Andrew Collins

Andrew Collins
The University of Newcastle, Australia · Discipline of Communication

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91
Publications
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Publications

Publications (91)
Article
Levels of DNA damage represent the dynamics between damage formation and removal. Therefore, to better interpret human biomonitoring studies with DNA damage endpoints, an individual’s ability to recognize and properly remove DNA damage should be characterized. Relatively few studies have included DNA repair as a biomarker and therefore, assembling...
Article
The comet assay is widely used for quantification of genomic damage in humans. Peripheral blood derived mononuclear cells (PBMCs) are the most often used cell type for this purpose. Since the comet assay can be performed in an enhanced throughput format, it can be applied to large sample collections such as biobanks. The European Prospective Invest...
Article
Full-text available
The comet assay or single cell gel electrophoresis, is the most common method used to measure strand breaks and a variety of other DNA lesions in human populations. To estimate the risk of overall mortality, mortality by cause, and cancer incidence associated to DNA damage, a cohort of 2,403 healthy individuals (25,978 person-years) screened in 16...
Article
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DNA integrity is considered an important parameter of semen quality and is of significant value as a predictor of male fertility. Currently, there are several methods that can assess sperm DNA integrity. One such assay is the comet assay, or single-cell gel electrophoresis, which is a simple, sensitive, reliable, quick and low-cost technique that i...
Article
Full-text available
The comet assay or single cell gel electrophoresis, is the most common method used to measure strand breaks and a variety of other DNA lesions in human populations. To estimate the risk of overall mortality, mortality by cause, and cancer incidence associated to DNA damage, a cohort of 2,403 healthy individuals (25,978 person-years) screened in 16...
Article
DNA damage and repair activity are often assessed in blood s#38les from humans in different types of molecular epidemiology studies. However, it is not always feasible to analyse the s#38les on the day of collection without any type of storage. For instance, certain studies use repeated s#38ling of cells from the same subject or s#38les from differ...
Article
Purpose: To assess whether the micronucleus cytome assay (MCyt) reliably detects DNA damage occurring in control and pathological superficial epithelial cells from human conjunctiva. Methods: Impression cytology samples from the bulbar conjunctiva of 33 healthy controls, eight patients with conjunctival intraepithelial neoplasia (CIN) and eight...
Article
The enzyme-modified comet assay was developed in order to detect DNA lesions other than those detected by the standard version (single and double strand breaks and alkali-labile sites). Various lesion-specific enzymes, from the DNA repair machinery of bacteria and humans, have been combined with the comet assay, allowing detection of different oxid...
Article
This optimized protocol (including links to instruction videos) describes a comet-based in vitro DNA repair assay that is relatively simple, versatile, and inexpensive, enabling the detection of base and nucleotide excision repair activity. Protein extracts from samples are incubated with agarose-embedded substrate nucleoids (‘naked’ supercoiled DN...
Article
Full-text available
The comet assay is a widely used test for the detection of DNA damage and repair activity. However, there are interlaboratory differences in reported levels of baseline and induced damage in the same experimental systems. These differences may be attributed to protocol differences, although it is difficult to identify the relevant conditions becaus...
Article
The comet assay is a popular assay in biomonitoring studies. DNA strand breaks (or unspecific DNA lesions) are measured using the standard comet assay. Oxidative stress-generated DNA lesions can be measured by employing DNA repair enzymes to recognise oxidatively damaged DNA. Unfortunately, there has been a tendency to fail to report results from a...
Article
The in vivo comet assay is an established genotoxicity test, with an OECD test guideline, but in its standard form it measures only DNA strand breaks. Including in the assay an additional step, in which the DNA is incubated with a lesion-specific enzyme, can provide important information about the nature of the DNA damage. Formamidopyrimidine DNA g...
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Full-text available
Purpose To determine the DNA protective effects of a standard coffee beverage in comparison to water consumption. Methods The single-blind, randomised controlled study with parallel design included healthy women (n = 50) and men (n = 50) recruited from the general Central European population. The subjects were randomised in a coffee and a control...
Article
The comet assay is a well-accepted biomonitoring tool to examine the effect of dietary, lifestyle, environmental and occupational exposure on levels of DNA damage in human cells. With such a wide range of determinants for DNA damage levels, it becomes challenging to deal with confounding and certain factors are inter-related (e.g. poor nutritional...
Article
The comet assay has become one of the methods of choice for the evaluation and measurement of DNA damage. It is sensitive, quick to perform and relatively affordable for the evaluation of DNA damage and repair at the level of individual cells. The comet assay can be applied to virtually any cell type derived from different organs and tissues. Even...
Article
The comet assay offers the opportunity to measure both DNA damage and repair. Various comet assay based methods are available to measure DNA repair activity, but some requirements should be met for their effective use in human biomonitoring studies. These conditions include i) robustness of the assay, ii) sources of inter- and intra-individual vari...
Article
The comet assay, also called single cell gel electrophoresis, is a sensitive, rapid and low-cost technique for quantifying and analysing DNA damage and repair at the level of individual cells. The assay itself can be applied on virtually any cell type derived from different organs and tissues of eukaryotic organisms. Although it is mainly used on h...
Article
Full-text available
Purpose To examine levels of oxidative DNA base damage and expression of selected genes and proteins related to DNA damage repair in human limbal epithelium engineered ex vivo. Methods Cells were expanded from limbal tissue on cell culture‐treated inserts in medium containing fetal bovine serum, recombinant growth factors, hormones and cholera tox...
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Full-text available
Purpose: Coffee is known to contain phytochemicals with antioxidant potential. The aim of this study was to investigate possible antioxidant effects of coffee in healthy human volunteers. Methods: A placebo-controlled intervention trial was carried out on 160 healthy human subjects, randomised into three groups, receiving 3 or 5 cups of study co...
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Full-text available
In the present study, we address the important issue of whether B-cells protected from irradiation-induced cell death, may survive with elevated levels of DNA damage. If so, such cells would be at higher risk of gaining mutations and undergoing malignant transformation. We show that stimulation of B-cells with the TLR9 ligands CpG-oligodeoxynucleot...
Data
γH2AX expression in TLR9/RA stimulated B-cells. B-cells were stimulated with CpG-ODNs (0.5 μg/ml) in the presence or absence of RA (200 nM) for 24 hours prior to irradiation (IR; 10 Gy). 2 hour after irradiation, the cells were subjected to immunofluorescence analysis as described in materials and methods. The results are presented as histograms of...
Data
TP53 levels in CVID-derived B-cells. Normal and CVID-derived B-cells were stimulated with CpG-ODNs (1 μg/ml) and anti-RP105 (1 μg/ml) for 72 hours prior to isolation of mRNA. The level of TP53 mRNA was quantified using RT-qPCR, and the amount of TP53 mRNA was related to the reference genes (TBP, B2M and 18s rRNA). The data represents mean 2-ΔCt val...
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Characteristics of the CVID patients. The table presents sex, age and clinical manifestations of the CVID patients included in the study. (DOC)
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Raw data. Raw data showing the individual data points behind the means, medians and variances presented in the results, tables and figures in the manuscript. (DOC)
Data
TP53 levels in TLR9/RA stimulated B-cells. B-cells were stimulated with CpG-ODN (0.5 μg/ml) in the presence or absence of RA (200 nM) for 24 hours prior to isolation of mRNA. The level of TP53 mRNA was quantified using RT-qPCR. The amount of TP53 mRNA was related to the reference gene (TBP) and quantified using the 2-ΔCt-method. The results are pre...
Data
mRNA expression of DDR-specific genes. B-cells were stimulated with CpG-ODNs (0.5 μg/ml) in the presence or absence of RA (200 nM) for 24 hours prior to irradiation (IR; 10 Gy). After additional 8 hours, the cells were harvested and subjected to RT-qPCR. The mRNA levels of target proteins were related to the reference gene (TBP) and quantified usin...
Data
Original uncropped Western blot of pATM. Original uncropped and unadjusted Western blot showing the level of pATM in Fig 3A. (TIF)
Data
Original uncropped Western blot of the expression of p53/p-p53. Original uncropped and unadjusted Western blot showing the level of p53 and p-p53 in Fig 2A. (TIF)
Data
Original uncropped Western blot of the expression of p21. Original uncropped and unadjusted Western blot blot showing the level of p21 in Fig 2C. (TIF)
Data
Original uncropped Western blot of pDNA-PKcs/pATR. Original uncropped and unadjusted Western blot showing the levels of pDNA-PKcs (upper panel) and pATR (lower panel) in Fig 3C. (TIF)
Chapter
The comet assay (single cell gel electrophoresis) is a sensitive, versatile method for detecting DNA damage in eukaryotic cells. The traditional comet assay format has 1 or 2 gels on a microscope slide, 1 sample per slide, and there is a limit of 40 gels per experiment given the size of a typical electrophoresis tank. To increase throughput, we hav...
Article
From a toxicological point of view, nanomaterials are of interest; because - on account of their great surface area relative to mass - they tend to be more reactive than the bulk chemicals from which they are derived. They might in some cases have the potential to damage DNA directly, or could act via the induction of oxidative stress. The comet as...
Article
Full-text available
[This corrects the article on p. 61 in vol. 6, PMID: 25774164.].
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Polyphenols are a very broad group of chemicals, widely distributed in plant foods, and endowed with antioxidant activity by virtue of their numerous phenol groups. They are widely studied as putative cancer-protective agents, potentially contributing to the cancer preventive properties of fruits and vegetables. We review recent publications relati...
Article
Full-text available
The comet assay has developed over the past 30 years and today, a variety of different DNA lesions and DNA repair can be measured by different versions of the assay (Collins, 2004). In the final step of the method, an image resembling a comet with a head (the nuclear core) and a tail (consisting of mainly single stranded DNA that has migrated out f...
Article
Abstract Surface coatings of nanoparticles (NPs) are known to influence advantageous features of NPs as well as potential toxicity. Iron oxide (Fe3O4) NPs are applied for both medical diagnostics and targeted drug delivery. We investigated the potential cytotoxicity and genotoxicity of uncoated iron oxide (U-Fe3O4) NPs in comparison with oleate-coa...
Article
Full-text available
Aim: Cultures for engineering of transplantable limbal epithelial grafts for treatment of ocular surface disorders may be initiated using dissociation of limbal epithelial cells by trypsin-EDTA or dispase or by a sequential incubation with these enzymes. The safety of such procedures is debated, and in the present study we examined levels of DNA da...
Article
Full-text available
The alkaline comet assay, when employed as a genotoxicity test, has relatively low sensitivity because it fails to detect—at non-cytotoxic concentrations—known genotoxins that do not induce breaks or alkali-labile sites. We demonstrate that this limitation is overcome by incorporating in the assay the DNA repair enzyme formamidopyrimidine DNA glyco...
Article
Full-text available
Among nanomaterials, silver nanoparticles (AgNPs) have the broadest and most commercial applications due to their antibacterial properties, highlighting the need for exploring their potential toxicity and underlying mechanisms of action. Our main aim was to investigate whether AgNPs exert toxicity by inducing oxidative damage to DNA in human kidney...
Article
Experiments were conducted to determine the validity of two common genotoxicity testing procedures, the comet assay and the micronucleus (MN) test, when applied to nanoparticles (NP). The comet assay is used to detect strand breaks (SB) induced in cellular DNA. There is a possibility of obtaining false positive results, if residual NP remain in pro...
Article
Experimental evidence indicates a strong connection between oxidative damage, cancer, and aging. Epidemiological observations suggest that a diet rich in fruits and vegetables is associated with lower incidence of some cancers and longer life expectancy; since fruits and vegetables contain natural antioxidants, a considerable effort has been dedica...
Article
Glutathione S-transferases (GSTs) are members of a multigene family of isoenzymes that are important in the control of oxidative stress and in phase II metabolism. Acting non-enzymically, GSTs can modulate signalling pathways of cell proliferation, cell differentiation and apoptosis. Using a molecular epidemiology approach, we have investigated a p...
Article
Full-text available
Among nanomaterials, silver nanoparticles (AgNPs) have the broadest and most commercial applications due to their anti-bacterial properties, highlighting the need for exploring their potential toxicity and underlying mechanisms of action. Our main aim was to investigate whether AgNPs exert toxicity by inducing oxidative damage to DNA in human kidne...
Article
Levels of oxidatively damaged cellular DNA and urinary excretion of damaged 2'-deoxyribonuclosides are widely measured in biomonitoring studies examining the role of oxidative stress induced by environmental exposures, lifestyle factors and development of disease. This has promoted efforts to harmonise measurements of oxidised guanine nucleobases b...
Article
It has been suggested that antioxidants attenuate oxidative stress and prevent oxidative stress-related diseases. Paradoxically, randomised controlled trials (RCT) using pharmacological doses of antioxidant supplements have demonstrated harmful effects in smokers. The aim of the present study was to test the compliance, tolerability and safety of t...
Article
Full-text available
As part of a project to develop high throughput versions of the comet assay (single cell gel electrophoresis), with a consequent need for more efficient scoring, we have compared the performance of visual scoring, automated and semi-automated image analysis when assessing comets in the same set of gels from dose-response experiments with typical DN...
Article
Lack of reliable assays for DNA repair has largely prevented measurements of DNA repair from being included in human biomonitoring studies. Using newly developed modifications of the comet assay we tested whether a fruit- and antioxidant-rich plant-based intervention could affect base excision repair (BER) and nucleotide excision repair (NER) in a...
Article
We used padlock probes to study the rate of gene specific repair of three genes, OGG1 (8-oxoguanine-DNA glycosylase-1), XPD (xeroderma pigmentosum group D), and HPRT (hypoxanthine-guanine phosphoribosyltransferase) in human lymphocytes, in relation to the repair rate of Alu repeats and total genomic DNA. Padlock probes offer highly specific detecti...
Data
Document S1: A full description of the methods for plasma antioxidant analysis, with references.
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Table S3: Gene sets in the C3 TFT collection regulated in the antioxidant-rich diet group and kiwifruit group when compared to controls
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Table S6: Gene transcripts downregulated in the antioxidant-rich diet-group vs. controls (LIMMA, p < 5%)
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Table S10: Biological processes significantly enriched among the upregulated gene transcripts in the kiwifruit group.
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Table S11: Biological processes significantly enriched among the downregulated gene transcripts in the kiwifruit group.
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Figure S3: The figure obtained using Metacore illustrates the leading edge (LE) genes (red bars) (contributing to the significance of the upregulated DNA and repair gene sets in GSEA) in the response to double -strand breaks-pathway. Red bars indicate LE genes from (1) comparing antioxidant-rich diet group to controls and (2) from comparing kiwifru...
Data
Table S1: Overview of the gene sets in the stress relevant gene set collections that were upregulated in the antioxidant-rich diet group when compared to controls (GSEA analysis). A brief description of each gene set is included with PubMed ID reference.
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Table S7: Gene transcripts downregulated in the kiwifruit -group vs. controls (LIMMA, p < 5%)
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Table S8: Biological processes significantly enriched among the upregulated gene transcripts in the antioxidant-rich diet group.
Data
Figure S1: The figure obtained using Metacore illustrates the leading edge (LE) genes (red bars) (contributing to the significance of the upregulated DNA and repair gene sets in GSEA) in the Nucleotide excision repair (NER) pathway. Red bars indicate LE genes from (1) comparing antioxidant-rich diet group to controls and (2) from comparing kiwifrui...
Data
Table S2: Overview of the gene sets in the stress relevant gene set collections that were upregulated in the kiwifruit group when compared to controls (GSEA analysis). A brief description of each gene set is included with PubMed ID reference.
Data
Table S9: Biological processes significantly enriched among the downregulated gene transcripts in the antioxidant-rich diet group.
Data
Figure S2: The figure obtained using Metacore illustrates the leading edge (LE) genes (red bars) (contributing to the significance of the upregulated DNA and repair gene sets in GSEA) represented in the Mismatch repair pathway. Red bars indicate LE genes from (1) comparing antioxidant-rich diet group to controls and (2) from comparing kiwifruit die...
Data
Table S4: Gene transcripts upregulated in the antioxidant-rich diet -group vs. controls (LIMMA, p < 5%)
Data
Table S5: Gene transcripts upregulated in the kiwifruit-group vs. controls (LIMMA, p < 5%)
Article
Full-text available
Plant-based diets rich in fruit and vegetables can prevent development of several chronic age-related diseases. However, the mechanisms behind this protective effect are not elucidated. We have tested the hypothesis that intake of antioxidant-rich foods can affect groups of genes associated with cellular stress defence in human blood cells. Trial r...
Article
This article summarises the results of human dietary intervention trials employing the comet assay (single cell gel electrophoresis, SCGE), which have been published in the last few years (i.e., between 2005 and 2008) and describes new trends and developments as well as current problems concerning the design of intervention trials and the interpret...
Article
We studied the in vitro antitumoral effect of a series of phenazine di- N-oxide derivatives, named 2-chloroacetylamino-7(8)-nitrophenazine N(5), N(10)-dioxide (1), 2-amino-7(8)-(1,3-dioxol-2-yl)phenazine N(5), N(10)-dioxide (2), 2-chloroacetylamino-7(8)-(1,3-dioxol-2-yl)phenazine N(5), N(10)-dioxide (3), and 2-amino-7(8)-methoxyphenazine N(5), N(10...
Article
In humans, epidemiological evidence suggests that increased consumption of fruits and vegetables can substantially enhance the protection against many common types of cancer. A molecular epidemiological study in 3 Slovak factories producing asbestos, glass fibres and rockwool was conducted. Altogether 388 subjects (239 exposed, 148 controls) were i...
Article
Full-text available
Single cell gel electrophoresis, or the comet assay, is widely used to measure DNA damage and repair. However, the behaviour of the DNA under the conditions used for the comet assay is not fully understood. In developing a method for studying specific gene sequences within comets, using ‘padlock probes’ (circularizable oligonucleotide probes), we h...