单糖组成分析方法的研究进展

单糖组成分析是对多糖以及糖蛋白中多种单糖组分的定性、定量分析。该分析方法可被用来分析多糖结构以及在多糖类药物研发或生产中起到质量控制的作用。就近几年来多糖以及糖蛋白中的单糖组成、分析方法进行了综述,包括对样品的水解方法以及不同色谱法和电泳法利弊的分析。     

Transgenic plants as factories for biopharmaceuticals

Plants have considerable potential for the production of biopharmaceutical proteins and peptides because they are easily transformed and provide a cheap source of protein. Several biotechnology companies are now actively developing, field testing, and patenting plant expression systems, while clinical trials are proceeding on the first biopharmaceuticals derived from them. One transgenic plant-derived biopharmaceutical, hirudin, is now being commercially produced in Canada for the first time. Product purification is potentially an expensive process, and various methods are currently being developed to overcome this problem, including oleosin-fusion technology, which allows extraction with oil bodies. In some cases, delivery of a biopharmaceutical product by direct ingestion of the modified plant potentially removes the need for purification. Such biopharmaceuticals and edible vaccines can be stored and distributed as seeds, tubers, or fruits, making immunization programs in developing countries cheaper and potentially easier to administer. Some of the most expensive biopharmaceuticals of restricted availability, such as glucocerebrosidase, could become much cheaper and more plentiful through production in transgenic plants.     

The monosaccharide composition and sequence of the carbohydrate moiety of human serum low density lipoproteins.

Human serum low density lipoprotein (d = 1.027-1.045) was delipidated with organic solvents and the apoprotein digested with thermolysin. The digest was fractionated by gel filtration and DEAE-cellulose chromatography. Two glycopeptides were obtained. One of the glycopeptides (GP-I) contained 2 residues of N-acetylglucosamine and 6 residues of mannose per mole of the glycopeptide, while the other contained 2 sialic acid, 5 mannose, 2 galactose, and 3 N-acetylglucosamine residues per mole of glycopeptide. The results of sequential enzymatic digestion with purified glycosidases, periodate oxidation, and partial acid hydrolysis lead us to propose the following sturctures for the two glycopeptides: (see article). These glycopeptides represent at least 50% of the carbohydrate moiety of LDL.     

蛹虫草多糖单糖组成的方法学研究

建立1-苯基-3-甲基-5-吡唑啉酮（PMP）柱前衍生HPLC法测定虫草多糖中单糖组分的通用性方法。本试验以9种单糖标准品为研究对象,通过单因素和响应面试验对衍生反应的温度、时间、pH和PMP用量进行了优化,并运用改进的方法测定了3批不同产地的蛹虫草多糖的单糖组分。结果表明：PMP与单糖摩尔比12:1、温度80℃、时间60min、 pH 8.2为最佳衍生条件,方法学验证证明该方法稳定、可靠、重现性良好。3批蛹虫草多糖中均稳定检测到甘露糖、半乳糖醛酸、葡萄糖、半乳糖和阿拉伯糖,摩尔比约为3.8:1.6:5.4:5.8:1,研究结果可为改善虫草多糖成分分析和构效关系研究提供支持。     

InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study

InterPro was developed as a new integrated documentation resource for protein families, domains and functional sites to rationalize the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects and has applications in computational functional classification of newly determined sequences lacking biochemical characterization and in comparative genome analysis. InterPro contains over 3500 entries, with more than 1000000 hits in SWISS-PROT and TrEMBL. The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. InterPro was used for whole proteome analysis of the pathogenic microorganism, Mycobacterium tuberculosis, and comparison with the predicted protein coding sequences of the complete genomes of Bacillus subtilis and Escherichia coli. 64.8% of the M. tuberculosis proteins in the proteome matched InterPro entries, and these could be classified according to function. The comparison with B. subtilis and E. coli provided information on the most common protein families and domains, and the most highly represented families in each organism. InterPro thus provides a useful tool for global views of whole proteomes and their compositions.     

A comparative analysis of nested subset patterns of species composition

We present a broad comparative assessment of nested subsets in species composition among ecological communities. We assembled presence-absence data from a broad range of taxa, geographic regions, and spatial scales; and subjected this collection of datasets to common analyses, including a variety of metrics for measuring nestedness and null hypotheses against which to evaluate them. Here we identify ecological patterns in the prevalence and strength of nested subset structure, and assess differences and biases among the available methodologies. In all, we compiled 279 presence-absence matrices, of which 163 do not overlap in their coverage of species and sites. The survey includes studies on vertebrates, arthropods, mollusks, plants, and other taxa; from north temperate, tropical, and south temperate latitudes. Our results were as follows. Statistically significant nestedness was common. Assemblages from landbridge archipelagos were strongly nested, and immigration experiments were least nested. This adds further empirical support to the hypothesis that extinction plays a major role in producing nested structure. Nestedness was positively correlated with the ratio of the areas of the largest and smallest sites, suggesting that the range in area of sites affects nestedness. Taxonomic differences in nestedness were weak. Higher taxonomic levels showed stronger nesting than their constituent lower taxa. We observed no effect of distance of isolation on nestedness; nor any effects of latitude. With regard to methodology, the metrics Nc and Ut yielded similar results, although Nc proved slightly more flexible in use, and deals differently with tied sites. Similarities also exist in the behavior of N0 (“N”) and Up, and between N1 and Ua. Standardized nestedness metrics were mostly insensitive to matrix size, and were useful in comparative analyses among presence-absence matrices. Most metrics were affected by the proportion of presences in the matrix. All analyses of nestedness, therefore, should test for bias due to matrix fill. We suggest that the factors controlling nested subset structure can be thought of as four filters that species pass to occur at a site: a sampling filter, a distance filter, a habitat filter, and an area filter – and three constraints on community homogeneity: evolutionary history, recent history, and spatial variation in the environment. The scale of examination can also have important effects on the degree of nestedness observed. Received: 13 September 1996 / Accepted: 16 September 1997     

Soybeans as bioreactors for biopharmaceuticals and industrial proteins

Plants present various advantages for the production of biomolecules, including low risk of contamination with prions, viruses and other pathogens, scalability, low production costs, and available agronomical systems. Plants are also versatile vehicles for the production of recombinant molecules because they allow protein expression in various organs, such as tubers and seeds, which naturally accumulate large amounts of protein. Among crop plants, soybean is an excellent protein producer. Soybean plants are also a good source of abundant and cheap biomass and can be cultivated under controlled greenhouse conditions. Under containment, the plant cycle can be manipulated and the final seed yield can be maximized for large-scale protein production within a small and controlled area. Exploitation of specific regulatory sequences capable of directing and accumulating recombinant proteins in protein storage vacuoles in soybean seeds, associated with recently developed biological research tools and purification systems, has great potential to accelerate preliminary characterization of plant-derived biopharmaceuticals and industrial macromolecules. This is an important step in the development of genetically engineered products that are inexpensive and safe for medicinal, food and other uses.     

Hydrogen breath test as a simple noninvasive method for evaluation of carbohydrate malabsorption during exercise

The aim of this study was to examine hydrogen (H₂) production with the hydrogen breath test (HBT) after ingesting primarily digestible carbohydrate (CHO) during 3 h of 75% maximal oxygen consumption exercise. This was done to indicate CHO overflow in the colon which may occur when gastric emptying, intestinal transit and CHO absorption are not matched and CHO accumulates in the colon where it is subject to bacterial degradation. Further, this study was designed to assess breath H₂ production as a function of the type of CHO ingested and the type of exercise. A group of 32 male triathletes performed three exercise trials at 1-week intervals with either a semi-solid (S) intake, an equal energy fluid intake (F) or a fluid placebo (P). Each trial consisted of cycling (sessions 1 and 3) and running (sessions 2 and 4). The mixed-expired H₂ concentrations in the resting and recovery periods (5 min after each session) did not change significantly in. time and did not differ among intakes. There were also no significant differences in H₂ concentrations between resting and recovery conditions. During exercise, H₂ concentrations decreased three to six-fold in comparison to resting and recovery levels and differed among intakes (ANOVA;P < 0.05). The H₂ on concentrations were almost continuously lower with P than with F and S. The H₂ concentrations were significantly higher during running than during cycling. During exercise, we found that CHO overflow could be compared among intakes and between exercise types by using the HBT, provided the influence of other factors on H₂ excretion — ventilation and intestinal blood flow — was similar for each condition.     

A simple and rapid preparation of alditol acetates for monosaccharide analysis

A simple and rapid method is described for the preparation of alditol acetates from monosaccharides. It can be performed in a single tube without transfers or evaporations. Monosaccharides are reduced with sodium borohydride in dimethyl sulphoxide and the resulting alditols acetylated using 1-methylimidazole as the catalyst. Removal of borate is unnecessary and acetylation is complete in 10 min at room temperature. Monosaccharides are quantitatively reduced and acetylated by this procedure. The alditol acetates are completely separated by glass-capillary, gas-liquid chromatography on Silar 10C. The method has been applied to the analysis of monosaccharides in acid hydrolysates of a plant cell-wall.     

Potential use of the monosaccharide composition of bacteria for their identification

The monosaccharide composition of cell hydrolysates can be used as a criterion for the chemical differentiation of gram-positive bacteria. The monosaccharide composition of six bacterial species belonging to the genus Bacillus has been determined using gas chromatography, mass spectrometry and computers. The qualitative composition was similar, glucose, galactose, ribose and glucosamine being the main components in all of the species. Some Bacillus species differed in their minor components. Although the monosaccharide composition appeared to be homogeneous, bacteria can be identified in terms of their carbohydrate profile using computers. To this end, the monosaccharide composition of bacterial cells is represented as a two-dimensional data file including the qualitative composition of components and the quantity of each component.     

A comparative test of a theory for the evolution of anisogamy

Why are sperm small and eggs large? The dominant explanation for the evolution of gamete size dimorphism envisages two opposing selection pressures acting on gamete size: small gametes are favoured because many can be produced, whereas large gametes contribute to a large zygote with consequently increased survival chances. This model predicts disruptive selection on gamete size (i.e. selection for anisogamy) if increases in zygote size confer disproportional increases in fitness (at least over part of its size range). It therefore predicts that increases in adult size should be accompanied by stronger selection for anisogamy. Using data from the green algal order Volvocales, we provide the first phylogenetically controlled test of the model''s predictions using a published phylogeny and a new phylogeny derived by a different method. The predictions that larger organisms should (i) have a greater degree of gamete dimorphism and (ii) have larger eggs are broadly upheld. However, the results are highly sensitive to the phylogeny and the mode of analysis used.     

Evaluation of exogenous siRNA addition as a metabolic engineering tool for modifying biopharmaceuticals

Traditional metabolic engineering approaches, including homologous recombination, zinc‐finger nucleases, and short hairpin RNA, have previously been used to generate biologics with specific characteristics that improve efficacy, potency, and safety. An alternative approach is to exogenously add soluble small interfering RNA (siRNA) duplexes, formulated with a cationic lipid, directly to cells grown in shake flasks or bioreactors. This approach has the following potential advantages: no cell line development required, ability to tailor mRNA silencing by adjusting siRNA concentration, simultaneous silencing of multiple target genes, and potential temporal control of down regulation of target gene expression. In this study, we demonstrate proof of concept of the siRNA feeding approach as a metabolic engineering tool in the context of increasing monoclonal antibody (MAb) afucosylation. First, potent siRNA duplexes targeting fut8 and gmds were dosed into shake flasks with cells that express an anti‐CD20 MAb. Dose response studies demonstrated the ability to titrate the silencing effect. Furthermore, siRNA addition resulted in no deleterious effects on cell growth, final protein titer, or specific productivity. In bioreactors, antibodies produced by cells following siRNA treatment exhibited improved functional characteristics compared to antibodies from untreated cells, including increased levels of afucosylation (63%), a 17‐fold improvement in FCgRIIIa binding, and an increase in specific cell lysis by up to 30%, as determined in an Antibody‐Dependent Cellular Cytoxicity (ADCC) assay. In addition, standard purification procedures effectively cleared the exogenously added siRNA and transfection agent. Moreover, no differences were observed when other key product quality structural attributes were compared to untreated controls. These results establish that exogenous addition of siRNA represents a potentially novel metabolic engineering tool to improve biopharmaceutical function and quality that can complement existing metabolic engineering methods. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29: 415–424, 2013     

A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis

Background

Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.

Methodology/Principal Findings

The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO₂ fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a β-1,3-glucan) outside of the plastids. We identified various β-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes.

Conclusions/Significance

Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.     

灵芝不同菌株胞外多糖的单糖组成和抗氧化活性分析

灵芝多糖是药用真菌灵芝的主要活性成分之一。早期研究发现不同灵芝子实体多糖的单糖组成和活性存在差异,但不同灵芝菌株胞外多糖的单糖组成和活性是否有区别仍不清楚。本研究通过液体发酵获得灵芝菌株5.26和5.616的胞外多糖,使用DEAE-cellulose和Sephadex G-200柱色谱分离纯化得到了两种多糖(5.26-2-1和5.616-2-1),并对5.26-2-1,5.616-2-1的单糖组成和抗氧化活性进行了分析。结果表明,5.26-2-1主要由甘露糖、半乳糖醛酸、半乳糖和葡萄糖组成,而5.616-2-1主要由甘露糖、半乳糖和葡萄糖组成。5.26-2-1中葡萄糖的摩尔百分比为63.97%,显著高于5.616-2-1(29.3%),但半乳糖的摩尔百分比为9.34%,显著低于5.616-2-1 (42.78%)。当多糖质量浓度为2 mg/mL时,5.26-2-1的Fe²⁺螯合能力、对1,1-二苯基-2-三硝基苯肼(DPPH)和羟自由基(·OH)的最大清除率分别为71.9%、71.3%和60.8%,显著高于5.616-2-1的值(63.5%、60.4%和51.8%...     

A comparative study on ceramide composition of cetacean brain gangliosides.

1. Ceramide composition and N-glycolylneuraminic acid content of gangliosides from gray and white matters and myelin of cerebrum and cerebellum were analyzed in eight species belonging to the suborder Odontoceti and two species to Mystacoceti. 2. The most characteristic feature was high contents of C20:0 (10-40%) and C24 species (5-40%). 3. Content of hydroxy fatty acid of C24 species was higher in cerebellum (5-20%) than cerebrum (0-3%). 4. Major component of long-chain base was dC18:1 (70-90%). 5. N-glycolylneuraminic acid was found in sperm whale, Dall's porpoise and killer whale (0.1-1.7%).     

Cyclosophoraose as a catalytic carbohydrate for methanolysis

A novel catalytic methanolysis can be induced by a natural cyclooligosaccharide, a cyclosophoraose (cyclic-(1-->2)-beta-D-glucan, Cys), which is a member of a family of unbranched cyclooligosaccharides produced as intra- or extraoligosaccharides by soil microorganisms of the genus, Rhizobium. Cys catalyzed the methanolysis for 5(4H)-oxazolones and various phospholipids. Cys enhanced the methanolysis reaction about 9200-fold for a benzylidene oxazolone or 250-fold for dipalmitoylphosphatidylcholine comparing with control. In this study, we describe that natural cyclosophoraoses isolated from the Rhizobium species function as catalytic carbohydrates for the methanolysis.     

Methylation analysis in glycoprotein chemistry: a comparative study of the carbohydrate structures of three hormone-binding glycoproteins from human serum

The structures of the carbohydrate moieties of three hormone-binding glycoproteins from human serum, namely, thyroxine-binding globulin, transcortin, and sex hormone-binding globulin, have been characterised using quantitative g.l.c. of the methylated monosaccharide derivatives obtained after methanolysis of the methylated glycoproteins.     

A latex agglutination test for the detection of Mycoplasma pneumoniae in respiratory exudates: a comparative study with a commercially available DNA-probe test.

We prepared polyclonal antibody specific to Mycoplasma pneumoniae. Using this antibody, we developed a latex agglutination test (LAT) for detecting the organism in respiratory exudates as rapid diagnosis of M. pneumoniae infection. Further, LAT was compared with DNA-probe test (DP) which was the only commercially available test for the rapid detection of the organism. In LAT, both M. pneumoniae and M. genitalium give positive agglutination, but the titer of M. genitalium was significantly lower than that of M. pneumoniae. The detection limit of LAT was 2 x 10(5) CFU/ml and that of DP was 5 x 10(4) CFU/ml in vitro. It was considered that target molecules in LAT were accumulated in the pharyngeal portion of the patients, because of their long half-life at 37 C. However, ribosomal RNA which was target molecule in DP was destroyed at 37 C much sooner, and the accumulation could not be expected. Actually, positive rate in LAT was higher than that in DP among clinical specimens in which M. pneumoniae was detected by culture method. The procedure of LAT is much easier and more rapid than that of DP in which radioactive isotope is required. LAT could be the choice of test for rapid diagnosis of M. pneumoniae infection.