1. Fusarium roseum �Graminearum� was the predominant fungus associated with stalk rot of maize in eastern Australia in the 1972, 1973 and 1974 growing seasons. All isolates of this pathogen were of the Group 2 type. Thus Group 2 contrasts with Group I which is normally isolated :Erora crown rot of wheat and grasses. Other fungi isolated in order of frequency were Diplodia maydis, F. rnoniliforme �Subglutinans�, Bipolaris sorokiniana, Nigrospora oryzac, F. roseum �Semitectum�, F. moniliforme, F. roseum �Equiseti�, F. roseum �Concolor�, Macrophomina phaseolina, Rhizoctonia sp., F. roseum �Acuminatum�, F. oxysporum, F. solani, F. tricinctum and F. roseum �Heterosporum�. The relative isolation frequencies of the fungi varied according to the seasonal conditions. Stalk rots were not of major importance in 1973, a relatively dry growing season. However, in 1974, a wet growing season, stalk rot diseases were common in all areas investigated. 2. Isolates of F. roseum �Graminearum�,derived mainly from wheat and maize but also from other sources and from various regions of eastern Australia, were examined for perithecia formation, colony characteristics, fertility, colony growth, conidia production and conidia size. The distribution of the fungus in field colonized maize and wheat plants was also studied. The Group 1 isolates did not produce perithecia, were heterothallic and very infertile, had a mean colony growth of 4.4 cm per 3 days (range, 3.9- 5.1) and produced relatively large numbers of conidia. In contrast, Group 2 isolates were homothallic and produced perithecia readily, had a mean colony growth of 5.4 cm per 3 days (range, 4.7�6.1) and produced relatively low numbers of conidia. Group 1 isolates were found to be commonly associated with crowns and roots of plants and Group 2 isolates were commonly associated with aerial plant parts. 3. The ability of a number of Group 1 and Group 2 isolates to produce the fungal hormone, zearalenone was assessed. Group I isolates produced three to four times more zearalenone than Group 2 isolates. In addition, a. culture which had previously produced perithecia but had lost that ability following numerous transfers, produced no detectable zearalenone. The results provided good evidence that the observed difference in perithecia formation was directly related to the ability to produce zearalenone. 4. The pathogenicity to wheat, maize and carnations of Group 1 isolates from crown rot affected wheat plants and Group 2 isolates from stalk rot affected maize plants was tested. Pathogenicity of 11 other isolates from teosinte, carnations, pearl millet, wheat and barley scab, banana, ginger and common wheat grass was also assessed. The results indicated that pathogenic specialization exists within F. roseum �Graminearum�. Wheat isolates were the most pathogenic to wheat, carnation isolates were the most pathogenic to carnations and all maize isolates were pathogenic to maize while those from wheat and common wheat grass were not as pathogenic to maize. Moreover, Group 2 isolates were more pathogenic when inoculated in aerial plant parts, and the Group I isolates were more pathogenic when inoculated in plant parts in soil. Inoculations on wheat seedlings in sterile field soil demonstrated that the inherent pathogenicity to wheat seedlings of isolates from wheat and maize were similar. 5. Some factors which could contribute to the observed pathogenic differences between isolates from wheat and maize to wheat seedlings in field soil were examined. Conidia volume, germination rate and inherent germinability in the soil were studied. The Group I isolates had the largest volume, the most rapid germination and the highest inherent germinability. Pathogenicity was positively correlated with conidium volume and inherent germinability. In addition, the inherent germinability and conidium volume were positively correlated. Thus, it was established that pathogenic behaviour of conidia of Group 1 and Group 2 reflected differences in conidia morphology.

1. Fusarium roseum �Graminearum� was the predominant fungus associated with stalk rot of maize in eastern Australia in the 1972, 1973 and 1974 growing seasons. All isolates of this pathogen were of the Group 2 type. Thus Group 2 contrasts with Group I which is normally isolated :Erora crown rot of wheat and grasses. Other fungi isolated in order of frequency were Diplodia maydis, F. rnoniliforme �Subglutinans�, Bipolaris sorokiniana, Nigrospora oryzac, F. roseum �Semitectum�, F. moniliforme, F. roseum �Equiseti�, F. roseum �Concolor�, Macrophomina phaseolina, Rhizoctonia sp., F. roseum �Acuminatum�, F. oxysporum, F. solani, F. tricinctum and F. roseum �Heterosporum�. The relative isolation frequencies of the fungi varied according to the seasonal conditions. Stalk rots were not of major importance in 1973, a relatively dry growing season. However, in 1974, a wet growing season, stalk rot diseases were common in all areas investigated. 2. Isolates of F. roseum �Graminearum�,derived mainly from wheat and maize but also from other sources and from various regions of eastern Australia, were examined for perithecia formation, colony characteristics, fertility, colony growth, conidia production and conidia size. The distribution of the fungus in field colonized maize and wheat plants was also studied. The Group 1 isolates did not produce perithecia, were heterothallic and very infertile, had a mean colony growth of 4.4 cm per 3 days (range, 3.9- 5.1) and produced relatively large numbers of conidia. In contrast, Group 2 isolates were homothallic and produced perithecia readily, had a mean colony growth of 5.4 cm per 3 days (range, 4.7�6.1) and produced relatively low numbers of conidia. Group 1 isolates were found to be commonly associated with crowns and roots of plants and Group 2 isolates were commonly associated with aerial plant parts. 3. The ability of a number of Group 1 and Group 2 isolates to produce the fungal hormone, zearalenone was assessed. Group I isolates produced three to four times more zearalenone than Group 2 isolates. In addition, a. culture which had previously produced perithecia but had lost that ability following numerous transfers, produced no detectable zearalenone. The results provided good evidence that the observed difference in perithecia formation was directly related to the ability to produce zearalenone. 4. The pathogenicity to wheat, maize and carnations of Group 1 isolates from crown rot affected wheat plants and Group 2 isolates from stalk rot affected maize plants was tested. Pathogenicity of 11 other isolates from teosinte, carnations, pearl millet, wheat and barley scab, banana, ginger and common wheat grass was also assessed. The results indicated that pathogenic specialization exists within F. roseum �Graminearum�. Wheat isolates were the most pathogenic to wheat, carnation isolates were the most pathogenic to carnations and all maize isolates were pathogenic to maize while those from wheat and common wheat grass were not as pathogenic to maize. Moreover, Group 2 isolates were more pathogenic when inoculated in aerial plant parts, and the Group I isolates were more pathogenic when inoculated in plant parts in soil. Inoculations on wheat seedlings in sterile field soil demonstrated that the inherent pathogenicity to wheat seedlings of isolates from wheat and maize were similar. 5. Some factors which could contribute to the observed pathogenic differences between isolates from wheat and maize to wheat seedlings in field soil were examined. Conidia volume, germination rate and inherent germinability in the soil were studied. The Group I isolates had the largest volume, the most rapid germination and the highest inherent germinability. Pathogenicity was positively correlated with conidium volume and inherent germinability. In addition, the inherent germinability and conidium volume were positively correlated. Thus, it was established that pathogenic behaviour of conidia of Group 1 and Group 2 reflected differences in conidia morphology.

In this study, the aim was enzymatic xylooligosaccharide production from cotton and sunflower stalks, two of main agricultural residues in Turkey. In first two parts of the study, alkali extracted xylan from both of the stalks was hydrolyzed by commercial xylanases Veron and Shearzyme. The effect of temperature, pH, enzyme and substrate concentrations were investigated to determine optimum enzymatic hydrolysis conditions of xylan. Sunflower and cotton stalk xylans were hydrolyzed by Shearzyme more efficiently than Veron under the conditions studied. Shearzyme produced different product profiles containing xylobiose (X2), xylotriose (X3), xylotetrose (X4) and xylopentose (X5) from cotton and sunflower stalk xylan. On the other hand, Veron hydrolyzed both xylan types to produce X2, X3, X5, X6 and larger xylooligosaccharides without any change in product profiles. In the third part of the study, home produced xylanase from Bacillus pumilus SB-M13, was also investigated for the production of xylooligosaccharides from both cotton and sunflower stalk xylan. The main products obtained by hydrolysis of both substrates by pure B. pumilus xylanase were X5 and X6, while crude B. pumilus xylanase generated X4 and X5 as the main products. Xylooligosaccharide production from pretreated cotton stalk without alkali extraction of xylan was the final part of the study. Three different pretreatment methods including biomass pretreatment by Phanerochaete chrysosporium fermentation, cellulase pretreatment and hydrothermal pretreatment were investigated to break down complex lignocellulosic structure of cotton stalk to improve the subsequent enzymatic hydrolysis of xylan in pretreated cotton stalk for xylooligosaccharide production. However, xylooligosaccharide was not effectively produced from pretreated cotton stalk. Shearzyme inhibiton was observed after all the pretreatment methods during further hydrolysis of pretreated cotton stalk probably due to production of inhibitory compounds of the enzyme.

Master of Science / Department of Agronomy / Tesfaye Tesso / Sorghum [Sorghum bicolor (L.) Moench] is listed as one of the potential feedstock sources for biofuel production. While sorghum grain can be fermented into ethanol in a similar way as maize, the greatest potential of the crop is based on its massive biomass and sugar rich juices. Thus development of the crop as alternative energy source requires improvement of these traits. The objectives of this study were (1) to determine the mode of inheritance of traits related to ethanol production and identify suitable genetic sources for use in breeding programs, and (2) to evaluate the potential of low lignin mutations for biomass feedstock production and assess biotic stress risks associated with deployment of the mutations. The study consisted of three related experiments: (i) estimating the combining ability of selected sweet and high biomass sorghum genotypes for biofuel traits and resistance to stalk lodging, (ii) determine the impact of brown mid-rib mutations on biofuel production and their reaction to infection by Macrophomina phaseolina and Fusarium thapsinum, and (iii) assess the reaction of low lignin mutants to green bug feeding. In the first experiment six sorghum genotypes of variable characteristics (PI193073, PI257602, PI185672, PI195754, SC382 and SC373) were crossed to three standard seed parent lines ATx3042, ATx623 and ATx399. The resulting hybrids and the parents were evaluated at four locations, three replications during 2009 and 2010 seasons. Data were collected on phenology, plant height, juice yield, °brix score and biomass production. In the second experiment, two brown mid-rib mutations (bmr6 and bmr12) and their normal versions were studied in four forage sorghum backgrounds (Atlas, Early Hegari, Kansas Collier and Rox Orange). The experiment was planted in four replications and at 14 d after flowering five plants in a plot were artificially infected with F. thapsinum and another five with M. phaseolina. The plants were harvested and rated for disease severity (lesion length and nodes crossed). Another five normal plants in each plot were harvested and used to determine biofuel traits (juice yield, ºbrix score and biomass). In the third experiment, a subset of entries evaluated in experiment II and three tolerant and susceptible checks were tested for greenbug feeding damage. Biotype K greenbug colony was inoculated to each genotype using double sticky foam cages. Feeding damage was assessed as percent chlorophyll loss using SPAD meter. There was significant general combining ability (GCA) effect among the male entries for juice yield, stem obrix and biomass production indicating that these traits are controlled by additive genes. Lines PI257602 and PI185672 in particular, had the highest GCA for all the traits and should serve as excellent breeding materials. There was no significant difference among the bmr mutants and between the bmr and normal genotypes for both stalk rot and greenbug damage. In conclusion, juice yield, °brix and biomass are largely controlled by additive genes and hence are amenable to genetic manipulation. The bmr mutations despite their impact on lignin content do not increase risk of attack by stalk rot pathogens and greenbugs and thus can be deployed for biofuel production without incurring losses to these factors.

Ribosome-inactivating proteins (RIPs) such as Shiga-like toxin 1 (SLT-1) halt protein synthesis in eukaryotic cells by depurinating a single adenine base in the sarcin-ricin loop of 28S rRNA. The molecular details involved in the ER lumenal escape and subsequent site-specific depurination are lacking, despite a general understanding of the biochemical basis of SLT-1 toxicity. Using a combination of yeast-2-hybrid and HeLa lysate pull-down followed by LC-MS/MS we have discovered yeast and human proteins that interact with the catalytic A1 chain of SLT-1. Yeast-2-hybrid library screens followed by the expression of full-length protein candidates and pull-down experiments yielded Cue2 as the only yeast cellular component that binds to the SLT-1 A1 chain. Further truncational analysis revealed that the known protein domains (two Cue domains and a Smr domain) within the primary sequence of Cue 2 were not essential for the interaction. Cue2 is a yeast monoubiquitin binding protein of no known function that is structurally homologous to the human ubiquitin-associated domain which has been implicated in intracellular routing and ER-associated degradation. Pull-down experiments indicated that the mechanism by which the catalytic domain of RIPs cleaves its substrate involves initial docking interactions with the ribosomal stalk by virtue of a conserved acidic C-terminal peptide domain common to all three stalk proteins P0, P1, and P2. The A1 chain of SLT-1 transiently binds to this peptide with a modest binding constant and rapid on and off rates. Mutagenesis of charged residues within the A1 chain identified a cationic surface that interacts with the peptide motif. In addition, phage-display was used to rapidly probe the importance of each residue within this C-terminal ribosomal peptide. The analysis revealed a complementary acidic surface and an additional hydrophobic motif involved in the interaction. Moreover, deletion mutagenesis performed on the ribosomal protein P0 revealed that the A1 chain binds to an alternate site on P0 in proximity to the contact sites for P1/P2 heterodimers. These results demonstrate that the catalytic chain of RIPs such as SLT-1 dock on ribosomes using two classes of binding sites located within the ribosomal stalk which may aid in orienting their catalytic domain in close proximity to the depurination site.

Ribosome-inactivating proteins (RIPs) such as Shiga-like toxin 1 (SLT-1) halt protein synthesis in eukaryotic cells by depurinating a single adenine base in the sarcin-ricin loop of 28S rRNA. The molecular details involved in the ER lumenal escape and subsequent site-specific depurination are lacking, despite a general understanding of the biochemical basis of SLT-1 toxicity. Using a combination of yeast-2-hybrid and HeLa lysate pull-down followed by LC-MS/MS we have discovered yeast and human proteins that interact with the catalytic A1 chain of SLT-1. Yeast-2-hybrid library screens followed by the expression of full-length protein candidates and pull-down experiments yielded Cue2 as the only yeast cellular component that binds to the SLT-1 A1 chain. Further truncational analysis revealed that the known protein domains (two Cue domains and a Smr domain) within the primary sequence of Cue 2 were not essential for the interaction. Cue2 is a yeast monoubiquitin binding protein of no known function that is structurally homologous to the human ubiquitin-associated domain which has been implicated in intracellular routing and ER-associated degradation. Pull-down experiments indicated that the mechanism by which the catalytic domain of RIPs cleaves its substrate involves initial docking interactions with the ribosomal stalk by virtue of a conserved acidic C-terminal peptide domain common to all three stalk proteins P0, P1, and P2. The A1 chain of SLT-1 transiently binds to this peptide with a modest binding constant and rapid on and off rates. Mutagenesis of charged residues within the A1 chain identified a cationic surface that interacts with the peptide motif. In addition, phage-display was used to rapidly probe the importance of each residue within this C-terminal ribosomal peptide. The analysis revealed a complementary acidic surface and an additional hydrophobic motif involved in the interaction. Moreover, deletion mutagenesis performed on the ribosomal protein P0 revealed that the A1 chain binds to an alternate site on P0 in proximity to the contact sites for P1/P2 heterodimers. These results demonstrate that the catalytic chain of RIPs such as SLT-1 dock on ribosomes using two classes of binding sites located within the ribosomal stalk which may aid in orienting their catalytic domain in close proximity to the depurination site.

As the most produced grain crop world-wide, 5% of corn is lost due to stalk lodging (above-ground structural failure of the stalk near the roots). Current modeling methods lack the ability to manipulate the stalk architecture. In contrast, parameterized models enable advanced analyses such as sensitivity and optimization studies. This thesis advances previous work on a parameterized cross-sectional model of maize stalk morphology and investigates the validity of a parameterized three-dimensional model. The parameterized cross-sectional model is based upon previous work that approximated the cross-section of maize stalks using an ellipse plus principal components. Validation of the cross-sectional model was done by evaluating the structural response in four loading cases: axial tension/compression, bending, transverse compression, and torsion. 2D prismatic extrusions of specimen specific cross-sections were tested under the load conditions and compared against 2D prismatic models of the parametrized cross-sections. Analysis of the 2D prismatic model consisted of a parameter sensitivity analysis to determine influential morphological features, and a load bearing analysis to quantify the proportion of load borne by each material tissue. Validation of the parameterized 3D model was completed by comparing the structural response of the parameterized 3D model against empirical test data. A comparison against CT-based finite element models was also done to quantify the level of predictive discrepancy caused by geometric parameterization. The elliptical 2D prismatic model responded with less than 5% error for axial tension/compression, bending, and transverse compression, suggesting that the ellipse model is sufficient for analyses and 3D parameterization. The 2D prismatic model maintained an error less than 10% under a torsion load. The parameter sensitivity analysis revealed that ellipse parameters are significantly more influential to stalk strength than material or finer geometric details. In the load bearing analysis, the rind bore a median of over 90% of the load in axial tension/compression, bending, and torsion, but less than 10% of the load in transverse compression. The parameterized 3D model validates yielding correlations with empirical test data resulting in R2 values of 0.82 in flexural stiffness, and in critical buckling a value of 0.71. Comparison with CT-based models resulted in very strong correlations with R2 values of 0.81 in flexural stiffness, and for critical buckling a value of 0.87. The parameterized 3D model validates and can be used in future studies.

Studies were conducted to determine if corn stalk strength had an effect on southwestern corn borer (Diatraea grandiosella Dyar) survival during different growth stages. In 2006 southwestern corn borer larvae were placed on corn during the tassel stage near the ear and base of the plant. Survival was higher near the ear than near the base of the plant. In 2007, five varieties of corn were planted at three locations in Mississippi. Plants were infested with five 3rd instar larvae at the ear zone during tassel, dough and dent development stages. After five days stalk strength and borer survival were measured. Survival decreased as the corn progressed from tassel to dent stage. Survival varied among corn varieties. The relationship between stalk strength and borer survival was not consistent, indicating that there are likely factors more directly limiting borer survival than physical stalk strength.

Cotton stalk lignin extractions were performed via alkaline methods at different conditions. Crude and post treated cotton stalk lignins, olive mill wastewater and garlic stalk juice were examined in terms of antimicrobial activity. Antimicrobial lignin was isolated depending on alkaline extraction conditions. Lignin extracted at 60&deg / C exhibited significant antimicrobial effect towards both Escherichia coli and Bacillus pumilus. However different post treatments such as ultrasonication and TiO2-assisted photocatalytic oxidation did not result in antimicrobial compounds. Olive mill wastewater and garlic stalk juice exerted substantial antimicrobial effects towards tested microorganisms. Xylan-based biodegradable films containing lignin, garlic stalk juice, tannic acid and olive mill wastewater were characterized against both B. pumilus and E. coli by means of their antimicrobial activities. E. coli exhibited lesser sensitivity to all tested antimicrobial xylan films except tannic acid-integrated xylan film than B. pumilus. Antimicrobial lignin integrated-xylan film exhibited stronger effect towards tested microorganisms than tannic acid-integrated film. In the case of both antimicrobial lignin and tannic acid integrated xylan films, 4% was found to be the maximum antimicrobial compound percentage in film forming solutions to observe continuous film formation. Lignin samples with/without antimicrobial activity were characterized by means of their chemical structure via FTIR and LC-MS. FTIR results revealed that cotton stalk lignins were significantly broken down via alkaline treatment and this breakdown resulted in the formation of new fractions and also ester &amp / ether bonds between antimicrobial hydroxycinnamic acids and lignin were cleaved during the alkaline treatments of cotton stalk lignins. By FTIR results, C=C bonds were found to be characteristic for antimicrobial lignin sample and it was suggested that these bonds might be the reason of the antimicrobial activity. By LC-MS qualitative mass analysis, antibacterial lignin fractions were found to be quite different from non-antibacterial lignin fractions. LC-MS results indicated that the antimicrobial lignin fractions might be lignin-derived oligomers and/or might be flavonoids. Cotton stalk lignin fractions demonstrated different antimicrobial activities depending on the method of isolation and chemical treatment.

No description available.