This thesis aims on comparison of rapid development frameworks Nette and Grails. Main objective of this paper is achieved by brief description of both languages (PHP, Groovy) and frameworks. Next is defined relatively complex set of criteria for comparison itself. Frameworks are then compared based on this set. Last part is development of the identical application on both platforms, thanks to which the practicle comparison may be done. The main contribution of this work is in comprehensive comparison of platforms Nette (PHP) and Grails (Groovy), which may be used for making decision about which platform to take for a development of new application. Comparision of course may serve like an information about that what developer should keep an eye on, what can make life easier or harder especially in contrast with that what offers concurent platform.

Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII and NotIII restriction enzymes produced 82,382,440 high quality reads used for genetic mapping, from which 5,265 Single Nucleotide Polymorphisms (SNPs) were discovered. The analysis revealed that the Keys’ populations are closely related with little population differentiation. In addition, the populations display evidence of inbreeding and low genetic diversity.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22286号 / 理博第4600号 / 新制||理||1660(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 工藤 洋, 教授 田村 実, 准教授 高山 浩司 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

The seeming lack of barriers to gene flow in the northwest Atlantic ocean has led to the general assumption that the population of the American lobster (Homarus americanus) is largely panmictic. However, morphological and genetic data presented in this dissertation suggest that lobster populations are less homogenous than once believed with potential for behavioral barriers to mating and selection of locally adaptive traits. Additionally, both long-term fishing pressures and the recent spread of a destructive epizootic shell disease may have impacted population structure. We developed a novel photographic technique to rapidly collect accurate morphological data with the ability to maintain a database of images for the purposes of re-sampling and testing additional hypotheses. During this study, we found significant morphometric differences between samples of lobsters from collection sites as close as 25km apart. Morphological differences may have originated due to differential selection or plastic responses to environmental variation. To analyze population genetic structure, I surveyed genetic variation using RADseq. Analysis of 1614 putatively neutral SNPs found little genetic difference (Average F¬ST=0.00137) between sample sites suggesting a high level of gene flow between regions. Several additional markers appeared to be under divergent selection between sample sites. A genome scan analysis of both neutral SNPs and SNPs under selection found several selected SNPs associated with principal components of morphological characters. A subsequent BLAST analysis identified a number of the selected SNPs lying in the H. americanus transcriptome, suggesting functional importance. Further experimentation is required to quantify the impacts of plasticity or local adaption in the origin of morphological differences between lobster populations, although the significant differences identified in this research are likely due to a combination of the two. The overarching conclusion is that lobster populations are, in fact, more differentiated than previously predicted and, as such, the findings presented here may have significant management implications.

Phylogenetics is crucial in the study of evolutionary processes and the determination of appropriate conservation units, and often these efforts are complicated by hybridization and introgression. Aliciella subsection Subnuda consists of seven species of herbaceous plants occurring in Utah and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of ITS and cpDNA regions and RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the cpDNA and ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny robustly resolves relationships between six clades, supportive of merging of two species. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results provide evidence of hybridization among and between all species in the subsection. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

<p>U radu su prikazani rezultati eksperimentalne primene samostalnog istraživačkog rada i laboratorijsko-eksperimentalne metode u obradi sadržaja nastave Prirode i dru&scaron;tva. Ispitan je uticaj takvog načina rada na osposobljavanje učenika za samostalan rad i njegovi efekti na kvalitet i trajnost znanja učenika. Izvr&scaron;eno je anketiranje učitelja i učenika eksperimentalne grupe kako bi se utvrdila njihova mi&scaron;ljenja o primeni istraživačkog pristupa i laboratorijsko-eksperimentalne metode u nastavi Prirode i dru&scaron;tva. Rezultati su potvrdili da pomenuti način rada doprinosi povećanju kvaliteta znanja učenika (posebno kada su u pitanju nivo prepoznavanja i reprodukcije), da pozitivno utiče na trajnost znanja učenika i da ga učenici vrlo pozitivno prihvataju. Njihovi odgovori govore u prilog činjenici da bi takav način rada trebalo da bude če&scaron;će zastupljen u praksi. Odgovori učitelja ukazuju na to da oni poznaju značaj i prednosti primene istraživačkog pristupa i laboratorijsko-eksperimentalne metode, upoznati su sa osnovnim didaktičko-metodičkim zahtevima koje je potrebno uvažavati prilikom primene takvog načina rada, ali su i svesni koliko je priprema i organizacija takvih časova zahtevan i složen posao.</p>

No description available.

The size and complexity of the oat genomes (Avena L., x = 7) have made genetic studies, including the discovery of molecular markers, difficult. Recent attention to these species has resulted in the development of many DArT -based markers in the tetraploid A. magna Murphy et Terrill (2n = 28, CCDD genomes), along with numerous RFLP's, SSR's, DArT's, and EST-based SNPs in hexaploid A. sativa L. (2n = 42, AACCDD). Here we report the first SNP markers for tetraploid oat based on genome reduction and high-throughput pyrosequencing in two inbred lines of A. magna: A-169 (wild) and Ba 13-13 (domesticated). Initially, the genomes were reduced using restriction digests with EcoRI and BfaI and sequenced to produce 706,426 reads for both genotypes that were subsequently assembled into 57,048 contigs with an average read length of 345 bp. Comparisons of the contigs between the two lines resulted in the detection of 31,304 in silico SNPs. High Resolution Melt (HRM) and KASPar assays were used to validate 1,108 of these in silico SNPs across a panel of diploid, tetraploid, and hexaploid oats. Of the assays, 119 were validated using HRM and 384 using KASPar genotyping in the Fluidigm EP1 system. Both sets of assays were then mapped on a population of 117 F2:8 recombinant inbred lines (RILs) developed from the A-169 x Ba 13-13 cross. A map of the A. magna genome was then constructed. The markers and map provide a new set of genomic tools for tetraploid and hexaploid oat breeding and allow for tracking of genes controlling traits of economic importance and other interesting genes through the evolution of Avena.

<p> Vaccination is arguably the most effective tool at our disposal to prevent the morbidity and mortality associated with infectious disease. However, there are currently several infectious diseases, notably HIV, malaria and tuberculosis, for which we do not posses effective vaccines. Further complicating matters, traditional methods to construct vaccines for these diseases have been unsuccessful. Advances in our understanding of adaptive immunity have demonstrated that vaccines for these diseases likely rely upon potent T cell immunity to be effective. Recombinant adenovirus (rAd) vectors have shown great promise as vaccination platforms since they are easily constructed, stable, well-tolerated and elicit robust T cell responses. The robust activity of rAd vectors based on the human serotype 5 virus (rHuAd5) in murine and simian models merits futher investigation as a prototypic T cell vaccine. To this end, we have undertaken a comprehensive evaluation of T cell immunity following rAd vaccination. Our previous observations determined that the CD8+ T cell response produced by rHuAd5 vaccines displayed a prolonged effector phase that was associated with long-lived antigen presentation. We have further investigated the mechanisms underlying the maintenance of this memory population. Our results have revealed that the memory phenotype is not due to continual recruitment of naive CD8+ T cells. Rather, the sustained effector phenotype appears to depend upon prolonged expression of the antigen-encoding transgene from the rHuAd5 vector. Interestingly, transgene expression was only required for 60 days after which point the memory population stabilized. Further investigation of the relationship between antigen structure and the CD8+ T cell response revealed that antigens which traffic through the ER produce a CD8+ T cell response that expands more rapidly and displays a more pronounced contraction phase than antigens which are produced within the cytosol. While the exact mechanism underlying this phenomenon is not known, we suspect that pathways related to ER stress may be involved. Despite the more dramatic contraction phase associated with antigens that traffic through the ER, the memory phenotype was unchanged. Interestingly, the CD4+ T cell response was not influenced by antigen structure and displays a sharp contraction phase regardless of whether the antigen traffics through the ER or is produced in the cytosol. We further investigated the relationship between CD4+ T cell help and CD8+ T cell immunity produced by rHuAd5. Based on the partially-exhausted phenotype of the CD8+ T cells produced by rHuAd5 (diminished TNF-a production and little IL-2 production), we suspected that inadequate CD4+ T cell help may have been responsible. However, removal of CD4+ T cells did not further impair the CD8+ T cell response produced by rHuAd5. Rather, a lack of CD4+ T cell help only impacted the magnitude of the primary CD8+ T cell response generated by rHuAd5; the functionality of the CD8+ T cell population, including the ability to proliferate following secondary stimulation, were not affected by the absence of CD4+ T cells. Thus, although CD8+ T cell expansion following immunization with rHuAd5 is dependent upon the availability of CD4+ T cell help, the memory functions of the CD8+ T cell population appears to be independent of CD4+ T cell help. Finally, we compared the magnitude of the CD8+ T cell response produced by rHuAd5 and recombinant vaccinia virus. Our results demonstrated that the functionality of the early T cell response produced by both vectors were identical. However, the primary transgene-specific CD8+ T cell responses produced by rHuAd5 were significantly larger than rVV because the vector specific responses were negligible in the case of rAd but very strong following rVV inoculation. This research has contributed to our understanding of T cell immunity following rAd immunization and will assist in the construction and implementation of future vaccines. </p> / Thesis / Doctor of Philosophy (PhD)

This study seeks to explore ideas about learning and how it happens in writing center tutorials. The questions posed for this research are the following: 1) What does learning look like in writing center consultations? and 2) What moves do tutors make to prompt learning moments? The study was created by video recording nine writing center consultations over the course of a single semester. The researcher conducted the sessions herself and worked with the same writer each time. Segments of sessions were transcribed to reveal patterns of learning at work. Reflective memos were also collected, as well as a final retrospective interview. The results of the study showed that learning happens when tutors and writers create learning moments both together and independently of each other. Tutors and writers prompt learning by addressing four elements of writing center sessions: session activities, writer moves with the text at hand, writing processes, and learning processes. Addressing these elements in sessions leads to conversations about learning, which leads to learning taking place. This research is useful for further developing the identity of the writing center as a space that values and strives for authentic learning to occur.