Taxonomic composition and spatio-temporal variability of macroinvertebrates inhabiting snags were examined from an 8-km segment of the Elm Fork of the Trinity River. Seventy-seven macroinvertebrate taxa were collected from submerged wood during the study. Assemblages were highly variable spatially and temporally, especially among seasons. An ordination of species and environment did not find snag taxa to have striking correlations with many of the selected environmental variables, although there were some trends in flow-mediated species distributions. There were significant seasonal differences in the abundances of some taxa, particularly among the Chironomidae (Diptera). The Tribe Orthocladiini was numerically abundant during the winter, while the Tribes Chironomini and Tanytarsini dominated the summer and autumn. Additionally, this study included a secondary production and microdistribution analysis of a population of the caddisfly Cyrnellus fraternus. Distributions of C. fraternus were restricted to snags, the most stable substratum for retreat building and for resisting periodic high waters. Larvae were not found in the soft sand and mud benthic habitats near submerged wood. The insects were multivoltine with a minimum of three generations per year. Pupae were collected July through September and adults emerged from May through October. The population overwintered as larvae. Estimated annual production was 1,015.4 mg/m2/yr. Mean standing stock biomass was 61.24 mg/m2, the cohort production/biomass ratio was 4.59, and the annual production/biomass rate was 16.58/yr for this population. Standing stock biomass ranged from 1.6 to 349.1 mg/m2 during the year and was significantly higher in autumn and summer than winter. Larvae were more abundant in the lower portions of the study area where flow was reduced for much of the year, than in the upper reaches, characterized by higher current velocities. C. fraternus larvae were found in their highest numbers on snags with dense deposits of silt and sand.

Distribution and life history characteristics of lacustrine-adfluvial bull trout (Salvelinus confluentus) were described in the North Fork Skokomish River Basin (including Lake Cushman, a reservoir) from 1994 to 1996. Day snorkeling was conducted in the river to determine initiation of the bull trout spawning migration, abundance of spawners, and duration of spawning. Declining photoperiod, increased river discharge, and decreased water temperature appeared to influence timing of migration and spawning. Lacustrine-adfluvial bull trout typically entered the North Fork Skokomish River in October although some fish entered as early as May. Mean lengths of spawners consistently increased from June to December 1996, and early migrating bull trout were shorter than those fish that entered after river discharge increased in October. The presence of two phases of the spawning migration may be indicative of two populations spawning in the river. Bull trout spawned between mid-September and December in the river and tributaries after water temperatures declined. All spawning occurred at temperatures less than 7.5��C. Comparisons with studies of other lacustrine-adfiuvial bull trout populations that inhabit river and reservoir complexes suggested that bull trout exhibit specific migratory strategies related to local environmental conditions. In the North Fork Skokomish River, changes in abundance of bull trout, mountain whitefish (Prosopium wilhamsom), cutthroat trout (Oncorhynchus dark), and rainbow trout (Oncorhynchus mykiss) revealed distinct temporal segregation among these species. Olympic National Park, a designated Biosphere Reserve, contains one of the largest remaining areas of relatively pristine habitat in the range of bull trout. Knowledge of responses of bull trout to changes in river discharge and temperature from relatively undisturbed systems, such as the North Fork Skokomish River, may be useful in understanding patterns observed in degraded environments. / Graduation date: 1998

No description available.

No description available.

In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks. Moreover, we have interrogated the role of forks interacting with individual sites of damage by using three damaging agents—MMS, 4NQO and bleomycin—that cause similar levels of replication slowing with very different frequency of DNA lesions. We find that the checkpoint slows replication by inhibiting origin firing, but not by decreasing fork rates. However, the checkpoint appears to facilitate replication of damaged templates, allowing forks to more quickly pass lesions. Finally, using a novel analytic approach, we rigorously identify fork stalling events in our combing data and show that they play a previously unappreciated role in shaping replication kinetics in response to DNA damage.

DNA is susceptible to various types of damage as a result of normal cellular metabolism or from environmental sources. In order to maintain genome stability a number of different, partially overlapping DNA repair pathways have evolved to tackle specific lesions or distortions in the DNA. Nucleotide excision repair (NER) is highly conserved throughout eukarya, bacteria and archaea and predominantly targets lesions that result from exposure to UV light, for example cyclobutane pyrimidine dimers and 6-4 photoproducts. The majority of archaea possess homologous of the eukaryotic repair genes and this thesis describes the isolation and the characterization of two XPB homologues identified in the crenarchaeon Sulfolobus solfataricus, SsoXPB1 and SsoXPB2. Human XPB is one of 10 proteins that make up the TFIIH transcription complex. The activity of XPB is tightly controlled by protein interactions, in particular with p52, which stimulates the ATPase activity of XPB. Rather than a conventional helicase, human XPB is thought to act as an ATP dependent conformational switch. Consistent with human XPB, however, the S. solfataricus proteins were unable to catalyse strand separation and the identification of an archaeal protein partner, Bax1, for SsoXPB2 was one of the focuses of this project. In order to maintain genome stability, the DNA must be replicated accurately with each cell cycle. When the advancing replication fork stalls at a lesion or a DNA break, it is crucial that the fork is reset and that replication continues to completion. The helicase Hel308 is thought to clear the lagging strand template of a stalled replication fork in order for replication restart to proceed via homologous recombination (HR). Although the specific function of Hel308 is not well understood, the possibilities are described in this thesis. Strand exchange proceeds to form a D-loop, followed by branch migration to increase regions of heterology during the synapsis stage of HR. No motors for branch migration have previously been recognised in archaea, although the identification of a possible candidate was investigated during this project.

This thesis aims toward developing strategies in the area of structural optimization and to implement these strategies in design processes. At   GM Powertrain Sweden where powertrains are designed and developed, two designs of a differential housing have been chosen for this thesis. The main tasks have been to perform a topology optimization of a model early in a design process, and a shape optimization on a model late in a design process. In addition the shape optimization strategies have also been applied on a fork shifter. This thesis covers the theory of different optimization strategies in general. The optimization processes are explained in detail and the results from the structural optimization of the differential housings as well as the fork shifter are shown and evaluated. The evaluation of the thesis provides enough arguments to suggest an implementation of the optimization strategies in design processes at GM Powertrain. A Structural Optimization group has great potential of closing the gap between structural designers and structural analysis engineers which in long terms mean that better structures can be developed in less time. To be competitive in the automotive industry these are two of the most important factors for being successful.

Durante o processo ensino/aprendizagem em Odontologia, é comum a ocorrência de inclinações do garfo de mordida em relação ao plano oclusal maxilar dos pacientes durante a tomada do arco facial realizada por alunos. Este trabalho avaliou a influência das inclinações do garfo de mordida para anterior e para posterior em relação ao plano oclusal na montagem do modelo maxilar em articuladores semi-ajustáveis do tipo arcon e não-arcon. Foram obtidos vinte modelos do arco maxilar de vinte pacientes, nos quais dois pontos foram marcados: um na aresta vestibular do canino direito e outro na aresta vestibular da cúspide mésio-vestibular do primeiro molar direito. Os registros no garfo de mordida foram realizados em três posições: garfo de mordida paralelo ao plano oclusal dos modelos, inclinado para anterior e para posterior (ambas 5º). Cada posição foi repetida cinco vezes, sendo o conjunto articulador/arco facial fixado em suporte especial para registro fotográfico. Cada fotografia foi levada ao programa Auto CAD, obtendo-se linhas de referências para a coleta de cinco medidas (uma angular e quatro lineares). Os dados obtidos foram submetidos à análise estatística paramétrica (Análise de Variância). Os resultados indicaram não haver diferença estatisticamente significante para inclinações do garfo de mordida tanto para anterior como para posterior em relação ao plano oclusal do modelo tanto para o articulador semi-ajustável do tipo arcon como para o não-arcon. O trabalho sugere que pequenas inclinações do garfo de mordida não comprometem a tomada do arco facial e sua transferência para articuladores semi-ajustáveis. / During the process teaching/learning in Dentistry, the occurrence of adverse inclinations of the bite fork concerned to maxillary occlusal plane of patients are current during the face-bow taking performed by students. This study evaluated the influence of the inclinations of bite fork to anterior and posterior related to oclusal plane on mounting of the maxillary cast in arcon and nonarcon semiadjustable articulators. Twenty casts of the maxillary arch from twenty patients were obtained, on which two points were marked: one on the vestibular edge of the right canine and another on the vestibular edge of mesiovestibular cusp of the right first molar. The records in the bite fork were made in three positions: the bite fork parallel to the castss plane occlusal, inclined to anterior and to posterior (both 5°). Each position was repeated five times, being the articulator/face-bow set fixed in special support for photographic register. Each photograph was introduced in Auto CAD program, resulting in lines of references for the collection of five measures (one angular and four linear). The data were subjected to statistical analysis parametric (Analysis of Variance). The results showed no significant statistical difference for inclinations of the bite fork to both anterior and to posterior related to the castss occlusal plane for the arcon and nonarcon semiadjustable articulators. The work suggests that small inclinations of bite fork do not compromise the face-bow taking and its transfer for the semiadjustable articulators.

Timely completion of DNA replication in each cell cycle is crucial for maintaining genomic integrity. This is often challenged by the presence of various replication fork barriers (RFBs). On collision with a RFB, the fate of the replication fork remains uncertain. In some cases, the integrity of the fork is maintained until the barrier is removed or the fork is rescued by merging with the incoming fork. However, fork stalling can cause dissociation of all of the associated replication proteins (fork collapse). If this occurs, the cell's recombination machinery can intervene to help restart replication in a process called recombination-dependent replication (RDR). Programmed protein-DNA barriers like the Replication Terminator Sequence-1 (RTS1) have been used to demonstrate that replication fork blockage can induce recombination. However, it remains unclear how efficiently this recombination gives rise to replication restart and whether the restarted replication fork exhibits the same fidelity as an origin-derived fork. It is also unknown whether accidental replication barriers induce recombination in the same manner as programmed barriers. In this study, I introduce recombination reporters at various sites downstream of RTS1 to obtain information on both the fidelity and efficiency of replication restart. I find that unlike break induced replication (BIR), the restarted fork gives rise to hyper-recombination at least 75 kb downstream of the barrier. Surprisingly, fork convergence, rather than inducing recombination, acts to prevent or curtail genetic instability associated with RDR. I also investigate a number of genetic factors that have a role in either preventing or promoting genome instability associated with the progression of the restarted fork. To compare RTS1 with an accidental protein-DNA barrier, a novel site-specific barrier system (called MarBl) was established based on the human mariner transposase, Hsmar1, binding to its transposon end. Replication fork blockage at MarBl strongly induces recombination, more so than at RTS1. This appears to be a general feature of accidental barriers as introduction of the E. coli TusB-TerB site-specific barrier in S. pombe gives rise to a similar effect. Here, I compare and contrast accidental barriers with programmed barriers. I observe that there is very little replication restart, if any, at MarBl measured by direct repeat recombination downstream. This points to the fact that accidental barriers do not trigger fork collapse in the same way as programmed RFBs and that the increased recombination that they cause may be a consequence of the inability of replication forks to terminate correctly, owing to the bi-directional nature of the barrier. Several genetic factors are assessed for their impact on MarBl-induced recombination, which further highlights both similarities and differences with RTS1-induced recombination.

Durante o processo ensino/aprendizagem em Odontologia, é comum a ocorrência de inclinações do garfo de mordida em relação ao plano oclusal maxilar dos pacientes durante a tomada do arco facial realizada por alunos. Este trabalho avaliou a influência das inclinações do garfo de mordida para anterior e para posterior em relação ao plano oclusal na montagem do modelo maxilar em articuladores semi-ajustáveis do tipo arcon e não-arcon. Foram obtidos vinte modelos do arco maxilar de vinte pacientes, nos quais dois pontos foram marcados: um na aresta vestibular do canino direito e outro na aresta vestibular da cúspide mésio-vestibular do primeiro molar direito. Os registros no garfo de mordida foram realizados em três posições: garfo de mordida paralelo ao plano oclusal dos modelos, inclinado para anterior e para posterior (ambas 5º). Cada posição foi repetida cinco vezes, sendo o conjunto articulador/arco facial fixado em suporte especial para registro fotográfico. Cada fotografia foi levada ao programa Auto CAD, obtendo-se linhas de referências para a coleta de cinco medidas (uma angular e quatro lineares). Os dados obtidos foram submetidos à análise estatística paramétrica (Análise de Variância). Os resultados indicaram não haver diferença estatisticamente significante para inclinações do garfo de mordida tanto para anterior como para posterior em relação ao plano oclusal do modelo tanto para o articulador semi-ajustável do tipo arcon como para o não-arcon. O trabalho sugere que pequenas inclinações do garfo de mordida não comprometem a tomada do arco facial e sua transferência para articuladores semi-ajustáveis. / During the process teaching/learning in Dentistry, the occurrence of adverse inclinations of the bite fork concerned to maxillary occlusal plane of patients are current during the face-bow taking performed by students. This study evaluated the influence of the inclinations of bite fork to anterior and posterior related to oclusal plane on mounting of the maxillary cast in arcon and nonarcon semiadjustable articulators. Twenty casts of the maxillary arch from twenty patients were obtained, on which two points were marked: one on the vestibular edge of the right canine and another on the vestibular edge of mesiovestibular cusp of the right first molar. The records in the bite fork were made in three positions: the bite fork parallel to the castss plane occlusal, inclined to anterior and to posterior (both 5°). Each position was repeated five times, being the articulator/face-bow set fixed in special support for photographic register. Each photograph was introduced in Auto CAD program, resulting in lines of references for the collection of five measures (one angular and four linear). The data were subjected to statistical analysis parametric (Analysis of Variance). The results showed no significant statistical difference for inclinations of the bite fork to both anterior and to posterior related to the castss occlusal plane for the arcon and nonarcon semiadjustable articulators. The work suggests that small inclinations of bite fork do not compromise the face-bow taking and its transfer for the semiadjustable articulators.