Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics.

Aphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC-MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.

Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea.

BACKGROUND: Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches. RESULTS: In this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor. CONCLUSIONS: This study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.

Fine mapping of Ae-Ps4.5, a major locus for resistance to pathotype III of Aphanomyces euteiches in pea.

KEY MESSAGE: QTL mapping and recombinant screening confirmed the major effect of QTL Ae-Ps4.5 on pea resistance to pathotype III of Aphanomyces euteiches and fine-mapped the QTL to a 3.06-Mb interval. Aphanomyces root rot, caused by Aphanomyces euteiches, is the most important disease of pea (Pisum sativum L.) worldwide. The development of pea-resistant varieties is a major challenge to control the disease. Previous linkage studies identified seven main resistance quantitative trait loci (QTL), including the QTL Ae-Ps4.5 associated with partial resistance in US nurseries infested by the pea pathotype III of A. euteiches. This study aimed to confirm the major effect of Ae-Ps4.5 on A. euteiches pathotype III, refine its interval, and identify candidate genes underlying the QTL. QTL mapping on an updated genetic map from the Puget × 90-2079 pea recombinant inbred line population identified Ae-Ps4.5 in a 0.8-cM confidence interval with a high effect (R2 = 89%) for resistance to the Ae109 reference strain of A. euteiches (pathotype III) under controlled conditions. However, the QTL mapping did not detect Ae-Ps4.5 for resistance to the RB84 reference strain of A. euteiches (pathotype I). Screening 224-pea BC5F2 plant progeny derived from three near-isogenic lines (NILs) carrying the 90-2079 allele at Ae-Ps4.5 in the Puget genetic background with 26 SNP markers identified 15 NILs showing recombination in the QTL interval. Phenotyping of the recombinant lines for resistance to the Ae109 strain of A. euteiches reduced the QTL to a physical interval of 3.06 Mb, containing 50 putative annotated genes on the Caméor pea genome V1a among which three candidate genes highlighted. This study provides closely linked SNP markers and putative candidate genes to accelerate pea breeding for resistant varieties to Aphanomyces root rot.

The functional role of Daphnia in the host-pathogen interaction of crayfish and the crayfish plague disease agent (Aphanomyces astaci).

Pathogen spores have been recognized as prey with implications for resource dynamics, energy transfer and disease transmission. In aquatic ecosystems, filter-feeders are able to consume such motile forms of pathogens that can cause severe disease in susceptible hosts. The interactions between European crayfish and the crayfish plague pathogen Aphanomyces astaci are of particular conservation interest. In this study, we aim to evaluate the ecological interactions between Ap. astaci, its host Astacus astacus and individuals of the genus Daphnia, filter-feeding planktonic crustaceans. Our focus was on the consumption of the motile zoospores by Daphnia individuals, but we also considered the potential of Daphnia as non-target hosts. We conducted a series of infection and life-history experiments with Ap. astaci, three Daphnia species (D. magna, D. galeata, and D. pulex) and the noble crayfish As. astacus. We did not observe any lethal effects in the infection experiments involving Ap. astaci and Daphnia. Only D. pulex showed differences in some life-history traits. The feeding experiment using the motile zoospores of Ap. astaci as alternative food source or as supplement to different amounts of algal food revealed their nutritional value: D. magna individuals survived, grew, and reproduced on a zoospore diet alone. When zoospores were supplemented to the regular algal diet, all life-history parameters have been significantly improved. However, this successful consumption of zoospores did not result in a reduced mortality of the susceptible crayfish As. astacus during the infection experiment. Nevertheless, the pathogen load of Ap. astaci in the tissues of As. astacus was significantly reduced as a consequence of the feeding activity of Daphnia. Our results indicate that an abundant filter-feeding community can reduce the amount of infective zoospores in the water body and thus be beneficial to susceptible crayfish hosts, potentially acting as a general buffer against zoospore-transmitted diseases in lentic waters.

Genomic characterization of three bacterial isolates antagonistic to the pea root rot pathogen Aphanomyces euteiches.

Microorganisms living in soil and rhizosphere or inside plants can promote plant growth and health. Genomic characterization of beneficial microbes could shed light on their special features. Through extensive field survey across Saskatchewan, Canada, followed by in vitro and greenhouse characterization, we identified several bacterial isolates antagonistic to pea root rot pathogen Aphanomyces euteiches. In this study, the genomes of three isolates-Pseudomonas sp. rhizo 66 (PD-S66), Pseudomonas synxantha rhizo 25 (Ps-S25), and Serratia sp. root 2 (TS-R2)-were sequenced, assembled, and annotated. Genome size of PD-S66 was 6 279 416 bp with 65 contigs, 59.32% GC content, and 5653 predicted coding sequences (CDS). Genome size of Ps-S25 was 6 058 437 bp with 66 contigs, a GC content of 60.08%, and 5575 predicted CDS. The genome size of TS-R2 was 5 282 152 bp, containing 26 contigs, a GC content of 56.17%, and 4956 predicted CDS. For the identification of the isolates, digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were determined, which confirmed PD-S66 and TS-R2 as potential new species, belonging to Pseudomonas and Serratia genera, respectively, while Ps-S25 belongs to species Pseudomonas synxantha. Biosynthetic gene clusters were predicted using antiSMASH. The genomic data provided insight into the genetics and biochemical pathways supporting the antagonistic activity against A. euteiches of these isolates.

Diversity and distribution of Aphanomyces astaci in a European hotspot of ornamental crayfish introductions.

Ornamental trade has become an important introduction pathway of non-native aquatic species worldwide. Correspondingly, there has been an alarming increase in the number of established crayfish of aquarium origin in Europe over the previous decade. The oomycete Aphanomyces astaci, the pathogen causing crayfish plague responsible for serious declines of European crayfish populations, is dispersed with introduced North American crayfish. The role of ornamental taxa in introducing and spreading different genotypes of this pathogen in open waters remains unclear. We investigated the distribution, prevalence, and diversity of A. astaci in Budapest, Hungary, which became a hotspot of aquarium crayfish introductions. Their establishment in this area was facilitated by locally abundant thermal waters. We screened for A. astaci in six host taxa from 18 sites sampled between 2018 and 2021: five cambarids (Cambarellus patzcuarensis, Faxonius limosus, Procambarus alleni, P. clarkii, P. virginalis) and one native astacid (Pontastacus leptodactylus). The pathogen was confirmed at five sampled sites in four host taxa: P. virginalis, P. clarkii, F. limosus, and for the first time in European open waters also in P. alleni. Genotyping was successful only in individuals from two different brooks where multiple host species coexisted but revealed unexpected patterns. Mitochondrial B-haplogroup of A. astaci, previously usually reported from Pacifastacus leniusculus or infected European species, was detected in P. virginalis at both sites, and in both F. limosus and P. virginalis sampled from a thermally stable tributary of Barát brook in 2018. In contrast, A-haplogroup of A. astaci was detected in coexisting F. limosus, P. virginalis and P. clarkii sampled in the same watercourse just a few hundred meters downstream in 2020. Additional genotyping methods indicated that a previously unknown A. astaci strain was associated with the latter haplogroup. One P. virginalis individual from 2020 was apparently co-infected by strains representing both mitochondrial haplogroups. The results indicated multiple sources of A. astaci in Budapest, likely directly associated with the introduction of ornamental species, interspecific transmission of this pathogen among ornamental hosts, and potential for a quick spatial or temporal turnover of dominant A. astaci strains at a certain locality. This highlights that in regions with high richness of potential A. astaci hosts, host taxon/pathogen genotype combinations become unpredictable, which might prevent reliable genotyping of pathogen sources in local crayfish mass mortalities.

Protocols for studying the crayfish plague pathogen, Aphanomyces astaci, and its host-pathogen interactions.

The crayfish plague caused by the pathogen Aphanomyces astaci has decimated the European and Asian populations of freshwater crayfish and represents an important threat to the other highly susceptible crayfish species in the world, such as the Australian, Madagascar, and South American species. The development and application of molecular methods addressed to the identification of A. astaci has increased exponentially during the last decades in contrast to a slow trend of the pathogen biology and host interaction. There is still a need for a better comprehension of the A. astaci-crayfish interactions, specifically the resistance and tolerance immune mechanism. These types of studies required a robust basic knowledge on the developmental biology of the pathogen in order to reproduce life stages and to perform infection experiments. A great piece of work in this area was carried out during the 1960 s to 80 s in University of Uppsala. Thus, the purpose of this work was to update previous protocols as well as to generate new guidelines to reproduce key developmental biology stages of A. astaci, to eventually identify crayfish populations with higher resistance and tolerance to this pathogen. This work also refers to other methodologies and guidelines for the diagnosis of crayfish plague, the pathogen isolation, and the in vitro production of zoospores.

eDNA monitoring as a tool for evaluating the reintroduction of Austropotamobius pallipes after a crayfish plague outbreak.

The crayfish plague, a severe disease caused by the oomycete Aphanomyces astaci, is responsible for most population declines of susceptible crayfish in Europe. This pathogen has been devastating native populations of Austropotamobius pallipes since the 1970s in the Iberian Peninsula. In this study, we report a massive mortality event in one of the most important Spanish populations of A. pallipes. We aimed to: (i) identify the cause of the mortality, and (ii) evaluate the reintroduction viability of the species. Over the course of six months, we used environmental DNA (eDNA) and traditional trap-based methods to detect the presence of A. astaci or of native or invasive crayfish in order to evaluate the reintroduction viability of A. pallipes to the affected population. We did not capture any live crayfish or detect the presence of A. astaci in the reservoir water during the six months following the mass mortality event. Our analyses indicated that it was feasible to initiate a reintroduction program at the site, which will continue to be monitored for three to five years and will help improve the conservation status of A. pallipes.

Molecular detection of Aphanomyces astaci - An improved species specific qPCR assay.

The parasitic oomycete Aphanomyces astaci is the causative agent of crayfish plague, a devastating disease for European freshwater crayfish. Species specific quantitative real-time PCR (qPCR) can offer rapid detection of the pathogen. However, the well established A. astaci qPCR assay recommended by the World Organization for Animal Health (WOAH) amplifies the recently described Aphanomyces fennicus. Consequently, false-positive results may occur. This calls for the improvement of the established species specific A. astaci qPCR assay in order to avoid amplifying A. fennicus while screening for A. astaci. We developed an improved species specific A. astaci qPCR assay and validated the assay across three laboratories, using established procedures including different qPCR master mixes for each respective laboratory. Genomic DNA from A. astaci, A. fennicus and closely related Aphanomyces spp. was analysed and compared with both the improved and established assay. Additionally, DNA from crayfish tissue and environmental samples were analysed with both assays. The improved assay showed similar sensitivity with the established assay for all sample types, while proving highly specific for A. astaci avoiding amplification of A. fennicus and the other tested Aphanomyces spp. Environmental DNA (eDNA) samples collected at River Lierelva in Norway amplified with the established assay, but not with the improved assay indicating false positive. We were able to sequence a 530 bp fragment of the ITS region from these eDNA samples and the consensus sequence showed 99.9-100 % pairwise identity with A. fennicus and 97.2-98 % pairwise identity with A. astaci, suggesting that the occurrence of A. fennicus is not limited to Finland, where it was first discovered.

Comparison of exoskeleton microbial communities of co-occurring native and invasive crayfish species.

Host-associated microbial communities are an important determinant of individual fitness and have recently been highlighted as one of the factors influencing the success of invasive species. Invasive hosts introduce their microbes into the new environment, and then both the host and its associated microbes enter into a series of interactions with the native macroscopic and microscopic biota. As these processes are largely unexplored, we aimed to compare the exoskeletal microbial communities of co-occurring and phylogenetically related crayfish: the native narrow-clawed crayfish Pontastacus leptodactylus and the invasive signal crayfish Pacifastacus leniusculus from the recently invaded Korana River, Croatia. The results of high-throughput 16S rRNA sequencing showed that the exoskeletal microbiome of both species is very diverse, significantly influenced by the local environment and dominated by low abundance bacterial families from the phylum Proteobacteria. Furthermore, the exoskeletal microbiomes of the crayfish species differed significantly in the composition and abundance of Amplicon Sequence Variants (ASVs), suggesting that they are to some extent shaped by species-specific intrinsic factors, despite sharing a common habitat. However, over 95% of the bacterial genera associated with the exoskeleton were detected in the exoskeleton samples of both native and invasive crayfish. We paid particular attention to two known crayfish pathogens, Aphanomyces astaci and Saprolegnia parasitica, and find that both species carry low amounts of both pathogens. On the side, we find that a non-standard ddPCR protocol outperforms standard qPCR test for A. astaci under low concentration conditions. Taken together, our results indicate the possibility of bidirectional mixing and homogenisation of exoskeleton microbiome. As such, they can serve as a baseline in future detangling of the processes that act together to shape the microbiomes of co-occuring native and invasive congeners during biological invasions.

Aphanomyces astaci in Mexico: A new haplotype from dwarf crayfish Cambarellus montezumae.

The crayfish plague is an emerging infectious disease caused by the pathogen Aphanomyces astaci (Oomycota), which is responsible for the decimation of Eurasian freshwater crayfish. This pathogen can coexist with the North American crayfish. These are chronic carriers of the disease as consequence of an immune response that can contain the growth of the pathogen without killing it. The origin of A. astaci locates in the southeastern United States and coincides with the origin of the family Cambaridae. This diverse family of decapods is distributed in North America from southern Canada to Honduras. However, only the native crayfish species from Canada and the USA have been examined for the presence of A. astaci. In this study, we describe for the first time the presence of A. astaci in Mexico in a population of the native species Cambarellus montezumae. By analyzing the small (rrnS) and large (rrnL) mitochondrial ribosomal regions, we showed the presence of two haplotypes of A. astaci within the same population (d1-haplotype and, a novel haplotype that was named, mex1-haplotype). The finding of A. astaci in Mexico confirms the occurrence of this pathogen within the range of the family Cambaridae. The individuals of C. montezumae appear to be chronic carriers of A. astaci, indicated by the lack of documented crayfish plague outbreaks in this population, similar to the pattern observed in other North American species. Thus, the results are of special concern to susceptible species of southern regions of America, i.e., Parastacidae. Therefore, this work emphasizes the need to better understand the distribution and genetic diversity of A. astaci within the distribution range of the natural carriers, i.e., North American species, especially the unexplored area of the family Cambaridae.

Austropotamobius pallipes can be infected by two haplotypes of Aphanomyces astaci: A key example from an outbreak at an ex-situ conservation facility.

The crayfish plague, caused by the pathogen Aphanomyces astaci, is a pandemic disease endemic to North America that has been devastating susceptible crayfish populations in Europe since the 19th century. In Spain, this disease has decimated populations of the native crayfish species Austropotamobius pallipes due to introductions of North American crayfish, which act as vectors of the pathogen. To combat against these losses, several regional governments have established ex-situ breeding programs to restock wild populations of the species. In this study, we report on an outbreak of A. astaci that occurred in one of the most important A. pallipes aquaculture centers in Spain. Using a variety of detection methods, we analyzed affected crayfish and environmental samples from the facilities over a period of six months and determined that the outbreak was caused by two haplotypes of A. astaci, d1 and d2, which are both associated with the North American crayfish species Procambarus clarkii. To our knowledge, this is the first report of a two-haplotype coinfection of A. astaci outside the native range of this pathogen.

Niche dynamics along two centuries of multiple crayfish invasions.

The realised ecological niches of species may change in response to dynamic abiotic and biotic environments, particularly under fast global change. To fully understand the dynamics of niche features and their drivers, it is essential to have a long-term view of species distributions and the factors that may have influenced them. Here, we analysed the distribution and niche dynamics of the Italian crayfish (Austropotamobius fulcisianus) in the Iberian Peninsula over the past 200 years. The Italian crayfish was introduced to Spain in the 16th century, and spread due to multiple stocking events until the 1970s, when two North American crayfish (red swamp crayfish Procambarus clarkii, and signal crayfish Pacifastacus leniusculus) were introduced. Both North American species are carriers of a pathogen (Aphanomyces astaci, the causal agent of crayfish plague) lethal to the Italian crayfish. We hypothesised that the realised niche of the Italian crayfish, both in breadth and in position, has changed over time following changes in its range. The distribution of the Italian crayfish expanded from the mid-19th century until the mid-20th century, in association with an enlargement of its realised niched, mostly towards less abrupt and more coastal-influenced areas. After the introduction of the North American crayfishes, the collapse of the Italian crayfish involved a niche shift towards rough terrains in mountain areas. North American crayfish have eventually occupied most of the Italian crayfish's niche space, with the few no-coexistence areas being relegated to the most abrupt and high-elevation territories. Our historical approach allowed us to document and understand the highly dynamic distribution and niche of the Italian crayfish in the presence of invader counterparts, and to explore the environmental conditions under which their coexistence is minimised.

Aquatic Peptide: The Potential Anti-Cancer and Anti-Microbial Activity of GE18 Derived from Pathogenic Fungus Aphanomyces invadans.

Small molecules as well as peptide-based therapeutic approaches have attracted global interest due to their lower or no toxicity in nature, and their potential in addressing several health complications including immune diseases, cardiovascular diseases, metabolic disorders, osteoporosis and cancer. This study proposed a peptide, GE18 of subtilisin-like peptidase from the virulence factor of aquatic pathogenic fungus Aphanomyces invadans, which elicits anti-cancer and anti-microbial activities. To understand the potential GE18 peptide-induced biological effects, an in silico analysis, in vitro (L6 cells) and in vivo toxicity assays (using zebrafish embryo), in vitro anti-cancer assays and anti-microbial assays were performed. The outcomes of the in silico analyses demonstrated that the GE18 peptide has potent anti-cancer and anti-microbial activities. GE18 is non-toxic to in vitro non-cancerous cells and in vivo zebrafish larvae. However, the peptide showed significant anti-cancer properties against MCF-7 cells with an IC50 value of 35.34 µM, at 24 h. Besides the anti-proliferative effect on cancer cells, the peptide exposure does promote the ROS concentration, mitochondrial membrane potential and the subsequent upregulation of anti-cancer genes. On the other hand, GE18 elicits significant anti-microbial activity against P. aeruginosa, wherein GE18 significantly inhibits bacterial biofilm formation. Since the peptide has positively charged amino acid residues, it targets the cell membrane, as is evident in the FESEM analysis. Based on these outcomes, it is possible that the GE18 peptide is a significant anti-cancer and anti-microbial molecule.

Development of a rapid and sensitive real-time diagnostic assay to detect and quantify Aphanomyces invadans, the causative agent of epizootic ulcerative syndrome.

The oomycete Aphanomyces invadans causes epizootic ulcerative syndrome (EUS), a World Organization for Animal Health (WOAH)-listed disease that has seriously impacted a wide range of fish worldwide. Currently, only three conventional polymerase chain reaction (PCR) assays are recommended for the detection of A. invadans. The robust quantitative PCR (qPCR) assay has recently become more important due to its highly accurate nature and the applicability of qPCR-based environmental DNA (eDNA) detection in the monitoring of pathogens in aquatic environments. Therefore, in this study, we developed a novel TaqMan probe-based qPCR method to sensitively and quantitatively detect A. invadans. The assay limit of detection was determined using 10-fold serial dilutions of linearized A. invadans plasmid. Assay sensitivity was assessed in the presence of interfering substances and compared to three WOAH-listed primers using the mycelia and zoospores of A. invadans with and without fish muscle tissue. The assay specificity was also theoretically and experimentally assessed against other oomycetes, fish muscle tissue, and water samples. The assay's repeatability and reproducibility were determined. In this study, the limit of detection of the developed assay was 7.24 copies of A. invadans genomic DNA per reaction (95% confidence interval (CI): 2.75 to 19.05 copies/reaction). The assay showed the same sensitivity in the presence of other substances. Compared to the WOAH-recommended PCR assays, this assay had 10-times higher sensitivity for all tested samples. There were no cross-reactions with other closely related oomycetes, fish muscle, or water samples, indicating that the assay was highly specific for A. invadans. The repeatability and reproducibility tests showed little variation, ranging from 0.1-0.9% and 0.04-1.1%, respectively, indicating the high consistency, repeatability, and reliability of the developed assay. This highly rapid, sensitive, specific, and consistent EUS qPCR assay would be of importance in transboundary disease management and the monitoring of pathogens in aquatic environments.

Epidemiology of epizootic ulcerative syndrome (EUS) in fish in the main water bodies of the Kavango-Zambezi and Great Limpopo transfrontier conservation areas of Zimbabwe.

A three-year study investigated the epidemiology of epizootic ulcerative syndrome (EUS) in fish from Kavango-Zambezi (KAZA) and Great Limpopo (GL) transfrontier conservation areas of Zimbabwe. A total of 38 sites comprising 27 wild fisheries and 11 aquacultures, from Mashonaland West, Matabeleland North and South, and Midlands were selected. Of the 27 wild fisheries, EUS-positive fish were detected from 9 (33.3%) and none from the 11 aquacultures. No positive cases were detected from Nile tilapia (Oreochromis niloticus) from both aquacultures and wild fisheries. A total of 9.9% (239/2423) fish from the nine positive fisheries had typical EUS lesions, and infection was confirmed in 15 species. Prevalence was significantly higher (p < 0.05) in KAZA (11.5%; 95% CI: 9.6-13.4) compared with GL (8.6%; 95% CI: 7.1-10.1). The most affected were Clarias, followed by Barbus and Oreochromis species. Most cases (>80%) were reported in winter when ambient temperature was low. Further studies are required to determine water parameters associated with EUS outbreaks. These results suggested that the African sharptooth catfish (Clarias gariepinus) could be used potentially as an indicator species for EUS surveillance programmes. Thus, implementation of surveillance and biosecurity programmes that take into consideration the epidemiology of EUS will be beneficial.

Anti-Cancer and Anti-Inflammatory Activities of a Short Molecule, PS14 Derived from the Virulent Cellulose Binding Domain of Aphanomyces invadans, on Human Laryngeal Epithelial Cells and an In Vivo Zebrafish Embryo Model.

In this study, the anti-cancer and anti-inflammatory activities of PS14, a short peptide derived from the cellulase binding domain of pathogenic fungus, Aphanomyces invadans, have been evaluated, in vitro and in vivo. Bioinformatics analysis of PS14 revealed the physicochemical properties and the web-based predictions, which indicate that PS14 is non-toxic, and it has the potential to elicit anti-cancer and anti-inflammatory activities. These in silico results were experimentally validated through in vitro (L6 or Hep-2 cells) and in vivo (zebrafish embryo or larvae) models. Experimental results showed that PS14 is non-toxic in L6 cells and the zebrafish embryo, and it elicits an antitumor effect Hep-2 cells and zebrafish embryos. Anticancer activity assays, in terms of MTT, trypan blue and LDH assays, showed a dose-dependent inhibitory effect on cell proliferation. Moreover, in the epithelial cancer cells and zebrafish embryos, the peptide challenge (i) caused significant changes in the cytomorphology and induced apoptosis; (ii) triggered ROS generation; and (iii) showed a significant up-regulation of anti-cancer genes including BAX, Caspase 3, Caspase 9 and down-regulation of Bcl-2, in vitro. The anti-inflammatory activity of PS14 was observed in the cell-free in vitro assays for the inhibition of proteinase and lipoxygenase, and heat-induced hemolysis and hypotonicity-induced hemolysis. Together, this study has identified that PS14 has anti-cancer and anti-inflammatory activities, while being non-toxic, in vitro and in vivo. Future experiments can focus on the clinical or pharmacodynamics aspects of PS14.

Evaluation of Effective Class-Balancing Techniques for CNN-Based Assessment of Aphanomyces Root Rot Resistance in Pea (Pisum sativum L.).

Aphanomyces root rot (ARR) is a devastating disease that affects the production of pea. The plants are prone to infection at any growth stage, and there are no chemical or cultural controls. Thus, the development of resistant pea cultivars is important. Phenomics technologies to support the selection of resistant cultivars through phenotyping can be valuable. One such approach is to couple imaging technologies with deep learning algorithms that are considered efficient for the assessment of disease resistance across a large number of plant genotypes. In this study, the resistance to ARR was evaluated through a CNN-based assessment of pea root images. The proposed model, DeepARRNet, was designed to classify the pea root images into three classes based on ARR severity scores, namely, resistant, intermediate, and susceptible classes. The dataset consisted of 1581 pea root images with a skewed distribution. Hence, three effective data-balancing techniques were identified to solve the prevalent problem of unbalanced datasets. Random oversampling with image transformations, generative adversarial network (GAN)-based image synthesis, and loss function with class-weighted ratio were implemented during the training process. The result indicated that the classification F1-score was 0.92 ± 0.03 when GAN-synthesized images were added, 0.91 ± 0.04 for random resampling, and 0.88 ± 0.05 when class-weighted loss function was implemented, which was higher than when an unbalanced dataset without these techniques were used (0.83 ± 0.03). The systematic approaches evaluated in this study can be applied to other image-based phenotyping datasets, which can aid the development of deep-learning models with improved performance.

Detecting aquatic pathogens with field-compatible dried qPCR assays.

Field-ready qPCR assays with extended shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here, we developed, validated, and tested the shelf-life of qPCR assays targeting Gyrodactylus salaris and Aphanomyces astaci with lyophilization and air-drying.