Winter rye produces ice-modifying antifreeze proteins upon cold treatment. Two of these antifreeze proteins are members of the large, highly conserved, ??-1,3-endoglucanase family. This project was designed to identify glucanase genes that are expressed during cold acclimation, wounding, pathogen infection, drought or treatment with the phytohormones ethylene and MeJa. Additionally, a more detailed proteomic analysis was to be carried out to evaluate the glucanase content of the apoplast of cold-acclimated (CA) winter rye. Results of 2D SDS-PAGE analysis revealed that non-acclimated whole leaf protein extracts contain at least two ??-1,3-endoglucanses while CA whole leaf protein extracts contain at least three ??-1,3-endoglucanses. Subsequent 2D SDS-PAGE analysis was conducted on the apoplast extracts of NA and CA winter rye plants revealed the limitations of standard 1D SDS-PAGE. The 2-dimensional gel analysis revealed that there is a minimum of 25 proteins within the apoplast of CA winter rye, including at least 5 ??-1,3-endoglucanases. Genome walking was used to isolate cold-responsive glucanase genes. The five genes isolated were designated scGlu6, scGlu9, scGlu10, scGlu11 and scGlu12. The cis-element pattern within the promoter of each gene was evaluated using online databases of documented plant cis elements. As expected, all of the promoters contained elements associated with cold, biotic and abiotic stresses, light regulation, and development. The expression patterns predicted by the cis elements in each promoter were compared to the mRNA abundance produced by each gene as detected by semi-quantitative reverse transcriptase PCR. In most cases, the abundance of transcripts arising from each gene loosely corresponded to the expression pattern predicted by the cis elements the corresponding promoter. Transcripts of scGlu9, 10 and 11 were present in cold-treated tissues and are candidates for ??-1,3-endoglucanases with antifreeze activity. The results presented in this thesis provide additional insight into the apoplast proteome of CA winter rye plants as well as the complexity of the signals controlling the proteins that reside there. Although there are still a number of unresolved questions, this research opens new directions for future studies in the cold acclimation process in winter rye and specifically for the contribution of ?? -1,3-endoglucanses.

Submitted by Francine Silva (francine.silva@unipampa.edu.br) on 2016-09-28T20:54:58Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Análise Transcricional de Physcomitrium Acutifolium Broth. Por meio da Técnica de RNA-SEG um enfoque sobre o estresse por frio em plantas.pdf: 2456403 bytes, checksum: f125855c91a08aa6e84cb53239871aa3 (MD5) / Made available in DSpace on 2016-09-28T20:54:58Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Análise Transcricional de Physcomitrium Acutifolium Broth. Por meio da Técnica de RNA-SEG um enfoque sobre o estresse por frio em plantas.pdf: 2456403 bytes, checksum: f125855c91a08aa6e84cb53239871aa3 (MD5) Previous issue date: 2015-05-29 / Os estresses abióticos são responsáveis pela indução de adaptações em plantas. Estas quando submetidas ao estresse, respondem através de mecanismos de sinalização nas rotas fisiológicas, desencadeando um processo de aclimatação. Entretanto, nem sempre este potencial de adaptação é expresso, mas se persistir ao longo do desenvolvimento da planta, torna-se uma adaptação oriunda de mudança genética. Consequentemente, essas alterações incipientes possam ser identificadas em nível transcricional, os precursores de algumas alterações genéticas importantes tais como splicing alternativo. Em ambientes polares a expressão de genes permitiu a adaptação das plantas a temperaturas de congelamento. Entre estas plantas estão os musgos, presentes nos ambientes de climas contrastantes, isto sugere que estes organismos tenham plasticidade fenotípica e genotípica. Ainda que haja poucos estudos destes organismos em relação a diferentes agentes estressores, é amplamente difundido que estes possuem potenciais de resistência aos estresses ambientais. Para descobrir estes potenciais de resistências é necessário estudar os genes relacionados especificamente com o fator estressor em questão, neste caso o estresse ao frio. Para tanto é necessário um processo de sequenciamento dos genes expressos quando a planta é submetida ao estresse. Neste estudo foram realizados testes com explantes cultivados in vitro do musgo Physcomitrium acutifolium Broth. em diferentes temperaturas, com 6 tratamentos variando de 0 a 25 ºC, seguidos das análises fenotípicas e posteriormente genômicas, incluindo processo de sequenciamento e identificação de genes expressos. Os resultados sugerem relação do estresse por baixas temperaturas e o potencial de expressão de genes relacionados ao estresse por frio neste musgo, principalmente por uma identificação de maiores ocorrências de splicing alternativo nas plantas cultivadas a temperatura mais baixa testada. Assim, o uso potencial de espécies de musgo em estudos relacionados à resistência ao congelamento em plantas, torna-se como uma alternativa interessante em processos de biotecnologia vegetal. / The abiotic stresses are responsible for inducing adaptations in plants. When subjected to stress, plants respond by signaling mechanisms in physiological pathways, starting a process of acclimatization. However, not every adaptation potential is identified in phenotypic level, but if the selection pressure led by the stress persist over plant development, there may be a change in genotypic level. Consequently, these incipient changes can be identified in transcriptional level, the precursors of some important genetic changes such as alternative splicing. In polar environments are noted that the plants were adapted to survive at low temperatures, this adjustment is related to the expression of genes, which confer them resistance to freezing. Among these plants are mosses, present in the environments of contrasting climates, this suggests that these organisms have phenotypic and genotypic plasticity. Even if there are few studies of these organisms in relation to different stressors, we know that these have the potential for resistance to environmental stresses. To discover these potential resistance is necessary to study the genes specifically related to the stressor in question, this study is the cold stress. Then you need a sequencing process is necessary genes expressed when the plant is subjected to stress. In this study were performed tests with cultured explants in vitro moss Physcomitrium acutifolium Broth. at different temperatures, with 6 treatments ranged from 0°C to 25°C, followed by phenotypic analysis and subsequently transcriptome analysis based in RNA sequencing process aiming to identify a differential gene expression. The results suggest stress relationship for low temperatures and the potential for expression of genes related to cold stress in this moss, mainly by an identification of a higher occurrences of alternative splicing in plants growing at lowest temperature tested. Thus, the potential use of moss species in studies related to plant resistance to freeze temperatures becomes as an interesting alternative in plant biotechnology processes.

The Southern Ocean is home to two major types of fishes: endemics in the suborder Notothenioidii and representatives of oceanic fish families that are widely distributed in the midwater and benthic environments elsewhere (e.g. bathylagids, myctophids, liparids, and zoarcids) In most regions of the coastal Antarctic, e.g. the Ross Sea, there is a distinct separation in the pelagic communities at the shelf break between the oceanics (off-shelf) and the endemics (on-shelf). Coincidentally, in much of the coastal Antarctic, the shelf break also marks the boundary between a water column entirely composed of the very cold (-2°C ) Ice Shelf Water and an oceanic profile that includes warmer Circumpolar Deep Water (2°C at 200 m) at intermediate depths. The distinct separation in pelagic communities observed in most coastal regions of the Antarctic is not seen on the western Antarctic Peninsula (WAP), where circumpolar deep water intrudes to form a warmer midwater and oceanic species are strongly represented. It was hypothesized that the cold ice-shelf water, lethal to fishes without antifreeze glycoproteins (AFGP's) in their blood, was excluding the oceanic species from most of the Antarctic continental shelf waters. To test the hypothesis, nine species of fish captured in WAP shelf waters were tested for the presence of AFGP's. The oceanic fish families analyzed: Myctophidae (Electrona and Gymnoscopelus), Zoarcidae (Melanostigma), Gempylidae (Paradiplospinus), Paralepididae (Notolepsis), and Bathylagidae (Bathylagus) showed no antifreeze activity. Two endemic species captured in the same sampling program did show antifreeze activity: the important pelagic species Pleuragramma antarcticum (Nototheniidae) and the Bathydraconid (Vomeridens). The absence of AFGP's in the blood of Antarctic oceanic species makes a strong case for temperature exclusion of oceanic fishes in the coastal Antarctic.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2005. / Bibliography: leaves 62-69.

I denna avhandling beskrivs tillverkning, karaktärisering och tillämpning av ett antal biomimetiska ytor. Biomimetik är att härma naturen och grundtanken är att titta på hur naturen löst liknande problemställningar. Två olika typer av modellsystem med inspiration från naturen har tagits fram för framtida tillämpningar inom bioanalys, biosensorer samt antifrysmaterial. Det ena typen av modellsystem innefattar fosforylerade ytor och det andra består av ytor som härmar antifrys(glyko)proteiner. Ytorna tillverkades av monolager av självorganiserande svavelorganiska molekyler och karaktäriserades före tillämpning med hjälp av ellipsometri, IR-spektroskopi, kontaktvinkelmätning och röntgenfotoelektronspektroskopi. Modellsystemen för att studera vattenfrysning på ytor inspirerades av antifrys(glyko)proteiner som bl.a. kan hittas i polarfiskar. Två modellsystem utvecklades och studerades med avseende på frysning av kondenserat vatten. Det ena designades att härma den aktiva domänen hos ett antifrysglykoproteiner (AFGP) och det andra härmade typ I antifrysproteiner (AFP I). Frysstudierna visade på signifi-kanta skillnader för AFGP-modellen jämfört med ett (OH/CH3) referenssystem med jämförbar vätbarhet, men inte för AFP Imodellen. Vattnet frös vid högre temperatur för AFGPmodellen. Modellsystemen med fosforylerade ytor inspirerades av fosforylering och biomineralisering. Två system utvecklades, ett med långa och ett med korta alkylkedjor på aminosyraanalogerna, både med och utan fosfatgrupp. En ny metod användes med skyddsgrupper på fosfaterna hos de långa analogerna innan bildandet av monolager. Skyddsgrupperna togs bort efter bildandet av monolager. Dessa monolager undersöktes också med elektrokemiska metoder och signifikant högre kapacitans observerades för de fosforylerade monolageren jämfört med de icke fosforylerade. / This thesis describes the preparation, characterization and application of a few biomimetic surfaces. Biomimetics is a modern development of the ancient Greek concept of mimesis, i.e. man-made imitation of nature. The emphasis has been on the preparation and characterization of two types of model systems with properties inspired by nature with future applications in bioanalysis, biosensors and antifreeze materials. One type of model system involves phosphorylated surfaces; the other consists of surfaces mimicking antifreeze (glyco)proteins. The surfaces were made by chemisorbing organosulfur substances to a gold surface into monomolecular layers, so called self-assembled monolayers (SAMs). The physicochemical properties of the SAMs were thoroughly characterized with null ellipsometry, contact angle goniometry, x-ray photoelectron spectroscopy and infrared spectroscopy prior to application. The work on antifreeze surfaces was inspired by the structural properties of antifreeze (glyco)proteins, which can be found in polar fish. Two model systems were developed and studied with respect to ice nucleation of condensed water layers. One was designed to mimic the active domain of antifreeze glycoproteins (AFGP) and the other mimicked type I antifreeze proteins (AFP I). Subsequent ice nucleation studies showed a significant difference between the AFGP model and a (OH/CH3) reference system displaying identical wetting properties, whereas the AFP I model was indistinguishable from the reference system. The model systems with phosphorylated surfaces were inspired from phosphorylations and biomineralization. Two systems were developed, short- and long-chained amino acid analogues, with and without a phosphate group. A novel approach with protected groups before attachment to gold were developed for the long-chained analogues. The protective groups could be removed successfully after assembly. The long-chained SAMs were evaluated with electrochemical methods and significantly higher capacitance values were observed for the phosphorylated SAMs compared to the non-phosphorylated.

The goal of our research is to generate cryopreservation agents derived from antifreeze glycoproteins. One postulated mechanism of cell cryo-injury is ice recrystallization. It is known that simple saccharides and cryopreservation agents (DMSO) display ice recrystallization inhibition (IRI). This study assessed the cytotoxicity and cryopreservation ability of these sugars in relation to their IRI. It was determined that compounds with greater IRI have increased cytotoxicity yet confer cryoprotection. To further investigate how structure is affecting IRI activity, several galactopyranoside derivatives were synthesized. A series of deoxy and α-Callyl- deoxy galactopyranoses were prepared. Testing determined that removal of any hydroxyl group removes IRI. 3-deoxy-β-thiophenyl galactose was also synthesized and had surprisingly better IRI than β-thiophenylgalactose. Also, 6-azido galactose had similar IRI to 6-deoxy galactose. Lastly, a series of β- thioalkylgalactosides was synthesized and testing gave contradicting results which suggest that predicting IRI based on hydrophilicity is more complicated than initially hypothesized.

One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.

The goal of our research is to generate cryopreservation agents derived from antifreeze glycoproteins. One postulated mechanism of cell cryo-injury is ice recrystallization. It is known that simple saccharides and cryopreservation agents (DMSO) display ice recrystallization inhibition (IRI). This study assessed the cytotoxicity and cryopreservation ability of these sugars in relation to their IRI. It was determined that compounds with greater IRI have increased cytotoxicity yet confer cryoprotection. To further investigate how structure is affecting IRI activity, several galactopyranoside derivatives were synthesized. A series of deoxy and α-Callyl- deoxy galactopyranoses were prepared. Testing determined that removal of any hydroxyl group removes IRI. 3-deoxy-β-thiophenyl galactose was also synthesized and had surprisingly better IRI than β-thiophenylgalactose. Also, 6-azido galactose had similar IRI to 6-deoxy galactose. Lastly, a series of β- thioalkylgalactosides was synthesized and testing gave contradicting results which suggest that predicting IRI based on hydrophilicity is more complicated than initially hypothesized.

One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.

The economic and safety hazards associated with the ability of gas hydrates to form in pipelines have prompted our interest in the inhibition of hydrate growth. Antifreeze proteins (AFPs) adsorb to ice surfaces and certain AFPs can also inhibit the growth of hydrates formed from water molecules organized in cage-like formations around a central small gas molecule. A Monte Carlo computational method for simulating the growth of ice crystals has been developed and it has proved useful in the understanding of the inhibition mechanism of these proteins. We have modified this crystal growth software in order to simulate the growth of large structure II gas hydrates, consisting of millions of water and gas molecules. This represents a first step towards investigating the effectiveness of novel compounds to inhibit hydrate growth in silico. Here, we describe these software modifications, and our efforts to incorporate type I AFP molecules into the hydrate growth simulations. Because both the docking interaction and inhibition mechanism for AFP towards hydrates remains unknown, we have set up a number of inhibitor screens to investigate possible AFP-hydrate docking models. Our goal is to reproduce the changes to gas hydrate morphology that have been observed in the presence of AFP, which will guide our choices for the binding alignment between AFPs and hydrates. This alignment will be instrumental for determining the AFPI-inhibition mechanism and should prove invaluable for the development of novel, hyperactive hydrate inhibitors.