Growth of bacteria in beer leads to turbidity and off-flavors, resulting in a spoiled and unpalatable product and thus economic loss. The most common beer-spoilage organisms (BSOs) are lactic acid bacteria (LAB), with Lactobacillus and Pediococcus species being the most problematic. Because of the harsh environment (low nutrients, antimicrobial compounds ethanol and hops, anaerobic), only select isolates are able to sustain growth in and spoil beer. To begin understanding the phenomenon of LAB adapting to overcome stresses in beer, ethanol tolerance, hop resistance, and nutrient acquisition mechanisms were investigated. First, ethanol tolerance was analyzed in the context of beer-spoilage ability, and it was found that it is intrinsically high in LAB, thus leading to the conclusion that LAB ability to spoil beer is not dependent on ethanol resistance levels. This was then followed by genome sequencing of the BSO Pediococcus claussenii ATCC BAA-344T (Pc344) to elucidate mechanisms being used to resist hops and acquire low abundance or alternative nutrients. Subsequent analysis of Pc344 and Lactobacillus brevis BSO 464 via reverse transcription quantitative PCR demonstrated the variability found among BSOs in the presence of beer-spoilage-related genes and their use during growth in beer. Further analysis of Pc344 was performed via RNA-sequencing to get a global view of gene expression during mid-logarithmic growth in beer. It was found that several alternative nutrients were being used by Pc344 to sustain growth, and that hop resistance was enabled by a variety of mechanisms including oxidative stress response and pH control. Finally, genomic comparison of BSOs determined that conservation is only present for closely related organisms and that no specific genes/proteins are indicative of an isolate’s beer-spoilage potential. It is more likely that horizontal gene transfer plays a major role in LAB adaption for growth in beer, and that plasmids are very important for this evolution, as was demonstrated by plasmid-variants of Pc344. The main conclusions of this thesis are therefore that hop resistance is the main factor determining ability to grow in beer, and that transfer of genetic elements is the driving force behind LAB evolving into BSOs.

Soil application of a known activator of Systemic Acquired Resistance (SAR), benzo(1,2,3)thiadiazole-7-carbothioic acid-S-methyl ester (BTH), and Harmonizer, a polychlorinated copper (II) phthalocyanine pigment, reduced severity of Colletotrichum orbiculare in Nicotiana benthamiana by 99% and 38%, respectively. BTH induced expression of nine SAR/progammed cell death-related genes and primed expression of two Induced Systemic Resistance (ISR)-related genes, while Harmonizer induced expression of only one SAR-related gene. Soil application of Harmonizer also reduced severity of Sclerotinia homoeocarpa in Agrostis stolonifera up to 39%, whereas BTH was ineffective. Next generation sequencing identified over 1000 genes in A. stolonifera with two-fold or higher increased expression following Harmonizer treatment relative to a water control, and induced expression of three defense-related genes was confirmed by relative RT-PCR. These results demonstrate that Harmonizer can activate systemic resistance in a dicot and a monocot, but changes in expression of genes indicated that it differed from BTH-activated SAR. / Petro-Canada, Natural Sciences and Engineering Research Council of Canada, Ontario Turfgrass Research Foundation

Both microRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate post- transcriptional events, but the post-transcriptional contribution to the global mammalian transcriptomes is still not well understood. In this study we study the synergistic interaction between microRNAs that inhibit gene production, and a special RBP, HuR, that positively regulates mRNA stability. We examined their relationship in terms of spatial, conservational and expressional perspective. We show comprehensive mapping of HuR binding sites by combination of its structural and sequential preferences; and cross-platform normalization method within a process of refining miRNA and HuR binding site mapping. Finally, we observed co-evolution of miRNA and HuR binding sites by looking at their proximity and conservation levels. Collectively, our data suggest that mammalian microRNAs and HuR, with seemingly opposing regulatory effects, cooperatively regulate their mutual targets.

Both microRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate post- transcriptional events, but the post-transcriptional contribution to the global mammalian transcriptomes is still not well understood. In this study we study the synergistic interaction between microRNAs that inhibit gene production, and a special RBP, HuR, that positively regulates mRNA stability. We examined their relationship in terms of spatial, conservational and expressional perspective. We show comprehensive mapping of HuR binding sites by combination of its structural and sequential preferences; and cross-platform normalization method within a process of refining miRNA and HuR binding site mapping. Finally, we observed co-evolution of miRNA and HuR binding sites by looking at their proximity and conservation levels. Collectively, our data suggest that mammalian microRNAs and HuR, with seemingly opposing regulatory effects, cooperatively regulate their mutual targets.

Gene finding in eukaryotic genomes is an essential part of a comprehensive approach to modern systems biology. Most methods developed in the past rely on a combination of computational prediction and external information about gene structures from transcript sequences and comparative genomics. In the past, external sequence information consisted of a combination of full-length cDNA and expressed sequence tag (EST) sequences. Much improvement in prediction of genes and gene isoforms is promised by availability of RNA-seq data. However, productive use of RNA-seq for gene prediction has been difficult due to challenges associated with mapping RNA-seq reads which span splice junctions to prevalent splicing noise in the cell. This work addresses this difficulty with the development of methods and implementation of two new pipelines: 1/ a novel pipeline for accurate mapping of RNA-seq reads to compact genomes and 2/ a pipeline for prediction of genes using the RNA-seq spliced alignments in eukaryotic genomes. Machine learning methods are employed in order to overcome errors associated with the process of mapping short RNA-seq reads across introns and using them for determining sequence model parameters for gene prediction. In addition to the development of these new methods, genome annotation work was performed on several plant genome projects.

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No description available.

This project concerns an exploration of the presence and interactions of long non-coding RNA transcripts in an experimental atherosclerosis mouse model with relevance for human abdominal aortic aneurysm development. 187 long noncoding RNAs, two of them entirely novel, were found to be differentially expressed between angiotensin II treated (developing abdominal aortic aneurysms) and non-treated apolipoprotein E deficient mice (not developing aneurysms) harvested after the same period of time. These transcripts were also studied with regards to co-expression network connections. Eleven previously annotated and two novel long non-coding RNAs were present in two significantly disease correlated co-expression groups that were further profiled with respect to network properties, Gene Ontology terms and MetaCore© connections.

Malaria is a pernicious disease that has greatly impacted and continues to affect the human population. While much research has been performed to understand the underlying nature of this disease, gaps in the knowledge-base persist. In order to address these deficiencies, a multi-disciplinary, multi-institutional project has been funded to study the systems biology of the host pathogen interaction during malaria infection in both humans and non-human primates. In the course of investigating the transcriptome during two 100-day experiments in Macaca mulatta, this work elucidated many of the underlying molecular pathways of the host and parasite that are affected by antimalarial drugs, as well as through host-pathogen interactions. The malaria-disease-related host pathways are related to, not surprisingly, immune-associated signalling and hematopoesis, and the altered parasite pathways demonstrate an association between disease severity and parasite life stage abundance. Continuing integration of this research with other data-types collected during the course of these experiments will improve our understanding of malaria systems biology and improve targeted malaria therapies.

Os microrganismos associados à cárie são, em sua maioria, microrganismos acidogênicos e acidúricos, anaeróbios estritos e facultativos. A presença de fungos é associada à microbiota de cárie radicular, sendo a espécie fúngica mais relacionada a Candida albicans. Embora estudos de cultivo e de análise de DNA comprovem a presença de fungos na microbiota associada a lesões de cárie radicular, demonstrando um gradiente crescente de colonização com a progressão da doença, pouco se sabe sobre o papel que estes microrganismos desempenham no processo de doença. O objetivo deste trabalho foi estudar o papel de Candida albicans na cárie radicular, através da análise de transcriptoma de biofilmes naturais de superfícies radiculares hígidas (n=10, SRS) e de lesão de cárie radicular ativa (n=9, RC). Foi avaliada a expressão diferencial de genes de Candida albicans, as funções específicas e vias metabólicas associadas a este microrganismo. O RNA total microbiano foi extraído e o mRNA isolado e sequenciado na plataforma Illumina Hi-Seq2500. Foram formados pool (grupamentos) das amostras com valores inferiores a 30ng/RNA para a construção de bibliotecas genômicas. Os dados gerados pelo sequenciamento de RNA-Seq foram compilados em uma tabela de contagem (reads) e mapeados com o genoma de referência (C. albicans SC5314) utilizando o software CLC Genomics Workbench 7.5.1. Para o cálculo do nível de expressão gênica os dados foram normalizados com o algoritmo DESeq. A expressão diferencial foi calculada com binomial negativa e False Discovery Rate (FDR<0,05). Os genes com maior expressão em RC e em SRS foram analisados pela mediana relativa de expressão (RME; Relative Median Expression) e expressão diferencial, assim como as vias metabólicas associadas a genes de virulência e metabolismo de açúcares. Dois genes (CaO19.610, FDR=0.009; CaO19.2506, FDR=0.018) apresentaram expressão diferencial significativa em superfície radicular hígida (SRS) e tem suas funções relacionadas a formação de biofilme. Enquanto que em superfície radicular cariada (RC) sete genes (UTP20, FDR=0.018; ITR1, FDR=0.036; DHN6, FDR=0.046; CaO19.7197, FDR=0.046; CaO19.7838, FDR=0.046; STT4, FDR=0.046; GUT1, FDR=0.046) apresentaram expressão diferencial significativa e tem suas funções relacionadas a atividade metabólica, transporte de açúcares, tolerância ao estresse, invasão e regulação de pH. Candida albicans é um microrganismo importante no desenvolvimento da doença cárie radicular. / The microbiota associated with root caries must be acidogenic and aciduric. S. mutans, Lactobacillus, Actinomyces, Veilonella, Bifidobacterium, and other bacteria play important roles in root caries biofilm. Yeasts are also present on carious and non-carious root biofilms, being the specie Candida albicans the most prevalent yeast found in root biofilms. Although the presence of Candida albicans is stablished in the literature, and there are an increasing gradient of Candida species. colonization with caries progression, the role of this microorganism in root caries has not being totally elucidated. The aim of this study is to analyse the role of Candida albicans in root caries thought a transcriptomic analysis of biofilms of sound root surfaces (n=10, SRS) and root caries lesions (n=9, RC) using a high-throughput sequencing of cDNA (RNA-Seq). The differential expression of genes of Candida albicans SC5314, the specific functions and pathways associated with the gene expression of the present study were investigated. The total bacterial RNA was extracted and the mRNA was isolated (Illumina Hi-Seq2500). Samples with low RNA concentration (less than 30ng/RNA) were pooled, yielding a final sample size of SRS=10 and RC=9. Sequence reads were compiled in a count table and mapped to C. albicans SC5314 genome of reference, using the software CLC Genomics Workbench 7.5.1. Gene expression was calculated in the algorithm DESeq, and the differential expression was calculated with binomial negative (Log2FoldChange) and False Discovery Rate (FDR<0,05). The genes with higher expression in RC and SRS were analysed by the Relative Median Expression (RME), and the virulence factors and pathways and sugar metabolization related with Candida albicans pathogenicity in root caries were analysed. Two genes (CaO19.610, FDR=0.009; CaO19.2506, FDR=0.018) are up-regulated in Sound Root Surface (SRS) have their functions related to biofilm formation and seven (UTP20, FDR=0.018; ITR1, FDR=0.036; DHN6, FDR=0.046; CaO19.7197, FDR=0.046; CaO19.7838, FDR=0.046; STT4, FDR=0.046; GUT1, FDR=0.046) are up-regulated in biofilm of carious dentin (RC) have functions related to metabolic activity, sugar transport, stress tolerance, invasion and pH regulation.