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No description available.

Astilbe (Saxifragaceae) is a genus of herbaceous perennials widely cultivated for their ornamental value. The genus is considered taxonomically complex because of its geographic distribution, variation within species, and the lack of adequate morphological characters to delineate taxa. To date, an inclusive investigation of the genus has not been conducted. This study was undertaken to (a) develop a well-resolved phylogeny of the genus Astilbe using an expanded morphological data set and sequences from the plastid gene matK, (b) use single nucleotide polymorphisms to determine the lineages of cultivated varieties, and (c) successfully culture Astilbe in vitro and evaluate potential somaclonal variation of resulting Astilbe microshoots. Phylogenetic trees generated from a morphological character matrix of 28 character states divided Astilbe into three distinct clades. Relationships were well resolved among the taxa, though only a few branches had greater than 50% bootstrap support. There is evidence from the phylogeny that some described species may actually represent variation within populations of species. From our analysis I propose an Astilbe genus with 13 to 15 species and offer a key for distinguishing species and varieties. There was little matK sequence variation among taxa of Astilbe. Phylogeny of Astilbe generated from the maximum parsimony and maximum likelihood analysis of matK sequences resulted in a polytomy of seven Astilbe species, with relationships within the genus poorly resolved. A second phylogeny of 21 taxa of Astilbe was more informative, aligning cultivated varieties near species from which they were derived. The matK sequence variation for Astilbe taxa was aligned to reveal DNA polymorphisms. Closely related taxa retained polymorphisms at the same sites within the gene sequence. These polymorphic sites could potentially be utilized to confirm the lineage of popular cultivated Astilbe varieties. Propagation of Astilbe seedlings in tissue culture gave rise to various numbers of microshoots from each of 15 seedlings. Multivariate and cluster analysis of morphological characters from 138 plants derived from 15 seedlings revealed potential somaclonal variants. These variants were characterized by one or more of the following traits: dwarf habit, dark green leaves (high chlorophyll content), increased flowering, or larger plant size. Somaclonal variants with desirable phenotypes may be valuable for cultivar development. / Ph. D.

With the development of sequencing technologies, more and more sequence variants are available for investigation. Different types of variants in the human genome have been identified, including single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and large structural variations such as large duplications and deletions. Of great research interest is the functional effects of these variants. Although many programs have been developed to predict the effect of SNPs, few can be used to predict the effect of indels or multiple variants, such as multiple SNPs, multiple indels, or a combination of both. Moreover, fine grained prediction of the functional outcome of variants is not available. To address these limitations, we developed a prediction framework, HMMvar, to predict the functional effects of coding variants (SNPs or indels), using profile hidden Markov models (HMMs). Based on HMMvar, we proposed HMMvar-multi to explore the joint effects of multiple variants in the same gene. For fine grained functional outcome prediction, we developed HMMvar-func to computationally define and predict four types of functional outcome of a variant: gain, loss, switch, and conservation of function. / Ph. D.

Breed characterization is a primary step in designing appropriate management and conservation programs of livestock in developing countries. Since cattle represent a major food animal species in Zambia, its conservation is a major goal for both the government and non-governmental organizations. To support the conservation effort, the objective of this thesis research was to assess the phenotypic and molecular characteristics of indigenous Zambian cattle breeds including Angoni, Barotse, Tonga, and Baila based on body measurements and randomly amplified polymorphic DNA (RAPD) markers, respectively. A total of 100 animals, 25 from each of the four breeds associated with different tribes and region of Zambia, were used in the molecular analysis research. Additionally, 10 Holstein x Jersey crossbred animals were used as a reference and to test the extent of cross-breeding, if any, of the indigenous stock with exotic breeds. To further compare the Zambian indigenous breeds, morphometric measurements including body length, heart girth, and height at withers on 50 animals of each breed were measured. Blood was collected from animals at randomly selected farms and DNA isolated by standard protocols in Zambia. A total of 10 primers, of the 20 evaluated for informativeness, were used in the RAPD-PCR analyses. Differences among the four breeds for all the three morphometric measurements were significant with the Barotse significantly higher than the other three (P<0.05). The average number of bands per primer was 7.1 and the percentage of polymorphic bands per primer ranged from 40 to 71.4 with an average of 64.8%. Breed divergence was highest between the Tonga and the Barotse and lowest between the Tonga and Baila breeds. Both the morphometric measurements and RAPD-based distance estimates suggest that the Barotse may be different from the other indigenous breeds while the Tonga and Baila were more closely related. In addition, the genetic distance estimates imply that the Holstein x Jersey crosses are different from the four Zambian indigenous cattle breeds evaluated. This thesis research provides, for the first time, the basic genetic information necessary for conservation of Zambian cattle breeds and the use of these populations for effective crossbreeding. The data suggest that though there is isolated by geographic distance and cultural differences among the tribes, two of the breeds are significantly related. / Master of Science

Trustworthy authentication of an object is of extreme importance for secure protocols. Traditional methods of storing the identity of an object using non-volatile memory is insecure. Novel chip-identifiers called Silicon Physical Unclonable Functions (PUFs) extract the random process characteristics of an Integrated Circuit to establish the identity. Though such types of IC identifiers are difficult to clone and provide a secure, yet an area and power efficient authentication mechanism, they suffer from instability due to variations in environmental conditions and noise. The decreased stability imposes a penalty on the area of the PUF circuit and the corresponding error correcting hardware, when trying to generate error-free bits using a PUF. In this thesis, we propose techniques to improve the popular delay-based PUF architectures holistically, with a focus on its stability. In the first part, we investigate the effectiveness of circuit-level optimizations of the delay based PUF architectures. We show that PUFs which operate in the subthreshold region, where the transistor supply voltage is maintained below the threshold voltage of CMOS, are inherently more stable than PUFs operating at nominal voltage because of the increased difference in characteristics of transistors at this region. Also, we show that subthreshold PUF enjoys higher energy and area efficiency. In the second part of the thesis, we propose a feedback-based supply voltage control mechanism and a corresponding architecture to improve the stability of delay-based PUFs against variations in temperature. / Master of Science

A Physical Unclonable Function (PUF) has shown a lot of promise to solve many security issues due to its ability to generate a random yet chip-unique secret in the form of an identifier or a key while resisting cloning attempts as well as physical tampering. It is a hardware-based challenge-response function which maps its responses to its challenges exploiting complex statistical variation in the logic and interconnect inside integrated circuits (ICs). An efficient PUF should generate a key that varies randomly from one chip to another. At the same time, it should reliably reproduce a key from a chip every time the key is requested from that chip. Moreover, a PUF should be robust to thwart any attack that aims to reveal its key. Designing an efficient PUF having all these qualities with a low cost is challenging. Furthermore, the efficiency of a PUF needs to be validated by characterizing it over a group of chips. This is because a PUF circuit is supposed to be instantiated in several chips, and whether it can produce a chip-unique identifier/key or not cannot be validated using a single chip. The main goal of this research is to propose a systematic approach to build a random, reliable, and robust PUF incurring minimal cost. With this objective, we first formulate a novel PUF system model that uncouples PUF measurement from PUF identifier formation. The proposed model divides PUF operation into three separate but related components. We show that the three PUF quality factors, randomness, reliability, and robustness, can be improved at each component of the system model resulting in an overall improvement of a PUF. We proposed three PUF enhancement techniques using the system model in this research. The proposed techniques showed significant improvements in a PUF. Second, we present a large-scale PUF characterization method to validate the efficiency of a PUF as a secure primitive. A compact and portable method measured a sizable set of around 200 chips. We also performed experiments to test a PUF against variations in operating conditions (temperature, supply voltage) and circuit aging. Third, we propose a method that can evaluate and compare the performance of different PUFs irrespective of their underlying working principles. This method can help a designer to select a PUF that is the most suitable one for a particular application. Finally, a novel PUF that exploits the variability in the pipeline of a microprocessor is presented. This PUF has a very low area cost while it can be easily integrated using software programs in an application having a microprocessor. / Ph. D.

Yes / There is a significant lack of geomagnetic field strength (archaeointensity) measurements for many archaeological time periods in the United Kingdom (UK). This not only makes past geomagnetic secular variation difficult to model but also limits the development of archaeointensity dating. This paper presents the first archaeointensity study on UK Neolithic material. In this study, twenty-five sherds of Neolithic Grooved Ware pottery from the Ness of Brodgar, Orkney, UK, some with direct radiocarbon dates, were subjected to a full archaeomagnetic investigation with the aim of increasing the amount of archaeointensity data for the UK. Both thermal Thellier and microwave palaeointensity experiments were used to determine which technique would be most suitable for British Neolithic pottery. Three successful archaeointensity results between 35 and 40μT were obtained using thermal Thellier method, which is consistent with the limited data available within a 15° radius and geomagnetic field model predictions from the same time. We separated the results into four different types with an intention of explaining the behaviours that determine the likelihood of achieving an acceptable archaeointensity estimate. The feasibility of obtaining geomagnetic field strength information during the UK Neolithic from ceramics has been demonstrated and the results provide a solid basis for improving our knowledge of geomagnetic secular variation during archaeological time in Britain. / The Andy Jagger Fund, University of Bradford, for supporting the stay at the University of Liverpool and Crafoord Grant, Sweden, No. 20160763. The radiocarbon dates were funded by AHRC NF/2017/2/7.

A survey of the genetic variation in the ability to produce brown pupae was conducted using 23 broods reared from wild caught females. In addition a selection experiment was designed to investigate the genetic basis of the dimorphism. It was concluded that the genetic basis of the dimorphism is a threshold trait with quantitative genetic variation underlying the two phenotypes of green and brown pupal color. It was further concluded that the dimorphism is maintained in nature by weak stabilizing selection, thus explaining the occurrence of mismatches in pupal and background color. / Master of Science

Repetitive tetramers of the DNA sequence 5'-CAAT-3' are present in several loci associated with lipooligosaccharide (LOS) phase variation in Haemophilus influenzae type b (Hib). In an attempt to identify H. somnus phase-variable LOS genes, the presence of CAAT repeats within the H. somnus 738 genome was confirmed using a (CAAT)7 probe. A 3.9 kb EcoRI fragment that reacted with the probe was cloned and sequenced. Sequence analysis confirmed the presence of 31 CAAT repeats downstream of two potential start codons, and indicated that small or large proteins would be encoded depending on the number of CAAT repeats. The larger gene products showed 46% amino acid homology to Lex2b from Hib, which influences LOS phase variation in that species. In H. somnus, this gene was named lob1 (lipooligosaccharide biosynthesis gene). Sequence analysis showed that randomly selected colonies most frequently contained 33 CAAT repeats in lob1, corresponding to a 294 amino acid product. Colonies selected for negative reactivity to mAb 5F5 were significantly more likely to have different numbers of CAAT repeats in lob1 than randomly selected colonies. The presence of lob1 in trans altered the LOS profile of a non-phase variable strain of H. somnus, and caused increased levels of reactivity to polyclonal antisera made to purified LOS from strain 738. Based on the ability of this gene to alter the LOS profile of a non-phase varying strain and the correlation of changes in CAAT repeats with mAb 5F5 reactivity, lob1 appears to be involved in LOS biosynthesis and phase variation. / Master of Science