Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays

Space assets and technology for bushfire management

The financial, emotional, and ecological impacts of bushfires can be devastating. This report was prepared by the participants of the Southern Hemisphere Space Studies Program 2021 in response to the topic: “How space assets and technologies can be applied to better predict and mitigate bushfires and their impacts.” To effectively reach the diverse set of stakeholders impacted by bushfires, Communication was identified as a key enabler central to any examination of the topic. The three pillars “predict”, “mitigate” and “communicate” were identified to frame the task at hand. Combining the diverse skills and experience of the class participants with the interdisciplinary knowledge gained from the seminars, distinguished lectures, and workshops during the SHSSP21 program, conducted a literature review With specific reference to the 2019-20 Australian fire season, we looked at the current state of the art, key challenges, and how bushfires can be better predicted and mitigated in the future. Comparing this to the future desired state, we identified gaps for each of the three domains, and worked across teams to reach consensus on a list of recommendations. Several of these recommendations were derived independently by two or more of the three groups, highlighting the importance of a holistic and collaborative approach. The report details a number of recommendations arising from this Where applicable, we also aligned our discussion with the experience and lessons from other countries and agencies to consider,learn from and respond to the international context, as others develop systems using space technology to tackle similar wildfire issues

Mammographic density and markers of socioeconomic status: a cross-sectional study

BACKGROUND: Socioeconomic status (SES) is known to be positively associated with breast cancer risk but its relationship with mammographic density, a marker of susceptibility to breast cancer, is unclear. This study aims to investigate whether mammographic density varies by SES and to identify the underlying anthropometric, lifestyle and reproductive factors leading to such variation. METHODS: In a cross-sectional study of mammographic density in 487 pre-menopausal women, SES was assessed from questionnaire data using highest achieved level of formal education, quintiles of Census-derived Townsend scores and urban/rural classification of place of residence. Mammographic density was measured on digitised films using a computer-assisted method. Linear regression models were fitted to assess the association between SES variables and mammographic density, adjusting for correlated variables. RESULTS: In unadjusted models, percent density was positively associated with SES, with an absolute difference in percent density of 6.3% (95% CI 1.6%, 10.5%) between highest and lowest educational categories, and of 6.6% (95% CI -0.7%, 12.9%) between highest and lowest Townsend quintiles. These associations were mainly driven by strong negative associations between these SES variables and lucent area and were attenuated upon adjustment for body mass index (BMI). There was little evidence that reproductive factors explained this association. SES was not associated with the amount of dense tissue in the breast before or after BMI adjustment. The effect of education on percent density persisted after adjustment for Townsend score. Mammographic measures did not vary according to urban/rural place of residence. CONCLUSIONS: The observed SES gradients in percent density paralleled known SES gradients in breast cancer risk. Although consistent with the hypothesis that percent density may be a mediator of the SES differentials in breast cancer risk, the SES gradients in percent density were mainly driven by the negative association between SES and BMI. Nevertheless, as density affects the sensitivity of screen-film mammography, the higher percent density found among high SES women would imply that these women have a higher risk of developing cancer but a lower likelihood of having it detected earlier

Motivators and barriers for dog and cat owners and veterinary surgeons in the United Kingdom to using preventative medicines

Routine use of preventative medicines is advocated as part of responsible dog and cat ownership. However, it has been suggested that the number of owners in the United Kingdom (UK) using preventative medicines to protect their pets is in decline. The aim of this novel study was to use a qualitative methodology to explore the attitudes of pet owners and veterinary surgeons in the UK to using preventative medicine products in dogs and cats. Preventative medicine was defined as “a drug or any other preparation used to prevent disease, illness or injury.” Semi-structured interviews were conducted by telephone with owners and veterinary surgeons who had recently participated in a preventative healthcare consultation. Thematic analysis of transcribed recordings of these interviews identified four themes. This paper reports the theme related to motivators and barriers to using preventative medicines. Owners’ understanding varied widely about the importance of preventative medicines for pets, as did their confidence in the safety of prescription products. A good relationship with their veterinary surgeon or practice, seeing adverts on the television about specific diseases, advice from a breeder and having personally seen infected animals appeared to be motivators for owners to use preventative medicines. Concern about adverse events and uncertainty about the necessity of using preventative medicines were barriers. Owners who trusted their veterinary surgeons to advise them on preventative medicine products described little use of alternative information sources when making preventative medicine choices. However, owners who preferred to do their own research described reading online opinions, particular in relation to the safety of preventative medicines, which they found confusing. In contrast, veterinary surgeons described broad confidence in the safety and efficacy of prescription preventative medicines and described protection of pet health as a strong motivator for their use. Several expressed some concern about being seen to “sell” products, which may present a barrier to their advocacy. Veterinary surgeons were unsure about owners’ level of understanding of the necessity of preventative medicines, particularly in relation to vaccinations, and few recalled instigating conversations with owners about product safety. Owner uncertainties about preventative medicine products may not be adequately addressed in the consulting room. This first qualitative study to investigate dog and cat preventative medicines suggests strategies are needed to increase discussion between pet owners and veterinary surgeons in the UK about the necessity, safety, efficacy and cost of preventative medicines

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Phylogeography of Blue Corals (Genus Heliopora) Across the Indo-West Pacific

10.3389/fmars.2021.714662Frontiers in Marine Science871466