ABSTRACT
Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.
Subject(s)
DNA/genetics , Fossils , High-Throughput Nucleotide Sequencing/methods , Livestock/genetics , Skin/chemistry , Animals , Base Sequence , DNA/history , England , High-Throughput Nucleotide Sequencing/trends , History, 17th Century , History, 18th Century , Mass Spectrometry , Molecular Sequence Data , Sequence Alignment , Sheep , Species SpecificityABSTRACT
AIMS: Three soils that varied in their physicochemical characteristics and microbial diversity were inoculated with Escherichia coli O157:H7 and Salmonella to determine the relative impact of abiotic and biotic factors on the pathogens' survival when the soil was held at 25°C. METHODS AND RESULTS: Three soils that were classified as having low, medium and high microbial diversity were divided into two batches for adjustment to 20% of water-holding capacity and to 40% of water-holding capacity. Soils were inoculated with both green fluorescent-labelled E. coli O157:H7 and red fluorescent-labelled Salmonella (5 log CFU g(-1) dry weight) and held at 25°C. Pathogens inoculated into an acidic soil died off within 9 weeks, whereas they were still detected in the other two soils by enrichment culture after 18 weeks. Moisture did not affect inactivation of E. coli O157:H7, but did affect Salmonella inactivation in soil having the greatest organic load and microbial diversity. Using multiple linear regression analysis, 98.7% of the variability in the inactivation rate for E. coli O157:H7 was explained by a model that included the variables of initial pH and electrical conductivity. Salmonella's inactivation rate was predicted by a model that included pH and initial cell numbers of copiotrophic and oligotrophic bacteria. CONCLUSION: This study provided evidence of specific properties that impact inactivation of E. coli O157:H7 and Salmonella in soils at 25°C. SIGNIFICANCE AND IMPACT OF THE STUDY: Identification of factors influential in the die-off of enteric pathogens will assist in developing guidelines for safe intervals between field contamination events and planting or harvesting of fresh-cut produce crops.
Subject(s)
Escherichia coli O157/physiology , Salmonella/physiology , Soil Microbiology , Soil/chemistry , Animals , Biodiversity , Biomass , Colony Count, Microbial , DNA, Ribosomal Spacer/analysis , Electric Conductivity , Humans , Hydrogen-Ion Concentration , Linear Models , Models, Biological , Phosphoric Monoester Hydrolases/analysis , Urease/analysis , Water/metabolism , beta-Glucosidase/analysisABSTRACT
The ability of enteropathogens such as Salmonella and Escherichia coli to adapt and survive acid stress is fundamental to their pathogenesis. Once inside the host, these organisms encounter life-threatening levels of inorganic acid (H+) in the stomach and a combination of inorganic and organic acids (volatile fatty acids) in the small intestine. To combat these stresses, enteric bacteria have evolved elegant, overlapping strategies that involve both constitutive and inducible defense systems. This article reviews the recent progress made in understanding the pH 3 acid tolerance systems of Salmonella and the even more effective pH 2 acid resistance systems of E. coli. Focus is placed on how Salmonella orchestrates acid tolerance by modulating the activities or levels of diverse regulatory proteins in response to pH stress. The result is induction of overlapping arrays of acid shock proteins that protect the cell against acid and other environmental stresses. Most notable among these pH-response regulators are RpoS, Fur, PhoP and OmpR. In addition, we will review three dedicated acid resistance systems of E. coli, not present in Salmonella, that allow this organism to survive extreme (pH 2) acid challenge.
Subject(s)
Adaptation, Biological , Escherichia coli/physiology , Salmonella typhimurium/physiology , Acids, Noncarboxylic/metabolism , Animals , Bacterial Proteins/metabolism , Carboxylic Acids/metabolism , Cattle , Escherichia coli O157/physiology , Gene Expression Regulation, Bacterial , Glucose-6-Phosphate Isomerase/genetics , Glucose-6-Phosphate Isomerase/metabolism , Heat-Shock Proteins/metabolism , Hydrogen-Ion Concentration , Sigma Factor/metabolismABSTRACT
An analysis of the Manufacturer and User Facility Device Experience database of the Food and Drug Administration was conducted to identify adverse event reports associated with pulmonary artery catheter use between 1993 and 1999. Of 714 adverse event reports, there were 48 deaths of which 42 (88%) were related to pulmonary artery rupture. A further analysis of risk factors was conducted and found "postmenopausal female" was a most significant finding. Further study is recommended to establish a causal relationship.