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131.
Summary A 1984 field experiment tested the effect of inoculation with a vesicular-arbuscular mycorrhizal fungus on yield of onions
(Allium cepa L. cv. Balstora) grown under commercial conditions from seedlings raised in peat modules. Roots in commercial blocking compost
(M 64) could not be infected, so a modified peat, containing 50% of sterilized clay soil, was used to produce mycorrhizal
seedlings. Treatments to seedlings were: uninoculated in M64 compost (K), uninoculated in modified medium (NM) and inoculated
withGlomus mosseae in modified medium (M). There were two blocks of plots, one irrigated, one not.
At harvest the yields of marketable (>20 mm bulb diameter) onions from M seedlings were generally about twice those from NM
seedlings. On non-irrigated plots M seedlings yielded 30.3 tha−1, slightly less than did K seedlings (36.6 t ha−1). On irrigated plots M seedlings yielded 35.3 t ha−1 and K seedlings 34.9 t ha−1, but this difference was not significant.
Differences in size of bulbs at harvest were small even though rates of vegetative growth differed markedly between treatments
during crop development. Variations in final yield arose largely from differences in numbers of onions that failed to bulb
(thicknecks). Irrigation increased mean bulb weight in all treatments but also markedly increased the number of thicknecks.
Unexpectedly, the increase in thicknecks was much less in inoculated plants. This effect of mycorrhizal infection did not
seem to be related to improved phosphorus nutrition. 相似文献
132.
Roman Brunecky Markus Alahuhta Yannick J. Bomble Qi Xu John O. Baker Shi‐You Ding Michael E. Himmel Vladimir V. Lunin 《Acta Crystallographica. Section D, Structural Biology》2012,68(3):292-299
The efficient deconstruction of lignocellulosic biomass remains a significant barrier to the commercialization of biofuels. Whereas most commercial plant cell‐wall‐degrading enzyme preparations used today are derived from fungi, the cellulosomal enzyme system from Clostridium thermocellum is an equally effective catalyst, yet of considerably different structure. A key difference between fungal enzyme systems and cellulosomal enzyme systems is that cellulosomal enzyme systems utilize self‐assembled scaffolded multimodule enzymes to deconstruct biomass. Here, the possible function of the X1 modules in the complex multimodular enzyme system cellobiohydrolase A (CbhA) from C. thermocellum is explored. The crystal structures of the two X1 modules from C. thermocellum CbhA have been solved individually and together as one construct. The role that calcium may play in the stability of the X1 modules has also been investigated, as well as the possibility that they interact with each other. Furthermore, the results show that whereas the X1 modules do not seem to act as cellulose disruptors, they do aid in the thermostability of the CbhA complex, effectively allowing it to deconstruct cellulose at a higher temperature. 相似文献
133.
Markus Alahuhta Yonghua Luo Shi‐You Ding Michael E. Himmel Vladimir V. Lunin 《Acta Crystallographica. Section F, Structural Biology Communications》2011,67(5):527-530
Here, a 2.0 Å resolution X‐ray structure of Clostridium thermocellum cellulase K family 4 carbohydrate‐binding module (CelK CBM4) is reported. The resulting structure was refined to an R factor of 0.212 and an Rfree of 0.274. Structural analysis shows that this new structure is very similar to the previously solved structure of C. thermocellum CbhA CBM4. Most importantly, these data support the previously proposed notion of an extended binding pocket using a novel tryptophan‐containing loop that may be highly conserved in clostridial CBM4 proteins. 相似文献
134.
Flint J Nurizzo D Harding SE Longman E Davies GJ Gilbert HJ Bolam DN 《Journal of molecular biology》2004,337(2):417-426
The structural and thermodynamic basis for carbohydrate-protein recognition is of considerable importance. NCP-1, which is a component of the Piromyces equi cellulase/hemicellulase complex, presents a provocative model for analyzing how structural and mutational changes can influence the ligand specificity of carbohydrate-binding proteins. NCP-1 contains two "family 29" carbohydrate-binding modules designated CBM29-1 and CBM29-2, respectively, that display unusually broad specificity; the proteins interact weakly with xylan, exhibit moderate affinity for cellulose and mannan, and bind tightly to the beta-1,4-linked glucose-mannose heteropolymer glucomannan. The crystal structure of CBM29-2 in complex with cellohexaose and mannohexaose identified key residues involved in ligand recognition. By exploiting this structural information and the broad specificity of CBM29-2, we have used this protein as a template to explore the evolutionary mechanisms that can lead to significant changes in ligand specificity. Here, we report the properties of the E78R mutant of CBM29-2, which displays ligand specificity that is different from that of wild-type CBM29-2; the protein retains significant affinity for cellulose but does not bind to mannan or glucomannan. Significantly, E78R exhibits a stoichiometry of 0.5 when binding to cellohexaose, and both calorimetry and ultracentrifugation show that the mutant protein displays ligand-mediated dimerization in solution. The three-dimensional structure of E78R in complex with cellohexaose reveals the intriguing molecular basis for this "dimeric" binding mode that involves the lamination of the oligosaccharide between two CBM molecules. The 2-fold screw axis of the ligand is mirrored in the orientation of the two protein domains with adjacent sugar rings stacking against the equivalent aromatic residues in the binding site of each protein molecule of the molecular sandwich. The sandwiching of an oligosaccharide chain between two protein modules, leading to ligand-induced formation of the binding site, represents a completely novel mechanism for protein-carbohydrate recognition that may mimic that displayed by naturally dimeric protein-carbohydrate interactions. 相似文献
135.
Karkehabadi S Hansson H Kim S Piens K Mitchinson C Sandgren M 《Journal of molecular biology》2008,383(1):144-154
The glycoside hydrolase (GH) family 61 is a long-recognized, but still recondite, class of proteins, with little known about the activity, mechanism or function of its more than 70 members. The best-studied GH family 61 member, Cel61A of the filamentous fungus Hypocrea jecorina, is known to be an endoglucanase, but it is not clear if this represents the main activity or function of this family in vivo. We present here the first structure for this family, that of Cel61B from H. jecorina. The best-quality crystals were formed in the presence of nickel, and the crystal structure was solved to 1.6 Å resolution using a single-wavelength anomalous dispersion method with nickel as the source of anomalous scatter. Cel61B lacks a carbohydrate-binding module and is a single-domain protein that folds into a twisted β-sandwich. A structure-aided sequence alignment of all GH family 61 proteins identified a highly conserved group of residues on the surface of Cel61B. Within this patch of mostly polar amino acids was a site occupied by the intramolecular nickel hexacoordinately bound in the solved structure. In the Cel61B structure, there is no easily identifiable carbohydrate-binding cleft or pocket or catalytic center of the types normally seen in GHs. A structural comparison search showed that the known structure most similar to Cel61B is that of CBP21 from the Gram-negative soil bacterium Serratia marcescens, a member of the carbohydrate-binding module family 33 proteins. A polar surface patch highly conserved in that structural family has been identified in CBP21 and shown to be involved in chitin binding and in the protein's enhancement of chitinase activities. The analysis of the Cel61B structure is discussed in light of our continuing research to better understand the activities and function of GH family 61. 相似文献
136.
Jacalin (Artocarpus integrifolia agglutinin) specifically recognizes thetumor-associated T-antigenic disaccharide structure,Gal13GalNAc. Porphyrins and their derivatives are currently used asphotosensitizers in photodynamic therapy to treat malignant tumors. In thisstudy, the interaction of several free base porphyrins and their metalderivatives with jacalin is investigated by absorption and fluorescencespectroscopy. Each lectin subunit was found to bind one porphyrin moleculeand the association constants were estimated to be in the range of2.4×103M–1 to 1.3×105M–1 at room temperaturefor the interaction of different porphyrins with jacalin. These values arein the same range as those obtained for the interaction of monosaccharidesto jacalin. Both free lectin and lectin saturated with the specificsaccharide were found to bind different porphyrins with comparable bindingstrength indicating that porphyrin binding takes place at a site differentfrom the sugar binding site. Further, both anionic and cationic porphyrinswere found to interact with the lectin with comparable affinity, clearlyindicating that the charge on the porphyrin does not play any role in thebinding process and that most likely the interaction is mediated byhydrophobic forces. These results suggest that jacalin and other lectins maypotentially be useful for targeted delivery of porphyrins to tumor tissuesin photodynamic therapy. 相似文献
137.
138.
Advances in high throughput 'omic technologies are starting to provide unprecedented insights into how components of biological systems are organized and interact. Key to exploiting these datasets is the definition of the components that comprise the system of interest. Although a variety of knowledge bases exist that capture such information, a major challenge is determining how these resources may be best utilized. Here we present a systematic curation strategy to define a systems-level view of the human extracellular matrix (ECM)--a three-dimensional meshwork of proteins and polysaccharides that impart structure and mechanical stability to tissues. Employing our curation strategy we define a set of 357 proteins that represent core components of the ECM, together with an additional 524 genes that mediate related functional roles, and construct a map of their physical interactions. Topological properties help identify modules of functionally related proteins, including those involved in cell adhesion, bone formation and blood clotting. Because of its major role in cell adhesion, proliferation and morphogenesis, defects in the ECM have been implicated in cancer, atherosclerosis, asthma, fibrosis, and arthritis. We use MeSH annotations to identify modules enriched for specific disease terms that aid to strengthen existing as well as predict novel gene-disease associations. Mapping expression and conservation data onto the network reveal modules evolved in parallel to convey tissue-specific functionality on otherwise broadly expressed units. In addition to demonstrating an effective workflow for defining biological systems, this study crystallizes our current knowledge surrounding the organization of the ECM. 相似文献
139.
Sacha Haywood 《Biological reviews of the Cambridge Philosophical Society》2013,88(4):895-911
Why different bird species lay different numbers of eggs is a question that has long been associated with factors external to the organism, that is, factors which operate on inherited variation in clutch size through the action of natural selection. Yet, while external factors are important, the extent of what is evolutionarily possible rests with the mechanisms developed by birds for clutch‐size control. Hitherto neglected, these mechanisms generate factors internal to the organism that are central to the origin of evolutionary change. They are related to the fact that a species‐specific range of clutch size arises from the differential survival of pre‐ovulatory follicles undergoing growth when the signal causing egg laying to end reaches the ovary. Herein, I examine three internal factors that, together with external factors, could impact the evolution of avian clutch size. Each factor acts by changing either the number of pre‐ovulatory follicles present in the ovary at the time of follicular disruption or the timing of this event. These changes to clutch size can be explained by the concept of heterochrony. In light of this, the role of phenotypic plasticity and genes determining clutch size is discussed. Finally, to account for the origin of evolutionary change in clutch size, I detail an hypothesis involving a process similar to Waddington's theory of genetic assimilation. 相似文献
140.
Ryuji Matsumura Jotaro Hirakawa Kaori Sato Toshiaki Ikeda Motoe Nagai Minoru Fukuda Yasuyuki Imai Hiroto Kawashima 《The Journal of biological chemistry》2015,290(24):15313-15326
Sialyl Lewis X (sLex) antigen functions as a common carbohydrate determinant recognized by all three members of the selectin family. However, its expression and function in mice remain undefined due to the poor reactivity of conventional anti-sLex monoclonal antibodies (mAbs) with mouse tissues. Here, we developed novel anti-sLex mAbs, termed F1 and F2, which react well with both human and mouse sLex, by immunizing fucosyltransferase (FucT)-IV and FucT-VII doubly deficient mice with 6-sulfo-sLex-expressing cells transiently transfected with an expression vector encoding CMP-N-acetylneuraminic acid hydroxylase. F1 and F2 specifically bound both the N-acetyl and the N-glycolyl forms of sLex as well as 6-sulfo-sLex, a major ligand for L-selectin expressed in high endothelial venules, and efficiently blocked physiological lymphocyte homing to lymph nodes in mice. Importantly, both of the mAbs inhibited contact hypersensitivity responses not only when administered in the L-selectin-dependent sensitization phase but also when administered in the elicitation phase in mice. When administered in the latter phase, F1 and F2 efficiently blocked rolling of mouse leukocytes along blood vessels expressing P- and E-selectin in the auricular skin in vivo. Consistent with these findings, the mAbs blocked P- and E-selectin-dependent leukocyte rolling in a flow chamber assay. Taken together, these results indicate that novel anti-sLex mAbs reactive with both human and mouse tissues, with the blocking ability against leukocyte trafficking mediated by all three selectins, have been established. These mAbs should be useful in determining the role of sLex antigen under physiological and pathological conditions. 相似文献