A diapause upregulated cDNA clone was isolated from a cDNA library generated from brain mRNA of diapausing Sarcophaga crassipalpis pupae. The clone hybridized to a 1600 bp transcript on a northern blot. The insert is 823 bp in length, has a tentative open reading frame of 615 bp, and codes for a 23 kDa protein. The clone has a high level of identity at the amino acid level with the four small heat shock proteins of Drosophila melanogaster. Northern analysis revealed no detectable expression of the transcript in diapause- or nondiapause-programmed wandering larvae, and only trace expression in nondiapausing pupae. But, the transcript was highly expressed beginning at the onset of diapause and continuing throughout diapause. Expression promptly decreased when diapause was terminated. In nondiapausing individuals the transcript was highly expressed in response to cold shock or heat shock, but temperature stress did not cause greater expression in diapausing pupae. The results imply that expression of this small heat shock protein, a response elicited by temperature stress in nondiapausing individuals, is a normal component of the diapause syndrome. The upregulation of this gene during diapause suggests that it plays an essential role during this overwintering developmental arrest.

<p>Using the model organism <em>Escherichia coli</em>, we discuss herein two novel antimicrobial targets: namely, the protein YjeE and the process of ribosome assembly.</p> <p>YjeE is essential for viability and widely conserved amongst bacterial pathogens and has no human homologue. We searched for a small molecule probe of the function of YjeE to help circumvent the inadequate genetic tools that are available for studying this protein. Sensitive methods for detecting ligand binding were optimized; however, this effort yielded no inhibitors. A second approach to studying the function of YjeE was the development of a reporter using a promoter that is directly upstream of <em>yjeE </em>in <em>E. coli</em>. The activity of this promoter was tested in the presence of small molecules of known function and in diverse gene deletion backgrounds. YjeE found to be linked to the inhibition of DNA and protein translation as well as central metabolism and respiration. These interactions prompted experiments that revealed YjeE to be dispensable under anaerobic conditions.</p> <p>Many antibiotics target ribosomal protein synthesis; however, no current antibiotics target the process of ribosome biogenesis. In order to identify new biogenesis factors, the non-essential fraction of the <em>E. coli </em>genome was screened for deletions that gave rise to cold-sensitive growth. We found that genes associated with ribosome function were the most represented cold sensitive factors amongst the genes of known function. We identified and present here two new putative ribosome biogenesis factors, <em>prfC</em> and <em>ychF</em>, which had phenotypes associated with ribosome assembly defects.</p> / Doctor of Philosophy (PhD)

No description available.

Les dinoflagellés sont un groupe très varié d’eucaryotes unicellulaires principalement retrouvés en milieu marin où ils ont un rôle écologique majeur dans la production primaire des océans et dans la formation des récifs coralliens. Ils sont aussi responsables de phénomènes néfastes comme les marées rouges et la production de toxines qui contaminent les crustacées et les poissons lorsque les conditions sont propices à leur multiplication rapide. Ces organismes possèdent des caractéristiques moléculaires uniques chez les eucaryotes, particulièrement en ce qui a trait au noyau. Le génome des dinoflagellés s’y retrouve condensé sous forme de cristal liquide stabilisé par des cations métalliques plutôt que sous forme de nucléosomes organisés par des histones. Cette forme condensée persiste tout au long du cycle cellulaire et limite la transcription des gènes à des boucles d’ADN qui se retrouvent à la périphérie des chromosomes. Ces caractéristiques inhabituelles, jumelées à une taille souvent imposante de leur génome, ont grandement limité l’étude des mécanismes moléculaires de base comme la régulation de la transcription. Afin de mieux caractériser ce processus chez ces organismes, le dinoflagellé Lingulodinium polyedrum, qui est étudié majoritairement pour ses multiples rythmes circadiens, a été utilisé. Tout d’abord, le séquençage à haut-débit a été utilisé afin de caractériser le transcriptome complet de l’organisme à quatre temps différents au cours d’une journée. De façon surprenante, ce séquençage a montré que très peu des transcrits varient entre les temps et que ces variations sont de faible amplitude, ce qui contraste fortement avec les résultats obtenus chez d’autres groupes d’organismes. Une inhibition pharmacologique de la transcription a aussi été effectuée et montre que les rythmes de photosynthèse et de bioluminescence continuent d’osciller de façon circadienne en absence de transcription. Ces résultats suggèrent que le modèle traditionnel de génération des rythmes circadiens par des boucles de rétroaction transcription/traduction est probablement absent chez Lingulodinium. La deuxième approche consiste en la caractérisation de deux protéines à domaine cold-shock (CSD), un domaine d’origine bactérienne qui est fortement surreprésenté chez les dinoflagellés et annoté comme potentiel facteur de transcription. Ces deux protéines ont une préférence pour la liaison de l’ADN simple brin versus l’ADN double brin tout en étant ii capable de lier de l’ARN. Par ailleurs, ces liaisons aux acides nucléiques ne sont pas spécifiques à une séquence particulière. L’analyse de leur abondance après un passage prolongé en condition froide n’a pas permis de déceler une augmentation importante de l’abondance des deux protéines et celles-ci sont également incapable de complémenter un quadruple mutant des protéines cold-shock chez E. coli. Ces données suggèrent que les CSDs des dinoflagellés ne sont probablement pas des facteurs de transcription séquence-spécifique et qu’ils ont également une fonction différente des protéines bactériennes. La troisième approche consiste en la réticulation in vivo des protéines interagissant avec la chromatine. Après réticulation, la chromatine a été purifiée et les protéines associées à ceux-ci ont été extraites et identifiées par spectrométrie de masse. Parmi les protéines identifiées, il y a un nombre réduit de protéines de liaison à l’ADN en comparaison avec des données similaires chez les animaux. Des peptides provenant d’une histone H4 ont aussi été identifiés, ce qui consiste en une des premières identifications de ce type de protéine chez les dinoflagellés. Plusieurs protéines de liaison à l’ARN ont été identifiées et pourraient permettre de réguler diverses étapes de la biologie des ARNm et ainsi moduler la traduction. Quelques protéines reliées au contrôle du cycle cellulaire et à la réparation de l’ADN ont aussi été identifiées. Mises ensemble, ces trois approches permettent de suggérer que la régulation de la transcription et de l’abondance des ARNm semblent avoir une importance moindre chez les dinoflagellés que chez les autres eucaryotes. / Dinoflagellates are a diverse group of unicellular eukaryotes found in marine habitat where they have a major role in the primary production of the ocean and in the formation of coral reefs. They are also responsible for some of the harmful algal blooms whose toxin production can contaminate crustacean and fish. Dinoflagellates possess unique molecular characteristics in eukaryotes, especially for their nucleus. For example, their genome is found in a permanently condensed liquid crystalline state stabilized by metallic cations instead of the nucleosome organized by histones. This condensed form persists throughout the cell cycle and limits transcription to DNA loops localized at the periphery of the chromosomes. These unusual characteristics, coupled with a generally large genome size, have greatly limited the study of basic molecular mechanisms such as transcription regulation. In order to better characterize this process for the dinoflagellates, I used Lingulodinium polyedrum, a dinoflagellate studied extensively for its circadian rhythms. As a first approach, high-throughput sequencing was used to characterize the complete transcriptome of the organism at four different times throughout the day. Surprisingly, this sequencing revealed that an extremely low number of transcripts vary in abundance between time points and that those variations are of low amplitude, a result in stark contrast with what has been observed in other organisms. A pharmacological inhibition of transcription was also done and shows that bioluminescence and photosynthesis rhythms persist in absence of transcription, suggesting that the classical transcription/translation feedback loop used to generate rhythmic timing in eukaryotes is probably absent in Lingulodinium. The second approach was the characterization of two proteins with a cold-shock domain (CSD), a type of domain strongly overrepresented in dinoflagellates and predicted to be a potential transcription factor. Those two proteins showed a preferential binding to single stranded DNA versus double stranded DNA while also being able to bind RNA, and were not specific to a particular sequence. Protein abundance analysis after a prolonged cold shock did not yield a massive increase in the abundance of those two proteins, as seen in E. coli. Furthermore, neither protein was able to complement a quadruple cold shock protein (CSP) mutant in E. coli. Data gathered here suggest that CSD proteins in dinoflagellates are probably iv not sequence-specific transcription factors and may also have a function different from bacterial CSP. The third approach consisted of the in vivo cross-linking of chromatin-interacting proteins. After cross-linking, the chromatin was purified and the proteins associated with it extracted and identified by mass spectrometry. Of the identified proteins, few DNA binding proteins were found, unlike similar studies done in animals. Peptides derived from a histone H4 were discovered, one of the first instances of histone identification in dinoflagellates. Multiple proteins able to bind RNA have been identified and could be used to regulate multiple steps of RNA biology and therefore modulate RNA translation. Some proteins related to cell cycle control and DNA repair were also identified. Taken together, these three approaches support the view that the transcriptional regulation and control over mRNAs abundance seem to have a lower importance in dinoflagellate than in other eukaryotes.

Les dinoflagellés sont une famille d'eucaryotes unicellulaires trouvés dans les écosystèmes marins et d'eau douce et sont d'importants producteurs primaires. Ils sont réputés pour plusieurs comportements distinctifs, notamment la formation de proliférations d'algues nuisibles appelées « marées rouges », l'émission de bioluminescence dans l'océan et leur contribution à la formation de récifs coralliens. Leur structure génomique est inhabituelle avec de grandes quantités d'ADN et des chromosomes condensés en permanence à toutes les étapes du cycle cellulaire. L’ADN est sans nucléosome et se trouve dans une structure de cristaux liquides. Plusieurs gènes sont codés dans de multiples répétitions situées dans des réseaux en tandem produisant des protéines pratiquement identiques sans aucun élément conservé détecté dans les régions présumées promotrices en amont de la séquence codante. Ces caractéristiques uniques rendent difficile à comprendre comment les cellules régulent l'expression des gènes. Cette thèse examine l’hypothèse que la régulation de transcription est difficile et peu utilisée chez les dinoflagellés. Les dinoflagellés présentent une rareté des facteurs de transcription, les protéines du domaine de choc froid (CSP) représentant la majorité des protéines de liaison à l'ADN potentielles dans le transcriptome de Lingulodinium polyedra et le génome de Symbiodinium kawagutii. Le potentiel des CSP de dinoflagellés à agir en tant que facteurs de transcription spécifiques à la séquence a été testé en utilisant des tests de déplacement de mobilité électrophorétique. Ces études ont révélé que quatre CSP différentes ont montré une préférence pour l'ARN par rapport à l'ADN simple et double brin. Une deuxième approche a examiné le ciblage de la séquence spécifique par des tests de sélection et de liaison d'amplification, et cela n'a révélé aucun motif consensus détectable dans la liaison à l'ADN. Nous concluons que les CSP dinoflagellés sont plus susceptibles de fonctionner comme des protéines de liaison à l'ARN que comme des facteurs de transcription. Il a été rapporté que l'expression de nombreux gènes chez plusieurs espèces de dinoflagellés était régulée par l'exposition à la lumière. Cela a été testé pour trois gènes, dont l'expression régulée par la lumière chez l'espèce formant des récifs Symbiodinium kawagutii. La régulation de ces gènes a été rapportée dans la littérature suggérant la possibilité d’identifier les éléments régulateurs dans le promoteur. Cependant, l'analyse par transfert de Northern n'a pas pu valider le modèle d'expression de ces trois gènes chez S. kawagutii. De plus, le séquençage d'ARN à haut débit a confirmé que ces trois gènes n'étaient pas induits par la lumière. Au total, seuls sept gènes ont été exprimés de manière différentielle à l'aube et au crépuscule en utilisant RNA-Seq, et tous étaient de moindre abondance à la fin de la période de lumière sur un 12: 12 cycle L: D. Trois des sept ont également été examinés en utilisant une analyse qPCR, et seule deux des trois ont pu être confirmés comme étant altérés, mais avec une différence de facteur inférieure à celle observée avec RNA-Seq. Nous en concluons qu'il y a peu de régulation lumineuse de l'expression génique dans cette espèce dinoflagellé. Dans l’ensemble, les études décrites ici appuient l’hypothèse que les dinoflagellés ont un moins grande dépendance sur la régulation transcriptionnelle que d’autres organismes. / Dinoflagellates are a large family of unicellular eukaryotes found in marine and freshwater ecosystems and are important primary producers in marine ecosystem. They are famous for several distinctive behaviors including forming harmful algal blooms called “red tides”, emission of bioluminescence in the ocean, and contributing to the formation of coral reefs. They have an unusual genome structure with large amounts of DNA and permanently condensed chromosomes throughout all stages of the cell cycle. The chromatin lacks observable nucleosomes and has a liquid crystal structure. Some genes are encoded in multiple repeats located in tandem arrays producing virtually identical proteins without any known conserved elements detected in the upstream promoter regions or intergenic spacers. These unique features make it difficult to understand how gene expression is regulated. This thesis describes two experimental tests for the hypothesis that transcriptional regulation is difficult and is not the primary means of regulating gene expression in dinoflagellates. Dinoflagellates show a paucity of transcription factors, and of these, cold shock domain proteins (CSPs) account for the majority of potential DNA binding proteins in the transcriptome. Here, the potential of dinoflagellate CSPs from free-living Lingulodinium polyedra and reef-forming Symbiodinium kawagutii (recently renamed to Fugacium kawagutii) to act as sequence specific transcription factors was tested. These studies using four different CSPs showed a preference for RNA over both single and double stranded DNA using electrophoretic mobility shift assays (EMSA). A second approach, testing for specific sequence binding by three cycles of selection and amplification binding (SAAB) did not enrich any consensus motif for any of the four proteins. We conclude dinoflagellate CSPs are more likely to function as RNA binding proteins than as transcription factors. Expression of many genes in many dinoflagellate species has been reported to be regulated by light. This was tested for three genes whose expression was reported to be light-regulated in Symbiodinium kawagutii. The availability of a genome sequence for this species suggested that it might be possible to identify potential regulatory elements in the promoter of these genes. However, Northern blot analysis was unable to confirm differential expression of these three genes over a 24 hour light-dark cycle. Furthermore, RNA-Seq of samples taken at the end of the day and night also indicated these three genes were not light-induced. In total, only seven genes were found to be differentially expressed at dawn and dusk using RNA-Seq in triplicate with a false discovery rate (FDR) of 0.1. All were of lower abundance at the end of the light period on a 12:12 L:D cycle suggesting possible repression by light. Three of these seven, picked at random, were examined using qPCR analysis. Only two of the three had lower abundance at the end of the day by this technique, and the fold difference was less than what was observed with RNA-Seq. We conclude from this that there is little light regulation of gene expression in this dinoflagellate species. Taken together, the studies described here support the hypothesis that dinoflagellates do not rely on regulation of genes at the transcriptional level to the same extent as other organisms.

The aim of this study was to induce the triploidy in pikeperch (Sander lucioperca) with use of a cold shock. To induce the triploidy, fertilised egg were (spawning temperature 14,5 °C) submerged in a cold bath at the temperature of 2 °C. Time of initiation was 1; 3; 5; 7 and 10 minutes post activation. The exposure time was 20 and 40 minutes. Ploidy level of freshly hatched larvae was assessed with use of the flow cytometry. In both exposure times, the hatching rate was getting lower with later time of initiation (20 minutes exposure, hatching rate: 58,4-13,4 %; 40 minutes exposure, hatching rate: 28- 9,6 %). Number of malformed larvae increased with later time of initiation and longer exposure time (20 minutes exposure, malformed larvae 0-47,2 %; 40 minutes exposure, malformed larvae 0-58,8 %). None of the tested combination of exposure time and time of initiation led to a population containing 100 % triploid larvae. However, percentage of triploid larvae grew up with longer exposure time and later time of initiation. The best cold shock combination with highest yield of triploids were after 20 minutes long treatment initiated 10 minutes post activation (57,1 +- 14,2 %) and after 40 minutes long treatment initiated 10 minutes post activation (61,9 +- 8,2 %). The most important finding of this study is that cold shock treatment leads to triploidy in pikeperch. To obtain 100% triploid larvae, shorter exposure time and different shock temperature might be applied. It may also eliminate low hatching rate and high appearance of malformed larvae.

We assessed influence of three acclimation regimes and influence of recovery after cold shock (exposure to 0°C for a period of time corresponding to Lt25) on the relative mRNA levels of selected stress proteins using qRT-PCR method. Larvae acclimated at 25°C showed relatively weak upregulation responses to cold shock. Much stronger responses were observed in the larvae that were cold-acclimated at 15°C or 15°C ? 6°C prior to cold shock. Two different general trends were distinguished in the response to cold acclimation and cold shock: (a) proteins from families SP70 and SP90 and splice variants c and d of the transcription factor HSF were upregulated in response to cold acclimation and the levels of their mRNA transcripts further increased after cold shock (for instance, the abundance of hsp70Aa mRNA increased up to 300-fold after cold shock (acclimation variant 15°C ? 6°C)); (b) four members of the small Hsp family (22, 23, 26 and 27 kDa) and splice variants a and b of the transcription factor HSF were down-regulated during cold acclimation (for instance, 10-fold in the case of hsp22) and the levels of their mRNA transcripts were either unchanged or increased only moderately after the cold shock. A third group of proteins, namely Hsc70, Hsp40 showed no or relatively small changes.

Cold adaptation in stationary phase in Bacillus subtilis One of the most important abiotic factor which influences life of bacterial cells is the ambient temperature. A decrease of this temperature is usually accompanied usually with the loss of the fluidity of bacterial cytoplasmatic membrane. While the mechanisms of the responses to the cold shock during the exponential phase of growth are well known for Bacillus subtilis, the responses of stationary phase cells had not been studied yet (despite the stationary phase is the most common state of microorganism in the nature). There are two independent mechanisms which restores much needed fluidity in Bacillus subtilis - short-term adaptation and long-term adaptation. Short-term adaptation is based on the function of fatty acid desaturase coded by des gene. Long-term adaptation relies on the change in ratio of iso- and anteiso- branched fatty acids. In this work we examinated membrane adaptation during stationary phase under two different conditions, namely under cultivation at stable low temperature and after cold shock. The highest activity of Pdes was observed for cultivation at 25 řC and for the cold shock applied from cultivation in 37 řC to 25 řC. Anisotropy measurements and fatty acids analysis were also performed. Results indicated, that the...

The nitrification process, the biologically mediated process of ammonia treatment in water resources recovery facilities (WRRF), remains the most common treatment process to mitigate the adverse effects of effluent ammonia discharges in surface water. However, it is well established that the temperature-sensitive process of nitrification remains hindered at low temperatures in conventional suspended growth technologies; specifically, passive treatment systems such as the lagoons, representing over 50% of Canadian treatment facilities in operation. As such, nitrification in lagoon facilities remains unreliable during the cold seasons with no nitrification occurring at 1°C. In contrast to suspended growth systems, attached growth technologies such as the moving bed biofilm reactors (MBBR) have recently been proven capable of achieving significant nitrification rates at temperatures as low as 1°C and are proposed as suitable upgrade systems to the common lagoon facility to reach year-long ammonia treatment targets. As such, the main objective of this research is to investigate and expand the current knowledge by investigating the key research questions lacking in the current literature on post-carbon, low temperature nitrifying MBBR systems. With this aim, a temperature-controlled study of attached growth nitrification kinetics was conducted to isolate the effects of low temperatures on nitrifying MBBR system performance down to 1°C. A removal rate of 98.44 ± 4.69 gN/m³d is identified as the 1°C intrinsic removal rate and the design removal rate for nitrifying MBBR systems at low temperatures. Considering this intrinsic rate at 1°C, an assessment of reactor efficiency at elevated TAN concentrations typical of non-combined sewer systems indicates that a two reactor in-series MBBR system configuration is recommended for retrofitting lagoon facilities connected to sanitary sewers. The study of the reactor performance to temperatures as low as 1°C demonstrates a non-linear decline in removal efficiency between 10°C and 1°C, with the existence of a kinetic threshold temperature delineated between 4°C and 2°C. As such, this delineated temperature range accounts for a significant decline in the performance of low carbon nitrifying MBBR systems during the onset of the cold seasons. This research identifies new recommended Arrhenius correction coefficient values taking into account this kinetic threshold temperature, with a coefficient of 1.049 being recommended above the kinetic threshold (≥4°C) and 1.149 below the threshold temperature at 1°C. Moreover, since the elapsed time to low temperature was identified as a key factor of attached growth nitrification kinetics, a modified theta model accounting for temperature and time is proposed in this research to accurately model the rate of nitrifying MBBR systems between 4°C and 1°C. Finally, with the severe adverse effects of sudden decreases in temperature, or cold shocks, on nitrification kinetics being previously demonstrated but not well understood, this research compares acclimatized and cold shocked MBBR reactors down to 1°C. The findings indicate 21% lower kinetics in the cold shocked reactor with reactor efficiencies never reaching those of the acclimatized reactor despite extended operation at 1°C. Thus, the research delineates the potentially lasting effects of extreme weather events such as cold air outbreaks and snowmelt periods on nitrifying MBBR system performance. On the other hand, these same findings demonstrate the resiliency of nitrifying MBBR reactors as nitrification was maintained within these systems despite being cold-shocked down from 10°C and 1°C. This study of attached growth kinetics was coupled with an investigation of the nitrifying biofilms, biomass, and microbiome responses to low temperatures and cold shock down to 1°C to provide an understanding of the changes occurring in these systems down to the cellular level. Comparisons of acclimatized and cold shocked nitrifying biofilms responses down to 1°C were characterized by increases in biofilm thickness, increases in biomass viability; and, greater shifts in microbiome communities occurring above 4°C in the acclimatized biofilm. Considering these observations, results also indicated a significant increase in nitrifiers per carrier above 4°C. As such, these findings suggested that the bulk of nitrifying biofilm adaptation to cold temperatures occurs above 4°C, a crucial adaptation phase in acclimatized systems. This adaptation phase is shown to be lacking in cold-shocked systems, with the cold shocked biofilm and microbiome demonstrating significant differences with the acclimatized systems’ biofilm and microbiome. This research was performed to answer the critical research questions relating to the design and operation of the post-carbon, low temperature nitrifying MBBR systems, with the first low temperature MBBR systems being scheduled to begin operation in the fall of 2020. This research expands the current knowledge on low temperature attached growth nitrification kinetics as well as cold shocked attached growth nitrification kinetics in MBBR systems down to 1°C. In addition, this research delineates the effects of low temperatures and cold shocks on the nitrifying MBBR system’s biofilms and their embedded cells.

Cold shock Y-box binding protein-1 (YB-1) coordinates several molecular processes between the nucleus and the cytoplasm and plays a crucial role in cell function. Moreover, it is involved in cancer progression, invasion, and metastasis. As trophoblast cells share similar characteristics with cancer cells, we hypothesized that YB-1 might also be necessary for trophoblast functionality. In samples of patients with intrauterine growth restriction, YB-1 mRNA levels were decreased, while they were increased in preeclampsia and unchanged in spontaneous abortions when compared to normal pregnant controls. Studies with overexpression and downregulation of YB-1 were performed to assess the key trophoblast processes in two trophoblast cell lines HTR8/SVneo and JEG3. Overexpression of YB-1 or exposure of trophoblast cells to recombinant YB-1 caused enhanced proliferation, while knockdown of YB-1 lead to proliferative disadvantage in JEG3 or HTR8/SVneo cells. The invasion and migration properties were affected at different degrees among the trophoblast cell lines. Trophoblast expression of genes mediating migration, invasion, apoptosis, and inflammation was altered upon YB-1 downregulation. Moreover, IL-6 secretion was excessively increased in HTR8/SVneo. Ultimately, YB-1 directly binds to NF-κB enhancer mark in HTR8/SVneo cells. Our data show that YB-1 protein is important for trophoblast cell functioning and, when downregulated, leads to trophoblast disadvantage that at least in part is mediated by NF-κB.