Search Results (49)

A high-throughput sequencing-based grapevine metagenomic survey was conducted across all grape-growing Canadian provinces (British Columbia, Ontario, Nova Scotia, and Québec) with the objective of better understanding the grapevine virome composition. In total, 310 composite grapevine samples representing nine Vitis vinifera red; five V. vinifera white; seven American–French red; and five white hybrid cultivars were analyzed. dsRNA, enriched using two different methods, was used as the starting material and source of viral nucleic acids in HTS. The virome status on the distribution and incidence in different regions and grapevine cultivars is addressed. Results from this study revealed the presence of 20 viruses and 3 viroids in the samples tested. Twelve viruses, which are in the regulated viruses list under grapevine certification, were identified in this survey. The major viruses detected in this survey and their incidence rates are GRSPaV (26% to 100%), GLRaV-2 (1% to 18%), GLRaV-3 (15% to 63%), GRVFV (0% to 52%), GRGV (0% to 52%), GPGV (3.3% to 77%), GFkV (1.5% to 31.6%), and GRBV (0% to 19.4%). This survey is the first comprehensive virome study using viral dsRNA and a metagenomics approach on grapevine samples from the British Columbia, Ontario, Nova Scotia, and Quebec provinces in Canada. Results from this survey highlight the grapevine virome distribution across four major grapevine-growing regions and their cultivars. The outcome of this survey underlines the need for strengthening current management options to mitigate the impact of virus spread, and the implementation of a domestic grapevine clean plant program to improve the sanitary status of the grapevine ecosystem. Full article

Background: Type 2 diabetes mellitus (T2DM) is an epidemic chronic disease that affects millions of people worldwide. This study aims to explore the impact of T2DM on the tear proteome, specifically investigating whether alterations occur before the development of diabetic retinopathy. Methods: Flush tear samples were collected from healthy subjects and subjects with preDM and T2DM. Tear proteins were processed and analyzed by mass spectrometry-based shotgun proteomics using a data-independent acquisition parallel acquisition serial fragmentation (diaPASEF) approach. Machine learning algorithms, including random forest, lasso regression, and support vector machine, and statistical tools were used to identify potential biomarkers. Results: Machine learning models identified 17 proteins with high importance in classification. Among these, five proteins (cystatin-S, S100-A11, submaxillary gland androgen-regulated protein 3B, immunoglobulin lambda variable 3–25, and lambda constant 3) exhibited differential abundance across these three groups. No correlations were identified between proteins and clinical assessments of the ocular surface. Notably, the 17 important proteins showed superior prediction accuracy in distinguishing all three groups (healthy, preDM, and T2DM) compared to the five proteins that were statistically significant. Conclusions: Alterations in the tear proteome profile were observed in adults with preDM and T2DM before the clinical diagnosis of ocular abnormality, including retinopathy. Full article

Black knot (BK) disease, caused by Apiosporina morbosa (Schwein.) v. Arx, significantly afflicts Japanese plums (Prunus salicina L.), resulting in substantial economic losses due to its destructive invasion of branches and trunks. Phenotyping for disease severity is critical to understanding resistance and susceptibility across diverse genotypes. In this study, 200 Japanese plum trees from a mixed lineage breeding program were phenotyped for BK severity using a rating scale from 0 to 5. Trees were rated by two independent raters and repeated on a second day, in early spring 2023, before leaf emergence, for peak visibility. The rating system was designed to capture varying levels of infection, with 0 representing no symptoms and 5 indicating severe infection with major effects to the tree’s overall health. Compared to data from 2015 and 2018, there was a noticeable increase in the number of heavily diseased trees relative to symptom-free trees. In 2023, the proportion of completely resistant trees remained the same as in 2018, suggesting true resistance. Median scores were calculated from four independent ratings per tree, comprised of two individuals on two different days, minimizing individual biases. Additionally, inter-rater reliability was assessed using the weighted Kappa statistic, which yielded a value of 0.903, indicating strong agreement between raters. This phenotypic assessment provides a robust dataset for correlation with genetic markers and supports further breeding efforts aimed at developing BK-resistant cultivars. Full article

The breast tissue microbiome has been increasingly recognized as a potential contributor to breast cancer development and progression. However, inconsistencies in microbial composition across studies have hindered the identification of definitive microbial signatures. We conducted a systematic review and meta-analysis of 11 studies using 16S rRNA sequencing to characterize the bacterial microbiome in 1260 fresh breast tissue samples, including normal, mastitis-affected, benign, cancer-adjacent, and cancerous tissues. Studies published until 31 December 2023 were included if they analyzed human breast tissue using Illumina short-read 16S rRNA sequencing with sufficient metadata, while non-human samples, non-breast tissues, non-English articles, and those lacking metadata or using alternative sequencing methods were excluded. We also incorporated microbiome data from The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort to enhance our analyses. Our meta-analysis identified Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota as the dominant phyla in breast tissue, with Staphylococcus and Corynebacterium frequently detected across studies. While microbial diversity was similar between cancer and cancer-adjacent tissues, they both exhibited a lower diversity compared to normal and mastitis-affected tissues. Variability in bacterial genera was observed across primer sets and studies, emphasizing the need for standardized methodologies in microbiome research. An analysis of TCGA-BRCA data confirmed the dominance of Staphylococcus and Corynebacterium, which was associated with breast cancer proliferation-related gene expression programs. Notably, high Staphylococcus abundance was associated with a 4.1-fold increased mortality risk. These findings underscore the potential clinical relevance of the breast microbiome in tumor progression and emphasize the importance of methodological consistency. Future studies to establish causal relationships, elucidate underlying mechanisms, and assess microbiome-targeted interventions are warranted. Full article

Background: To progress research into the biological mechanisms that link mammographic breast density to breast cancer risk, fibroglandular breast density can be used as a surrogate measure. This study aimed to develop a computational tool to classify fibroglandular breast density in hematoxylin and eosin (H&E)-stained breast tissue sections using deep learning approaches that would assist future mammographic density research. Methods: Four different architectural configurations of transferred MobileNet-v2 convolutional neural networks (CNNs) and four different models of vision transformers were developed and trained on a database of H&E-stained normal human breast tissue sections (965 tissue blocks from 93 patients) that had been manually classified into one of five fibroglandular density classes, with class 1 being very low fibroglandular density and class 5 being very high fibroglandular density. Results: The MobileNet-Arc 1 and ViT model 1 achieved the highest overall F1 scores of 0.93 and 0.94, respectively. Both models exhibited the lowest false positive rate and highest true positive rate in class 5, while the most challenging classification was class 3, where images from classes 2 and 4 were mistakenly classified as class 3. The area under the curves (AUCs) for all classes were higher than 0.98. Conclusions: Both the ViT and MobileNet models showed promising performance in the accurate classification of H&E-stained tissue sections across all five fibroglandular density classes, providing a rapid and easy-to-use computational tool for breast density analysis. Full article

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high resistance to chemotherapy. Doxorubicin is commonly used, but its efficacy is limited by variable sensitivity and resistance. Bacopaside II, a saponin compound, has shown anti-cancer potential. This study evaluates the effects of doxorubicin and bacopaside II, both individually and in combination, across TNBC subtypes to explore mechanisms of resistance and enhanced drug efficacy. Methods: The growth-inhibitory effects of doxorubicin and bacopaside II were assessed in four TNBC cell lines. IC50 values were determined using dose–response assays, and doxorubicin accumulation was measured via spectral flow cytometry. ATP-binding cassette (ABC) transporter expression (ABCB1, ABCC1, ABCC3, and ABCG2) was analyzed for correlations with drug sensitivity. In silico docking assessed the binding affinity of bacopaside II to ABC transporters. A 3D culture model simulated drug-resistant TNBC, and combination effects were evaluated with live-cell imaging. Results: Doxorubicin sensitivity varied across TNBC molecular subtypes, correlating to intracellular accumulation. Bacopaside II inhibited growth across subtypes, inducing apoptosis in sensitive cells and necrosis in resistant cells. Bacopaside II increased doxorubicin accumulation, independent of P-glycoprotein (ABCB1), possibly through interactions with other ABC transporters. In drug-resistant 3D cultures, bacopaside II maintained efficacy and enhanced doxorubicin accumulation, counteracting ABC transporter-mediated resistance. The doxorubicin and bacopaside II combination showed synergistic growth inhibition. Conclusions: Bacopaside II enhances doxorubicin efficacy in TNBC by increasing drug accumulation and overcoming ABC transporter-mediated resistance, suggesting its potential as an adjuvant in TNBC treatment. These findings support further investigation of bacopaside II, particularly for resistant TNBC subtypes. Full article

Fire blight is an infectious disease found in apple and pear orchards. While managing the disease is critical to maintaining orchard health, identifying symptoms early is a challenging task which requires trained expert personnel. This paper presents an inspection technique that targets individual symptoms via deep learning and density estimation. We evaluate the effects of including multi-spectral sensors in the model’s pipeline. Results show that adding near infrared (NIR) channels can help improve prediction performance and that density estimation can detect possible symptoms when severity is in the mid-high range. Full article

Chlorophyll has long been used as a natural indicator of plant health and photosynthetic efficiency. Laser-induced fluorescence (LIF) is an emerging technique for understanding broad spectrum organic processes and has more recently been used to monitor chlorophyll response in plants. Previous work has focused on developing a LIF technique for imaging moss mats to identify metal contamination with the current focus shifting toward application to moss fronds and aiding sample collection for chemical analysis. Two laser systems (CoCoBi a Nd:YGa pulsed laser system and Chl-SL with two blue continuous semiconductor diodes) were used to collect images of moss fronds exposed to increasing levels of Cu (1, 10, and 100 nmol/cm²) using a CMOS camera. The best methods for the preprocessing of images were conducted before the analysis of fluorescence signatures were compared to a control. The Chl-SL system performed better than the CoCoBi, with dynamic time warping (DTW) proving the most effective for image analysis. Manual thresholding to remove lower decimal code values improved the data distributions and proved whether using one or two fronds in an image was more advantageous. A higher DTW difference from the control correlated to lower chlorophyll a/b ratios and a higher metal content, indicating that LIF, with the aid of image processing, can be an effective technique for identifying Cu contamination shortly after an event. Full article

This paper presents a number of lessons learned while designing a proposed sterilization system for Mars Sample Return. This sterilization system is needed to inactivate any potentially hazardous Mars material on the exterior surface of the vessel containing sealed sample tubes filled with Mars rock cores, regolith and atmosphere. These returned samples would provide information on the geologic history of Mars, the evolution of its climate and the potential for ancient life. Mars Sample Return is categorized at Planetary Protection Category V Restricted Earth Return, so it is required to protect the Earth–Moon system from the biological impact of returning samples from Mars to Earth. This article reviews lessons learned in the development of a particular engineering implementation to support the protection of the Earth–Moon biosphere: the use of in situ ultraviolet LED illumination. The details of the biological efficacy of this approach or the policy-related impacts are outside of the scope of this manuscript. The lessons learned presented here include establishing design requirements for the system, the selection of a light source, optical design options, contamination control and approaches to thermal and power management. Full article

Dietary practices of masters athletes (MAs) may promote healthy ageing; however, they are poorly understood. The aims of this systematic review were to synthesise the literature on the dietary intakes of MAs and undertake comparisons between younger (35–50 years) and older (>50 years) MAs and the general population. A search was conducted across seven databases to identify relevant publications for screening and data extraction. Averages for energy intake (EI), macronutrients, and micronutrients were compared with data from the 2011–2012 Australian Health Survey (general population). Twenty-six studies (n = 2819) were included. Energy intake was higher for older (8908 kJ/d versus 7792 kJ/d) but not younger MAs (9073 kJ/d versus 8872 kJ/d) versus the general population. Younger versus older male MAs had higher energy and macronutrient intakes. Energy intake for older was comparable to younger female MAs (7819 kJ/d versus 7485 kJ/d), but older had higher protein, lower carbohydrate, and higher micronutrient intakes. Micronutrient intake was higher in MAs than the general population. Similar EIs for older MAs and younger general population may indicate potential for a higher-quality diet. Younger female MAs may restrict or misreport EI, requiring further investigation. There is a need for more comprehensive assessments of dietary intake in MAs to ascertain diet quality in relation to health. Full article

This study investigated the transmission of grapevine viruses, specifically grapevine red blotch virus (GRBV) and grapevine Pinot gris virus (GPGV), in vineyards in Niagara Region, Ontario, Canada. Forty sentinel vines that were confirmed free of GRBV and GPGV by both high-throughput sequencing (HTS) and endpoint polymerase chain reaction (PCR) were introduced to two vineyards (one organic and one conventional) that were heavily infected with both GRBV and GPGV. Four months post-introduction, the sentinel vines were relocated to a phytotron. The HTS results from 15 months post-introduction revealed a widespread infection of GPGV among the sentinel vines but did not detect any GRBV. The GPGV infection rate of sentinel vines in the organic vineyard (13/18) was higher than in the conventional vineyard (1/19). The possibility of an alternative viral reservoir was assessed by testing the most abundant plants in between rows (Medicago sativa, Trifolium repens, Cirsium arvense and Taraxacum officinale), perennial plants in border areas (Fraxinus americana, Ulmus americana, Rhamnus cathartica) and wild grape (unknown Vitis sp.). The HTS result showed that cover crops and perennial plants did not harbor any grapevine viruses, while 4/5 wild grapes tested positive for GPGV but not GRBV. A pairwise sequence identity analysis revealed high similarities between the GPGV isolates found in the established vines on the vineyard and the newly contracted GPGV isolates in the sentinel vines, implicating a recent transmission event. This work provides novel insights into the spread of grapevine viruses in Niagara Region and is also the first direct proof of the spread of GPGV in natural vineyard conditions in North America. Full article

The ability to detect, measure, and locate the source of contaminants, especially heavy metals and radionuclides, is of ongoing interest. A common tool for contaminant identification and bioremediation is vegetation that can accumulate and indicate recent and historic pollution. However, large-scale sampling can be costly and labor-intensive. Hence, non-invasive in-situ techniques such as laser-induced fluorescence (LIF) are becoming useful and effective ways to observe the health of plants through the excitation of organic molecules, e.g., chlorophyll. The technique presented utilizes images collected of LIF in moss to identify different metals and environmental stressors. Analysis through image processing of LIF response was key to identifying Cu, Zn, Pb, and a mixture of the metals at nmol/cm² levels. Specifically, the RGB values from each image were used to create density histograms of each color channel’s relative pixel abundance at each decimal code value. These histograms were then used to compare color shifts linked to the successful identification of contaminated moss samples. Photoperiod and extraneous environmental stressors had minimal impact on the histogram color shift compared to metals and presented with a response that differentiated them from metal contamination. Full article

Background: Erectile dysfunction (ED) is common after prostate cancer treatment. It has been studied for conventional radiotherapy, but associations in the hypofractionated radiotherapy context are less clear. This study aimed to determine which factors are predicted for worsening ED after highly conformal, modestly hypofractionated radiotherapy to the prostate. Methods: Two hundred and twelve patients treated with 6000 cGy in twenty fractions across four centers were included in this study. Demographic, clinical, and dosimetry factors were then evaluated for post-treatment declines in erectile function using logistic regression and an explainable machine learning-based neural network. Results: 212 patients with a median follow-up of 3.6 years were evaluated. A total of 104 (49%) patients received androgen deprivation therapy. Prior to treatment, 52 (25%) patients were on ED medication. Mean doses to the penile bulb, penile crus, and penile shaft were 2490 (IQR: 1529–3656) cGy, 2095 (1306–3036) cGy, and 444 (313–650) cGy, respectively. Fifty-nine (28%) patients had a worsening of ED after treatment. On multivariable analysis, only the mean dose to the penile shaft [OR >345 vs. ≤345: 4.47 (1.43–13.99); p = 0.010] and pretreatment use of ED medication [OR yes vs. no: 12.5 (5.7–27.5; p < 0.001)] predicted for worsening ED. The neural network confirmed that the penile shaft mean dose and pre-treatment ED medication use are the most important factors in predicting ED. Conclusions: Pre-treatment ED and penile shaft dosimetry are important predictors for ED after hypofractionated radiotherapy for prostate cancer. Full article

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada. Full article

Physical activity is consistently recognized as a key component of healthy aging. The current study aimed to investigate the prospective association between social support specific for physical activity (SSPA) and physical activity across nine years among adults aged 60–65 years at baseline (n = 1984). An observational longitudinal design was used, with mail surveys administered to a population-based sample across four waves. SSPA was measured using a score ranging from 5–25, and physical activity was assessed as time spent in walking, or engaging in moderate and vigorous activity, during the previous week. Data were analyzed using linear mixed-effects models. The results demonstrated a positive significant relationship between SSPA and physical activity, accounting for sociodemographic and health variables. Each unit of increase in SSPA was associated with 11 extra minutes of physical activity per week (p < 0.001). There was a significant interaction between SSPA and wave at the final timepoint, such that the relationship was weaker (p = 0.017). The results highlight the value of even small increases in SSPA. SSPA could be targeted to promote physical activity among older adults, but may be more impactful in young-old adults. More research is needed to understand impactful sources of SSPA, underlying mechanisms between SSPA and physical activity, and potential moderation by age. Full article