Cassettes for PCR-mediated construction of green, yellow, and cyan fluorescent protein fusions in Candida albicans.

We have developed a set of plasmids containing fluorescent protein cassettes for use in PCR-mediated gene tagging in Candida albicans. We engineered YFP and CFP variants of the GFP sequence optimized for C. albicans codon usage. The fluorescent protein sequences, linked to C. albicans auxotrophic marker sequences, were amplified by PCR and transformed directly into yeast. Gene-specific sequence was incorporated into the PCR primers, such that the tag-cassette integrates by homologous recombination at the 3'-end of the gene of interest. This technique was used to tag Cdc3 and Tub1 with GFP, YFP and CFP, which were readily visualized by fluorescence microscopy and localized as expected. In addition, Tub1-YFP and Cdc3-CFP were visualized in the same cells. Thus, this technique directs one-step construction of multiple fluorescent protein fusions, facilitating the study of protein co-expression and co-localization in C. albicans cells in vivo.     

Cooking DNA: the effect of ‘domestic’ cooking methods on detection of GM potato

The ability to detect GM material in otherwise unprocessed foods cooked using domestic methods is important should ‘ready‐to‐eat’ foods require labelling. This study addresses the issue of DNA degradation in foods as a result of cooking. A number of ‘domestic’ cooking methods were shown to affect the length of DNA sequences able to be PCR amplified from potato samples and the degree of degradation was treatment‐specific. However, a. real‐time PCR assay was developed and. GM material was positively identified in all cooked GM potato samples. This confirms that GM material should be able to be detected in otherwise unprocessed food samples cooked using domestic methods, even if the cooking process has partially degraded the DNA. Results indicate, however, that there may be implications of the cooking process on the ability to accurately quantify GM content in some cooked samples.     

基于转录组学分析酸胁迫影响鼠伤寒沙门氏菌耐酸能力的机理

目的：探究酸胁迫和非酸胁迫条件下鼠伤寒沙门氏菌（Salmonella typhimurium）的转录组反应,分析差异基因（differentially expressed genes,DEGs）表达水平,阐明酸胁迫影响鼠伤寒沙门氏菌耐酸反应（acid tolerance response,ATR）的相关代谢通路。方法：对鼠伤寒沙门氏菌进行酸胁迫处理,利用转录组测序技术和生物信息学分析相关DEGs,并通过实时聚合酶链式反应（real-time polymerase chain reaction,real-time PCR）进行验证。结果：经酸胁迫后,共筛选到683 个DEGs,其中上调343 个,下调340 个。其中涉及细胞运动、氨基酸代谢、细胞膜组成等通路上调能够使鼠伤寒沙门氏菌快速适应酸环境;碳水化合物代谢相关通路上调能够为鼠伤寒沙门氏菌快速适应酸环境提供更多的能量,与此同时,嘧啶代谢等能量代谢通路下调能够使鼠伤寒沙门氏菌降低能量消耗以维持上述的必需代谢过程;细菌应激调控相关通路上调赋予鼠伤寒沙门氏菌交叉保护抗性;鞭毛、外膜蛋白、脂多糖等毒力相关基因表达上调增强了鼠伤寒沙门氏菌的毒力。real-time PCR验证结果与转录组测序分析表达趋势一致。结论：酸胁迫显著提高了鼠伤寒沙门氏菌的耐酸能力,其中与代谢和细胞过程相关的通路发挥主要作用,本研究结果为进一步了解该菌的酸胁迫反应及更好地控制其在食品中的污染提供了理论依据。     

A PCR Assay for Specific Detection of the Pandemic Vibrio parahaemolyticus O3:K6 Clone from Shellfish

: The current standard method for identifying Vibrio parahaemolyticus serotype O3:K6, an emerging pathogen with apparent enhanced virulence characteristics, typically takes 4 to 6 d to complete and requires serotyping. To provide a more rapid strategy, we optimized a polymerase chain reaction (PCR)‐based assay for specific detection of V. parahaemolyticus O3:K6. Of 78 V. parahaemolyticus isolates and other related species; only strains classified into the V. parahaemolyticus O3:K6 clonal group (n= 39) showed positive results in the PCR assay. The assay detected 2.3 cells/PCR reaction and 310 cells/g using bacterial cultures and inoculated oyster samples, respectively. Sensitive and specific detection of V. parahaemolyticus O3:K6 was possible following a 6‐h enrichment.     

The Chemistry of PCR Primers: Concept and Application

DNA is a typical organic compound with marked differences from other chemicals and biopolymers because DNA can be amplified by the enzyme polymerase. DNA can be, in principle, amplified from a single copy by the polymerase chain reaction (PCR). In this review, we focus our attention on the chemistry of PCR primers. Because PCR is basic technology in biology research fields, we sometimes use chemically labeled primers without any awareness of the chemistry they leave behind. We would like to emphasize that chemically labeled primers contain a lot of potential for different chemistry ideas and much study is still necessary to advance PCR for single-nucleotide polymorphism (SNP) typing, genetic diagnosis, and other fields. Two categories of primers, affinity-capture primers and signaling primers, are discussed from the viewpoints of their chemical concepts and applications. Affinity-capture primers are used for purification, isolation, and manipulation of PCR products by high specificity and affinity to the cognate molecules by molecule molecule interactions, whereas signaling primers report the hybridization and/or progress of PCR amplification by a signal change, in most cases by a fluorescence change. The content of this review may be useful for a better understanding of the chemistry of PCR primers and, more importantly, for the invention of novel PCR chemistry.     

Short communication: Recovery of viable Mycobacterium avium subspecies paratuberculosis from retail pasteurized whole milk in Brazil

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a chronic granulomatous enteritis that affects all ruminants worldwide. Some researchers have indicated a possible role of MAP in Crohn's disease. Despite extensive research and large and important advances in the past few decades, the etiology of Crohn's disease remains indefinite. The most probable transmission route of MAP from animals to humans is milk and dairy products. Mycobacterium avium ssp. paratuberculosis has already been detected in milk samples worldwide, and some studies have reported that MAP is resistant to pasteurization. In Brazil, MAP has been reported in raw milk samples; however, Brazilian retail pasteurized milk has not yet been tested for viable MAP. The aim of this study was to investigate MAP in pasteurized milk in the region of Viçosa (Minas Gerais, Brazil). Thirty-seven samples were collected and processed for culture of MAP. One colony similar to MAP was observed and confirmed by IS900-nested PCR and sequencing. Analysis revealed 97 to 99% identity with the MAP K-10 strain. This study is the first report of the presence of MAP in retail pasteurized whole milk in Brazil.     

Development of a method for the quantification of haddock (Melanogrammus aeglefinus) in commercial products using real-time PCR

A method is presented for the quantification of haddock in complex food matrices based on real-time PCR. The proportion of haddock muscle tissue to the numbers of a single copy gene has been shown to remain relatively constant, throughout the year and across a number of fishing grounds, using conventional muscle nitrogen content as a comparator. This indicates that quantification of fish, based upon nitrogen content or the numbers of a single copy gene, would return data with a similar degree of accuracy. Thus, a haddock-specific, real-time PCR primer and probe set was designed and optimised, and when used in conjunction with a haddock calibration curve was shown to be able to quantify model samples to within 7% of the true percentage. This is the first report of a real-time assay for the quantification of white fish, which would allow enforcement of the legislation in a complex food matrix containing haddock with other fish species.