东北旱田土壤中Anabaena伴生细菌的分离与鉴定

[背景]鱼腥藻(Anabaena)在农田土壤中广泛分布,具有固碳和固氮功能。明确伴生细菌与蓝细菌的关系,对提高农田土壤中Anabaena的功能具有重要意义。[目的]从东北不同旱田土壤中分离Anabaena sp.PCC7120的伴生细菌,初步鉴定伴生细菌的分类归属,推测伴生细菌的功能,为明确旱田土壤蓝细菌与伴生细菌的关系提供数据支撑。[方法]采用平板分离、PCR-DGGE、克隆测序技术测定并分析不同旱田土壤中伴生细菌的16S rRNA基因序列,确定伴生细菌的分类地位。[结果]PCR-DGGE图谱显示东北旱田14个土样中分离获得Anabaena sp.PCC7120伴生细菌数量和种类不同;PCR-克隆测序获得伴生细菌的16S rRNA基因序列37条,可鉴定到种水平的菌株36条,主要归为鞘氨醇盒菌属(Sphingopyxis)、贪噬菌属(Variovorax)、黄杆菌属(Flavobacterium)和红球菌属(Rhodococcus)等,推测这些伴生细菌具有适应寡营养、富集微量元素、清除毒素等功效。[结论]东北旱田不同土壤中Anabaena sp.PCC7120伴生细菌种类和数量各异,这...     

A genome-wide association analysis of quantitative trait loci for protein fraction content in Tibetan wild barley

The genetic associations and differences of four protein fractions were investigated in Tibetan wild barley. Albumin, globulin and hordein contents were under genetic control probably via multiple genes/quantitative trait loci. A correlation analysis showed that globulin was significantly associated with albumin, glutelin and hordein, while hordein was closely correlated with glutelin. Forty-nine diversity array technology (DArT) markers, which were distributed over seven chromosomes, were associated with the protein fraction contents. Those DArT markers associated with hordein were the same as those associated with globulin and glutelin. Only five markers associated with hordein, globulin and glutelin were also associated with albumin. Most of the protein fraction contents are therefore controlled by same genes which may contribute to total protein content. The discovery of new markers associated with specific protein fractions could be used to detect genes controlling protein content in the barley germplasm.     

Structural plasticity associated with the beta-propeller architecture

The beta-propeller architecture observed in protein tertiary structure and classified into the five different types according to number of 'blades' (or beta-sheets) and a sixth type classified according to the secondary structure composition of the blades (the beta beta alpha beta-molecular unit) is characterized by variations (or plasticity) in the structure. These correspond to the number of beta-strands associated with the blade, the number of amino acid residues associated with equivalent beta-strands in the different blades and the presence of alpha-helices and twisted beta-strands. We have generated a beta-sheet associated beta-strand pattern that may be important for protein structure prediction and modeling. Analysis of the beta-propellers extracted primarily from the SCOP database revealed there are 179 beta-propellers. The examination of the secondary structure corresponding to the beta-propeller using PDBsum that was useful to define the beta-sheet associated beta-strand pattern, combined with visualization on graphics display revealed structural plasticity associated with the beta-propeller architecture. Particularly, the type 6- and 7-bladed beta-propellers known to be associated with sequence and functional diversity are more common and associated with relatively more structural variations compared to the other beta-propeller types.     

p68 Sam is a substrate of the insulin receptor and associates with the SH2 domains of p85 PI3K.

The 68 kDa Src substrate associated during mitosis is an RNA binding protein with Src homology 2 and 3 domain binding sites. A role for Src associated in mitosis 68 as an adaptor protein in signaling transduction has been proposed in different systems such as T-cell receptors. In the present work, we have sought to assess the possible role of Src associated in mitosis 68 in insulin receptor signaling. We performed in vivo studies in HTC-IR cells and in vitro studies using recombinant Src associated in mitosis 68, purified insulin receptor and fusion proteins containing either the N-terminal or the C-terminal Src homology 2 domain of p85 phosphatidylinositol-3-kinase. We have found that Src associated in mitosis 68 is a substrate of the insulin receptor both in vivo and in vitro. Moreover, tyrosine-phosphorylated Src associated in mitosis 68 was found to associate with p85 phosphatidylinositol-3-kinase in response to insulin, as assessed by co-immunoprecipitation studies. Therefore, Src associated in mitosis 68 may be part of the signaling complexes of insulin receptor along with p85. In vitro studies demonstrate that Src associated in mitosis 68 associates with the Src homology 2 domains of p85 after tyrosine phosphorylation by the activated insulin receptor. Moreover, tyr-phosphorylated Src associated in mitosis 68 binds with a higher affinity to the N-terminal Src homology 2 domain of p85 compared to the C-terminal Src homology 2 domain of p85, suggesting a preferential association of Src associated in mitosis 68 with the N-terminal Src homology 2 domain of p85. This association may be important for the link of the signaling with RNA metabolism.     

Three-dimensional reconstruction of tubulin in zinc-induced sheets: II. Consequences of removal of microtubule associated proteins

The three-dimensional structure of zinc-induced tubulin sheets freed of microtubule associated proteins has been determined to 20 Å resolution by electron microscopy and image reconstruction. The determination was carried out with porcine brain tubulin separated from microtubule associated proteins by phosphocellulose chromatography. Negatively stained samples were tilted using the goniometer stage of the electron microscope to provide images of the tubulin sheets ranging in tilt from ?60 ° to +60 °. The micrographs were digitized and subjected to a cross-correlation analysis to compensate for smooth curvature of the lattice in the sheets. For each angle of tilt, an average unit cell was obtained from the cross-correlation analysis and subsequently a Fourier transform was computed for inclusion in the three-dimensional Fourier data set. The transforms of 47 tilted images plus the average of five untilted sheets were combined and an inverse Fourier transform was applied to give a threedimensional reconstruction of the microtubule associated protein-free tubulin sheets. Comparison of the protofilament structure in these sheets with the previously published protofilament structure of zinc-induced tubulin sheets containing microtubule associated proteins reveals a number of consequences of the removal of microtubule associated proteins. (1) The extensive internal contact along the protofilament observed in microtubule associated protein-containing tubulin sheets is maintained in microtubule associated protein-free tubulin sheets. (2) In projection, the protofilaments in microtubule associated protein-free tubulin sheets are 2.2 Å closer together than in microtubule associated protein-tubulin sheets. (3) The deviations of adjacent protofilaments from the plane of the sheets when viewed end-on are more pronounced in the absence of microtubule associated proteins. Differences are also observed at the level of individual tubulin subunits. In particular, the distinct cleft which was found in one class of subunits in tubulin sheets with microtubule associated proteins is absent in the microtubule associated protein-free tubulin sheets. The loss of this cleft and some changes in the shape of the tubulin subunits upon removal of microtubule associated proteins suggest a possible site for the interaction of tubulin with microtubule associated proteins.     

Engineering Chinese hamster ovary (CHO) cells to achieve an inverse growth – associated production of a foreign protein, β-galactosidase

Protein synthesis in mammalian cells can be observed in two strikingly different patterns: 1) production of monoclonal antibodies in hybridoma cultures is typically inverse growth associated and 2) production of most therapeutic glycoproteins in recombinant mammalian cell cultures is found to be growth associated. Production of monoclonal antibodies has been easily maximized by culturing hybridoma cells at very low growth rates in high cell density fed- batch or perfusion bioreactors. Applying the same bioreactor techniques to recombinant mammalian cell cultures results in drastically reduced production rates due to their growth associated production kinetics. Optimization of such growth associated production requires high cell growth conditions, such as in repeated batch cultures or chemostat cultures with attendant excess biomass synthesis. Our recent research has demonstrated that this growth associated production in recombinant Chinese hamster ovary (CHO) cells is related to the S (DNA synthesis)-phase specific production due to the SV40 early promoter commonly used for driving the foreign gene expression. Using the stably transfected CHO cell lines synthesizing an intracellular reporter protein under the control of SV40 early promoter, we have recently demonstrated in batch and continuous cultures that the product synthesis is growth associated. We have now replaced this S-phase specific promoter in new expression vectors with the adenovirus major late promoter which was found to be active primarily in the G1-phase and is expected to yield the desirable inverse growth associated production behavior. Our results in repeated batch cultures show that the protein synthesis kinetics in this resulting CHO cell line is indeed inverse growth associated. Results from continuous and high cell density perfusion culture experiments also indicate a strong inverse growth associated protein synthesis. The bioreactor optimization with this desirable inverse growth associated production behavior would be much simpler than bioreactor operation for cells with growth associated production. This revised version was published online in August 2006 with corrections to the Cover Date.     

Comparison of non histone proteins selectively associated with nucleosomes with proteins released during limited DNase digestions.

Cultured mammary cells from GR mouse were used to analyse proteins associated with the mononucleosomes and released by a short micrococcal DNase treatment of nuclei. On metrizamide density gradients, mononucleosomes appear to be heterogeneous according to their content of associated non-histone proteins. Proteins associated with the denser fraction (1.22 - 1.24 g/ml) were analysed by two dimensional electrophoresis and compared to the proteins released by DNase I treatment. All the proteins associated with mononucleosomes were also released by DNase I treatment. It could then be assumed that these proteins are associated with the active part of the genome. Additional proteins were released by micrococcal DNase treatment of the nuclei. They could be involved in a higher order organization of chromatin.     

Auditory imagery associated with Japanese onomatopoeic representation

When we want to express the subjective impression of sound, we usually use onomatopoeias. We investigated the relationship between the impression of auditory imagery associated with Japanese onomatopoeic representation and onomatopoeic features. Subjects rated the impressions of auditory imageries associated with 40 onomatopoeias on semantic differential scales. Principal component analysis was applied to the rating data and the scales were integrated to the components of beauty, potency and sharpness. We determined the relationship between phonetic features of onomatopoeias and tonal features of the auditory imageries on the obtained principal components. Onomatopoeic representations that included voiced consonants were associated with a "dirty" impression. Onomatopoeic representations that contained approximant sounds were associated with a "powerful" impression. The vowel /i/ was associated with a "sharp" impression and vowels /u/ and /o/ were associated with a "dull" impression. The obtained tendencies confirmed that some onomatopoeic features reflected particular impressions of auditory imagery.     

The relationship between psychosocial stress, age, BMI, CRP, lifestyle, and the metabolic syndrome in apparently healthy subjects

The aim of this cross-sectional study was to examine the factors which may be associated with the metabolic syndrome by exploring the relationship between psychosocial stress, age, body mass index (BMI), C-reactive protein (CRP), lifestyle factors, and the components of the metabolic syndrome, such as glycated hemoglobin (HbA1c), fasting blood sugar (FBS), body fat percentage, and triglyceride concentration, among apparently healthy subjects. Psychosocial stress was measured by the use of the inventory to measure psychosocial stress (IMPS). One thousand four hundred and ninety-nine people out of 1,941 public school workers admitted to a hospital for a medical check-up responded to the IMPS, yielding a response rate of 77.2%. A total of 1,201 workers excluding 298 who were taking medication for various diseases were analyzed with the use of hierarchical multiple regression models. It was found that IMPS-measured stress score, age, BMI, and smoking habit were associated with an increase in glycated hemoglobin among men, while alcohol consumption was associated with a decrease in glycated hemoglobin. Stress score, age, BMI, and alcohol consumption were found to be associated with an increase in FBS among men, while smoking and exercise habits were associated with a decrease in FBS. CRP was found to be associated with an increase in body fat percentage among men, though stress score was not associated with an increase in body fat percentage. Stress score, age, and BMI were associated with an increase in triglyceride concentration among women. The findings of the present study seem to be in line with the hypothesis that psychosocial stress plays an important role in developing the metabolic syndrome, which may be associated with inflammatory processes in the vascular wall, resulting in atherosclerosis and cardiovascular disease.     

Adenosine kinase and cardiovascular fetal programming in gestational diabetes mellitus

Gestational diabetes mellitus (GDM) is a detrimental condition for human pregnancy associated with endothelial dysfunction and endothelial inflammation in the fetoplacental vasculature and leads to increased cardio-metabolic risk in the offspring. In the fetoplacental vasculature, GDM is associated with altered adenosine metabolism. Adenosine is an important vasoactive molecule and is an intermediary and final product of transmethylation reactions in the cell. Adenosine kinase is the major regulator of adenosine levels. Disruption of this enzyme is associated with alterations in methylation-dependent gene expression regulation mechanisms, which are associated with the fetal programming phenomenon. Here we propose that cellular and molecular alterations associated with GDM can dysregulate adenosine kinase leading to fetal programming in the fetoplacental vasculature. This can contribute to the cardio-metabolic long-term consequences observed in offspring after exposure to GDM.     

Tree diversity patterns in successive vegetation types along an elevation gradient in the Mountains of Eastern Mexico

Tree species richness changes along elevation gradients in response to underlying environmental conditions. Our hypothesis was that richness is associated with climatic variables and decreases with elevation. The objective was to identify trends in species, genus and family richness, diversity and vegetation structure in relation to climate variables along an elevation gradient with successive types of forest in Veracruz, Mexico. Trees were identified and measured in 0.1 ha at 15 sites located from 140 to 4000 m a.s.l. Generalized linear models were used to fit richness, diversity, basal area and density as a function of elevation; the best model was selected using Akaike’s Information Criterion. Multivariate analyses were used to explore climatic variables associated to composition of groups of sites along the gradient. Along the entire elevation gradient, species, genus and family richness decreased unimodally, and diversity decreased monotonically. Richness was positively correlated with temperature but not with precipitation. Basal area increased monotonically and highest basal area was associated with high humidity and certain tree species (Quercus and Abies). Ordinations indicated three groups of sites: lower elevation dry forest associated with temperature seasonality, mid-elevation cloud forest associated with precipitation-related variables, and coniferous forest at the top of the gradient associated with elevation. Our study shows that different plant communities are associated with certain climatic conditions and harbour different tree species, genera and families. The results support the hypothesis that species richness is associated with climate, and decreases with elevation.     

Sarco(endo)plasmic reticulum and plasmalemmal Ca(2+)-ATPase activities in cremaster muscles and sacs differ according to the associated inguinal pathology

Sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) and plasmalemmal Ca(2+)-ATPase (PMCA) activities in cremaster muscles and sacs, which have been subjected to different autonomic tonuses, were determined and compared. Samples of cremaster muscles and sacs associated with male or female inguinal hernia, hydrocele or undescended testis were obtained from children during operations and activities of SERCA and PMCA were determined. While highest SERCA and PMCA activities were encountered among cremaster muscles and sacs associated with undescended testis, least activities were encountered among structures associated with hydrocele. The alterations in SERCA and PMCA activities in cremaster muscles associated with undescended testis appear to reflect the attempts at maintaining the levels of cytosolic calcium. Despite similar total calcium contents, lower SERCA and PMCA activities were found in sacs associated with hydrocele compared to those associated with undescended testis suggest a difference among the levels of cytosolic calcium.     

An independent validation study of loci associated with nematode resistance in sheep

Gastrointestinal nematode infection is a constraint on sheep production worldwide. Selective breeding programmes to enhance resistance to nematode infection are currently being implemented in a number of countries. Identification of loci associated with resistance to infection or causative mutations for resistance would enable more effective selection. Loci associated with indicator traits for nematode resistance has been identified in previous studies. In this study, Scottish Blackface, Texel and Suffolk lambs were used to validate the effects at eight genomic regions previously associated with nematode resistance (OAR3, 4, 5, 7, 12, 13, 14, 21). No SNP was significantly associated with nematode resistance at the region‐wide level but seven SNPs in three of the regions (OAR4, 12, 14) were nominally associated with trichostrongyle egg count in this study and six of these were also significant when fitted as single SNP effects. Nematodirus egg count was nominally associated with SNPs on OAR3, 4, 7 and 12.     

Retrotransposon insertions in rice gene pairs associated with reduced conservation of gene pairs in grass genomes

Small-scale changes in gene order and orientation are common in plant genomes, even across relatively short evolutionary distances. We investigated the association of retrotransposons in and near rice gene pairs with gene pair conservation, inversion, rearrangement, and deletion in sorghum, maize, and Brachypodium. Copia and Gypsy LTR-retrotransposon insertions were found to be primarily associated with reduced frequency of gene pair conservation and an increase in both gene pair rearrangement and gene deletions. SINEs are associated with gene pair rearrangement, while LINEs are associated with gene deletions. Despite being more frequently associated with retrotransposons than convergent and tandem pairs, divergent gene pairs showed the least effects from that association. In contrast, convergent pairs were least frequently associated with retrotransposons yet showed the greatest effects. Insertions between genes were associated with the greatest effects on gene pair arrangement, while insertions flanking gene pairs had significant effects only on divergent pairs.     

The function of proteins that interact with mRNA

Specific proteins are associated with mRNA in the cytoplasm of eukaryotic cells. The complement of associated proteins depends upon whether the mRNA is an integral component of the polysomal complex being translated, or, alternatively, whether it is part of the non-translated free mRNP fraction. By subjecting cells to ultraviolet irradiation in vivo to cross-link proteins to mRNA, mRNP proteins have been shown to be associated with specific regions of the mRNA molecule. Examination of mRNP complexes containing a unique mRNA has suggested that not all mRNA contain the same family of associated RNA binding proteins. The function of mRNA associated proteins may include a role in providing stability for mRNA, and/or in modulating translation. With the recent demonstrations that both free and polysomal mRNPs are associated with the cytoskeletal framework, specific mRNP proteins may play a role in determining the subcellular localization of specific mRNPs.     

Proteins associated with rabbit reticulocyte mRNA caps during translation as investigated by photocrosslinking.

This laboratory previously detected by UV crosslinking a number of proteins associated with cytoplasmic mRNA in mammalian cells, and the data suggested that they are involved in translation. To find out which proteins are associated with caps we made use of reticulocyte mRNA specifically labeled in the cap with 32P together with a cell-free translation system and UV crosslinking. Approximately 8 bands corresponding to proteins crosslinked to the cap itself have been detected by polyacrylamide gel electrophoresis after UV crosslinking and digestion with RNases or tobacco pyrophosphatase. All but one were specific for methylated caps. One was similar in size and partial peptide map to a cap-binding protein, CBP I, previously identified in other laboratories, and most of the others corresponded to proteins previously known to be associated with mRNA but not known to be associated with caps. The results suggest that most mRNA-associated proteins are associated with caps or poly(A). Also, the number of cap-associated proteins may be greater than previously suspected.     

Fenofibrate induces HDL-associated PAF-AH but attenuates enzyme activity associated with apoB-containing lipoproteins

Human plasma platelet-activating factor acetylhydrolase (PAF-AH) is an enzyme associated mainly with the apolipoprotein B (apoB)-containing lipoproteins and primarily with LDL. A small proportion of enzymatic activity is also associated with HDL. Plasma paraoxonase 1 (PON1) is an esterase exclusively associated with HDL. The effect of fenofibrate on PAF-AH and PON1 activities in patients with dyslipidemias of Types IIA, IIB, and IV were studied. Fenofibrate reduced plasma PAF-AH activity in all patient groups. In Type IIA patients, this reduction was mainly due to a fall in enzyme activity associated with the dense LDL subspecies, whereas in Type IIB and Type IV patients, it was due to the decrease in PAF-AH activity associated with both the VLDL+IDL and dense LDL subspecies. Drug therapy in Type IIB and Type IV patients significantly increased the HDL-associated PAF-AH activity due to the increase in enzyme activity associated with the HDL-3c subfraction. Fenofibrate did not affect serum PON1 activities toward paraoxon and phenylacetate in either patient group. The fenofibrate-induced elevation of HDL-associated PAF-AH activity in dyslipidemic patients of Type IIB and Type IV, as well as the reduction in enzyme activity associated with atherogenic apoB-containing lipoproteins in all patient groups, may represent a new and important antiatherogenic effect of this potent lipid-modulating agent.