Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

An investigation of implicit measurement techniques amongst low risk and forensic samples

There are difficulties with utilising self- report and physiological measures of assessment amongst forensic populations. This study investigates implicit based measures amongst sexual offenders, nonsexual offenders and low risk samples. Implicit measurement is a term applied to measurement methods that makes it difficult to influence responses through conscious control. The test battery includes the Implicit Association Test (IAT), Rapid Serial Visual Presentation (RSVP), Viewing Time (VT) and the Structured Clinical interview for disorders. The IAT proposes that people will perform better on a task when they depend on well-practiced cognitive associations. The RSVP task requires participants to identify a single target image that is presented amongst a series of rapidly presented visual images. RSVP operates on the premise that if two target images are presented within 500milliseconds of each other, the possibility that the participant will recognize the second target is significantly reduced when the first target is of salience to the individual. This is the attentional blink phenomenon. VT is based on the principle that people will look longer at images that are of salience. Results showed that on the VT task, child sexual offenders took longer to view images of children than low risk groups. Nude over clothed images induced a greater attentional blink amongst low risk and offending samples on the RSVP task. Sexual offenders took longer than low risk groups on word pairing tasks where sexual words were paired with adult words on the IAT. The SCID highlighted differences between the offending and non offending groups on the sub scales for personality disorders. More erotic stimulus items on the VT and RSVP measures is recommended to better differentiate sexual preference between offending and non offending samples. A pictorial IAT is recommended. Findings provide the basis for further development of implicit measures within the assessment of sexual offenders.