Academic literature on the topic 'Cell hybridisation'

Multicolour fluorescence in situ hybridisation (FISH) analysis of interphase nuclei in cleavage stage human embryos has highlighted a high incidence of postzygotic chromosomal mosaicism, including both aneuploid and ploidy mosaicism. Indeed, some embryos appear to have a chaotic chromosomal complement in a majority of nuclei, suggesting that cell cycle checkpoints may not operate in early cleavage. Most of these studies, however, have only analysed a limited number of chromosomes (3–5), making it difficult to distinguish FISH artefacts from true aneuploidy. We now report analysis of 11 chromosomes in five sequential hybridisations with standard combinations of two or three probes and minimal loss of hybridisation efficiency. Analysis of a series of arrested human embryos revealed a generally consistent pattern of hybridisation on which was superimposed frequent deletion of one or both chromosomes of a specific pair in two or more nuclei indicating a clonal origin and continued cleavage following chromosome loss. With a binucleate cell in a predominantly triploid XXX embryo, the two nuclei remained attached during preparation and the chaotic diploid/triphoid status of every chromosome analysed was the same for each nucleus. Furthermore, in each hybridisation the signals were distributed as a mirror-image about the plane of attachment, indicating premature decondensation during anaphase consistent with a lack of checkpoint control.

This paper presents the development of a control strategy for a fuel cell and supercapacitor hybrid power system for application in a city driving bus. This aims to utilise a stable fuel cell power output during normal operation whilst allowing variations to the power output based on the supercapacitor state-of-charge. This provides flexibility to the operation of the system, protection against over-charge and under-charge of the supercapacitor and gives flexibility to the sizing of the system components. The proposed control strategy has been evaluated using validated Simulink models against real-world operating data collected from a double-decker bus operating in London. It was demonstrated that the control strategy was capable of meeting the operating power demands of the bus and that a wide range of degrees of hybridisation are viable for achieving this. Comparison between the degree of hybridisation proposed in this study and those in operational fuel cell (FC) hybrid buses was carried out. It was found that the FC size requirement and FC variation can be significantly reduced through the use of the degree of hybridisation identified in this study.

Fluorescence in situ hybridisation has been used to follow replication of the short arm of human chromosome 11 using chromosome anomalies to distinguish the maternally-and paternally-derived homologues. The temporal difference in replication timing within and between chromosomes has been estimated by combining S phase detection with dual colour fluorescence in situ hybridisation. Proximal regions of 11p, including the WT1 gene, tend to replicate earlier on the maternally-derived chromosome than on the paternally-derived homologue. More distal parts of 11p (including the IGF2 gene) have the opposite imprint. The average difference in replication timing between homologous loci in the population of cells is small compared to the differences between loci along a single chromosome. The imprint is not strictly adhered to since many nuclei have hybridisation patterns opposite to the trend within the population. The nature of the imprinting signal has been investigated. Absolute replication time, but not the imprint, was affected by azacytidine, an inhibitor of DNA methylation. The replication imprint was modified by treatments that inhibit histone deacetylation. We suggest that replication imprinting reflects differences in chromatin structure between homologues.

Abstract Quantum dots (QDs) are fluorescent semiconductor nanocrystals (2–10-nm core diameter) possessing the unique properties of extremely high fluorescence efficiency, lack of photobleaching and long fluorescence lifetime, making them an ideal tool for bioimaging. We have developed a novel technique for in situ hybridisation (ISH) using biotinylated oligonucleotides conjugated to streptavidin coated QD, and used them in this study to label bone marrow trephine samples. 50-mer long oligonucleotide probes were conjugated to QDs prior to ISH and conjugation efficiency was demonstrated by gel electrophopresis. ISH conditions and molar ratio of QDs to probe were optimised using a polyT probe. Images were captured using a CRI Nuance spectral imaging system and signal intensity was semi-quantitated using IPLab software. Specific oligonucleotide hybridisation was demonstrated using a probe for myeloperoxidase (MPO) in 40 bone marrow sections infiltrated by acute myeloid leukaemia (AML), acute lymphoblastic leukaemia (ALL), chronic myeloid leukaemia (CML) as well as reactive bone marrow. In each case hybridisation signal was consistent with the distribution of MPO by standard immunohistochemistry - MPO was strongly expressed by myeloid blasts and absent in lymphoid blasts; in CML, most, but not all, cells were positive for MPO, in comparison to many fewer positive cells in reactive marrow. Duplex ISH was demonstrated using a probe for bcl-2 together with MPO in 5 bone marrow sections infiltrated by follicular lymphoma (FL). Strong hybridisation signal for bcl-2 was detected in all cells of the paratrabecular aggregates of FL but showed only scattered positivity in the remainder of the bone marrow. Conversely, MPO was absent in the paratrabecular aggregates and present in the myeloid cells in the remainder of the marrow. This pattern was present in both single and duplex ISH for MPO and bcl-2 in the marrow infiltrated by FL. Duplex ISH was performed both by sequential hybridisation with bcl-2 followed by MPO, and simultaneously with a mix of bcl-2 and MPO probes. As negative controls, scrambled oligonucleotide probes for the corresponding genes were used in each case and did not show hybridisation. In summary, we have developed a generic method for QD labelling and semi-quantitative detection of oligonucleotide ISH in routinely processed clinical tissue samples. Although, in this study we primarily used bone marrow trephine samples, this technique can be applied to any tissue. It has the potential to facilitate transfer of microarray-identified gene signatures to clinical research and diagnostics, whilst the ability of spectral imaging to resolve multiple signals offers the possibility of multiplexed probe detection.

A pair of orthogonal coiled coils templates highly specific live cell bioconjugation of two different proteins. PNA tagging and hybridisation with fluorophore–DNA reporters enables rapid dual receptor internalisation analysis of EGFR and ErbB2.

A series of 3'-linked conjugates between an oligodeoxyribonucleotide 13mer and cholic, folic, lipoic and pantothenic acids, cholesterol, vitamin E and a viral fusion peptide have been prepared in an attempt to enhance the cellular uptake properties of the nucleic acid. It was envisaged that the 4 biological acids may improve the cellular uptake of the oligonucleotide through natural receptor-mediated uptake mechanisms, whilst cholesterol, vitamin E and the fusion peptide may enhance interaction of the conjugate with cellular membranes. In the course of preparing conjugates involving cholic, folic, lipoic and panthothenic acids, a methodology was developed that allowed for simple and effective conjugation between moieties bearing a carboxylic acid group and an oligonucleotide sequence, achieving linkage through disulfide and thioether bonds. All of the 3'-linked conjugates were characterised by reverse phase HPLC and electrospray mass spectrometry, and were found to have increased stability towards nucleases present in serum. The solid phase synthesis of a small library of peptides composed of the cationic amino acids lysine, ornithine, histidine and arginine, the hydrophobic amino acid tryptophan, and alanine as a spacer, and their subsequent coupling through an N-terminal cysteine residue to a 5'-maleimide-modified 8mer was also accomplished. The preparation of 49 peptide-oligonucleotide conjugates was achieved in good yield and purity with a simple gel filtration employed as the only purification step. Melt analysis of the hybridisation properties of the constructs indicated that increasing the number of cationic residues within the peptide segment led to elevated T_m values on binding with a 16mer target. The binding affinities of the peptide segments were found to be stronger when bound to single-stranded rather than duplex DNA, and dependent on salt concentration and pH. Thermodynamic analysis revealed enhanced free energies of binding for cationic peptide-oligonucleotides compared to the unmodified 8mer.

Non-small cell lung carcinoma is a leading cause of cancer mortality worldwide. There are gender and smoking associated differences both in tumour types and clinical outcome. Squamous cell carcinomas (SCC) are more frequent among smoking men while females develop adenocarcinomas (ADCA). NSCLC among never smokers are mainly ADCA, and occurs mostly in females. The present thesis elucidates the role of estrogen receptor (ER) and epidermal growth factor receptor family (EGFR/HER2-4) in NSCLC in the perspective of gender and histology as well as the influence of smoking on those biomarkers. A recently developed technique, tissue micro array (TMA), was employed.The question of how much of a tumour tissue that needed to be included in a TMA for biomarker analysis was analyzed by a statistical approach. Data indicates a sample size of three cylinders of tumour tissue with a diameter of 0.6 mm each as being appropriate and cost-effective. In order to optimally use the up to thousands of different tumour samples within a TMA, it would be optimal to serially cut and store slides before performing in situ detection of proteins and nucleic acids. Applying up to date methodology, and by evaluation with image analysis, data are presented that shows that such handling of TMA slides would be possible without any loss of biomarker information. ERα is more frequently observed in ADCA and in females and a local estradiol synthesis is supported by the presence of aromatase. ERβ is identified as a positive prognostic marker in ADCA. Smoking is associated to increased levels of ERβ mRNA. EGFR over expression is associated with a ligand. Independent phosporylation of ERα. HER-4 intracellular domain may also act as a co-activator to ERα in ADCA, especially among neversmokers. The question of ER and EGFR family signalling crosstalk as a potential target for combined targeted therapy is raised.

Im ersten Teil der Arbeit wurden Strategien zur Analyse von Transkripten erarbeitet. Die ersten Versuche zielten darauf ab, in mit Glaskapillaren genommenen Einzelzellproben verschiedener Gewebeschichten RT-PCR durchzuführen, um spezifische Transkripte nachweisen zu können. Dies gelang für eine Reihe von Genen aus verschiedenen Pflanzenspezies. Dabei konnten sowohl Transkripte stark wie auch schwach exprimierter Gene nachgewiesen werden.
Für die Erstellung von Gewebe-spezifischen Expressionsprofilen war es notwendig, die in vereinigten Zellproben enthaltene mRNA zunächst zu amplifizieren, um eine ausreichende Menge für Arrayhybridisierungen zu erhalten. Vor der Vermehrung wurde die mRNA revers transkribiert. Es wurden daran anschließend verschiedene Amplifikationsstrategien getestet: Die neben Tailing, Adapterligation und anderen PCR-basierenden Protokollen getestete Arbitrary-PCR hat sich in dieser Arbeit als einfache und einzige Methode herausgestellt, die mit so geringen cDNA-Mengen reproduzierbar arbeitet. Durch Gewebe-spezifische Array-hybridisierungen mit der so amplifizierten RNA konnten schon bekannte Expressionsmuster verschiedener Gene, vornehmlich solcher, die an der Photosynthese beteiligt sind, beobachtet werden. Es wurden aber auch eine ganze Reihe neuer offensichtlich Gewebe-spezifisch exprimierter Gene gefunden. Exemplarisch für die differentiell exprimierten Gene konnte das durch Arrayhybridisierungen gefundene Expressionsmuster der kleinen Untereinheit von Rubisco verifiziert werden. Hierzu wurden Methoden zum Gewebe-spezifischen Northernblot sowie semiquantitativer und Echtzeit-Einzelzell-RT-PCR entwickelt.
Im zweiten Teil der Arbeit wurden Methoden zur Analyse von Metaboliten einschließlich anorganischer Ionen verwendet. Es stellte sich heraus, daß die multiparallele Methode der Gaschromatographie-Massenspektrometrie keine geeignete Methode für die Analyse selbst vieler vereinigter Zellinhalte ist. Daher wurde auf Kapillarelektrophorese zurückgegriffen. Eine Methode, die mit sehr kleinen Probenvolumina auskommt, eine hohe Trennung erzielt und zudem extrem geringe Detektionslimits besitzt. Die Analyse von Kohlenhydraten und Anionen erfordert eine weitere Optimierung. Über UV-Detektion konnte die K+-Konzentration in verschiedenen Geweben von A. thaliana bestimmt werden. Sie lag in Epidermis und Mesophyll mit ca. 25 mM unterhalb der für andere Pflanzenspezies (Solanum tuberosum und Hordeum vulgare) publizierten Konzentration. Weiter konnte gezeigt werden, daß zwölf freie Aminosäuren mittels einer auf Kapillarelektrophorese basierenden Methode in vereinigten Zellproben von Cucurbita maxima identifiziert werden konnten. Die Übertragung der Methode auf A. thaliana-Proben muß jedoch weiter optimiert werden, da die Sensitivität selbst bei Laser induzierter Fluoreszenz-Detektion nicht ausreichte.
Im dritten und letzten Teil der Arbeit wurde eine Methode entwickelt, die die Analyse bekannter wie unbekannter Proteine in Gewebe-spezifischen Proben ermöglicht. Hierzu wurde zur Probennahme mittels mechanischer Mikrodissektion eine alternative Methode zur Laser Capture Microdissection verwendet, um aus eingebetteten Gewebeschnitten distinkte Bereiche herauszuschneiden und somit homogenes Gewebe anzureichern. Aus diesem konnten die Proteine extrahiert und über Polyacrylamidgelelektrophorese separariert werden. Banden konnten ausgeschnitten, tryptisch verdaut und massenspektrometrisch die Primärsequenz der Peptidfragmente bestimmt werden. So konnten als Hauptproteine im Mesophyll die große Untereinheit von Rubisco sowie ein Chlorophyll bindendes Protein gefunden werden.
Die in dieser Arbeit entwickelten und auf die Modellpflanze Arabidopsis thaliana angewandten Einzelzellanalysetechniken erlauben es in Zukunft, physiologische Prozesse besser sowohl räumlich als auch zeitlich aufzulösen. Dies wird zu einem detaillierteren Verständnis mannigfaltiger Vorgänge wie Zell-Zell-Kommunikation, Signalweiterleitung oder Pflanzen-Pathogen-Interaktionen führen.
The subject of this thesis was the analysis of single plant cells in respect to their contents of i) transcripts, ii) inorganic cations and anions, iii) metabolites like amino acids and carbohydrates as well as iv) proteins. One task was the transfer of existing methods to single cell analysis on leaf tissues of the model plant Arabisopsis thaliana L., the second one was the refinement and the development, respectively, of new protocols for the analysis of such picoliter samples. For cell type specific sampling two different complimentary methods were applied: Using micro glass capillaries specific single cell contents could be harvested from intact plants, whereas typical sample volumes were in the picoliter range. Even the sampling of inner cell types such as companion cells could be demonstrated. Using mechanical micro dissection of embedded tissue a larger amount of homogenous tissue could be collected.
Because single cell samples contain only femtogram amounts of mRNA, direct detection of transcripts is impossible. Therefore, two amplification protocols were applied to the cell samples: The first procedure makes use of specifically primed RT-PCR for amplification. Several genes derived from different plants and tissues could be detected after successful RT-PCR, including high as well as low expressed genes. The second method was developed to monitor the activity of many genes in parallel using array hybridisation with filters containing the cDNA of as many as 16.000 ESTs. For this purpose, unspecific RT-PCR as it is applied in the differential display was used to amplify different transcripts in just one reaction. However, in these tissue specific array hybridisations the expression patterns of several hundreds genes could be monitored. These included known tissue specific expression patterns (of mainly photosynthesis related genes) as well as a couple of unknown expression patterns. To verify the tissue specificity of gene activity some results were reconsidered using tissue specific northern blot hybridisations and real time RT-PCR, respectively.
Secondly, metabolites (including inorganic ions) were investigated: Because gas chromatography-mass spectrometry does not reveal the sensitivity which in necessary for the analysis of even multiple pooled single cell samples capillary electrophoresis was applied for these studies. This method has a high potential as it needs only small amounts of starting material, has uncomparable low detection limits and exhibits a high number of theoretical plates.
The analysis of inorganic anions and carbohydrates needs further optimisations. Using UV absorption-detection potassium could be detected in different cell types whereas the concentrations in mesophyll and epidermis were found around 25 mM each. These concentrations are lower than in other species as Solanum tuberosum or Hordeum vulgare. For investigations of amino acids the cell samples were derivatized to make the use of laser induced fluorescence-detection capable. In samples derived from pumpkin (Cucurbita maxima) mesophyll twelve amino acids could be detected and identified. The transfer of this method to A. thaliana derived samples exhibited no results which may be due to the low concentration of free amino acids in these plants.
Finally, a method was developed with which the existence of known and unknown proteins in tissue specific samples could be monitored. For this, mechanical micro dissection was used to: After embedding and sectioning the tissue of interest was cut out by an vibrating steel chisel to get homogenous samples. The proteins contained in these tissue pieces were extracted and separated by one dimensional SDS polyacrylamid gel electrophoresis. Several protein bands could be detected after staining with either silver or coomassie blue stain. These bands were cut out and sequenced by mass spectrometry. The large subunit of rubisco as well as one chlorophyll binding protein could be identified as the major proteins within the mesophyll.
The single cell analysis methods which were developed and applied to the model plant A. thaliana in this thesis allow a better spatial as well as temporal resolution of analysis. This will lead to a more detailed understanding of physiological processes like cell to cell communication, signalling or plant-pathogen interactions.

The availability of DNA samples that are of adequate quality and quantity is essential for any genetic analysis. The fields of forensic biology and clinical diagnostic pathology testing often suffer from limited samples that yield insufficient DNA material to allow extensive analysis. This study examined the utility of a recently introduced whole genome amplification method termed Multiple Displacement Amplification (MDA) for amplifying a variety of limited sample types that are commonly encountered in the fields of forensic biology and clinical diagnostics. The MDA reaction, which employs the highly processive bacteriophage φ29 DNA polymerase, was found to generate high molecular weight template DNA suitable for a variety of downstream applications from low copy number DNA samples down to the single genome level. MDA of single cells yielded sufficient DNA for up to 20,000,000 PCR assays, allowing further confirmatory testing on samples of limited quantities or the archiving of precious DNA material for future work. The amplification of degraded DNA material using MDA identified a requirement for samples of sufficient quality to allow successful synthesis of product DNA templates. Furthermore, the utility of MDA products in comparative genomic hybridisation (CGH) assays identified the presence of amplification bias. However, this bias was overcome by introducing a novel modification to the MDA protocol. Future directions for this work include investigations into the utility of MDA products in short tandem repeat (STR) assays for human identifications and application of the modified MDA protocol for testing of single cell samples for genetic abnormalities.

In the late 1990s, a series of landmark publications described RNA interference (RNAi) and related RNA silencing phenomena in nematodes, plants and fungi. By manipulating RNA silencing, biologists have been able to create tools for specifically inactivating genes. In organisms from trypanosomes to insects, RNA silencing is now indispensible for studying gene function. RNA silencing has been used in a project aimed at systematically knocking out all genes in the model plant Arabidopsis thaliana. RNA silencing has a natural role in defending eukaryotic cells against virus replication. By assembling virus DNA sequences in a form that triggers RNA silencing, biologists have created plants resistant to specific viruses. In this study, we set out to test if a similar approach would protect plants against infection by the agriculturally important Brassica pathogen, Plasmodiophora brassicae. P. brassicae is an obligate intracellular biotroph, from the little studied eukaryotic supergroup, the Rhizaria. To identify the gene sequences that would be starting material for P. brassicae RNA silencing, new P. brassicae genes were gathered by cDNA cloning or genomic PCR-walking. Using suppression subtractive hybridisation (SSH) and oligo-capping cloning of full-length cDNAs, 76 new gene sequences were identified. A large proportion of the cDNAs were predicted to contain signal peptides for ER translocation. In addition to the new cDNA identified here, partial sequences for the P. brassicae actin and TPS genes were published by other researchers close to the beginning of this study. Using PCR-walking, full-length genomic DNA sequences from both genes were obtained. Later, genomic DNA sequences spanning or flanking a total of 24 P. brassicae genes were obtained. The P. brassicae genes were rich in typical eukaryotic spliceosomal introns. Transcription of P. brassicae genes also appears likely to begin from initiator elements rather than TATA-box-containing promoters. A segment of the P. brassicae actin gene was assembled in hairpin format and transformed into Arabidopsis thaliana. Observation of simultaneous knockdown of the GUS marker gene as well as detection of siRNAs indicated that the hpRNA sequences induced RNA silencing. However, inoculation of these plants with P. brassicae resulted in heavy club root infection. We were unable to detect decreases in actin gene expression in the infecting P. brassicae, at either early or late stages of infection. We conclude that, within the limits of the techniques used here, there is no evidence for induction of RNA silencing in P. brassicae by in planta produced siRNAs.

The intimate relationship between the higher-order chromatin organisation and the regulation of gene expression is increasingly attracting attention in the scientific community. Thanks to high-resolution microscopy, genome-wide molecular biology tools (3C, ChIP-on-chip), and bioinformatics, detailed structures of chromatin loops, territories, and nuclear domains are gradually emerging. However, to fully reveal a comprehensive map of nuclear organisation, some fundamental questions remain to be answered in order to fit all the pieces of the jigsaw together. The underlying mechanisms, precisely organising the interaction of the different parts of chromatin need to be understood. Previous work in our lab hypothesised and verified the “transcription factory” model for the organisation of mammalian genomes. It is widely assumed that active polymerases track along their templates as they make RNA. However, after allowing engaged polymerases to extend their transcripts in tagged precursors (e.g., Br-U or Br-UTP), and immunolabelling the now-tagged nascent RNA, active transcription units are found to be clustered in nuclei, in small and numerous sites we call “transcription factories”. Previous work suggested the transcription machinery acts both as an enzyme as well as a molecular tie that maintains chromatin loops, and the different classes of polymerases are concentrated in their own dedicated factories. This thesis aims to further characterise transcription factories. Different genes are transcribed by different classes of RNA polymerase (i.e., I, II, or III), and the resulting transcripts are processed differently (e.g., some are capped, others spliced). Do factories specialise in transcribing particular subsets of genes? This thesis developed a method using replicating minichromosomes as probes to examine whether transcription occurs in factories, and whether factories specialise in transcribing particular sets of genes. Plasmids encoding the SV40 origin of replication are transfected into COS-7 cells, where they are assembled into minichromosomes. Using RNA fluorescence in situ hybridisation (FISH), sites where minichromosomes are transcribed are visualised as discrete foci, which specialise in transcribing different groups of genes. Polymerases I, II, and III units have their own dedicated factories, and different polymerase II promoters and the presence of an intron determine the nuclear location of transcription. Using chromosome conformation capture (3C), minichromosomes with similar promoters are found in close proximity. They are also found close to similar endogenous promoters and so are likely to share factories with them. In the second part of this thesis, I used RNA FISH to confirm results obtained by tiling microarrays. Addition of tumour necrosis factor alpha (TNF alpha) to human umbilical vein endothelial cells induces an inflammatory response and the transcription of a selected sub-set of genes. My collaborators used tiling arrays to demonstrate a wave of transcription that swept along selected long genes on stimulation. RNA FISH confirmed these results, and that long introns are co-transcriptionally spliced. Results are consistent with one polymerase being engaged on an allele at any time, and with a major checkpoint that regulates polymerase escape from the first few thousand nucleotides into the long gene.

At present, prostate cancer is a significant public health issue throughout the world and is the second leading cause of cancer deaths in older men. The prostate specific antigen or PSA (which is encoded by the kallikrein 3/KLK3 gene) test is the current most valuable tool for the diagnosis and management of prostate cancer. However, it is insufficiently sensitive and specific for early diagnosis, for staging of prostate cancer or for discriminating between benign prostatic hyperplasia (BPH) and prostate cancer. Recent research has revealed another potential tumour marker, glandular kallikrein 2 (KLK2 gene/hK2 protein), which may be used alone or in conjunction with PSA to overcome some of the limitations of the PSA test. Twelve new kallikrein gene family members have been recently identified and, like hK2 and PSA, many of these genes have been suggested to be involved in carcinogenesis. In this study, the cellular localisation and level of expression of several of these newer kallikreins (KLK4, KLK5, KLK7, KLK8 and KLK11) was examined in prostate tissue, to provide an understanding of the association of their expression with prostatic diseases and their potential as additional biomarkers. Like PSA and hK2, the present observation indicated that each of these proteins, hK4, hK5, hK7, hK8 and hK11, was detected within the cytoplasm of the secretory cells of the prostate glands. For the first time, all of these newly-identified proteins were shown to be expressed in prostatic intraepithelial neoplasia (PIN) lesions, in comparison to normal glands and cancer lesions. In addition to cytoplasmic secretory cell expression, the localisation of hK4 to the basal cells and nuclei in prostatic lesions was intriguing. The intensity of hK4 staining in prostate tissue was strongest in comparison to the other newly-identified kallikrein proteins (hK5, hK7, hK8 and hK11). Therefore, KLK4/hK4 expression was characterised further to define this cellular localisation and examined in non-prostatic tissue and also in a larger number of prostate tissues in an attempt to determine its potential value as a biomarker for prostate disease. Three hK4 antipeptide polyclonal antibodies, derived against N-terminal, mid-region and C-terminal hK4 amino acid sequences, were used. The hK4 N-terminal antipeptide antibody was used to demonstrate the cellular localisation of hK4 in kidney, salivary glands, liver, testis, colon carcinoma, heart, endometrium and ovarian cancer, for the first time. The presence of hK4 in these non-prostate tissues was consistent with the previous reports using RT-PCR. The dual cytoplasmic and nuclear localisation of hK4 observed in the prostate above was also seen in these tissues. Although hK4 was found widely expressed in many human tissue types, indicating that it is not prostate specific in its expression, the highest expression level of hK4 was seen in the prostate. Therefore, detailed expression patterns and levels of KLK4 mRNA and hK4 protein in the normal prostate and prostatic diseases and histopathological lesions were investigated and reported for the first time in this study. Twelve benign prostatic hyperplasia (BPH), 19 adenocarcinoma (Gleason grade 2-5) and 34 bone metastases from prostate cancer were analysed. Using in situ hybridisation, the expression of KLK4 mRNA was detected in the cytoplasm of the secretory cells of both normal and diseased prostate tissue. KLK4 mRNA was also noted in both secretory and basal cells of PIN lesions, but the basal cells of normal glands were negative. Using the hK4 N-terminal and mid-region antipeptide antibodies, hK4 was predominantly localised in the cytoplasm of the secretory cells. The intensity of hK4 staining appeared lowest in normal and BPH, and increased in PIN lesions, high Gleason grade prostate cancer and bone metastases indicating the potential of hK4 as a histopathological marker for prostatic neoplasias. Further studies are required with a larger cohort to determine its utility as a clinical biomarker. Small foci of atypical cells, which were found within normal glands, were also intensely stained. Surprisingly, hK4 protein was found in the nucleus of the secretory cells (but not the basal cells) of high grade PIN and Gleason grade 3 prostate cancer. The detection of KLK4 mRNA and hK4 protein in PIN lesions and small foci of atypical cells suggests that up-regulation of KLK4 expression occurs early in the pathology of prostate carcinogenesis. The finding of basal cell expression is not typical for the kallikreins and it is not clear what role hK4 would play in this cell type. With the use of the hK4 C-terminal antipeptide antibody, the staining was mainly localised in the nuclei of the secretory cells of the prostate glands. Although the nuclear localisation was readily noted in more than 90% of epithelial cells of the prostate gland with the C-terminal antibody, no difference in staining intensity was observed among the histopathological lesions of the prostate. The prominent nuclear localisation with the C-terminal antipeptide antibody was also shown to be distributed throughout the nucleus by using confocal microscopy. Further, by using gold-labelled particles for electron microscopy, the intracellular localisation of these hK4 antipeptide antibodies was reported here for the first time. Similar to the immunohistochemical results, the cytoplasm was the major site of localisation with the N-terminal and mid-region antipeptide antibodies. To further characterise the involvement of KLK4/hK4 in human prostate cancer progression, the transgenic adenocarcinoma mouse prostate (TRAMP) model was used in this study. In this study, mouse KLK4 (also known as enamel matrix serine protease -1, EMSP-1) was shown to be expressed in the TRAMP prostate for the first time. Previous studies had only shown the developing tooth as a site of expression for EMSP-1. The level of EMSP-1 mRNA expression was increased in PIN and prostate cancer lesions of the TRAMP model, while negative or low levels of EMSP-1 mRNA were seen in normal glands or in control mouse prostate tissue. The normal mouse prostate did not stain with any the three hK4 antipeptide antibodies. hK4 N-terminal and mid-region antipeptide antibodies showed positive staining in the cytoplasm of the epithelial cells of PIN and cancer lesions of the mouse prostate. The C-terminal antipeptide antibody showed distinctively nuclear staining and was predominantly localised in the nuclei of the glandular cells of PIN and cancer lesions of the mouse prostate. The expression patterns of both the mRNA and protein level for mouse KLK4 strongly supported the observations of KLK4/hK4 expression in the human prostate and further support the utility of the TRAMP model. Overall, the findings in this thesis indicate a clear association of KLK4/hK4 expression with prostate cancer progression. In addition, several intriguing findings were made in terms of cellular localisation (basal as well as secretory cells; nuclear and cytoplasmic) and high expression in atypical glandular cells and PIN, perhaps indicating an early involvement in prostate disease progression and, additionally, utility as basal cell and PIN histological markers. These findings provide the basis for future studies to confirm the utility of hK4 as a biomarker for prostate cancer progression and identify functional roles in the different cellular compartments.

Genomic DNA extraction is the starting point for various downstream molecular biology applications viz. PCR, restriction analysis, hybridisation etc. Numerous problems like DNA degradation, co-isolation of viscous polysaccharides, polyphenols and other secondary metabolites causing damage to DNA, inhibiting restriction enzymes, DNA polymerases etc, are routinely encountered during DNA isolation from plants. Quinone compounds resulting from oxidation of polyphenols lead brown the DNA preparations and can also damage proteins and DNA’s due to their oxidizing properties. This results in a poor yield of high molecular weight DNA. The protocol below explains the extraction of DNA via the CTAB method, involving three major steps viz lysis of cell wall and membranes, extraction of genomic DNA and precipitation of DNA.

The increasing demand on primary energy and the increasing concern on climatic change demand immediately a sustainable development, but still there remain open questions regarding its technical realisation. The second law of thermodynamics is a very simple but efficient way to define the principle design rules of sustainable technologies in minimising the irreversible entropy production. The ideal, but real process chain is defined by a still reversible structure or logic of the process chain—the reversible reference process chain—but consisting of real components with an irreversible entropy production on a certain level. It can easily be shown for energy conversion and for transportation that hybridisation in general can be indeed a measure to meet the reversible process chain and to minimise the entropy flow to the environment. Fuel cells are principal reversible converters of chemical energy and thus a key element within hybridisation. Depending on application, CHP may be a hybridisation step or only a slight improvement. There is a fundamental difference in heating a house or in supplying an endothermic chemical reaction with reaction entropy. The use of heat recovery and isolation is a necessary measure to minimise the entropy flow to the environment and can be described by a reversible reference process as well. The application of reversible reference process chains shows that hybrid systems with fuel cells are a technical feasibility to approach very closely the thermodynamic potential. This development differs from the past where the technical possibilities of materials and manufacturing limited the technology to meet reversibility and thus sustainability.

Micro-scale polymerase chain reaction (micro-PCR) systems offer substantial advantages over macro-scale systems. Smaller sample volumes are required, and faster process times are feasible. Thermal control of micro-PCR systems is a substantial technical challenge, however. The PCR process requires the fluid sample to be cycled through three temperature ranges — typically 90–95°C, 50–65°C and 72–77°C for denaturation, hybridisation and replication respectively. Durations of the three steps are required to be in the ratio of 4:4:9. In this paper, the thermal analysis of a continuous flow micro-PCR device is reported. The objective of the analysis is to optimize the thermal performance of the device for fast amplification cycles with high efficiency - an efficient PCR features rapid heating and cooling between steps, and good temperature uniformity within each step. The device comprises an array of parallel microchannels formed within a polypropylene substrate to carry fluid, with the base of the substrate mounted on an aluminium carrier. Substrate depth is 500 micron, and each channel is 60 micron wide by 40 micron deep. Thermoelectric cells (TECs) are bonded to the carrier, and powered by a thermoelectric controller with feedback from sensors embedded in the carrier. A Pyrex Glass slide is bonded to the substrate to form closed channels. Arrays of film heaters mounted on the slide adjacent to the channel are used to establish the required temperature regions along the channel. By pumping the fluid at a fixed flow rate, temperature cycling of specific period is achieved. Thermal analysis of the substrate is performed using an approximate closed-form solution, in conjunction with Finite Element (FE) and Computational Fluid Dynamics (CFD) simulations. The analysis is used to conduct a parametric study in order to determine the optimum configurations of substrate materials, cooling conditions, heaters and flow rates required to impose specific temperature cycles. The use of thermoelectric cells is shown to increase the rate of change of temperature between the various regions, improving the efficiency and decreasing the cycle time of the PCR process. Cycle times of 6s or less are shown to be feasible, yielding benefits in time saved for multiple amplifications. Finally, the analysis is also used to identify the dimensionless parameters which govern the thermal characteristics of the device, illustrating the importance of the Biot number.