Rapid advances in high-throughput molecular profiling techniques enabled large-scale genomics, transcriptomics, and proteomics-based biomedical studies, generating an enormous amount of multi-omics data. Processing and summarizing multi-omics data, modeling interactions among biomolecules, and detecting condition-specific dysregulation using multi-omics data are some of the most important yet challenging analytics tasks. In the case of detecting somatic DNA copy number aberrations using bulk tumor samples in cancer research, normal cell contamination becomes one significant confounding factor that weakens the power regardless of whichever methods used for detection. To address this problem, we propose a computational approach – BACOM 2.0 to more accurately estimate normal cell fraction and accordingly reconstruct DNA copy number signals in cancer cells. Specifically, by introducing allele-specific absolute normalization, BACOM 2.0 can accurately detect deletion types and aneuploidy in cancer cells directly from DNA copy number data. Genes work through complex networks to support cellular processes. Dysregulated genes can cause structural changes in biological networks, also known as network rewiring. Genes with a large number of rewired edges are more likely to be associated with functional alteration leading phenotype transitions, and hence are potential biomarkers in diseases such as cancers. Differential dependency network (DDN) method was proposed to detect such network rewiring and biomarkers. However, the existing DDN method and software tool has two major drawbacks. Firstly, in imbalanced sample groups, DDN suffers from systematic bias and produces false positive differential dependencies. Secondly, the computational time of the block coordinate descent algorithm in DDN increases rapidly with the number of involved samples and molecular entities. To address the imbalanced sample group problem, we propose a sample-scale-wide normalized formulation to correct systematic bias and design a simulation study for testing the performance. To address high computational complexity, we propose several strategies to accelerate DDN learning, including two reformulated algorithms for block-wise coefficient updating in the DDN optimization problem. Specifically, one strategy on discarding predictors and one strategy on accelerating parallel computing. More importantly, experimental results show that new DDN learning speed with combined accelerating strategies is hundreds of times faster than that of the original method on medium-sized data. We applied the DDN method on several biomedical datasets of omics data and detected significant phenotype-specific network rewiring. With a random-graph-based detection strategy, we discovered the hub node defined biomarkers that helped to generate or validate several novel scientific hypotheses in collaborative research projects. For example, the hub genes detected by the DDN methods in proteomics data from artery samples are significantly enriched in the citric acid cycle pathway that plays a critical role in the development of atherosclerosis. To detect intra-omics and inter-omics network rewirings, we propose a method called multiDDN that uses a multi-layer signaling model to integrate multi-omics data. We adapt the block coordinate descent algorithm to solve the multiDDN optimization problem with accelerating strategies. The simulation study shows that, compared with the DDN method on single omics, the multiDDN method has considerable advantage on higher accuracy of detecting network rewiring. We applied the multiDDN method on the real multi-omics data from CPTAC ovarian cancer dataset, and detected multiple hub genes associated with histone protein deacetylation and were previously reported in independent ovarian cancer data analysis. / Doctor of Philosophy / We witnessed the start of the human genome project decades ago and stepped into the era of omics since then. Omics are comprehensive approaches for analyzing genome-wide biomolecular profiles. The rapid development of high-throughput technologies enables us to produce an enormous amount of omics data such as genomics, transcriptomics, and proteomics data, which makes researchers swim in a sea of omics information that once never imagined. Yet, the era of omics brings new challenges to us: to process the huge volumes of data, to summarize the data, to reveal the interactions between entities, to link various types of omics data, and to discover mechanisms hidden behind omics data. In processing omics data, one factor that weakens the strengths of follow up data analysis is sample impurity. We call impure tumor samples contaminated by normal cells as heterogeneous samples. The genomic signals measured from heterogeneous samples are a mixture of signals from both tumor cells and normal cells. To correct the mixed signals and get true signals from pure tumor cells, we propose a computational approach called BACOM 2.0 to estimate normal cell fraction and corrected genomics signals accordingly. By introducing a novel normalization method that identifies the neutral component in mixed signals of genomic copy number data, BACOM 2.0 could accurately detect genes' deletion types and abnormal chromosome numbers in tumor cells. In cells, genes connect to other genes and form complex biological networks to perform their functions. Dysregulated genes can cause structural change in biological networks, also known as network rewiring. In a biological network with network rewiring events, a large quantity of network rewiring linking to a single hub gene suggests concentrated gene dysregulation. This hub gene has more impact on the network and hence is more likely to associate with the functional change of the network, which ultimately leads to abnormal phenotypes such as cancer diseases. Therefore, the hub genes linked with network rewiring are potential indicators of disease status or known as biomarkers. Differential dependency network (DDN) method was proposed to detect network rewiring events and biomarkers from omics data. However, the DDN method still has a few drawbacks. Firstly, for two groups of data with unequal sample sizes, DDN consistently detects false targets of network rewiring. The permutation test, which uses the same method on randomly shuffled samples is supposed to distinguish the true targets from random effects, however, is also suffered from the same reason and could let pass those false targets. We propose a new formulation that corrects the mistakes brought by unequal group size and design a simulation study to test the new formulation's correctness. Secondly, the time used for computing in solving DDN problems is unbearably long when processing omics data with a large number of samples scale or a large number of genes. We propose several strategies to increase DDN's computation speed, including three redesigned formulas for efficiently updating the results, one rule to preselect predictor variables, and one accelerating skill of utilizing multiple CPU cores simultaneously. In the timing test, the DDN method with increased computing speed is much faster than the original method. To detect network rewirings within the same omics data or between different types of omics, we propose a method called multiDDN that uses an integrated model to process multiple types of omics data. We solve the new problem by adapting the block coordinate descending algorithm. The test on simulated data shows multiDDN is better than single omics DDN. We applied DDN or multiDDN method on several datasets of omics data and detected significant network rewiring associated with diseases. We detected hub nodes from the network rewiring events. These hub genes as potential biomarkers help us to ask new meaningful questions in related researches.

Pure rotational spectra of the rare isotopologues of titanium oxide, (TiO)-Ti-46, (TiO)-Ti-47, (TiO)-Ti-49, and (TiO)-Ti-50, have been recorded using a combination of Fourier transform millimeter-wave (FTmmW) and millimeter/submillimeter direct absorption techniques in the frequency range 62-538 GHz. This study is the first complete spectroscopic characterization of these species in their X-3 Delta(r) ground electronic states. The isotopologues were created by the reaction of N2O or O-2 and titanium vapor, produced either by laser ablation or in a Broida-type oven, and observed in the natural Ti isotopic abundances. Between 10 and 11 rotational transitions J + 1 <-> J were measured for each species, typically in all 3 spin-orbit ladders Omega-1,2, and 3. For (TiO)-Ti-47 and (TiO)-Ti-49, hyperfine structure was resolved, originating from the titanium-47 and titanium-49 nuclear spins of I = 5/2 and 7/2, respectively. For the Omega = 1 and 3 components, the hyperfine structure was found to follow a classic Lande pattern, while that for Omega = 2 appeared to be perturbed, likely a result of mixing with the nearby isoconfigurational a(1)Delta state. The spectra were analyzed with a case (a) Hamiltonian, and rotational, spin-orbit, and spin-spin parameters were determined for each species, as well as magnetic hyperfine and electric quadrupole constants for the two molecules with nuclear spins. The most abundant species, (TiO)-Ti-48, has been detected in circumstellar envelopes. These measurements will enable other titanium isotopologues to be studied at millimeter wavelengths, providing Ti isotope ratios that can test models of nucleosynthesis.

New laboratory measurements of hydrides have been carried out using terahertz direct absorption spectroscopy. Spin components of the N = 2 <- 1 transition of the free radical CrH (X (6)Sigma(+)) have been recorded in the range 730-734 GHz, as well as a new measurement of the J = 2 <- 1 line of AlH (X (1)Sigma(+)) near 755 GHz. Both species were created in an AC discharge of H-2, argon, and metal vapor. For CrH, the chromium source was Cr(CO)(6), while AlH was produced from Al(CH3)3. The J = 4.5 <- 3.5 and 3.5 <- 2.5 fine-structure components were recorded for CrH, each which consists of resolved proton hyperfine doublets. For AlH, the two main quadrupole components, F = 4.5 <- 3.5 and 3.5 <- 2.5, of the J = 2 <- 1 transition were observed as blended features. These data were analyzed with previous 1 <- 0 millimeter/submillimeter measurements with (6)Sigma and (1)Sigma Hamiltonians for chromium and aluminum hydrides, respectively, and rotational, fine-structure (CrH only), and hyperfine constants were derived. The new measurements have resulted in refined spectroscopic parameters for both species, as well as direct measurement of the respective 2 <- 1 rotational transitions. This work also resolves a 10 MHz discrepancy in the frequency of the AlH line. CrH and AlH have already been observed in the photospheres of stars via their electronic transitions. These data will facilitate their discovery at submillimeter/terahertz wavelengths in circumstellar envelopes and perhaps in diffuse clouds.

Thysanotus R.Br. (Asparagales; Laxmanniaceae) is a genus native to Australia with c. 50 species distributed chiefly in Australia. To date, Thysanotus lacks proper and detailed systematic studies based on molecular and/or non-molecular data. Therefore, carrying out a detailed systematic study using molecular and/or non-molecular data seemed important. Furthermore, generic placement of Murchisonia Brittan has always been controversial and this placement required testing under a phylogenetic framework. The generic relationships within Laxmanniaceae/Lomandraceae are considered uncertain; therefore, a phylogenetic analysis using molecular and morphological data is necessary to properly understand the generic relationships of Laxmanniaceae. Detailed studies on stem anatomy and morphology were carried out in order to understand the systematic significance and phylogenetic signal of these characters. The cp DNA (trnL intron and trnL–F intergenic spacer) and nuclear ITS2 gene regions were amplified and the results compared and combined with a morphological analysis. Phylogenetic analyses were carried out using Arthropodium R.Br and Eustrephus R.Br as outgroup taxa. There was sufficient variation in general morphology, seed micromorphology and stem anatomy and were potentially useful in understanding phylogenetic relationships of Thysanotus. A number of synapomorphies based on general morphology and stem anatomy such as absence of pendent flowers and absence of irregular shaped epidermal cells were recognised. The molecular data and the combined data yielded highly resolved consensus trees and enabled us to recognise three main lineages within the genus, each representing life history adaptations. Murchisonia was consistently nested within Thysanotus in all analyses showing a need for the return of both species to Thysanotus. Insights to intraspecific variation were also discernable from morphological, molecular and the combined analyses in species such as T. patersonii and T. juncifolius. Two new Thysanotus species, T. unicupensis and T. racemoides are also described. Our data strongly support the current circumscription of Laxmanniaceae, but suggest that there are three main lineages within the family, rather than the two previously recognised subfamilies. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1524476 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Apesar da monofilia de Pentatomidae ter sido amplamente demonstrada, as relações infrafamiliares precisam ser esclarecidas. Por exemplo, um dos maiores táxons da família, a subfamília Pentatominae, ainda não é reconhecido como um grupo monofilético. Para resolver estes problemas é necessário, além de conhecer a diversidade do grupo, realizar estudos cladísticos nos níveis genéricos e cladísticos. Na presente Tese são descritas cinco novas espécies do gênero Chloropepla (Pentatominae): C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 e Chloropepla sp. nov. 3. As espécies são caracterizadas, principalmente, por atributos da genitália de machos e fêmeas. Uma chave ampliada para a identificação das espécies do gênero é fornecida. A distribuição setentrional do grupo é expandida da Venezuela para a Costa Rica. Uma sinopse de Chloropepla também é apresentada, com uma descrição ampliada do gênero e diagnose das espécies, ambas baseadas em análise de parcimônia das 12 espécies conhecidas. Esta análise cladística confirmou a monofilia do grupo, baseada no peritrema ostiolar longo e evanescente, hypandrium amplo com projeções dorsais atingindo o X segmento, parâmeros cilíndricos, dirigidos dorsalmente, conjuntiva membranosa reduzida, quase que inteiramente obscurecida pela phallotheca. A relação filogenética resultante entre as espécies de Chloropepla foi submetida à BPA com as subregiões e províncias da região Neotropical como terminais. Esta análise demonstrou uma relação próxima entre as áreas amazônicas e indicou uma natureza híbrida da sub-região chaquenha. Finalmente, a relação entre oito gêneros de Pentatominae é investigada: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia e Rhyncholepta. Duas análises de parcimônia foram realizadas: uma baseada somente em caracteres morfológicos e outra baseada em morfologia e em sequências ribossomais (evidencia total). Um fragmento de rDNA mitocondrial 16S e dois de rDNA nuclear 28S foram sequenciados e analisados utilindo-se o método de optimização direta. As análises apresentaram diferentes relações entre os gêneros. Contudo, algumas relações se mantêm em ambos os cladogramas: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). Os resultados obtidos enfatizam a necessidade de estudos futures sobre o uso de dados moleculares em análises genéricas e específicas em Pentatominae. Além disto, as homologias também precisam ser melhor investigas e testadas, com base em estudos cladísticos, dentro de Pentatomidae, Pentatominae e tribos. / The monophyly of Pentatomidae was already highly confirmed. However, the infra-family relationships still need to be clarified. For example, one of the largest taxa of the family, the sub-family Pentatominae is not recognized as a monophyletic group. To solve these problems is necessary to know the diversity of the group as well as to perform cladistics studies at the level of genera and species. In this thesis, five new species of the genus Chloropepla (Pentatominae) are described: C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 and Chloropepla sp. nov. 3. The species are mainly characterized by features of male and female genitalia. An extended key to identification of the species of the genus is provided. The northern distribution of the group is expanded from Venezuela to Costa Rica. A synopsis of Chloropepla is also presented, with an extended description of the genus and diagnosis for the species, both based in a parsimonious analysis of the 12 know species. This cladistics analysis confirmed the monophyly of the group, based on ostiolar ruga long and evanescent, wide hypandrium, with dorsal projections flanking the segment X, parameres cylindrical, dorsally directed, membranous conjunctiva reduced, almost entirely obscured by the phallotheca. The resultant phylogenetic relationship of Chloropepla species were submitted to a BPA with the sub-regions and provinces of Neotropical region as terminals. This analysis showed a near relation among the Amazonian areas and indicated a hybrid nature of the Chacoan subregion. Finally, the relationship of eight Pentatominae genera is investigated: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia and Rhyncholepta. Two parsimony analyses were performed: one based solely on morphological characters and other based on morphological plus ribosomal DNA sequences (total evidence). One fragment of 16S mitochondrial and two of 28S nuclear rDNA were sequenced and analyzed using the direct optimization method. The results of both analysis differed in the relationships of the genera. However, some relations are recovered in both cladograms: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). The results here obtained emphasize the necessity of further studies on the use of molecular data in analyses on genera and species levels in Pentatominae. Besides, the homologies also need to be better investigated and tested within Pentatomidae, Pentatominae and tribes levels, based on cladistics studies.

Apesar da monofilia de Pentatomidae ter sido amplamente demonstrada, as relações infrafamiliares precisam ser esclarecidas. Por exemplo, um dos maiores táxons da família, a subfamília Pentatominae, ainda não é reconhecido como um grupo monofilético. Para resolver estes problemas é necessário, além de conhecer a diversidade do grupo, realizar estudos cladísticos nos níveis genéricos e cladísticos. Na presente Tese são descritas cinco novas espécies do gênero Chloropepla (Pentatominae): C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 e Chloropepla sp. nov. 3. As espécies são caracterizadas, principalmente, por atributos da genitália de machos e fêmeas. Uma chave ampliada para a identificação das espécies do gênero é fornecida. A distribuição setentrional do grupo é expandida da Venezuela para a Costa Rica. Uma sinopse de Chloropepla também é apresentada, com uma descrição ampliada do gênero e diagnose das espécies, ambas baseadas em análise de parcimônia das 12 espécies conhecidas. Esta análise cladística confirmou a monofilia do grupo, baseada no peritrema ostiolar longo e evanescente, hypandrium amplo com projeções dorsais atingindo o X segmento, parâmeros cilíndricos, dirigidos dorsalmente, conjuntiva membranosa reduzida, quase que inteiramente obscurecida pela phallotheca. A relação filogenética resultante entre as espécies de Chloropepla foi submetida à BPA com as subregiões e províncias da região Neotropical como terminais. Esta análise demonstrou uma relação próxima entre as áreas amazônicas e indicou uma natureza híbrida da sub-região chaquenha. Finalmente, a relação entre oito gêneros de Pentatominae é investigada: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia e Rhyncholepta. Duas análises de parcimônia foram realizadas: uma baseada somente em caracteres morfológicos e outra baseada em morfologia e em sequências ribossomais (evidencia total). Um fragmento de rDNA mitocondrial 16S e dois de rDNA nuclear 28S foram sequenciados e analisados utilindo-se o método de optimização direta. As análises apresentaram diferentes relações entre os gêneros. Contudo, algumas relações se mantêm em ambos os cladogramas: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). Os resultados obtidos enfatizam a necessidade de estudos futures sobre o uso de dados moleculares em análises genéricas e específicas em Pentatominae. Além disto, as homologias também precisam ser melhor investigas e testadas, com base em estudos cladísticos, dentro de Pentatomidae, Pentatominae e tribos. / The monophyly of Pentatomidae was already highly confirmed. However, the infra-family relationships still need to be clarified. For example, one of the largest taxa of the family, the sub-family Pentatominae is not recognized as a monophyletic group. To solve these problems is necessary to know the diversity of the group as well as to perform cladistics studies at the level of genera and species. In this thesis, five new species of the genus Chloropepla (Pentatominae) are described: C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 and Chloropepla sp. nov. 3. The species are mainly characterized by features of male and female genitalia. An extended key to identification of the species of the genus is provided. The northern distribution of the group is expanded from Venezuela to Costa Rica. A synopsis of Chloropepla is also presented, with an extended description of the genus and diagnosis for the species, both based in a parsimonious analysis of the 12 know species. This cladistics analysis confirmed the monophyly of the group, based on ostiolar ruga long and evanescent, wide hypandrium, with dorsal projections flanking the segment X, parameres cylindrical, dorsally directed, membranous conjunctiva reduced, almost entirely obscured by the phallotheca. The resultant phylogenetic relationship of Chloropepla species were submitted to a BPA with the sub-regions and provinces of Neotropical region as terminals. This analysis showed a near relation among the Amazonian areas and indicated a hybrid nature of the Chacoan subregion. Finally, the relationship of eight Pentatominae genera is investigated: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia and Rhyncholepta. Two parsimony analyses were performed: one based solely on morphological characters and other based on morphological plus ribosomal DNA sequences (total evidence). One fragment of 16S mitochondrial and two of 28S nuclear rDNA were sequenced and analyzed using the direct optimization method. The results of both analysis differed in the relationships of the genera. However, some relations are recovered in both cladograms: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). The results here obtained emphasize the necessity of further studies on the use of molecular data in analyses on genera and species levels in Pentatominae. Besides, the homologies also need to be better investigated and tested within Pentatomidae, Pentatominae and tribes levels, based on cladistics studies.

Apesar da monofilia de Pentatomidae ter sido amplamente demonstrada, as relações infrafamiliares precisam ser esclarecidas. Por exemplo, um dos maiores táxons da família, a subfamília Pentatominae, ainda não é reconhecido como um grupo monofilético. Para resolver estes problemas é necessário, além de conhecer a diversidade do grupo, realizar estudos cladísticos nos níveis genéricos e cladísticos. Na presente Tese são descritas cinco novas espécies do gênero Chloropepla (Pentatominae): C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 e Chloropepla sp. nov. 3. As espécies são caracterizadas, principalmente, por atributos da genitália de machos e fêmeas. Uma chave ampliada para a identificação das espécies do gênero é fornecida. A distribuição setentrional do grupo é expandida da Venezuela para a Costa Rica. Uma sinopse de Chloropepla também é apresentada, com uma descrição ampliada do gênero e diagnose das espécies, ambas baseadas em análise de parcimônia das 12 espécies conhecidas. Esta análise cladística confirmou a monofilia do grupo, baseada no peritrema ostiolar longo e evanescente, hypandrium amplo com projeções dorsais atingindo o X segmento, parâmeros cilíndricos, dirigidos dorsalmente, conjuntiva membranosa reduzida, quase que inteiramente obscurecida pela phallotheca. A relação filogenética resultante entre as espécies de Chloropepla foi submetida à BPA com as subregiões e províncias da região Neotropical como terminais. Esta análise demonstrou uma relação próxima entre as áreas amazônicas e indicou uma natureza híbrida da sub-região chaquenha. Finalmente, a relação entre oito gêneros de Pentatominae é investigada: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia e Rhyncholepta. Duas análises de parcimônia foram realizadas: uma baseada somente em caracteres morfológicos e outra baseada em morfologia e em sequências ribossomais (evidencia total). Um fragmento de rDNA mitocondrial 16S e dois de rDNA nuclear 28S foram sequenciados e analisados utilindo-se o método de optimização direta. As análises apresentaram diferentes relações entre os gêneros. Contudo, algumas relações se mantêm em ambos os cladogramas: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). Os resultados obtidos enfatizam a necessidade de estudos futures sobre o uso de dados moleculares em análises genéricas e específicas em Pentatominae. Além disto, as homologias também precisam ser melhor investigas e testadas, com base em estudos cladísticos, dentro de Pentatomidae, Pentatominae e tribos. / The monophyly of Pentatomidae was already highly confirmed. However, the infra-family relationships still need to be clarified. For example, one of the largest taxa of the family, the sub-family Pentatominae is not recognized as a monophyletic group. To solve these problems is necessary to know the diversity of the group as well as to perform cladistics studies at the level of genera and species. In this thesis, five new species of the genus Chloropepla (Pentatominae) are described: C. paveli, C. stysi, Chloropepla sp. nov. 1, Chloropepla sp. nov. 2 and Chloropepla sp. nov. 3. The species are mainly characterized by features of male and female genitalia. An extended key to identification of the species of the genus is provided. The northern distribution of the group is expanded from Venezuela to Costa Rica. A synopsis of Chloropepla is also presented, with an extended description of the genus and diagnosis for the species, both based in a parsimonious analysis of the 12 know species. This cladistics analysis confirmed the monophyly of the group, based on ostiolar ruga long and evanescent, wide hypandrium, with dorsal projections flanking the segment X, parameres cylindrical, dorsally directed, membranous conjunctiva reduced, almost entirely obscured by the phallotheca. The resultant phylogenetic relationship of Chloropepla species were submitted to a BPA with the sub-regions and provinces of Neotropical region as terminals. This analysis showed a near relation among the Amazonian areas and indicated a hybrid nature of the Chacoan subregion. Finally, the relationship of eight Pentatominae genera is investigated: Arvelius, Chlorocoris, Chloropepla, Eludocoris, Fecelia, Loxa, Mayrinia and Rhyncholepta. Two parsimony analyses were performed: one based solely on morphological characters and other based on morphological plus ribosomal DNA sequences (total evidence). One fragment of 16S mitochondrial and two of 28S nuclear rDNA were sequenced and analyzed using the direct optimization method. The results of both analysis differed in the relationships of the genera. However, some relations are recovered in both cladograms: Loxa + Mayrinia + Chlorocoris (Monochrocerus), Arvelius + E. humeralis + R. humeralis and Chlorochoris (Chlorocoris) + Fecelia + Chlorochoris (Arawacoris). The results here obtained emphasize the necessity of further studies on the use of molecular data in analyses on genera and species levels in Pentatominae. Besides, the homologies also need to be better investigated and tested within Pentatomidae, Pentatominae and tribes levels, based on cladistics studies.

Les données moléculaires précises, comme les taux de collisions, sont très important pour interpréter les observations de raies moléculaires, et par conséquent, pour estimer la abondance moléculaire dans le milieu interstellaire. Nous avons utilisé différents approximations quantiques pour étudier les excitations rotationnelles de AlCN(1Σ), AlNC(1Σ), MgCN(2Σ), MgNC(2Σ), SiCN(2∏) et SiNC(2∏) à cause des collisions avec atomes de He . On a utilisé He pour simuler les collisions avec H2 en multipliant les taux par un facteur d'échelle. Nous avons aussi étudié le excitation rotationnel de HCN(1Σ) à cause des collisions avec H2. Puis, des calculs de transfert radiatif on été faite pour estimer la abondance relative du isomères dans différentes régions du milieu interstellaire. Malgré les caractéristiques spectroscopiques semblables des isomères, ce travail démontre l'importance d'effectuer des calculs des taux de collisions séparément pour chaque isomère, afin d'obtenir leur abondances. / Accurate molecular data, such collisional rate coefficients, are essential to model molecular lines and then to estimate molecular abundances in the interstellar medium (ISM). For this reason, we have used quantum approximations to study the rotational (de-)excitation of AlCN(1Σ), AlNC(1Σ), MgCN(2Σ), MgNC(2Σ), SiCN(2∏) and SiNC(2∏) molecules by collisions with He, as a model of H2. We have also considered the rotational (de-)excitation of HCN(1Σ) molecules by ortho-H2 and para-H2 molecules.Then, we have performed radiative transfer calculations in order to estimate the relative abundances of cyanide/isocyanide species in the ISM. The impact of our molecular data in the simulation of molecular emissions is discussed. Despite the similar spectroscopic characteristics of the isomers, this work demonstrates the importance of conducting separate collisional rate calculations for each isomer in order to obtain their abundances.

Barnadesioideae é uma subfamília monofilética subordinada a família Asteraceae, que consiste em 9 gêneros e 85 espécies endêmicos da América do Sul. O interesse em Barnadesioideae vem aumentando consideravelmente desde que resultados em biologia molecular revelaram que constituem o grupo irmão para o restante das Asteraceae. Hipóteses filogenéticas para Barnadesioideae vêm sendo propostas nas últimas duas décadas com resultados incongruentes, especialmente em relação à monofilia de Dasyphyllum e sua classificação infragenérica. O intuito desde projeto é propor hipóteses filogenéticas baseadas em dados moleculares a fim de testar a monofilia de Dasyphyllum, de sua classificação infragenérica e as relações filogenéticas de D. diacanthoides, D. excelsum, D. hystrix (incertae sedis) e D. capixaba. As análises filogenéticas foram baseadas em duas regiões não codificantes do cpDNA, trnL-trnF e psbA-trnH, e uma região nuclear, ITS. As regiões plastidiais e nuclear foram analisadas separadamente e combinadas, sob os critérios de parcimônia e análise Bayesiana. Os resultados obtidos demonstram que Dasyphyllum não é um grupo monofilético pelo posicionamento de D. diacanthoides e D. excelsum em um clado como grupo irmão de Fulcaldea e Arnaldoa e distante filogeneticamente das outras espécies do gênero. Além disso, a monofilia de Dasyphyllum seção Macrocephala e Dasyphyllum seção Dasyphyllum em sua circunscrição atual foram rejeitadas. Visando a monofilia de Dasyphyllum, Dasyphyllum subgênero Archidasyphyllum é elevado ao status de gênero, Archidasyphyllum, com duas novas combinações, Archidasyphyllum diacanthoides e Archidasyphyllum excelsum. / Barnadesioideae is a monophyletic subfamily of Asteraceae, which includes 9 genera and 85 species endemic to South America. The interest in Barnadesioideae increased considerably since results with molecular data revealed this subfamily is the sister group to the other Asteraceae. Phylogenetic hypotheses for Barnadesioideae have been proposed in the last two decades with inconsistent results, especially regarding the monophyly of Dasyphyllum and its infrageneric classification. The objectives of this study were to propose phylogenetic hypotheses based on molecular data to test the monophyly of Dasyphyllum, its infrageneric classification, besides the phylogenetic relationships of D. diacanthoides, D. excelsum, D. hystrix (incertae sedis) and D. capixaba. The phylogenetic analyzes were based on two non-coding regions of cpDNA, trnL-trnF and psbA-trnH, and a nuclear region, ITS. The nuclear and plastid regions were analyzed separately and combined under the parsimony criterion and with Bayesian analysis. The results have shown that Dasyphyllum is not a monophyletic group by the positioning of D. diacanthoides and D. excelsum in a clade as sister group of Fulcaldea and Arnaldoa and phylogenetically distant from the other species of the genus. In addition, the monophyly of Dasyphyllum section Macrocephala and Dasyphyllum section Dasyphyllum in its current circumscription were rejected. In order to achieve the monophyly of Dasyphyllum, Dasyphyllum subgenus Archidasyphyllum is elevated to the status of genus, Archidasyphyllum, with two new combinations, Archidasyphyllum diacanthoides and Archidasyphyllum excelsum.

by Lam Fung Ming. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 45-47). / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter CHAPTER 2 --- BACKGROUND --- p.4 / Section 2.1 DNA Cloning --- p.5 / Section 2.1.1 Principles of cell-based DNA cloning --- p.5 / Section 2.1.2. Polymerase Chain Reaction --- p.8 / Section 2.2 DNA Libraries --- p.10 / Section 2.3. Expressed Sequence Tags --- p.11 / "Section 2.4 dbEST - Database for ""Expressed Sequence Tag""" --- p.13 / Chapter CHAPTER 3 --- REDUCTION OF PARTIAL SEQUENCE REDUNDANCY AND CDNA ALIGNMENT --- p.15 / Section 3.1 Materials --- p.15 / Section 3.2 Our Algorithm --- p.16 / Section 3.3 Data Storage --- p.24 / Section 3.4 Criterion of Alignment --- p.27 / Section 3.5 Pairwise Alignment --- p.29 / Chapter CHAPTER 4 --- RESULTS AND DISCUSSION --- p.32 / Chapter CHAPTER 5 --- CONCLUSION AND FUTURE DEVELOPMENT --- p.42 / REFERENCES --- p.45 / APPENDIX --- p.i