Mutagenesis study on the zebra fish SOX9 high-mobility group: comparison of sequence and non-sequence specific HMG domains

A unique class of proteins, containing high-mobility group (HMG) domain(s), recognizes unusual DNA structures and/or bends specific to AT-rich linear double-stranded DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high degrees of sequence similarity, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared in an effort to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in the sequence specific HMG domain. The differences in pI values, the instability index, and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.     

The limitations of immunoenzyme approaches to distinguish between 'specific' and 'non-specific' antibody-forming cells, with particular respect to immunocytochemical studies on the in situ immune response

After antigenic stimulation, specific antibody-forming cells can be detected in situ in tissue sections of lymphoid organs using an antigen specific immunoenzyme approach. Immunoglobulin-forming cells staining positively with a particular antigen-enzyme conjugate are considered to be specific antibody-forming cells (provided that the right control conjugates show a negative staining). Immunoglobulin-forming cells, staining negatively with the same antigen-enzyme conjugate, may do so for two reasons: (i) they are in fact specific antibody-forming cells, but are not detected as such because of limitations of the technique; (ii) they are real-nonspecific immunoglobulin producing cells. In this paper, the limitations of the technique are discussed.     

Age versus size determination of radial variation in wood specific gravity: lessons from eccentrics

Radial increases in wood specific gravity have been shown to characterize early successional trees from tropical forests. Here, we develop and apply a novel method to test whether radial increases are determined by tree age or tree size. The method compares the slopes of specific gravity changes across a short radius and a long radius of trees with eccentric trunks. If radial changes are determined by size, then the slope of the change should be the same on both radii. If radial changes are determined by age, then the slope should be greater on the short radius. For 30 trees from 12 species with eccentricity of at least 4%, the ratio of the slopes of the linear regressions of specific gravity on radial distance (short radius slope/long radius slope) was regressed on the ratio of radii lengths (long radius/short radius). The regression was highly significant, and the faster increase in specific gravity on the short radius was sufficient to compensate for the difference in radius lengths, so the specific gravity of wood along the short radius was equal to the specific gravity on the long radius at any given proportional distance on the radius. Therefore, trees that are producing xylem faster on one radius than another produce wood of comparable specific gravity on both radii at the same time, so radial increases in specific gravity are dependent on tree age, not tree size.     

Experimental approaches to the study of the biogenesis of mammalian mitochondrial proteins

Mitochondrial proteins are synthesized in mitochondria and on cytosolic ribosomes. Several approaches used to establish the site of synthesis and the identity of mitochondrially synthesized proteins are described. These include the specific inhibition of mitochondrial translation by inhibitors or mutation and the specific elimination of cytosolic translation either by using isolated mitochondria or specific inhibitors. Experimental approaches to study the import of proteins into mitochondria are also discussed.     

江滩与兴林垦种区钉螺体内几种酶活性的比较

在自动化分析仪上分析了兴林垦种林区内钉螺和草和滩钉螺的总蛋白（ＴＰｒ）含量和谷丙转氨酶（ＧＰＴ）、谷草转氨酶（ＧＯＴ）以及碱性磷酸脂酶（ＡＬＰ）的活力和比活力,及其受林地地下水位高度的影响,结果表明,林地钉螺的ＧＯＴ、ＧＰＴ酶活力和比活力均比滩于钉螺显著提高,ＡＬＰ活力较稳定,但比活力增加,林地内随地下水位降低,钉螺体内总蛋白含量下降,ＧＯＴ、ＧＰＴ比活力均显著升高。     

Monoclonal antibodies specific against tumors and viral infections

Monoclonal antibodies are monospecific antibodies. They are generated also by hybridoma technology. They are useful in target specific therapy against dangerous diseases. This property of monoclonal antibody offers us a new hope to combat deadly diseases where chemotherapy fails to produce specific treatment without adverse effects. This review article deals with the use of monoclonal antibodies specific against tumors and viral infections.     

Y enriched and Y specific DNA sequences from the genome of the mediterranean fruit fly,Ceratitis capitata

DNA sequences that are enriched or specific to the genome of the male medfly, Ceratitis capitata, have been isolated using a differential hybridization approach. Twelve phage clones from a genomic library have been identified that consistently display more intense hybridization with a genomic DNA probe from males as opposed to one from females. Southern DNA blot analysis reveals that these recombinant clones contain at least one EcoRI fragment that is either specific to the male genome, or more highly represented in it, as compared with the female genome. These EcoRI fragments, when used as probes, all generate a similar pattern of intense multiple bands in genomic DNA of males. This suggests the presence of repetitive sequences that are at least partially homologous in these regions of the genome that are specific to or enriched in males. In situ hybridization to mitotic chromosomes confirms a Y chromosomal origin for the male specific repetitive sequences. Data on the genomic organization, representation and evolutionary conservation of these sequences that are specific to or enriched in males are presented. Studies of the genomic organization and representation of flanking sequences that are not male specific are presented as well.by R. Appels     

Quantitative Assessment of Specificity in Immunoelectron Microscopy

In immunoelectron microscopy (immuno-EM) on ultrathin sections, gold particles are used for localization of molecular components of cells. These particles are countable, and quantitative methods have been established to estimate and evaluate the density and distribution of “raw” gold particle counts from a single uncontrolled labeling experiment. However, these raw counts are composed of two distinct elements: particles that are specific (specific labeling) and particles that are not (nonspecific labeling) for the target component. So far, approaches for assessment of specific labeling and for correction of raw gold particle counts to reveal specific labeling densities and distributions have not attracted much attention. Here, we discuss experimental strategies for determining specificity in immuno-EM, and we present methods for quantitative assessment of (1) the probability that an observed gold particle is specific for the target, (2) the density of specific labeling, and (3) the distribution of specific labeling over a series of compartments. These methods should be of general utility for researchers investigating the distribution of cellular components using on-section immunogold labeling. (J Histochem Cytochem 58:917–927, 2010)     

Conservation analysis of class‐specific positions in cytochrome P450 monooxygenases: Functional and structural relevance

Cytochrome P450 monooxygenases (CYPs) constitute a ubiquitous, highly divergent protein family. Nevertheless, all CYPs share a common fold and conserved catalytic machinery. Based on the electron donor system, 10 classes of CYPs have been described, but most CYPs are members of class I accepting electrons from ferredoxin which is being reduced by FAD‐containing reductase, or class II accepting electrons from FAD‐ and FMN‐containing CPR‐type reductase. Because of the low sequence conservation inside the two classes, the conserved class‐specific positions are expected to be involved in aspects of electron transfer that are specific to the two types of reductases. In this work we present results from a conservation analysis of 16,732 CYP sequences derived from an updated version of the Cytochrome P450 Engineering Database (CYPED), using two class‐specific numbering schemes. While no position was conserved on the distal, substrate‐binding surface of the CYPs, several class‐specific residues were found on the proximal, reductase‐interacting surface; two class I‐specific residues that were negatively charged, and three class II‐specific residues that were aromatic or charged. The class‐specific conservation of glycine and proline residues in the cysteine pocket indicates that there are class‐specific differences in the flexibility of this element. Four heme‐interacting arginines were conserved differently in each class, and a class‐specific substitution of a heme‐interacting tyrosine by histidine was found, pointing to a link between heme stabilization and the reductase type. Proteins 2014; 82:491–504. © 2013 Wiley Periodicals, Inc.     

基因组织特异性相关研究进展

研究基因的组织特异性是了解生命活动进程和组织功能的重要一步.尽管对于看家基因和组织特异基因的研究由来已久,但是对于它们仍缺少统一的定义方式和检测方法.在定义方式上,可以从基因的组织表达数和在各组织间的表达变化情况来分别定义看家基因和组织特异基因.通常将在大多数正常组织中有表达,且表达水平较稳定的基因称为看家基因,而将在一个或少数组织中优势表达的基因定义为组织特异基因或组织选择基因.在检测方法上,高通量实验技术,包括基因芯片、RNA-seq和质谱技术等已成为检测基因组织特异性的主要方法.通过比较多个典型研究的实验结果,发现不同检测方法的覆盖度和灵敏度存在很大差异,其中RNA-seq技术最为灵敏,获得的看家基因数目最多,质谱技术检测出来的看家基因和组织特异基因数目较少,而基因芯片方法给出的多个检测结果间差别较大.尽管不同的定义方式和检测方法所导致的看家基因(或组织特异基因)的集合不完全一致,但不同的看家基因数据集(或组织特异基因)却展现出非常一致的功能和特性.看家基因通常实现所有组织和细胞都必须的基本功能,而看家基因与其他组织表达基因间的相互作用以及组织特异基因间的相互作用则实现了组织的特有功能.同时,基因的组织特异性与疾病之间具有密切联系,相比其他基因,看家基因更有可能成为癌基因,而组织特异基因则更有希望发展成为药物靶标.     

Comparison of physical chemical properties of llama VHH antibody fragments and mouse monoclonal antibodies

Antigen specific llama VHH antibody fragments were compared to antigen specific mouse monoclonal antibodies with respect to specificity, affinity and stability. The llama VHH antibody fragments and the mouse monoclonal antibodies investigated were shown to be highly specific for the protein antigen hCG or the hapten antigen RR-6. The affinity of the interaction between monovalent llama VHH antibody fragments and their antigen is close to the nanomolar range, similar to the bivalent mouse monoclonal antibodies studied. Llama VHH antibody fragments are similar to mouse monoclonal antibodies with respect to antigen binding in the presence of ammonium thiocyanate and ethanol. The results show that relative to antigen specific mouse monoclonal antibodies, antigen specific llama VHH fragments are extremely temperature stable. Two out of six llama VHHs are able to bind antigen specifically at temperatures as high as 90 degrees C, whereas four out of four mouse monoclonal antibodies are not functional at this temperature. Together with the finding that llama VHH fragments can be produced at high yield in Saccharomyces cerevisiae, these findings indicate that in the near future antigen specific llama VHH fragments can be used in for antibodies unexpected products and processes.     

The use of base pair specific DNA binding agents as affinity labels for the study of mammalian chromosomes

The fluorochromes Hoechst 33258 and olivomycin are base pair specific DNA binding agents. The fluorescence enhancement of Hoechst 33258 and olivomycin in the presence of DNA can be directly related to the A-T and G-C content of the interacting DNA respectively. Cytological observations of metaphase chromosomes treated with these two compounds suggest that the fluorescent banding patterns produced are the reverse of one another. —Non-fluorescent base pair specific DNA binding agents have been used as counterstains in chromosome preparations to enhance the contrast of the banding patterns produced by the base specific fluorochromes. The non-fluorescent G-C specific antibiotic actinomycin-D enhanced the resolution of fluorescent bands produced by the A-T specific fluorochrome Hoechst 33258. Similarly the non-fluorescent A-T specific antibiotic netropsin was found to enhance resolution of the bands produced by the G-C specific fluorochrome olivomycin. Netropsin was also found to increase the differential fluorescent enhancement of complexes of olivomycin with DNAs of various base composition in solution. These findings suggest that counterstaining agents act through a base sequence dependent inhibition of subsequent binding by base pair specific fluorochromes.—The base specific DNA binding agents have been used to differentiate different types of constitutive heterochromatin in mammalian species, and to facilitate chromosome identification in somatic cell hybrids.     

Crystal structures of receptors involved in small molecule transport across membranes

This paper briefly reviews contemporary protein crystallography and focuses on six receptor proteins of membrane-intrinsic ATP binding cassette (ABC) transporters. Three of these receptors are specific for carbohydrates and three for amino acids. The receptor GacH of the transporter GacFGH from Streptomyces glaucescens is specific for acarbose and its homologs, and MalE of Salmonella typhimurium is specific for maltose but also forms a complex with acarbose, and the third receptor is the highly specific d-galactose receptor AcbH of the transporter AcbFGH from Actinoplanes sp. Concerning the receptors for amino acids, ArtJ belongs to the ArtJ-(MP)(2) transporter of Geobacillus stearotermophilus and recognizes and binds to positively charged arginine, lysine, and histidine with different sizes of side chains, contrasting the receptors Ngo0372 and Ngo2014 from Neisseria gonorrhaeae that are highly specific for cystine and cysteine, respectively. The differences in the rather unspecific receptors GacH, MalE and ArtJ are compared with the highly specific receptors AcbH, Ngo0372 and Ngo2014.     

异质性荧光染色的巨噬细胞功能研究I．异质性荧光染色的巨噬细胞吞噬活性

利用淀粉多糖和免疫促进剂（白喉类毒素和卡介苗）诱导和活化小鼠腹腔巨噬细胞,观察了四种异质性荧光染色的巨噬细胞非特异性和特异性吞噬活性。实验证明,深蓝色和淡蓝色荧光的巨噬细胞是分化程度低的幼稚细胞,非特异性吞噬功能较弱,但在特异性吞噬过程中呈现了活跃的吞噬活性,特别是在免疫促进剂的活化下,它们的特异性吞噬功能显著增强、淡蓝绿色荧光的巨噬细胞是分化程度较高、非特异性和特异性吞噬功能最旺盛的巨噬细胞,而黄色荧光的巨噬细胞是分化程度最高、特异性吞噬功能较减退的巨噬细胞。     

采用花器喷雾法并基于Cre/lox系统定点整合拟南芥Rps2基因的技术体系研究

To improve site?specific integration technology system, site?specific integration of Rps2 target gene in Arabidopsis thaliana (Linn.) Heynh. was carried out based on Cre/lox system by floral spraying method. The results show that 1495 site?specific integration candidate plants are obtained by this method with a site?specific integration efficiency of about 0076%. After PCR and histochemical staining experiment verification, the positive plants of precise integration account for 8604%, in which, 6334% positive plants are single copy transformed plants. The results of quantitative real?time PCR (qRT?PCR) and hypersensitive reaction (HR) show that the site?specific integrated Rps2 gene can be transcribed and expressed normally. It is suggested that this system can greatly improve the stability and efficiency of site?specific integration genetic transformation system in plants.     

Use of a structured kinetic model of antibody synthesis and secretion for optimization of antibody production systems: I. Steady-state analysis

Steady-state simulations using our previously developed structured kinetic model of antibody synthesis and secretion by hybridoma cells are used here in conjunction with factorial design analysis to identify intracellular parameters important in determining the specific antibody secretion rate and predict the dependence of this rate on cell specific growth rate. Simulation results suggest that the specific growth rate, the assembly rate of the heavy and light chains and the heavy- and -chain gene dosage can significantly affect the rate of antibody secretion. Based on these results, environmental and/or genetic manipulation approaches are proposed for maximizing the specific antibody secretion rate and the antibody volumetric productivity in large-scale antibody production systems.     

Direct Haplotype‐Specific DNA Sequencing

Abstract

Determining haplotype‐specific DNA sequence information is very important in a wide range of research fields. However, no simple and robust approaches are currently available for determining haplotype‐specific sequence information. We have addressed this problem by developing a very simple and robust haplotype‐specific sequencing approach. We utilise the fact that DNA sequencing polymerases are sensitive to 3′end mismatches in the sequencing primer. By using two sequencing primers with 3′end corresponding to the two alleles in a given SNP locus, we are able to obtain allele‐specific DNA sequences from both alleles.

We evaluated this direct haplotype‐specific approach by determining haplotypes within the intron 2 sequence of the fructan‐6‐fructosyltransferase (6‐ft) gene in Lolium perenne L. We obtained reliable haplotype‐specific sequences for all primers and genotypes evaluated. We conclude that the haplotype‐specific sequencing is robust, and that the approach has a potentially very wide application range for any diploid organism.     

Aspecific and specific intermolecular interactions in aqueous media

Aspecific as well as specific interactions involve the same noncovalent forces, consisting of Lifshitz-van der Waals, Lewis acid/base, electrostatic, and thermal or Brownian movement interactions. In vivo, aspecific interactions between, e.g., cells and/or biopolymers usually are repulsive, while specific interactions are always attractive. The differences between the two classes of interactions can be shown to lie in the fact that aspecifically interacting bodies are large, while specifically interacting sites are small, or have a small radius of curvature, and in the fact that aspecifically interacting surfaces are homogeneous, whereas specific sites have a heterogeneous composition.