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• 131. [Article] Early Identification of At-Risk Children in a Rural School District Using Multiple Predictor Variables

  The purpose of this study was to determine if data routinely collected during the kindergarten year and at entry into first grade could be used to predict whether a child would be perceived as successful ...

  Citation × Citation Citation Abstract Copy Title: Early Identification of At-Risk Children in a Rural School District Using Multiple Predictor Variables Author: Wilde, Richard Wayne Year: 1991 The purpose of this study was to determine if data routinely collected during the kindergarten year and at entry into first grade could be used to predict whether a child would be perceived as successful or not successful by the end of first grade. The need for immediate continued research on this topic was established through the review of literature, which highlighted the extent of the at-risk problem both locally and nationally. The growing number of at-risk students combined with the minimal impact of the educational programs mandates the need to identify these students in time to prevent school failure. However, clear identification procedures are not currently available and previous studies have raised substantial questions regarding the accuracy of early identification procedures. The presenting problem of this study was to determine the sensitivity and specificity of a set of predictor variables, and then to analyze these findings as to whether or not they were accurate enough for use as an initial identification process for subsequent classes. The primary research approach of this study was a longitudinal data collection and correlational analysis, with discriminant analysis techniques used to determine predictive accuracy. The study was limited to data on the class of 2001 from two elementary schools within the Washougal School District. The data collected and the subsequent analysis were used to answer six exploratory research questions. No hypothesis was proposed. This study used ratings and scores obtained from the administration of the Preschool Screening system, kindergarten teacher ratings, the School Success Rating Scale, and the Gates-MacGinitie Reading Readiness Tests as predictor variables. Criterion measures of school success/failure were: placement into special programs or grade retention, and end-of-first-grade evaluations of individual student success (report cards, teacher ratings, Gates-MacGinitie Reading Achievement, and the School Success Ratings Scale). The demographic variables of gender, age, parent marital status, and eligibility for free or reduced lunch were analyzed for their potential to exceed or enhance the accuracy of the predictor variables. Three types of measurement were defined and required in order for a predictor or predictor combination to be considered adequate for use in an identification process. These were overall accuracy, criterion sensitivity and specificity accuracy, and prediction sensitivity and specificity accuracy. An 80 percent accuracy level was desired on all three types of measurement. Findings of this study indicated that no single or combination of predictor, and/or demographic variables produced all three desired levels of accuracy. Various combinations of the predictor and demographic variables produced overall accuracy rates exceeding 80 percent for each of the criterion variables. Criterion measured sensitivity and specificity were found to be adequate for use in the prediction of at-risk students. Prediction measured specificity was also found to be highly accurate. Prediction sensitivity, however, was below the desired 80 percent level, indicating that the predictor variables over identify at-risk students. It was concluded that the predictor variables could be used in an identification process if mild over-identification of at-risk students was acceptable to the district. Any use of these identification procedures is assumed to be in connection with ethical intervention practices. Recommendations from this study included cross validation of the results and continuation of the study regarding the predictive accuracy of the identified variables as the students move through higher grade levels. The study also encouraged the Washougal School District to develop a formal collection and processing procedure for their routinely collected data. Title: Early Identification of At-Risk Children in a Rural School District Using Multiple Predictor Variables Author: Wilde, Richard Wayne Year: 1991 The purpose of this study was to determine if data routinely collected during the kindergarten year and at entry into first grade could be used to predict whether a child would be perceived as successful or not successful by the end of first grade. The need for immediate continued research on this topic was established through the review of literature, which highlighted the extent of the at-risk problem both locally and nationally. The growing number of at-risk students combined with the minimal impact of the educational programs mandates the need to identify these students in time to prevent school failure. However, clear identification procedures are not currently available and previous studies have raised substantial questions regarding the accuracy of early identification procedures. The presenting problem of this study was to determine the sensitivity and specificity of a set of predictor variables, and then to analyze these findings as to whether or not they were accurate enough for use as an initial identification process for subsequent classes. The primary research approach of this study was a longitudinal data collection and correlational analysis, with discriminant analysis techniques used to determine predictive accuracy. The study was limited to data on the class of 2001 from two elementary schools within the Washougal School District. The data collected and the subsequent analysis were used to answer six exploratory research questions. No hypothesis was proposed. This study used ratings and scores obtained from the administration of the Preschool Screening system, kindergarten teacher ratings, the School Success Rating Scale, and the Gates-MacGinitie Reading Readiness Tests as predictor variables. Criterion measures of school success/failure were: placement into special programs or grade retention, and end-of-first-grade evaluations of individual student success (report cards, teacher ratings, Gates-MacGinitie Reading Achievement, and the School Success Ratings Scale). The demographic variables of gender, age, parent marital status, and eligibility for free or reduced lunch were analyzed for their potential to exceed or enhance the accuracy of the predictor variables. Three types of measurement were defined and required in order for a predictor or predictor combination to be considered adequate for use in an identification process. These were overall accuracy, criterion sensitivity and specificity accuracy, and prediction sensitivity and specificity accuracy. An 80 percent accuracy level was desired on all three types of measurement. Findings of this study indicated that no single or combination of predictor, and/or demographic variables produced all three desired levels of accuracy. Various combinations of the predictor and demographic variables produced overall accuracy rates exceeding 80 percent for each of the criterion variables. Criterion measured sensitivity and specificity were found to be adequate for use in the prediction of at-risk students. Prediction measured specificity was also found to be highly accurate. Prediction sensitivity, however, was below the desired 80 percent level, indicating that the predictor variables over identify at-risk students. It was concluded that the predictor variables could be used in an identification process if mild over-identification of at-risk students was acceptable to the district. Any use of these identification procedures is assumed to be in connection with ethical intervention practices. Recommendations from this study included cross validation of the results and continuation of the study regarding the predictive accuracy of the identified variables as the students move through higher grade levels. The study also encouraged the Washougal School District to develop a formal collection and processing procedure for their routinely collected data. Close

• 132. [Article] An Experimental Study of Scotopic Sensitivity Irlen Syndrome in Learning Disabled Students

  This study examined the effect on reading performance of a controversial treatment for a dysfunction of visual perception known as Scotopic sensitivity/lrlen Syndrome. The treatment, referred to as spectral ...

  Citation × Citation Citation Abstract Copy Title: An Experimental Study of Scotopic Sensitivity Irlen Syndrome in Learning Disabled Students Author: Farber, Kathleen Hickam Year: 1994 This study examined the effect on reading performance of a controversial treatment for a dysfunction of visual perception known as Scotopic sensitivity/lrlen Syndrome. The treatment, referred to as spectral modification, involved the use of colored transparent overlays for reading by four elementary school children in their actual school environments. The diagnostic, prescriptive and remediation procedures used in this study were originally developed by Helen Irlen, a California psychologist and researcher. Irlen conceptualized Scotopic Sensitivity Syndrome as a difficulty in visual processing of the printed page when perceived through full spectrum light. Spectral modification techniques were considered controversial in that they were employed prior to scientific validation of the syndrome. Previous research used pre-test/post-test experimental designs to test the effect of spectral modification on reading performance. The research problem addressed here was that the technique had not been systematically examined over time in the school setting, and from the practitioner's point of view. Sample selection involved pre-screening and screening phases. The pre-screening procedures of teacher recommendation and file review resulted in a pool of 26 children who were screened with the Irlen Differential Perceptual Interview Survey. Four subjects were selected who were in separate school settings, who demonstrated Irlen Syndrome to a significant extent, and whose profiles did not present variables which would compromise their participation. These four underwent comprehensive vision evaluations as a preliminary assessment procedure. A four-strand single-subject experimental design was used to generate data on subjects' rate and accuracy of oral reading, and comprehension of silent reading. Performance changes during experimental reading trials varied between the four, although three subjects exhibited positive performance change on one indicator. A supporting procedure was that subjects were pre and post-tested on the three performance indicators. Post-test results corroborated the changes demonstrated by three subjects Interview formats were employed to obtain qualitative data from teachers, parents, and the subjects themselves. Recommendations for practitioners intending to implement spectral modification techniques were generated from this data. Title: An Experimental Study of Scotopic Sensitivity Irlen Syndrome in Learning Disabled Students Author: Farber, Kathleen Hickam Year: 1994 This study examined the effect on reading performance of a controversial treatment for a dysfunction of visual perception known as Scotopic sensitivity/lrlen Syndrome. The treatment, referred to as spectral modification, involved the use of colored transparent overlays for reading by four elementary school children in their actual school environments. The diagnostic, prescriptive and remediation procedures used in this study were originally developed by Helen Irlen, a California psychologist and researcher. Irlen conceptualized Scotopic Sensitivity Syndrome as a difficulty in visual processing of the printed page when perceived through full spectrum light. Spectral modification techniques were considered controversial in that they were employed prior to scientific validation of the syndrome. Previous research used pre-test/post-test experimental designs to test the effect of spectral modification on reading performance. The research problem addressed here was that the technique had not been systematically examined over time in the school setting, and from the practitioner's point of view. Sample selection involved pre-screening and screening phases. The pre-screening procedures of teacher recommendation and file review resulted in a pool of 26 children who were screened with the Irlen Differential Perceptual Interview Survey. Four subjects were selected who were in separate school settings, who demonstrated Irlen Syndrome to a significant extent, and whose profiles did not present variables which would compromise their participation. These four underwent comprehensive vision evaluations as a preliminary assessment procedure. A four-strand single-subject experimental design was used to generate data on subjects' rate and accuracy of oral reading, and comprehension of silent reading. Performance changes during experimental reading trials varied between the four, although three subjects exhibited positive performance change on one indicator. A supporting procedure was that subjects were pre and post-tested on the three performance indicators. Post-test results corroborated the changes demonstrated by three subjects Interview formats were employed to obtain qualitative data from teachers, parents, and the subjects themselves. Recommendations for practitioners intending to implement spectral modification techniques were generated from this data. Close

• 133. [Article] Spatial and temporal population dynamics of Cantharellus formosus, the Pacific Golden chanterelle, in Oregon

  This dissertation was undertaken to improve the understanding of the population dynamics of the Pacific Golden chanterelle, Cantharellus formosus. It addresses the longevity of individuals over a 12 year ...

  Citation × Citation Citation Abstract Copy Title: Spatial and temporal population dynamics of Cantharellus formosus, the Pacific Golden chanterelle, in Oregon Author: Collins, Kelly Patrice This dissertation was undertaken to improve the understanding of the population dynamics of the Pacific Golden chanterelle, Cantharellus formosus. It addresses the longevity of individuals over a 12 year period and the limits of gene flow within the area of a 6,400 hectare watershed at the H.J. Andrews Long Term Ecological Research site and the 112 km square Willamette Valley of Oregon. I found that certain genets (i.e. genotypic individuals), called predominant genets, were able to survive for many years and inhabited an area of approximately 4 meters in diameter. Predominant genets produced sporocarps nearly every year, but many related and unrelated genets appeared and disappeared within the boundaries of that genet (as measured by sporocarps), especially in abundant or "good" years of sporocarp production. There was very little differentiation found between 9 plots in the the 6,400 hectare watershed (FST=0.001-0.008). Most differentiation was driven by one or two plots that differed in each of the years sampled (1998, 2000). Migration rates and genetic diversity also differed within the two years sampled. These results demonstrate the differences that occur between abundant years, when many different genets produce a single sporocarp, and less abundant years, when only the predominant genets produce sporocarps. The trend of little differentiation continued at the larger scale when the Willamette Valley was tested as a barrier to dispersal. I found no barrier to dispersal between the Coast Mountain Range and the Cascade Mountain Range that border the Willamette Valley. The two northernmost populations on the Coast Range showed somewhat larger differentiation, as did parameters between populations when evaluated by region. Analysis of molecular variance partitioned nearly twice the amount of variance to regions when calculated by genotypic frequencies (11%) as opposed to allelic frequencies (6%). This suggests that there is a tendency for genetic exchange between close populations. Differentiation was not supported by low estimated migration rates. These findings support a heirarchical dispersal scenario in which the majority of spores fall close to the parental sporocarp and mate with close neighbors. Other spores are captured in surface air currents and dispersed to other populations nearby. A few spores are transported to higher convection layers that disperse them many miles. The overall factor that limits the dispersal of C. formosus is not capacity to disperse, but more likely environmental factors such as availability of host trees like Douglas fir, Hemlock, and Sitka Spruce, proper moisture conditions of the soil, and low exchangeable acidity. Title: Spatial and temporal population dynamics of Cantharellus formosus, the Pacific Golden chanterelle, in Oregon Author: Collins, Kelly Patrice This dissertation was undertaken to improve the understanding of the population dynamics of the Pacific Golden chanterelle, Cantharellus formosus. It addresses the longevity of individuals over a 12 year period and the limits of gene flow within the area of a 6,400 hectare watershed at the H.J. Andrews Long Term Ecological Research site and the 112 km square Willamette Valley of Oregon. I found that certain genets (i.e. genotypic individuals), called predominant genets, were able to survive for many years and inhabited an area of approximately 4 meters in diameter. Predominant genets produced sporocarps nearly every year, but many related and unrelated genets appeared and disappeared within the boundaries of that genet (as measured by sporocarps), especially in abundant or "good" years of sporocarp production. There was very little differentiation found between 9 plots in the the 6,400 hectare watershed (FST=0.001-0.008). Most differentiation was driven by one or two plots that differed in each of the years sampled (1998, 2000). Migration rates and genetic diversity also differed within the two years sampled. These results demonstrate the differences that occur between abundant years, when many different genets produce a single sporocarp, and less abundant years, when only the predominant genets produce sporocarps. The trend of little differentiation continued at the larger scale when the Willamette Valley was tested as a barrier to dispersal. I found no barrier to dispersal between the Coast Mountain Range and the Cascade Mountain Range that border the Willamette Valley. The two northernmost populations on the Coast Range showed somewhat larger differentiation, as did parameters between populations when evaluated by region. Analysis of molecular variance partitioned nearly twice the amount of variance to regions when calculated by genotypic frequencies (11%) as opposed to allelic frequencies (6%). This suggests that there is a tendency for genetic exchange between close populations. Differentiation was not supported by low estimated migration rates. These findings support a heirarchical dispersal scenario in which the majority of spores fall close to the parental sporocarp and mate with close neighbors. Other spores are captured in surface air currents and dispersed to other populations nearby. A few spores are transported to higher convection layers that disperse them many miles. The overall factor that limits the dispersal of C. formosus is not capacity to disperse, but more likely environmental factors such as availability of host trees like Douglas fir, Hemlock, and Sitka Spruce, proper moisture conditions of the soil, and low exchangeable acidity. Close

• 134. [Article] Influence of lidar, Landsat imagery, disturbance history, plot location accuracy, and plot size on accuracy of imputation maps of forest composition and structure

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier ...

  Citation × Citation Citation Abstract Copy Title: Influence of lidar, Landsat imagery, disturbance history, plot location accuracy, and plot size on accuracy of imputation maps of forest composition and structure Author: Braaten, Justin, Gregory, Matthew J., McGaughey, Robert J., Roberts, Heather M., Henderson, Emilie B., Ohmann, Janet L., Zald, Harold S. J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/remote-sensing-of-environment/. Title: Influence of lidar, Landsat imagery, disturbance history, plot location accuracy, and plot size on accuracy of imputation maps of forest composition and structure Author: Braaten, Justin, Gregory, Matthew J., McGaughey, Robert J., Roberts, Heather M., Henderson, Emilie B., Ohmann, Janet L., Zald, Harold S. J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/remote-sensing-of-environment/. Close

• 135. [Article] Degradation kinetics of taxol using mass spectroscopy

  Paclitaxel is a very important anticancer drug commonly called Taxol®. We know from previous work (Hoffman, et al., 1998) that Taxol exists in filbert, Corylus avellana L. material. Quantification of ...

  Citation × Citation Citation Abstract Copy Title: Degradation kinetics of taxol using mass spectroscopy Author: Zhang, Jun Paclitaxel is a very important anticancer drug commonly called Taxol®. We know from previous work (Hoffman, et al., 1998) that Taxol exists in filbert, Corylus avellana L. material. Quantification of Taxol in filbert plant material is painstaking and hitherto was accomplished by rapidly processing single batches in a complicated procedure (Hoffman, et al., 1998), which seemingly unavoidably, was accompanied by some degradation. However for extraction, testing, plant physiological and horticultural purposes a simplified method of determining Taxol yield is required. All simplified methods tested were found limited by rapid degradation of Taxol. Under these conditions not only is the sought product broken down, but we were unable to distinguish Taxol precursors from degradation products. Thus it was decided to go back to first principles and study the degradation of Taxol in vitro. Degradation kinetics of Taxol was studied using electrospray ionization mass spectrometry (ESIMS) to identify possible Taxol adducts and degradation products. Our preparation for ESIMS analysis by experimental necessity involved various other components. Since some of these components interacted with the degradation products, we developed a program to distinguish these putative adducts from spurious components found in the system and we were able to plot the pH dependence of Taxol degradation in this system at room temperature (approximately 25oC). The results of the mass spectrometric analysis of these degradants were found dependent on pH and time. Our results show major degradation at pH 9 and beyond, plus minor degradation at pH 5. Two optimum pHs for stability were found at pH 4 and pH 7. This data varies slightly from the published results Dordunoo and Burt (1996). Our smoother curves define two pHs events in this pH range which to our knowledge, have not been reported and our temperature was lower. We hope that this information will help us extract Taxol more efficiently with greater yield from novel plant sources, e.g. hazel (filbert) tree, Corylus avellana L. The possibility of Taxol dimer formation in solution and perhaps in vivo can be inferred, but not proven, in this work. This dimer, may exist, in dynamic equilibrium with parent compound, Taxol. Title: Degradation kinetics of taxol using mass spectroscopy Author: Zhang, Jun Paclitaxel is a very important anticancer drug commonly called Taxol®. We know from previous work (Hoffman, et al., 1998) that Taxol exists in filbert, Corylus avellana L. material. Quantification of Taxol in filbert plant material is painstaking and hitherto was accomplished by rapidly processing single batches in a complicated procedure (Hoffman, et al., 1998), which seemingly unavoidably, was accompanied by some degradation. However for extraction, testing, plant physiological and horticultural purposes a simplified method of determining Taxol yield is required. All simplified methods tested were found limited by rapid degradation of Taxol. Under these conditions not only is the sought product broken down, but we were unable to distinguish Taxol precursors from degradation products. Thus it was decided to go back to first principles and study the degradation of Taxol in vitro. Degradation kinetics of Taxol was studied using electrospray ionization mass spectrometry (ESIMS) to identify possible Taxol adducts and degradation products. Our preparation for ESIMS analysis by experimental necessity involved various other components. Since some of these components interacted with the degradation products, we developed a program to distinguish these putative adducts from spurious components found in the system and we were able to plot the pH dependence of Taxol degradation in this system at room temperature (approximately 25oC). The results of the mass spectrometric analysis of these degradants were found dependent on pH and time. Our results show major degradation at pH 9 and beyond, plus minor degradation at pH 5. Two optimum pHs for stability were found at pH 4 and pH 7. This data varies slightly from the published results Dordunoo and Burt (1996). Our smoother curves define two pHs events in this pH range which to our knowledge, have not been reported and our temperature was lower. We hope that this information will help us extract Taxol more efficiently with greater yield from novel plant sources, e.g. hazel (filbert) tree, Corylus avellana L. The possibility of Taxol dimer formation in solution and perhaps in vivo can be inferred, but not proven, in this work. This dimer, may exist, in dynamic equilibrium with parent compound, Taxol. Close

• 136. [Article] Selective control of Cirsium arvense (L.) Scop. in Mentha piperita L. with 3,6-dichloropicolinic acid

  A series of field experiments was conducted during 1975 and 1976 to examine peppermint tolerance and Canada, thistle response to Dowco 290 (3, 6- dichloropicolinic acid). Peppermint oil yield and Canada ...

  Citation × Citation Citation Abstract Copy Title: Selective control of Cirsium arvense (L.) Scop. in Mentha piperita L. with 3,6-dichloropicolinic acid Author: Whitesides, Ralph E. A series of field experiments was conducted during 1975 and 1976 to examine peppermint tolerance and Canada, thistle response to Dowco 290 (3, 6- dichloropicolinic acid). Peppermint oil yield and Canada thistle density were considered most important in evaluating experimental results. Peppermint tolerance to Dowco 290 was studied in weed-free peppermint (cv. Mitcham).. Rates of 0.25 lb/A or more reduced peppermint oil yield. Time of application appeared to be less critical than rate of herbicide as oil production decreased with increasing rates. Mint injury was sufficiently severe at high rates to cause yield reductions the year of treatment, but recovery was good and no reduction in oil yield was found 1 year later. Spring application of Dowco 290 to peppermint (cv. Mitcham and Todd's Mitcham) infested with Canada thistles resulted in erratic oil yield but good thistle control. Oil yield was difficult to evaluate because of the variability of the peppermint stand. All rates of Dowco 290 tested gave good short-term thistle control and rates of 0.5 lb/A or more gave excellent seasonal control, There was no advantage to split applications of Dowco 290 (fall plus spring) over a single application in the spring. An excellent combination of good thistle control and high oil yield was obtained from sequential treatments in the spring when 0.125 lb/A was applied 10 weeks prior to harvest and 0.063 lb/A was applied 2 weeks later. Trans location of Dowco 290 through underground thistle parts was demonstrated by treating parent plants and observing the response in a connected daughter plant. The herbicide was not lethal at rates that translocated to connected plants, but it did cause abnormal floral development. Dowco 290 was sufficiently active when applied at 0.25 lb/A to control all underground plant parts of test thistles even when treated plant parts were removed as soon as 1 hour after treatment. Root mortality was measured by a modified tetrazolium test. Seedling Canada thistle plants were slightly more sensitive to Dowco 290 than plants which developed from mature rootstock. After seedling plants had developed a more complex root system, regrowth from rootstock of plants grown from seed and from mature rootstock was similar. Title: Selective control of Cirsium arvense (L.) Scop. in Mentha piperita L. with 3,6-dichloropicolinic acid Author: Whitesides, Ralph E. A series of field experiments was conducted during 1975 and 1976 to examine peppermint tolerance and Canada, thistle response to Dowco 290 (3, 6- dichloropicolinic acid). Peppermint oil yield and Canada thistle density were considered most important in evaluating experimental results. Peppermint tolerance to Dowco 290 was studied in weed-free peppermint (cv. Mitcham).. Rates of 0.25 lb/A or more reduced peppermint oil yield. Time of application appeared to be less critical than rate of herbicide as oil production decreased with increasing rates. Mint injury was sufficiently severe at high rates to cause yield reductions the year of treatment, but recovery was good and no reduction in oil yield was found 1 year later. Spring application of Dowco 290 to peppermint (cv. Mitcham and Todd's Mitcham) infested with Canada thistles resulted in erratic oil yield but good thistle control. Oil yield was difficult to evaluate because of the variability of the peppermint stand. All rates of Dowco 290 tested gave good short-term thistle control and rates of 0.5 lb/A or more gave excellent seasonal control, There was no advantage to split applications of Dowco 290 (fall plus spring) over a single application in the spring. An excellent combination of good thistle control and high oil yield was obtained from sequential treatments in the spring when 0.125 lb/A was applied 10 weeks prior to harvest and 0.063 lb/A was applied 2 weeks later. Trans location of Dowco 290 through underground thistle parts was demonstrated by treating parent plants and observing the response in a connected daughter plant. The herbicide was not lethal at rates that translocated to connected plants, but it did cause abnormal floral development. Dowco 290 was sufficiently active when applied at 0.25 lb/A to control all underground plant parts of test thistles even when treated plant parts were removed as soon as 1 hour after treatment. Root mortality was measured by a modified tetrazolium test. Seedling Canada thistle plants were slightly more sensitive to Dowco 290 than plants which developed from mature rootstock. After seedling plants had developed a more complex root system, regrowth from rootstock of plants grown from seed and from mature rootstock was similar. Close

• 137. [Article] Genetic patterns of demography and diversity in eastern North Pacific rockfishes (genus Sebastes)

  The 100 North Pacific rockfish species in the genus Sebastes are highly diverse. Rockfishes fertilize their eggs internally and release swimming larvae. Complex courting behaviors may allow female rockfish ...

  Citation × Citation Citation Abstract Copy Title: Genetic patterns of demography and diversity in eastern North Pacific rockfishes (genus Sebastes) Author: Johansson, Mattias Lars The 100 North Pacific rockfish species in the genus Sebastes are highly diverse. Rockfishes fertilize their eggs internally and release swimming larvae. Complex courting behaviors may allow female rockfish to be selective about their mates and may promote and maintain speciation. In this study, I applied genetic techniques to survey the factors that structure rockfish populations and have potential to affect speciation. First, I used microsatellites to test the hypothesis that the rangewide signal of isolation-by-distance previously identified in copper rockfish is the result of localized habitat or oceanographic breaks. I found significant population divergence at both the whole-coast and Oregon-coast scales. I also identified a weak but significant barrier to larval migration south of Newport, Oregon. Second, I used a candidate gene approach to assess the possibility that olfactory receptor related to class A, type 2 (Ora2) genes could differentiate species at mating. I characterized sequence variation in Ora2 genes between five distantly-related rockfishes and tested for evidence of positive selection. My results suggest that rockfishes possess a single, highly conserved Ora2 gene. Although evidence of positive selection was found for nine amino acids, shared alleles were found across all five study species. This suggests that the Ora2 gene in isolation could not differentiate species during mating season. Finally, I tested the hypothesis that rockfishes mate non-randomly based on major histocompatibility complex (MHC) genotype, as has been seen in other fishes. I characterized MHC genotypes of copper and quillback rockfish in a captive-mating population, identified parents of fourteen broods, and drew inferences about mate choice based on known parentage. I found a significant proportion of multiple-fathered broods, a high degree of hybridization, and that these two species possess multiple, highly-variable MHC genes. I did not find strong evidence that females selected males based on MHC. This may be because larval survival is stochastic, which promotes a bet-hedging strategy, rather than a high degree of selectivity. This work complements our understanding of the population genetics of nearshore rockfishes, and offers a first look at two gene families that may function in mate choice to avoid hybridization and improve larval quality. Title: Genetic patterns of demography and diversity in eastern North Pacific rockfishes (genus Sebastes) Author: Johansson, Mattias Lars The 100 North Pacific rockfish species in the genus Sebastes are highly diverse. Rockfishes fertilize their eggs internally and release swimming larvae. Complex courting behaviors may allow female rockfish to be selective about their mates and may promote and maintain speciation. In this study, I applied genetic techniques to survey the factors that structure rockfish populations and have potential to affect speciation. First, I used microsatellites to test the hypothesis that the rangewide signal of isolation-by-distance previously identified in copper rockfish is the result of localized habitat or oceanographic breaks. I found significant population divergence at both the whole-coast and Oregon-coast scales. I also identified a weak but significant barrier to larval migration south of Newport, Oregon. Second, I used a candidate gene approach to assess the possibility that olfactory receptor related to class A, type 2 (Ora2) genes could differentiate species at mating. I characterized sequence variation in Ora2 genes between five distantly-related rockfishes and tested for evidence of positive selection. My results suggest that rockfishes possess a single, highly conserved Ora2 gene. Although evidence of positive selection was found for nine amino acids, shared alleles were found across all five study species. This suggests that the Ora2 gene in isolation could not differentiate species during mating season. Finally, I tested the hypothesis that rockfishes mate non-randomly based on major histocompatibility complex (MHC) genotype, as has been seen in other fishes. I characterized MHC genotypes of copper and quillback rockfish in a captive-mating population, identified parents of fourteen broods, and drew inferences about mate choice based on known parentage. I found a significant proportion of multiple-fathered broods, a high degree of hybridization, and that these two species possess multiple, highly-variable MHC genes. I did not find strong evidence that females selected males based on MHC. This may be because larval survival is stochastic, which promotes a bet-hedging strategy, rather than a high degree of selectivity. This work complements our understanding of the population genetics of nearshore rockfishes, and offers a first look at two gene families that may function in mate choice to avoid hybridization and improve larval quality. Close

• 138. [Article] Pyramiding quantitative trait loci conditioning partial resistance to Sclerotinia sclerotiorum in bush blue lake green beans (Phaseolus vulgaris)

  Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic pathogen capable of causing white mold, a severe disease in common bean. White mold is of particular concern to the Oregon snap bean processing ...

  Citation × Citation Citation Abstract Copy Title: Pyramiding quantitative trait loci conditioning partial resistance to Sclerotinia sclerotiorum in bush blue lake green beans (Phaseolus vulgaris) Author: Barrett, Miles Andrew Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic pathogen capable of causing white mold, a severe disease in common bean. White mold is of particular concern to the Oregon snap bean processing industry, where processors allow less than 3% incidence in harvested shipments. Breeding for white mold resistance in beans has been difficult due to quantitative inheritance and low heritability. We combined two quantitative trait loci (QTL) for physiological resistance to white mold: a QTL located on linkage group 7 from G122 and a B8 QTL from NY6020. The B7 QTL is linked to phaseolin for which a sequence characterized amplified region (SCAR) marker phaseolin has been used successfully to transfer the QTL in dry bean. The transfer in snap bean is more challenging because this QTL is also linked to the p locus which conditions the white-seeded trait. While most snap beans have T phaseolin seed protein, the OSU bush blue lake (BBL) materials have the S form of phaseolin, facilitating the use of T phaseolin as a selectable marker in breeding for white mold resistance. Thus, transfer of this QTL has to be coupled with breaking the linkage between colored seed and the resistance QTL. The B8 QTL is linked to the SS18₁₆₅₀ SCAR and AW19₁₂₀₀ random amplified polymorphic DNA (RAPD) markers. Oregon State University BBL bean germplasm originally developed with single QTL were crossed to pyramid the two resistance QTL. The assumptions made in combining these two sources of resistance are that the QTL are non-allelic and are additive. OSU 6229, OSU 6230, and OSU 6241 are advanced breeding lines that have the SS18₁₆₅₀ allele from NY6020 and show statistically significant higher levels of resistance in the field and greenhouse (straw) test compared to susceptible cultivars. White-seeded, T phaseolin types were selected from a OR 91G x G122 BC₂F₃ population. The selected lines showed levels of resistance significantly better than the susceptible check cultivars in the straw test. The two sources were crossed and the progeny were subjected to three or more generations of phenotypic selection in the straw test. One hundred and forty eight families were planted in a randomized complete block design (RCBD). All families had been previously genotyped using the PHAS and SS18₁₆₅₀ SCAR molecular markers. Plants were inoculated using actively growing mycelium of S. sclerotiorum and scored using a modified straw test to test for genetic additivity among marker classes. None of the lines were statistically more resistant than G122, a QTL donor and standard resistant check. In a separate study, data collected in NY6020-5 x OR 91G and NY6020-5 x OSU 5613 populations suggest that NY6020-5 has a B7 QTL equivalent to G122. Other researchers have presented evidence that G122 has a B8 QTL equivalent to NY6020. Finally in a mixed linear model study we identified two markers, B18₁₅₀₀ and C8₁₂₀₀, which should prove useful in breeding for white mold resistance. While the material that we developed does not show significantly higher levels of resistance than the resistant parents, we have transferred the resistance QTL into a bush blue lake background, and the lines derived from this work should have significantly higher levels of resistance than existing commercial cultivars. We also present evidence of a QTL not previously identified in NY6020-5. Title: Pyramiding quantitative trait loci conditioning partial resistance to Sclerotinia sclerotiorum in bush blue lake green beans (Phaseolus vulgaris) Author: Barrett, Miles Andrew Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic pathogen capable of causing white mold, a severe disease in common bean. White mold is of particular concern to the Oregon snap bean processing industry, where processors allow less than 3% incidence in harvested shipments. Breeding for white mold resistance in beans has been difficult due to quantitative inheritance and low heritability. We combined two quantitative trait loci (QTL) for physiological resistance to white mold: a QTL located on linkage group 7 from G122 and a B8 QTL from NY6020. The B7 QTL is linked to phaseolin for which a sequence characterized amplified region (SCAR) marker phaseolin has been used successfully to transfer the QTL in dry bean. The transfer in snap bean is more challenging because this QTL is also linked to the p locus which conditions the white-seeded trait. While most snap beans have T phaseolin seed protein, the OSU bush blue lake (BBL) materials have the S form of phaseolin, facilitating the use of T phaseolin as a selectable marker in breeding for white mold resistance. Thus, transfer of this QTL has to be coupled with breaking the linkage between colored seed and the resistance QTL. The B8 QTL is linked to the SS18₁₆₅₀ SCAR and AW19₁₂₀₀ random amplified polymorphic DNA (RAPD) markers. Oregon State University BBL bean germplasm originally developed with single QTL were crossed to pyramid the two resistance QTL. The assumptions made in combining these two sources of resistance are that the QTL are non-allelic and are additive. OSU 6229, OSU 6230, and OSU 6241 are advanced breeding lines that have the SS18₁₆₅₀ allele from NY6020 and show statistically significant higher levels of resistance in the field and greenhouse (straw) test compared to susceptible cultivars. White-seeded, T phaseolin types were selected from a OR 91G x G122 BC₂F₃ population. The selected lines showed levels of resistance significantly better than the susceptible check cultivars in the straw test. The two sources were crossed and the progeny were subjected to three or more generations of phenotypic selection in the straw test. One hundred and forty eight families were planted in a randomized complete block design (RCBD). All families had been previously genotyped using the PHAS and SS18₁₆₅₀ SCAR molecular markers. Plants were inoculated using actively growing mycelium of S. sclerotiorum and scored using a modified straw test to test for genetic additivity among marker classes. None of the lines were statistically more resistant than G122, a QTL donor and standard resistant check. In a separate study, data collected in NY6020-5 x OR 91G and NY6020-5 x OSU 5613 populations suggest that NY6020-5 has a B7 QTL equivalent to G122. Other researchers have presented evidence that G122 has a B8 QTL equivalent to NY6020. Finally in a mixed linear model study we identified two markers, B18₁₅₀₀ and C8₁₂₀₀, which should prove useful in breeding for white mold resistance. While the material that we developed does not show significantly higher levels of resistance than the resistant parents, we have transferred the resistance QTL into a bush blue lake background, and the lines derived from this work should have significantly higher levels of resistance than existing commercial cultivars. We also present evidence of a QTL not previously identified in NY6020-5. Close

• 139. [Article] Genetic variation and mating system of ponderosa pine in the Willamette Valley of Oregon

  The population genetic structure of ponderosa pine (Pinus ponderosa Dougi.) in the Willamette Valley of Oregon was investigated. Cones were collected from native stands of ponderosa pine from the Willamette ...

  Citation × Citation Citation Abstract Copy Title: Genetic variation and mating system of ponderosa pine in the Willamette Valley of Oregon Author: Gooding, Geoffrey David The population genetic structure of ponderosa pine (Pinus ponderosa Dougi.) in the Willamette Valley of Oregon was investigated. Cones were collected from native stands of ponderosa pine from the Willamette Valley, eastern Oregon, southwest Oregon and the Puget Sound Basin of Washington. Seeds were subjected to isozyme analysis of 12 enzyme systems controlled by 20 different loci. Population genetic parameters for progeny, parent trees and pollen were estimated from isozyme data using BIOSYS-2, a population genetic statistical software package. For progeny data, total gene diversity (HT) was 0.249; average genic diversity within stands (Hs) was 0.231; average genic diversity among stands (DST) was 0.017; the proportion of total genic diversity due to differences among stands (GST) was 0.067. Based on gene diversity statistics and genetic distances, stands of Willamette Valley ponderosa pine do not differ substantially from one another or from other populations of ponderosa pine in Washington and Oregon. These results suggest that protection of the Willamette Valley population can be accomplished by conserving a large number of individuals in a few large stands or many small stands. Multilocus and single-locus estimates of outcrossing rate were determined for six stands within the Willamette Valley. Outcrossing rates were estimated for seven polymorphic loci using MLTR, a mating system analysis software package. Estimates of multilocus outcrossing for these stands (mean 0.642; range 0.365 to 0.879) were substantially lower than estimates previously reported for other populations of ponderosa pine, other pine species, and other species in the family Pinaceae. No significant difference was detected among stands in outcrossing rate. The high level of inbreeding observed in this population could be attributable to population fragmentation due to human activities, or to reduced levels of pollen production in this population compared to other populations of ponderosa pine. Genetic conservation strategies for this population should include the protection of the large native stands that remain and the use of local, adapted sources for afforestation. Management of pollen in a seed orchard should improve the genetic quality of seed over wild stand seed by reducing inbreeding levels. Title: Genetic variation and mating system of ponderosa pine in the Willamette Valley of Oregon Author: Gooding, Geoffrey David The population genetic structure of ponderosa pine (Pinus ponderosa Dougi.) in the Willamette Valley of Oregon was investigated. Cones were collected from native stands of ponderosa pine from the Willamette Valley, eastern Oregon, southwest Oregon and the Puget Sound Basin of Washington. Seeds were subjected to isozyme analysis of 12 enzyme systems controlled by 20 different loci. Population genetic parameters for progeny, parent trees and pollen were estimated from isozyme data using BIOSYS-2, a population genetic statistical software package. For progeny data, total gene diversity (HT) was 0.249; average genic diversity within stands (Hs) was 0.231; average genic diversity among stands (DST) was 0.017; the proportion of total genic diversity due to differences among stands (GST) was 0.067. Based on gene diversity statistics and genetic distances, stands of Willamette Valley ponderosa pine do not differ substantially from one another or from other populations of ponderosa pine in Washington and Oregon. These results suggest that protection of the Willamette Valley population can be accomplished by conserving a large number of individuals in a few large stands or many small stands. Multilocus and single-locus estimates of outcrossing rate were determined for six stands within the Willamette Valley. Outcrossing rates were estimated for seven polymorphic loci using MLTR, a mating system analysis software package. Estimates of multilocus outcrossing for these stands (mean 0.642; range 0.365 to 0.879) were substantially lower than estimates previously reported for other populations of ponderosa pine, other pine species, and other species in the family Pinaceae. No significant difference was detected among stands in outcrossing rate. The high level of inbreeding observed in this population could be attributable to population fragmentation due to human activities, or to reduced levels of pollen production in this population compared to other populations of ponderosa pine. Genetic conservation strategies for this population should include the protection of the large native stands that remain and the use of local, adapted sources for afforestation. Management of pollen in a seed orchard should improve the genetic quality of seed over wild stand seed by reducing inbreeding levels. Close

• 140. [Article] Breeding for bruchid resistance in common bean (Phaseolus vulgaris L.) : interspecific introgression of lectin-like seed proteins from tepary bean (P. acutifolius A. Gray), genetic control and bruchid resistance characterization.

  Interspecific hybridization was initiated between wild P. acutifolius accession G40199 and P. vulgaris to introgress resistance to Acanthoscelides obtectus (bean seed weevil). F1 interspecific hybrids ...

  Citation × Citation Citation Abstract Copy Title: Breeding for bruchid resistance in common bean (Phaseolus vulgaris L.) : interspecific introgression of lectin-like seed proteins from tepary bean (P. acutifolius A. Gray), genetic control and bruchid resistance characterization. Author: Kusolwa, Paul Mbogo Interspecific hybridization was initiated between wild P. acutifolius accession G40199 and P. vulgaris to introgress resistance to Acanthoscelides obtectus (bean seed weevil). F1 interspecific hybrids were recovered by embryo rescue and maintained until flowering. Mostly sterile hybrids were backcrossed twice to common bean cultivar ICA Pijao to recover sufficient fertility for the lines to reproduce without assistance. The inheritance of a 33 kDa seed storage protein from accession G40199 was studied in an F2 intraspecific population from a cross of G40199 and a cultivated Brown Tepary accession. G40199 possessed the protein but Brown Tepary did not. The protein was inherited as a single dominant gene in a F2 population of 116 individuals. Following these observations, interspecific hybrids were progeny tested for the introgression of a 33 kDa protein from accession G40199. Backcross interspecific introgression lines were used as bridge parents to transfer the 33 kDa protein into the large red seeded cultivar Rojo adapted to Tanzania, and into a phaseolin null backcross breeding line of Rojo with the objective of introgressing resistance to A. obtectus into a Sub-Saharan Africa variety. Genomic, proteomic and phylogenetic characterization of genes associated with the 33 kDa proteins were conducted in order to identify the mechanism of resistance found in accession G40199. Genomic DNA encoding a family of lectin-like seed storage proteins (the complex APA locus) was amplified by PCR using primers for arcelin, phytohaemagglutinin and alpha amylase inhibitors. The PCR products were used as molecular markers and co-segregated with the 33 kDa protein. Analyses of mRNA expression identified two arcelin variants, ARL-3pa and ARL-4pa, as expressed in G40199 and its derived interspecific hybrids. MS-MS proteomic analysis of seed protein profiles in G40199 demonstrated the presence of protein peptides with amino acid sequences corresponding to the two arcelin variants and phytohaemagglutinin (PHA) protein subunits. Essentially similar protein peptides were observed in the introgression lines. Phylogenetic analysis demonstrated the difference of the two arcelin variants in G40199 that clustered with P. acutifolius arcelin-like proteins and were separated from those of P. vulgaris. Seeds from G40199 and BC2F3 interspecific hybrid lines were subjected to an A. obtectus feeding trial at OSU. Introgression lines expressing the homozygous 33 kDa protein demonstrated significant bruchid resistance. This resistance was exhibited as delayed insect emergence with a mean of 63 days for 50% F1 adults after inoculation compared to 44 days to 50% adult for ICA Pijao. In addition, reduced size and weight of adults, and reduced number of adults was observed in a period of 72 days after bruchid infestation. G40199 was completely resistant with no emerging adults. The 33 kDa protein which is linked to co-expression of ARL-3pa, ARL-4pa and PHA protein subunits is a contributing factor to the observed resistance to A. obtectus among interspecific hybrids. Title: Breeding for bruchid resistance in common bean (Phaseolus vulgaris L.) : interspecific introgression of lectin-like seed proteins from tepary bean (P. acutifolius A. Gray), genetic control and bruchid resistance characterization. Author: Kusolwa, Paul Mbogo Interspecific hybridization was initiated between wild P. acutifolius accession G40199 and P. vulgaris to introgress resistance to Acanthoscelides obtectus (bean seed weevil). F1 interspecific hybrids were recovered by embryo rescue and maintained until flowering. Mostly sterile hybrids were backcrossed twice to common bean cultivar ICA Pijao to recover sufficient fertility for the lines to reproduce without assistance. The inheritance of a 33 kDa seed storage protein from accession G40199 was studied in an F2 intraspecific population from a cross of G40199 and a cultivated Brown Tepary accession. G40199 possessed the protein but Brown Tepary did not. The protein was inherited as a single dominant gene in a F2 population of 116 individuals. Following these observations, interspecific hybrids were progeny tested for the introgression of a 33 kDa protein from accession G40199. Backcross interspecific introgression lines were used as bridge parents to transfer the 33 kDa protein into the large red seeded cultivar Rojo adapted to Tanzania, and into a phaseolin null backcross breeding line of Rojo with the objective of introgressing resistance to A. obtectus into a Sub-Saharan Africa variety. Genomic, proteomic and phylogenetic characterization of genes associated with the 33 kDa proteins were conducted in order to identify the mechanism of resistance found in accession G40199. Genomic DNA encoding a family of lectin-like seed storage proteins (the complex APA locus) was amplified by PCR using primers for arcelin, phytohaemagglutinin and alpha amylase inhibitors. The PCR products were used as molecular markers and co-segregated with the 33 kDa protein. Analyses of mRNA expression identified two arcelin variants, ARL-3pa and ARL-4pa, as expressed in G40199 and its derived interspecific hybrids. MS-MS proteomic analysis of seed protein profiles in G40199 demonstrated the presence of protein peptides with amino acid sequences corresponding to the two arcelin variants and phytohaemagglutinin (PHA) protein subunits. Essentially similar protein peptides were observed in the introgression lines. Phylogenetic analysis demonstrated the difference of the two arcelin variants in G40199 that clustered with P. acutifolius arcelin-like proteins and were separated from those of P. vulgaris. Seeds from G40199 and BC2F3 interspecific hybrid lines were subjected to an A. obtectus feeding trial at OSU. Introgression lines expressing the homozygous 33 kDa protein demonstrated significant bruchid resistance. This resistance was exhibited as delayed insect emergence with a mean of 63 days for 50% F1 adults after inoculation compared to 44 days to 50% adult for ICA Pijao. In addition, reduced size and weight of adults, and reduced number of adults was observed in a period of 72 days after bruchid infestation. G40199 was completely resistant with no emerging adults. The 33 kDa protein which is linked to co-expression of ARL-3pa, ARL-4pa and PHA protein subunits is a contributing factor to the observed resistance to A. obtectus among interspecific hybrids. Close