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James Robertson

Publications and source records attributed to James Robertson.

At least 19 recordsLinked to original sources
PubMed2026

Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.

Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.

Metagenomics↗
PubMed2006

Chemical profiling of heroin recovered from the North Korean merchant vessel Pong Su.

Heroin samples, seized from the North Korean merchant vessel Pong Su in Australian waters, were analyzed to determine geographic origin. Duplicate samples were analyzed by the National Measurement Institute's Australian Forensic Drug Laboratory and the United States Drug Enforcement Administration's Special Testing and Research Laboratory. Alkaloid ratios were determined by both liquid chromatography-diode array detection (LC-DAD) and capillary electrophoresis-diode array detection (CE-DAD) techniques. Acid/neutral manufacturing by-products were determined by solvent extraction followed by gas chromatography-mass spectrometry (GC-MS). Solvents, trapped in the heroin particles during manufacture, were detected by both static headspace GC-MS and purge and trap GC-MS. The alkaloid ratios obtained were consistent with heroin of a Southeast Asian (SEA) origin and principal component analysis of the alkaloid results demonstrated the presence of at least four subgroupings within the seizure. The solvent analysis detected diethyl ether and ethyl acetate, solvents typically seen in SEA heroin. However, the acid/neutral analysis revealed compounds not normally seen in heroin of a SEA origin. Furthermore, sterol-like molecules, always detected in the acid/neutral analysis of SEA heroin, were absent from the Pong Su samples. The Pong Su heroin, although similar to SEA heroin, has sufficient differences to classify it as having an unknown origin at the time of this writing.

Journal Article↗
PubMed2005

Short tandem repeat (STR) genotyping of keratinised hair. Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles.

A feasibility study of short tandem repeat (STR) genotyping of telogen phase hairs in particular, and hair shaft in general, is presented. A number of extraction procedures in common use were investigated and the quantities of nuclear DNA (nuDNA) delivered were quantified via a real-time PCR assay. The extracts were subjected to two variations on AmpFlSTR Profiler Plus PCR amplification strategies (extended cycles, two rounds of PCR) and the genotypes compared. Nuclear DNA was found to persist in human hair shafts, albeit at very low levels. Full Profiler Plus profiles consistent with the hair donor were obtained from 100 mg hair shaft samples (bleached and unbleached). These were, however, mixed profiles, indicating low copy number (LCN) contamination in the extracts. Single telogen hair clubs and single hair shafts delivered partial profiles with usually only one allele of heterozygous loci. Telogen phase hairs yielded the same amount of nuDNA (and no more) as hair shafts (either anagen or telogen). Whether hair shafts dissolved or not in lysis buffer had no effect on either the quantitated yield of DNA or on the chance of obtaining a correct genotype. These results provide evidence that genomic DNA resides on the exterior of the hair shaft and we use this information to suggest an optimal procedure for nuDNA extraction from keratinised hair samples: soaking hairs in simple digestion buffers containing Tris-HCl, a salt and a chelating agent without prior cleaning of the hair shafts. It is proposed that cleaning removes most of the recoverable DNA. This procedure was applied to obtain genotypes from 3 cm hair shafts which matched reference profiles from the donors at up to 9 out of 10 AmpFlSTR Profiler Plus STR loci. When the genotyping success was measured by counting the number of matches between the two dominant alleles at each locus for each extract with the reference DNA profile of the hair donor, the success was found to be highly dependent on the donor. The number of matching alleles varied between not less than 10 for one donor to no more than two for another donor. These results may well be linked to the environmental experience of the hairs from each donor prior to removal.

DNA↗
PubMed2005

Short tandem repeat (STR) genotyping of keratinised hair. Part 1. Review of current status and knowledge gaps.

We present a review of the literature on procedures for obtaining short tandem repeat (STR) genotypes from keratinised hair, being either hair shaft or telogen phase (naturally shed) hairs without associated scalp, follicle or sheath cells. Both the hair shaft and the telogen hair club have been subjected to the DNA-degrading keratinisation process and are more likely to be found at a crime scene than anagen (plucked) or catagen phase hairs. We discuss human hair structure, the human hair growth cycle, the keratinisation process and their implications for DNA extraction procedures, PCR amplification strategies and the interpretation of STR genotypes. Knowledge gaps and areas requiring research are identified and are the subject of a second article in this series.

DNA↗
PubMed2005

Decreased stability and translation of T cell receptor zeta mRNA with an alternatively spliced 3'-untranslated region contribute to zeta chain down-regulation in patients with systemic lupus erythematosus.

The molecular mechanisms involved in the aberrant expression of T cell receptor (TCR) zeta chain of patients with systemic lupus erythematosus are not known. Previously we demonstrated that although normal T cells express high levels of TCR zeta mRNA with wild-type (WT) 3' untranslated region (3' UTR), systemic lupus erythematosus T cells display significantly high levels of TCR zeta mRNA with the alternatively spliced (AS) 3' UTR form, which is derived by splice deletion of nucleotides 672-1233 of the TCR zeta transcript. Here we report that the stability of TCR zeta mRNA with an AS 3' UTR is low compared with TCR zeta mRNA with WT 3' UTR. AS 3' UTR, but not WT 3' UTR, conferred similar instability to the luciferase gene. Immunoblotting of cell lysates derived from transfected COS-7 cells demonstrated that TCR zeta with AS 3' UTR produced low amounts of 16-kDa protein. In vitro transcription and translation also produced low amounts of protein from TCR zeta with AS 3' UTR. Taken together our findings suggest that nucleotides 672-1233 bp of TCR zeta 3' UTR play a critical role in its stability and also have elements required for the translational regulation of TCR zeta chain expression in human T cells.

3' Untranslated Regions↗
PubMed2005

Innate IL-10 promotes the induction of Th2 responses with plasmid DNA expressing HIV gp120.

Like most DNA vaccines, intramuscular immunization with plasmid DNA coding for influenza virus haemagglutinin (HApDNA) induced Th1 responses and IgG2a antibodies in mice. However, plasmid DNA coding for HIV gp120 (gp120pDNA) induced Th2-biased responses and predominantly IgG1 antibodies. Responses to gp120pDNA switched to a Th1-type in IL-10-defective mice and to exclusively IgG2a antibodies in IL-4-defective mice. Conversely, antigen-specific IFN-gamma production induced by gp120pDNA or HApDNA was reduced in IL-12-defective mice, whereas addition of plasmid DNA coding for IL-12 enhanced Th1 responses. Plasmid DNA stimulated IL-10 and IL-12 production by macrophages and dendritic cells (DCs) in vitro and anti-IL-10 antibodies enhanced IL-12 production and DC maturation in response to gp120pDNA. Our findings suggest that T cell responses induced by DNA vaccines is influenced by the nature of the antigen, and that the induction of Th2-biased responses with gp120pDNA is mediated in part through the stimulation of innate IL-10, which inhibits activation of DCs that direct the induction of Th1 cells.

Animals↗
PubMed2004

Hospital bioterrorism preparedness linkages with the community: improvements over time.

BACKGROUND: Strong linkages between hospitals and community response entities such as fire safety, law enforcement, emergency management agencies, emergency medical services, public health, and local government administration are an essential element of overall hospital preparedness. These pre-established relationships enable an integrated community response during an emergency. METHODS: This pilot study assessed changes in linkages between hospitals and key community entities related to preparedness for a bioterrorism (BT) event before and after the events of fall 2001. A 51-item questionnaire was mailed to two consecutive hospital samples scheduled for accreditation surveys (April-May 2001 and May-June 2002; n=68 and n=97 responses, respectively). On-site visits by surveyors verified the presence of a plan addressing bioterrorism issues. RESULTS: Substantial improvement in collaborative planning for surge capacity and lab/pharmacy issues occurred. Hospital plans that addressed BT increased significantly (47.1% to 90.7%), as did awareness of community BT-related plans (48.5% to 74.2%). Hospitals that conducted a BT-related drill increased from 19.1% to 48.5%. CONCLUSIONS: Adequate resources are needed, but opportunities remain to further improve collaborative planning, such as agreements with other hospitals on a single media spokesperson or development of a protocol for pharmaceutical distribution. Additional guidance is needed on expected levels of performance regarding linkages.

Bioterrorism↗
PubMed2004

Rates of claims for cumulative trauma disorder of the upper extremity in Ontario workers during 1997.

Surveillance of work-related cumulative trauma disorder of the upper extremity (CTDUE) requires valid and reliable claim extraction strategies and should examine for confounding and interaction. This research estimated crude and specific rates of CTDUE claims in Ontario workers during 1997 while acknowledging misclassification and testing for confounding and interaction. Lower and upper limit event estimates were obtained by means of an algorithm applied to the Ontario Workplace Safety and Insurance Board (OWSIB) database and were combined with "at-risk" estimates obtained from the Canadian Labour Force Survey (LFS). Poisson regression was used to evaluate confounding and interaction. The method used to identify CTDUE claims had a substantial impact on the magnitude of rates, female to male rate ratios, the most commonly affected part of the upper extremity and the highest risk occupational categories. Poisson regression identified sex interactions. It allowed rigorous evaluation of the data and indicated that rates should be examined separately for men and women. Researchers should clearly define extraction strategies and examine the impact of misclassification.

Adolescent↗
PubMed2003

Public health. Building microbial forensics as a response to bioterrorism.

Combating bioterrorism is a challenge to all of us. To be proactive, the U.S. Government has formalized the discipline of "microbial forensics" to deter and attribute perpetrators of such acts. This Policy Forum describes the foundations of the microbial forensics program: the creation of a national bioforensics laboratory, a partnership laboratory network, and a peer-consensus scientific working group and the promulgation of quality assurance guidelines.

Advisory Committees↗
PubMed2003

An evaluation of the Maxcan fibre finder version 3.3 on cotton fibres.

The Maxcan fibre finder system is a product of Cox Analytical Systems, Sweden, and has been developed for the primary purpose of searching for fibres on tape lifts. This paper evaluates the ability of the Maxcan system to search for different fibre types and colours under varying conditions. The system performed effectively in most situations, although it did have problems with some search combinations that a human operator would also find difficult in a manual search. The Maxcan system has the added advantages of being objective, consistent and able to do large batch searches unattended. These attributes make it very useful where a large number of tapes need to be searched in casework and also in research where large quantities of data need to be gathered within a reasonable time.

Journal Article↗
PubMed2003

Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations.

Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.

Alleles↗
PubMed2003

Identifying cumulative trauma disorders of the upper extremity in workers' compensation databases.

BACKGROUND: Impeding the use of workers' compensation databases for surveillance of cumulative trauma disorder of the upper extremity (CTDUE) is the lack of valid and reliable extraction strategies. METHODS: Using the Z795-96 Coding of Work Injury or Disease Information standard, an algorithm was developed to classify claims as definite, possible, or non-CTDUE. Reliability was assessed with standardized claim reviews. RESULTS: Moderate to substantial agreement (Kappa = 0.48, 95% CI 0.42-0.54, n = 328; weighted Kappa = 0.75, 95% CI 0.70-0.80, n = 328) was demonstrated. The algorithm produced relatively homogeneous groups of definite and non-CTDUE claims but 29.1% of the possible CTDUE claims were categorized as definite CTDUE by claim review. Part of body agreement was almost perfect (Kappa = 0.81-1.00) when determining whether the upper extremity or specific parts of the upper extremity were involved. CONCLUSIONS: The algorithm can be used to estimate the number of CTDUE and extract homogeneous groups of definite and non-CTDUE claims. Furthermore, certain upper extremity part of body codes can be used to target anatomically defined claims.

Algorithms↗
PubMed2002

Work-related cumulative trauma disorders of the upper extremity: navigating the epidemiologic literature.

BACKGROUND: Cumulative trauma disorder of the upper extremity (CTDUE) is an umbrella term used to describe disorders resulting from repeated use of the upper extremity over time rather than a specific incident. The primary purpose of this article is to summarize the literature regarding the rate of work-related CTDUE, while drawing attention to the various factors contributing to the wide range of reported findings. METHODS: The Cumulative Index to Nursing and Allied Health and Medline databases were searched for articles focusing on etiology or rates of occurrence of work-related CTDUE and their findings were summarized. RESULTS: Potential reasons for rising rates, a gender differential, and the substantial range in rates and rate ratios are delineated and important factors to consider when interpreting rates derived from workers' compensation data are detailed. CONCLUSIONS: Future research should attempt to correctly identify more specific categories of CTDUE in well-defined and accurately-quantified "at risk" populations to provide more meaningful information regarding the epidemiology of CTDUE and the effectiveness of control activities.

Adult↗
PubMed2002

Influence of an artificial cervical joint compared with fusion on adjacent-level motion in the treatment of degenerative cervical disc disease.

OBJECT: The authors report the preservation of motion at surgically treated and adjacent spinal segments after placing an artificial cervical joint (ACJ) and they describe the influence of interbody fusion on changes in angulation occurring in the sagittal plane at adjacent levels in the treatment of cervical spondylosis. METHODS: The authors conducted a prospective nonrandomized study of patients in whom an ACJ was placed or autologous bone graft interbody fusion was performed. Angular measurements at levels adjacent to that surgically treated were calculated using plain flexion-extension radiographs obtained at 6-month intervals. Analyses of qualitative data, such as increase or decrease in adjacent-level motion, and the degree of disc degeneration were performed. Quantitative data were also analyzed. In the fusion group a significant increase in adjacent-level movement was demonstrated at the 12-month follow-up visit compared with the group of patients in whom ACJs were placed (p < 0.001). The increase in movement occurred predominantly at intervertebral discs that were preoperatively regarded as normal (p < 0.02). An overall reduction in adjacent-level movement was observed in patients who underwent joint replacement, although this was compensated for by the movement provided by the ACJ itself. CONCLUSIONS: Fusion results in increased motion at adjacent levels. The increase in adjacent-level motion derives from those discs that appear radiologically normal prior to surgery. It remains unknown whether ACJs have a protective influence on adjacent intervertebral discs.

Adult↗
PubMed2002

Estimating the population at risk for Ontario Workplace Safety and Insurance Board-covered injuries or diseases.

Difficulty in quantifying the population at risk for a work-related injury or disease limits the usefulness of workers' compensation data for surveillance. This article presents a method of obtaining estimates of the Ontario Workplace Safety and Insurance Board (OWSIB)- covered workforce using the Canadian Labour Force Survey (LFS). The method involves extracting that class of worker most likely to be insured by the OWSIB and using actual hours worked to estimate full-time equivalents at risk. Compared to population at risk estimates readily available from published tables, the refined crude estimate was 26% lower and ranged from 15 to 79% lower depending on the age group. The percentage decrease from published estimates was generally greater for women compared to men, particularly in the 25 to 39 year age categories. Consequently, the method of deriving population at risk estimates should be considered when comparing rates across sexes, ages, industries or occupations.

Adolescent↗
PubMedDate not supplied

The population of coloured textile fibres in domestic washing machines.

A population survey was carried out to analyse examples of the coloured fibre population that may be expected to exist in both front- and top-loading domestic washing machines during Spring, in Sydney, Australia. White cotton T-shirts were washed both individually, and with a normal household wash load, then taped to recover extraneous fibres transferred during the wash cycle. Twelve thousand one hundred and seventy-eight fibres were classified according to length, colour and generic class. Cotton fibres were most prevalent (69.4%), followed by man-made fibres (24.2%). The most common colour/generic class combinations were black/grey cotton (27%), blue cotton (20%) and red cotton (15.6%). Other combinations generally represented under 2% of the total fibre population. Two thirds (65.9%) of the recovered fibres were under 2 mm in length, the proportion of fibres decreasing with increasing fibre length. Variations in machine type did not affect the distribution of fibres with respect to fibre type, colour or length.

Journal Article↗