Identification of Mycoplasmatales: Procedures for Both Characterization and Purification

Procedures with potential value for identification and purification of Mycoplasma were applied to over 240 cultures representing 11 of the 12 known avian serotypes. Growth was tested at pH 5.5 and 9.5, at 25 and 42 C, in serum-free media, and in the presence of (i) 1% bile salts, (ii) 3% NaCl, and (iii) 0.02% methylene blue. One avian Mycoplasma serotype grew in broth containing 1% bile salts. Two of 11 avian serotypes were resistant to 0.02% methylene blue. A number of Mycoplasma strains grew at 42 C or in a pH 9.5 medium. Usefulness of these procedures for purifying cultures of Mycoplasma is discussed.     

Microcalorimetric detection of growth of Mycoplasmatales.

A static ampoule microcalorimeter was used to study the growth of mycoplasmas, acholeplasmas and ureaplasmas. Growth as indicated by thermograms was compared with the results of conventional methods, namely, terminal dilution counts, plate counts, turbidimetric measurements, glucose consumption and pH changes. Removal of oxygen had little effect on mycoplasma growth. The microcalorimetric method is potentially useful for identifying and enumerating the members of the Mycoplasmatales.     

Characterization of Mycoplasmatales Virus <Emphasis Type="Italic">laidlawii</Emphasis> 1

A recent report¹ described for the first time the isolation of a virus that infects a species of mycoplasma. This agent, now designated MVL1, has been purified, examined in the electron microscope and its nucleic acid type determined. Cultures of M. laidlawii strain BN1 (ref. 1), grown in glucose serum broth or agar², were inoculated with virus during their log phase and incubated at 37° C for 18–24 h. On solid medium, plaques were observed in the mycoplasmal lawn from which virus was harvested by flooding the plate with phosphate buffered saline (PBS), pH 7.3, for 3–5 h. The titre of the virus was estimated as previously reported¹.     

Mycoplasmatales virus,MV-M1: Discovery inAcholeplasma modicum and preliminary characterization

A new virus, Mycoplasmatales virus-modicum 1 (MV-M1), was recovered from spontaneous plaques in lawns ofAcholeplasma modicum. Strain “mod” produced plaques onA. modicum strains but not on strains ofAcholeplasma laidlawii. Only MV-L3 of the three knownA. laidlawii viruses (MV-L1, MV-L2, and MV-L3) produced plaques onA. modicum. The MV-M1 virus was serologically distinct from the threeA. laidlawii viruses; filterable at 0.1 μm; partially sensitive to heat and Nonidet P-40; and chloroform labile. Spherical particles ranging from 105 to 160 nm were observed in electron micrographs of negatively stained preparations.     

Ecto-ATPase of Mammalian Synaptosomes: Identification and Enzymic Characterization

Intact synaptosomes isolated from mammalian brain tissues (rat, mouse, gerbil, and human) have an ATP hydrolyzing enzyme activity on their external surface. The synaptosomal ecto-ATPase(s) possesses characteristics consistent with those that have been described for ecto-ATPases of various other cell types. The enzyme has a high affinity for ATP (the apparent Km values are in the range of 2-5 X 10(-5) M), and is apparently stimulated equally well by either Mg2+ or Ca2+ in the absence of any other cations. The apparent activation constant for both divalent cations is approximately 4 X 10(-4) M in all mammalian brain tissues studied. The involvement of a non-specific phosphatase in the hydrolysis of externally added ATP is excluded. ATP hydrolysis is maximal in the pH range 7.4-7.8 for both divalent cation-dependent ATPase activities. Dicyclohexylcarbodiimide, 2,4-dinitrophenol, trifluoperazine, chlorpromazine, and p-chloromercuribenzoate (50 microM) inhibit the ecto-ATPase, whereas ouabain (1 mM) and oligomycin (3.5 micrograms X mg-1 protein) show little or no inhibition of this enzyme activity. Inhibitor data suggest that the Mg2+- and Ca2+-dependent ecto-ATPase may represent two different enzymes on the surface of synaptosomes.     

Acholeplasma axanthum, sp. n.: a new sterol-nonrequiring member of the Mycoplasmatales

Mycoplasmas recovered from tissue cultures and previously shown to belong to the sterol-nonrequiring group of mycoplasmas have been further characterized. The biological and serological properties of these strains show them to be clearly distinct from Acholeplasma laidlawii and A. granularum, two species of sterol-nonrequiring mycoplasmas recently reclassified. It is proposed that the newly described mycoplasmas be designated Acholeplasma axanthum, sp. n.     

Amylopectin Synthase of Eimeria tenella: Identification and Kinetic Characterization

ABSTRACT. A soluble enzyme amylopectin synthase (UDP-glucose-α 1,4-glucan α-4-glucosyltransferase) which transfers glucose from uridine 5'-diphosphate glucose (UDP-glucose) to a primer to form α-I,4-glucosyl linkages has been identified in the extracts of unsporulated oocysts of Eimeria tenella . UDP-glucose and not ADP-glucose was the most active glucosyl donor. Corn amylopectin, rabbit liver glycogen, oyster glycogen and corn starch served as primers; the latter two were less efficient. The enzyme has an apparent pH optimum of 7.5 and exhibited typical Michaelis-Menten kinetics with dependence on both the primer and substrate concentrations. The Michaelis constants (Km). with respect to UDP-glucose, was 0.5 mM; and 0.25 mg/ml and 1.25 mg/ml with respect to amylopectin and rabbit liver glycogen. The product formed by the reaction was predominantly a glucan containing α-1,4 linkages. The specificity of the enzyme suggests that this enzyme is similar to glycogen synthase in eukaryotes and has been designated as amylopectin synthase (UDP-glucose-α-1,4-glucosetransferase EC 2.4.1.11).     

Optimization of Proteomic Sample Preparation Procedures for Comprehensive Protein Characterization of Pathogenic Systems

Mass spectrometry-based proteomics is a powerful analytical tool for investigating pathogens and their interactions within a host. The sensitivity of such analyses provides broad proteome characterization, but the sample-handling procedures must first be optimized to ensure compatibility with the technique and to maximize the dynamic range of detection. The decision-making process for determining optimal growth conditions, preparation methods, sample analysis methods, and data analysis techniques in our laboratory is discussed herein with consideration of the balance in sensitivity, specificity, and biomass losses during analysis of host-pathogen systems.     

Pyrosequencing for Microbial Identification and Characterization

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.     

猪博卡病毒环状附加体的发现与鉴定

为了证实博卡病毒可以环状附加体形式存在于宿主体内,本研究利用半巢式PCR方法在健康猪粪便标本中筛查出2株猪博卡病毒环状附加体PBoV_G2-episome和PBoV_G3-episome。通过反复测序和序列拼接得到其末端非编码区序列（405nt和511nt）。经过对其进行序列分析及二级结构的预测,发现PBoV_G2-episome与人博卡病毒3附加体（HBoV3-episome）结构相似,而PBoV_G3-episome与博卡病毒属其他成员的末端二级结构存在较大差别。猪博卡病毒环状附加体的发现证实了有些博卡病毒与其他细小病毒的复制方式存在一定差异,也为今后博卡病毒感染性克隆的构建提供了一条研究思路。     

Characterization of New Punch Mutations: Identification of Two Additional Mutant Classes

The Punch locus of Drosophila melanogaster which encodes the pteridine biosynthetic enzyme, GTP cyclohydrolase, is genetically complex. Lethal alleles of the locus resolve into an array of interallelic complementation groups, and at least one class of mutations is developmentally specific, affecting GTP cyclohydrolase activity only in the heads of adults. All previously isolated Punch alleles were identified on the basis of a mutant eye color phenotype. By screening mutagenized chromosomes over Punch region deficiencies, we have now isolated new alleles on the basis of lethal and visible phenotypes. Most of these alleles fall into previously identified genetic classes, but two new classes of mutations were also found. One class contains two alleles that behave as dominant lethal mutations in some genetic backgrounds. The other class represents a second developmentally specific set of alleles that affect the function of the Punch locus only during embryogenesis.     

Proceedings: Preservation of Mycoplasmatales and L-phase variants in the American type culture collection by freezing and freeze-drying

The ATCC collection of Mycoplasmatales (with the exception of Thermoplasma) have been freeze-dried using a final concentration of 12% sucrose in the recommended growth media. Longevity studies show that storage at ?30 °C results in acceptable viability. Improved methods for the preservation of strains of Neissera L-phase variants are being investigated.     

Powers of Multiple-Testing Procedures for Identification of Genes Significantly Differentially Expressed in Microarray Experiments

Because of the high operation costs involved in microarray experiments, the determination of the number of replicates required to detect a gene significantly differentially expressed in a given multiple-testing procedure is of considerable significance. Calculation of power/replicate numbers required in multiple-testing procedures provides design guidance for microarray experiments. Based on this model and by choice of a multiple-testing procedure, expression noises based on permutation resampling can be considerably minimized. The method for mixture distribution model is suitable to various microarray data types obtained from single noise sources, or from multiple noise sources. By using the biological replicate number required in microarray experiments for a given power or by determining the power required to detect a gene significantly differentially expressed, given the sample size, or the best multiple-testing method can be chosen. As an example, a single-distribution model of t-statistic was fitted to an observed microarray dataset of 3 000 genes responsive to stroke in rat, and then used to calculate powers of four popular multiple-testing procedures to detect a gene of an expression change D. The results show that the B-procedure had the lowest power to detect a gene of small change among the multiple-testing procedures, whereas the BH-procedure had the highest power. However, all multiple-testing procedures had the same power to identify a gene having the largest change. Similar to a single test, the power of the BH-procedure to detect a small change does not vary as the number of genes increases, but powers of the other three multiple-testing procedures decline as the number of genes increases.     

Synaptic Protein Tyrosine Kinase: Partial Characterization and Identification of Endogenous Substrates

The subcellular distribution of protein tyrosine kinase in rat forebrain was determined using [Val5]-angiotensin II as exogenous substrate. Enzyme activity was present in each of the fractions analyzed and was enriched in synaptic membranes (SMs) and the synaptosomal soluble fraction (2.2- and 2.5-fold over the homogenate, respectively). SMs also phosphorylated polyglutamyltyrosine (pGT; molar ratio of 4:1), the Vmax for angiotensin and pGT phosphorylation being 26.3 +/- 1.6 and 142 +/- 4 pmol/min/mg, respectively. Extraction of SMs with several different detergents resulted in enhanced enzyme activity and the solubilization of 33-37% of the angiotensin and 43-70% of the pGT-phosphorylating activity. Isolated postsynaptic densities (PSDs) contained tyrosine kinase and phosphorylated angiotensin and pGT. The Vmax values for angiotensin and pGT phosphorylation by PSDs were 17 +/- 5 and 23 +/- 1 pmol/min/mg, respectively. Six putative endogenous substrates for SM tyrosine kinase, with molecular weights of 205K, 180K, 76K, 60K, 50K, and 45K, were identified. Each of these proteins, except p76, was phosphorylated in the detergent-insoluble residue obtained following the extraction of SMs with Triton X-100 as well as in PSDs, indicating that the postsynaptic apparatus is an active site of tyrosine phosphorylation. The phosphorylation of p76 was localized to the Triton X-100 extract and also occurred in the synaptosomal soluble fraction. The results indicate that tyrosine kinase and its substrates are located in both pre- and postsynaptic compartments and suggest a role for this enzyme in synaptic function.     

多重检验法在基因芯片研究中鉴定差异表达基因的统计功效

鉴于基因芯片实验的造价,在基因芯片实验设计中,首要考虑的因素是需要多少重复才能检测出一个具有显著差异表达的基因。计算多重检验法要求的重复数（样本大小）或功效可为基因芯片实验设计提供重要的参考。为此,本文基于置换重抽样法构建了一种基因表达噪声混合分布模型。该方法适用各类基因表达数据,即无论是基因表达单噪声源或是多噪声源都可行。应用混合模型和多重检验法并给定统计功效。研究者能在基因芯片实验中获得所需要的最少生物学重复数：或者根据样本大小来确定测定一个显著差异表达的基因所具有的检验功效;或者根据样本大小和统计检验功效,选择最好的统计测验方法。本文以一组在老鼠中与中风有关的3000个基因的基因芯片实验所获得的数据为例,应用该方法拟和后组建了一个单分布模型（即表达单噪声源的分布模型）。根据该模型,我们计算了4种多重检验法在鉴定一个具有表达差异（D）值的基因中所需要的统计功效。结果表明。检测一个小的差异D值,4种多重检验法中B方法的统计功效最低,而BH方法最高。但是,对于鉴定一个具有最大表达差异的基因时,4种方法有相同的鉴定功效。与传统的单个检验法一样,BH方法检测一个小的变化所需要的效率不会随基因数目增加而改变,其他3种多重检验法的检测功效则随基因数目增加而降低。     

Identification and Characterization of Rhizosphere-Competent Bacteria of Wheat

To obtain rhizosphere-competent bacteria which could subsequently be modified for the development of biological control agents, bacteria were isolated from the rhizosphere and rhizoplane of wheat and barley plants by standard techniques. Of these isolates, 60 were selected for field testing as spring wheat seed inoculants in 1985. Isolates were marked genetically for resistance to antibiotics via selection of spontaneous mutants to detect and monitor isolates in the field. Forty-three days after planting, the average log₁₀ CFU/mg (dry weight) of roots and rhizosphere soil for the mutant isolates sampled ranged from 0 to 3.4. Twenty mutant isolates were retested in 1986. A total of 4 isolates were not detected, but the other 16 had an average root colonization value of log₁₀ 2.1 CFU and a range of log₁₀ 0.9 CFU to log₁₀ 3.2 CFU when sampled 32 days after planting. The average colonization value dropped to log₁₀ 1.1 CFU 51 days later. Some isolates detected previously were not detected in the second sampling; others had root colonization values similar to those obtained in the first sampling. Mutant isolates of rhizosphere bacteria included Bacillus pumilus, Bacillus subtilis, Pseudomonas fluorescens, Streptomyces spp., Xanthomonas maltophilia, and a saprophytic coryneform. Mixtures of isolates from different genera and species were compatible on seeds and roots.