A report on the study of land-sourced pollutants and their impacts on water quality in and adjacent to the Great Barrier Reef: an assessment to guide the development of management plans to halt any decline in the water quality of river catchments draining to the Reef, as a result of land-based pollution, and to achieve the long-term goal of reversing any trend in declining water quality

Includes 'Summary statement of the Reef Science Panel regarding water quality in and adjacent to the Great Barrier Reef

The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism.

High-throughput sequencing (HTS) has successfully identified novel resistance genes in enterococci and determined clonal relatedness in outbreak analysis. We report the use of HTS to investigate two concurrent outbreaks of glycopeptide-resistant Enterococcus faecium (GRE) with an uncharacterised resistance mechanism to quinupristin-dalfopristin (QD).Seven QD-resistant and five QD-susceptible GRE isolates from a two-centre outbreak were studied. HTS was performed to identify genes or predicted proteins that were associated with the QD-resistant phenotype. MLST and SNP typing on HTS data was used to determine clonal relatedness.Comparative genomic analysis confirmed this GRE outbreak involved two distinct clones (ST80 and ST192). HTS confirmed the absence of known QD resistance genes, suggesting a novel mechanism was conferring resistance. Genomic analysis identified two significant genetic determinants with explanatory power for the high level of QD resistance in the ST80 QD-resistant clone: an additional 56aa leader sequence at the N-terminus of the lsaE gene and a transposon containing seven genes encoding proteins with possible drug or drug-target modification activities. However, HTS was unable to conclusively determine the QD resistance mechanism and did not reveal any genetic basis for QD resistance in the ST192 clone. This study highlights the usefulness of HTS in deciphering the degree of relatedness in two concurrent GRE outbreaks. Although HTS was able to reveal some genetic candidates for uncharacterised QD resistance, this study demonstrates the limitations of HTS as a tool for identifying putative determinants of resistance to QD

Evaluation of a low-cost optical particle counter (Alphasense OPC-N2) for ambient air monitoring

A fast growing area of research is the development of low-cost sensors for measuring air pollutants. The affordability and size of low-cost particle sensors makes them an attractive option for use in experiments requiring a number of instruments such as high density spatial mapping. However, for these low-cost sensors to be useful for these types of studies their accuracy and precision needs to be quantified. We evaluated the Alphasense OPC-N2, a promising low-cost miniature optical particle counter, for monitoring ambient airborne particles at typical urban background sites in the UK. The precision of the OPC-N2 was assessed by co-locating 14 instruments at a site to investigate the variation in measured concentrations. Comparison to two different reference optical particle counters as well as a TEOM-FDMS enabled the accuracy of the OPC-N2 to be evaluated. Comparison of the OPC-N2 to the reference optical instruments demonstrated reasonable agreement for the measured mass concentrations of PM1, PM2.5 and PM10. However, the OPC-N2 demonstrated a significant positive artefact in measured particle mass during times of high ambient RH (> 85 %) and a calibration factor was developed based upon κ-Kohler theory, using average bulk particle aerosol hygroscopicity. Application of this RH correction factor resulted in the OPC-N2 measurements being within 33 % of the TEOM-FDMS, comparable to the agreement between a reference optical particle counter and the TEOM-FDMS (20 %). Reasonable inter-unit precision for the 14 OPC-N2 sensors was observed. Overall, the OPC-N2 was found to accurately measure ambient airborne particle mass concentration provided they are i) correctly calibrated and ii) corrected for ambient RH. The reasonable level of precision demonstrated between multiple OPC-N2 suggests that they would be suitable device for applications where the spatial variability in particle concentration was to be determined

Comparison of Plankton Catch by Three Light-Trap Designs in the Northern Gulf of Mexico

The ichthyoplankton catch and zooplankton biomass estimates of three light-trap designs-cylindrical, quatrefoil, and rectangular-were compared over three consecutive nights at an offshore petroleum platform in the northern Gulf of Mexico. The quatrefoil light trap had higher fish and zooplankton abundance estimates than the other two designs. Categorical analysis of the two abundant fish taxa, Opisthonema oglinum and Anchoa spp., indicated that catch by the quatrefoil and rectangular traps was similar, capturing more larvae than juveniles and more O. oglinum than Anchoa spp. relative to cylindrical trap catch. Across all fish species, the quatrefoil captured a greater percentage of larvae. Other ontogenetic and species-specific differences were noted among the light-trap designs. Samples from vertical plankton tows underestimated larger size classes compared to light-trap catch. Light-trap catch per unit effort (CPUE) declined through the night, especially for the quatrefoil, and increased with depth. In contrast, the percentage of larvae captured across all traps increased through the night and decreased with depth, indicating that CPUE was related mostly to juvenile catch. The percentage of larvae also decreased with increasing water current speed

First Trimester Plasma Glucose Values in Women without Diabetes are Associated with Risk for Congenital Heart Disease in Offspring

In a retrospective study of 19 171 mother-child dyads, elevated random plasma glucose values during early pregnancy were directly correlated with increased risk for congenital heart disease in offspring. Plasma glucose levels proximal to the period of cardiac development may represent a modifiable risk factor for congenital heart disease in expectant mothers without diabetes.Peer reviewe

Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

<p>Abstract</p> <p>Background</p> <p>Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species <it>Daphnia pulex</it>, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.</p> <p>Results</p> <p>Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the <it>Daphnia </it>genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of <it>D. pulex </it>MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.</p> <p>Conclusion</p> <p>The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in <it>Daphnia </it>genomics will enable the further development of this species as a model organism for the environmental sciences.</p

Real-World Concordance between Germline and Tumour <i>BRCA1/2</i> Status in Epithelial Ovarian Cancer

Patients diagnosed with epithelial ovarian cancer may undergo reflex tumour BRCA1/ 2 testing followed by germline BRCA1/2 testing in patients with a positive tumour test result. This testing model relies on tumour BRCA1/ 2 tests being able to detect all types of pathogenic variant. We analysed germline and tumour BRCA1/2 test results from patients treated for epithelial ovarian cancer at our specialist oncological referral centre. Tumour BRCA1/2 testing was performed using the next-generation sequencing (NGS)-based myChoice ® companion diagnostic (CDx; Myriad Genetics, Inc.). Germline BRCA1/2 testing was performed in the North West Genomic Laboratory Hub using NGS and multiplex ligation-dependent probe amplification. Between 11 April 2021 and 11 October 2023, 382 patients were successfully tested for tumour BRCA1 and BRCA2 variants. Of these, 367 (96.1%) patients were tested for germline BRCA1/ 2 variants. In those patients who underwent tumour and germline testing, 15.3% (56/367) had a BRCA1/ 2 pathogenic variant (36 germline and 20 somatic). All germline BRCA1/2 pathogenic small sequencing variants were detected in tumour DNA. By contrast, 3 out of 8 germline BRCA1/2 pathogenic large rearrangements were not reported in tumour DNA. The overall concordance of germline BRCA1/2 pathogenic variants detected in germline and tumour DNA was clinically acceptable at 91.7% (33/36). The myChoice ® CDx was able to detect most germline BRCA1/2 pathogenic variants in tumour DNA, although a proportion of pathogenic large rearrangements were not reported. If Myriad's myChoice ® CDx is used for tumour BRCA1/2 testing, our data supports a testing strategy of germline and tumour BRCA1/2 testing in all patients diagnosed with epithelial ovarian cancer aged &lt; 79 years old, with germline BRCA1/2 testing only necessary for patients aged ≥ 80 years old with a tumour BRCA1/2 pathogenic variant. </p