The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel methylation patterns corresponding to nine recognition sequences were detected (26695, 3; J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and expression of candidate methyltransferases (MTases) permitted not only the functional characterization of multiple, yet undescribed, MTases, but also revealed novel features of both Type I and Type II R-M systems, including frameshift-mediated changes of sequence specificity and the interaction of one MTase with two alternative specificity subunits resulting in different methylation patterns. The methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori R-M systems in limiting transformation as well as in gene regulation and host interaction.
MYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far.
We report on the first foodborne outbreak of Shigella sonnei described in Austria. On July 14 2008, AGES was informed of a cluster of 22 laboratory-confirmed cases of infection with S. sonnei restricted to public health district X in the province of Salzburg. All cases had attended a youth-group trip to a small village in the province of Tyrol from July 7 to July 9. An outbreak case among the trip participants was a person who (1) attended the trip and (2) fell ill with diarrhea in the period between July 8 and July 12. Among the 61 trip participants, 42 fitted the outbreak case definition, including 31 culture-confirmed cases. A household outbreak case was a person who (1) did not participate in the trip, (2) fell ill with diarrhea not before July 10 and (3) had household contact with an outbreak case between one and three days before onset of illness. Of the 11 household outbreak cases, 10 were tested by stool culture and four of these had a laboratory-confirmed S. sonnei infection. In addition, one of the two hostel staff tested positive for S. sonnei. All 36 isolates were biotype gl, lysotype 12, and were indistinguishable from each other by PFGE. A cohort study among the trip participants revealed a risk ratio of 2.71 for consumption of salad (on at least 1 of the 3 days of the trip) (95% CI: 1.38-5.32, P = 0.004). Among the 42cases, 34 could be explained by consumption of salad. The landlady of the hostel, who prepared the salad with bare hands, was a carrier and was assumed to be the source of contamination of the salad. Without proper epidemiological analytical investigation of this shigellosis outbreak, its association with food consumption would not have been identified.
In April 2008, a general foodborne outbreak of Salmonella Enteritidis phage type 6 affected nine persons (two households in Salzburg and one household in Tyrol; eight microbiologically confirmed cases and one possible case). Epidemiological investigation revealed that all cases had eaten lunch together at a farm. Homemade bread dumpling loaf, prepared with eggs from the farm, was the most likely vehicle for the pathogen. Six eggs were bacteriologically tested and yielded the outbreak strain on the egg shells. The farms egg laying flock consisted of 12 hens, which were identified as the source of infection by isolating the outbreak strain from samples of hen fecal material and dust. Molecular subtyping using multiple loci variable number of tandem repeats analysis (MLVA) revealed a pattern unique to isolates from the outbreak, different from nine epidemiologically unrelated isolates tested for comparison. The laying hens were culled and no further cases of salmonellosis were associated with the farm. This example demonstrates the considerable potential of outbreak investigation to elucidate the transmission of infection along the food chain and to provide information essential for implementation of targeted measures for prevention of foodborne illness.
Norovirus is increasingly recognized as a leading cause of outbreaks of foodborne disease. We report on an outbreak in Austria that reached a total of 176 cases, affecting pupils and teachers from four schools on a skiing holiday in a youth hostel in the province of Salzburg in December 2007. A questionnaire was sent to the four schools in order to obtain data from persons attending the school trip on disease status, clinical onset, duration of illness and hospitalization. A cohort study was undertaken to identify the sources of infection. The school trip attendees were interviewed by questionnaire or face-to-face on their exposure to food items from the menu provided by the hostel owner. Of the 284 school holiday-makers, 176 fitted the definition of an outbreak case (attack rate 61.9%). A total of 264 persons on the ski holiday participated in the cohort study (response rate 93%). The day-by-day food-specific analyses did not find any food items served on any of five days (December 8-12) of the holiday to be associated with infection risk. The day-specific risk analyses revealed Monday December 10 (RR: 9.04; 95% CI: 6.02-13.6; P < 0.001) and Tuesday December 11 (RR: 3.37; 95% CI: 2.56-4.43; P < 0.001) as the two most risky days for having being exposed to norovirus. According to the epidemiological investigation, airborne transmission of norovirus originating from the first vomiting case most probably initiated this outbreak; foodborne genesis was excluded. During recent years, norovirus has become increasingly established as the most important causative agent of epidemic gastroenteritis in holiday-makers all over Europe. Tourism is one of the primary industries in Austria. Timely involvement of the relevant public health authorities is essential in any outbreak of norovirus gastroenteritis, irrespective of its genesis.
Most oesophageal carcinomas (>70%) are squamous cell carcinomas (SCC) arising from the surface epithelial lining. In the gastro-oesophageal junction (GEJ) adenocarcinomas occur in the setting of Barrett oesophagus (BE). These carcinomas typically present with surface ulceration. The authors report a rare case of a SCC of the GEJ with completely intramural growth underneath intact non-dysplastic oesophageal squamous epithelium and BE without dysplasia. The sharply demarcated tumour was located in the muscularis propia with infiltration of perioesophageal tissue nearly reaching the diaphragm. Intramural squamous carcinomas are very rare with only three reported cases. In this study, the authors discuss this finding and review the relevant literature. Intramural carcinomas are a diagnostic challenge for clinicians and pathologist, since preoperative biopsies mostly fail to establish the diagnosis and surgical explorations must be considered.
Strategies of groundwater protection in agricultural dominated areas are mainly based on a general reduction of the input of nutrients like nitrate. However, preventive measures in different parts of the catchment may provide very different effects on raw water quality. Exemplified on the case study Liedern (BEW GmbH Bocholt, Germany) it is shown that hydrogeochemical processes along the flow path and in the well strongly affect the results of agricultural measures in terms of modality and efficiency. Thus, a reduction of fertilization in the vicinity of the well gallery leads to a decrease of nitrate concentration in the raw water. Whereas agricultural measures in the eastern part of the catchment do not influence nitrate, but cause a reduction of the iron concentration and rate of incrustation in the wells after 18 years. In this study we present a management tool that enables assessment of future trends in raw water quality. The tool is based on a reactive transport model which considers land use dynamics as an instrument to influence groundwater/raw water quality. A thermodynamic equilibrium approach is applied for modelling hydrogeochemical processes between aqueous, solid and gaseous phases. Kinetically controlled reactions like the microbial degradation of organic carbon are expressed by multiplicative Michaelis-Menten equations.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.