Engineering evaluations and studies. Volume 3: Exhibit C

High rate multiplexes asymmetry and jitter, data-dependent amplitude variations, and transition density are discussed

Structural investigations of hydroxylase proteins and complexes in bacterial multicomponent monooxygenase systems

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008.Vita.Includes bibliographical references.Bacterial multicomponent monooxgenases (BMMs) such as toluene/o-xylene monooxygenase (ToMO), phenol hydroxylase (PH), and soluble methane monooxygenase (sMMO) catalyze hydrocarbon oxidation reactions at a carboxylatebridged non-heme diiron center common to many systems in biology, as discussed in the first and subsequent chapters of this document. Chapter 1 provides a summary of various relationships between structure and activity in BMMs, as they have been determined through decades of research into BMM hydrocarbon catalysis. Presented in Chapter 2 are the structures of the native (ToMOH) and manganese(ll)-reconstituted (Mn(ll)-ToMOH) ToMO hydroxylase, at 1.85 A and 2.20 A resolution, respectively. The structure of Mn(ll)-ToMOH reveals an active site coordination and geometry similar to that in diferrous and manganese(ll)-reconstituted MMOH, indicating that it represents an analog of the diferrous ToMOH structure. Through comparison of the native ToMOH and Mn(II)-ToMOH structures, a collection of metal site oxidation state dependent conformational changes in conserved residues on the surface of the hydroxylase a-suibunit are observed, suggesting a relationship between active site oxidation state and component interactions in BMMs. Through analysis of the 1.85 A ToMOH structure, a series of hydrophobic cavities through the asubunit connecting the active site to the protein surface analogous to those previously noted in MMOH were also discovered as part of this work. Chapter 3 describes three X-ray crystal structures of ToMOH T201X mutants, and four structures of ToMOH N202X mutants at resolutions ranging from 1.90 to 2.90 A.(cont.) These data reveal alterations in the ToMOH active site pocket surface topology and malformed hydrogen bonding interactions resulting from the various mutations that may respectively be responsible for substrate hydroxylation regiospecificity and proton translocation differences observed of the mutant proteins in future biochemical studies when compared to the wild-type system. Reported in Chapter 4 is a 1.95 A X-ray crystal structure of the xenon gas pressurized PH hydroxylase (Xe-PHH), along with computational analyses of the various surface-to-diiron center cavities, channels, and pores in the a-subunits of all three structurally characterized BMM hydroxylase proteins. The structure of Xe-PHH reveals extensive xenon binding in the conserved a-subunit hydrophobic cavities and suggests a role for the pathway in dioxygen transport to the active site during catalysis. Computational analyses of surface-to-diiron center cavities, channels, and pores in the BMM hydroxylase a-subunits supports findings from the Xe-PHH structure, and provides insight into how the various molecular substrate transport pathways may have been carved into the different hydroxylase proteins through evolution.by Michael S. McCormick.Ph.D

Fuzzy cognitive map modelling the adoption of educational software in schools

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This thesis focuses on modelling factors in the adoption of educational software in schools based on the perceptions of key stakeholders. Findings indicate educational software adoption in UK secondary schools is unsatisfactory. Given the potential of educational software to affect the learning process; the government's emphasis on developing software content for learning purposes and the concern that scarce resources in schools are wasted on software that is inappropriately used or not used at all, there is a need to ensure the successful take-up of educational software. This study aims to provide schools the means to facilitate better management of resources and achieve greater utilisation of educational software. The study in recognising the importance of stakeholders in any technological adoption considers modelling educational software adoption in schools, based on key stakeholders' perceptions. Fuzzy cognitive maps (FCMs), considered extensions of cognitive maps used for modelling complex chains of casual relationships, are used as a modelling approach in this study. A mixed methods research approach is adopted. Participants, include students; a range of teachers; ICTCoordinators and ICT-Technicians, drawn from three UK secondary schools. The resulting FCM model offers a visual medium providing insight into the factors required in the take-up of educational software. Some factors identified include the availability and accessibility to IT facilities and equipment; the availability of educational software; software ability to satisfy learning requirements and to meet curriculum requirements. The model provides the means to identify factors which have a greater impact on educational software adoption, so scarce resources can be directed accordingly. As a holistic model it provides insight into the context of educational software adoption in schools. As a dynamic model it allows the opportunity to explore `what-if possibilities relating to policy and investment options. The model can act as a guide for planners, decision-makers and software developers

Genetic improvement of grain quality for bread making in triticale

Triticale (X Triticosecale Wittmack) is a high-yielding and vigourous interspecific hybrid between wheat and cereal rye. The crop is known for tolerance of abiotic stresses and high biomass production, and thus it has the potential to increase the profitability and productivity of growers in marginal environments and to help address the food production challenges of the 21st century. The original cultivars from the 1960s and 1970s usually produced grain with flour properties in between triticale’s progenitor species, and thus produced dough inferior to wheat and unsuitable for a range of food products, including loaf bread, flat bread, cakes, biscuits and crackers. However over the last 40 years, grain yield and grain quality for animal feed have been significantly improved through breeding and selection, and hence indirect improvements (or at the least, genetic drift in quality alleles) in its potential to produce good food products could be expected. Furthermore, significant advances in wheat quality research have produced vast amounts of information, methodology and technology that can be easily used to improve triticale quality, and the tastes of the modern consumer are different to those of 40 years ago. This thesis aimed to characterise the flour properties of a range of modern triticale cultivars and compare them to wheat, then investigate genetic, agronomic and post-harvest strategies to improve the value of the grain for a human food market. Focus was given to the two major scientific issues which have historically hindered the use of triticale flour in food products – poor gluten strength and high α-amylase activity – and to other quality traits of commercial significance. The grain and flour quality was quantified in up to 17 modern triticale cultivars grown in four environments over 2 years – Greendale, NSW in 2009 (JP09), Cowra, NSW in 2010 (COW10), both of which are typical triticale growing environments with poor soil and minimal fertiliser, Narrabri, NSW in 2010 (NARR10), which is a high yielding, high quality environment known for producing Australian Prime Hard wheat, and Stirling, SA in 2011 (SA11) which is a high protein, low yielding environment. Field plots were arranged in a randomised complete block design at JP09, COW10 and NARR10 with minimal irrigation; rust was controlled with fungicide. The three varieties from SA11 were sourced from commercial seed production lots. Grain was milled to wholemeal flour on a Newport Scientific hammer mill with 0.5mm screen, and to white flour on both a Quadrumat® Junior Mill and a Bühler experimental mill. Glutenin and secalin subunits were characterised by SDS-PAGE and the gluten properties were investigated using the SDS-sedimentation test and mixographs. α-Amylase activity was investigated spectrophotometrically and using the falling number test. These vi measurements were compared to estimations of grain protein, non-starch polysaccharides (NSP), starch content and fibre content using near-infrared transmittance (NIT). Flour protein was estimated by NIR (near-infrared reflectance). The pasting properties of milled flours were evaluated on a Newport Scientific Rapid Visco Analyzer according to AACC 76-21, except 10 mM AgNO3 was used in place of DI water to inhibit α-amylase activity. Grain hardness was measured by the Single-Kernel Characterisation System and moisture and ash content by standard oven methods. Colour of Junior milled flour was assessed using a Minolta Chroma meter CR-400. Finally, plain cookies were baked according to a standard recipe used to assess soft wheats. Variability in the glutenin and secalin subunits was small relative to global diversity amongst triticale cultivars, and reflects the narrow genetic base of material in Australian breeding programs. The gluten quality of these triticale cultivars was inferior to bread wheat but similar to soft wheat; however the protein content of triticale flour was significantly lower than wheat flour. Lower triticale protein content represents a change from early cultivars and reduces its capacity to form viscoelastic gluten. Cultivars Hawkeye and Vicuna were recommended for breeding to improve gluten strength in locally adapted germplasm. Much greater variability in starch and NSP characteristics were found in triticale compared to wheat, and the ranges overlapped between species. The cultivars Tobruk, Yukuri and Berkshire expressed equivalent α-amylase activity to wheat; cultivars Jaywick and Yukuri were found to have partially waxy starch. Triticale generally exhibited higher NSP, equivalent pasting properties, higher α-amylase activity and lower falling number than wheat checks. However, low falling number was not indicative of high α-amylase activity; this contradicts the assumptions on which previous triticale research was based and has implications for the interpretation of research and the use of falling number to compare triticale to wheat. Furthermore, an unexpected negative correlation was observed with NSP, where higher NSP reduced the slurry viscosity measured in the falling number test. Modification of the falling number test is recommended before it can be used in triticale breeding programs. Nevertheless, the observed genetic variability in starch characteristics and α-amylase activity indicates some triticale cultivars have waxy properties conducive to the production of noodles, and that certain lines exhibited similar late-maturity α-amylase activity to modern wheat cultivars: an indirect benefit of breeding and selection over the past few decades. Like starch properties, great variation was found amongst triticale cultivars for hardness, colour and milling yield. Berkshire displayed a grain hardness equivalent to durum wheat, suggesting a null allele at the rye softness protein locus (Sin locus); the remaining cultivars exhibited a grain hardness between soft wheat and bread wheat. The high milling yield and low fibre content of Tobruk (milling yield was even higher than bread wheat) suggested this line has a thin seed coat and thus would be an excellent parent for the genetic improvement of triticale milling yield. Average flour ash content was significantly higher vii than wheat in both statistical and practical terms, and a different bench mark needs to be used for low ash triticale flour compared to low ash wheat. Apart from Vicuna and Yukuri, triticale cultivars produced darker flour than wheat, however with modern consumer preferences tending towards ‘healthy-looking’ foods, darker flour should not be a hindrance to its utility. The overall results confirmed previous suggestions that triticale is suited to soft wheat products such as cookies, and hence their cookie quality was investigated. Although the dough behaviour and water absorption of triticale was different to soft wheat (specifically, triticale dough tended to loose large amounts of water during sheeting), triticale cookies were found to be equivalent to soft wheat cookies. Overall, the survey of quality amongst modern triticale cultivars suggested two things: firstly, sufficient genetic variation exists amongst current lines to breed triticale cultivars with significantly improved flour quality (comparable to wheat for some quality traits); secondly, there is a clear need to classify current cultivars into suitability for various end uses. This would facilitate efficient marketing to the milling industry and subsequent use in food products. Improvement of the the poor gluten strength in triticale was attempted by backcrossing locally-adapted spring breeding lines to DH265, a winter line which contained a modified 1R chromosome carrying two translocations from 1D of bread wheat – the Glu-D1d allele from 1DL (which simultaneously removed Glu-R1) and the Gli-D1/Glu-D3 locus from the distal end of 1DS. Single plant and plot selection was performed on five cross populations grown in multiple environments and the yield, protein content and gluten strength was analysed on F4-derived F7 grain. Lines containing the translocation had a slightly lower yield compared to the null lines and the triticale checks; but similar to the wheat checks for all except one cross (which was significantly less). This may reflect a loss of root system vigour, head length or higher selection pressure due to lower transmission rate of the translocation to offspring. The translocation slightly increased protein content in two populations and increased SDS-sedimentation height in one population (after accounting for the influence of higher protein content). However, no difference was detected between the overall average SDS-sedimentation height of the null lines and the wheat and triticale checks. This is partially due to large variability in SDS-sedimentation height within each cross population resulting from significant variability at other glutenin and secalin loci. Nevertheless, several lines were identified with grain yield equivalent to current triticale cultivars (and significantly higher than wheat) plus equivalent SDS-sedimentation height to wheat. Thus the translocation is a potential solution to the generally poor gluten strength of modern triticale cultivars. The viability of using existing variability for secaloglutenin alleles in the progenitor species was investigated as a means of creating new germplasm (‘primary triticales’) with high gluten strength. The HMW glutenins of five durum lines, and the HMW secalins and 75k γ- secalins of two rye lines, were defined using SDS-PAGE. These lines were then crossed, new primaries were produced, and grain was tested for the expression of secaloglutenin viii alleles, protein content and SDS-sedimentation height as an estimation of secalogluten strength. The secaloglutenin alleles were simply inherited from the parental plants and all were expressed normally in the offspring, however it was possible that mixed oligomers were formed between glutenins and secalins at the macromolecular level. Significant differences were observed in the SDS-sedimentation height of primaries originating from different durum parents, suggesting that selection of durum parents with high SDSsedimentation is a viable method for producing triticale flour with superior gluten properties. In south-eastern Australia, dual-purpose cropping is commonly used by growers to manage risk in mixed enterprise operations. A preliminary report of lower ash content but comparable protein content in triticale produced in dual-purpose systems was reported in Bangladesh and hence an experiment was conducted to assess the effect of biomass removal on grain yield, test weight, protein content and ash content of grain from four Australian dual-purpose triticale lines grown in five year-site environments (ash content is correlated with nutritional value, milling yield and flour colour). Ash content was either unaffected or increased by removal of biomass and both protein content and grain yield were reduced. It was concluded that although ash content was lower in some lines cut late in the season, the general effect was detrimental to quality and even when ash content was reduced, the effect was not large enough to reduce the level to that of wheat. Hence similar to wheat, dual-purpose triticale systems are not recommended for production of grain for a milling market. Poor milling yield in triticale is a key concern for millers. However, the high variability of grain hardness in triticale, historic problems with grain shrivelling, and lack of varietal classification has meant milling is usually conducted without adjusting settings to batch characteristics. Hence the importance of tempering moisture was investigated in three triticale varieties of varying hardness grown in two environments alongside a wheat standard. Milling yield and ash content both increased as tempering moisture was decreased from 15% to 11%. Triticale flour could be produced at a similar extraction rate as bread wheat provided there was no detrimental effect of high flour ash content. Surface area of larger triticale grain may also influence ideal tempering moisture, however further investigation is required. Tempering triticale to a moisture content appropriate to its physical grain hardness was essential in the optimisation of the milling process. The results of this thesis suggests that it is possible to produce triticale cultivars with flour properties equivalent to wheat, either through traditional plant breeding, chromosomal modification or creation of new primary triticales. However, with a changing market, many of the flour requirements have changed since triticale was first investigated in food products e.g. increased popularity of darker/wholemeal flours. Furthermore, general improvement of the crop over the last few decades has indirectly improved the grain e.g. breeding for plump grain has increased starch content and milling yield. Many of the current concerns of millers such as insufficient protein content, sticky dough, high α- ix amylase production, and low milling yield, can be overcome through fertilizer management, classification of varieties into grain hardness, milling yield and protein quality classes, and sourcing batches of grain with low α-amylase activity (avoiding measurement using the falling number test). There is a clear need to develop a marketing pathway for triticale flour in which cultivars and agronomic conditions that optimise milling quality are clearly communicated to growers. This is a prerequisite for the establishment of a price premium for batches of grain that meet the requirements of millers, processers and consumers. The higher yield and abiotic stress tolerance of triticale suggests that with focused breeding and an industry-wide push for efficient flour marketing, this crop could address some of the food production challenges of the 21st century

Highly Excited States of Small Molecules and Negative Atomic Ions

Excited states of atoms and molecules exhibit a rich array of diverse phenomena. This dissertation examines two exotic states of atoms at such excited levels: Rydberg molecules and atomic negative ions. Rydberg molecules are formed by a Rydberg atom and one or more ground state atoms, and can be highly polar due to their unusual electronic wave functions and enormous bond lengths. This dissertation expands the theory of these molecules by studying the formation and structure of polyatomic molecules, multichannel Rydberg molecules formed from divalent atoms, and spin effects and relativistic interactions. It also details intermolecular forces between Rydberg molecules, their manipulation via external fields, and their dependence on the intricacies of electron-atom scattering. This electron-atom interaction is also the main component of the latter portion of this thesis, which studies doubly excited states of alkali negative ions in very polarizable and nearly degenerate atomic states. Photodetachment of these states reveals electron correlation and long-range forces stemming from their high excitation

Polymer structure and mechanical properties

Mechanical properties, morphology, and relaxation processes in elastomers and crystalline polymer

Interspecific Hybridization in Plant Biology

Many crop gene pools are derived from a small number of founders. As a consequence of long histories of strong directional selection, crop gene pools have narrow genetic diversity available to provide inherent solutions to changing needs or challenges. Notoriously, plants can mate across taxonomically-determined species boundaries, and interspecific hybridization is widely used in plant genetics research. Interspecific hybridizations have conferred practical improvements to crops, some of which are unexpected based on the phenotypes of the parents. Genomics has provided insights into the fundamental consequences of interspecific hybridization for plant biology. Additionally, genomics has allowed the development of molecular tools for dissecting the genetic control of phenotypic variation in interspecific hybrid populations and manipulating interspecific introgressions in crop improvement. This Research Topic aims to publish peer-reviewed research to interspecific hybridization and its consequences, both fundamental and applied. While such work is prominent in plants, consideration will also be given to salient work in other taxa. A key threshold for publication will be the extent to which findings are of cross-cutting interest and importance, i.e. not only to those working on the target taxon but to a wide range of biological scientists.Peer reviewe

Allocating patrolling resources to effectively thwart intelligent attackers

This thesis considers the allocation of patrolling resources deployed in an effort to thwart intelligent attackers, who are committing malicious acts at unknown locations which take a specified length of time to complete. This thesis considers patrolling games which depend on three parameters; a graph, a game length and an attack length. For patrolling games, the graph models the locations and how they are connected, the game length corresponds to the time-horizon in which two players, known as the patroller and attacker, act and the attack length is the time it takes an attacker to complete their malicious act. This thesis defines patrolling games (as first seen in [16]) and explains its known properties and how such games are solved. While any patrolling game can be solved by a linear program (LP) when the number of locations or game length is small, this becomes infeasible when either of these parameters are of moderate size. Therefore, strategies are often evaluated by knowing an opponent’s response and with this, patroller and attacker strategies give lower and upper bounds on the optimal value. Moreover, when tight bounds are given by strategies these are optimal strategies. This thesis states known strategies giving these bounds and classes for which patrolling games have been solved. Firstly, this thesis introduces new techniques which can be used to evaluate strategies, by reducing the strategy space for best responses from an opponent. Extensions to known strategies are developed and their respective bounds are given using known results. In addition we develop a patroller improvement program (PIP) which improves current patroller strategies by considering which locations are currently under performing. Secondly, these general techniques and strategies are applied to find solutions to a certain class of patrolling games which are not previously solved. In particular, classes of the patrolling game are solved when the graph is multipartite or is an extension of a star graph. Thirdly, this thesis conjectures that a developed patroller strategy known as the random minimal full-node cycle is optimal for a large class of patrolling games, when the graph is a tree. Intuitive reasoning behind the conjecture is given along with computational evidence, showing the conjecture holds when the number of locations in the graph is less than 9. Finally, this thesis looks at three extensions to the scenario modelled by the patrolling game. One extension models varying distances between locations rather than assuming locations are a unitary distance apart. Another extension allows the time needed for an attacker to complete their malicious act to vary depending on the vulnerability of the location. For the final extension of multiple players we look at four variants depending on how multiple attackers succeed in the extension. In each extension we find some properties of the game and show that it possible to relate # extensions to the classic patrolling game in order to find the value and optimal strategies for certain classes of such games

Annual Wheat Newsletter. Volume 56

The Annual Wheat Newsletter is edited by W.J. Raupp and published by the Wheat Genetic and Genomic Resources Center at Kansas State University. The scope of the Newsletter includes current project activities, cultivar releases, special reports, and publications of wheat researchers worldwide. The Newsletter annually has over 100 contributors from more than 30 countries