The mechanism of solvent effect on the positional selectivity of Candida antarctica lipase B during 1,3-diolein synthesis by esterification

We investigated the influence of solvent on the positional selectivity of Novozym 435 which was the immobilized Candida antarctica lipase B (CALB) during the esterification of oleic acid with glycerol for 1,3-diolein preparation previously. Herein, molecular modeling was used to elucidate the underlying mechanism of the solvent effect on the positional selectivity of the enzyme. The results showed that the binding energy of sn-1 hydroxyl of glycerol molecular with CALB became higher, and the binding energy of sn-2 hydroxyl of glycerol molecular with CALB became lower along with the increase of the solvent log P. It was demonstrated that, increasing log P of the solvent, the enzyme selectivity to sn-1 hydroxyl of glycerol molecular grew weaker, and the selectivity to sn-2 hydroxyl of glycerol molecular grew stronger.     

Effect of pH on the molecular weight of poly-3-hydroxybutyric acid produced by Alcaligenes sp.

Summary The molecular weight of a polymer is an important parameter characterizing the physical properties of the polymer. The effect of pH on the molecular weight of poly-3-hydroxybutyric acid (PHB) produced by Alcaligenes sp. K-912 were investigated. PHB having higher molecular weight was obtained when cultivated under high pH conditions compared to the results cultivated under low pH conditions. The polydispersity index was almost the same as 1.6. But the cell mass was decreased as the pH became higher. The molecular weight was mainly determined in the early cultivation period and molecular weight difference could be explained by calculating the number of polymer chains.     

Fluorescence spectroscopic analysis on interaction of fleroxacin with pepsin

The interaction between fleroxacin (FLX) and pepsin was investigated by spectrofluorimetry. The effects of FLX on pepsin showed that the microenvironment of tryptophan residues and molecular conformation of pepsin were changed based on fluorescence quenching and synchronous fluorescence spectroscopy in combination with three‐dimensional fluorescence spectroscopy. Static quenching was suggested and it was proved that the fluorescence quenching of pepsin by FLX was related to the formation of a new complex and a non‐radiation energy transfer. The quenching constants K_SV, binding constants K and binding sites n were calculated at different temperatures. The molecular interaction distance (r = 6.71) and energy transfer efficiency (E = 0.216) between pepsin and FLX were obtained according to the Forster mechanism of non‐radiation energy transfer. Hydrophobic and electrostatic interaction played a major role in FLX–pepsin association. In addition, the hydrophobic interaction and binding free energy were further tested by molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.     

花器官发育的分子机制研究进展

经典的ABC模型成功地解释了模式植物拟南芥和金鱼草因同源异型基因突变而引起的植物花器官的变异。随后,大量花器官特征基因和新突变体的研究不断完善和发展了ABC模型。该文综述了近年来花器官发育分子模型及花器官同源基因的调控机理等方面的最新研究成果,并对未来的研究方向进行了展望,以期为深入了解花发育的分子机理和遗传机制奠定基础。     

Physicochemical Studies on Sulfated Polysaccharides Extracted from Seaweeds at Various Temperatures

Sulfated polysaccharides (SPS) were extracted from three species of seaweeds of Ulvacea (Ulva pertusa, Ulva conglobata and Entromorpha prolifera) for 4 hr at various temperatures and their physicochemical properties were studied using viscometric and equilibrium sedimentation measurements in order to determine the optimum extracting condition.

Sulfated polysaccharides extracted at various temperatures from the seaweed of U. pertusa had the same physicochemical properties, while the larger molecular components of SPS was not extracted from U. conglobata and E. prolifera, at the low temperature of 30~40°C. This was confirmed by analyses of their viscosity and molecular weight and by gel filtration chromatography, in which each SPS showed two or three peaks.

The larger molecular component of SPS could be extracted at the high temperature of 80~90°C in the thermostable form.     

Studies on iron uptake and its effect on the outer membrane proteins ofPseudomonas stuzeri RC-7

Pseudomonas stutzeri RC-7, grown under iron-deficient conditions, produced catecholtype siderophore. Iron uptake was enhanced by the presence of its own siderophore. The production of iron-binding protein with molecular weight of 55,000 in the outer membrane was found to be suppressed in iron-supplemented conditions. In contrast, another protein with molecular weight of 42,000 was induced under the same conditions.     

基于转录组的冬虫夏草菌微循环产孢研究

为研究冬虫夏草菌（Ophiocordyceps sinensis）微循环产孢过程中的分子机理,采用高通量测序技术,对微循环产孢前后冬虫夏草菌的转录组进行研究。筛选获得差异表达基因6 902个。Gene Ontology（GO）功能聚类分析表明,差异表达基因主要参与分子功能、胞内运输、核糖核蛋白复合体等生物学通路。京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG)功能富集分析结果表明,差异表达基因参与了核糖体、嘧啶代谢、蛋白酶体、嘌呤代谢、甘氨酸代谢等过程。Mmc、Mcb、MaH1、MaPP5、MaAGA、Pyk等候选基因不同程度的参与了冬虫夏草菌微循环产孢过程,其中Mcb家族基因可能起到关键作用。通过qRT PCR验证差异表达基因,定量结果与转录组测序结果一致。本研究为进一步揭示冬虫夏草菌微循环产孢分子机制以及关键基因的调控提供了重要信息。     

Effects of hyaluronan treatment on lipopolysaccharide-challenged fibroblast-like synovial cells

Numerous investigations have reported the efficacy of exogenous hyaluronan (HA) in modulating acute and chronic inflammation. The current study was performed to determine the in vitro effects of lower and higher molecular weight HA on lipopolysaccharide (LPS)-challenged fibroblast-like synovial cells. Normal synovial fibroblasts were cultured in triplicate to one of four groups: group 1, unchallenged; group 2, LPS-challenged (20 ng/ml); group 3, LPS-challenged following preteatment and sustained treatment with lower molecular weight HA; and group 4, LPS-challenged following pretreatment and sustained treatment with higher molecular weight HA. The response to LPS challenge and the influence of HA were compared among the four groups using cellular morphology scoring, cell number, cell viability, prostaglandin E₂ (PGE₂) production, IL-6 production, matrix metalloproteinase 3 (MMP3) production, and gene expression microarray analysis. As expected, our results demonstrated that LPS challenge induced a loss of characteristic fibroblast-like synovial cell culture morphology (P < 0.05), decreased the cell number (P < 0.05), increased PGE₂ production 1,000-fold (P < 0.05), increased IL-6 production 15-fold (P < 0.05), increased MMP3 production threefold (P < 0.05), and generated a profile of gene expression changes typical of LPS (P < 0.005). Importantly, LPS exposure at this concentration did not alter the cell viability. Higher molecular weight HA decreased the morphologic change (P < 0.05) associated with LPS exposure. Both lower and higher molecular weight HA significantly altered a similar set of 21 probe sets (P < 0.005), which represented decreased expression of inflammatory genes (PGE₂, IL-6) and catabolic genes (MMP3) and represented increased expression of anti-inflammatory and anabolic genes. The molecular weight of the HA product did not affect the cell number, the cell viability or the PGE₂, IL-6, or MMP3 production. Taken together, the anti-inflammatory and anticatabolic gene expression profiles of fibroblast-like synovial cells treated with HA and subsequently challenged with LPS support the pharmacologic benefits of treatment with HA regardless of molecular weight. The higher molecular weight HA product provided a cellular protective effect not seen with the lower molecular weight HA product.     

Molecular histoproteomy by MALDI mass spectrometry imaging to uncover markers of the impact of Nosema on Apis mellifera

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful technology used to investigate the spatio-temporal distribution of a huge number of molecules throughout a body/tissue section. In this paper, we report the use of MALDI IMS to follow the molecular impact of an experimental infection of Apis mellifera with the microsporidia Nosema ceranae. We performed representative molecular mass fingerprints of selected tissues obtained by dissection. This was followed by MALDI IMS workflows optimization including specimen embedding and positioning as well as washing and matrix application. We recorded the local distribution of peptides/proteins within different tissues from experimentally infected versus non infected honeybees. As expected, a distinction in these molecular profiles between the two conditions was recorded from different anatomical sections of the gut tissue. More importantly, we observed differences in the molecular profiles in the brain, thoracic ganglia, hypopharyngeal glands, and hemolymph. We introduced MALDI IMS as an effective approach to monitor the impact of N. ceranae infection on A. mellifera. This opens perspectives for the discovery of molecular changes in peptides/proteins markers that could contribute to a better understanding of the impact of stressors and toxicity on different tissues of a bee in a single experiment.     

Genetic characterization of apospory in tetraploid Paspalum notatum based on the identification of linked molecular markers

Tetraploid Paspalum notatum (bahiagrass) is a valuable forage grass with aposporous apomictic reproduction. In a previous study, we showed that apospory in bahiagrass is under the control of a single dominant gene with a distorted segregation ratio. The objective of this work was to identify molecular markers linked to apospory in tetraploid P. notatum and establish a preliminary syntenic relationship with the genomic region associated with apospory in P. simplex. A F₁ population of 290 individuals, segregating for apospory, was generated after crossing a completely sexual plant (Q4188) with a natural aposporous apomictic plant (Q4117). The whole progeny was classified as sexual or aposporous by embryo sacs analysis. A bulked segregant analysis was carried out to identify molecular markers co-segregating with apospory. Four hundred RAPD primers, 30 AFLP primers combinations and 85 RFLP clones were screened using DNA from both parental genotypes and aposporous and sexual bulks. Linkage analysis was performed with cytological and genetic information from the complete progeny. Cytoembryological analysis showed 219 sexual and 71 aposporous F₁ individuals. Seven different molecular markers (2 RAPD, 4 AFLP and 1 RFLP) were found to be completely linked to apospory. The RFLP probe C1069, mapping to the telomeric region of the long arm of rice chromosome 12, was one of the molecular markers completely linked to apospory in P. notatum. This marker had been previously associated with apospory in P. simplex. A preliminary map of the chromosome region carrying the apospory locus was constructed.     

Influence of Molecular Sizes of Cryptococcus neoformans Capsular Polysaccharide on Phagocytosis

The role of capsular polysaccharides (CPS) of Cryptococcus neoformans in phagocytosis by murine alveolar macrophages was investigated in four strains of C. neoformans serotype A, YC-11, YC-5, YC-27 and YC-13. Phagocytosis rates increased markedly after adding 10% mouse serum, compared to fetal calf serum. The reverse relation between capsular thickness of C. neoformans and phagocytosis by alveolar macrophages was observed except in YC-27, which had thin capsules and high virulence. The phagocytosis rate in mice serum was 17.3% in YC-11 (capsule thickness 2.8-3.5 μm), 39.8% in YC-5 (capsule size 0.8-1.5 μm), 20.3% in YC-27 (capsule size 0.6-1.1 μm), and 62.8% in YC-13 (capsule not detected microscopically). The CPS of YC-11, YC-5, and YC-27 analyzed by gel-filtration using CL-2B showed high molecular fractions near the void volume. However, the CPS of YC-13 showed only low molecular fractions. The widely eluted CPS of YC-11 was separated into 3 fractions and each fraction was added in the phagocytosis assay of YC-13. Phagocytosis was markedly suppressed particularly by the addition of a higher molecular fraction. These results suggest that phagocytosis of C. neoformans by alveolar macrophages is influenced by the molecular sizes of the CPS.     

The phylogenetic position of Apterosperma (Theaceae) based on morphological and karyotype characters

Classifications of Theaceae have usually placed the endangered monotypic genus Apterosperma in tribe Schimeae (x=18), whereas recent molecular phylogenetic evidence supports its transfer to tribe Theeae (x=15). Molecular data have not resolved the phylogenetic position of Apterosperma within Theeae. We investigated the chromosome number and karyotype of Apterosperma in the context of molecular and morphological phylogenetic evidence to provide further insight into the placement of Apterosperma within Theaceae. The chromosome number and karyotype was found to be 2n = 30 = 26m + 4sm, consistent with the transfer of Apterosperma to tribe Theeae. When the chromosome data were incorporated into a data set of 46 other nonmolecular characters, Apterosperma was placed as the first-diverging lineage within the clade comprising tribe Theeae. This supports its placement based on molecular data. The low intrachromosomal asymmetry (type 1A) of Apterosperma, presumably ancestral for the family, is also consistent with this placement. Character optimization strongly supports a base chromosome number of x=15 for tribe Theeae. Because of variable and sometimes conflicting chromosome count reports of species in tribes Schimeae and Stewartieae, the base chromosome number of Theaceae could be either x=15 or 17.     

Cryptic species in the Pyropia yezoensis complex (Bangiales,Rhodophyta): Sympatric occurrence of two cryptic species even on same rocks

In a previous study on wild populations of Pyropia, the occurrence of two possible new species (Pyropia sp. 2 and Pyropia sp. 3) which are closely related to the two commercially important Pyropia species, P. yezoensis and P. tenera, was confirmed as the result of molecular phylogenetic analyses. To characterize the morphological features of the two wild Pyropia species, we collected Pyropia blades in a natural population in which Pyropia sp. 3 was known to occur, and carried out molecular identification before detailed morphological observations. Through the molecular identification we found, unexpectedly, that Pyropia sp. 2 blades grew sympatrically in the same site. Therefore, after molecular identification, we examined in detail the external morphology and anatomy of the two wild Pyropia species using more than 10 blades each. As a result, it is concluded that all of the blades of the two species are morphologically identical to P. yezoensis, but distinct from P. tenera. It is therefore considered that both of the two wild Pyropia species are cryptic species within the P. yezoensis complex. Furthermore, this study revealed that the two cryptic species grew sympatrically, even on the same rocks within the natural habitat.     

Antifungal effects of chitosan with different molecular weights on in vitro development of Rhizopus stolonifer (Ehrenb.:Fr.) Vuill

Determination of the molecular weight of three types of chitosan was carried out by HPSEC-RI. The effect of low, medium and high molecular weight chitosan was evaluated on development of three isolates of Rhizopus stolonifer. Image analysis and electronic microscopy observations were done in spores of this fungus. Germination of R. stolonifer in potato dextrose broth with chitosan was also evaluated. Results pointed out that the low molecular weight chitosan was more effective for inhibition of mycelial growth while the high molecular weight chitosan affected spore shape, sporulation and germination. Studies of scanning and transmission electron microscopy revealed numerous and deeper ridge ornamentations of the chitosan-treated spore.     

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae,Chlorophyta) based on chloroplast genomes

Filamentous green algae Chaetophorales present numerous taxonomic problems as many other green algae. Phylogenetic analyses based on nuclear genes have limited solutions. Studies with appropriate chloroplast molecular markers may solve this problems; however, suitable molecular markers for the order Chaetophorales are still unknown. In this study, 50 chloroplast genomes of Chlorophyceae, including 15 of Chaetophorales, were subjected to single protein-coding gene phylogenetic analyses, and substitution rate and evolutionary rate assays, and PCR amplification verification was conducted to screen the suitable molecular markers. Phylogenetic analyses of three chloroplast representative genes (psaB, tufA, and rbcL) amplified from 124 strains of Chaetophorales showed that phylogenetic relationships were not improved by increasing the number of samples, implying that the genes themselves, rather than limited samples, were the reason for the unsupported Topology I. Seven genes (atpF, atpI, ccsA, cemA, chlB, psbB, and rpl2) with robust support were selected to be the most suitable molecular markers for phylogenetic analyses of Chaetophorales, and the concatenated seven genes could replace the time-consuming and labor-intensive phylogenetic analyses based on chloroplast genome to some extent. To further solve the taxonomic problems of Chaetophorales, suitable chloroplast markers combined with more taxon-rich approach could be helpful and efficient.     

Studies on the Bacterial Spore Coat

Properties of alkali-soluble components from the spore coat of Bacillus megaterium were examined by physicochemical methods. They were composed of acidic polypeptides of various molecular weights with small amounts of phosphorus and sugar. They were allowed to dissociate to unit components by incubation with SDS. The major component was partially purified by gel filtration, and shown to have a mean molecular weight of about 11,000.     

Construction of cytoplasmic molecular markers distinguishing Danio rerio from Gobiocypris rarus at high identity domains based on MP-PCR strategy and Sybr Green I detection

To distinguish the cytoplasm of Danio rerio from that of Gobiocypris rarus, we cloned G. rarus COXI and constructed cytoplasmic molecular markers at the high identity domains of COXI by mutated primer PCR (MP-PCR for short). Then Sybr Green I was used to detect the single amplicon. As a result, we succeeded in getting the cytoplasmic molecular markers, G.M COXI and Z.M COXI, by MP-PCR strategy. They were used to detect the sperm-derived mtDNA in the sexual hybrid embryos (D. rerio ♀ × G. rarus ♂) before the sphere stage. In the present study, all results demonstrate that MP-PCR approach and Sybr Green I detection are feasible to construct the molecular markers to identify genes that shared high identity.     

Influence of the reaction medium on the product distribution of peroxidase-catalysed oxidation of p-cresol

Summary p-Cresol was oxidized by hydrogen peroxide in a reaction catalysed by horseradish peroxidase and the low molecular weight products were investigated. In aqueous media Pummerer's ketone (I) was the dominating product but in organic media the product distribution was quite different; 2,2'-dihydroxy-5,5'-dimethyldiphenyl (II) was the main low molecular weight product. Similar product distributions were obtained with peroxidase adsorbed on a solid support and suspended in toluene and with peroxidase solubilized in a microemulsion containing the same solvent. The best selectivity for the formation of (II) was obtained when the enzyme was adsorbed on Celite and suspended in water-saturated chloroform with 0.5% (v/v) extra water added. The yield of low molecular weight products in this case was 28%; of this fraction, 95% was (II). Offprint requests to: P. Adlercreutz     

Combined molecular and morphological phylogeny of Eulophidae (Hymenoptera: Chalcidoidea), with focus on the subfamily Entedoninae

A new combined molecular and morphological phylogeny of the Eulophidae is presented with special reference to the subfamily Entedoninae. We examined 28S D2–D5 and CO1 gene regions with parsimony and partitioned Bayesian analyses, and examined the impact of a small set of historically recognized morphological characters on combined analyses. Eulophidae was strongly supported as monophyletic only after exclusion of the enigmatic genus Trisecodes. The subfamilies Eulophinae, Entiinae (=Euderinae) and Tetrastichinae were consistently supported as monophyletic, but Entedoninae was monophyletic only in combined analyses. Six contiguous bases in the 3e′ subregion of the 28S D2 rDNA contributed to placement of nominal subgenus of Closterocerus outside Entedoninae. In all cases, Euderomphalini was excluded from Entiinae, and we suggest that it be retained in Entedoninae. Opheliminae n. stat. is raised from tribe to subfamily status. Trisecodes is removed from Entedoninae but retained as incertae sedis in Eulophidae until its family placement can be determined new placement . The genera Neochrysocharis stat. rev. and Asecodes stat. rev. are removed from synonymy with Closterocerus because strong molecular differences corroborate their morphological differences. Closterocerus (Achrysocharis) germanicus is transferred to the genus Chrysonotomyia n. comb. based on molecular and morphological characters.     

Designing of enzyme inhibitors based on active site specificity: lessons from methyl gallate and its lipoxygenase inhibitory profile

Methyl gallate was purified, by lipoxygenase (LOX) inhibitory activity-guided method since its alleged anti-inflammatory property, from Bergenia ligulata (Wall), a plant used in the traditional, Ayurvedic system of medicine extensively. The LOX inhibitory property of methyl gallate was studied by enzyme kinetics, isothermal titration calorimetry and molecular docking followed by molecular simulation studies. The wet-laboratory experiments and in silico studies showed complete agreement, and promise of methyl gallate as a drug-lead molecular scaffold for anti-inflammatory therapy, based on LOX inhibition. The expressed work shows the need of nonactive site binding parameters to be considered while designing of inhibitors based on the specificities toward active sites of enzymes.