A PCR test for detecting Escherichia coli O157:H7 based on the identification of the small inserted locus (SILO157)

AIMS: This paper provides identification of a DNA sequence derived from Shiga toxin-producing Escherichia coli (STEC) O157:H7 and information on its utilization for detecting STEC O157 by PCR. METHODS AND RESULTS: Random Amplified Polymorphic DNA and DNA library were used to identify in STEC O157:H7 (strain EDL 933) a 2634-bp Small Inserted Locus, designated SILO157. Analysis of 211 bacterial strains showed that the PCR assays amplifying the SILO157 region could be used to detect STEC O157 with a good specificity. CONCLUSIONS: Characterization of a novel locus in STEC O157 is attractive since the serotype O157:H7 of STEC is still by far the most important serotype associated with more serious diseases. This island encodes putative proteins and especially one that is predicted to be an outer membrane protein designated IHP1. SIGNIFICANCE AND IMPACT OF THE STUDY: Further investigations could now be developed to appreciate the role of the SILO157 in pathogenicity.     

HPLC analysis of plant DNA methylation: a study of critical methodological factors.

HPLC analysis of nucleosides is important for determining total DNA methylation in plants and can be used to help characterise epigenetic changes during stress, growth and development. This is of particular interest for in vitro plant cultures as they are highly susceptible to genetic change. HPLC methodologies have been optimised for mammalian and microbial DNA, but not for plants. This study examines critical methodological factors in the HPLC analysis of plant DNA methylation using in vitro cultures of Ribes ciliatum. HPLC revealed that complete removal of RNA from plant DNA extractions is difficult using RNase (A and T1) digestions and LiCl precipitation. This suggests that base analysis should be avoided when using these RNA removal techniques, as bases from residual RNA fragments will inflate peak areas for DNA-derived bases. Nucleoside or nucleotide analysis is therefore recommended as a more suitable option as RNA and DNA constituents can be readily separated. DNA digestion was also a critical factor as methylation was under-estimated following incomplete nuclease digestion and over-estimated following incomplete phosphatase digestion. The units of enzyme required for complete DNA digestion was optimised and found to be 20-200 times less for nuclease P1 and 15 times less for alkaline phosphatase as compared with previous protocols. Digestion performance was conveniently monitored using marker peaks that indicate incomplete digestion products. This study identifies critical components of HPLC analysis and offers a comprehensive guide for the stringent analysis of DNA methylation in plants.     

Detection of Escherichia coli serogroup O103 by real-time polymerase chain reaction

AIMS: The aims of the study were to identify the specific genes of O-antigen gene cluster from Shiga toxin-producing Escherichia coli (STEC) O103 and to provide the basis for a specific real-time PCR test for rapid detection of E. coli O103. METHODS AND RESULTS: The published primers complementary to JUMPstart and gnd gene, the conserved flanking sequences of O-antigen genes clusters in E. coli and related species, were used to amplify the 12-kbp O103 O-antigen biosynthesis locus of STEC O103. A DNA library representative of this cluster allowed two O103-specific probes to be identified in the flippase (wzx) and UDP-galactose-4-epimerase (galE) genes. Two specific O103 serotyping real-time PCR tests based on these two genes were successfully developed. CONCLUSIONS: These results confirm that the O-antigen gene cluster sequences of E. coli allow rapidly a specific O-antigen real-time PCR assay to be designed. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings increase the number of real-time PCR-assays available to replace the classical O-serotyping among E. coli O-antigen.     

Dynamics of a memory trace: effects of sleep on consolidation

BACKGROUND: There is evidence that sleep is important for memory consolidation, but the underlying neuronal changes are not well understood. We studied the effect of sleep modulation on memory and on neuronal activity in a memory system of the domestic chick brain after the learning process of imprinting. Neurons in this system become, through imprinting, selectively responsive to a training (imprinting) stimulus and so possess the properties of a memory trace. RESULTS: The proportion of neurons responsive to the training stimulus reaches a maximum the day after training. We demonstrate that sleep is necessary for this maximum to be achieved, that sleep stabilizes the initially unstable, selective responses of neurons to the imprinting stimulus, and that for sleep to be effective, it must occur during a particular period of time after training. During this period, there is a time-dependent increase in EEG activity in the 5-6 Hz band, that is, in the lower range of the theta bandwidth. The effects of sleep disturbance on consolidation cannot be attributed to fatigue or to stress. CONCLUSIONS: We establish that long-term trace consolidation requires sleep within a restricted period shortly after learning. Undisturbed sleep is necessary for the stabilization of long-term memory, measured at the behavioral and neuronal levels, and of long-term but not short-term neuronal responsiveness to the training stimulus.     

Cold susceptibility and disinfestation of Bactrocera invadens (Diptera: Tephritidae) in oranges

To develop a cold disinfestation treatment for the fruit fly Bactrocera invadens Drew, Tsuruta & White (Diptera: Tephritidae) that is rapidly spreading across Africa, research was conducted in Nairobi, Kenya, using flies from a laboratory culture and 'Valencia' orange (Citrus sinensis L. Osbeck) as the host. The developmental rate of B. invadens in Valencia oranges was determined at 28 degrees C, and the third instar was found to be the least susceptible of the egg and larval life stages to cold treatment at 1.1 degrees C in oranges. When 22,449 B. invadens third instars were exposed in oranges to a cold treatment with an approximate midpoint of 1.1 +/- 0.5 degrees C, the results suggested that a period of 16 d would be worthwhile verifying on a larger scale in oranges. Results from the first replicate of 16,617 larvae showed no survivors, but the second replicate of 23,536 larvae had three survivors. Because a longer cold treatment based on a mean temperature of 1.1 degrees C would create logistical difficulties for some export markets, further replicates were conducted at an approximate midpoint of 0.5 degrees C and at mean hourly maximum of 0.9 +/- 0.5 degrees C, for 16 d. After three replicates, in which 65,752 B. invadens third instars in total were treated with no survivors, the Japanese requirement of 99.99% mortality at the 95% confidence level was surpassed. The following treatment protocol for B. invadens larvae in oranges can therefore be recommended: fruit pulp to be maintained at temperatures of 0.9 degrees C or lower for 16 consecutive days.     

Survival of shoot meristems of tomato seedlings frozen in liquid nitrogen

An explant containing the primary shoot meristem was dissected from intact tomato seedlings after thawing from liquid nitrogen. Surviving explants produced shoots directly by normal meristem growth when cultured in the presence of gibberellic acid. Without gibberellic acid all surviving explants produced callus tissue and subsequently adventitious shoots, with no direct outgrowth of the primary meristem.Dimethyl sulphoxide (15%) in culture medium and a cooling rate changing continuously from 20 to 55 °C min^?1 between 0 and ?120 °C were required for optimal survival.Nonfrozen material produced shoots directly without the requirement for gibberellic acid indicating that hormonal regulation of organised growth by the shoot meristem had been altered by the freeze/ thaw process.     

Development of a 5'-nuclease PCR assay for detecting Shiga toxin-producing Escherichia coli O145 based on the identification of an 'O-island 29' homologue

AIMS: A DNA sequence, from Escherichia coli STEC O145, homologous to O-island 29 from STEC O157 is described, together with a real-time PCR assay for detecting it. METHODS AND RESULTS: PCR and sequencing were used to identify the 'O-island 29' homologous DNA sequence from STEC O145 (strain VTH34). The sequence divergence between the STEC O145 and O157 'O-island 29' allowed a STEC O145 5'-nuclease PCR assay to be developed. CONCLUSIONS: The characterization of a novel locus in STEC O145 has allowed a specific O145 serogroup 5'-nuclease PCR assay to be designed. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings increase the number of serogroup PCR assays available as alternatives to classical O-serotyping of E. coli.     

Identification of the O-antigen biosynthesis genes of Escherichia coli O91 and development of a O91 PCR serotyping test

AIMS: The aims of the study were to characterize the O91 O-antigen gene cluster from Shiga toxin-producing Escherichia coli (STEC) O91 and to provide the basis for a specific PCR test for rapid detection of E. coli O91. METHODS AND RESULTS: The published primers complementary to JUMPstart and gnd gene, the conserved flanking sequences of O-antigen genes clusters in E. coli and related species were used to amplify the 10-kbp O91 O-antigen biosynthesis locus of STEC O91. A DNA library representative of this cluster allowed two O91 specific probes to be identified, and two specific PCR O91 serotyping tests to be successfully developed. CONCLUSIONS: These results confirm that the O-antigen gene cluster sequences of E. coli allow rapidly a specific O-antigen PCR assay to be designed. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings increase the number of PCR-assays available to replace the classical O-serotyping among E. coli O-antigen.