Software forking---creating a variant product by copying and modifying an existing project---is often considered an ad hoc, low cost alternative to principled product line development. To maintain forked projects, developers need to manually port existing features or bug-fixes from one project to another. Such manual porting is not only tedious but also error-prone. When the contexts of the ported code vary, developers often have to adapt the ported code to fit its surroundings. Faulty adaptations or inconsistent updates of the ported code could potentially introduce subtle inconsistencies in the codebase. To build a deeper understanding to cross-system porting and porting related errors, this dissertation investigates: (1) How can we identify ported code from software version histories? (2) What is the overhead of cross-system porting required to maintain forked projects? (3) What is the extent and characteristics of porting errors that occur in practice? and (4) How can we detect and characterize potential porting errors? As a first step towards assessing the overhead of cross-system porting, we implement REPERTOIRE, a tool to analyze repeated work of cross-system porting across peer projects. REPERTOIRE can detect ported edits between program patches with high accuracy of 94% precision and 84% recall. Using REPERTOIRE, we study the temporal, spatial, and developer dimensions of cross-system porting using 18 years of parallel evolution history of the BSD product family. Our study finds that cross-system porting happens periodically and the porting rate does not necessarily decrease over time. The upkeep work of porting changes from peer projects is significant and currently, porting practice seems to heavily depend on developers doing their porting job on time. Analyzing version histories of Linux and FreeBSD, we derive five categories of porting errors, including incorrect control- and data-flow, code redundancy, and inconsistent identifier and token renamings. Leveraging this categorization, we design a static control- and data-dependence analysis technique, SPA, to detect and characterize porting inconsistencies. SPA detects porting inconsistencies with 65% to 73% precision and 90% recall, and identify inconsistency types with 58% to 63% precision and 92% recall on average. In a comparison with two existing error detection tools, SPA outperforms them with 14% to 17% better precision. / text

Planar cell polarity (PCP) is the organization of cellular characteristics within the plane of a tissue. PCP manifests both structurally, as in the directionality of insect bristles or mammalian skin hair, or dynamically, as in vertebrate neurulation, gastrulation, and oriented cell division in the kidney. Two well-conserved pathways are known to regulate PCP in invertebrates and in vertebrates: the Frizzled/PCP pathway and the Fat-Dachsous (Ft-Ds) pathway. The latter consists of the cadherins Ft and Ds, along with the Golgi kinase Four-jointed (Fj) and the transcriptional co-repressor Atrophin (Atro). Ft and Ds can bind each other, suggesting a mechanism for signal transduction. Fj phosphorylates Ft and Ds, modulating their binding affinities for each other. Atro is proposed to link Ft-Ds signaling with downstream events in the nucleus during eye development. The details of Ft-Ds binding, and the consequences of their interactions with other members of the pathway are poorly understood. In this work, I quantitatively analyzed Ft-Ds pathway mutant clones for their effects on ommatidial polarity in the Drosophila eye. My findings suggest that the Ft-Ds pathway regulates PCP independently of asymmetric cellular accumulation of Ft or Ds. I found that Atro has a position-specific role in regulating polarity in the eye, that Fj dampens clonal polarity signals, and that asymmetric accumulation of the atypical myosin Dachs is not essential for production and propagation of a long-range PCP signal. My observations suggest that Ft and Ds interact to modulate a secondary signal that regulates long-range polarity, that signaling by the Ds intracellular domain is dependent on Ft, and that ommatidial fate specification is genetically separable from long-range signaling.

Darbo tikslas Nustatyti paprastosios pušies (Pinus sylvestris L.) klonų išsilaikymą ir fenologijos ypatumus lokalios amoniako taršos sąlygomis. Darbo objektas Tyrimai 2011 m. vykdyti Jonavos miškų urėdijos, Pagelažių girininkijos teritorijoje, esančiose sėklinėje plantacijoje, kuri nuo AB „Achemos yra nutolusi 6 km. Sėklinė plantacija buvo įveista 1966-1971 m. Pasodinta 30 vietinės kilmės pliusinių medžių klonų, naudota kvadratinė schema. Metodika Buvo išmatuoti visų medžių skersmenys Šiaurės-Pietų ir Vakarų-Rytų kryptimis bei įvertinta defoliacija. Apskaičiuoti visų medžių klonų vidurkiai, F kriterijus, bei paveldėjimo koeficientas. Duomenų analizei panaudota programa STATISTICA. Darbo rezultatai Tarp nagrinėjamų parametrų tarp atskirų klonų buvo esminiai genetiniai skirtumai. Paveldėjimo koeficientas − nuo 0.13 iki 0.18. Defoliacijos paveldėjimo koeficientas buvo didesnis negu skersmens. Išskirti atskiri klonai, kurių parametrai turi esminį skirtumą. Mažesnės defoliacijos klonai buvo didesnio skersmens. Darytina prielaida, kad šie klonai gerai toleruoja aplinkos taršą. Šiai hipotezei patvirtinti reikalinga klonų metinio radialinio prieaugio genetinio salygotumo tyrimas, skirtingose oro amoniako taršos koncentracijose. / Purpose The aim of the study was to determine retenton and phenology of Scots pine (Pinus sylvestris L.) clones under local ammonia pollution condition. Object Investigation was accomplised in seed plantation of Pageleziai forestry of Jonava forestry district distance 6 km from nitrogen fertilizer factory. Seed plantation was created in 1966-1971 m. There was planted 30 local genesis plus trees of Scots pine clones and exposition of field with quadratic scheme. Methods During investigation was measured all trees diametrical values of the North-South and West-East direction and the same valued defoliation. All trees were calculated means, F-test, and heritage coefficient. Describing data analysis used STATISTICA. Results Investigation between all parameters and individual clones assessed significant genetics differences. Heritage coefficient range between 0.13 and 0.18. Heritage coefficient of the defoliation were larger than diametrical values. Seperation of the individual clones parameters showed significant diferences. Clones with less defoliation were larger diameters. Assumption of this study is that these clones can tolerate environmental pollution. The hypothesis confirmed are needed annual radial increment of the clones study of the genetic conventionality under different concentration of air ammonia pollution.

Planar cell polarity (PCP) is the organization of cellular characteristics within the plane of a tissue. PCP manifests both structurally, as in the directionality of insect bristles or mammalian skin hair, or dynamically, as in vertebrate neurulation, gastrulation, and oriented cell division in the kidney. Two well-conserved pathways are known to regulate PCP in invertebrates and in vertebrates: the Frizzled/PCP pathway and the Fat-Dachsous (Ft-Ds) pathway. The latter consists of the cadherins Ft and Ds, along with the Golgi kinase Four-jointed (Fj) and the transcriptional co-repressor Atrophin (Atro). Ft and Ds can bind each other, suggesting a mechanism for signal transduction. Fj phosphorylates Ft and Ds, modulating their binding affinities for each other. Atro is proposed to link Ft-Ds signaling with downstream events in the nucleus during eye development. The details of Ft-Ds binding, and the consequences of their interactions with other members of the pathway are poorly understood. In this work, I quantitatively analyzed Ft-Ds pathway mutant clones for their effects on ommatidial polarity in the Drosophila eye. My findings suggest that the Ft-Ds pathway regulates PCP independently of asymmetric cellular accumulation of Ft or Ds. I found that Atro has a position-specific role in regulating polarity in the eye, that Fj dampens clonal polarity signals, and that asymmetric accumulation of the atypical myosin Dachs is not essential for production and propagation of a long-range PCP signal. My observations suggest that Ft and Ds interact to modulate a secondary signal that regulates long-range polarity, that signaling by the Ds intracellular domain is dependent on Ft, and that ommatidial fate specification is genetically separable from long-range signaling.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2002. / Härtill 5 uppsatser.

Submitted by Reginaldo Soares de Freitas (reginaldo.freitas@ufv.br) on 2017-05-05T15:56:30Z No. of bitstreams: 1 texto completo.pdf: 399359 bytes, checksum: ae716e36f544e5e13da15f5717608860 (MD5) / Made available in DSpace on 2017-05-05T15:56:30Z (GMT). No. of bitstreams: 1 texto completo.pdf: 399359 bytes, checksum: ae716e36f544e5e13da15f5717608860 (MD5) Previous issue date: 2002-04-30 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / As variedades de cana-de-açúcar têm sido obtidas tanto por meio de acasalamentos biparentais como por policruzamentos. Entretanto, são poucos os relatos na literatura sobre as estimativas de parâmetros genéticos e os resultados da seleção confrontando os diferentes sistemas de acasalamento. As sementes foram derivadas de 15 famílias provenientes dos acasalamentos biparentais, policruzamento e autofecundação e foram semeadas em casa de vegetação. Após aproximadamente 20 a 30 dias as plântulas foram transplantadas individualmente para campo espaçadas no sulco a 0,50m. As mudas para instalação do experimento foram obtidas na soca, em fevereiro de 2000. Neste mesmo mês, o experimento foi implantado no Campo Experimental Fundão, próximo ao aeroporto, pertencente à Universidade Federal de Viçosa. Cada unidade experimental foi constituída de um sulco de 2m de comprimento, espaçados 1,40m entre si. Em cada unidade, foram plantadas 36 gemas. O delineamento empregado foi o de blocos aumentados, com as variedades RB855536 e SP80-1816 como tratamentos comuns em todos os blocos. Foram avaliados os caracteres: número de colmos, peso médio de colmos, Brix, comprimento médio de colmos, diâmetro médio de colmos, tonelada de colmos por hectare, tonelada de Brix por hectare e produção estimada de colmos em kg. A partir das análises intrablocos, foram obtidas as médias ajustadas dos tratamentos regulares e essas foram utilizadas para compor duas novas análises de variância. O teste F foi significativo para todos os caracteres, indicando variabilidade genética entre os sistemas de acasalamento. As médias do acasalamento biparental não diferiram estatisticamente das médias do policruzamento. As médias das famílias obtidas por autofecundação para os caracteres Brix e número de colmos não apresentaram diferença acentuada em relação aos outros sistemas de acasalamentos. Já para os outros caracteres há evidências de elevada depressão endogâmica. As estimativas das variâncias genéticas e herdabilidades para os sistemas de acasalamentos foram de magnitudes semelhantes. A variância genética dentro de família representou grande parte da variância genética total para todos os caracteres, exceto para TCH, para o qual a variância genética entre famílias representou 78% da variância genética total. A herdabilidade da família foi maior do que a herdabilidade de clone para quase todos os caracteres. / The sugar cane varieties have been obtained both by biparental matings and by mid-parents. However, there are few reports in literature on the estimates of genetic parameters and the results of the selection confronting the different mating systalks. The seeds were derived from 15 coming families of the biparental matings, midparent and selfing and they were sowed in greenhouse. After approximately 20 to 30 days, the plantules were transplanted individually for field placed in the furrow with a half-meter space. The seedlings for installation of the experiment were obtained in a ratton in February 2000. In this same month, the experiment was implanted in “Campo Experimental Fundão”, close to the airport, belonging to the Universidade Federal de Viçosa. Each experimental unit was constituted of a furrow of 2m of length, spaced 1,40m amongst themselves. In each unit, 36 yolks were planted. The experimental design was augmented blocks with the varieties RB855536 and SP80-1816 as common treatments in all of the blocks. The characters evaluated were: number of stalks, average stalk weight, Brix, average stalk length , average stalk diameter, stalk tons for hectare, Brix tons for hectare and estimated stalk production in kg. The adjusted averages of the regular treatments were obtained from the intrablocks and were used to compound two new variance analyses. The F test was significant for all of the characters, indicating genetic variability among the mating systalks. The averages of the biparental mating didn't differ statistically from the midparent averages. The families’ averages obtained by selfing for the characters Brix and number of stalks didn't differ much in relation to the other mating systalks. However, for the other characters, there are evidences of high endogamic depression. The estimates of the genetic variances and heritability for the mating systalks had similar magnitudes. The genetic variance in the family represented a great part of the total genetic variance for all of the characters, except for TCH, for which the genetic variance among families represented 78% of the total genetic variance. The family heritability was larger than the clone one for almost all of the characters. / Não foi localizado o currículo lattes do autor.

No description available.

Rhizomania, caused by beet necrotic yellow vein virus (BNYVV), has been considered as an economically important disease around the world because of the extreme reduction in sugar beet yield and sugar content in affected plants. The spread of rhizomania all over the world, including the emergence of resistance- breaking virus isolates, have been become a major concern for the plant pathologists and plant breeders aiming at improving sugar beet resistance to   BNYVV as well as better understanding sugar beet-virus interactions during disease development. The main focus of this project is to elucidate the role of P25-interacting partner, the VIP1 transcription factor, in activation of transcription.  The isolation of the gene-of-interest (VIP1) was performed by RT-PCR on total RNA preparations extracted from root tissue of sugar beet (Beta vulgaris ssp. vulgaris).  The isolated gene of interest was cloned using gateway system into a binary expression vector and the obtained construct was then transformed into Agrobacterium tumefaciens for analysing transient expression in the experimental host (Nicotinana benthamiana).  Dual-luciferase promoter activity assay was performed on isolated leaf discs co-expressing P25 and VIP1 and compared to appropriate controls.  Six promoter constructs were tested. However, we observed an increase in luciferase activity (1.8-4.2-fold) upon co-expression of P25 and VIP1 only for two constructs tested, although the increase was not supported by Student’s t-test at 0.05 significance level. Nevertheless, the luciferase activity assay data for these two constructs were consistent with RNA-seq and RT-qPCR data obtained previously showing upregulation of the expression of these two specific sugar beet genes during BNYVV infection in sugar beets.     Thus, the results support our hypothesis that the interaction of the virus virulence factor P25 with VIP1 transcription factor is needed to activate transcription of certain genes in the nucleus for the virus benefit.

L’amélioration de l’efficacité de l’utilisation de l’eau (WUE) s’avère un élément clé afin d’augmenter la durabilité des plantes cultivées lors de périodes de sécheresse. Dans ce contexte, cette thèse a étudié la relation entre la conductance du mésophylle au CO2 (gm), un élément contraignant l’assimilation en carbone, et l’hydraulique chez des peupliers hybrides, espèces à forte croissance et haute transpiration. Il a été démontré, à l’aide d’une méthode améliorée, que gm reste constante durant les premières étapes d’un stress hydrique jusqu’à un seuil de conductance stomatique (gs) d’environ 0,15 mol m−2 s−1. En diminuant expérimentalement les limitations causées par les stomates, gm et la conductance hydraulique des feuilles n’ont pas été altérées, suggérant une isolation hydraulique partielle du mésophylle. L’application d’acide abscissique (ABA) exogène et la cavitation du xylème ont mis en évidence le délai de réaction de gm par rapport à gs, suggérant également l’isolation hydraulique du mésophylle. L’isolation hydraulique serait en cause et entrainerait un délai dans l’acheminement de l’ABA, retardant ainsi la fermeture d’aquaporines et entrainant une déviation de l’eau vers la voie apoplastique et une diminution irréversible de gm. Toutefois, une diminution de la turgescence résultant de la cavitation entraine une diminution de gm réversible par pressurisation d’eau dans le xylème, suggérant un effet réversible au niveau de la membrane plasmique. Ces deux mécanismes peuvent également être observés lors d’un stress hydrique de plus longue durée. Ainsi, la diminution de gm est retardée de quelques jours par rapport à gs, suggérant un effet de l’ABA endogène. Toutefois, une variation diurne de gm après plus d’une semaine de stress suggère une réaction au changement journalier de turgescence. La variation de réponse de gs entre différents génotypes de peupliers et le délai de réaction de gm permettent d’augmenter le ratio gm/gs, et ce dernier est corrélé positivement à l’efficacité de transpiration, une composante foliaire de WUE. Ainsi, le ratio gm/gs serait un trait à favoriser dans l’amélioration de WUE afin d’augmenter la résilience des plantes cultivées à la sécheresse, surtout dans un contexte de changements climatiques où la fréquence et l’intensité des périodes de séchesse sont prédits d’augmenter. / Increasing water use efficiency (WUE) is a key objective to improve the sustainability of cultivated plants to drought. In that context, this thesis has studied the relation between leaf hydraulics and mesophyll conductance to CO2 (gm), a component that restricts carbon assimilation, in hybrid poplar clones, plants with high growth rates and transpiration. It was first shown, using an improved measurement method, that gm remained constant during the early stages of water stress and declined only below a stomatal conductance (gs) threshold of ~0.15 mol m−2 s−1. Removing stomatal limitations experimentally did not improve gm or leaf hydraulic conductance (Kleaf), which suggests a partial hydraulic isolation of the mesophyll. Furthermore, adding xylem-fed abscisic acid (ABA) or inducing xylem cavitation again showed a delayed gm response and hydraulic isolation of the mesophyll. Two mechanisms would be at play. First, in the case of ABA, hydraulic isolation would delay its delivery and eventually induce mesophyll aquaporins gating and a shift towards the apoplastic water pathway, thus decreasing gm. However, it is only with a decline in turgor caused by xylem cavitation that pressurizing water allows for a full restoration of gm, which suggests a reversible change at the plasma membrane level. Those two mechanisms can be observed during a longer water stress period. Thus, the delay in gm decline by a few days compared to gs suggests an ABA response and the partial hydraulic isolation of the mesophyll. After more than a week of water stress, diurnal changes in gm indicate a daily turgor variation. The variation in gs response to drought and the delay in the decline of gm increase the gm/gs ratio, which is positively correlated to transpiration efficiency, a foliar component of WUE. Thus, the gm/gs ratio was used to discriminate between five poplar genotypes, and the results suggest that it should be improved to increase WUE and the resilience of cultivated plants to drought, which is more than ever critical since drought events are predicted to increase in frequency and intensity under climate change.

Thesis (M. Tech. (Agriculture)) -- Central University of Technology, Free State, 2013 / ntroduction: Good quality Eucalyptus is of importance to South Africa’s pulp and paper industry. Limited land is available for forestry, therefore Eucalyptus with genotypes for good pulp and paper qualities, particularly hybrids, are bred and cloned via cuttings. Although these Eucalyptus clones keep the favourable genotypes in the population, many have difficulty with rooting. Research has shown that rhizobacteria can improve rooting. Thus, one strategy to enhance the rooting of cuttings is to use rhizobacterial preparations. The aim of this study was to characterise rhizobacterial communities of Eucalyptus hybrid and species and identify possible plant-growth promoting rhizobacteria (PGPR). Materials and methods: Rhizospheric samples were collected from Eucalyptus hybrids and species. The rhizobacterial communities were characterised using fatty acid methyl esters (FAME) analysis and denaturing gradient gel electrophoresis (DGGE). DGGE fragments were further sequenced to identify rhizobacteria. Results and discussion: FAME analysis successfully achieved a broad characterisation of the Eucalyptus hybrid and species rhizobacterial communities based on their fatty acid composition. Myristic acid (C14:0) was the most abundant fatty acid. DGGE profiles gave a molecular profile of the Eucalyptus hybrid and species rhizobacterial communities based on their DNA composition. Nitrosomona eutropha was present in all samples which illustrates a nitrogen-rich environment. Adhaenbacter aquaticus was unique to the better rooting Eucalyptus hybrid GU111. Conclusion: This study provided some insight into the diversity of rhizobacterial communities of Eucalyptus hybrids and species. Possible PGPR were identified and the observation made that the nature of the soil environment changes with the aging of the associated host. These findings allow further investigation into the formulation of potential rhizobacterial preparations for rooting enhancement of Eucalyptus cuttings.