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51.
Jarrod A Chapman Martin Mascher Ayd?n Bulu? Kerrie Barry Evangelos Georganas Adam Session Veronika Strnadova Jerry Jenkins Sunish Sehgal Leonid Oliker Jeremy Schmutz Katherine A Yelick Uwe Scholz Robbie Waugh Jesse A Poland Gary J Muehlbauer Nils Stein Daniel S Rokhsar 《Genome biology》2015,16(1)
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users. 相似文献52.
Michael MichailidesGerasimos Christou Christos S. AkratosAthanasia G. Tekerlekopoulou Dimitrios V. Vayenas 《International biodeterioration & biodegradation》2011,65(3):560-564
The composting of olive leaves and olive pomace from a three-phase olive mill was tested as a method for solid waste reuse. The process was carried out using a compost windrow and mixing olive leaves and pomace at a ratio of 1:2. Compost was retained in the windrow for 60 days during which thermophilic temperatures developed for the first 40 days. The compost was then placed into a closed area to mature for another 60 days. The final product proved to be high quality amendment with C/N 27.1 and high nutrient concentrations (N, 1.79%; P, 0.17%; K, 4.97%; Na, 2.8%). Mature compost presented the highest germination index (198%) reported to date, as the germination index in the majority of previous studies is under 80%. Furthermore, tests revealed that addition of 31.5 tons of compost per ha, could increase lettuce yield by 145%. 相似文献
53.
Nikolaos P Polyzos Human M Fatemi Apostolos Zavos Grigoris Grimbizis Dimitra Kyrou Juan-Garcia Velasco Paul Devroey Basil Tarlatzis Evangelos G Papanikolaou 《Reproductive biology and endocrinology : RB&E》2011,9(1):1-5
Background
Serum anti-Mullerian hormone (AMH) is currently considered the best marker of ovarian reserve and of ovarian responsiveness to gonadotropins in in-vitro fertilization (IVF). AMH assay, however, is not available in all IVF Units and is quite expensive, a reason that limits its use in developing countries. The aim of this study is to assess whether the "ovarian sensitivity index" precisely reflects AMH so that this index may be used as a surrogate for AMH in prediction of ovarian response during an IVF cycle.Methods
AMH serum levels were measured in 61 patients undergoing IVF with a "long" stimulation protocol including the GnRH agonist buserelin and recombinant follicle-stimulating hormone (rFSH). Patients were divided into four subgroups according to the percentile of serum AMH and their ovarian stimulation was prospectively followed. Ovarian sensitivity index (OSI) was calculated dividing the total administered FSH dose by the number of retrieved oocytes.Results
AMH and OSI show a highly significant negative correlation (r = -0.67; p = 0.0001) that is stronger than the one between AMH and the total number of retrieved oocytes and than the one between AMH and the total FSH dose.Conclusions
OSI reflects quite satisfactory the AMH level and may be proposed as a surrogate of AMH assay in predicting ovarian responsiveness to FSH in IVF. Being very easy to calculate and costless, its use could be proposed where AMH measurement is not available or in developing countries where limiting costs is of primary importance. 相似文献54.
Palmfeldt J Vang S Stenbroen V Pavlou E Baycheva M Buchal G Monavari AA Augoustides-Savvopoulou P Mandel H Gregersen N 《Journal of proteome research》2011,10(5):2389-2396
Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and revealed seven differentially regulated proteins compared with healthy controls. Two proteins involved in pathways of detoxification and oxidative/reductive stress were underrepresented in EE patient samples: mitochondrial superoxide dismutase (SOD2) and aldehyde dehydrogenase X (ALDH1B). Sulfide:quinone oxidoreductase (SQRDL), which takes part in the same sulfide pathway as ETHE1, was also underrepresented in EE patients. The other differentially regulated proteins were apoptosis inducing factor (AIFM1), lactate dehydrogenase (LDHB), chloride intracellular channel (CLIC4) and dimethylarginine dimethylaminohydrolase 1 (DDAH1). These proteins have been reported to be involved in encephalopathy, energy metabolism, ion transport, and nitric oxide regulation, respectively. Interestingly, oxidoreductase activity was overrepresented among the regulated proteins indicating that redox perturbation plays an important role in the molecular mechanism of EE. This observation may explain the wide range of symptoms associated with the disease, and highlights the potency of the novel gaseous mediator sulfide. 相似文献
55.
56.
Plants and microbes produce multiple carotenoid pigments with important nutritional roles in animals. By unraveling the basis of carotenoid biosynthesis it has become possible to modulate the key metabolic steps in plants and thus increase the nutritional value of staple crops, such as rice (Oryza sativa), maize (Zea mays) and potato (Solanum tuberosum). Multigene engineering has been used to modify three different metabolic pathways simultaneously, producing maize seeds with higher levels of carotenoids, folate and ascorbate. This strategy may allow the development of nutritionally enhanced staples providing adequate amounts of several unrelated nutrients. By focusing on different steps in the carotenoid biosynthesis pathway, it is also possible to generate plants with enhanced levels of several nutritionally-beneficial carotenoid molecules simultaneously. 相似文献
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58.
The active sites of feruloyl esterases from mesophilic and thermophilic sources were probed using methyl esters of phenylalkanoic acids. Only 13 out of 26 substrates tested were significant substrates for all the enzymes. Lengthening or shortening the aliphatic side chain while maintaining the same aromatic substitutions completely abolished activity for both enzymes, which demonstrates the importance of the correct distance between the aromatic group and the ester bond. Maintaining the phenylpropanoate structure but altering the substitutions of the aromatic ring demonstrated that the type-A esterase from the mesophilic fungus Fusarium oxysporum (FoFaeA) showed a preference for methoxylated substrates, in contrast to the type-B esterase from the same source (FoFaeB) and the thermophilic type-B (StFaeB) and type-C (StFaeC) from Sporotrichum thermophile, which preferred hydroxylated substrates. All four esterases hydrolyzed short chain aliphatic acid (C2-C4) esters of p-nitrophenol, but not the C12 ester of laurate. All the feruloyl esterases were able to release ferulic acid from the plant cell wall material in conjunction with a xylanase, but only the type-A esterase FoFaeA was effective in releasing the 5,5' form of diferulic acid. The thermophilic type-B esterase had a lower catalytic efficiency than its mesophilic counterpart, but released more ferulic acid from plant cell walls. 相似文献
59.
60.
Efstathopoulos N Bathrellos E Giamarellos-Bourboulis EJ Lazarettos J Papalois A Grecka P Nikolaou V 《Prostaglandins, leukotrienes, and essential fatty acids》2005,72(5):357-362
Immunonutrition with diets enriched in polyunsaturated fatty acids (PUFAs) are becoming mandatory for multiple trauma patients. Solutions containing single n-6 PUFAs were administered intravenously in an experimental model of trauma. Thirty-five rabbits were studied; 13 controls; 10 administered gamma-linolenic acid (GLA) 30 min after fracture of the right femor; and 12 arachidonic acid (AA). Systolic, diastolic and mean arterial pressures and heart rate were recorded; serum levels of tumor necrosis factor-alpha (TNFalpha), malondialdehyde (MDA) and nitrate were estimated before and after therapy. Mean survival of controls, of animals treated with GLA and of animals treated with AA was 0.80, 1.41 and 3.60 days, respectively. Administration of PUFAs induced higher levels of blood pressure; that of AA decreased serum TNFalpha and tissue bacterial load compared to controls. Intravenous administration of n-6 PUFAs conferred hemodynamic stability and increased survival in a model of trauma rendering further research mandatory. 相似文献