In the last decade the lowered Acoustic Doppler Current Profiler (LADCP) has become an important instrument in measuring full-water-depth profile of velocity in the open ocean. The basic principle of the LADCP is to lower one or two self-contained ADCP, one looking downward and the other looking upward, together with the CTD rosette during the hydrographic cast. After careful analysis of the ADCP data it is possible to retrieve surface ¡Vto-bottom profile of horizontal current velocity. In the present study we have conducted three cruises (21-25 April, 7-10 July and 11-13 October of 2007) in the Lanyu area to survey the Kuroshio flow structure by using the first set of LADCP in Taiwan. A total of 34 LADCP/CTD casts were completed. The results indicate that a major branch of the Kuroshio is located at the region between Taiwan and Lanyu, with a seasonal variation of flow intensity and vertical extent. Surface currents can reach a maximum speed of 70-140 cm/s northward. Kuroshio has a strongest speed (~140 cm/s) in October followed by July (~100 cm/s) and April (~90 cm/s). The vertical extent of the Kuroshio can extend to 400-m depth in October, 600-m depth in July and 400-m depth in April. A southward reverse current can be observed off the southeast Taiwan coast in depths between 200 and 800 m and the speed ranges between 30 and 60 cm/s. This southward flow is strongest in April (~60 cm/s), followed by July (~40 cm/s) and October (~30 cm/s). A cyclonic, cold eddy was observed in the eastern side of Lanyu from the shipboard ADCP data during the April cruise. The Kuroshio flows to the northwest during ebbs and to the northeast during floods from the LADCP observations at different tidal phases in July. Finally, analysis of the temperature-salinity characteristics of the CTD data reveals that the South China Sea waters can penetrate into and mix with the Kuroshio waters more significantly in summertime than in other season.

This study investigates the variations of flow field and water mass due to the influence of topographic effect in the Kaoping Submarine Canyon. The data used in this study are collected from five cruises of field observations using research vessel OR3. Instruments deployed include ship-board ADCP¡BCTD¡Btow-ADCP, moored ADCP and vertical arrays of temperature loggers. The collected data are analyzed through a variety of time series analysis technique, such as harmonic analysis¡Blow-pass filter¡BFFT and EOF analysis. The results show that (1) the flow in the Kao-ping Canyon was dominated by semi-diurnal tide. Harmonic analysis shows that both bottom layer and the shelf region are dominated by the M2 tide. The amplitude increases with canyon depth, and the major axis of tidal current align with canyon orientation. (2) Water mass are moving around by the oscillation tidal current along the canyon. During flood, surface water flow to southeast, while bottom flow is up canyon. During ebb, surface water goes to northwest, while bottom flow is down canyon. (3) The low-pass flows indicate a counter-clockwise rotation from surface down, which is explained due to bottom frictional effect. (4) EOF analysis of CTD profiles suggested that the first mode (semi-diurnal tide) can explain 88% of the variations.

<p>Eukaryotic RNA polymerase II (RNAPII) not only synthesizes mRNA, but also coordinates transcription-related processes through the post-translational modification of its unique C-terminal repeat domain (CTD). The CTD is an RNAPII specific extension of the enzyme's largest subunit and consists of multiple repeating heptads with the consensus sequence Y₁S₂P₃T₄S₅P₆S₇. In <italic>Saccharomyces cerevisiae (Sc)</italic>, RNAPII committed to productive elongation is phosphorylated at the S₂ positions of the CTD, primarily by CTDK-I (composed of the CDK-like Ctk1, the cyclin-like Ctk2, and Ctk3) the principal elongation-phase CTD kinase in <italic>Sc</italic>. Although responsible for the bulk of S₂ phosphorylation <italic>in vivo</italic>, Ctk1 coexists with the essential kinase Bur1 which also contributes to S₂ phosphorylation during elongation. In higher eukaryotes there appears to be only one CTD S₂ kinase: P-TEFb, which had been suggested to reconstitute the activity of both of the <italic>Sc</italic> S₂ CTD kinases. Based on comparative genomics, we hypothesized that the previously-unstudied <italic>Drosophila</italic> CDK12 (dCDK12) and little-studied human CDK12 and CDK13 (hCDK12 and hCDK13) proteins are CTD elongation-phase kinases, the metazoan orthologs of yeast Ctk1. Using fluorescence microscopy we show that the distribution of dCDK12 on formaldehyde-fixed polytene chromosomes is virtually identical to that of hyperphosphorylated RNAPII, but is distinct from that of P-TEFb. Chromatin immunoprecipitation experiments confirm that dCDK12 is present on the transcribed regions of active <italic>Drosophila</italic> genes in a pattern reminiscent of a S₂ CTD kinase. Appropriately, we show that dCDK12, hCDK12, and hCDK13 purified from nuclear extracts manifest CTD kinase activity <italic>in vitro</italic> and associate with CyclinK, implicating it as the cyclin subunit of the kinase. Most importantly we demonstrate that RNAi knockdown of dCDK12 in <italic>Drosophila</italic> cell culture and hCDK12 in human cell lines alters the phosphorylation state of the CTD. In an effort to further characterize the transcriptional roles of human CDK12/CyclinK we overexpress, purify to near homogeneity, and characterize, full-length hCDK12/CyclinK. Additionally, we also identify hCDK12 associated proteins via mass spectrometry, revealing interactions with multiple RNA processing factors, and attempt to engineer an analog sensitive CDK12 human cell line. Overall, these results demonstrate that CDK12 is a major elongation-associated CTD kinase, the ortholog of yCtk1. Our findings clarify the relationships between two yeast CDKs, Ctk1 and Bur1, and their metazoan homologues and draw attention to major metazoan CTD kinase activities that have gone unrecognized and unstudied until now. Furthermore, the results suggest that hCDK12 affects RNA processing events in two distinct ways: Indirectly through generating factor-binding phospho-epitopes on the CTD of elongating RNAPII and directly through binding to specific factors.</p> / Dissertation

In addition to AtCPL1-4, the genome of Arabidopsis thaliana encodes a large number of putative acid phosphatases. The predicted Arabidopsis SCP1-like small phosphatases (SSP) are highly homologous to the catalytic domain of eukaryotic RNA polymerase II carboxyl terminal domain (pol II CTD) phosphatases. Among the family members, SSP4, SSP4b and SSP5 form a unique group characterized by long N-terminal extensions. These three SSPs showed similar and ubiquitous gene expression. SSP4 and SSP4b were localized exclusively in the nuclei, while SSP5 accumulated both in the nucleus and cytoplasm. In vitro observation revealed that SSP4 and SSP4b dephosphorylated the pol II CTD-PO4 at both Ser2 and Ser5 in the conserved heptad repeats; however, SSP5 dephosphorylated only Ser5 of CTD-PO4. These results indicate that Arabidopsis SSP family encodes active CTD phosphatases similarly to animal SCP1 family proteins and plant CPLs family proteins, but with distinct substrate specificities. ssp mutants did not exhibit phenotypic abnormalities under normal growth conditions. However, ssp5 single mutants and ssp4 ssp4b ssp5 triple mutants showed enhanced sensitivity to ABA and glucose during seed germination. Yet, increased ABA-inducible gene expressions were not distinguishable in triple mutants compared to wild type plants upon ABA treatment. Unlike the ssp mutations, the cpl1 mutation strongly induced RD29A expression in response to cold, ABA and NaCl treatments. Thus, the cpl1 mutant is an ideal genetic background for an inducible gene expression system, in which the detrimental effect to host plants caused by a conventional constitutive expression could be avoided. Production of flavonoid such as anthocyanins in Arabidopsis is relatively easy to monitor and is regulated by transcription factors such as PAP1. PAP1 activates the expression of multiple enzymes in the anthocyanin biosynthesis pathway; however, high level of flavonoid production could cause vegetative growth retardation. To optimize flavonoid accumulation, a three-component system was designed consisting of a cold inducible RD29A-PAP1 expression cassette, a feedforward effector RD29A-CBF3, and a mutation in host repressor CPL1. Transgenic cpl1 plants containing both homozygous PAP1 and CBF3 transgenes produced 30-fold higher level of total anthocyanins than control plants upon cold treatment. LC/MS/MS analysis showed the flavonoid profile in cold-induced transgenic plants resembled that of previously reported pap1-D plants but were enriched for kaempferol derivatives. Furthermore, PAP1 and environmental signals synergistically regulate flavonoid pathway to produce a flavonoid blend that has not been produced by PAP1 overexpression or cold treatment alone. These results delineate the usability of the three-component inducible system in plant metabolic engineering.

This study investigates the structures of flow field in the mouth of Kao-Ping River, southwest Taiwan. The data used in this study are collected from several cruises of field observations using research vessel OR3 and fishing boats. Instruments deployed include bmADCP, sbADCP, towADCP, Aquadopp, CTD, XR420 and Seacat37. Spatial and temporal variations of flow, sea level, temperature and salinity data are sampled. The collected data are analyzed through harmonic analysis, low-pass filter and FFT. Results from previously study showed that cold water flowed eastward into the canyon during flood, and westward out of the canyon during ebb. This study shows that the canyon head is not the channel for bottom layer water to climb up into the shallow bank or the river (perhaps the bottom water climb up over shelf at the turning of the canyon 5 km offshore). The summaries are: (1)Water mass are moving around dominated by the oscillation M2 tidal current. There are 3 hours lag between sea level and flow. Maximum out canyon flow found at the peak of flood, while in canyon flow found at the low water. (2)The coastal surface water flows southeast during flood, and goes to northwest during ebb. (3)Tide current is the primary dynamic in the Kaoping River.During flood, lower temperature and higher salinity seawater is up river. During ebb, higher temperature and lower salinity is down the river. Amplitude of tidal current decreases with depth (likely due to bottom friction) at river mouth depth of 3 meters.

No description available.

La plus grosse sous-unité (Rpb1) de l'ARN polymérase II est caractérisée par une structure unique et flexible au niveau du domaine C-terminal (CTD) qui consiste en une répétition en tandem d'une séquence consensus heptapeptidique Y1-S2-P3-T4-S5-P6-S7. Le CTD est essentiel pour pour la viabilité cellulaire et est requis pour d'importantes activités associées avec la transcription par l'ARN Pol II, dont la régulation de la synthèse de l'ARN et des événements de maturation co-transcriptionnels (mise en place de la coiffe 5', épissage, terminaison en 3'... etc). Forts d'un système permettant l'expression conditionnelle de mutants du CTD, nous disséquons le CTD afin de comprendre l'implication de résidus/répétitions spécifiques sur la transcription dans des cellules mammifères. Nos résultats montrent que le CTD est crucial pour le contrôle de la transcription pervasive et indiquent une implication inédite des complexes Mediateur et Integrateur dans le processus de terminaison de la transcription. / The largest subunit (Rpb1) of RNA polymerase II has a unique and flexible structure at its C-terminal domain (CTD) that consists of tandem repeats with the consensus heptad sequence Y1-S2-P3-T4-S5-P6-S7. The CTD is essential for cellular viability and is required for important activities associated with RNA pol II transcription, including the regulation of RNA synthesis and co-transcriptional processing events (5’ capping, splicing, 3’ termination…etc). Using a conditional CTD mutant expression system, we dissect the importance of specific residues/repeats on transcription in mammalian cells. Our results indicate the importance of the CTD in the control of pervasive transcription and hints to novel roles of the Mediator and Integrator complexes in transcription termination processes.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

RNA polymerase II (Pol II) is responsible for the transcription of all protein-coding and some non-coding genes in eukaryotes. Its largest subunit, Rpb1, contains a unique C-terminal domain (CTD) which consists of repeats of the heptad YSPTSPS. It acts as a binding platform for proteins that control the different stages of transcription and their recruitment is regulated mainly by differential phosphorylation of residues contained within the CTD. Previous studies could unveil proteins containing a CTD-interacting domain (CID) as important players that specifically bind to certain phosphorylation types of the CTD. More precisely, they were shown to be important for the last step of transcription, termination. Despite extensive research over the past 30 years, the exact mechanism of how these proteins facilitate the dislodgement of Pol II from the DNA template, still remains unknown. The work presented here contains detailed studies of the CID-containing protein Seb1 from the fission yeast Schizosaccharomyces pombe, revealing an unexpectedly broad role of this protein in transcription termination. In addition to a CID, Seb1 also contains an RNA recognition motif (RRM) which allows direct binding to RNA. Here, I present high-resolution crystal structures of both domains of Seb1. While the CID has a very conserved fold, the RNA binding regions contains an unusual arrangement of a canonical RRM intertwined with a second domain that are both important for RNA binding. Structure-based mutations were introduced and a combination of in vitro and genome-wide in vivo studies uncover Seb1 as an essential player in transcription termination. Importantly, both domains are required to promote the full function of Seb1. Despite its homology to the well-studied budding yeast protein Nrd1, the role of Seb1 in fission yeast is quite different. This thesis therefore provides important insight into the mechanisms that underlie eukaryotic transcription termination.

The aim of this master thesis has been to design, and partly manufacture and evaluate, a highly miniaturized, on-chip conductivity-temperature-depth (CTD) sensor system for deepwater analysis also including electrodes for pH and chloride ion concentration measurements. The microtechnology-based sensor system will be a vital instrument onboard the Deeper Access, Deeper Understanding submersible, which will be small enough for deployment through bore holes into the subglacial lakes of Antarctica. Design of the complete 15 x 30 mm chip, including variations of each sensor type (in total 39 sensors), is presented. Salinity (through conductivity), temperature, chloride ion concentration and pH sensors have been manufactured using conventional lithography, evaporation, wet etching and lift off techniques. Simulations of the pressure sensors (not manufactured) show how the set of four bossed membranes with integrated strain gauges combine to cover, yet withstand, pressures of 1-100 atm. Salinity is measured conductively with gold electrodes. The temperature sensor is a platinum thermoresistor. Chloride ion concentration and pH are measured potentiometrically with ion-selective microelectrodes of silver/silver chloride and iridium oxide, respectively. Tests of the conductivity sensor gave good results also on sea water samples of known salinity. The temperature sensor showed good linearity to a reference sensor in the tested range of 5-35 C. Issues with evaporation and lift off are discussed, and a process identification document is attached. / DADU