Harmonising the human biobanking consent process: an Irish experience.

Biobanks are repositories of human biological samples and data. They are an important component of clinical research in many disease areas and often represent the first step toward innovative treatments. For biobanks to operate, researchers need human participants to give their samples and associated health data.

What GDPR and the Health Research Regulations (HRRs) mean for Ireland: "explicit consent"-a legal analysis.

Background: Irish Health Research Regulations (HRRs) were introduced following the commencement of the General Data Protection Regulation (GDPR) in 2018. The HRRs set out supplementary regulatory requirements for research. A legal analysis presented under the auspices of the Irish Academy of Medical Sciences (IAMS) on April 8 and November 25, 2019 at the Royal College of Surgeons in Ireland welcomed the introduction of GDPR and the HRRs.

What GDPR and the Health Research Regulations (HRRs) mean for Ireland: a research perspective.

Background: Irish Health Research Regulations (HRRs) were introduced following the European Union (EU) General Data Protection Regulation (GDPR) in 2018. The HRRs described specific supplementary regulatory requirements for research regarding governance, processes and procedure that impact on several facets of research. The numerous problems that the HRRs and particularly "explicit consent" inadvertently created were presented under the auspices of the Irish Academy of Medical Sciences (IAMS) on November 25, 2019, at the Royal College of Surgeons in Ireland.

Development and progress of Ireland's biobank network: Ethical, legal, and social implications (ELSI), standardized documentation, sample and data release, and international perspective.

Biobank Ireland Trust (BIT) was established in 2004 to promote and develop an Irish biobank network to benefit patients, researchers, industry, and the economy. The network commenced in 2008 with two hospital biobanks and currently consists of biobanks in the four main cancer hospitals in Ireland. The St.

Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples.

The Saint James's Hospital Biobank was established in 2008, to develop a high-quality breast tissue BioResource, as a part of the breast cancer clinical care pathway. The aims of this work were: (1) to ascertain the quality of RNA, DNA, and protein in biobanked carcinomas and normal breast tissues, (2) to assess the efficacy of AllPrep(®) (Qiagen) in isolating RNA, DNA, and protein simultaneously, (3) to compare AllPrep with RNEasy(®) and QIAamp(®) (both Qiagen), and (4) to examine the effectiveness of Allprotect(®) (Qiagen), a new tissue stabilization medium in preserving DNA, RNA, and proteins. One hundred eleven frozen samples of carcinoma and normal breast tissue were analyzed.

Aldo-keto reductase from Helicobacter pylori--role in adaptation to growth at acid pH.

Pyridine-linked oxidoreductase enzymes of Helicobacter pylori have been implicated in the pathogenesis of gastric disease. Previous studies in this laboratory examined a cinnamyl alcohol dehydrogenase that was capable of detoxifying a range of aromatic aldehydes. In the present work, we have extended these studies to identify and characterize an aldoketo reductase (AKR) enzyme present in H.

Neuraminidase production by Erysipelothrix rhusiopathiae.

In order to characterise neuraminidase activity by Erysipelothrix, 85 isolates of Erysipelothrix spp. from a variety of sources including human clinical, marine and terrestrial animals, and the environment were investigated for neuraminidase production. Neuraminidase activity was detected by a peanut lectin haemagglutination method.

Characterization of cinnamyl alcohol dehydrogenase of Helicobacter pylori. An aldehyde dismutating enzyme.

Cinnamyl alcohol dehydrogenases (CAD; 1.1.1.

Identifying cloned Helicobacter pylori promoters by primer extension using a FAM-labelled primer and GeneScan analysis.

The transcriptional start sites of 27 promoters in Helicobacter pylori strain 4187E have been successfully identified using a non-radioactive primer extension protocol. The technique involves reverse transcribing mRNA with a sequence-specific FAM-labelled primer. The length of the FAM-labelled cDNA primer extension product can be analysed on a standard DNA sequencer using GeneScan software.

Tolerance of Pseudomonas aeruginosa to Melaleuca alternifolia (tea tree) oil is associated with the outer membrane and energy-dependent cellular processes.

Objectives: The essential oil of Melaleuca alternifolia (tea tree oil) and its components have antimicrobial activity against a wide range of Gram-positive and Gram-negative bacteria, fungi and viruses. The mechanism(s) by which Pseudomonas aeruginosa NCTC 10662 maintains a decreased susceptibility to tea tree oil and components was investigated.

Results: Ethylene diamine tetraacetic acid enhanced the antimicrobial activity of tea tree oil and terpinen-4-ol against stationary phase P.

Cellular fatty acid profile distinguishes Burkholderia pseudomallei from avirulent Burkholderia thailandensis.

Burkholderia pseudomallei, the cause of melioidosis, can be distinguished from the closely related but nonpathogenic Burkholderia thailandensis by gas chromatography (GC) analysis of fatty acid derivatives. A 2-hydroxymyristic acid derivative (14:0 2OH) was present in 95% of B. pseudomallei isolates and no B.

Extended-spectrum beta-lactamase enzymes in clinical isolates of Enterobacter species from Lagos, Nigeria.

Over a 9-month period, 8 of 40 nonduplicate isolates of Enterobacter spp. producing extended-spectrum beta-lactamase (ESBL) were detected for the first time from two hospitals in Lagos, Nigeria. Microbiologic and molecular analysis confirmed the presence of ESBL.

Persistence of biofilm-associated Escherichia coli and Pseudomonas aeruginosa in groundwater and treated effluent in a laboratory model system.

This study was based on the hypothesis that groundwater-derived biofilms may provide a reservoir for coliform or pathogenic bacteria as has been observed in drinking water distribution systems. Escherichia coli, labelled with green fluorescent protein, was found to colonize all layers of mixed-population biofilms developed in association with indigenous groundwater micro-organisms in a laboratory-scale reactor. Biofilm-associated E.

Escherichia coli survival in groundwater and effluent measured using a combination of propidium iodide and the green fluorescent protein.

Aims: The aim of this study was to deterimine the survival of an enteric bacterium in anaerobic groundwater and effluent microcosms using the green fluorescent protein (GFP) marker gene in combination with the viability indicator propidium iodide (PI).

Methods And Results: The pEGFP vector (Clontech) was transformed into Escherichia coli DH5alpha and was stable for at least 100 generations of growth in nonselective medium at 28 degrees C and 37 degrees C. Using an epifluorescent microscope, GFP cells could be detected under blue light (450-490 nm) and the numbers of PI-positive GFPs could be detected under green light (530-560 nm).

Mechanism of action of Melaleuca alternifolia (tea tree) oil on Staphylococcus aureus determined by time-kill, lysis, leakage, and salt tolerance assays and electron microscopy.

The essential oil of Melaleuca alternifolia (tea tree) has broad-spectrum antimicrobial activity. The mechanisms of action of tea tree oil and three of its components, 1,8-cineole, terpinen-4-ol, and alpha-terpineol, against Staphylococcus aureus ATCC 9144 were investigated. Treatment with these agents at their MICs and two times their MICs, particularly treatment with terpinen-4-ol and alpha-terpineol, reduced the viability of S.

The detection and recovery of Erysipelothrix spp. in meat and abattoir samples in Western Australia.

Aims: To investigate the occurrence of Erysipelothrix rhusiopathiae and other Erysipelothrix spp. in abattoir and meat samples in Western Australia.

Methods And Results: Samples were collected from various parts of pig and sheep carcasses, as well as different sections of slaughtering line, pen soil and effluent.

Desulfosporosinus meridiei sp. nov., a spore-forming sulfate-reducing bacterium isolated from gasolene-contaminated groundwater.

Eight strains of spore-forming, sulfate-reducing bacteria, isolated from groundwater contaminated with motor fuel [mostly benzene, toluene ethylbenzene and xylene (BTEX) compounds] in sandy soil near Perth, Australia, were closely related to Desulfosporosinus (previously Desulfotomaculum) orientis DSM 765T (95.3-97.3% 16S rDNA sequence similarity).

Identification of genes associated with copper tolerance in an adhesion-defective mutant of Aeromonas veronii biovar sobria.

TnphoA mutagenesis was used to identify adhesins of Aeromonas veronii biovar sobria 3767, a strain isolated from a diarrhoeal stool specimen. Six mutants, from a library of 154, exhibited significantly reduced levels of adhesion to HEp-2 cells. Primers to the terminal regions of TnphoA were used for inverse PCR and the product from one mutant was cloned into pBluescript and partial sequence data obtained.

Spore-forming, Desulfosporosinus-like sulphate-reducing bacteria from a shallow aquifer contaminated with gasoline.

Previous studies on the geochemistry of a shallow unconfined aquifer contaminated with hydrocarbons suggested that the degradation of some hydrocarbons was linked to bacterial sulphate reduction. There was attenuation of naphthalene, 1,3,5-trimethylbenzene (TMB), toluene, p-xylene and ethylbenzene in the groundwater with concomitant loss of sulphate. Here, the recovery of eight strains of sulphate-reducing bacteria (SRB) from the contaminated site is reported.

The identification of response regulators of Branhamella catarrhalis using PCR.

Potential response regulator gene fragments from the genome of Branhamella (Moraxella) catarrhalis were isolated by PCR using degenerate oligonucleotide primers. DNA sequence analysis of several cloned PCR products with similar restriction endonuclease analysis (REA) patterns revealed that the cloned gene fragment had significant homology to members of the OMPR sub-family of response regulator genes, including 61% identity with the phoB gene of Haemophilus influenzae. The derived amino acid sequence showed greatest similarity to the PhoB response regulator protein of Pseudomonas aeruginosa.

Moraxella catarrhalis: clinical significance, antimicrobial susceptibility and BRO beta-lactamases.

Moraxella catarrhalis is an important pathogen of humans. It is a common cause of respiratory infections, particularly otitis media in children and lower respiratory tract infections in the elderly. Colonisation of the upper respiratory tract appears to be associated with infection in many cases, although this association is not well understood.

Characterization of the roles of hemolysin and other toxins in enteropathy caused by alpha-hemolytic Escherichia coli linked to human diarrhea.

Escherichia coli strains producing alpha-hemolysin have been associated with diarrhea in several studies, but it has not been clearly demonstrated that these strains are enteropathogens or that alpha-hemolysin is an enteric virulence factor. Such strains are generally regarded as avirulent commensals. We examined a collection of diarrhea-associated hemolytic E.

Identification of clinical isolates of indole-positive Klebsiella spp., including Klebsiella planticola, and a genetic and molecular analysis of their beta-lactamases.

In a collection of 43 indole-positive Klebsiella clinical isolates, which were initially identified as Klebsiella oxytoca, there were 18 isolates which exhibited a pattern characteristic of extended-spectrum beta-lactamase (ESBL) resistance. This study aimed to confirm their identity by biochemical tests and by PCR and to determine the genetic basis for their resistance to the beta-lactams and broad-spectrum cephalosporins. Chromosomal beta-lactamase genes were analyzed by PCR, and plasmid-mediated beta-lactamase genes were analyzed by conjugation and transformation.