Academic literature on the topic 'Glycan code'
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Journal articles on the topic "Glycan code"
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Jones, Christopher J., and Cynthia K. Larive. "Cracking the glycan sequence code." Nature Chemical Biology 7, no. 11 (October 18, 2011): 758–59. http://dx.doi.org/10.1038/nchembio.696.
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Kaltner, Herbert, José Abad-Rodríguez, Anthony P. Corfield, Jürgen Kopitz, and Hans-Joachim Gabius. "The sugar code: letters and vocabulary, writers, editors and readers and biosignificance of functional glycan–lectin pairing." Biochemical Journal 476, no. 18 (September 24, 2019): 2623–55. http://dx.doi.org/10.1042/bcj20170853.
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Abstract Ubiquitous occurrence in Nature, abundant presence at strategically important places such as the cell surface and dynamic shifts in their profile by diverse molecular switches qualifies the glycans to serve as versatile biochemical signals. However, their exceptional structural complexity often prevents one noting how simple the rules of objective-driven assembly of glycan-encoded messages are. This review is intended to provide a tutorial for a broad readership. The principles of why carbohydrates meet all demands to be the coding section of an information transfer system, and this at unsurpassed high density, are explained. Despite appearing to be a random assortment of sugars and their substitutions, seemingly subtle structural variations in glycan chains by a sophisticated enzymatic machinery have emerged to account for their specific biological meaning. Acting as ‘readers’ of glycan-encoded information, carbohydrate-specific receptors (lectins) are a means to turn the glycans’ potential to serve as signals into a multitude of (patho)physiologically relevant responses. Once the far-reaching significance of this type of functional pairing has become clear, the various modes of spatial presentation of glycans and of carbohydrate recognition domains in lectins can be explored and rationalized. These discoveries are continuously revealing the intricacies of mutually adaptable routes to achieve essential selectivity and specificity. Equipped with these insights, readers will gain a fundamental understanding why carbohydrates form the third alphabet of life, joining the ranks of nucleotides and amino acids, and will also become aware of the importance of cellular communication via glycan–lectin recognition.
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Klein, Joshua, Luis Carvalho, and Joseph Zaia. "Application of network smoothing to glycan LC-MS profiling." Bioinformatics 34, no. 20 (May 22, 2018): 3511–18. http://dx.doi.org/10.1093/bioinformatics/bty397.
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Abstract Motivation Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting. Existing tools for interpreting the resulting data do not take into account related glycans when evaluating individual observations, limiting their sensitivity. Results We developed an algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans. Our algorithm optimizes a set of likelihood scoring functions based on glycan chemical properties but uses network Laplacian regularization and optionally prior information about expected glycan families to smooth the likelihood and thus achieve a consistent and more representative solution. Our method was able to identify as many, or more glycan compositions compared to previous approaches, and demonstrated greater sensitivity with regularization. Our network definition was tailored to N-glycans but the method may be applied to glycomics data from other glycan families like O-glycans or heparan sulfate where the relationships between compositions can be expressed as a graph. Availability and implementation Built Executable http://www.bumc.bu.edu/msr/glycresoft/ and Source Code: https://github.com/BostonUniversityCBMS/glycresoft. Supplementary information Supplementary data are available at Bioinformatics online.
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Kellman, Benjamin P., Yujie Zhang, Emma Logomasini, Eric Meinhardt, Karla P. Godinez-Macias, Austin W. T. Chiang, James T. Sorrentino, et al. "A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)." Beilstein Journal of Organic Chemistry 16 (October 27, 2020): 2645–62. http://dx.doi.org/10.3762/bjoc.16.215.
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Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable glycan structure representation, is such a language. For this reason, Linear Code was adapted to represent reaction rules, but the syntax has drifted from its original description to accommodate new and originally unforeseen challenges. Here, we delineate the consensuses and inconsistencies that have arisen through this adaptation. We recommend options for a consensus-based extension of Linear Code that can be used for reaction rule specification going forward. Through this extension and specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code.
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Gabius, Hans-Joachim. "Glycans: bioactive signals decoded by lectins." Biochemical Society Transactions 36, no. 6 (November 19, 2008): 1491–96. http://dx.doi.org/10.1042/bst0361491.
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The glycan part of cellular glycoconjugates affords a versatile means to build biochemical signals. These oligosaccharides have an exceptional talent in this respect. They surpass any other class of biomolecule in coding capacity within an oligomer (code word). Four structural factors account for this property: the potential for variability of linkage points, anomeric position and ring size as well as the aptitude for branching (first and second dimensions of the sugar code). Specific intermolecular recognition is favoured by abundant potential for hydrogen/co-ordination bonds and for C–H/π-interactions. Fittingly, an array of protein folds has developed in evolution with the ability to select certain glycans from the natural diversity. The thermodynamics of this reaction profits from the occurrence of these ligands in only a few energetically favoured conformers, comparing favourably with highly flexible peptides (third dimension of the sugar code). Sequence, shape and local aspects of glycan presentation (e.g. multivalency) are key factors to regulate the avidity of lectin binding. At the level of cells, distinct glycan determinants, a result of enzymatic synthesis and dynamic remodelling, are being defined as biomarkers. Their presence gains a functional perspective by co-regulation of the cognate lectin as effector, for example in growth regulation. The way to tie sugar signal and lectin together is illustrated herein for two tumour model systems. In this sense, orchestration of glycan and lectin expression is an efficient means, with far-reaching relevance, to exploit the coding potential of oligosaccharides physiologically and medically.
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Alocci, Davide, Pavla Suchánková, Renaud Costa, Nicolas Hory, Julien Mariethoz, Radka Vařeková, Philip Toukach, and Frédérique Lisacek. "SugarSketcher: Quick and Intuitive Online Glycan Drawing." Molecules 23, no. 12 (December 5, 2018): 3206. http://dx.doi.org/10.3390/molecules23123206.
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SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The “quick mode” allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The “normal mode” integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.
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Dumych, Tetiana, Clarisse Bridot, Sébastien Gouin, Marc Lensink, Solomiya Paryzhak, Sabine Szunerits, Ralf Blossey, Rostyslav Bilyy, Julie Bouckaert, and Eva-Maria Krammer. "A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin." Molecules 23, no. 11 (October 28, 2018): 2794. http://dx.doi.org/10.3390/molecules23112794.
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The fimbrial lectin FimH from uro- and enteropathogenic Escherichia coli binds with nanomolar affinity to oligomannose glycans exposing Manα1,3Man dimannosides at their non-reducing end, but only with micromolar affinities to Manα1,2Man dimannosides. These two dimannoses play a significantly distinct role in infection by E. coli. Manα1,2Man has been described early on as shielding the (Manα1,3Man) glycan that is more relevant to strong bacterial adhesion and invasion. We quantified the binding of the two dimannoses (Manα1,2Man and Manα1,3Man to FimH using ELLSA and isothermal microcalorimetry and calculated probabilities of binding modes using molecular dynamics simulations. Our experimentally and computationally determined binding energies confirm a higher affinity of FimH towards the dimannose Manα1,3Man. Manα1,2Man displays a much lower binding enthalpy combined with a high entropic gain. Most remarkably, our molecular dynamics simulations indicate that Manα1,2Man cannot easily take its major conformer from water into the FimH binding site and that FimH is interacting with two very different conformers of Manα1,2Man that occupy 42% and 28% respectively of conformational space. The finding that Manα1,2Man binding to FimH is unstable agrees with the earlier suggestion that E. coli may use the Manα1,2Man epitope for transient tethering along cell surfaces in order to enhance dispersion of the infection.
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Lopes, Nuno, Viviana G. Correia, Angelina S. Palma, and Catarina Brito. "Cracking the Breast Cancer Glyco-Code through Glycan-Lectin Interactions: Targeting Immunosuppressive Macrophages." International Journal of Molecular Sciences 22, no. 4 (February 17, 2021): 1972. http://dx.doi.org/10.3390/ijms22041972.
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The immune microenvironment of breast cancer (BC) is composed by high macrophage infiltrates, correlated with the most aggressive subtypes. Tumour-associated macrophages (TAM) within the BC microenvironment are key regulators of immune suppression and BC progression. Nevertheless, several key questions regarding TAM polarisation by BC are still not fully understood. Recently, the modulation of the immune microenvironment has been described via the recognition of abnormal glycosylation patterns at BC cell surface. These patterns rise as a resource to identify potential targets on TAM in the BC context, leading to the development of novel immunotherapies. Herein, we will summarize recent studies describing advances in identifying altered glycan structures in BC cells. We will focus on BC-specific glycosylation patterns known to modulate the phenotype and function of macrophages recruited to the tumour site, such as structures with sialylated or N-acetylgalactosamine epitopes. Moreover, the lectins present at the surface of macrophages reported to bind to such antigens, inducing tumour-prone TAM phenotypes, will also be highlighted. Finally, we will discuss and give our view on the potential and current challenges of targeting these glycan-lectin interactions to reshape the immunosuppressive landscape of BC.
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Kaltner, Herbert, and Hans-Joachim Gabius. "Sensing Glycans as Biochemical Messages by Tissue Lectins: The Sugar Code at Work in Vascular Biology." Thrombosis and Haemostasis 119, no. 04 (January 8, 2019): 517–33. http://dx.doi.org/10.1055/s-0038-1676968.
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AbstractAlthough a plethora of players has already been revealed to be engaged in the haemostatic system, a fundamental consideration of the molecular nature of information coding can give further explorations of the mechanisms of blood clotting, platelet functionality and vascular trafficking direction. By any measures, looking at ranges of occurrence and of potential for structural versatility, at strategic positioning to influence protein and cell sociology as well as at dynamics of processing and restructuring for phenotypic variability, using sugars as an alphabet of life for generating the glycan part of glycoconjugates is a success story. The handiwork by the complex system for glycan biosynthesis renders biochemical messages of exceptionally high coding capacity available. They are read and translated into cellular effects by receptors termed lectins. The different levels of regulation on both sides, that is, glycan and lectin, establish an intriguingly fine-tuned capacity for functional pairing. The emerging insights into the highly branched routes of glycosylation, into lectin structures up to complete characterization in solution and the shape of lectin networks, first obtained for the three selectins, now extended to considering many other C-type lectins, galectins and siglecs, as well as into intra- and inter-family cross-talk and cooperations are sure to push boundaries in our understanding of the molecular basis of haemostasis.
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Yusufi, Faraaz Noor Khan, Wonjun Park, May May Lee, and Dong-Yup Lee. "An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins." Bioprocess and Biosystems Engineering 32, no. 1 (May 6, 2008): 97–107. http://dx.doi.org/10.1007/s00449-008-0226-4.
Full textDissertations / Theses on the topic "Glycan code"
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Lopes, Valéria Stefania. "Caracterização da família de genes HSP20 em Glycine max." Universidade Estadual de Londrina, EMBRAPA. Centro de Ciências Exatas. Programa de Pós-Graduação em Biotecnologia, 2012. http://www.bibliotecadigital.uel.br/document/?code=vtls000175506.
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As pequenas proteínas de choque térmico (HSP20) são frequentemente associadas com a resposta das plantas ao estresse causado por fatores abióticos e, mais recentemente, têm sido também associadas a resposta aos estresses bióticos. Nas plantas, os genes Hsp20 representam a classe mais abundante dentre as proteínas de choque térmico, mas ainda pouco se conhece sobre essa família de genes em soja. Devido à suas aparentes multifuncionalidades, essas proteínas são alvos promissores para o desenvolvimento de variedades agrícolas melhor adaptadas a condições de estresses abióticos e bióticos, até mesmo quando combinados. Dessa forma, o presente trabalho realizou a caracterização molecular in silico das regiões codificadoras e reguladoras da família de genes codificadores para HSP20 de soja, com foco em sua distribuição no genoma, localização subcelular, divisão em subfamílias, estrutura secundária e regulação frente a estresses bióticos e abióticos, além da identificação de padrões de cis elementos, potencialmente envolvidos na resposta da soja a nematóides. Após a prospecção de genes anotados em bancos de dados do genoma da soja como Hsp20, foram obtidos 76 modelos gênicos. Dentre estes, apenas 52 modelos gênicos fizeram parte dos potenciais candidatos a GmHsp20 (Glycine max-Hsp20), devido as suas características estruturais, de cis elementos e de expressão. Em seguida, foram identificados, a partir das análises in vivo, 45 genes como Hsp20 de soja, distribuídos em 11 subfamílias. Para cada uma dessas, foi possível observar padrões de estrutura secundária específicos. Dentre os 45 genes GmHsp20 responsivos ao estresse de calor, 5 foram também responsivos ao estresse de frio e outros 5 ao estresse por infecção pelo nematóide M. javanica. Além disso, foram observados mais dois genes responsivos ao estresse biótico, mas não ao choque térmico. Obtiveram-se modelos operacionais de promotores para os genes responsivos a cada tipo de estresse analisado. Entre os cis elementos identificados nos Hsp20, que respondem a infecção por M. javanica, estão os Wbox, CAAT box, ABRE e MYB, além do elemento HSE/Heat. Os promotores responsivos ao estresse biótico seguiram padrões de composição e distribuição de cis elementos, descritos na literatura como relacionados a esse tipo de estresse e outros. Tais resultados irão auxiliar na geração de tecnologias de expressão dirigida, ainda mais avançadas, e novos genótipos de soja cada vez mais adaptados a condições combinadas de estresse.The small heat shock proteins (HSP20) are often associated in plant stress response caused by abiotic factors and, more recently, have also been associated with response to biotic stresses. The Hsp20 genes represent, in plants, the most abundant class among the heat shock proteins, but little is known about this gene family in soybean. Due their apparent multifunctionality, these proteins are promising targets to the crop varieties development for better conditions adapted to biotic and abiotic stresses, even when they are combined. Thus, the present study conducted an in silico molecular characterization of regulatory and coding regions of HSP20 genes from soybean, focus in its genome distribution, subcellular localization, division into subfamilies, secondary structure and regulation under biotic and abiotic stresses, besides the identification patterns to cis elements potentially involved in the response to nematodes. After the exploration of Hsp20 genes annotation in soybean genome databases, 76 gene models were obtained. After in silico analysis, just 52 gene models were part of the GmHsp20 potencial candidates due to their structural characteristics of cis elements and expression profile. In addition, based on in vivo analysis, 45 soybean Hsp20 genes were identified, distributed in 11 subfamilies, for which is possible to observe a specific secondary structure for each one. Among the 45 GmHsp20 genes heat stress responsives, 5 genes were cold stress responsive and other five were nematode infection by M. javanica responsive. Moreover, two genes were observed being responsive to biotic stress, but they weren't responsive to thermal shock. Operational Models of Hsp20 promoters were obtained to responsive genes to each stress condition examined in this study. Among the identified cis elements in Hsp20 soybean genes that were responsive to M. javanica infection were W box, CAAT box, ABRE and MYB, besides the HSE / Heat element. Promoters responsive to biotic stress in soybean follows composition and distribution standards of cis elements, as described in the literature to be related to this type of stress. These results, such as responsive genes and promoters to many different stresses, can assist in generation of expression directed technologies even more advanced and new soybean genotypes more adapted to under combined stress conditions.
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Rachid, Breno Francovig. "Identificação de novos locos de resistência à ferrugem asiática (Phakopsora pachyrhizi) em soja (Glycine max)." Universidade Estadual de Londrina. IAPAR. EMBRAPA. Centro de Ciências Biológicas. Programa de Pós-Graduação em Genética e Biologia Molecular, 2008. http://www.bibliotecadigital.uel.br/document/?code=vtls000154641.
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No Brasil, a ferrugem asiática, causada pelo fungo Phakopsora pachyrhizi, vem provocando perdas de produtividade e aumento no custo de produção pelo uso intensivo de fungicidas em lavouras de soja. A utilização de variedades resistentes é uma ferramenta importante no combate à doença. Atualmente existem cinco locos relatados contendo genes de resistência à doença, denominados rpp1 a rpp5. A resistência conferida por alguns genes presentes nos locos rpp1 e rpp3 foi quebrada, no Brasil, por uma nova raça do fungo. O presente estudo teve como objetivo realizar testes de alelismo entre fontes de resistência identificadas no banco de germoplasma da Embrapa Soja e que não mapeiam nos locos rpp2 e rpp4. Para tanto, 20 fontes cujos genes de resistência mapeiam fora dos locos rpp2 e rpp4 (Laperuta, 2007) foram separados em um grupo com quatro testadoras cruzadas entre si e com o outro grupo composto pelas outras 16 fontes. As gerações parentais e F2 derivadas desses cruzamentos foram inoculadas e avaliadas em casa-de-vegetação. Cada planta foi classificada de acordo com a reação de resistência (lesões RB) ou de suscetibilidade (lesões TAN). Com base na ausência de segregação ou no padrão de segregação observados na geração F2, foi possível concluir que das quatro fontes utilizadas como testadoras, três delas (PI 200487 ou Kinoshita, PI 200526 ou Shira Nui e GC 84058-18-4) possuem pelo menos um gene de resistência no mesmo grupo de ligação (GL), enquanto a outra testadora (PI 203398 ou Abura) possui um gene de resistência em loco independente. Das demais fontes testadas, duas delas (PI 416764 e PI 423966) pertencem ao grupo da Kinoshita, três (PI 416810, PI 417421 e PI 398777) pertencem ao grupo da Abura, e cinco (PI 397618TC1, PI 417074, PI 417503, Nova Santa Rosa e Hyuuga) obtiveram segregação independente em relação ao grupo da Kinoshita e Abura, indicando que apresentam pelo menos um gene de resistência segregando independentemente em relação aos GL testados. As fontes GC 84058-21-4 e GC 84051-9-1 não segregaram em cruzamentos com a testadora GC84058-18-4 enquanto a PI416819 não segrega com a testadora PI 200526, as quais devem conter pelo menos um gene próximo ao GL da Kinoshita. Outras três fontes (PI 471904, PI 200455 e PI 417115) não segregam em cruzamentos com Abura, mas não foi possível concluir sobre o GL já que a PI 471904 também não segrega com o grupo Kinoshita, enquanto a PI 200455 também não segrega com as 16 testadoras PI 200526 e PI 200487 do grupo da Kinoshita e, finalmente, a PI 417115 também não segrega com a PI 200487 do grupo da Kinoshita. É possível, em função desses resultados, que estejamos lidando com um novo grupo de genes de resistência a doenças, no GL N.In Brazil, the soybean rust, caused by Phakopsora pachyrhizi, has caused yield losses and increased the cost of production by the intensive use of fungicides in soybean fields. The use of resistant varieties is an important tool to control the disease. Currently five different loci have been reported containing genes for resistance to disease, called rpp1 to rpp5. A new race of the fungus broke the resistance conferred by some genes present in the loci rpp1 and rpp3 in Brazil. This study aimed to perform allelism tests between sources of resistance identified in the germplasm bank of Embrapa Soybean, whose genes do not belong to rpp4 and rpp2 loci. To accomplish this objective, 20 sources of resistance genes mapping out of the loci rpp2 and rpp4 (Laperuta, 2007) were divided into a group with four testers, which were crossed between them, and with the other 16 sources. The parentals and F2 generations from these crosses were inoculated and evaluated in a greenhouse. Each plant was classified according to the reaction of resistance (RB lesion) or susceptibility (TAN lesion). Based on the segregation observed in the F2 generation, it was possible to conclude that among the four sources used as testers, three of them (PI 200487 or "Kinoshita," PI 200526 or "Shira Nui" and GC 84058 18-4) have at least one gene of resistance in the same linkage group (LG), while the other tester (PI203398 or "Abura") has a gene of resistance in an independent locus. Among the other sources tested, three of them (PI 416764 and PI 423966) belong to the group "Kinoshita," three (PI 416810, PI 417421 and PI 398777) belong to the group "Abura", and five (PI 397618TC1, PI 417074, PI 417503, Nova Santa Rosa and Hyuuga) segregated independently in relation to the groups "Kinoshita" and "Abura," which indicates that they have at least one gene of resistance mapping out of the loci 17 tested. The sources GC 84058-21-4 and GC 84051-9-1 didnt segregat in crosses with the tester GC 84058-18-4 and must contain at least one gene next to the LG of "Kinoshita." Three other sources (PI 471904, PI 200455 and PI 417115) not segregated in crosses with "Abura," but it was not possible to conclude about their LG, because the PI 471904 also do not segregate with "Kinoshita, while the PI 200455 do not segregate with the testers PI 200526 and PI 200487 of the group "Kinoshita" and, finally, the PI417115 also do not segregate with PI 200487 of the group "Kinoshita." According to these results, it is possible that we are dealing with a new cluster of genes for disease resistance in LG-N.
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Kuwano, Biana Harumi. "Encarquilhamento foliar em soja (Glycine max (L.) Merr.) no Paraná : fatores envolvidos e possíveis causas." Universidade Estadual de Londrina. Centro de Ciências Agrárias. Programa de Pós-Graduação em Agronomia, 2017. http://www.bibliotecadigital.uel.br/document/?code=vtls000218129.
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Áreas produtoras de soja (Glycine max L. Merr.) no Paraná têm apresentado plantas com sintomas de encarquilhamento foliar, semelhante a toxicidade de Mn, com redução de porte, geralmente observados em reboleiras. O objetivo desse trabalho foi analisar propriedades químicas e microbiológicas do solo relacionadas à ciclagem de Mn e investigar se a alta disponibilidade desse nutriente pode ter causado o encarquilhamento foliar em áreas comerciais de soja. Foram coletadas amostras de solo e planta em áreas de reboleiras com sintomas e áreas sadias adjacentes de nove propriedades na safra 2012/13 e três na safra 2013/14. Na parte aérea das plantas foram determinados: a massa seca e os teores foliares de P, K, Ca, Mg, S, B, Cu, Fe, Mn e Zn. As amostras de solo foram coletadas nas profundidades de 0-5, 5-10, 10-20 e 20-40 cm, secas ao ar e analisadas quanto ao pH (CaCl2), C orgânico, P disponível, Ca, Mg, K, Al, H+Al, soma de bases, CTC, saturação por bases, teores de B, Cu, Fe, Mn e Zn. As análises microbiológicas foram realizadas nas amostras de solo de 0-5, 5-10 cm e na rizosfera. Foram avaliados o número de unidades formadoras de colônias (UFC) de bactérias oxidantes e redutoras de Mn, sendo que os isolados representativos tiveram a região rDNA 16S sequenciada para identificação. O C da biomassa microbiana (CBM), a respiração basal e colonização micorrízica também foram avaliados. As plantas com encarquilhamento foliar apresentaram redução na massa da parte aérea e na produtividade de grãos. Em adição, apresentaram teores foliares mais elevados de P, Ca, Mg, Mn e B e menores teores de K. No solo das áreas sem sintomas, a SB, a CTC, os teores de Ca, Mg e Fe (0-5 cm) foram maiores, enquanto o os teores de P e Zn (10-20 cm) foram mais baixos. Na safra 2012/13, o CBM foi significativamente maior nas áreas sem sintoma de encarquilhamento foliar. O número de UFC de bactérias oxidantes de Mn foi maior no solo da área sem sintomas (0-5 cm, rizosfera) enquanto que o número de bactérias redutoras foi maior na área com sintomas. A maior população de bactérias redutoras de Mn da área com sintomas coincidiu com maiores teores de Mn na planta, ligeiramente superiores aos encontrados nas plantas sem sintomas. Entre as bactérias redutoras de Mn, predominou o gênero Streptomyces enquanto diversos gêneros representaram as bactérias oxidantes de Mn: Arthrobacter, Streptomyces, Bacillus, Novosphingobium, Agrobacterium, Variovorax, Acinetobacter e Pseudomonas. O teor de P diferiu entre as áreas tanto no solo como na planta, enquanto os teores de Ca e Mg diferiram apenas no solo, sugerindo que o sintomas podem não estar relacionados a um nuntriente em particular, mas pode ser o resultado da interação de vários fatores. Apesar de os teores de Mn na planta e no solo, tanto nas áreas com sintomas como nas áreas sem sintomas serem considerados altos, não foram apontados como causa direta do problema. É provável haver uma interação multifatores na manifestação dos sintomas que precisa ser mais bem estudada.Soybean (Glycine max L. Merr.) producing fields in Paraná State have presented plants with leaf crinkle, similar to symptoms of Mn toxicity, resulting in growth reduction, generally observed in spots. The aim of this work was to analyze soil chemical and microbiological properties related with Mn cycling and investigate if high amounts of this nutrient have caused the "crinkle leaf" in commercial areas of soybean. Soil and plant samples were collected in spots with symptoms and adjacent healthy areas of nine fields in 2012/13 season and three in 2013/14 season. In the shoots, the dry weight and foliar concentrations of P, K, Ca, Mg, S, B, Cu, Fe, Mn and Zn were determined. Soil samples were collected at depths of 0-5, 5-10, 10-20 and 20-40 cm, air-dried and analyzed for pH (CaCl2), organic C, available P, Ca, Mg, K, Al, H + Al, Sum of bases, CEC, base saturation, B, Cu, Fe, Mn and Zn concentrations. Microbiological analyzes were carried out in soil samples from 0-5, 5-10 cm and rhizosphere. The number of colony forming units (CFU) of oxidizing and Mn reducing bacteria was evaluated, and the most representative isolates had the 16S rDNA region sequenced for identification. Microbial biomass C (MBC), basal respiration and mycorrhizal colonization were also assessed. Plants with foliar crinkling presented lower shoot dry weight and grain yield. In addition, showed higher foliar concentrations of P, Ca, Mg, Mn and B, and lower concentrations of K. The values of SB, CEC, Ca, Mg and Fe concentrations (0-5 cm) were higher in the soil of plants without symptoms, whereas P and Zn (10-20 cm) were lower. In the 2012/13 season, MBC was significantly higher in the soils of plants without symptoms. The number of CFUs of Mn-oxidizing bacteria was higher in the soil of the symptomless area (0-5 cm, rhizosphere), whereas the number of Mn-reducing bacteria was higher in the area with plants showing symptoms. The largest population of Mn-reducing bacteria in the area with symptoms coincided with slightly higher concentrations of Mn in plant leaves, compared with plants without symptoms. The genus Streptomyces predominated among the Mn-reducing bacteria, while several genera represented the Mn-oxidizing bacteria: Arthrobacter, Streptomyces, Bacillus, Novosphingobium, Agrobacterium, Variovorax, Acinetobacter and Pseudomonas. The P concentrations differed between both soil and plants, while Ca and Mg differed only in the soil, suggesting that the symptom may not be related to a particular nutrient, but may depend on the interaction between several factors. Despite the concentrations of Mn in plants and in the soil are considered high, they could not be considered the sole cause of the problem. A multifactorial interaction probably occurs and must be more deeply studied.
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Rosset, Michele. "Hidrólise enzimática de carboidratos de soja [Glycine max (L.) Merrill] e efeitos em tofu tipo silken." Universidade Estadual de Londrina, 2011. http://www.bibliotecadigital.uel.br/document/?code=vtls000168335.
Full textAbstract:
A adição de Viscozyme L na suspensão de soja pode resultar em um tofu com características diferentes do tradicional. Devido à ação da enzima, material da parede celular (polissacarídeos) poderá ser parcialmente hidrolisado liberando mono e oligossacarídeos, os quais serão transferidos para o tofu, provavelmente modificando sua composição e textura. O objetivo deste trabalho foi estudar os efeitos, em tofu tipo silken, da hidrólise de carboidratos de soja realizada pelo complexo enzimático Viscozyme L. Na primeira etapa, foi realizada a otimização da temperatura de ação de Viscozyme L e foi verificado que, a 55 oC, os teores dos açúcares redutores aumentaram em até 4 vezes, comparado ao controle. Estaquiose foi o oligossacarídeo predominante no tofu tratado (4,58 g/100 g) e o conteúdo de rafinose foi de 1,22 e 0,75 g/100 g nos tofus tratado e controle, respectivamente. O nível de glicose, aproximadamente, duplicou no tofu tratado (1,66 g/100 g) em relação ao controle (0,74 g/100 g). O tofu tratado apresentou maior quantidade de compostos fenólicos que o controle (173 e 161 mg equivalentes de ácido gálico/100 g de tofu liofilizado, respectivamente) e maior atividade antioxidante pelo teste ABTS e DPPH. O conteúdo total de isoflavonas (92 mMol/100 g tofu) não apresentou diferença entre as amostras, mas o tofu tratado apresentou maior concentração de malonil glicosídeos e o controle de ?-glicosídeos. Os tofus apresentaram diferenças sensoriais como maior odor de soja e menor uniformidade da superfície (tofu tratado), mas não houve preferência de uma amostra em relação à outra. O tofu tratado teve maior quantidade de glicose e frutose que o controle, porém não foram verificadas diferenças nos gostos (ácido e amargo) das amostras. Isto pode ter ocorrido pelo fato dos tofus terem sido coagulados com glucona-delta-lactona, um coagulante ácido que pode ter mascarado o sabor doce do tofu tratado com enzima. As condições ideais de temperatura e concentração de Viscozyme L para extração de proteína foram 60 oC e 30 FBG (Fungal Beta Glucanase) por 30 minutos. O pré-tratamento enzimático para extração de proteínas resultou em rendimento de 56,27%, superior ao método alcalino tradicional, 33,04%; o efeito da temperatura de pré-tratamento foi a variável mais importante. Para hidrólise de carboidratos, as condições ótima de temperatura e concentração de enzima foram 45 oC e 45 FBG/10 g de farinha desengordurada de soja, respectivamente. Ambas amostras de tofu apresentaram aglomerados de microestruturas globulares de proteínas e estrutura tridimensional fibrosa, típica de tofus.The addition of Viscozyme L in soy suspension may result in a tofu with characteristics differents from traditional. Due to the presence of the enzyme, cell wall material (polysaccharides) may be partially hydrolyzed to release mono-and oligosaccharides, which will be transferred to the tofu and probably influencing composition and texture. The aim of this work was to study the effects, in silken tofu, of the hydrolysis of soy carbohydrates by the enzyme complex of Viscozyme L. First, this study investigated the enzymatic pre-treatment of soy slurry to optimize conditions of the enzyme action. The optimum temperature of Viscozyme L was 55 oC and it was found that the levels of reducing sugars increased up to 4 times compared to the control. Stachyose was the predominant oligosaccharide in treated tofu 4.58 g/100 g, and of raffinose was 1.22 and 0.75 g/100 g in treated tofu and control, respectively. The glucose level was approximately doubled in the treated tofu (1.66 g/100 g) compared to control (0.74 g/100 g). The treated tofu had a higher amount of phenolic compounds compared to the control, 173 and 161 mg of gallic acid equivalent/100 g of dried tofu, and higher antioxidant activity by ABTS and DPPH test. The total content of isoflavonas (92 mMol/100 g tofu) did not differ between the samples but the treated tofu had a higher concentration of malonyl glycosides and the control of ?-glycosides. The tofus showed sensory differences as the largest soybean odor and less uniform surface (treated tofu), but there was no preference for one sample over the other. The treated tofu had higher amount of glucose and fructose than the control, but there was no observed differences in the taste (acid and bitter) of the samples. This may have occurred because the tofus were coagulated with glucona-delta-lactone, an acid coagulant that may have masked the sweet taste of treated tofu. The optimum conditions of temperature and concentration of Viscozyme L for protein extraction were 60 ° C and 30 FBG (Fungal Beta glucanase), during 30 minutes. Enzimatic pre-treatment for proteins extraction resulted in a yield of 56.27%, higher than the traditional alkaline method, 33.04%; the effect of the pre-treatment temperature was the most important variable. For carbohydrate hydrolysis the optimal conditions of temperature and enzyme concentration were 45° C and 45 g of FBG/10 g defatted soy flour. All tofu samples had a globular microstructure of protein which was integrated into clumps and showed a fibrous three-dimensional network structure, typical of tofu.
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Almeida, Adriély Alves de. "Tratamento de sementes como alternativa para o controle de Meloidogyne javanica em soja Glycine max (L.) Merril." Universidade Estadual de Londrina. Centro de Ciências Agrárias. Programa de Pós-Graduação em Agronomia, 2014. http://www.bibliotecadigital.uel.br/document/?code=vtls000196041.
Full textAbstract:
O tratamento de sementes tem sido evidenciado com boas perspectivas como medida complementar no controle de fitonematoides. Portanto, o objetivo desse trabalho foi verificar o efeito de produtos utilizados no tratamento de sementes de soja sobre o nematoide de galhas Meloidogyne javanica. Foram realizados ensaios in vitro e em casa de vegetação compostos pela combinação dos tratamentos: Testemunhas (inoculada e não inoculada com M. javanica para o ensaio em casa de vegetação); Abamectina; Tiametoxam; Fludioxonil + Metalaxil-M + Tiabendazol; Abamectina + Tiametoxam; Abamectina + Fludioxonil + Metalaxil-M + Tiabendazol; Tiametoxam + Fludioxonil + Metalaxil-M + Tiabendazol; e Abamectina + Tiametoxam + Fludioxonil + Metalaxil-M + Tiabendazol. O ensaio in vitro foi realizado com o objetivo de verificar o efeito de produtos sobre a eclosão, mobilidade e mortalidade dos juvenis de segundo estádio (J2) do nematoide. Para o ensaio em casa de vegetação, as sementes de soja cv. BRS 133 foram previamente tratadas conforme descrito anteriormente. A semeadura foi realizada em vasos com capacidade para 3 litros de substrato, com uma planta por vaso. Aos 15 dias da inoculação, avaliou-se o efeito dos tratamentos sobre o desenvolvimento das plantas e a penetração dos J2 pelo método de coloração com fucsina ácida. Após 30 e 60 dias, foram tomadas novamente medidas de desenvolvimento das plantas, bem como o número de galhas e massas de ovos, população final, fator de reprodução e número de nematoides por grama de raiz. Os tratamentos contendo Abamectina foram os mais eficientes em reduzir a taxa de eclosão dos J2, bem como os que apresentaram maiores taxas de imobilização e mortalidade sobre os juvenis, diferindo da testemunha. Aos 15 dias da inoculação, observou-se melhor desenvolvimento radicular, comprimento de parte aérea e massa fresca de parte aérea em plantas provenientes de sementes tratadas. Para o número de nematoides/g de raiz observou-se significativa diferença entre plantas provenientes de sementes tratadas e a testemunha inoculada, destacando-se os tratamentos contendo Abamectina, isolada, ou em combinação com os demais produtos. Após 30 dias, confirmou-se a eficiência do tratamento de sementes em reduzir a população do nematoide nos tratamentos 3 (Abamectina) e 9 (Abamectina + Tiametoxam + Fludioxonil + Metalaxil-M + Tiabendazol), apresentando menores valores para as variáveis população final, fator de reprodução e nematoides/g de raiz. No entanto, aos 60 dias, não observou-se eficiência dos tratamentos em manter baixa a população do nematoide. Portanto, a partir dos resultados obtidos confirmou-se que o tratamento de sementes é uma importante medida, auxiliar, a ser utilizada no manejo integrado dos fitonematoides.The seed treatment have been demonstrated good prospects as a complementary measure to control nematodes. Therefore, this study aimed to investigate the effect of products used in the seeds treatment of soybean on root-knot nematode Meloidogyne javanica. To accomplish this, experiments were conducted in vitro and on greenhouse consisted of combinations of treatments: Control (inoculated and non-inoculated, for the test in a greenhouse with nematode and without seed treatment); Abamectin; Tiametoxam; Fludioxonil + Metalaxyl-M + Tiabendazole; Abamectin + Tiametoxam; Abamectin + Fludioxonil + Metalaxyl-M + Tiabendazole; Tiametoxam + Fludioxonil + Metalaxyl -M + Tiabendazole, and Abamectin + Tiametoxam + Fludioxonil + Metalaxyl-M + Tiabendazole. The in vitro assay was performed in order to verify the effect of chemicals on hatching, mobility and mortality of nematode second stage juveniles ( J2 ) . For the experiment in greenhouse, seeds were pretreated by the method of plastic bag with the following combination of treatment. The sowing was performed in glass with a capacity of 3 liters of substrate, leaving one plant per pot. At 15 days after inoculation, the treatment effect on plant growth and nematode penetration was evaluated by th the acid fuchsin method. After 30 and 60 days, were taken measures of plant development again, as well as the number of galls and egg masses, final population, reproduction factor and number of nematodes per gram of root. Treatments containing abamectin were the most effective in reducing the hatching rate of J2, as well as those which had higher immobilization and mortality rates on juveniles, differing from control. At 15 days, there was greater root development, length of shoot and fresh weight of shoots in plants grown from treated seeds. For the number of nematodes/g of root was observed significant difference among plants grown from treated seeds and inoculated control highlighting the treatments containing abamectin, isolated or in combination with other products. After 30 days, it was confirmed the effect of seed treatment on reducing nematode populations with treatment 3 (Abamectin) and 9 (Abamectin + Tiametoxam + Fludioxonil + Metalaxyl -M + Tiabendazole), with smaller values for final population factor, reproduction factor and nematodes/g of root. However, at 60 days, after inoculation, there was no effect of treatments on maintaining low nematode populations. Therefore, from the results obtained it can be concluded that the seeds treatment may be a measure that assists in the nematode integrated management.
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Santos, Esmael Lopes dos. "Influência do genótipo sobre as concentrações de proteína e óleo em sementes de soja [Glycine max (L.) Merrill]." Universidade Estadual de Londrina. Centro de Ciências Agrárias. Programa de Pós-Graduação em Agronomia, 2006. http://www.bibliotecadigital.uel.br/document/?code=vtls000117318.
Full textAbstract:
A soja [Glycine max (L.) Merrill] a cada ano vem confirmando a sua posição ímpar como produto agrícola brasileiro de maior importância, quer na geração de divisas para o país, quer no incremento das atividades da agroindústria, da produção de carnes, de óleo e derivados. A principal utilização da soja, tanto no Brasil como no restante do mundo, é como matéria prima para a indústria de esmagamento que produz óleo degomado e farelo. O óleo é utilizado como matéria prima para a indústria alimentícia na produção de óleo refinado, e seus derivados, e o farelo é utilizado, principalmente, na indústria de rações como enriquecedor protéico. A qualidade do farelo de soja é dada pelo seu conteúdo de proteína. O farelo obtido da soja produzida no Brasil, especialmente na região Sul, tem apresentado conteúdo de proteína abaixo das especificações exigidas pelo mercado, o que tem depreciado seu valor. A concentração de óleo e proteína na semente de soja é herdada como uma característica quantitativa que sofre grande influência do meio ambiente. Em condições de cultivo in vivo é difícil controlar precisamente o fornecimento de carbono e nitrogênio destinado às sementes. Com o objetivo de avaliar a influência de genótipos de soja sobre a concentração de proteína e óleo na semente com desenvolvimento in vivo e in vitro, sementes imaturas das cultivares CD 202 e CD 206 foram retiradas da planta mãe no estádio R5, cultivadas in vitro em meio de cultura líquido, contendo 20, 40 e 60 mM de glutamina. As sementes foram incubadas em frascos de vidro em constante agitação, por oito dias a 25 . 0,2.C, com concentração de sacarose de 204,5 mM. Após esse período de incubação, foi determinado o ganho de massa fresca das sementes. Posteriormente, foi determinado o teor de óleo e proteína das sementes desenvolvidas in vitro e das desenvolvidas in vivo. O ganho de massa fresca não apresentou diferença significativa (P>0,05) em uma mesma cultivar quando houve alteração da concentração de glutamina. Entre as cultivares o ganho de massa fresca apresentou diferença significativa (P<0,05) nas concentrações de 40 e 60 mM de glutamina na cultivar CD 206 em relação à CD 202. A porcentagem de proteína na concentração de 20 mM de glutamina não apresentou diferença significativa (P>0,05) na cultivar CD 206 cultivada in vitro quando comparada com a cultivada in vivo. Porém o inverso ocorreu para as concentrações de 40 e 60 mM de glutamina. A cultivar CD 202 quando cultivada in vitro na concentração de 20 mM apresentou porcentagem de proteína menor que as sementes cultivadas in vivo. Porém, acima da concentração de 20 mM de glutamina, a cultivar CD 202 apresentou uma alta porcentagem de proteína, respondendo positivamente ao aumento da concentração de glutamina. Com suprimento adequado de nitrogênio para as sementes com desenvolvimento in vitro o genótipo não limitou o acúmulo de proteína. Entre as duas cultivares estudadas, a proteína se apresentou sempre em maior porcentagem na cultivar CD 206. As concentrações de óleo e proteína foram inversamente relacionadas. O genótipo influencia na composição da semente de soja, pois mesmo quando houve variação no suprimento de nitrogênio para as sementes com desenvolvimento in vitro diferenças estatísticas apresentadas na porcentagem de proteína e óleo, foram mantidas entre os genótipos.Soybean [Glycine max (L.) Merrill] confirms every year its unparalleled position of most important agricultural Brazilian product as regards the flow of money to the country and the increasing of agro-industry activities and also meat, oil and respective sub products production. In Brazil as well as in the rest of the world, soybean is mainly used as raw material of the grinding industry which produces degummed oil and meal. Soybean oil is the raw material of the food industry for the production of refined oil and its sub products and the meal is mainly used to increase the protein content in animal food. The quality of soybean meal is evaluated by its protein content. Meal resulting from soybean produced in Brazil, specifically in southern region of Brazil, has been presenting a protein content lower than the demands of the market, what results in the product?s devaluation. The concentration of oil and protein in soybean seed is an inherited qualitative trait, but it is greatly influenced by the environment .Under the condition of cultivation in vitro it is difficult to control precisely the supply of carbon and nitrogen destined for the seeds. With the purpose of evaluating soybean?s genotype on the concentration of protein and oil of seeds developed in vivo and in vitro, immature seeds of cultivars CD 202 and CD 206 were removed from the mother-plant in the stage R5 and were cultivated in vitro, in a liquid milieu of cultivation which contained 20, 40 and 60 mM of glutamine. The seeds were incubated in glass flasks and agitated constantly during eight days at 25± 0,2 º C with 204,5 mM sucrose concentration. After that period of incubation it was determined the gain of fresh mass of the seeds. Afterwards it was also determined the oil and protein contents of the seeds developed in vitro and those developed in vivo. The fresh mass gain did not present a significant difference ( P>0,05) in the same cultivar when the glutamine concentration was altered , but between the two cultivars, fresh mass gain showed a significant difference (P<0,05) in the concentration of 40 and 60 mM of glutamine in the cultivar CD 206 as compared to the cultivar CD 202. The protein percentage in the 20 mM glutamine concentration did not present a significant difference (P>0,05) in the cultivar CD 206 cultivated in vivo. Nevertheless the opposite occurs in 40 and 60 mM of glutamine concentrations. Cultivar 202 when cultivated in vitro in 20 mM concentration showed a lower protein percentage than that of the seed cultivated in vivo. However, over 20 mM glutamine concentration, the cultivar CD 202 showed a high percentage of protein, what represents a good response to the increase of glutamine concentration. With an adequate supply of nitrogen for the seeds cultivated in vitro, the genotype did not limit the protein gain. Between the studied cultivars, protein percentage was always higher in the cultivar CD 206. Oil and protein concentrations were inversely related. The genotype has influence on soybean seeds composition, since it was observed that statistical differences in the oil and protein percentage remained unchanged even when a variation in the nitrogen supply to the seeds developed in vitro ocurred.
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Santos, Maria Aparecida dos. "Identificação de QTL associados à simbiose entre bradyrhizobium japonicum/B. elkanii e a soja [Glycine max(L.) Merr.]." Universidade Estadual de Londrina. Centro de Ciências Biológicas. Programa de Pós-Graduação em Microbiologia, 2005. http://www.bibliotecadigital.uel.br/document/?code=vtls000108570.
Full textAbstract:
O nitrogênio (N) necessário para a soja [Glycine max (L.) Merril] pode ser suprido pelo processo de fixação biológica do nitrogênio (FBN) com estirpes de Bradyrhizobium japonicum/ B. elkanii, de tal forma que, hoje, não se recomenda o uso de fertilizantes nitrogenados para essa cultura no Brasil. Contudo, nos últimos anos, os parâmetros de FBN não vêm sendo avaliados nos programas de melhoramento, que priorizam o rendimento de grão e a resitência a doenças. O objetivo deste estudo foi identificar QTL (Quantitative Trait Loci), utilizando marcadores microssatélites (SSR), relacionados com a FBN em uma população F2:7 de 157 linhagens endogâmicas recombinantes derivadas do cruzamento entre as cultivares contrastantes quanto as características de nodulação e crescimento de plantas, relacionadas com a FBN, Bossier (alta) x Embrapa 20 (média). As linhagens foram avaliadas em casa de vegetação quanto às características relacionadas com o crescimento da planta (massa da parte aérea seca, MPAS) e nodulação (massa de nódulos secos, MNS; número de nódulos, NN e massa média de nódulos secos, MNS/NN). Todas as características avaliadas apresentaram diferenças significativas (p = 0,05), indicando a existência de variabilidade genética entre as linhagens. A cultivar Bossier apresentou as maiores médias para todas as características avaliadas. Foram mapeados 16 marcadores distribuídos em seis dos vinte grupos de ligação, cobrindo uma região de 5% do genoma da soja (151,6 cM). A análise de regressão identificou doze associações significativas em quatro grupos de ligação (B1, C2, D1b, e H): três para a massa da parte aérea, quatro para número de nódulos, duas para massa de nódulos e três para a massa média de nódulos. Todos os QTL detectados foram de efeitos menores (R2 variando de 2,5% a 8,0%), semelhante ao encontrado na população F2:3 de Embrapa 20 (média) x BRS 133 (baixa) ( Nicolas et al., 2005). Contudo, sete marcadores foram confirmados nas duas populações, indicativo de uso potencial em programas de melhoramento visando a FBN.Nitrogen (N) demand of soybean [Glycine max (L.) Merrill] can be supplied via biological nitrogen fixation (BNF) through the inoculation with selected Bradyrhizobium japonicum/B. elkanii strains, such that today no N-fertilizer is recommended for the crop in Brazil. However, traits related to BNF have not been lately evaluated in soybean breeding programs, with priority given to yield and resistance to diseases. The objective of this study was the identification of QTL (Quantitative Trait Loci) related to BNF using microsatellites (SSR) markers, in an F2:7 population of 157 Recombinant Imbred Lines (RILs), derived from the cross between parental cultivars with contrasting capacities of BNF, Bossier (high) and Embrapa 20 (medium). Soybean lines were grown under greenhouse conditions for the evaluation of the parameters of plant growth (shoot dry weight, SDW), and nodulation (nodule number, NN; nodule dry weight, NDW and the relation nodule dry weight/nodule number, NDW/NN). All parameters evaluated showed statistical differences (P= 0.05), indicating genetic variability among soybean lines. Sixteen markers located in six out of the twenty soybean linkage groups have been mapped, covering about 5% of the genome (151.6 cM). The regression analysis identified twelve significant associations in four linkage groups (B1, C2, D1b and H): three for shoot weight, four for nodule number, four for nodule weight and three for the medium value of nodule weight. All QTL had minor effects (R2 = 2,5 to 8,0%) similar to previous reports in an F2:3 of BRS 133 (low) x Embrapa 20 (medium) (Nicolás et al., 2005). However, seven QTL were confirmed in both populations, indicating that they might be effective in increasing BNF in soybean breeding programs.
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Seibel, Neusa Fátima. "Caracterização, fracionamento e hidrólise enzimática dos componentes do resíduo do processamento da soja [Glycine Max (L.) Merrill], fibras dos cotilédones." Universidade Estadual de Londrina. Centro de Ciências Agrárias. Programa de Pós-Graduação em Ciência de Alimentos, 2006. http://www.bibliotecadigital.uel.br/document/?code=vtls000118533.
Full textAbstract:
Ingredientes derivados de soja, fibras de cotilédones, farinha desengordurada e concentrado protéico foram avaliados quanto às características químicas e propriedades funcionais. O macromineral de maior concentração foi o potássio e o micromineral foi o ferro em todos os ingredientes. O maior percentual de ácido fítico estava nas amostras protéicas, assim como as isoflavonas, no entanto, as fibras apresentaram mais genisteína e daidzeína e o total de isoflavonas correspondeu a 45% do valor encontrado na farinha. As fibras alimentares tiveram as melhores propriedades de hidratação e as propriedades relacionadas com o óleo foram similares à da farinha de soja, mesmo tendo menores percentuais de proteínas. A parede celular das fibras dos cotilédones de soja foi fracionada e o componente majoritário foi a hemicelulose, correspondendo a 55%, em média. Com a constituição dos monossacarídeos das frações houve a distinção de dois grupos: (1) celulose e (2) pectina e hemiceluloses. A classificação das proteínas foi baseada na solubilidade em diferentes solventes, a farinha desengordurada de soja apresentou a maior fração extraída com solução salina e o concentrado protéico, assim como as fibras de cotilédones, com solução alcalina. A eletroforese apresentou as proteínas majoritárias da soja, ß-conglicinina e glicinina nas fibras de cotilédones e nos ingredientes protéicos. A proteína extraída das fibras também revelou bandas com peso molecular próximo aos 30KDa, sendo provavelmente glicoproteínas de parede celular, ricas em hidroxiprolina. Após a determinação das melhores condições, as fibras de soja foram hidrolisadas com carboidrase e com protease. As frações sólidas das fibras hidrolisadas com carboidrase tiveram maior quantidade de proteínas e aumento nas propriedades hidrofílicas, enquanto que a fração solúvel teve 73% dos carboidratos e 50% dos ácidos urônicos da quantidade inicial das amostras. A protease foi capaz de solubilizar 54% do total das proteínas, produzindo uma fração sólida contendo 76% de fibras alimentares totais. A fração solúvel teve peptídeos de baixo peso molecular, menor que 10KDa e uma banda de peso molecular próximo aos 25KDa. As micrografias da MEV confirmaram a redução das partículas na amostra micronizada em relação à original. A estrutura física da fibra original hidrolisada com protease ficou mais porosa superficialmente do que a fibra micronizada. As amostras hidrolisadas com carboidrase apresentaram uma estrutura mais compactada.Soybean derived ingredients: cotyledon fibers, defatted flour and protein concentrate were evaluated for chemical characteristics and functional properties. Potassium was the macro and iron the micro mineral in highest concentration in all the ingredients. The highest concentration of phytic acid was in the protein concentrate, as well as the highest concentration of isoflavones, however, the fibers had more genistin and daidzein and the total isoflavones in the fibers corresponded to 45% of the amount in the defatted flour. Dietary fibers had the best hydration properties and in properties related to oil emulsification had similar indexes to soybean flour, despite the lower protein concentration. The cell wall soybean cotyledon fiber was fractioned and the major component was hemicellulose, corresponding to 55% on the average. Based on monosaccharide composition of the cell wall fractions there were two groups: (1) cellulose and (2) pectin and hemicelluloses. Protein classification due to solubility in different solvents showed that defatted flour had a major protein fraction extracted with salt solution while the protein concentrate and dietary fibers had higher protein solubility with alkaline solution. The electrophoresis presented the major soybean proteins, ß-conglicinin and glicinin in cotyledon fibers and in protein ingredients. The protein extracted from fibers also reveled bands with molecular weigh next 30KDa, probably cell wall hydroxyproline-rich glycoproteins. After identifying the best conditions, the soybean fibers were hydrolyzed with carbohydrase and protease. The solid fraction of carbohydrase hydrolyzed fiber had higher protein concentration and increased hydrophilic properties, while the soluble fraction had 73% carbohydrates and 50% uronic acids of the initial quantity in samples. The protease hydrolyzed 54% of the total protein in the fiber samples, producing a solid fraction with 76% total dietary fiber. The soluble fraction had peptides of low molecular weigh, lower than 10KDa, and one band of molecular weigh close to 25KDa. The SEM micrographies confirmed the reduced particle in the milled sample in relation to the original sample. The physical structure of the original fiber hydrolyzed with protease had more superficial porosity than the reduced particle fiber. The hydrolyzed samples with carbohydrase presented a more compact structure.
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Aoyagi, Luciano Nobuhiro. "Caracterização estrutural e transcricional dos fatores de transcrição R2R3-MYB no genoma da soja (Glycine max) em resposta a doenças." Universidade Estadual de Londrina. Centro de Ciências Exatas. Programa de Pós-Graduação em Biotecnologia, 2013. http://www.bibliotecadigital.uel.br/document/?code=vtls000188152.
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A soja representa uma das mais importantes culturas para a economia, uma vez que é o principal produto do setor agropecuário e de exportação do Brasil. A Ferrugem asiática da soja (FAS), causada por Phakopsora pachyrhizi, representa além de um um fator limitante para a expansão da cultura, uma ameaça devido ao seu potencial em causar perdas na produção de grãos e aumento nos custos do cultivo. O controle baseado em produtos quimicos, além de ser despendioso, causa impactos indesejáveis ao homem e ao ambiente, criando a necessidade de se buscar formas alternativas e igualmente eficazes de controle. A compreensão dos mecanismos de defesa e resistência de plantas de soja, bem como a busca de genes ligados a esses processos, representam um caminho para encontrar formas de se transpor os problemas causados por este e outros patógenos. Estudos da interação (transcritoma) de soja com FAS indicam que fatores de transcrição (FT) da família MYB são expressos com frequência e diferencialmente em plantas resistentes. Em Arabidopsis, MYBs são amplamente estudados e muitos apresentam funções bem determinadas, incluindo o controle sobre as respostas de defesa. Apesar das evidências apontarem a possível participação destes FTs no controle de importantes processos em soja, incluindo a resposta de defesa, existe uma grande escassez de conhecimento, em comparação. Atualmente MYB é a maior família de FT de G. max, assim como a maior entres as plantas, indicando grande potencial de conter candidatos que atuem no controle de importantes processos, assim como é observado em Arabidopsis. Objetivando aumentar o conhecimento sobre estes FT, bem como seu real papel e funções para soja, o presente estudo, analisou a família de fatores de transcrição MYB. GmMYBs da classe R2R3 foram identificados a partir do genoma da soja por meio ferramentas de bioinformática (SMART, Pfam e MEME), e a função putativa foi determinada com base na contrução de árvore filogenética e classificação dos GmMYBs em subfamílias, utilizando guias (AtMYB) com funções conhecidas. Todas as subfamilias MYB de Arabidopsis thaliana e algumas de soja observadas em trabalhos prévios foram formadas, assim como novo subgrupos. A expressão e o perfil transcricional dos GmMYBs R2R3 em ensaios com P. pachyrhizi, Aphis glycines, Heterodera glycines, Pratilenchus brachyurus e Phytophthora sojae, através de análises em bancos de transcritomas (Soybase, LGE-Genosoja, Genevestigator), foi realizada e associada a determinação das funções putativas em busca de potenciais genes envolvidos no controle de mecanismos de defesa. Após a seleção dos modelos gênicos alvos, a indução pela infecção com P. pachyrhizi foi avaliada, por meio de PCR quantitativo em tempo real.
tilizando três genótipos, dois resistentes, PI230970 e Shiranui que possuem o gene Rpp2 e Rpp5, respectivamente, e Williams 82 como modelo suscetível. Entre os genes avaliados, houve destaque para aqueles ligados a síntese de lignina, com três GmMYBs induzidos em plantas resistentes em maior nível e mais rapidamente, um GmMYB com função desconhecida e outro possivelmente ligado a modulação de genes responsivos a quitina, ambos induzidos por um período mais prologando na planta resistente. Analises funcionais futuras irão ser conduzidas para confirmar o envolvimento desses genes na resposta a infecção por patógenos em soja.Soybean is one of the most important crops for the economy, since it is the main product of the agricultural sector and export of Brazil. Asian soybean rust caused by Phakopsora pachyrhizi, is a limiting factor for the crop expansion and a threat because of its potential yield losses and increase in cultivation costs. The control carried out with chemicals is expensive and cause undesirable impacts to humans and the environment, creating the need to seek for alternatives and equally effective control. A more profound understanding of the mechanisms of defense and resistance of soybean plants, as well as the search for genes associated with these processes represent a path to find ways to overcome the problems caused by FAS and other pathogens. Studies of the interaction of soybeans with FAS indicate that transcription factors (TF) MYB family are differentially expressed in resistant plants. In Arabidopsis, MYBs are extensively studied and have well-defined functions, including control over the defense of the plant. Despite evidence suggest a possible role of these TFs in controlling important processes in soybean, including defense response, there is a lack of knowledge, compared with Arabidopsis. MYB is currently the largest family of FT of G. max, and also in plants, indicating great potential to contain candidates that act to control important processes. Aiming to increase knowledge about these mechanisms, in this work we evaluated the family of MYB transcription factors. GmMYBs class R2R3 were identified from the soybean genome using bioinformatics (SMART, Pfam and MEME), and putative function was determined on the basis of phylogenetic tree construction and classification of subfamilies in GmMYBs using guides (AtMYB) with functions known. All MYB subfamilies of Arabidopsis thaliana and some soybean seen in previous works were formed, as well as new subgroups. The expression and transcriptional profile of GmMYBs R2R3 assays with FAS through analysis in banks of transcritomas (Soybase, LGE-Genosoja, Genevestigator) was performed and associated with determining the putative functions for search potential genes involved in the control mechanism defense. After the selection of target genes, induction by infection with FAS was assessed by quantitative PCR in real time at different times of inoculum (12, 24, 48, 72 and 96 hai) into two treatments (with or without inoculum of spores of P. pachyrhizi). Assays were performed in three genotypes, two resistant PI230970 (resistant) having Rpp2 allele and the allele that has Shiranui Rpp5, and showing lesions of the type RB in response to FAS and Williams 82 (susceptible) having TAN type lesions. Among the genes evaluated, there was especially those related to lignin synthesis with three GmMYBs induced in plant resistance in higher levels and faster, one GmMYB with unknown function and other possibly connected to modulation of responsive genes chitin, both induced by a longer period in the plant resistant.
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Godoy, Leandro Pereira de. "Panorama genômico da estirpe semia 5079 (=CPAC 15) de Bradyrhizobium Japonicum, recomendada comercialmente para a cultura da soja (Glycine max (L) merr.)." Universidade Estadual de Londrina. Centro de Ciências Biológicas. Programa de Pós-Graduação em Microbiologia, 2007. http://www.bibliotecadigital.uel.br/document/?code=vtls000125585.
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O processo de fixação biológica do nitrogênio atmosférico (FBN) com bactérias das espécies Bradyrhizobium japonicum e B. elkanii é fundamental para a viabilidade econômica da cultura da soja no Brasil. Com a expansão da cultura no País, no início dos anos 1960, também teve início um programa de seleção de estirpes adaptadas às condições ambientais e às cultivares nacionais e a estirpe SEMIA 5079 (=CPAC 15), pertencente à espécie B. japonicum, destacou-se por sua eficiência, competitividade e adaptação às condições ambientais estressantes, passando a ser utilizada em inoculantes comerciais desde 1992. Nesta última década, o seqüenciamento de alguns genomas de rizóbios permitiu obter grandes avanços no conhecimento da genética dessas bactérias, e este estudo teve por objetivo o seqüenciamento parcial do genoma da estirpe SEMIA 5079, visando a identificação de genes relacionados à capacidade saprofítica, à competitividade e à eficiência do processo de FBN. As leituras dos clones de bibliotecas do tipo "shotgun", construídas a partir do DNA total da SEMIA 5079, resultaram em uma cobertura real de 13,17 % do genoma, com um total de 1.371 CDSs ("coding sequences") anotadas, sendo 729 de função conhecida, 312 hipotéticas conservadas e 330 hipotéticas. A classificação funcional das CDSs pelo banco de dados COG ("Clusters of Orthologous Groups of proteins") mostrou genes putativos em quase todas as classes. Em relação ao banco KEGG ("Kyoto Encyclopedia of Genes e Genomes"), houve similaridade das seqüências anotadas na SEMIA 5079 com outros 71 organismos, e a maior similaridade foi constatada com a estirpe USDA 110 de B. japonicum, e com as estirpes BTAi1 e ORS278 de Bradyrhizobium sp. Quatorze transposases foram encontradas, a maioria relacionada a seqüências de inserção, indicativo de plasticidade elevada do genoma da SEMIA 5079; além disso, 4,54% das CDSs foram identificadas como genes parálogos, também relacionados à adaptação ambiental. Várias CDSs foram anotadas como genes que codificam proteínas relacionadas à nodulação, como os genes nodB, nodD2 e nodW e à FBN, como os genes nifE, fixP, fixQ, fixR e fixO, além de outras proteínas envolvidas no ciclo do N. No seqüenciamento parcial do genoma da estirpe SEMIA 5079, 5,76 % das CDSs válidas codificam enzimas que participam de quase todas as vias de biodegradação de xenobióticos, podendo representar um reservatório importante de genes com potencial biotecnológico.The biological nitrogen fixation (BNF) process with bacteria belonging to the species Bradyrhizobium japonicum and B. elkanii is crucial for the economical viability of the soybean crop in Brazil. A strain selection program began with the crop expansion in the earlier 1960s, aiming at the identification of bacteria adapted to the local environmental conditions and to the Brazilian cultivars; strain SEMIA 5079 (= CPAC 15) of B. japonicum was then recognized by its efficiency, competitiveness and adaptability to stressful environmental conditions, therefore it has been employed in commercial inoculants since 1992. Few rhizobial genomes were completly sequenced in the last decade, and allowed an impressive increase in the genetic knowledge of these bacteria. In this context, this study aimed at the partial sequencing of the genome of strain SEMIA 5079, searching for genes related to the saprophytic capacity, competitiveness and efficiency of the BNF process. The readings of shotgun libraries built with SEMIA 5079 total DNA resulted in a real covering of 13.17% of the genome, with a total of 1.371 CDSs (coding sequences) annotated, 729 with known functions, 312 classified as conserved hypothetical and 330 as hypothetical. The functional classification of the CDSs in the database COG (Clusters of Orthologous Groups of proteins) identified putative genes in almost all classes. Furthermore, the comparison with strain USDA 110 of B. japonicum, sequenced in 2002 by Japanese researchers, has also demonstrated similar percentages of CDSs classified in the categories of COG, an important indication to support the strategy of partial genome sequencing of a bacterium. In relation to the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, the CDSs of SEMIA 5079 have shown similarity with the sequences of 71 other organisms, but in a higher number with B. japonicum strain USDA 110, and with Bradyrhizobium sp. strains BTAi1 and ORS278. Fourteen transposases were found, most related to insertion sequences, indicating high plasticity of the genome of SEMIA 5079; furthermore, 4.54% of the CDSs were classified as paralog genes, also favoring environmental adaptation. Several CDSs were annotated as genes that codify proteins related to the nodulation, as nodB, nodD2 and nodW genes, and to the BNF, as nifE, fixP, fixQ, and fixR genes, in addition to other proteins involved in the cycle of N. The partial sequencing of the genome of strain SEMIA 5079 has also identified 5.76% of CDSs participating in almost all pathways of xenobiotic biodegradation, and might represent a reservoir of important genes with biotechnological potential.
Books on the topic "Glycan code"
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Potsdam, Germany) International Beilstein Symposium on Glyco-Bioinformatics (2nd 2011. Proceedings of the 2nd Beilstein Symposium on Glyco-Bioinformatics: Cracking the sugar code by navigating the glycospace : June 27th-July 1st, 2011, Potsdam, Germany. Berlin: Logos Verlag Berlin GmbH, 2012.
Find full textBook chapters on the topic "Glycan code"
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Šebestík, Jaroslav, Milan Reiniš, and Jan Ježek. "Sugar Code (Glycocode)." In Biomedical Applications of Peptide-, Glyco- and Glycopeptide Dendrimers, and Analogous Dendrimeric Structures, 23–27. Vienna: Springer Vienna, 2012. http://dx.doi.org/10.1007/978-3-7091-1206-9_3.
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Lechner, J. T., J. Stierstorfer, and T. M. Klapötke. "Crystal Structure and Characterization of the Well-Known Plasticizers Ethylene Glycol Dinitrate, Diethylene Glycol Dinitrate and Triethylene Glycol Dinitrate." In Future Developments in Explosives and Energetics, 57–12. Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/9781839162350-00057.
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Ethylene glycol dinitrate (EGDN), diethylene glycol dinitrate (DEGDN) and triethylene glycol dinitrate (TEGDN) are used as plasticizers in propellant mixtures and have been known for more than 100 years. Despite the industrial application and the long history of these compounds, the crystal structures of all three compounds, which are liquids at room temperature, have not yet been determined. Therefore, in this work the crystal structures were determined by low-temperature X-ray diffraction and thus the bonding properties and crystal packing in the solid state could be compared. The densities at room temperature were measured by gas-pycnometry and the energetic properties were calculated using the EXPLO5 code.
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Lechner, J. T., J. Stierstorfer, and T. M. Klapötke. "Crystal Structure and Characterization of the Well-Known Plasticizers Ethylene Glycol Dinitrate, Diethylene Glycol Dinitrate and Triethylene Glycol Dinitrate." In Future Developments in Explosives and Energetics, 57–12. Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/9781788017855-00057.
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Ethylene glycol dinitrate (EGDN), diethylene glycol dinitrate (DEGDN) and triethylene glycol dinitrate (TEGDN) are used as plasticizers in propellant mixtures and have been known for more than 100 years. Despite the industrial application and the long history of these compounds, the crystal structures of all three compounds, which are liquids at room temperature, have not yet been determined. Therefore, in this work the crystal structures were determined by low-temperature X-ray diffraction and thus the bonding properties and crystal packing in the solid state could be compared. The densities at room temperature were measured by gas-pycnometry and the energetic properties were calculated using the EXPLO5 code.
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Coppens, Philip. "Electron Density Studies of Molecular Crystals." In X-Ray Charge Densities and Chemical Bonding. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195098235.003.0014.
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Small molecules consisting of light-, few-electron atoms were the first species beyond atoms to yield to quantum-mechanical methods. Similarly, crystals of small light-atom molecules have served as most useful test cases of charge density mapping. The small number of core electrons in first-row atoms enhances the relative contribution of valence electron scattering to the diffraction pattern. Early studies, done just after automated diffractometers became widely available, were concerned with molecular crystals such as uracil (Stewart and Jensen 1967), s-triazine (Coppens 1967), oxalic acid dihydrate (Coppens et al. 1969), decaborane (Dietrich and Scheringer 1978), fumaramic acid (Hirshfeld 1971), glycine (Almlof et al. 1973), and tetraphenylbutatriene (Berkovitch-Yellin and Leiserowitz 1976). While thermal motion is often pronounced in molecular crystals, advances in low-temperature data collection have done much to alleviate this disadvantage. In recent years, subliquid-nitrogen cooling techniques have been increasingly applied. Among the most interesting aspects of molecular crystals are the influence of intermolecular interactions on the electronic structure. Physically meaningful Coulombic parameters pertinent to a molecule in a condensed environment can be obtained from the diffraction analysis, and can be used in the modeling of macromolecules. The enhancement of the electrostatic moments relative to those of the isolated species has been noted in chapter 7. But, beyond these considerations, molecular crystals are important in their own right. For example, crystals of aromatic molecules substituted with π-electron donor and acceptor groups are among the most strongly nonlinear optical solids known, considerably exceeding the nonlinearity of inorganic crystals such as potassium titanyl phosphate (KTP); while mixed-valence organic components of low-dimensional solids can become superconducting at low temperatures. The relation between such properties of molecular crystals and their charge distribution provides a continuing impetus for further study. The suitability of light-atom crystals for charge density analysis can be understood in terms of the relative importance of core electron scattering. As the perturbation of the core electrons by the chemical environment is beyond the reach of practically all experimental studies, the frozen-core approximation is routinely used. It assumes the intensity of the core electron scattering to be invariable, while the valence scattering is affected by the chemical environment, as discussed in chapter 3.
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Kelly, Alan. "Consistency and Change." In Molecules, Microbes, and Meals. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780190687694.003.0006.
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Proteins are, in my view, the most impressive molecules in food. They influence the texture, crunch, chew, flow, color, flavor, and nutritional quality of food. Not only that, but they can radically change their properties and how they behave depending on the environment and, critically for food, in response to processes like heating. Even when broken down into smaller components they are important, for example giving cheese many of its critical flavor notes. Indeed, I would argue that perhaps the most fundamental phenomenon we encounter in cooking or processing food is the denaturation of proteins, as will be explained shortly. Beyond food, the value of proteins and their properties is widespread across biology. Many of the most significant molecules in our body and that of any living organism (including plants and animals) are proteins. These include those that make hair and skin what they are, as well as the hemoglobin that transports oxygen around the body in our blood. Proteins are built from amino acids, a family of 20 closely related small molecules, which all have in chemical terms the same two ends (chemically speaking, an amino end and an acidic end, hence the name) but differ in the middle. This bit in the middle varies from amino acid to amino acid, from simple (a hydrogen atom in the case of glycine, the simplest amino acid) to much more complex structures. Amino acids can link up very neatly, as the amino end of one can form a bond (called a peptide bond) with the acid end of another, and so forth, so that chains of amino acids are formed that, when big enough (more than a few dozen amino acids), we call proteins. Our bodies produce thousands of proteins for different functions, and the instructions for which amino acids combine to make which proteins are essentially what the genetic code encrypted in our DNA specifies. We hear a lot about our genes encoding the secrets of life, but what that code spells is basically P-R-O-T-E-I-N. Yes, these are very important molecules!
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Becker, Richard C., and Frederick A. Spencer. "Novel Anticoagulants." In Fibrinolytic and Antithrombotic Therapy. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780195155648.003.0023.
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While all anticoagulants have, to a certain extent, novel properties, the development of agents that inhibit specific coagulation proteases through structural affinity and can be inhibited themselves by the concomitant production of antidotes (drug–antidote pair construct) has the potential to revolutionize the field. With the evolution of our thinking toward hemostasis and thrombosis has come new pharmacologic constructs for safe and effective treatment. Aptamers are single-stranded nucleic acids that inhibit a protein’s function by folding into a specific three-dimensional structure that defines high-affinity binding to the target protein (White et al., 2000). The term aptamer (from the Latin aptus, “to fit”) was coined by Ellington and Szostak (1990) following their pioneering work published originally in Nature. Based on iterative selection techniques, aptamers that bind essentially any protein or small molecule can be generated. A high-affinity, specific inhibitor that interacts with functional groups (on both the nucleic acid and the protein) can be constructed if a small amount of pure target is available. The initiation point for aptamer development is a combinatorial library composed of single-stranded nucleic acids (RNA, DNA, or modified RNA), typically containing 20 to 40 randomized positions (1024 different sequences). Isolation of high-affinity nucleic acid ligands involves a process known as SELEX (systemic evolution of ligands by exponential enrichment). The starting library is incubated with the protein of interest. Nucleic acid molecules that adopt conformations that allow target protein binding are subsequently partitioned from other sequences (that do not bind the protein). The bound sequences are removed and amplified by reverse transcription and polymerase chain reaction (PCR) (for RNA-based libraries) or PCR alone (for DNA-based libraries). After repeating the process several times, the selected ligands are secured and evaluated for binding affinity and ability to inhibit activity (of the target protein). Postselection optimization steps typically include (1) reduction in aptamer length (from a starting molecule of 80–100 nucleotides to 40 nucleotides); (2) enhanced stability in biologic systems (achieved by substitution of ribonucleotides with 2-amino, 2´-fluoro, or 2´-0-alkyl nucleotides and protection from exonuclease digestion by 3´ end capping); and (3) reduced renal clearance (achieved by increasing the molecules’ mo lecular weight through site-specific addition of polyethylene glycol moieties or other hydrophobic groups.
Conference papers on the topic "Glycan code"
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Schuberth, Ralf, Ingo Prahl, Harald Weiss, and Carlo Unverzagt. "SYNTHESIS OF THE LEC-10 NONASACCHARIDE, A BISECTED AND CORE-FUCOSYLATED N-GLYCAN." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.407.
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Mehta, Anand S., Mary Ann Comunale, Siddhartha Rawat, Jessica Garner, Lucy Betesh, Mengjun Wang, Laura Steel, and Michael Bouchard. "Abstract 4982: Increased core fucosylation, a glycan alteration associated with cancer, is the result of hepatocyte dedifferentiation." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4982.
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Jokar, Amir, Steven J. Eckels, and Mohammad H. Hosni. "Evaluation of Heat Transfer and Pressure Drop for the Heater-Core in an Automotive Heat Pump System." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-60824.
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The heat transfer and pressure drop results for a heater-core of an automotive system are presented and discussed in this article. The heater-core is a type of compact heat exchanger that is used as part of an automobile heating-cooling system for heating the passenger cabin on cold seasons. The automotive heating-cooling system in this study includes a standard refrigeration cycle consists of a condenser, an evaporator, a compressor and an expansion valve using the refrigerant R134a as the working fluid. Furthermore, the system uses two separate secondary fluid loops using a 50% glycol-water mixture to exchange energy with the main refrigeration loop. During the cold weather season, the system is operated in the heat pump mode and one of the fluid loops is used to transfer heat from the condenser to the heater-core for heating the passenger cabin. The heat transfer from the heater-core to the passenger cabin is accomplished using air flow through the heater-core openings in an unmixed and cross-flow fashion. The air-side of the heater-core has a unique louver system that is intended to enhance the air-side heat transfer while the glycol-side has a twisted wire inserts to enhance flow turbulence and heat transfer. Semi-empirical correlations for the heat transfer and pressure drop for both glycol-water mixture and air flows in the heater-core are proposed. The flow of the glycol-water mixture in the heater-core is a single-phase flow within a bundle of parallel circular tubes with the twisted wire inserts. The flow of air through the heater-core is approximated as a flow across a finned-tube compact heat exchanger with continuous plate-fins. A modified Wilson plot technique is applied to determine correlations for heat transfer on both glycol-water mixture and air sides. The frictional pressure drop on the glycol-side is calculated from the total measured pressure drop and adjusted for pressure drops within manifolds and inlet/outlet ports. The results for the heat transfer and pressure drop analyses are finally plotted, discussed and compared with the relevant previous studies. These results show that the heat transfer rate is increased in the glycol-side due to the twisted wire inserts, in comparison with the smooth circular tubes. The air-side heat transfer rate is also enhanced due to the louvers in the air passages, as compared to flat-plate fins in compact heat exchangers.
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Woo, Kyoungja, and Byeong-Seon Kim. "Synthesis and bioconjugation of CdSe/CdS core/shell nanoparticles to poly(ethylene glycol) analogues." In Microelectronics, MEMS, and Nanotechnology, edited by Dan V. Nicolau. SPIE, 2005. http://dx.doi.org/10.1117/12.637955.
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Sano, T., and H. Schmidt. "Dual wavelength optofluidic distributed feedback dye laser on a single PDMS chip." In CLEO: Applications and Technology. Washington, D.C.: Optica Publishing Group, 2023. http://dx.doi.org/10.1364/cleo_at.2023.jw2a.1.
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We demonstrate two liquid-core distributed feedback (DFB) lasers operating side-by-side simultaneously at two different wavelengths with sub-mW thresholds from Rhodamine 6G dissolved in ethylene glycol and 4-(Dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran in dimethyl sulfoxide on a single polydimethylsiloxane device.
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Saini, Simarjeet S., Chris Stanford, Juhee Park, Phillip DeShong, William E. Bentley, and Mario Dagenais. "APTES and APES Detection and Glyco Sensing Using Etched Core Fiber Bragg Grating Sensors." In Optical Fiber Sensors. Washington, D.C.: OSA, 2006. http://dx.doi.org/10.1364/ofs.2006.thf4.
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Ebong, E. E., D. C. Spray, and J. M. Tarbell. "The Roles of HS and Its Glypican-1 Core Protein in Flow-Induced Endothelial NOS Activation and Cell Remodeling." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53294.
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Endothelial cell (EC) glycocalyx (GCX) is an endovascular protective coat that is degraded in disease. GCX heparan sulfate (HS) proteoglycan is essential for flow-induced nitric oxide (NO) release and cell remodeling, but the HS core proteins involved in these mechanotransduction events are unknown. We hypothesize that the glypican-1 (GPC1) HS core protein mediates flow-induced EC NO synthase (eNOS) activation and is less important for flow-induced cell remodeling, because GPC1 is located in the caveolae where eNOS resides but, to our knowledge, GPC1 has no direct association with the cytoskeleton. We tested our hypotheses by exposing monolayers of bovine aortic EC (BAEC) with intact GCX, heparinase III (HepIII) enzymatically degraded HS, and RNA-silenced GPC1 to 12–15 dyne/cm2 average shear stress for 3 and 24 hours. HS removal by HepIII and GPC1 inhibition by shRNA equally blocked shear-induced eNOS activation that occurs in shear-conditioned BAEC with fully intact GCX. EC remodeling in response to flow was attenuated by HS degradation, but preserved with GPC1 knockdown. These results suggest that while HS is involved in both centralized and decentralized GCX-mediated mechanotransduction mechanisms, GPC1 plays a role in only centralized GCX-mediated mechanotransduction.
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Woo, Hee-Suk, Yun-Seok Hong, Young-Soon Lim, Jung-Yean Park, Hee-Jae Ahn, and Choong-Dong Lee. "Structural Analysis for Ethylene Oxide Reactor." In ASME 2007 Pressure Vessels and Piping Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/pvp2007-26486.
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The structural safety of the Ethylene Oxide (EO) reactor of an ethylene glycol plant project should be verified by computational analysis. The heat transfer analysis has been performed using the finite volume method program, Fluent and the stress analysis has been performed using the finite element program, ANSYS. The applied loads are dead weight, internal pressure, nozzle load, earthquake load, wind load and thermal load. The analysis results for the main load conditions are presented. In addition, abnormal operating conditions such as runaway, pre-ignition and post-ignition are analyzed. The structural integrity of an EO reactor is investigated in accordance with the ASME Boiler and Pressure Vessel Code, Section VIII, Div. 2. It is concluded that the design of the EO reactor complies with the design criteria for all design load conditions.
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Fork, Richard L., H. L. Fragnito, P. C. Becker, and C. H. Hirlimann. "Multipass amplifier for femtosecond optical pulses." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1988. http://dx.doi.org/10.1364/oam.1988.mn1.
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We describe a multipass optical amplifier based on a double confocal geometry1 which we have used to amplify femtosecond optical pulses to energies of 90 nJ using only 0.7 W of pump power from a Metalaser copper vapor laser operated at 10 kHz. We use four mirrors of 20-cm radius arranged so that an incident train of pulses passes six times through a gain jet containing a mixture of rhodamine 640 and sulforhodamine 640 in ethylene glycol. The amplified pulses, which have durations of ~50 fs, are sufficiently intense to generate white light continuum pulses in an optical fiber with a 4-μm core.
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Kornhauser, Alan A. "Aqua-Ammonia as an Environmentally Acceptable Low Temperature Brine." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-62684.
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In many industrial processes, cooling with brines is preferable to cooling with an evaporating refrigerant. For medium and high temperatures (above about −35°C/−30°F), aqueous solutions of calcium chloride, sodium chloride, ethylene glycol, propylene glycol, and methanol have typically been used. For very low temperatures (down to about −80°C/-110°F) halocarbon refrigerants methylene chloride and trichloroethylene have generally been used. In recent years, both methylene chloride and trichloroethylene have come under increasingly strict regulation because of their toxicity. While many plants continue to use these brines, most are searching for alternates. This study was begun in response to the needs of a plant that was replacing methylene chloride with aqueous calcium chloride. The high viscosity of the calcium chloride brine caused design and operational problems. The above-mentioned brines, as well as aqua-ammonia, polydimethylsiloxane, and d-limonene, were compared for cost, toxicity, flammability, environmental safety, and energy efficiency. The energy efficiency comparison included comparisons of heat transfer coefficient, mass flow rate, volume flow rate, frictional pressure drop, inertial pressure drop, and pumping power. The comparisons indicated that aqua-ammonia was the best choice as a replacement for methylene chloride and trichloroethylene in some temperature ranges.
Reports on the topic "Glycan code"
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George and Hawley. PR-015-10602-R01 Effects of Liquid Contamination on Ultrasonic Flow Meter Performance. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), August 2012. http://dx.doi.org/10.55274/r0010787.
Full textAbstract:
A known cause of error in in-line ultrasonic meters is the presence of liquid contamination on transducer faces. These liquids can come from unconventional or poor-quality gas supplies, but compressor oil or glycol can also enter the natural gas stream due to problems with upstream equipment. It has been suspected that liquid contamination produces a fundamental measurement error in ultrasonic pulse transit time, which leads to biases in the measured sound speed of the gas and, ultimately, flow measurement errors. Operators presently observe such differences in measured sound speeds, but often do not understand that they may be linked to the presence of liquids. Having such an understanding could lead to solutions to manage the problem, such as diagnostics to identify the cause of the liquid contamination and prompt maintenance on the equipment producing the liquids. Such diagnostics could reduce the resulting measurement errors and related lost-and-unaccounted-for (LAUF) gas amounts. This report documents a research project to characterize ultrasonic meter response to liquid contaminants produced by pipeline operations, particularly compressor oil and glycol. Tests were performed using multiple brands of ultrasonic meters and multiple types of transducers, with flow data and diagnostics collected from each meter. The data were analyzed to answer three questions: (1) how the diagnostic ability of the meter depends upon the meter and transducer designs, (2) whether ultrasonic meter diagnostics can identify liquid contaminant types, and (3) how various liquid contaminants affect measurement accuracy.
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Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, August 2013. http://dx.doi.org/10.32747/2013.7593398.bard.
Full textAbstract:
The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist biophores (ii) to develop an arsenal of amphiphilic topically active PK/PBAN antagonists with an array of different time-release profiles based on the previously developed prototype analog; (iii) to develop rationally designed non-peptide SMLs based on the antagonist biophore determined in (i) and evaluate them in cloned receptor microplate binding assays and by pheromonotropic, melanotropic and pupariation in vivo assays. (iv) to clone PK/PBAN receptors (PK/PBAN-Rs) for further understanding of receptor-ligand interactions; (v) to develop microplate binding assays for screening the above SMLs. In the course of the granting period A series of amphiphilic PK/PBAN analogs based on a linear lead antagonist from the previous BARD grant was synthesized that incorporated a diverse array of hydrophobic groups (HR-Suc-A[dF]PRLa). Others were synthesized via the attachment of polyethylene glycol (PEG) polymers. A hydrophobic, biostablePK/PBAN/DH analog DH-2Abf-K prevented the onset of the protective state of diapause in H. zea pupae [EC50=7 pmol/larva] following injection into the preceding larval stage. It effectively induces the crop pest to commit a form of ‘ecological suicide’. Evaluation of a set of amphiphilic PK analogs with a diverse array of hydrophobic groups of the formula HR-Suc-FTPRLa led to the identification of analog T-63 (HR=Decyl) that increased the extent of diapause termination by a factor of 70% when applied topically to newly emerged pupae. Another biostablePK analog PK-Oic-1 featured anti-feedant and aphicidal properties that matched the potency of some commercial aphicides. Native PK showed no significant activity. The aphicidal effects were blocked by a new PEGylated PK antagonist analog PK-dF-PEG4, suggesting that the activity is mediated by a PK/PBAN receptor and therefore indicative of a novel and selective mode-of-action. Using a novel transPro mimetic motif (dihydroimidazole; ‘Jones’) developed in previous BARD-sponsored work, the first antagonist for the diapause hormone (DH), DH-Jo, was developed and shown to block over 50% of H. zea pupal diapause termination activity of native DH. This novel antagonist development strategy may be applicable to other invertebrate and vertebrate hormones that feature a transPro in the active core. The research identifies a critical component of the antagonist biophore for this PK/PBAN receptor subtype, i.e. a trans-oriented Pro. Additional work led to the molecular cloning and functional characterization of the DH receptor from H. zea, allowing for the discovery of three other DH antagonist analogs: Drosophila ETH, a β-AA analog, and a dF analog. The receptor experiments identified an agonist (DH-2Abf-dA) with a maximal response greater than native DH. ‘Deconvolution’ of a rationally-designed nonpeptide heterocyclic combinatorial library with a cyclic bis-guanidino (BG) scaffold led to discovery of several members that elicited activity in a pupariation acceleration assay, and one that also showed activity in an H. zea diapause termination assay, eliciting a maximal response of 90%. Molecular cloning and functional characterization of a CAP2b antidiuretic receptor from the kissing bug (R. prolixus) as well as the first CAP2b and PK receptors from a tick was also achieved. Notably, the PK/PBAN-like receptor from the cattle fever tick is unique among known PK/PBAN and CAP2b receptors in that it can interact with both ligand types, providing further evidence for an evolutionary relationship between these two NP families. In the course of the granting period we also managed to clone the PK/PBAN-R of H. peltigera, to express it and the S. littoralis-R Sf-9 cells and to evaluate their interaction with a variety of PK/PBAN ligands. In addition, three functional microplate assays in a HTS format have been developed: a cell-membrane competitive ligand binding assay; a Ca flux assay and a whole cell cAMP ELISA. The Ca flux assay has been used for receptor characterization due to its extremely high sensitivity. Computer homology studies were carried out to predict both receptor’s SAR and based on this analysis 8 mutants have been generated. The bioavailability of small linear antagonistic peptides has been evaluated and was found to be highly effective as sex pheromone biosynthesis inhibitors. The activity of 11 new amphiphilic analogs has also been evaluated. Unfortunately, due to a problem with the Heliothis moth colony we were unable to select those with pheromonotropic antagonistic activity and further check their bioavailability. Six peptides exhibited some melanotropic antagonistic activity but due to the low inhibitory effect the peptides were not further tested for bioavailability in S. littoralis larvae. Despite the fact that no new antagonistic peptides were discovered in the course of this granting period the results contribute to a better understanding of the interaction of the PK/PBAN family of Nps with their receptors, provided several HT assays for screening of libraries of various origin for presence of PK/PBAN-Ragonists and antagonists and provided important practical information for the further design of new, peptide-based insecticide prototypes aimed at the disruption of key neuroendocrine physiological functions in pest insects.