19 research outputs found
Next-generation methods for early disease detection in crops. A review
No full textBackground: Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. Herein, in this review were presented and discussed the traditional and innovative methods for early detection of the pathogen. In addition, they highlighted the major advantages and limitations of current technologies. Results: traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in the field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. Conclusion: The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially can revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. This article is protected by copyright. All rights reserved
Next‐generation methods for early disease detection in crops. A review
No full text: Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry
Sviluppo di una metodica su dispositivo portatile per la determinazione in situ di biomarcatori espressi in seguito a stress biotico provocato dall’infezione da Spilocaea oleagina in olivo (Olea europaea L.)
No full textProposta di un manuale di buona prassi (GHP) per trippai e lampredottai secondo il regolamento CE 852/2004
No full textQuesto manuale si propone l’obiettivo di essere d’aiuto a tutti coloro che gestiscono la piccola impresa di trippaio e di lampredottaio, tenendo conto che tale lavoro trova le sue radici nella tradizione storica toscana. Il punto di riferimento è il Regolamento (CE) n.852/2004 che è integrato con la normativa nazionale e regionale nelle fasi non contemplate. Viene descritto il metodo seguito per arrivare alla stesura di un programma HACCP.
Trippa e lampredotto sono suscettibili di contaminazione ben prima della vendita al consumatore, con pericoli di origine biologica e chimica insiti nella sua produzione e preparazione primaria. Tali possibili contaminazioni sono prese in considerazione nello studio del pericolo per fornire un approccio globale al prodotto. Viene dedicata particolare attenzione alla contaminazione secondaria e sono state compilate schede di valutazione del rischio per ogni fase del processo di produzione. Sono messe a disposizione dell’operatore del settore alimentare (OSA) schede di verifica da utilizzare per l’applicazione del manuale.
Abstract
This guide is aimed at helping who works in a small tripe and lampredotto business, bearing in mind the historical tradition of this job in Tuscany. Regulation (EC) No 852/2004 is the guideline; national and regional legislation integrate the main regulation for parts that are not considered in it. A method is described to create a HACCP-based program.
Tripe and lampredotto can be contaminated long before be sold to the final consumer. There are biological and chemical hazards present at the level of primary production. These contaminations are examined in the hazard analysis to get a global approach. Much attention has been focused on the secondary contamination. Schedules of risk assessment are filled for every phases of the production process. Verification sheets are made available for food business operators to apply this guide
Development of a Real-Time Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Olea Europaea Geminivirus
No full textA real-time loop-mediated isothermal amplification (LAMP) assay was developed for simple, rapid and efficient detection of the Olea europaea geminivirus (OEGV), a virus recently reported in different olive cultivation areas worldwide. A preliminary screening by end-point PCR for OEGV detection was conducted to ascertain the presence of OEGV in Sicily. A set of six real-time LAMP primers, targeting a 209-nucleotide sequence elapsing the region encoding the coat protein (AV1) gene of OEGV, was designed for specific OEGV detection. The specificity, sensitivity, and accuracy of the diagnostic assay were determined. The LAMP assay showed no cross-reactivity with other geminiviruses and was allowed to detect OEGV with a 10-fold higher sensitivity than conventional end-point PCR. To enhance the potential of the LAMP assay for field diagnosis, a simplified sample preparation procedure was set up and used to monitor OEGV spread in different olive cultivars in Sicily. As a result of this survey, we observed that 30 out of 70 cultivars analyzed were positive to OEGV, demonstrating a relatively high OEGV incidence. The real-time LAMP assay developed in this study is suitable for phytopathological laboratories with limited facilities and resources, as well as for direct OEGV detection in the field, representing a reliable method for rapid screening of olive plant material
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Bayesian Methods for Multi-Outcome Analysis and a Study of Gender Bias in Medical Articles
No full textIn Chapter 1, we present Multi-Outcome Regression with Tree-structured Shrinkage (MOReTreeS), a novel framework for Bayesian multi-response regression when the outcomes are related according to a known tree or hierarchy [Thomas et. al, 2020]. Examining the impact of an exposure on a large number of health outcomes is statistically challenging. Analyzing each outcome separately ignores relationships among pathologies, leads to multiple testing problems, and introduces bias when only the strongest associations are reported. MOReTreeS addresses these limitations using a tree-structured prior for the regression coefficients of each outcome that enables: (1) borrowing of strength across related outcomes; (2) data-driven discovery of groups of outcomes that are similarly affected by the exposure, and; (3) estimation of a single, interpretable effect for each outcome group. Through simulations, we find that MOReTreeS can reduce the root mean squared error of the effect estimates compared to standard regression methods while still providing significant dimensional reduction, thereby enhancing interpretability of the estimates. We apply MOReTreeS to study the effect of short-term exposure to fine particulate matter (PM2.5) on risk of hospitalization due to 432 cardiovascular diseases categorized by the hierarchical International Classification of Diseases, Revision 9.
In Chapter 2, we apply MOReTreeS to a more in-depth analysis of PM2.5 and hospitalizations due to cardiovascular and respiratory disease in Medicare beneficiaries. Our objectives were (1) to discover groups of related causes of hospitalization such that PM2.5 associations are similar within but different between groups; (2) to introduce MOReTreeS to an audience of epidemiologists, and; (3) to introduce an R package, moretrees, for fitting MOReTreeS models to matched case-control and case-crossover data. We conducted a time-stratified case-crossover study of hospitalizations from 2000 through 2014 among Medicare beneficiaries aged 65+ living in the contiguous United States. Cause of hospitalization was defined using hierarchical Clinical Classification Software (CCS) codes. Daily PM2.5, temperature, and relative humidity data were linked to Medicare data via residential ZIP codes. Statistical models used a MOReTreeS prior and conditional logistic likelihood with nonlinear control for temperature and humidity. Our dataset included 6,007,293 hospitalizations for 57 cardiovascular causes and 8,690,837 hospitalizations for 32 respiratory causes. MOReTrees grouped 51 of 57 cardiovascular diseases into one group with a positive PM2.5 association. Compared to this group, heart failure exhibited a stronger positive association. Negative associations were observed for certain aneurysms and intracranial hemorrhage. 31 of 32 respiratory outcomes were grouped and were positively associated with PM2.5. Influenza exhibited a negative association.
In Chapter 3, we present an analysis of gender bias in authorship of invited commentaries in medical journals [Thomas et al., 2019]. In peer-reviewed medical journals, authoring an invited commentary on an original article is a recognition of expertise. Women author fewer invited publications than men. However, it is unknown whether this disparity is due to gender differences in characteristics that drive invitations, such as field of expertise, seniority, and scientific output. We aimed to estimate the odds ratio (OR) of authoring an invited commentary for women compared to men with similar expertise, seniority, and publication metrics. We used a matched case-control study design of all articles published from 2013 through 2017 in an English-language medical journal, or medical articles published in a multidisciplinary journal. Cases were defined as corresponding authors of invited commentaries in a given journal during the study period. Controls were matched to cases on scientific expertise by calculating a similarity index for abstracts published 2013 through 2017 using natural language processing. Genderize.io was used to predict gender from author first name and country of origin. Invited commentaries were defined as publications that cite another publication within the same journal volume and issue. The OR for gender was estimated adjusting for field of expertise, publication output, citation impact, and years since first publication (years active), with an interaction between gender and years active. The final dataset included 43,235 cases across 2,549 journals. For researchers who had been active for the median number of years (16), the OR for invited commentary authorship was 0.79 for women compared to men with similar scientific expertise, number of publications, and citation impact (95% confidence interval (CI): 0.77 to 0.81). For every one decile increase in years active, this OR decreased further by a factor of 0.97 (95%CI: 0.96 to 0.98).Biostatistic
Addition of Olive Leaf Extract (OLE) for Producing Fortified Fresh Pasteurized Milk with an Extended Shelf Life
No full textAn olive leaf extract (OLE) has been tested in vitro for its antibacterial activity and ability to inhibit α-glucosidase enzyme. OLE was also evaluated for its potential, when added to pasteurized milk, to preserve nutritional parameters and to limit microbial growth, thus prolonging shelf life. In vitro assays demonstrated a strong antibacterial efficacy of OLE mainly against Bacillus cereus and the capacity to inhibit α-glucosidase enzyme (IC50) when used at 0.2 mg oleuropein/mL. The milk fortification with OLE at 3.6 mg of oleuropein/mL of milk reduced total mesophilic bacteria at undetectable level after 6 d (expiration date) and by 1 log CFU/mL after 10 d. Moreover, OLE addition at 1.44 and 3.6 mg of oleuropein/mL of milk significantly reduced fat and lactose losses up to 10 d. The results motivate the use of the OLE to make a new functional milk with an extended shelf life
A systematic review of evidence on malignant spinal metastases : natural history and technologies for identifying patients at high risk of vertebral fracture and spinal cord compression
No full textBackground: Spinal metastases can lead to significant morbidity and reduction in quality of life due to spinal cord compression (SCC). Between 5% and 20% of patients with spinal metastases develop metastatic spinal cord compression during the course of their disease. An early study estimated average survival for patients with SCC to be between 3 and 7 months, with a 36% probability of survival to 12 months. An understanding of the natural history and early diagnosis of spinal metastases and prediction of collapse of the metastatic vertebrae are important.
Objective: To undertake a systematic review to examine the natural history of metastatic spinal lesions and to identify patients at high risk of vertebral fracture and SCC.
Data sources: The search strategy covered the concepts of metastasis, the spine and adults. Searches were undertaken from inception to June 2011 in 13 electronic databases [MEDLINE; MEDLINE In-Process & Other Non-Indexed Citations; EMBASE; Cochrane Database of Systematic Reviews; Cochrane Central Register of Controlled Trials (CENTRAL); Database of Abstracts of Reviews of Effects (DARE), NHS Economic Evaluation Database (NHS EED), HTA databases (NHS Centre for Reviews and Dissemination); Science Citation Index and Conference Proceedings (Web of Science); UK Clinical Research Network (UKCRN) Portfolio Database; Current Controlled Trials; ClinicalTrials.gov].
Review methods: Titles and abstracts of retrieved studies were assessed by two reviewers independently. Disagreement was resolved by consensus agreement. Full data were extracted independently by one reviewer. All included studies were reviewed by a second researcher with disagreements resolved by discussion. A quality assessment instrument was used to assess bias in six domains: study population, attrition, prognostic factor measurement, outcome measurement, confounding measurement and account, and analysis. Data were tabulated and discussed in a narrative review. Each tumour type was looked at separately.
Results: In all, 2425 potentially relevant articles were identified, of which 31 met the inclusion criteria. No study examined natural history alone. Seventeen studies reported retrospective data, 10 were prospective studies, and three were other study designs. There was one systematic review. There were no randomised controlled trials (RCTs). Approximately 5782 participants were included. Sample sizes ranged from 41 to 859. The age of participants ranged between 7 and 92 years. Types of cancers reported on were lung alone (n= 3), prostate alone (n= 6), breast alone (n= 7), mixed cancers (n= 13) and unclear (n= 1). A total of 93 prognostic factors were identified as potentially significant in predicting risk of SCC or collapse. Overall findings indicated that the more spinal metastases present and the longer a patient was at risk, the greater the reported likelihood of development of SCC and collapse. There was an increased risk of developing SCC if a cancer had already spread to the bones. In the prostate cancer studies, tumour grade, metastatic load and time on hormone therapy were associated with increased risk of SCC. In one study, risk of SCC before death was 24%, and 2.37 times greater with a Gleason score 7 than with a score of < 7 (p= 0.003). Other research found that patients with six or more bone lesions were at greater risk of SCC than those with fewer than six lesions [odds ratio (OR) 2.9, 95% confidence interval (CI) 1.012 to 8.35, p= 0.047]. For breast cancer patients who received a computerised tomography (CT) scan for suspected SCC, multiple logistic regression in one study identified four independent variables predictive of a positive test: bone metastases 2 years (OR 3.0 95% CI 1.2 to 7.6; p= 0.02); metastatic disease at initial diagnosis (OR 3.4, 95% CI 1.0 to 11.4; p= 0.05); objective weakness (OR 3.8, 95% CI 1.5 to 9.5; p= 0.005); and vertebral compression fracture on spine radiograph (OR 2.6, 95% CI 1.0 to 6.5; p= 0.05). A further study on mixed cancers, among patients who received surgery for SCC, reported that vertebral body compression fractures were associated with presurgery chemotherapy (OR 2.283, 95% CI 1.064 to 4.898; p= 0.03), cancer type [primary breast cancer (OR 4.179, 95% CI 1.457 to 11.983; p= 0.008)], thoracic involvement (OR 3.505, 95% CI 1.343 to 9.143; p= 0.01) and anterior cord compression (OR 3.213, 95% CI 1.416 to 7.293; p= 0.005).
Limitations: Many of the included studies provided limited information about patient populations and selection criteria and they varied in methodological quality, rigour and transparency. Several studies identified type of cancer (e.g. breast, lung or prostate cancer) as a significant factor in predicting SCC, but it remains difficult to determine the risk differential partly because of residual bias. Consideration of quantitative results from the studies does not easily allow generation of a coherent numerical summary, studies were heterogeneous especially with regard to population, results were not consistent between studies, and study results almost universally lacked corroboration from other independent studies.
Conclusion: No studies were found which examined natural history. Overall burden of metastatic disease, confirmed metastatic bone involvement and immediate symptomatology suggestive of spinal column involvement are already well known as factors for metastatic SCC, vertebral collapse or progression of vertebral collapse. Although we identified a large number of additional possible prognostic factors, those which currently offer the most potential are unclear. Current clinical consensus favours magnetic resonance imaging and CT imaging modalities for the investigation of SCC and vertebral fracture. Future research should concentrate on: (1) prospective randomised designs to establish clinical and quality-of-life outcomes and cost-effectiveness of identification and treatment of patients at high risk of vertebral collapse and SCC; (2) Service Delivery and Organisation research on magnetic resonance imaging (MRI) scans and scanning (in tandem with research studies on use of MRI to monitor progression) in order to understand best methods for maximising use of MRI scanners; and (3) investigation of prognostic algorithms to calculate probability of a specified event using high-quality prospective studies, involving defined populations, randomly selected and clearly identified samples, and with blinding of investigators
Table_3_NGS transcriptomic analysis uncovers the possible resistance mechanisms of olive to Spilocea oleagina leaf spot infection.xlsx
No full textSpilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock’s eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages—”zero sign of disease” and “evident sign of infection”. Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. ‘Koroneiki’ showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in ‘Koroneiki’, while ‘Nocellara del Belice’ was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.</p
Image_1_NGS transcriptomic analysis uncovers the possible resistance mechanisms of olive to Spilocea oleagina leaf spot infection.tiff
No full textSpilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock’s eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages—”zero sign of disease” and “evident sign of infection”. Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. ‘Koroneiki’ showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in ‘Koroneiki’, while ‘Nocellara del Belice’ was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.</p
