荧光定量PCR方法检测白酒发酵过程中Aspergillus tubingensis生物量

【目的】为了更好地分析霉菌在白酒发酵过程中的作用,需要快速准确地测定发酵过程中霉菌生物量的变化,本实验以白酒酿造中常用的塔宾曲霉(Aspergillus tubingensis)为例,建立一套快速准确定量塔宾曲霉生物量的方法。【方法】优化从酒醅中提取基因组的方法,设计和验证专一性引物,建立实时荧光定量PCR(Real-time quantitative PCR)方法,验证方法的有效性并应用于白酒发酵过程中塔宾曲霉生物量的检测。【结果】用原位机械破碎法提取酒醅中总基因组,其DNA的浓度能够达到1.060×105 ng/g酒醅;同时建立了一套快速准确测定固态基质中霉菌生物量的方法,并应用于白酒生产(制曲、堆积发酵和窖池发酵过程)中塔宾曲霉生物量的定量。【结论】实时荧光定量PCR方法能够快速准确地测定固态基质中霉菌的生物量,且检测限较低,对今后的相关研究具有借鉴意义。     

Rapid radiometric method for detection of Salmonella in foods.

A radiometric method for the detection of Salmonella in foods has been developed which is based on Salmonella poly H agglutinating serum preventing Salmonella from producing 14CO2 from [14C]dulcitol. The method will detect the presence or absence of Salmonella in a product within 30 h compared to 4 to 5 days by routine culture methods. The method has been evaluated against a routine culture method using 58 samples of food. The overall agreement was 91%. Five samples negative for Salmonella by the routine method were positive by the radiometric method. These may have been false positives. However, the routine method may have failed to detect Salmonella due to the presence of large numbers of lactose-fermenting bacteria which hindered isolation of Salmonella colonies on the selective agar plates.     

免疫-PCR法检测梅毒螺旋体特异性抗体

以梅毒螺旋体重组蛋白为抗原,应用免疫-PCR方法检测梅毒螺旋体抗体,并同常规ELISA法进行比较,探讨免疫-PCR方法检测梅毒螺旋体特异性抗体的可行性。结果免疫-PCR法敏感性是常规ELISA法的104倍,阳性检出率高于ELISA法;对照血清标本梅毒螺旋体抗体检测为阴性。表明免疫-PCR方法具有较高敏感性和特异性,有一定的临床推广价值,对梅毒患者的早期诊断及时治疗等具有重要意义。     

Detection of Enterobacter sakazakii in dried infant milk formula by cationic-magnetic-bead capture

Enterobacter sakazakii has been associated with life-threatening infections in premature low-birth-weight infants. Contaminated infant milk formula (IMF) has been implicated in cases of E. sakazakii meningitis. Quick and sensitive methods to detect low-level contamination sporadically present in IMF preparations would positively contribute towards risk reduction across the infant formula food chain. Here we report on the development of a simple method, combining charged separation and growth on selective agar, to detect E. sakazakii in IMF. This protocol can reliably detect 1 to 5 CFU of E. sakazakii in 500 g of IMF in less than 24 h.     

TaqMan-MGB 探针检测GSTP1外显子5SNP可行性研究

目的：评估TaqMan-MGB探针基因分型方法检测已知SNP的可行性,并与传统的PCR-RFLP方法比较。方法：高通量的TaqMan-MGB探针基因分型方法已被用来检测单核苷酸多态性（SNP）。在321倒样本中,同时用TaqMan-MGB探针基因分型方法和PCR—RFLP方法检测GSTP1外显子5SNP。结果：2种方法所得结果完全一致。野生型（AA）226例（70．4％）,杂合子（AG）92例（28．7％）,纯合突变型3例（O．9％）。结论：TaqMan-MGB探针基因分型方法是一种能快速、高度特异性、高度自动化检测SNP的方法。可用于大规模的基因分型。     

De Novo Identification of Single Nucleotide Mutations in Caenorhabditis elegans Using Array Comparative Genomic Hybridization

Array comparative genomic hybridization (aCGH) has been used primarily to detect copy-number variants between two genomes. Here we report using aCGH to detect single nucleotide mutations on oligonucleotide microarrays with overlapping 50-mer probes. This technique represents a powerful method for rapidly detecting novel homozygous single nucleotide mutations in any organism with a sequenced reference genome.     

Detection of depolymerase isoenzymes after electrophoresis or electrofocusing, or in titration curves

The cup-plate technique makes it possible to detect enzyme activities after diffusion into buffered, substrate-containing agar gels. This technique has been used after nondenaturing blotting transfer in order to detect depolymerizing enzyme activities once analytical protein separation (e.g., by electrophoresis, electrofocusing, or titration curves) has been completed. This rapid and very sensitive method was successfully applied to the enzymes polygalacturonate lyase, polygalacturonate hydrolase, endoglucanase, and xylan hydrolase. Other possible applications are presented.     

A supersensitive dot-hybridization method: rapid and quantitative detection of host-derived DNA in recombinant products at the one picogram level

We have developed a highly sensitive method of DNA dot-blotting hybridization to detect host-derived DNA (nuclear DNA and plasmid DNA) in a recombinant product. This method has two distinctive features compared to the conventional hybridization method: firstly, a highly specific radioactive probe is prepared by using ultrasonicated DNA, instead of untreated DNA, as a template for the oligo-labeling reaction; secondly, the signal to noise ratio is increased by the use of lambda phage DNA as non-homologous DNA. This method enabled us to detect host-derived DNA at the one picogram level without using a radioisotope of high specific activity and long exposure times.     

A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation

The discovery and characterization of microRNAs (miRNAs) and other families of short RNAs has led to a rapid expansion of research directed at elucidating their expression patterns and regulatory functions. Here, we describe a convenient, sensitive, and straightforward method to detect and quantitate specific miRNA levels in unfractionated total RNA samples. The method, based on splinted ligation, does not require specialized equipment or any amplification step, and is significantly faster and more sensitive than Northern blotting. We demonstrate that the method can be used to detect various classes of small regulatory RNAs from different organisms.     

Ultrastructural localization of 5'-nucleotidase in guinea pig neutrophils based upon the use of cerium as capturing agent

A cytochemical method for 5'-nucleotidase localization in which cerium serves as the capture agent in order to enzymatically detect liberated inorganic phosphate has been developed. The method has been established in cell-free model systems and in guinea pig neutrophils where 5'-nucleotidase is restricted to the plasmalemma as an ectoenzyme. This cerium-based method gives better results for ultrastructural localization of 5'-nucleotidase than conventional lead-based methods.     

How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach

Background  

It has been recognized that replicates of arrays (or spots) may be necessary for reliably detecting differentially expressed genes in microarray experiments. However, the often-asked question of how many replicates are required has barely been addressed in the literature. In general, the answer depends on several factors: a given magnitude of expression change, a desired statistical power (that is, probability) to detect it, a specified Type I error rate, and the statistical method being used to detect the change. Here, we discuss how to calculate the number of replicates in the context of applying a nonparametric statistical method, the normal mixture model approach, to detect changes in gene expression.     

应用不同方法检测食品中大肠菌群结果的比较

评价检测食品中大肠菌群不同方法。比较国家标准、行业标准和显色培养基检测方法检测大肠菌群结果的差别。国家标准和行业标准检测结果基本一致,但有差异,应用显色培养基检测大肠菌群优于目前使用的国家标准和出口食品检验行业标准方法。检测食品中大肠菌群,显色培养基检测方法快速、灵敏、特异。     

Detecting protein atom correlations using correlation of probability of recurrence

The dynamic cross‐correlation Map(DCCM) technique has been used extensively to study protein dynamics. In this work, we introduce the use of the method of correlation of probability of recurrence (CPR) as a complementary method to detect correlations between protein residue atoms. Time series of the distances of the C_α atoms of the β‐lactamase inhibitory protein (BLIP) from a reference position are analyzed using CPR and mutual information (MI). The results are compared to those provided by DCCM. In comparison to MI, CPR is found to detect more of the correlations present in DCCM. It is also able to detect a small number of significant correlations between distant residues that are not detected by DCCM. Proteins 2014; 82:2180–2189. © 2014 Wiley Periodicals, Inc.     

Multilocus variable number tandem repeat analysis (MLVA) of Streptococcus pyogenes

We tested 21 polymorphic loci encoded by the genome of Streptococcus pyogenes (group A Streptococcus, GAS). Seven of them were chosen for the MLVA scheme. The primer pairs, designed for selected loci, detect from few to several alleles, and the method has a Simpson's Index of diversity of 0.957. To test the overall performance of the method, multiplex PCR reactions were carried out for over 700 GAS strains. Using the method we were able to detect differences between highly clonal strains that share the same emm, MLST and PFGE types. The most diverse strains were M4, M2, M3 and M28.We developed a typing method that can be employed to differentiate between GAS strains. The method has high resolution and measures diversity of the GAS core chromosome, on the contrary to methods such as PFGE.     

Detection of diarrhetic shellfish poisoning toxins from tropical shellfish using liquid chromatography-selected reaction monitoring mass spectrometry

A negative mode liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) method was developed to detect low concentrations of the diarrhetic shellfish poisoning (DSP) toxins okadaic acid and dinophysistoxin-1 (DTX-1). Detection relies upon monitoring the transition of negative precursor ions [M - H]- to a common fragment ion of m/z 255. Our limit of detection for okadaic acid with this method is 0.5 pg on column. LC-SRM MS has allowed us to detect persistent, low concentrations of DSP toxins from Singapore shellfish.     

Glycosphingolipid immunostaining: detection of antibody binding with an avidin-biotin enzyme system

Glycosphingolipids carrying carbohydrate sequences recognized by antibodies and lectins can be detected on thin layer chromatograms using an avidin-biotin enzyme system (ABC reagents). This same method can be used to detect glycosphingolipids blot-transferred from thin layer chromatograms to nitrocellulose. This method has certain advantages over the original radioimmunoassay method, including development of positive bands in minutes after incubation with the substrate, avoidance of handling hazardous radioactive materials and stability of reagents. We have demonstrated the usefulness of this method for immunostaining glycosphingolipids with both monoclonal and polyclonal anti-carbohydrate antibodies. These reagents have previously been used to detect carbohydrate antigens in tissues and isolated cells and now it is possible to use the same reagents for the detection of glycosphingolipid antigens on chromatograms.     

Detection of multiple QTL with epistatic effects under a mixed inheritance model in an outbred population

A quantitative trait depends on multiple quantitative trait loci (QTL) and on the interaction between two or more QTL, named epistasis. Several methods to detect multiple QTL in various types of design have been proposed, but most of these are based on the assumption that each QTL works independently and epistasis has not been explored sufficiently. The objective of the study was to propose an integrated method to detect multiple QTL with epistases using Bayesian inference via a Markov chain Monte Carlo (MCMC) algorithm. Since the mixed inheritance model is assumed and the deterministic algorithm to calculate the probabilities of QTL genotypes is incorporated in the method, this can be applied to an outbred population such as livestock. Additionally, we treated a pair of QTL as one variable in the Reversible jump Markov chain Monte Carlo (RJMCMC) algorithm so that two QTL were able to be simultaneously added into or deleted from a model. As a result, both of the QTL can be detected, not only in cases where either of the two QTL has main effects and they have epistatic effects between each other, but also in cases where neither of the two QTL has main effects but they have epistatic effects. The method will help ascertain the complicated structure of quantitative traits.     

Use of pseudosubstrate affinity to measure active protein kinase A

Traditional cAMP-dependent protein kinase (also known as protein kinase A [PKA]) assays, which are based on substrate phosphorylation, often have high background activity from other kinases, thereby limiting sensitivity and making it difficult to detect low levels of active PKA in cell lysates. Therefore, a better technique that measures active PKA in crude cell lysates undoubtedly is necessary. We developed an efficient and sensitive assay to compare active PKA levels based on binding of the active PKA catalytic subunit to its pseudosubstrate domain inhibitor (PKI) fused with glutathione S-transferase (GST-PKI). This pseudosubstrate affinity assay can detect variations in the active PKA levels in the presence of common inducers of PKA activity such as forskolin and prostaglandins. It has resolution to detect a concentration-dependent curve of active PKA in a linear range, and it also has sensitivity to detect up to 2.5 ng of active enzyme. An observed change in the binding affinity between PKA and PKI in the presence of the PKA inhibitor N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide (H89) shows that this assay can be successfully used to measure how active PKA is affected by specific inhibitors. We conclude that this method is a simple, inexpensive, and nonhazardous method to compare active PKA levels with high sensitivity and specificity with negligible background.