Equine infectious anemia virus (EIAV) is an important animal model to study the contribution of macrophages in viral persistence during lentiviral infections. EIAV is unique amongst the lentiviruses in that it causes a rapid, rather than the very slow disease progression, characteristic of other lentiviral infections. The accessory gene, S2, unique to EIAV, is an important determinant in viral pathogenesis. A functional S2 gene is required to achieve high-titer viremia and the development of disease in infected horses. Despite its essential role, the mechanisms by which S2 influences EIAV pathogenesis remain elusive. The goal of this research was to gain insight into the role of S2 in pathogenesis. To accomplish this goal we: (i) Examined the effects of EIAV and its S2 protein in the regulation of the cytokine and chemokine responses in macrophages, (ii) Assessed the influence of EIAV infection and the effect of S2 on global gene expression in macrophages and (iii) Identified host cellular proteins that interact with S2 as a starting point for the identification of host factors implicated in S2 function. The results from this study provide evidence for a role of S2 in enhancing a proinflammatory cytokine and chemokine response in infected macrophages. Specifically, S2 enhances the expression of IL-1 alpha, IL-1 beta IL-8, MCP-2, MIP-1 beta, IP-10 and a newly discovered cytokine, IL-34. Involvement of S2 in cytokine and chemokine dysregulation may contribute to disease development by optimizing the host cell environment to promote viral dissemination and replication. Microarray analyses revealed an interesting set of differentially expressed genes upon EIAV infection. Genes affected by EIAV were involved in the immune response, transcription, translation, cell cycle and cell survival. Finally, we used the yeast two-hybrid system to identify S2 host cellular interacting proteins. We identified osteosarcoma amplified 9 (OS-9) and proteasome 26S ATPase subunit 3 (PSMC3) proteins as interacting partners of S2. Additional evidence is needed to demonstrate the physiological relevance of these interactions in vivo. In summary, the results from this study contribute towards our understanding of the role S2 in disease expression and allow the formulation of new hypotheses as to the potential mechanisms of action of S2 during EIAV infection.

Behavior is a complex process resulting from the integration of genetic and environmental information. Thus, the genetically tractable Drosophila melanogaster was utilized to better understand the interplay between these factors since Drosophila males and females exhibit sex-specific courtship behaviors that are innate yet modifiable. These sex-specific behaviors, as well as sexually dimorphic development, are regulated, in part, by the somatic sex-determination hierarchy. Since reproductive behaviors rely on the rapid integration of multiple sensory cues, it is likely that the perception and integration of such cues and mating-induced physiological changes are mediated in part by changes in gene expression. Therefore, it was hypothesized that assaying gene expression changes in response to courtship or mating in Drosophila males would uncover new targets of the sex-determination hierarchy and other behaviorally important loci. We took a novel approach to find these behaviorally-responsive loci by utilizing microarray technology to assess courtship- or mating-induced gene expression changes in Drosophila male whole bodies or heads. Mutations in candidate loci were tested for effects on reproductive behaviors and present the first data showing that egghead (egh) and female-specific independent of transformer (fit) affect male reproductive behavior. egh is up regulated in male heads 20 min after courting and is required post-developmentally in a subset of neurons for robust male courtship behavior. fit, a fat body-expressed sex-determination hierarchy target gene, is up regulated in male whole bodies after 5 min of courtship. fit is also up regulated in male heads after 20 min of courtship or 2 hrs after mating. Mutations in fit result in male-male courtship; more specifically, fit mutants direct courtship towards males and also elicit courtship from wild-type males. By analyzing fit's role in courtship behavior, we also shed light on the role the fat body plays in modulating behavior. These studies provide the first pieces of evidence that gene expression changes occur in Drosophila males performing reproductive behaviors. This novel approach identified behaviorally important loci that are expressed in the nervous system and the fat body, indicating that both tissues modulate behavior. Also identified were sex-determination hierarchy target genes and it is likely that further analysis of the remaining candidates will reveal more members of this genetic cascade.

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) is a phytoestrogenic component of Rheum plant extracts which has been used for medical treatment since ancient times. It has been shown to have anti-inflammatory and anti-cancer effects. In our research, we aimed to study the biological effects of emodin on MCF-7 and MDA-231 cell lines. Cytotoxicity assays showed that emodin treatment for 48hours caused a concentration dependent decrease in viable cell numbers of both cell lines. As determined by cell counting with tryphan blue, IC50 values were 8.40 and 12.17 &micro / g/ml for MCF-7 and MDA-231 cells, respectively. Apoptotic effects of emodin was investigated by measuring the changes in apoptotic and antiapoptotic gene expressions by qRT-PCR. In MCF-7 cells, Bax expression increased with increasing emodin concentrations, while Bcl-2 expression was downregulated. Bax/Bcl-2 ratio was calculated as 9.2 fold at 10&micro / g emodin/ml treatment for 48 hours, indicating stimulation of apoptosis. However, Bax/Bcl-2 ratio was found 1.6 fold for MDA-231 cells. These results were in accordance with the results obtained from microarray analysis of related gene expressions. MCF-7 cells were more apoptotic in comparison to MDA-231 cells. DNA fragmentation was observed in MCF-7 cells by TUNEL method. GST enzyme activity that was measured using CDNB as substrate, was increased 100% with respect to control up to 5&micro / g emodin/ml treatment of MCF-7 cells for 48 hours. However, effect of emodin on GST activity in MDA-231 cells was found insignificant. According to microarray analysis results, emodin affected the gene expressions of GST isozymes in MCF-7 cells much more than in MDA-231 cells.

ABSTRACT TRANSFORMATION OF POTATO WITH MYB4 TRANSCRIPTION FACTOR AND EVALUATION OF ABIOTIC STRESS TOLERANCE AND GENE EXPRESSION PROFILES IN TRANSGENIC PLANTS Kalemtas, G&uuml / ls&uuml / m Ph.D., Department of Biology Supervisor: Prof. Dr. H&uuml / seyin Avni &Ouml / ktem February 2011, 257 pages Potato (Solanum tuberosum L. cv. Kennebec) was transformed via Agrobacterium tumefaciens (EHA105) harbouring two different binary vectors containing Oryza sativa myb4 gene, which encodes MYB4 transcription factor / under the control of CaMV35S promoter or cold inducible COR15a promoter. The transgenic plants were not growth retarded and there was no significant difference (p&lt / 0.05) in their tuber yield compared to wild-type plants. Wild-type and transgenic plants were subjected to abiotic stresses to compare their stress tolerances. There was no significant difference in boron, freezing and drought tolerances of wild-type and transgenic lines. Two of the transgenic lines were more salt tolerant than wild-type with respect to growth parameters. Transcriptomes of wild-type and these two lines, one expressing myb4 under the control of 35S promoter and the other COR15a promoter, were analyzed to elucidate the myb4-regulated processes and downstream target genes in potato. Differentially regulated genes in transgenic lines showed that myb4 controls a large and complex transcriptional network associated with diverse cellular processes, primarily defense and rescue, metabolism and development. Genes involved in sucrose synthesis, some peroxidases and CBF3 transcription factor were up-regulated in transgenic plants upon exposure to freezing stress. This suggested that myb4 may configure freezing response in potato primarily by oxidative stress defence mechanisms, osmotic adjustment or activation of CBF3 regulated genes that may confer cold tolerance. Despite up-regulation of these stress related genes, transgenic potato was not more drought or freezing tolerant compared to WT under the tested conditions. Further experiments should be conducted to better elucidate the involvement of these genes in regulation of stress response in transgenic potato expressing myb4.

Wheat is the most important grain crop grown in our country providing greatest part of the daily nutritional requirement. Abiotic factors including salinity, drought, cold and heat stresses affect quality and yield of wheat varieties used for the production of both bread and pasta flour. NAC proteins form one of the widest families of plant specific transcription factors. Members of this family are related with development, defense and abiotic stress responses. TaNAC69-1 and TtNAM-B2 genes were isolated from T.aestivum and T.turgidum, respectively. Then they were cloned into different monocot and dicot expression vectors to be used for further wheat and tobacco genetic transformation studies. To understand effects of salinity, drought, cold and heat stresses on expression profiles of TaNAC69-1 and TtNAM-B2 genes, quantitative real time PCR was performed. The time series expression profiles of TaNAC69-1 show that it was signi

The experimental factors such as the cell type and the treatment may have different impact on expression levels of individual genes which are quantitative measurements from microarrays. The measurements can be collected at a few unevenly spaced time points with replicates. The aim of this study is to consider cell type, treatment and short time series attributes and to infer about their effects on individual genes. A mixed effects model (LME) was proposed to model the gene expression data and the performance of the model was validated by a simulation study. Realistic data sets were generated preserving the structure of the sample real life data studied by Nymark et al. (2007). Predictive performance of the model was evaluated by performance measures, such as accuracy, sensitivity and specificity, as well as compared to the competing method by Smyth (2004), namely Limma. Both methods were also compared on real life data. Simulation results showed that the predictive performance of LME is as high as 99%, and it produces False Discovery Rate (FDR) as low as 0.4% whereas Limma has an FDR value of at least 32%. Moreover, LME has almost 99% predictive capability on the continuous time parameter where Limma has only about 67% and even it cannot handle continuous independent variables.

This study presents a CMOS integrated sensor chip suitable for sensing biological samples like DNA. The sensing part of the chip consists of a 32 X 32 pixel array with a 15 &micro / m pixel pitch. Pixels have 5 &micro / m X 5 &micro / m detector electrodes implemented with the top metal of the CMOS process, and they are capable of detecting charge transferred or induced on those electrodes with a very high sensitivity. This study also includes development of an external electronics containing ADC for analog to digital data conversion. This external circuitry is implemented on a PCB compatible with the Opal Kelly XM3010 FPGA that provides data storage and transfer to PC. The measured noise of the overall system is 6.7 e- (electrons), which can be shrunk down to even 5.1 e- with an over sampling rate. This kind of sensitivity performance is very suitable for DNA detection, as a single nucleotide of a DNA contains 1 or 2 e- and as 10 to 20 base pair long DNA&rsquo / s are usually used in microarray applications. The measured dynamic range of the system is 71 dB, in other words, at most 24603 e- per frame (20 ms) can be detected. The measured leakage is 31 e-/frame, but this does not have a dramatic effect on the sensitivity of the system, noting that the leakage is a predictable quantity. DNA detection tests are performed with the chip in addition to electronic performance measurements. The surface of the chip is covered with a nitride passivation layer to prevent the pixel crosstalk and is modified with an APTES polymer for suitable DNA immobilization. DNA immobilization and hybridization tests are performed with 5&rsquo / -TCTCACCTTC-3&rsquo / probe and its complementary 3&rsquo / -AGAGTGGAAG-5&rsquo / target sequences. Hybridization performed in 1 pM solution is shown to have a larger steady state leakage than the immobilization in a 13 &micro / M solution, implying the ability to differentiate between the full match and full mismatch sequences. To best of our knowledge, the measured pM sensitivity has not yet been reported with any label free CMOS DNA microarrays in literature, and it is comparable with the sensitivity of techniques like QCM or the fluorescence imaging. The 1 pM sensitivity is not a theoretical limit of the sensor, since theoretically the sensitivity level of 6.7 e- can offer much better results, down to the aM level, as far as the noise of electronics is considered, nevertheless the sensitivity is expected to be limited by DNA immobilization and hybridization probabilities which are determined by the surface modification technique and applied protocol. Improving those can lead to much smaller detection limits, such as aM level as stated above.

Rhodobacter capsulatus DSM1710 is a purple non-sulfur bacterium capable of hydrogen production via photofermentation. Biohydrogen is a clean and renewable way of hydrogen production, which can be achieved by PNS bacteria in outdoor large scale photobioreactors using sun light. In outdoor conditions bacteria can be exposed to heat and cold stress. In this study in order to understand the effects of heat and cold stress on photofermentative hydrogen production and gene expression profile of R.capsulatus on acetate as the carbon source, microarray analysis was carried out. Since there is no commercially available microarray chip for R.capsulatus, an Affymetrix GeneChip&reg / was designed and it was manufactured by Affymetrix.The experiments were conducted at 30

Microarray technology enables researchers to measure the expression levels of thousands of genes simultaneously to understand relationships between genes, extract pathways, and in general understand a diverse amount of biological processes such as diseases and cell cycles. While microarrays provide the great opportunity of revealing information about biological processes, it is a challenging task to mine the huge amount of information contained in the microarray datasets. Generally, since an accurate model for the data is missing, first a clustering algorithm is applied and then the resulting clusters are examined manually to find genes that are related with the biological process under inspection. We need automated methods for this analysis which can be used to eliminate unrelated genes from data and mine for biologically important genes. Here, we introduce a general methodology which makes use of traditional clustering algorithms and involves integration of the two main sources of biological information, Gene Ontology and interaction networks, with microarray data for eliminating unrelated information and find a clustering result containing only genes related with a given biological process. We applied our methodology successfully on a number of different cases and on different organisms. We assessed the results with Gene Set Enrichment Analysis method and showed that our final clusters are highly enriched. We also analyzed the results manually and found that most of the genes that are in the final clusters are actually related with the biological process under inspection.

The first part of this research focused on wide-cross whole-genome radiation hybrid (WWRH) mapping of the cotton (Gossypium) genome. Radiation hybrid mapping has been used extensively to map the genomes of human and certain animal species, but not plant species. In lieu of in vitro hybrid cell line technologies for plants, we developed a novel approach for radiation hybrid mapping based on wide-cross in vivo hybridization. Flowers from one species of cotton, either G. hirsutum or G. barbadense, were -irradiated and then used to pollinate the other species. The resulting hybrid plants were assessed as a mapping tool. Two WWRH mapping panels were constructed from 5- and 8-krad -irradiation treatments. Both panels demonstrated that the WWRH mapping method can be used to map the cotton genome, and that this method complements traditional linkage mapping approaches. The second part of this research focused on the identification of cold-responsive genes using spotted oligo-gene microarray analysis. Increased cold-tolerance in cotton would promote early and uniform seedling establishment, expand the growing season, decrease susceptibility to fungal infections and certain diseases, and increase fiber yield and quality. BLAST searches of the cotton database using amino acid sequences of 93 drought/cold-related genes from Arabidopsis and several other plant species led to 806 cotton orthologous cDNAs and expressed sequence tags (ESTs). Eight hundred and six cotton 70-mer oligos were designed and included in an oligo-gene microarray containing 1,536 70-mer oligos, each representing a cDNA or EST from cotton, or one of 121 chloroplast genes or 66 mitochondrial genes from Arabidopsis. Thirty-eight cotton cDNAs and ESTs were identified as cold-responsive genes based on experimental treatment and oligo-gene microarray analysis. Expression was up-regulated for 36 genes and down-regulated for two genes by cold treatment. Results from microarray analysis were tested and confirmed by northern blot analysis for 16 genes. Our data suggest that Arabidopsis orthologous genes can be used to identify homologous cotton genes. The oligo-gene microarray is a valid approach to study transcriptional changes in cotton.