cannula and either infected (CIF) or concurrently infected and immuno-suppressed as described previously (CISIF). The development of immunity in IF animals was accompanied by a 0.17 proportional decrease in feed intake between days 15 to 28 of infection (p<0.05) and a 0.20 proportional reduction in nutrient utilization (p=0.07), none of which were observed in ISIF animals. While FEC and worm burdens indicated successful immunosuppression in ISIF animals, both serum IgA and total antibody production were not reduced. The development of immunity in CIF was reflected in an increase in both mast cells and globule leukocytes in serial abomasal tissue biopsies, both of which were reduced in CISIF (p<0.01 for both). In serial biopsy tissue, immuno-suppression did prevent a rise in tissue IgA that was apparent in CIF animals (p<0.01) although these changes were not reflected in serum IgA levels. It appears that the alleviation of the reduction in feed intake and nutrient utilization in young lambs through the use of corticosteroid induced immuno-suppression may be a universal phenomenon for both intestinal and abomasal parasites, but the association with and/or role of IgA during infection with T. circumcincta is unclear. In summary, the reduction in feed intake and nutrient utilization in sheep during infection with both the abomasal nematode T. circumcincta and the small intestine nematode T. colubriformis appears to be associated with a component(s) of the acquisition phase of the host immune response, rather than, as conventionally assumed, the direct mechanical damage of the parasite per se. It is hypothesised that the nutritional disturbance as a consequence of infection in young lambs may be the result of pro-inflammatory cytokines involved in immunological signalling that may also be associated with the production of IgA, the effects of which can be reduced through the provision of adequate MP. These studies provide evidence that the immune response to gastrointestinal parasites is nutritionally costly to the animal and have implications for application of manipulations that are intended to promote the development of a strong immune reaction in high producing animals.

<p>The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance.</p><p>Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe,</p><p>DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast.</p><p>In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results.</p><p>Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis</p><p>than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.</p>

<p>B cell lymphomas and leukemias are heterogeneous tumors with different cellular origins. Analysis of immunoglobulin (Ig) genes enables insight into the B cell progenitor, as Ig somatic hypermutation correlates with antigen-related B cell transit through the germinal center (GC). Also, restricted Ig variable heavy chain (V_H) gene repertoires in B cell malignancies could imply antigen selection during tumorigenesis. The length of telomeres has been shown to differ between GC B cells and pre/post-GC B cells, possibly representing an alternative angle to investigate B cell tumor origin. </p><p>Mantle cell lymphoma (MCL), previously postulated to derive from a naïve, pre-GC B cell, was shown to have an Ig-mutated subset (18/110 MCLs, 16%), suggestive of divergent cellular origin and GC exposure. Another subset of MCL (16/110, 15%), characterized by V_H3-21/V_λ3-19 gene usage, alludes to a role for antigen(s) in pathogenesis, also possible for hairy cell leukemia (HCL) in which the V_H3-30 gene (6/32, 19%) was overused. HCL consisted mainly of Ig-mutated cases (27/32, 84%) with low level intraclonal heterogeneity, contrasting with the proposed post-GC origin, for both Ig-mutated and Ig-unmutated HCLs. For MCL and HCL, derivation from naïve or memory marginal zone B cells which may acquire mutations without GC transit are tempting speculations, but currently little is known about this alternative immunological pathway. Heavily mutated Ig genes without intraclonal heterogeneity were demonstrated in lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia (13/14, 93%), confirming that the precursor cell was transformed after GC affinity maturation. Telomere length analysis within 304 B cell tumors revealed variable lengths; shortest in the Ig-unmutated subset of chronic lymphocytic leukemia, longest in the GC-like subtype of diffuse large B cell lymphoma, and homogeneous in MCL regardless of Ig mutation status. However, telomere length is complex with regard to GC-related origin.</p><p>In summary, this thesis has provided grounds for speculation that antigens play a role in MCL and HCL pathogenesis, although the potential antigens involved are currently unknown. It has also enabled a more informed postulation about the cellular origin of B cell tumors, which will ultimately enhance understanding of the biological background of the diseases. </p>

Der "Leukocyte Receptor Complex" (LRC) ist ein DNA-Sequenzabschnitt auf dem Chromosom 19 des Menschen, der eine Länge von über 900.000 Basenpaaren umfaßt. In diesem Chromosomenabschnitt ist eine Vielzahl von Genen lokalisiert, die für die Funktion verschiedener weißer Blutzellen (Leukozyten) von entscheidender Bedeutung sind. Bei den aus diesen Genen synthetisierten Proteinen (Eiweißen) handelt es sich um Strukturen, die auf der Oberfläche dieser Zellen lokalisiert sind und zur Interaktion der Leukozyten mit ihrer Umgebung dienen. Diese auch als Rezeptoren bezeichneten Proteine können mit Oberflächenproteinen auf anderen Körperzellen wechselwirken und daraus resultierende Signale in das Innere der Blutzelle weiterleiten. <br /> In der vorliegenden Doktorarbeit wurde der LRC im Detail untersucht. Hierzu wurde zunächst der gesamte Chromosomenabschnitt aus kleineren, einander überlappenden DNA-Fragmenten rekonstruiert. Aufgrund der in diesen DNA-Fragmenten enthaltenen DNA-Sequenzen war es möglich, den gesamten Chromosomenabschnitt ähnlich einem Puzzle zusammenzusetzen. Die anschließende Analyse des LRC zeigte, daß sich dieser in drei Bereiche, sogenannte Cluster, unterteilen läßt. Diese Cluster sind dadurch gekennzeichnet, daß in ihnen jeweils nur Gene eines Rezeptortyps vorkommen. Hierbei handelt es sich um ‚immunoglobulin-like transcript′ -Gene (ILT) und ‚killer cell Ig-like receptor′-Gene (KIR). Die KIR- und ILT-Cluster werden von weiteren stammesgeschichtlich verwandten Genen unterbrochen und flankiert. Je nach Individuum können im LRC bis zu 31 solcher verwandten Rezeptorgene lokalisiert sein. Auf der Grundlage der Kartierungsdaten und von Daten des humanen Genomprojekts war es zudem möglich, evolutionäre Untersuchungen zur Entwicklung des LRC durchzuführen. Dabei wurde eine Hypothese zur Entstehung des LRC entworfen und zu anderen Spezies in Beziehung gesetzt. <br /> Im zweiten Teil der Arbeit habe ich aufbauend auf der sogenannten HRCA-Methode eine Technik entwickelt, die es erlaubt kleinste Unterschiede zwischen DNA-Sequenzen, sogenannte Einzelbasenpaaraustausche, nachzuweisen. Die entwickelte Methode kann verwendet werden, um sehr ähnliche DNA-Sequenzen, wie z.B. verschiedene KIR-Sequenzen, zu unterscheiden und ihre Menge zu bestimmen. Sie ist außerdem geeignet Mutationen, die mit bestimmten Krankheiten assoziiert sind, nachzuweisen und könnte somit in der Diagnostik Anwendung finden. / The Leukocyte Receptor Complex (LRC) is a DNA region on human chromosome 19 with a length of approximately 900.000 base pairs. A number of genes, which are located in this chromosomal region, are known to be important for the function of some types of white blood cells (leukocytes). The products of theses genes are proteins, which are located on the surface of these cells and enable them to interact with their environment. These proteins are also called receptors. They can bind to cell surface proteins on other cells and transmit resulting signals into the leukocyte. <br /> During my work I analyzed the chromosomal organization of the LRC in detail. To do so, I reconstructed the whole chromosomal region from smaller overlapping DNA fragments. Due to the DNA sequences contained within these fragments it was possible to put the whole chromosomal region together like a puzzle. The following analyses of the LRC showed that it is mainly composed of three regions, so called clusters. These clusters are characterised by the presence of only one receptor family. These are the immunoglobulin-like transcripts (ILTs) and the killer cell Ig-like receptors (KIR) respectively. In the LRC the KIR- and ILT-Clusters are flanked by additional receptor genes, which are evolutionary related to KIRs and ILTs. The number of receptor genes in the LRC varies between individuals, their can be up to 31 genes on each chromosome. <br /> On the basis of the data obtained in this work as well as data from the human genome project it was also possible to draw conclusions concerning the evolutionary development of the LRC. I developed a hypothesis of the origin of the LRC and discussed this in comparison to other species. <br /> In the second part of my thesis I developed a new technique based on the so-called ’hyper-branched rolling circle amplification′ (HRCA). This technique allows the detection of small differences between two or more DNA molecules, so called ’single nucleotide polymorphisms′ (SNPs). With this newly developed method it is possible to distinguish very similar variants of a gene, e.g. two KIR sequences, and to determine their relative concentration. The method can also be used to detect mutations, which are associated with certain diseases and could therefore be used for diagnostic purposes.

The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance. Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe, DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast. In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results. Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.

B cell lymphomas and leukemias are heterogeneous tumors with different cellular origins. Analysis of immunoglobulin (Ig) genes enables insight into the B cell progenitor, as Ig somatic hypermutation correlates with antigen-related B cell transit through the germinal center (GC). Also, restricted Ig variable heavy chain (VH) gene repertoires in B cell malignancies could imply antigen selection during tumorigenesis. The length of telomeres has been shown to differ between GC B cells and pre/post-GC B cells, possibly representing an alternative angle to investigate B cell tumor origin. Mantle cell lymphoma (MCL), previously postulated to derive from a naïve, pre-GC B cell, was shown to have an Ig-mutated subset (18/110 MCLs, 16%), suggestive of divergent cellular origin and GC exposure. Another subset of MCL (16/110, 15%), characterized by VH3-21/Vλ3-19 gene usage, alludes to a role for antigen(s) in pathogenesis, also possible for hairy cell leukemia (HCL) in which the VH3-30 gene (6/32, 19%) was overused. HCL consisted mainly of Ig-mutated cases (27/32, 84%) with low level intraclonal heterogeneity, contrasting with the proposed post-GC origin, for both Ig-mutated and Ig-unmutated HCLs. For MCL and HCL, derivation from naïve or memory marginal zone B cells which may acquire mutations without GC transit are tempting speculations, but currently little is known about this alternative immunological pathway. Heavily mutated Ig genes without intraclonal heterogeneity were demonstrated in lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia (13/14, 93%), confirming that the precursor cell was transformed after GC affinity maturation. Telomere length analysis within 304 B cell tumors revealed variable lengths; shortest in the Ig-unmutated subset of chronic lymphocytic leukemia, longest in the GC-like subtype of diffuse large B cell lymphoma, and homogeneous in MCL regardless of Ig mutation status. However, telomere length is complex with regard to GC-related origin. In summary, this thesis has provided grounds for speculation that antigens play a role in MCL and HCL pathogenesis, although the potential antigens involved are currently unknown. It has also enabled a more informed postulation about the cellular origin of B cell tumors, which will ultimately enhance understanding of the biological background of the diseases.

Basigin and Embigin are members of the immunoglobulin superfamily that function as cell adhesion molecules. Studies of Basigin null mice revealed reproductive sterility, increased pain sensitivity, and blindness. It is thought that the mechanism causing blindness involves misexpression of monocarboxylate transporter 1 (MCT1) in the absence of Basigin. It is known that the transmembrane domain of Basigin interacts with MCT1. In the absence of Basigin, MCT1 does not localize to the plasma membrane of expressing cells and photoreceptor function is disrupted. Studies of the Basigin null mouse brain suggest that MCT1 is properly expressed, which suggests a separate mechanism causes the increased pain sensitivity in these animals, and also that a different protein directs MCT1 to the plasma membrane of expressing cells in mouse brain. Embigin is known to interact with MCT2 in neurons and with MCT1 in erythrocytes. It is not known, however, if Embigin normally interacts with MCT1 in the mouse brain or if Embigin acts to compensate for the lack of Basigin in the Basigin null animals. Therefore, the purpose of this study was to determine if Embigin normally interacts with MCT1, 2, or 4 in the mouse brain and if so, whether the interaction is similar to that between Basigin and MCT1. Expression of Basigin, Embigin, MCT1, MCT2, and MCT4 in mouse brain was assessed via immunoblotting and immunohistochemical analyses. In addition, recombinant protein probes corresponding to the Embigin transmembrane domain were generated for ELISA binding assays using endogenous mouse brain MCTs. It was determined that the proteins in question are rather ubiquitously expressed throughout the mouse brain, and that the cell adhesion molecules Basigin and Embigin may be co-expressed in the same cells as the MCT2 and MCT4 transporter proteins. In addition, it was determined that the Embigin transmembrane domain does not interact with the MCTs. The data therefore suggest that MCTs do not require Basigin or Embigin for plasma membrane expression in mouse brain.

Mass spectrometry (MS) is a power analytical tool which is capable of analyzing biomolecules in great detail, both structurally and quantitatively. With regards to glycans, special considerations regarding sample preparation are necessary in order to achieve reproducible identification and relative quantification of these analytes. A workflow for isolation at the glycopeptide level and subsequent detection at the glycan level with phenylhydrazine, demonstrated that monoclonal antibodies (mAbs) containing a specific amino acid mutation were able to express approximately an additional 50% of the α2,6 disialylated glycan compared to their non-mutant analogues. In a second experiment using mAbs, an azide modified glycan (Ac4ManAz) was introduced both metabolically and enzymatically during mAb production. This glycan is a precursor in the sialic acid pathway and the azide moiety allows for specific chemistry post-production including the potential for highly specific enrichment. The results of this workflow demonstrated that [100 μM] of Ac4ManAz precursor added to the cell media was necessary for metabolic expression. More complex samples however, may contain multiple sites of glycosylation. To conserve the site of attachment, these molecules are often studied at the glycopeptide level, and require enrichment of glycopeptides to improve the lower signal intensity observed in the presence of co-eluting peptides. Carboxymethyl chitosan (CMCH) as well as amine-functionalized magnetic-nanoparticles (MNP) were developed as novel materials for this purpose. CMCH is naturally occurring, and therefore is cost-effective and readily available. In a 12 protein mixture CMCH demonstrated the bulk enrichment of glycopeptides yielding an approximately 20% higher enrichment of sialylated species as compared to a commercially available glycopeptide kit through the use of tandem mass tags for relative quantification. In the same approach, amine functionalized MNP were produced and used to enrich glycopeptides from tryptic digests. This approach was fast (about 10 mins) and quantitatively demonstrated improved retention for sialylated species. Examples of these techniques and their applications are reported in this work. / October 2015

Poor water quality is a global health concern affecting one billion people around the world. It is important to monitor water sources in order to maintain the quality of our drinking water and to avoid disease outbreaks. Targeting Escherichia coli as a faecal indicator is a widely used procedure, but the current methods are time consuming and not adequate to prevent spreading of faecal influence.   This Master thesis demonstrates the development of a near infrared fluorescence flow cytometer sensor system targeting Escherichia coli, using fluorescently labeled chicken IgY antibodies. The near infrared light was chosen to avoid fluorescence from blue-green algae that are present in the water source.   The hardware was developed with a 785  nm laser line to detect Alexa Fluor 790 labeled antibodies, using a photomultiplier tube or two different CMOS cameras. The antibodies were labeled using a commercial labeling kit, and evaluated using antibody binding assays and the developed hardware.   The IgY antibodies were successfully labeled with Alexa Fluor 790 and the function was maintained after the labeling process. The result demonstrates the principles of the sensor system and how it solved to the problem with fluorescence from blue-green algae. An aperture was used to overcome the suboptimal laser and filter setup, and to increase the sensitivity of the system. However, only a small fraction of the cells could be detected, due to challenges with the focal depth and loss of sensitivity in the photomultiplier tube at near infrared wavelengths. Further development is required to create a working product.