Pyrenophora semeniperda is a generalist fungal pathogen that occurs primarily on monocot seed hosts. It is in the phylum Ascomycota, which includes both self-compatible (homothallic) and self-incompatible (heterothallic) species. Homothallic fungal species contain complementary mating-type (MAT) idiomorphs in a single unikaryotic strain, while heterothallic strains contain a single MAT idiomorph requiring interaction between strains of complementary mating-types for sexual reproduction to occur. Because the majority of P. semeniperda strains contained either MAT1 or MAT2, this species was provisionally categorized as heterothallic. However, many strains contain both MAT idiomorphs and appear to be homothallic. These results warranted a closer look at the MAT idiomorphs and the structure of the P. semeniperda genome in order to assure accurate characterization of the MAT locus. Additionally, an assessment of the geographic distribution of MAT idiomorphs provides us with insight into the genetic diversity of P. semeniperda and the reproductive strategies that it employs. In this study, we characterized the P. semeniperda MAT locus and assessed the idiomorph distribution of 514 isolates from 25 P. semeniperda populations collected from infected Bromus tectorum (cheatgrass) seeds. Additionally, we used simple sequence repeat (SSR) and MAT idiomorph length polymorphisms to demonstrate the existence of dikaryotic strains and pseudohomothallism in this fungus. We identified a unique variable number tandem repeat (VNTR) within each idiomorph of the MAT locus of P. semeniperda. Presence of the VNTR in all MAT loci analyzed from strains collected in the Intermountain West suggests ancient proliferation of this repeat. The persistence and effectiveness of P. semeniperda strains in the cheatgrass pathosystem depend not only on the density of the fungus in the soil, but also on the genetic heterogeneity of each population. Our study suggests that P. semeniperda genetic diversity is increased both through MAT locus-dependent sexual reproduction and asexually through anastomosis.

Sovietinio laikotarpio Lietuvos istorijai skirtuose tyrimuose savo vietą atranda naujos arba ankščiau mažai tyrinėtos temos. Viena tokių temų – žydų tapatumas sovietų okupacijos Lietuvoje laikotarpiu – atskleidžiama ir šiame darbe. Keliamas tikslas – remiantis šaltiniais bei istoriografija probleminiu būdu išanalizuoti sovietinio laikotarpio Lietuvos žydų tapatumą bei jo santykį su repatriacijos į Izraelį procesu XX a. aštuntuoju ir devintuoju dešimtmečiais. Tokios chronologijos pasirinkimas sąlygotas būtent paskutiniaisiais SSRS gyvavimo dešimtmečiais padidėjusio iš Lietuvos bei kitų sovietinių respublikų išvykstančių žydų skaičiaus. Tokį pagausėjimą nulėmė sušvelninta Sovietų Sąjungos emigracijos politika, kuria siekta sumažinti įtampą tarp jos ir Vakarų valstybių, o ypač JAV. Suvokiant, kad Izraelio valstybė bei persikėlimas į ją nuolatiniam gyvenimui – aliyah – yra glaudžiai susiję su žydų tapatumo klausimu, darbe tam skiriamas pagrindinis dėmesys. Siekiama nustatyti, kaip Lietuvos žydų bendruomenė apibrėžė savo tautinį tapatumą paskutiniaisiais SSRS gyvavimo dešimtmečiais, kaip jis kito ir ar kito. Į žydų tautinį tapatumą mėginama žvelgti per keletą žymenų: kalbą, pačios žydų bendruomenės sudėties kaitą bei visuomenės, valdžios požiūrį į juos. Jeigu pirmieji du aspektai akcentuoja vidinius bendruomenės gyvenimo procesus, tai pastarajame išskiriamas individo ir jų grupių santykis su supančia aplinka bei jos poveikis individualaus, bendruomeninio tapatumo kaitai. Darbe... [toliau žr. visą tekstą] / Nowadays new or less known historical topics easily find their place in researches of Soviet Lithuanian history. One of these new topics – Jewish identity during Soviet occupation period in Lithuania – has been revealed in this research. The main goal of this research is to analyze the identity of Lithuanian Jews and its‘ relations with the process of repatriation to Israel on 8th and 9th decades of the 20th Century. This chronology was chosen because of strong increase in numbers of Jews emigrating from Soviet Union during last two decades of Soviet state existence. This increase was conditioned by subdued USSR emigration policy, as an attempt to reduce tension between Soviet Union and the West, especially United States of America. State of Israel and resettlement to this place for constant living – aliyah – are closely linked with Jewish identity topic, on which we will be concentrating the most. The aim is to determine how Lithuanian Jewish community defined their ethnical identity on the last decades of USSR existence, how did it change, if it did at all. Ethnical identity is analyzed through language, inner changes of Jewish community, society and authority attitude towards them. While the first two mentioned aspects emphasize inner processes of community life, the other one highlights the relation of individuals and their groups with surrounding environment and its‘ effect to personal or communal identity transformation. This research seeks to unpack the motives which... [to full text]

Marker-Assisted Verification of Hybrids in Pearl Millet-Napiergrass (Pennisetum glaucum [L.] R. Br. x Pennisetum purpureum Schumach.). (December 2011) Charlie D. Dowling, III, B.S., College of Agriculture and Life Sciences Chair of Advisory Committee: Dr. Russell W. Jessup A high-biomass perennial grass that is directly seeded using existing farm equipment can reduce both planting and overall input costs. Three cytoplasmic male-sterile cms A-lines and four fertile genotypes of pearl millet (Pennisetum glaucum [L.] R. Br.) and one novel pearl millet selection from the Perennial Grass Breeding Program at Texas A&M University were selected to cross with napiergrass (Pennisetum purpureum Schumach.). The pearl millet parents were chosen based on characteristics such as basal tillering, plant height, and days to anthesis. Three napiergrass accessions from the Perennial Grass Breeding Program and the cultivar Merkeron were used as pollinators for these crosses. The cms and fertile pearl millet accessions produced full heads of seed when pollinated with napiergrass. There were a large range of seed sizes and weights for each hybrid family, and the seed were separated into four size classes. The weight differences from the largest to smallest class of seed varied by more than 30%. All of the seed classes germinated, and seed size, in this case, was completely unrelated to the ability to germinate. 100% germination was observed in five seed size classes for both PMN iv hybrids, and 90% germination was observed in three of the eight classes. Essentially all of the hybrid seed recovered from the original pearl millet x napiergrass crosses germinated, but all of the F 1 hybrids were sterile in that none of them produced viable seed. Flow cytometry could not be used to identify the hybrids because the DNA content of pearl millet and napiergrass were essentially the same even though distinct 2C and 4C peaks were seen from the diploid pearl millet. From the 58 EST-SSRs surveyed in the bulked segregate analysis, several were heterozygous dominant and many were homozygous dominant and hemizygous at its particular loci. Seven hemizygous EST-SSRs were identified for Merkeron, seven for PEPU09FL01, eight for PEPU09FL02, and six for PEPU09FL03. These markers are extremely valuable to any pearl millet x napiergrass hybridization program because they provide a means whereby the hybrids can be easily identified. Identification of hemizygous pearl millet markers will also assist in future DNA sequencing and also in a marker-assisted breeding program.

Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

The main task of the thesis is the practical verification of the ultrasonic sealing method for producing bags with a higher probability of goods in the sealing area. Most of the work deals with programming a block for the overall operation of an ultrasonic generator. Part of the solution is creation of visualization of the generator user interface. The last part is designing and implementing a reporting system to help customers get production data.

Suicide is a significant public health issue in the US. Despite national and international prioritization since 1996, little definitive progress has been made in terms of identification and intervention in cases of elevated suicide risk. Forty percent of those who died by suicide attended an emergency department within a year of death. Therefore, universal suicide risk screening in emergency departments could prove a vital component to a national suicide prevention strategy. The present study empirically evaluated the universal suicide risk screening program recently implemented at Parkland Health and Hospital System. The sample consisted of patients over 18 years of age (N=333,855; Mage=42.7, 32% male) screened as part of routine clinical care from May 4th, 2015, through November 3rd, 2015. The Parkland Algorithm for Suicide Screening (PASS) is part of a clinical decision support system for responses to Columbia - Suicide Severity Rating Scale Clinical Practice Screener (C-SSRS) items, leading to an automated clinical response via three suicide risk stratification levels: no action for no risk identified, psychiatric social worker assessment for moderate risk identified, and psychiatrist/psychologist interview for high risk identified. The present study used receiver operating characteristic (ROC) curve analysis, which found the PASS predicted disposition (z=30.46, p<.001, AUC=.78, CI95=.77, .81). This study also evaluated the cutpoints separating suicide risk stratification and levels of clinical response. The results supported the first cutpoint and highlighted a need for additional data to address the second cutpoint. The results of the present study suggest that the universal suicide risk screening program at Parkland Health and Hospital System is an important step toward addressing suicide prevalence in the US.

Quinoa (Chenopodium quinoa Willd.) is an important food crop for subsistence farmers in the Altiplano (high plains) of Peru, Bolivia, and Argentina. Saponins are part of a diverse family of secondary metabolites that are found in high concentrations in the pericarp of many varieties of quinoa. Due to their bitter taste and anti-nutritive properties, saponins must be removed before the quinoa grain is consumed. There are ‘sweet’ varieties of quinoa that have significantly reduced levels of saponin. Previous research suggests saponin production is controlled by a single locus. The major objective of this research was to elucidate the genetic components in the saponin biosynthesis pathway. Thus, we report the development and annotation of the first large scale expressed sequence tag (EST) collection for quinoa based on Sanger and 454 pyrosequencing of maturing seed tissue expressing saponins. Sanger sequencing produced 18,325 reads with an average read length of 693 nucleotides, while 454 GS-FLX pyrosequencing generated 295,048 reads with an average read length of 202 nucleotides. A hybrid assembly of all sequences generated 39,366 unigenes, consisting of 16,728 contigs and 22,638 singletons. Repeat sequence analysis of the unigene set identified 291 new microsatellite markers. From the unigene set, a custom microarray was developed and used to assay transcriptional changes in developing seeds of saponin-containing and saponin-free quinoa lines. The microarray consisted of 102,834 oligonucleotide probes representing 37,716 sequences of the unigenes set. Three different statistical comparisons, based on comparisons of ‘sweet’ vs. ‘bitter’ seed tissue at two developmental stages, were assayed on the custom array. Using a p-value cutoff threshold of 0.01, we identified a list of 198 significantly differentially expressed candidate genes common to all three comparisons. We also identified a list of candidate genes (p-value ≤ 0.05) that are known to be associated with identified triterpenoid (saponin) biosynthetic pathways that were differentially expressed in all three comparisons. Included in this list are candidate genes that share homology to cytochrome P450s (20), cytochrome P450 monooxygenases (10), and glycosyltransferases (49) suggesting that transcriptional differences in the saponin biosynthesis pathway possibly responsible for the absence or presence of saponin in quinoa are determined after the formation of the β-amyrin skeleton. These candidate genes are suggested for use in future studies in the production of saponin in quinoa.

Big sagebrush (Artemisia tridentata) is one of the ecologically most important shrub species in western North America. The species serves as a major source of food and habitat for the near-threatened sage grouse and various other fauna. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is considered as a serious threat to sustainability of the big sagebrush ecosystem. Because of its importance, restoration of this species is very crucial to those dependent on big sagebrush community. However, restoration of big sagebrush carried out by using diverse seed source can lead to imbalance and degradation in the native ecosystem. Therefore, restoration works aided by understanding of adaptive traits of big sagebrush using molecular markers will aid successful restoration. The major objective of this research was to create a substantial resource of nuclear sequence data and identify markers that can be used in future studies in big sagebrush. We report the development and annotation of the first expressed sequence tag (EST) collection for big sagebrush based on 454 sequencing of leaf tissue. Expressed genes of subspecies tridentata and vaseyana were sequenced using the 454 GS-FLX titanium platform, which produced 823,392 reads with an average read length of 404 bp and 702,001 reads with an average read length of 333 bp for sspp. tridentata and vaseyana, respectively. Assembly of the reads resulted in 212,102 consensus sequences in ssp. tridentata and 199,439 in ssp. vaseyana. A combined assembly of both subspecies sequences generated 29,541 contigs with an average length of 796 bp and 275,866 singletons with an average length of 370 bp. A BLASTx search against the non-redundant (NR) protein database using the contigs obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). Gene Ontology (GO) IDs were assigned to 18,397 sequences. A total of 20,952 SNPs were detected between the two subspecies and 1,182 SNPs were confirmed in tetraploid ssp. wyomingensis. In addition, 1,003 and 507 SSRs were detected in ssp. tridentata contigs and ssp. vaseyana contigs, respectively.

Diploid potato populations between a primitive cultivated species, <I>Solanum phureja</I>, and a weedy species, <I>S. chacoense</I>, were used to examine the segregation of microsatellite markers and three traits in backcrosses. Two of the traits, anther culture competence and 2<I>n</I> pollen production, originated from <I>S. phureja</I> whereas the third, leptine production (a specific glycoalkaloid known to convey resistance to the Colorado potato beetle) originated from <I>S. chacoense</I>. Using CP2, a self-incompatible F₁ hybrid originating from a cross between <I>S. chacoense</I> clone 80-1 and <I>S. phureja</I> clone 1-3, three populations were developed: 1-3 x CP2 (PBCp), CP2 x 1-3 (PBCc), and CP2 x 80-1 (CBC). For the microsatellite study, four simple sequence repeat (SSR) primer pairs that amplified fragments within potato sequences found in the GenBank were used to look at segregation ratios in our backcross populations and to eliminate possible spurious genotypes bearing non-parental alleles in these populations. Seventeen spurious genotypes were discarded from PBCp; none was found in PBCc or CBC. Two SSR loci showed skewed segregation in PBCp (favoring transmissnion of the allele originally found in 80-1), PBCc showed normal segregation at all loci, and CBC showed distorted segregation at one locus (revealing a deficiency of homozygotes). In the study of anther culture, three components of ACR were investigated in a preliminary study: 1) embryos produced per anther (EPA), 2) embryo regeneration rate and 3) percentage of monoploids (2<I>n</I>=1<I>x</I>=12) among regenerants. CP2 was intermediate, 80-1 was low, and 1-3 was high for ACR. Only EPA was selected for further characterization in our populations. PBCp (78 genotypes) and CBC (57 genotypes), were characterized for anther culture response ACR/EPA in a series of studies. Nine high and ten low selections were identified in CBC, and ten high and ten low selections were identified in PBCp. EPA selections were used for bulk segregant analysis (BSA) using 214 RAPD primers. Two bands, one amplified by OPQ-10 and another by OPZ-4 were linked in coupling and in repulsion, respectively, to ACR in PBCp. One band amplified by OPW-14 primer was linked in coupling to ACR in CBC. One-way ANOVAs for data from remaining genotypes of the populations verified linkage of the markers to ACR/EPA. For 2n pollen production, a total of 77 PBCp genotypes was characterized; 80-1 produces low % 2<I>n</I> pollen, and 1-3 produces high % 2<I>n</I> pollen. Pollen samples were stained with propidium iodide and examined by flow cytometry. The frequency of 2n pollen varied continuously from 1.7 % to 40.6 % among the 41 genotypes that flowered sufficiently to allow three separate pollen collections. Variation due to the environment was observed where the frequency of 2n pollen appeared greater over a range of genotypes on single collection days. BSA could not be used due to limited population size and a low number of selections at the extremes of the distribution of phenotypes. The continuous variation for 2<I>n</I> pollen production suggests multigenic control of the trait. In the study of leptine content in reciprocal backcross populations, 87 genotypes within PBCp, and 42 genotypes within PBCc were characterized using gas chromatography of leaf samples. CP2 was intermediate, 1-3 had zero, and 80-1 was high for leptine content in the foliage. Leptines were present in low levels in 43 of 87 genotypes in PBCp, indicating simple genetic control. In PBCc, only 7 of 42 genotypes expressed leptines, generally at a higher level than in PBCp, indicating cytoplasmic inheritance. Ten high and ten nil selections within PBCp, and seven high and eight nil selections within PBCc were used for BSA using 214 RAPD primers. Three primers OPQ-2, OPT-16 and OPT-20 amplified bands segregating with high bulks in both populations. These markers were linked in coupling to leptine content in PBCp. Linkage was verified by ANOVAs for leptine content in the entire population. / Ph. D.

No description available.