Pisolithus is an ectomycorrhizal (ECM) fungal genus that exists in native and plantation forests worldwide. Despite many aspects of the genus having been studied over the years, there is limited knowledge of the genetic population structure of Pisolithus spp. The major aim of this study was to begin to elucidate the genetic structure of populations of Pisolithus native to the eastern states of Australia. Initially, the number of species represented in the University of Western Sydney Pisolithus culture collection was investigated using ITS-RFLP and previously developed simple sequence repeat (SSR) markers. From these analyses, two clear groupings emerged with the RFLP groups corresponding to the SSR groups identified. To study genetic population structure, appropriate markers were required and SSR markers were considered to be most suited to this end. The developed SSR markers were successfully used to amplify P. microcarpus and P. albus DNA from ECM root tips and soil samples. Therefore, these markers will be a useful tool for future investigations into the population structure of above and below-ground structures of P. microcarpus and P. albus populations. / Doctor of Philosophy (PhD)

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 164-176).

Molecular DNA markers have become widely used in all areas of genetic research. The objectives of this thesis were to develop polymorphic markers in sunflower and utilize the markers for genetic and candidate gene analyses. Amplified fragment length polymorphism (AFLP) markers were used to estimate genetic similarities and assess the genetic diversity among 24 public oilseed inbred lines of sunflower (Helianthus annuus L.). A total of 359 AFLP markers were scored by using six AFLP primer combinations. Genetic similarities ranged from 0.70 to 0.91, polymorphism rate ranged from 7 to 24%, and polymorphic information contents (PICs) ranged from 0.0 to 0.5. Principal coordinate and cluster analysis separated the lines into two groups, B-lines and R-lines, illustrating breeding history, basic heterotic pattern and the widespread practice of using each group to develop new lines. ��9 stearoyl-ACP desaturase (SAD) and ��l2 oleate desaturase (OLD) cDNAs were cloned and sequenced. DNA fragment length polymorphism (DFLP), single strand conformational polymorphism (SSCP), and simple sequence repeat (SSR) markers were developed for the SAD6 and SAD17 genes among eight elite inbred lines. PICs for DFLP, SSCP, and SSR markers were 0.18, 0.37, and 0.30, respectively. Length variants were due to long monomeric repeats, insertions, and deletions in intron sequences, thereby producing polymorphic markers. OLD desaturates 18:1-PC (oleoyl phosphatidylcholine) to 18:2-PC, thereby converting oleic to linoleic acid. It is a likely candidate gene to be causing the high oleic phenotype in mutant sunflower. The expression of OLD7 in developing seeds was greatly reduced in mutant as opposed to wildtype backcross-derived lines. The restriction fragment length polymorphism (RFLP) patterns suggest that OLD7 is duplicated and rearranged in mutant lines. Utilizing sunflower SAD gene sequences and 27 inbred lines, intron fragment length polymorphism (IFLP) markers were developed for automated genotyping. These IFLP markers with ~470 to ~850 bp in length had a mean PIC score of 0.414, versus 0.336 for DFLP markers, and 0.582 for SSCP markers. One and two nucleotide length polymorphisms were reliably detected in PCR fragments up to ~150 and ~680 bp, respectively. / Graduation date: 1998

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2004. / Thesis documentation sheet inserted. Appendix reprints five manuscripts and papers co-authored with others. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix.

the majority of patients with early breast cancer receive some form of systemic adjuvant therapy (chemo-, endocrine, and/or targeted therapy). Despite the increase in adjuvant therapy prescription, little progress has been made with respect to assisting oncologists to determine which breast cancer patients, particularly those deemed at “lower risk” of relapse, require chemotherapy or other systemic therapy and which women can safely be treated with loco-regional treatment alone. For these reasons, the identification of prognostic and predictive markers that will assist the clinician in selecting the most suitable form of medical therapy has become very high priority as well as a real challenge in translational research. Unfortunately, several problems have hampered the identification and/or clinical usefulness of prognostic and predictive markers. In Chapter 1, we sought to address some of the specific questions regarding prognosis: - Are gene expression signatures robust and reproducible? - Do the different gene signatures have similar prognostic performance? Are they concordant in their prediction for the individual patient? - What is the role of individual genes in a signature and what is their biological interpretation? - What is the relationship between the molecular classification defined by cluster analysis and the different prognostic signatures? Through the following specific aims: 1. Independent validation study of a prognostic gene signature derived from microarray technology, to demonstrate its reproducibility, robustness and clinical utility compared with classical breast cancer prognostic factors in an appropriate validation cohort (Chapter 1A); 2. Independent comparison of three prognostic gene signatures (Chapter 1B); 3. Characterization of the biological foundation of the different prognostic signatures and refinement of our knowledge regarding breast cancer prognosis according to the molecular subgroups defined by ER and HER2 through a meta-analysis of publicly available gene expression data (Chapter 1C). In Chapter 2, we sought to address some specific questions regarding the prediction of response for the most commonly given breast cancer treatments: - What is the importance of proliferation genes in predicting clinical outcome in patients treated with endocrine therapy? - What is the value of TOP2A in predicting the efficacy of anthracycline therapy? - Can we identify a list of genes associated with response to anthracyline therapy? - What is the best method and cutoff to determine HER2-positive patients eligible for trastuzumab therapy? Would an alternative quantitative method for HER2 expression and homodimerization discriminate patients with significantly different probabilities of clinical outcome following treatment with trastuzumab? Through the following specific aims: 1. Investigation of molecular markers of response to endocrine therapy in hormono-sensitive patients (Chapter 2A); 2. Prospective evaluation of the predictive value of TOP2A and identification of genes associated with response in a cohort of patients treated with anthracyclines (Chapter 2B); 3. Investigation of the best method to select patients who should be treated by trastuzumab-based therapy and evaluation of a new technique to quantitatively assess HER2 expression (Chapter 2C).

Coronary Artery Bypass Grafting (CABG) is an effective and invasive cardiac surgery to salvage blocked coronary artery. Cardiopulmonary bypass (CPB) is usually applied to support circulation during temporary cardiac arrest. Studies have demonstrated that cardiac injury, inflammation, and oxidative stress could be induced during CABG with CPB. We conducted two studies to investigate the release of cardiac biochemical markers and inflammatory response as well as to compare the effect of different coating biomaterial of CPB on the induction of inflammation and oxidative stress during CPB. We investigated the release patterns and the serum levels of cardiac markers as well as inflammatory markers in patients undergoing elective CABG at different time points after initiation of CPB. In this study, we demonstrated that cardiac markers such as creatine kinase isoenzyme MB (CK-MB), and cardiac troponin I (cTnI) and inflammatory markers such as tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and high sensitivity C-reactive protein (hsCRP) were highly elevated after CPB. Moreover, we confirmed that cTnI is still a better biochemical marker for cardiac injury than others following CABG with CPB. Other nonspecific but highly sensitive markers such as lactate dehydrogenase (LDH), lactate, TNF-alpha, IL-6, and hsCRP could be potential surrogate markers for evaluation of cardiac injury following CPB. Based on these findings, we conducted a further investigation to demonstrate our hypothesis that different biocompatible materials used in CPB may affect the inflammation and oxidative stress differently. Biocompatible materials are thinly coated on CPB tubes to provide similar environment like endothelial cells during cardiac surgery. There are several biocompatible materials available in the market. Each of them has unique characteristics. Inflammatory response is one of the bodys fundamental defense mechanisms against foreign invaders. However, inappropriate or excessive response can lead to harmful, potentially life-threatening consequences due to severe inflammatory tissue destruction. CPB-induced inflammatory response can be one of the factors, which can affect surgical outcomes. Depending on the presence of different biocompatible materials in CPB circuits, the degree of immunoreactions can be varied. In this study, we analyzed hsCRP, an acute phase protein, and tau protein, a marker of neurocognitive deficiency. Furthermore we analyzed inflammatory cytokines including TNF-alpha, IL-6, IL-10, and interferon-gamma (IFN-gamma) to evaluate the levels of inflammation. Serum levels of oxidized nitric oxide as a marker of oxidative stress were also assessed. We demonstrated that different biocompatible material has different impacts on inflammation and oxidative stress. In the aspect of anti-inflammation, heparin-coated biocompatible material is better than others whereas surface-modifying additives biocompatible material is worse than others. Overall, different coating biomaterial of CPB results in various inflammatory response. In terms of oxidative stress, we did not observe significant difference between different biomaterial-coated CPB.

Aquesta tesis doctoral està basada en estudiar la resposta immunològica dels peixos en models d'estrès i d'activació del sistema immune des la genòmica funcional. L'aplicació de tecnologies moleculars com el Differential Display van permetre identificar y clonar por primera vegada en orades (Sparus aurata) y en altres especies de peix, el gen enolasa. Aquest enzim glucolític s'ha plantejat per primera vegada com un bon marcador molecular per estudiar el benestar dels peixos. Per mitjà de l'ús d'una plataforma de microarrays dissenyada específicament per a salmònids, i altres metodologies biomoleculars, es va comprovar que els nivells d'enolasa eren regulats en diferents teixits y en diferents especies de peix, com també en adverses situacions per l'animal. D'altra banda, s'han estudiat diferents gens immunològics candidats a ser possibles gens per l'estudi del sistema immunològic dels peixos. Aquests gens s'han estudiat a nivell d'expressió en teixits de truites (Oncorhynchus mykiss) mitjançant PCR convencional i PCR quantitativa, i l'ús de metodologies biomoleculars i bioinformàtiques. Entre ells, destaca el factor de transcripció PU.1, un gen indispensable per el desenvolupament de l'hematopoesi. Aquest gen, s'ha clonat i caracteritzat per primera vegada en salmònids. L'expressió de PU.1 s'ha estudiat mitjançant l'ús d'hibridacions in situ en ronyó anterior y en cervell de truita. A més, l'ús de microarray en aquest dos teixits han permès fer un estudi exhaustiu i pioner a nivell de transcriptòmica en peixos. Les anàlisis del xip de microarray, ha revelat que grups de gens s'activen o s'inhibeixen com a conseqüència d'un estrès immunològic.En resum, aquesta tesis doctoral ha aplicat el desenvolupament de noves tecnologies moleculars pioneres en peixos, com el microarray, la clonació de noves seqüències gèniques i la bioinformàtica, per estudiar la genòmica funcional dels peixos en situacions d'activació dels mecanismes d'estrès i del sistema immune. / The main results of the present thesis can be integrated to a better understanding the stress and the immune responses in fish at a transcriptional level. The application of functional genomic tools, which encloses from using simple PCR analysis to more modern, sophisticate and fashionable microarray technique, allowed us to identified transcriptional regulations of certain set of genes which are enhanced or repressed under stress conditions. Our findings contribute to increase knowledge of molecular mechanism involved in coping the stress and immune responses in fish and provides a better understanding of fish physiology when fish health is threatened. Furthermore, thesis results may be interesting for aquaculture which looks for good biomolecular markers that may improve fish production and fish quality. The isolation, characterization and gene expression study with further microarray analysis of the enolase gene, allowed us to describe enolase as a possible biomolecular marker to determine fish welfare. The in situ hybridization study of the hematopoietic transcription factor PU.1, contributed to amplify the knowledge of the development of the fish immune system. Throughout this thesis, DNA sequences and mRNA expression levels of several genes studied, have contributed to enlarged genomic fish database. In summary, this thesis described from a transcriptional level, gene expression and molecular mechanisms activated or repressed when fish welfare is threatened and contributes to a better understanding of transcriptiomic mechanisms required to cope with the stress.

Objective: The purpose of the study is to explore and illustrate how ultrasound midwives and medical specialist in obstetrics and gynecology believe the information given to parents about the genetic soft markers should be handled. Design: A quantitative questionnaire study with cross-sectional design. Participants: 44 ultrasound midwives and 37 medical specialists in obstetrics and gynecology. Findings: Most of the participants would like to inform before the ultrasound starts that they will be looking for genetic softmarkers during the ultrasound. Likewise the majority wanted to inform the parents about possible increases in the risk for chromosomal abnormalities based on findings on the routine ultrasound. There was a difference in frequency between those who responded that they would like to inform before the ultrasound that they will be looking for genetic softmarkers and those who responded that they believe the future parents wants information before the examination. Key conclusions: It could help health care professionals in their role as information providers if there were common recommendations for the information to be given to future parents about genetic softmarkers in connection with the routine ultrasound. / Syfte: Syftet med studien är att undersöka och belysa hur ultraljudbarnmorskor och specialistläkare inom obstetrik och gynekologi anser att informationen som ges till blivande föräldrar kring genetiska ultraljudsmarkörer bör hanteras. Design: En kvantitativ enkätstudie med tvärsnittsdesign. Deltagare: 44 ultraljudsbarnmorskor och 37 specialistläkare inom obstetrik och gynekologi. Resultat: Merparten av deltagarna vill informera innan ultraljudundersökningen börjar om att de kommer att titta efter genetiska ultraljudmarkörer under rutinultraljudet. Likaså ville majoriteten informera de blivande föräldrarna om eventuella riskökningar för kromosomavvikelser utifrån upptäckter på rutinultraljudet. Det fanns en skillnad i frekvens mellan de som svarat att de ville informera innan ultraljudsundersökningen om att de kommer att titta efter genetiska ultraljudsmarkörer och de som svarat att de tror att de blivande föräldrarna vill ha denna information innan undersökningen. Slutsats: Det skulle kunna hjälpa hälso-och sjukvårdspersonal i sin uppgift som informationsgivare om det fanns genomsamma rekommendationer för vilken information som skall ges till blivande föräldrar kring genetiska ultraljudsmarkörer i samband med rutinultraljudet. På det sättet skulle vi erbjuda en mer jämställd information och vård till hela befolkningen oberoende av var de bor.

Coronary Artery Bypass Grafting (CABG) is an effective and invasive cardiac surgery to salvage blocked coronary artery. Cardiopulmonary bypass (CPB) is usually applied to support circulation during temporary cardiac arrest. Studies have demonstrated that cardiac injury, inflammation, and oxidative stress could be induced during CABG with CPB. We conducted two studies to investigate the release of cardiac biochemical markers and inflammatory response as well as to compare the effect of different coating biomaterial of CPB on the induction of inflammation and oxidative stress during CPB. We investigated the release patterns and the serum levels of cardiac markers as well as inflammatory markers in patients undergoing elective CABG at different time points after initiation of CPB. In this study, we demonstrated that cardiac markers such as creatine kinase isoenzyme MB (CK-MB), and cardiac troponin I (cTnI) and inflammatory markers such as tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and high sensitivity C-reactive protein (hsCRP) were highly elevated after CPB. Moreover, we confirmed that cTnI is still a better biochemical marker for cardiac injury than others following CABG with CPB. Other nonspecific but highly sensitive markers such as lactate dehydrogenase (LDH), lactate, TNF-alpha, IL-6, and hsCRP could be potential surrogate markers for evaluation of cardiac injury following CPB. Based on these findings, we conducted a further investigation to demonstrate our hypothesis that different biocompatible materials used in CPB may affect the inflammation and oxidative stress differently. Biocompatible materials are thinly coated on CPB tubes to provide similar environment like endothelial cells during cardiac surgery. There are several biocompatible materials available in the market. Each of them has unique characteristics. Inflammatory response is one of the bodys fundamental defense mechanisms against foreign invaders. However, inappropriate or excessive response can lead to harmful, potentially life-threatening consequences due to severe inflammatory tissue destruction. CPB-induced inflammatory response can be one of the factors, which can affect surgical outcomes. Depending on the presence of different biocompatible materials in CPB circuits, the degree of immunoreactions can be varied. In this study, we analyzed hsCRP, an acute phase protein, and tau protein, a marker of neurocognitive deficiency. Furthermore we analyzed inflammatory cytokines including TNF-alpha, IL-6, IL-10, and interferon-gamma (IFN-gamma) to evaluate the levels of inflammation. Serum levels of oxidized nitric oxide as a marker of oxidative stress were also assessed. We demonstrated that different biocompatible material has different impacts on inflammation and oxidative stress. In the aspect of anti-inflammation, heparin-coated biocompatible material is better than others whereas surface-modifying additives biocompatible material is worse than others. Overall, different coating biomaterial of CPB results in various inflammatory response. In terms of oxidative stress, we did not observe significant difference between different biomaterial-coated CPB.

The Gossypium genus includes 45 diploid and 5 tetraploid cotton species of which only 2 diploids and 2 tetraploids are cultivated in different parts of the tropics and sub-tropics, leaving the remaining diploid and tetraploid species as potential genetic sources for novel trait introgression. The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) poses significant problems to US cultivated Upland cottons (Gossypium hirsutum L., 2n=52), all of which lack high resistance. This work was in collaboration with the USDA-ARS team that focussed on introgressing reniform nematode-resistance from a diploid cotton species, Gossypium longicalyx Hutch. & Lee into G. hirsutum by creating a tri-species hybrid, HLA and backcross breeding (Bell et al., 2007; Robinson et al., 2007). The main objectives of this work were [1] to cytogenetically evaluate and help select superior types at each introgressed generation; [2] to identify molecular markers tightly linked to the reniform nematode-resistance gene and to map the resistance loci; [3] (A) to introgress germplasm on a genome-wide basis, (B) to evaluate introgressed germplasm for traits of economic importance other than reniform nematode resistance, and (C) to evaluate breeding methodologies in terms of this specialized breeding material. Reniform nematode resistant plants were of diverse cytogenetic constitution but individuals that modally formed 26II chromosomal configuration were identified at BC2F1, BC3F1, BC4F1, and BC5F1 generations. Three SSR markers, BNL3279_114, BNL1066_156, and BNL836_215 and one phenotypic marker, green-colored fuzz (Fzglon), were identified to be tightly-linked to the resistance locus. Extension of the association analysis and linkage estimation to 16 susceptible self progeny (BC1S1, BC3S1 and BC6S1) and 374 susceptible backcross hybrids (BC2F1-BC8F1) mapped the resistance locus to chromosome 11 of cotton with BNL3279_114 on one side and Fzglon on the other at 0.8 cM and 2.8 cM, respectively. Besides reniform nematode-resistance introgression, genome-wide introgression efforts were also conducted. Low micronaire and high fiber strength were the two most promising traits identified in the HLA-derived introgressed generations. Most of the introgressed generations had high variability for the fiber-quality traits than the commercial checks, thus providing more opportunities for selection and improvement.