Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum

Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1× coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40–70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP–dROX, we assembled a physical map for P.chrysogenum, with 2–3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.     

Bacillus daqingensis sp. nov. isolated from near poultry farm soil

A novel bacterial strain, designated PFS-5^T, was isolated from the soil environment with feces of a live poultry farm located in Cheonan, Republic of Korea. Strain PFS-5^T was Gram-staining-positive, motile, strictly aerobic bacterium, rod-shaped, and endospore-forming. The strain contained meso-diaminopimelic acid in their peptidoglycan and MK-7 menaquinone. The major fatty acids were anteiso-C_15:0 (44.2%), C_16:0 (22.2%), and iso-C_15:0 (16.7%). The DNA G+C content was 40.1 mol%. Comparative 16S rRNA gene sequence analysis identified strain PFS-5^T in the genus Bacillus, exhibiting the highest level of sequence similarity with type strain of B. herbersteinensis D-1,5a^T (96.9%), B. humi LMG 22167^T (96.7%), B. alkalitelluris BA288^T (96.1%), B. litoralis SW-211^T (96.0%), and B. luteolus YIM93174^T (95.5%). The major polar lipids of PFS-5^T were diphosphatidylglycerol and phosphatidylglycerol. On the basis of result from poly-phasic data, strain PFS-5^T represents a novel species, for which the name Bacillus cheonanensis sp. nov. is proposed (Type strai PFS-5^T = KACC 17469^T = JCM19333^T).     

Environmental specimen banking

Biological Trace Element Research - The risk of environmental damage from the countless chemicals and chemical combinations is estimated by monitoring the air, water, soil, and biota and comparing...     

猪PEG1基因多态性及其遗传印记

PEG1基因影响动物胚胎生长及母性行为,多数动物PEG1为父方表达的遗传印记特征,但出生后猪的PEG1印记表达尚不清楚。因此,文章选取长白、大白和蓝塘3个品种共166头纯种猪,在猪的PEG1基因外显子12区域内寻找SNP,采用PCR-SSCP方法对其多态性进行检测和基因频率分析;取带有PEG1基因该位点SNP为杂合的仔猪3头,对其胃、胸腺、胰、脾、肺、肌肉、肝、舌、肾、脑、膀胱、心脏等组织器官和胎盘的mRNA产物分别进行RT-PCR-SSCP分析,结果表明:PEG1基因外显子12存在一个由G突变为A的单核苷酸多态性位点;PEG1的外显子12在3头仔猪的主要组织器官仅表达父亲来源的等位基因,表明猪的PEG1基因呈母方印记、父方表达的遗传特征。     

Sequential analysis of cell differentials and IFN-gamma production of splenocytes from mice infected with Toxoplasma gondii

To assess the relationship between the changes of cellular components and the production of Th1 cytokine in the immune tissue, inbred C57BL/6 mice were orally infected with 40 cysts of 76K strain of Toxoplasma gondii. The sequential change of cell differentials and IFN-gamma production of splenocytes were analyzed by Diff-Quik stain and RT-PCR. There were no significant proportional changes of cellular components of splenocytes until day 4 postinfection (PI) as compared to those of day 0, and the relative percentage of macrophages and neutrophils/eosinophils increased significantly (p < 0.01) thereafter. The expression of IFN-gamma mRNA of CD3- cells was observed from day 1 PI at a low level. However, IFN-gamma production of CD3+ cells increased significantly from day 4 PI (p < 0.01) which progressively increased thereafter. These findings provide the relative percentages of granulocytes and macrophages were increased in conjunction with increase of total number of splenocytes after oral infection with T. gondii in the susceptible murine hosts, and lymphocytes were the major cellular components and the important source of IFN-gamma.     

Quantitation of efletirizine in human plasma and urine using automated solid-phase extraction and column-switching high-performance liquid chromatography

A heart-cut column-switching, ion-pair, reversed-phase HPLC system was used for the quantitation of efletirizine (EFZ) in biological fluids. The analyte and an internal standard (I.S.) were extracted from human EDTA plasma by C₁₈ solid-phase extraction (SPE) using a RapidTrace^® workstation. The eluent from the SPE was evaporated, reconstituted and injected onto the HPLC column. Urine samples were diluted and injected directly without the need of extraction. The compounds of interest were separated from most of the extraneous matrix materials by the first C₁₈ column, and switched onto a second C₁₈ column for further separation using a mobile phase of stronger eluting capability. Linearity range was 10–2000 ng ml⁻¹ for plasma and 0.05–10 μg ml⁻¹ for urine. The lower limit of quantitation (LOQ) was 10 ng from 1 ml of plasma, with a signal-to-noise ratio of 15:1. Inter-day precision and bias of quality control samples (QCs) were <5% for plasma and <7% for urine. Selectivity was established against six other antihistamines, three analogs of efletirizine, and on 12 control plasma lots and nine control urine lots. Recovery was 90.0% for EFZ and 89.5% for I.S. from plasma. One hundred samples can be processed in every 2.75 h on a 10-module RapidTrace^® workstation with minimal human attention. Method ruggedness were tested on three brands of SPE and six different lots of one SPE brand. Performance ruggedness was demonstrated by different analysts on multiple HPLC systems. Analyte stability through sample storage, extraction process (benchtop, freeze–thaw, refrigeration after extraction) and chromatography (on-system, reinjection) was established.     

Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

Background  

Homologous recombination mediated by the λ-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the λ-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these λ-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains.     

Monitoring the activation of neuronal nitric oxide synthase in brain tissue and cells with a potentiometric immunosensor

An all solid state potentiometric immunosensor (ASPI) has been developed to study the activation process of neuronal nitric oxide synthase (nNOS), the enzyme involved in the synthesis of nitric oxide generated under physiological conditions. At first, an all solid state H⁺-selective ISE was fabricated with the carboxylated poly(vinyl chloride) (PVC-COOH) film containing H⁺ ionophore, antibody was then immobilized on the polymer layer. The immunocomplex formation was detected by monitoring pH change due to interaction between urease labeled secondary antibody and antigen. Experimental parameters such as the amount of phosphorylated nNOS immobilized on the electrode surface and pH responses due to the antibody–antigen reaction were studied in detail. The calibration plot of the potentiometric potential vs. phosphorylated nNOS concentration exhibited a linear relationship in the range of 3.4–340.0 μg/ml. The calibration sensitivity of the phosphorylated nNOS immunosensor was −0.073 ± 0.002 mV/μg ml⁻¹. The detection limit of nNOS was determined to be 0.2 μg/ml based on five-time measurements (95% confidence level, k = 3, n = 5). The reliability of the immunosensor was examined with rat brain tissues as well as neuronal cells, and the results shown were good, implying a promising approach for a novel electrochemical immunosensor platform with potential applications to clinical diagnosis.