Chemical Ecology of Nematodes

Nematodes represent the most abundant group of metazoans on earth. They utilize diverse chemicals to interact with con-specific and hetero-specific organisms, and are also impacted by compounds produced by other interacting organisms. In the first part of this review we discuss how nematode-derived glycolipids modulate their behavior and development, as well as the interactions with other organisms. Furthermore, we provide a short overview about other secondary metabolites produced by nematodes that affect different life traits of free-living nematodes. In the second part of this review we discuss how different bacteria-, nematode-, and plant-derived chemicals such as volatile organic compounds, root exudates, and plant defenses regulate the interaction between entomopathogenic nematodes, their symbiotic bacteria, insect prey, predators, and plants

The role of soluble sugars and starch in plant-herbivore interactions: signaling and ecological consequences

Insect attack leads to a strong reconfiguration of plant metabolome, which influences the performance of the attacker. While the causes and consequences of induced changes in plant secondary metabolites are well studied, less is known about primary metabolites. To contribute to filling this gap of knowledge, I studied the role of sugars and starch in the interaction between Nicotiana attenuata and Manduca sexta. I found that M. sexta attack decreases soluble carbohydrates in N. attenuata leaves and roots. I did not observe this effect in jasmonate-deficient plants, suggesting that jasmonates are a plant signal that reprograms carbohydrate metabolism. Based on the above, I evaluated the ecological consequences of the observed jasmonate-dependent carbohydrate depletion in the context of plant resistance and tolerance by asking: Does the impact of M. sexta attack on leaf carbohydrates affect plant nutritional value and plant resistance? And does it reduce the capacity of roots to supply energy for regrowth and herbivore tolerance? Finally, I evaluated the degree of phylogenetic conservatism of the impact of M. sexta attack on both root carbohydrate reconfiguration and tolerance in the Solanaceae. My results suggest that i) lower sugar concentrations in the leaves lead to an increased M. sexta growth, suggesting that leaf carbohydrate depletion constrains rather than enhances plant resistance against herbivores; ii) the depletion of root carbohydrates significantly constrains the plant’s regrowth capacity and fitness, indicating that root carbohydrate depletion constrains tolerance to herbivory; and iii) changes in soluble root carbohydrate pools are strongly correlated with regrowth capacity across several solanaceous plant species and iv) that both traits do not show a phylogenetic signal, indicating that root carbohydrates are important determinants of tolerance to aboveground herbivory and that these two traits are subject of rapid evolution in the Solanaceae

Adaptations and responses of the common dandelion to low atmospheric pressure in high‐altitude environments

Atmospheric pressure is an important, yet understudied factor that may shape plant ecology and evolution. By growing plants under controlled conditions at different experimental stations in the Swiss alps, we evaluated the impact of ecologically realistic atmospheric pressures between 660 and 950 hPa on the growth and defence of different dandelion populations. Low atmospheric pressure was associated with reduced root growth and defensive sesquiterpene lactone production. Defence suppression only occurred in populations originating from lower altitudes. Populations from higher altitudes constitutively produced less sesquiterpene lactones and did not suffer from suppression under low atmospheric pressure. Synthesis. We conclude that atmospheric pressure modulates root growth and defence traits, and that evolutionary history shapes plant phenotypic responses to atmospheric pressure. Our findings have important implications for our understanding of altitudinal gradients and the future use of plants as a source of food and bioactive metabolites in extraterrestrial habitats

Searching for the most variable m/z values in grape development in a Portuguese vineyard

Each vineyard is known to have a strong impact on the metabolic compounds of grapes due to its external factors, named terroir [1]. Furthermore, knowledge on the metabolic behavior of vines in response to the terroir effect can help to assess, in advance, the optimal maturity of grapes. The aim of this work was to obtain a metabolic profile of vines in different locations and consequently associate it with the external conditions present during grapes’ development using an untargeted approach. Samples were collected in eight sites of a Portuguese vineyard during different developmental stages and analyzed using a metabolomic protocol based on liquid chromatography coupled to tandem mass spectrometry [2]. Briefly, samples were grounded and extracted using a mixture of water/methanol/chloroform (20:40:40, v/v/v). The aqueous methanol fraction was used for further analysis. An Agilent Eclipse plus C18 column (RRHD 1.8 µm, 2.1 mm × 100 mm) was used for chromatographic separation and elution was achieved in gradient mode. Water and acetonitrile both containing 0.1% (v/v) formic acid were used as mobile phase. Mass spectrometry analysis was performed in positive and negative ionization mode and data were acquired in scan mode to maximize the number of detected m/z values. MZmine software was chosen for data analysis due to its robustness in fragment selection. A baseline correction was applied to equalize baselines and an alignment algorithm was used to equalize retention times aiming to compare m/z values from different samples. Statistical and chemometric tools were used to exclude m/z values attributed to blanks and to establish a metabolic profile, respectively. Preliminary results confirm that the methodology chosen for data analysis is fast and accurate for the viable selection of the most significant m/z features. Regarding currently analyzed samples, the proposed methodology allowed the identification of several m/z features presenting a statistically significant variation among sampling points, which will be further investigated as indicators of the maturity state.info:eu-repo/semantics/publishedVersio

A Preliminary Investigation into Search and Matching for Tumour Discrimination in WHO Breast Taxonomy Using Deep Networks

Breast cancer is one of the most common cancers affecting women worldwide. They include a group of malignant neoplasms with a variety of biological, clinical, and histopathological characteristics. There are more than 35 different histological forms of breast lesions that can be classified and diagnosed histologically according to cell morphology, growth, and architecture patterns. Recently, deep learning, in the field of artificial intelligence, has drawn a lot of attention for the computerized representation of medical images. Searchable digital atlases can provide pathologists with patch matching tools allowing them to search among evidently diagnosed and treated archival cases, a technology that may be regarded as computational second opinion. In this study, we indexed and analyzed the WHO breast taxonomy (Classification of Tumours 5th Ed.) spanning 35 tumour types. We visualized all tumour types using deep features extracted from a state-of-the-art deep learning model, pre-trained on millions of diagnostic histopathology images from the TCGA repository. Furthermore, we test the concept of a digital "atlas" as a reference for search and matching with rare test cases. The patch similarity search within the WHO breast taxonomy data reached over 88% accuracy when validating through "majority vote" and more than 91% accuracy when validating using top-n tumour types. These results show for the first time that complex relationships among common and rare breast lesions can be investigated using an indexed digital archive

Impact of simulated in vitro gastrointestinal digestion on bioactive compounds, bioactivity and cytotoxicity of melon (Cucumis melo L. inodorus) peel juice powder

The objectives of this research work were to evaluate the effect of in vitro gastrointestinal digestion (GIT) on melon peel juice (MPJ) powder from fruit processing industry by-products, considering (i) the recovery and accessibility indexes, (ii) the changes on antioxidant activity, and (iii) the prebiotic effect. Throughout exposition to GIT conditions a decrease on the total phenolic content (TPC = 65.31%) and antioxidant activity by ABTS = 39.77% and DPPH = 45.91% were observed. However, these both parameters exhibited stable accessibility, accounting with 81.89%, 76.55%, and 54.07% for TPC, ABTS and DPPH, respectively. After gastrointestinal digestion, the non-absorbed fraction exhibited a positive impact on the growth of Bifidobacterium and Lactobacillus strains, possibly associated with the high content of simple sugar (glucose and fructose). This fraction also showed to be safe on Caco-2 intestinal cells. These findings suggest that MPJ might be used as a potential food functional ingredient.info:eu-repo/semantics/publishedVersio

Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level.

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included wholegenome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and wholeproteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes

Entomopathogenic potential of bacteria associated with soil-borne nematodes and insect immune responses to their infection

Soil-borne nematodes establish close associations with several bacterial species. Whether they confer benefits to their hosts has been investigated in only a few nematode-bacteria systems. Their ecological function, therefore, remains poorly understood. In this study, we isolated several bacterial species from rhabditid nematodes, molecularly identified them, evaluated their entomopathogenic potential on Galleria mellonella larvae, and measured immune responses of G. mellonella larvae to their infection. Bacteria were isolated from Acrobeloides sp., A. bodenheimeri, Heterorhabditis bacteriophora, Oscheius tipulae, and Pristionchus maupasi nematodes. They were identified as Acinetobacter sp., Alcaligenes sp., Bacillus cereus, Enterobacter sp., Kaistia sp., Lysinibacillus fusiformis, Morganella morganii subsp. morganii, Klebsiella quasipneumoniae subsp. quasipneumoniae, and Pseudomonas aeruginosa. All bacterial strains were found to be highly entomopathogenic as they killed at least 53.33% G. mellonella larvae within 72h post-infection, at a dose of 106 CFU/larvae. Among them, Lysinibacillus fusiformis, Enterobacter sp., Acinetobacter sp., and K. quasipneumoniae subsp. quasipneumoniae were the most entomopathogenic bacteria. Insects strongly responded to bacterial infection. However, their responses were apparently little effective to counteract bacterial infection. Our study, therefore, shows that bacteria associated with soil-borne nematodes have entomopathogenic capacities. From an applied perspective, our study motivates more research to determine the potential of these bacterial strains as biocontrol agents in environmentally friendly and sustainable agriculture

Phase-field models in interfacial pattern formation out of equilibrium

Preprin

Influência do ritmo circadiano na morte súbita inesperada em epilepsia

Universidade de São Paulo Faculdade de Medicina de Ribeirão Preto Departamento de Neurologia, Psiquiatria e PsicologiaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de FisiologiaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Disciplina de Neurologia ExperimentalUNIFESP, EPM, Depto. de FisiologiaUNIFESP, EPM, Disciplina de Neurologia ExperimentalSciEL