Exploring the hidden hot world of long non-coding RNAs in thermophilic fungus using a robust computational pipeline.

Long noncoding RNAs (lncRNAs) are versatile RNA molecules recently identified as key regulators of gene expression in response to environmental stress. Our primary focus in this study was to develop a robust computational pipeline for identifying structurally identical lncRNAs across replicates from publicly available bulk RNA-seq datasets. In order to demonstrate the effectiveness of the pipeline, we utilized the transcriptome of the thermophilic fungus Thermothelomyces thermophilus and assessed the expression pattern of lncRNAs in conjunction with Heat Shock Proteins (HSP), a well-known protein family critical for the cell's response to high temperatures. Our findings demonstrate that the identification of structurally identical transcripts among replicates in this thermophilic fungus ensures the reliability and accuracy of RNA studies, contributing to the validity of biological interpretations. Furthermore, the majority of lncRNAs exhibited a distinct expression pattern compared to HSPs. Our study contributes to advancing the understanding of the biological mechanisms comprising lncRNAs in thermophilic fungi.

Environmental conditions affect the nutritive value and alkaloid profiles of Lupinus forage: Opportunities and threats for sustainable ruminant systems.

The identification of crops that simultaneously contribute to the global protein supply and mitigate the effects of climate change is an urgent matter. Lupins are well adapted to nutrient-poor or contaminated soils, tolerate various abiotic stresses, and present relevant traits for acting as ecosystem engineers. Lupins are best studied for their seeds, but their full foraging potential needs further evaluation. This study evaluated the effects of location and sowing date on forage production, proximate composition, and the detailed mineral and alkaloid profiles of three species of Lupinus (L. albus cv. Estoril, L. angustifolius cv. Tango, and L. luteus cv. Cardiga). Sowing date and location and their interaction with the plant species significantly affected the vast majority of measured parameters, emphasizing the effects of climate and soil conditions on these crops. The relatively high crude protein and in vitro digestibility support the potential of the lupin species studied as sustainable forage protein sources in diets for ruminant animals. The content of individual essential macro and trace elements was below the maximum tolerable levels for cattle and sheep. Lupanine, smipine, and sparteine were the most abundant quinolizidine alkaloids in L. albus cv. Estoril, lupanine, and sparteine in L. angustifolius cv. Tango, and lupinine, gramine, ammodendrine, and sparteine in L. luteus cv. Cardiga. Based on the maximum tolerable levels of total quinolizidine alkaloid intake, the dietary inclusion of forages of L. albus cv. Estoril and L. angustifolius cv. Tango does not pose a risk to the animals, but the high alkaloid content of L. luteus cv. Cardiga may compromise its utilization at high levels in the diet. Overall, the results reveal a high potential for lupins as protein forage sources well adapted to temperate regions and soils with lower fertility, with a relevant impact on livestock sustainability in a climate change era.

FTA-LAMP based biosensor for a rapid in-field detection of Globodera pallida-the pale potato cyst nematode.

The combination of a sensitive and specific magnetoresistive sensing device with an easy DNA extraction method and a rapid isothermal amplification is presented here targeting the on-site detection of Globodera pallida, a potato endoparasitic nematode. FTA-cards were used for DNA extraction, LAMP was the method developed for DNA amplification and a nanoparticle functionalized magnetic-biosensor was used for the detection. The combinatorial effect of these three emerging technologies has the capacity to detect G. pallida with a detection limit of one juvenile, even when mixed with other related species. This combined system is far more interesting than what a single technology can provide. Magnetic biosensors can be combined with any DNA extraction protocol and LAMP forming a new solution to target G. pallida. The probe designed in this study consistently distinguished G. pallida (∆Vac binding/Vac sensor above 1%) from other cyst nematodes (∆Vac binding/Vac sensor below 1%). It was confirmed that DNA either extracted with FTA-cards or Lab extraction Kit was of enough quantity and quality to detect G. pallida whenever present (alone or in mixed samples), ensuring probe specificity and sensitivity. This work provides insights for a new strategy to construct advanced devices for pathogens in-field diagnostics. LAMP runs separately but can be easily integrated into a single device.

Exploring the relationship between emotion regulation, inhibitory control, and eating psychopathology in a non-clinical sample.

OBJECTIVE: The present study aimed to explore the relationship between difficulties in emotion regulation and deficits in inhibitory control, and the role of these processes in eating psychopathology in a non-clinical sample. We also explored the specificity in which deficits in inhibitory control may underlie eating psychopathology, namely whether they can be conceptualised as context specific or more extensive in nature. METHOD: Participants were 107 healthy individuals recruited at a major Portuguese university, aged between 18 and 43 years-old (M = 21.23, SD = 4.79). Two computerised neuropsychological tasks (i.e., emotional go/no-go and food go/no-go tasks) were used to assess response inhibition in the presence of general versus context-specific stimuli. A set of self-report measures was used to assess variables of interest such as emotion regulation and eating psychopathology. RESULTS: Results indicated higher response inhibition deficits among participants with higher difficulties in emotion regulation comparing to those with lower difficulties in emotion regulation, particularly in the context of food-related stimuli. In addition, the relationship between difficulties in emotion regulation and eating psychopathology was moderated by inhibitory control deficits in both the context of food and pleasant stimuli. CONCLUSIONS: The present findings highlight inhibitory control as an important process underlying the relationship between difficulties in emotion regulation and eating psychopathology in non-clinical samples. Findings have important implications for clinical practice and the prevention of eating psychopathology in healthy individuals and individuals with eating disorders.

Historical line of airglow observations at Comandante Ferraz Brazilian Station: measurements of temperature and studies on gravity waves.

The thermal dynamics of the upper atmosphere, especially in the mesosphere, have been improving our understanding about the effects of climate change, as well as how the dynamics and general circulation in the upper atmosphere are driven by different types of waves, such as the atmospheric gravity waves, planetary waves and atmospheric tides. In order to study the upper atmospheric temperature variability and gravity waves, several research groups have been employing the remote technique of observing the airglow emissions originated in the upper mesosphere and lower thermosphere, besides emissions from the ionosphere. INPE's airglow group started the studies on emissions from the upper atmosphere to investigate temperature and dynamics in the mesosphere, thermosphere/ionosphere at the end of 70's. However, only in 2001 this group sent the first airglow experiment to the Brazilian Antarctic Station Comandante Ferraz (EACF) to measure the OH (8-3) emission and temperature. From that year to 2014, several other experiments were carried out at EACF, not only to measure the temperature and airglow intensities, but also to observe gravity waves, winds and other related phenomena. This paper presents airglow experiments at EACF from 2001 to the present, including illustrations, examples of already published results, and unpublished data.

Corrigendum: Severe and enduring' stage in anorexia nervosa: comparing eating attitudes, impairment and associated psychopathology.

[This corrects the article DOI: 10.3389/fnut.2022.867401.].

International consensus on patient-centred outcomes in eating disorders.

The effectiveness of mental health care can be improved through coordinated and wide-scale outcome measurement. The International Consortium for Health Outcomes Measurement has produced collaborative sets of outcome measures for various mental health conditions, but no universal guideline exists for eating disorders. This Position Paper presents a set of outcomes and measures for eating disorders as determined by 24 international experts from professional and lived experience backgrounds. An adapted Delphi technique was used, and results were assessed through an open review survey. Final recommendations suggest outcomes should be tracked across four domains: eating disorder behaviours and cognitions, physical health, co-occurring mental health conditions, and quality of life and social functioning. Outcomes are collected using three to five patient-reported measures. For children aged between 6 years and 12 years, the measures include the Children's Eating Attitude Test (or, for those with avoidant restrictive food intake disorder, the Eating Disorder in Youth Questionnaire), the KIDSCREEN-10, and the Revised Children's Anxiety and Depression Screener-25. For adolescents aged between 13 years and 17 years, the measures include the Eating Disorder Examination Questionnaire (EDE-Q; or, for avoidant restrictive food intake disorder, the Nine-Item Avoidant Restrictive Food Intake Disorder Screener [NIAS]), the two-item Patient Health Questionnaire (PHQ-2), the nine-item Patient Health Questionnaire (PHQ-9), the two-item Generalised Anxiety Disorder (GAD-2), the seven-item Generalised Anxiety Disorder (GAD-7), and the KIDSCREEN-10. For adults older than 18 years, measures include the EDE-Q (or, for avoidant restrictive food intake disorder, the NIAS), the PHQ-2, the PHQ-9, the GAD-2, the GAD-7, the Clinical Impairment Assessment, and the 12-item WHO Disability Assessment Schedule 2.0. These questionnaires should be supplemented by information on patient characteristics and circumstances (ie, demographic, historical, and clinical factors). International adoption of these guidelines will allow comparison of research and clinical interventions to determine which settings and interventions work best, and for whom.

A magnetic nanoparticle-based microfluidic device fabricated using a 3D-printed mould for separation of Escherichia coli from blood.

Herein, A microfluidic device is described, produced with a 3D-printed master mould that rapidly separates and concentrates Escherichia coli directly from whole blood samples, enabling a reduction in the turnaround time of bloodstream infections (BSIs) diagnosis. Moreover, it promotes the cleansing of the blood samples whose complexity frequently hampers bacterial detection. The device comprises a serpentine mixing channel with two inlets, one for blood samples (spiked with bacteria) and the other for magnetic nanoparticles (MNPs) functionalized with a (bacterio)phage receptor-binding protein (RBP) with high specificity for E. coli. After the magnetic labelling of bacteria throughout the serpentine, the microchannel ends with a trapping reservoir where bacteria-MNPs conjugates are concentrated using a permanent magnet. The optimized sample preparation device successfully recovered E. coli (on average, 66%) from tenfold diluted blood spiked within a wide range of bacterial load (102 CFU to 107 CFU mL-1). The non-specific trapping, tested with Staphylococcus aureus, was at a negligible level of 12%. The assay was performed in 30 min directly from diluted blood thus presenting an advantage over the conventional enrichment in blood cultures (BCs). The device is simple and cheap to fabricate and can be tailored for multiple bacterial separation from complex clinical samples by using RBPs targeting different species. Moreover, the possibility to integrate a biosensing element to detect bacteria on-site can provide a reliable, fast, and cost-effective point-of-care device.

Upcycling post-harvest biomass residues from native European Lupinus species: from straws and pod shells production to nutritive value and alkaloids content for ruminant animals.

The production of Lupinus seeds for food and feed is increasing worldwide, which results in large amounts of post-harvest biomass residues, considered of low value and left in the field to be burned or incorporated in the soil. To valorize these agricultural wastes, this work aimed to assess their potential as an alternative feed for ruminants. Thus, the production yield, nutritive value, and alkaloid content of straws and pod shells from three native European Lupinus species, L. albus 'Estoril' (white), L. angustifolius 'Tango' (narrow-leafed), and L. luteus 'Cardiga' (yellow), cultivated in two locations, were evaluated. The dry matter (DM) yield of straws and pod shells were the highest for L. albus 'Estoril' (4.10 t ha-1) and the lowest for L. angustifolius 'Tango' (1.78 t ha-1), suggesting a poor adaptation of narrow-leafed lupin to the particularly dry and warm agronomic year. Despite species-specific differences, lupin biomass residues presented higher crude protein (53.0-68.9 g kg-1 DM) and lignin (103-111 g kg-1 DM) content than cereal straws usually used in ruminant feeding, thus resulting in higher metabolizable energy (6.43-6.58 MJ kg-1 DM) content. In vitro digestibility was similar among lupin species (47.7-50.6%) and higher in pod shells (53.7%) than in straws (44.6%). Lupinus albus 'Estoril' and L. luteus 'Cardiga' presented considerable amounts of alkaloids in straws (23.9 and 119 mg kg-1 DM) and pod shells (20.5 and 298 mg kg-1 DM), while no alkaloids were detected in L. angustifolius 'Tango' biomass residues. Considering the combined production of straw and pod shells per lupin species, it is anticipated that lupin biomass residues produced per ha can fulfill 85% of the energy and nearly 50% of protein requirements of a flock of 4 to 9 dry and mid-pregnancy sheep with 50 kg body weight for one year. No negative effects on small (ovine) and large (bovine) ruminant species due to alkaloids are expected, even if biomass residues are consumed at up to 85% DM intake. The large production yield along with its nutritive value unveils the potential of lupin biomass residues valorization as alternative fodder for ruminants, promoting sustainability under a circular economy approach.

Machine learning-aided LiDAR range estimation.

Automotive light detection and ranging (LiDAR) requires accurate and computationally efficient range estimation methods. At present, such efficiency is achieved at the cost of curtailing the dynamic range of a LiDAR receiver. In this Letter, we propose using decision tree ensemble machine learning models to overcome such a trade-off. Simple and yet powerful models are developed and proven capable of performing accurate measurements across a 45-dB dynamic range.

Bromelain does not provide significant analgesic and anti-inflammatory benefits over placebo in cats undergoing ovariohysterectomy.

OBJECTIVE: To evaluate the efficacy and safety of bromelain to control pain and inflammation in cats undergoing ovariohysterectomy. ANIMALS: 30 client-owned cats undergoing ovariohysterectomy. PROCEDURES: In a randomized, blinded clinical study, cats were assigned to receive either oral bromelain suspension (40 mg/kg [18 mg/lb]; BG, n = 15) or placebo solution (0.1 mL/kg [0.045 mL/lb]; PG, 15), which were administered 90 minutes before and 12 hours after surgery. The anesthetic protocol included acepromazine, meperidine, propofol, and isoflurane. Pain and sedation were assessed at various time points up to 24 hours post-extubation using the UNESP-Botucatu multidimensional composite pain scale, the Glasgow feline composite measure pain scale, and a descriptive numerical scale. Surgical wound inflammation was measured at the same time points, using a numeric rating scale. Morphine was administered as rescue analgesia. Laboratory data (urea, creatinine, gamma-glutamyl transferase, alkaline phosphatase, the prothrombin time, and the fecal occult blood) were analyzed preoperatively and 24 hours after surgery. RESULTS: Pain/inflammation scores, and analgesic requirements did not differ between groups. Shorter recovery time and lower sedation scores were recorded during the first hour post-extubation in the BG than the PG. Postoperatively, serum creatinine and gamma-glutamyl transferase were lower in the BG compared to PG. Compared to baseline values, all biochemistry variables decreased at 24 hours in the BG. The prothrombin time and fecal occult blood did not differ between groups or over time. CLINICAL RELEVANCE: Bromelain did not provide significant analgesic and anti-inflammatory benefits over placebo in cats undergoing ovariohysterectomy.

Eating disorders during lockdown: the transcultural influence on eating and mood disturbances in Ibero-Brazilian population.

BACKGROUND: COVID-19 pandemic has implied exceptional restrictive measures to contain its widespread, with adverse consequences on mental health, especially for those people with a background of mental illness, such as eating disorders (EDs). In this population, the influence of socio-cultural aspects on mental health has been still underexplored. Then, the main aim of this study was to assess changes in eating and general psychopathology in people with EDs during lockdown regarding the ED subtype, age, and provenance, and considering socio-cultural aspects (e.g., socioeconomical factors such as work and financial losses, social support, restrictive measures, or health accessibility, among others). METHODS: The clinical sample was composed of 264 female participants with EDs (74 anorexia nervosa (AN), 44 bulimia nervosa (BN), 81 binge eating disorder (BED), and 65 other specified feeding and eating disorder (OSFED)), with a mean age of 33.49 years old (SD = 12.54), from specialized ED units in Brazil, Portugal, and Spain. The participants were evaluated using the COVID-19 Isolation Eating Scale (CIES). RESULTS: A global impairment in mood symptoms and emotion regulation was reported in all the ED subtypes, groups of age, and countries. Spanish and Portuguese individuals seemed more resilient than Brazilian ones (p < .05), who reported a more adverse socio-cultural context (i.e., physical health, socio-familial, occupational, and economic status) (p < .001). A global trend to eating symptoms worsening during lockdown was observed, regardless of the ED subtype, group of age, and country, but without reaching statistical significance. However, the AN and BED groups described the highest worsening of the eating habits during lockdown. Moreover, individuals with BED significantly increased their weight and body mass index, similarly to BN, and in contrast to the AN and OSFED groups. Finally, we failed to find significant differences between groups of age although the younger group described a significant worsening of the eating symptoms during lockdown. CONCLUSIONS: This study reports a psychopathological impairment in patients with EDs during lockdown, being socio-cultural aspects potential modulatory factors. Individualized approaches to detect special vulnerable groups and long-term follow-ups are still needed.

Effective Management of Powdery Mildew in Cantaloupe Plants Using Nighttime Applications of UV Light.

Ultraviolet light at wavelengths from 254 to 283 nm/has been reported to effectively suppress powdery mildews in several crops, including some cucurbits. Its use to suppress powdery mildew (Podosphaera xanthii) specifically in cantaloupe has not been previously reported. We evaluated the foregoing technology in cantaloupe fields for suppression of powdery mildew and possible effects on plant growth and yield. In a controlled laboratory study, greenhouse-grown cantaloupe plants were exposed to a gradient of UV-C (254 nm) doses during darkness, and the effects upon powdery mildew development and the plant were evaluated. We also evaluated the efficacy of nighttime applications of UV-C at 100 and 200 J/m2 against powdery mildew on adaxial leaf surfaces in greenhouse, high-tunnel, and open-field plantings. UV-C at the foregoing doses reduced sporulation and germination of P. xanthii conidia without damaging plants. On cantaloupe seedlings in the greenhouse, disease severity was equivalently suppressed at all doses and frequencies of applications of the light. In high-tunnel and open-field experiments, the most effective control of powdery mildew was provided by UV-C applied at 200 J/m2 twice every week, where suppression provided by UV-C was generally equal to and sometimes better than the fungicide treatment. The foregoing UV-C dose and frequency of application also provided the highest yield under field conditions, indicating that UV-C treatment is a promising technology for commercially relevant suppression of powdery mildew on cantaloupe in a variety of growing systems.

Dependence of Sensitivity, Derivative of Transfer Curve and Current on Bias Voltage Magnitude and Polarity in Tunneling Magnetoresistance Sensors.

The sensitivity of tunneling magnetoresistance sensors is an important performance parameter. It depends on the derivative of resistance versus magnetic field (transfer curve) and the current and is expressed as the product of the two factors. Previous research has demonstrated that the bias voltage has a significant impact on the sensitivity. However, no research has been conducted into the dependence of current and the derivative on bias voltage magnitude and polarity, and their contribution to the sensitivity. Thus, this paper investigates the dependence of sensitivity, derivative of resistance versus magnetic field curve and current on bias voltage magnitude and polarity in CoFeB/MgO/CoFeB-based tunneling magnetoresistance sensors with weak, strong and no voltage-controlled perpendicular magnetic anisotropy modification. It demonstrates that the sensitivity dependence on bias voltage for sensors with voltage controlled magnetic anisotropy modification showed no saturation up to 1 V. Moreover, the sensitivity asymmetry with respect to bias polarity changed significantly with bias, reaching a ratio of 6.7. Importantly, the contribution of current and the derivative of resistance versus magnetic field curve to the sensitivity showed a crossover. The current dominated the bias dependence of sensitivity below the crossover voltage and the derivative above the voltage. Furthermore, the crossover voltage in sensors without voltage controlled magnetic anisotropy modification did not depend on polarity, whereas in sensors with voltage controlled magnetic anisotropy modification, it appeared at significantly higher voltage under positive than negative polarity.

Association between Polymorphism of Genes IL-1A, NFKB1, PAR1, TP53, and UCP2 and Susceptibility to Non-Small Cell Lung Cancer in the Brazilian Amazon.

Non-small cell lung cancer (NSCLC) accounts for the vast majority of cases of lung neoplasms. It is formed in multiple stages, with interactions between environmental risk factors and individual genetic susceptibility and with genes involved in the immune and inflammatory response paths, cell or genome stability, and metabolism, among others. Our objective was to evaluate the association between five genetic variants (IL-1A, NFKB1, PAR1, TP53, and UCP2) and the development of NSCLC in the Brazilian Amazon. The study included 263 individuals with and without lung cancer. The samples were analyzed for the genetic variants of NFKB1 (rs28362491), PAR1 (rs11267092), TP53 (rs17878362), IL-1A (rs3783553), and UCP2 (INDEL 45-bp), which were genotyped in PCR, followed by an analysis of the fragments, in which we applied a previously developed set of informative ancestral markers. We used a logistic regression model to identify differences in the allele and the genotypic frequencies among individuals and their association with NSCLC. The variables of gender, age, and smoking were controlled in the multivariate analysis to prevent confusion by association. The individuals that were homozygous for the Del/Del of polymorphism NFKB1 (rs28362491) (p = 0.018; OR = 0.332) demonstrate a significant association with NSCLC, which was similar to that observed in the variants of PAR1 (rs11267092) (p = 0.023; OR = 0.471) and TP53 (rs17878362) (p = 0.041; OR = 0.510). Moreover, the individuals with the Ins/Ins genotype of polymorphism IL-1A (rs3783553) demonstrated greater risk for NSCLC (p = 0.033; OR = 2.002), as did the volunteers with the Del/Del of UCP2 (INDEL 45-bp) (p = 0.031; OR = 2.031). The five polymorphisms investigated can contribute towards NSCLC susceptibility in the population of the Brazilian Amazon.

Mosquito vector competence for dengue is modulated by insect-specific viruses.

Aedes aegypti and A. albopictus mosquitoes are the main vectors for dengue virus (DENV) and other arboviruses, including Zika virus (ZIKV). Understanding the factors that affect transmission of arboviruses from mosquitoes to humans is a priority because it could inform public health and targeted interventions. Reasoning that interactions among viruses in the vector insect might affect transmission, we analysed the viromes of 815 urban Aedes mosquitoes collected from 12 countries worldwide. Two mosquito-specific viruses, Phasi Charoen-like virus (PCLV) and Humaita Tubiacanga virus (HTV), were the most abundant in A. aegypti worldwide. Spatiotemporal analyses of virus circulation in an endemic urban area revealed a 200% increase in chances of having DENV in wild A. aegypti mosquitoes when both HTV and PCLV were present. Using a mouse model in the laboratory, we showed that the presence of HTV and PCLV increased the ability of mosquitoes to transmit DENV and ZIKV to a vertebrate host. By transcriptomic analysis, we found that in DENV-infected mosquitoes, HTV and PCLV block the downregulation of histone H4, which we identify as an important proviral host factor in vivo.

Long non-coding RNAs: definitions, functions, challenges and recommendations.

Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.

A Lab-on-a-Chip Approach for the Detection of the Quarantine Potato Cyst Nematode Globodera pallida.

The potato cyst nematode (PCN), Globodera pallida, has acquired significant importance throughout Europe due to its widespread prevalence and negative effects on potato production. Thus, rapid and reliable diagnosis of PCN is critical during surveillance programs and for the implementation of control measures. The development of innovative technologies to overcome the limitations of current methodologies in achieving early detection is needed. Lab-on-a-chip devices can swiftly and accurately detect the presence of certain nucleotide sequences with high sensitivity and convert the presence of biological components into an understandable electrical signal by combining biosensors with microfluidics-based biochemical analysis. In this study, a specific DNA-probe sequence and PCR primers were designed to be used in a magnetoresistive biosensing platform to amplify the internal transcribed spacer region of the ribosomal DNA of G. pallida. Magnetic nanoparticles were used as the labelling agents of asymmetric PCR product through biotin−streptavidin interaction. Upon target hybridization to sensor immobilized oligo probes, the fringe field created by the magnetic nanoparticles produces a variation in the sensor's electrical resistance. The detection signal corresponds to the concentration of target molecules present in the sample. The results demonstrate the suitability of the magnetic biosensor to detect PCR target product and the specificity of the probe, which consistently distinguishes G. pallida (DV/V > 1%) from other cyst nematodes (DV/V < 1%), even when DNA mixtures were tested at different concentrations. This shows the magnetic biosensor's potential as a bioanalytical device for field applications and border phytosanitary inspections.

Phosphite Is More Effective Against Phytophthora Crown Rot and Leather Rot Caused by Phytophthora cactorum than P. nicotianae.

Phytophthora crown rot (PhCR) and leather rot (LR) caused by Phytophthora spp. are major threats to strawberry production worldwide. In the United States, these diseases are mainly caused by Phytophthora cactorum; however, P. nicotianae has also been recently reported causing PhCR. Growers have relied on three different chemical products (i.e., mefenoxam and phosphites for PhCR and LR, and azoxystrobin for LR). Because resistance to mefenoxam and azoxystrobin has been reported, this study aimed to assess the in vitro sensitivity of Phytophthora spp. isolates from strawberry to phosphites and investigate its efficacy on in vivo assays. In vitro sensitivity of P. cactorum (n = 128) and P. nicotianae (n = 24) isolates collected from 1997 to 2018 was assessed for phosphite at 10, 50, 100, 150, and 300 µg/ml. Regardless of the Phytophthora sp. and isolation organ, most of the isolates (75% for P. cactorum and 54.2% for P. nicotianae) had effective concentration that inhibits pathogen growth by 50% (EC50) values ranging from 50 to 100 µg/ml. In vivo tests with strawberry fruit and plants revealed that commercial formulations of phosphite applied at the highest field rate controlled P. cactorum isolates but failed to control PhCR and LR caused by some isolates of P. nicotianae. In this study, EC50 results from in vitro assay did not truly translate the efficacy of phosphites on controlling LR and PhCR caused by P. cactorum and P. nicotianae. Our findings support the hypothesis that the product acts in a dual way: direct on the pathogen and stimulating the plant immune system. Moreover, this has important implications for disease management, highlighting the importance of a correct diagnosis before phosphite recommendations, because its efficacy varies within Phytophthora spp.

Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches.

The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as a sensor to initiate the damaged DNA checkpoint. It is a conserved domain widely distributed in eukaryotic organisms and is present in several DNA-binding proteins from all kingdoms. Here we showed that distant species have important differences in key residues that affect affinity for ssDNA. Based on these findings, we hypothesized that different HIRAN domains might affect fork reversal and translesion synthesis through different metabolic processes. To address this question, we predicted the tertiary structure of both yeast and human HIRAN domains using molecular modeling. Structural dynamics experiments showed that the yeast HIRAN domain exhibited higher structural denaturation than its human homolog, although both domains became stable in the presence of ssDNA. Analysis of atomic contacts revealed that a greater number of interactions between the ssDNA nucleotides and the Rad5 domain are electrostatic. Taken together, these results provide new insights into the molecular mechanism of the HIRAN domain of Rad5 and may guide us to further elucidate differences in the ancient eukaryotes HIRAN sequences and their DNA affinity.Communicated by Ramaswamy H. Sarma.