Camera trap data collected to model daily trapping rates (DTRs) of terrestrial avian species at arid zone waterholes in central Australia in relation to daily maximum temperature and days since last rainfall.
Contributors:Corey Goodwin, Andrew Wotherspoon, Michelle Gahan, Dennis McNevin
Forensic genotyping can be impeded by gamma-irradiation of biological evidence in the event of radiological crime. Oxidative effects within the mitochondria elicit greater damage to mitochondrial DNA (mtDNA) than nuclear DNA (nuDNA) at low doses. This study presents a novel approach for the assessment of nuDNA versus mtDNA damage from a comparison of genotype and quantity data, while exploring likely mechanisms for differential damage after high doses of gamma-irradiation.
Liquid (hydrated) and dried (dehydrated) whole blood samples were exposed to high doses of gamma-radiation (1-50 kilogray, kGy). The GlobalFiler PCR Amplification Kit was used to evaluate short tandem repeat (STR) genotyping efficacy and nuDNA degradation; a comparison was made to mtDNA degradation measured using real-time PCR assays. Each assay was normalised before comparison by calculation of integrity indices relative to unirradiated controls. For nuDNA, a subset of autosomal STR markers were selected for relative size consistency with three mtDNA targets (86, 190 and 452 bp), including loci of low molecular weight (D2S441, ~75-110 bp), intermediate molecular weight (vWA and D1S1656, ~150-210 bp), and high molecular weight (TPOX and SE33, ~310-450 bp). For STR size groups containing multiple loci, the average peak heights of alleles for each marker were determined. Integrity indices were calculated from the peak height or quantity ratios of increasing amplicon size difference, comprising intermediate/short (Index A), long/intermediate (Index B), and long/short loci (Index C).
Full STR profiles were attainable up to the highest dose, although DNA degradation was noticeable after 10 and 25 kGy for hydrated and dehydrated blood, respectively. This was manifested by heterozygote imbalance more than allele dropout. Degradation was greater for mtDNA than nuDNA, as well as for hydrated than dehydrated cells, after equivalent doses.
Findings suggest that oxidative effects due to water radiolysis and mitochondrial function are dominant mechanisms of differential damage to nuDNA versus mtDNA after high-dose gamma-irradiation. While differential DNA damage was reduced by cell desiccation, its persistence after drying indicates innate differences between nuDNA and mtDNA radioresistance and/or continued oxidative effects within the mitochondria. Degradation of mtDNA is more severe after gamma-irradiation than nuDNA; this does not adversely impact on genotyping success of blood samples up to 50 kGy.
Contributors:Berenice Talamantes Becerra, Jason Carling, Karina Kennedy, Michelle E. Gahan, Arthur Georges
These compressed directories contain fastA files of complexity-reduced genotyping by sequencing data of bacterial isolates from a public hospital in Australia. Sequencing data of a total of 165 bacterial isolates are included in these data sets of the following species: Enterococcus faecium, Staphylococcus aureus, Enterobacter cloacae complex, Citrobacter freundii, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter asburiae, Escherichia coli, Morganella morganii, Citrobacter amalonaticus, Enterobacter aerogenes, Enterococcus faecalis, Hafnia alvei, Providencia rettgeri and Serratia marcescens. Additionally, this dataset includes sequencing results of genomic DNA of E. coli O157 (EDL 933) IRMM449 Sigma-Aldrich certified reference. All bacterial isolates were processed with the following combination of restriction enzymes: PstI with MseI, PstI with HpaII and MseI with HpaII. Some samples contain technical replicates and the certified reference contains six technical replicates. Each directory contains a Microsoft Excel Comma Separated Values File with bacterial isolate information, including an internal unique identity number (TargetID), the sample name (Genotype), material used for DNA extraction (Tissue), complexity-reduced genotyping method (Comment), and other details produced after sequencing (e.g. extract plate barcode, extract well, flowcell ID, flowcell lane). For a detailed description of how this data was obtained, please refer to the article "Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping (2019) Berenice Talamantes-Becerra, Jason Carling, Karina Kennedy, Michelle E. Gahan, Arthur Georges. Journal of Microbiological Methods, Volume 160, May 2019, Pages 11-19. https://doi.org/10.1016/j.mimet.2019.03.016
Contributors:Pawel Waryszak, Tanja Lenz, Michelle Leishman, Paul Downey
The data was generated in the "Elevated CO2 and herbicide tolerance" experiment (2012). The experiment followed a randomised fully factorial design, with the factors being CO2 concentration (ambient or elevated) and herbicide treatment (recommended and double recommended label rate). Four glasshouses were used: two at the ambient and two at the elevated CO2 concentration.
Ten replicates of each weed species for each CO2 × herbicide treatment combination were grown. These were evenly split between the treatment glasshouses. Additionally, six replicates of each weed species were grown under each CO2 treatment to assess the biomass allocation each species at the time of herbicide application. This could not be done after herbicide treatment due to plant mortality. These plants were harvested into their above- and belowground components on the day of herbicide application and oven-dried at 60oC to constant weight (48 – 72 hours) before being weighed.
Pots were randomly rearranged within the glasshouses each fortnight to minimise any within-glasshouse effects. All pots were evenly spaced to minimise shading from neighbouring plants. As Lantana camara and I. indica were propagated from cuttings, they were re-potted into 2.8 L pots after eight weeks and six weeks respectively to allow them ample space for root development. The vine species A. cordifolia and I. indica were trained onto stakes. Pots were mist watered for one minute four times daily.
The elevated CO2 treatment was maintained by a dosing and monitoring system (Canary Company Pty Ltd, Lane Cove, NSW, Australia) at 550 ppm, from 6 am to 6 pm, with air continuously circulated within each glasshouse. The elevated CO2 treatment represents the predicted atmospheric CO2 concentration by 2030 under most emissions scenarios (IPCC, 2001). The ambient CO2 treatment was 380 ppm. The glasshouse temperature was set to 17°C at night and 24°C during the day.