The Omics Hunt for Novel Molecular Markers of Resistance to Phytophthora infestans

Wild Solanum accessions are a treasured source of resistance against pathogens, including oomycete Phytophthora infestans, causing late blight disease. Here, Solanum pinnatisectum, Solanum tuberosum, and the somatic hybrid between these two lines were analyzed, representing resistant, susceptible, and moderately resistant genotypes, respectively. Proteome and metabolome analyses showed that the infection had the highest impact on leaves of the resistant plant and indicated, among others, an extensive remodeling of the leaf lipidome. The lipidome profiling confirmed an accumulation of glycerolipids, a depletion in the total pool of glycerophospholipids, and showed considerable differences between the lipidome composition of resistant and susceptible genotypes. The analysis of putative resistance markers pinpointed more than 100 molecules that positively correlated with resistance including phenolics and cysteamine, a compound with known antimicrobial activity. Putative resistance protein markers were targeted in an additional 12 genotypes with contrasting resistance to P. infestans. At least 27 proteins showed a negative correlation with the susceptibility including HSP70-2, endochitinase B, WPP domain-containing protein, and cyclase 3. In summary, these findings provide insights into molecular mechanisms of resistance against P. infestans and present novel targets for selective breeding.

Response of physiological parameters in Dionaea muscipula J. Ellis teratomas transformed with rolB oncogene

Background Plant transformation with rol oncogenes derived from wild strains of Rhizobium rhizogenes is a popular biotechnology tool. Transformation effects depend on the type of rol gene, expression level, and the number of gene copies incorporated into the plant’s genomic DNA. Although rol oncogenes are known as inducers of plant secondary metabolism, little is known about the physiological response of plants subjected to transformation. Results In this study, the physiological consequences of rolB oncogene incorporation into the DNA of Dionaea muscipula J. Ellis was evaluated at the level of primary and secondary metabolism. Examination of the teratoma (transformed shoots) cultures of two different clones (K and L) showed two different strategies for dealing with the presence of the rolB gene. Clone K showed an increased ratio of free fatty acids to lipids, superoxide dismutase activity, synthesis of the oxidised form of glutathione, and total pool of glutathione and carotenoids, in comparison to non-transformed plants (control). Clone L was characterised by increased accumulation of malondialdehyde, proline, activity of superoxide dismutase and catalase, total pool of glutathione, ratio of reduced form of glutathione to oxidised form, and accumulation of selected phenolic acids. Moreover, clone L had an enhanced ratio of total triglycerides to lipids and accumulated saccharose, fructose, glucose, and tyrosine. Conclusions This study showed that plant transformation with the rolB oncogene derived from R. rhizogenes induces a pleiotropic effect in plant tissue after transformation. Examination of D. muscipula plant in the context of transformation with wild strains of R. rhizogenes can be a new source of knowledge about primary and secondary metabolites in transgenic organisms.

Features of the intestinal microbiota functional status in early-aged children with rotavirus infection

The aim is to assess the intestinal microflora functional and structural disorders in early-aged children in the dynamics of rotavirus infection by studying intestinal metabolites in faeces – short-chain fatty acids (SCFA). Materials and methods. The study included 60 breastfed children aged 1-24 months with rotavirus infection (the study group) and 30 healthy children, representative by age and sex (the comparison group). Determination of SCFA (acetate, propionate, butyrate) in faeces was carried out in all children of the study group three times in the dynamics of the disease (on the 3rd, 5th and 10th day) and in healthy children once. Results. The total concentration of SCFA in children with rotavirus infection was 3 and 2.2 times lower than in healthy children in the acute period of the disease (p<0.01 on the 3rd and 5th day, respectively), increasing on the 10th day (p<0.05), however, not reaching the normal level (p<0.01). The decrease in the total pool of SCFA occurred due to all volatile acids (C2, C3, C4), the concentrations of which were lower than in healthy children (p<0.01). Violation of the volatile acids ratio in their general pool was observed from the first days of rotavirus gastroenteritis in the form of an increase in the C2 relative concentration (p˂0.05) and a decrease in C3 and C4 profiles (p˂0.05). Correspondingly, a decrease in anaerobic index was noted. It was equal to 0.04 [0.01; 0.11] on the 3rd and 5th day of the disease, constituting only 1/5 of the healthy children values (p˂0,01), increasing on the 10th day to 0,09 [0,02; 0.17], however, remaining twice as lower than in children of the comparison group (p˂0,01). Conclusions. There is a violation of the intestinal microflora functional condition in early-aged children from the first days of rotavirus infection, which is expressed by depletion of the total pool of SCFA and concentrations of each of them, as well as structural disorders of intestinal microbiocinosis in the form of reducing its anaerobiosis. These changes are most pronounced during the first five days of rotavirus gastroenteritis and last up to 10th day of illness.

Artificial Intelligence and Capsule Endoscopy: Automatic Detection of Small Bowel Blood Content Using a Convolutional Neural Network

<b><i>Introduction:</i></b> Capsule endoscopy has revolutionized the management of patients with obscure gastrointestinal bleeding. Nevertheless, reading capsule endoscopy images is time-consuming and prone to overlooking significant lesions, thus limiting its diagnostic yield. We aimed to create a deep learning algorithm for automatic detection of blood and hematic residues in the enteric lumen in capsule endoscopy exams. <b><i>Methods:</i></b> A convolutional neural network was developed based on a total pool of 22,095 capsule endoscopy images (13,510 images containing luminal blood and 8,585 of normal mucosa or other findings). A training dataset comprising 80% of the total pool of images was defined. The performance of the network was compared to a consensus classification provided by 2 specialists in capsule endoscopy. Subsequently, we evaluated the performance of the network using an independent validation dataset (20% of total image pool), calculating its sensitivity, specificity, accuracy, and precision. <b><i>Results:</i></b> Our convolutional neural network detected blood and hematic residues in the small bowel lumen with an accuracy and precision of 98.5 and 98.7%, respectively. The sensitivity and specificity were 98.6 and 98.9%, respectively. The analysis of the testing dataset was completed in 24 s (approximately 184 frames/s). <b><i>Discussion/Conclusion:</i></b> We have developed an artificial intelligence tool capable of effectively detecting luminal blood. The development of these tools may enhance the diagnostic accuracy of capsule endoscopy when evaluating patients presenting with obscure small bowel bleeding.

Screening for Health-Promoting Fatty Acids in Ascidians and Seaweeds Grown under the Influence of Fish Farming Activities

The present study aimed to contrast the fatty acid (FA) profile of ascidians (Ascidiacea) and seaweeds (sea lettuce, Ulva spp. and bladderwrack, Fucus sp.) occurring in a coastal lagoon with versus without the influence of organic-rich effluents from fish farming activities. Our results revealed that ascidians and seaweeds from these contrasting environments displayed significant differences in their FA profiles. The n-3/n-6 ratio of Ascidiacea was lower under the influence of fish farming conditions, likely a consequence of the growing level of terrestrial-based ingredients rich on n-6 FA used in the formulation of aquafeeds. Unsurprisingly, these specimens also displayed significantly higher levels of 18:1(n-7+n-9) and 18:2n-6, as these combined accounted for more than 50% of the total pool of FAs present in formulated aquafeeds. The dissimilarities recorded in the FAs of seaweeds from these different environments were less marked (≈5%), with these being more pronounced in the FA classes of the brown seaweed Fucus sp. (namely PUFA). Overall, even under the influence of organic-rich effluents from fish farming activities, ascidians and seaweeds are a valuable source of health-promoting FAs, which confirms their potential for sustainable farming practices, such as integrated multi-trophic aquaculture.

STUDIES OF ALTERATIONS OF THE CELLULAR MEMBRANE BARRIER FUNCTION AT LARYNGEAL CANCER

Introduction. Cellular membrane barrier alterations lead to metabolic and functional disorders. However, in the case of laryngeal cancer (LC) they are insufficiently studied. The aim of the study – to learn the nature of the interaction of erythrocyte membranes with introduced spin probes as an indicator of changes in the barrier function of membranes at LC. Research Methods. Samples of the erythrocyte membranes from 40 patients with LC stages II and III and 20 healthy volunteers were probed by EPR with AdTEMPO test. Microviscosity of erythrocyte membranes was determined by the τeff and the decreasing in RSSI. The content of MWM was identified in the blood plasma and in erythrocyte. The partition coefficient between blood plasma proteins and erythrocyte glycocalyx was calculated. SCEM was evaluated by amount of unabsorbed methylene blue. Results and Discussion. It was established that LC patient’s endogenous intoxication is characterized by excessive accumulation of the total pool of MWM both in blood plasma and glycocalyx of erythrocyte. SCEM was significantly decreased in samples of both LC stages in comparison to control. The most apparent decline in τeff was observed prior to washing of erythrocytes for 5 min after probe insertion. The deceleration after 60 min was observed only in LC stage II. The value of τeff was at control values levels after washing of erythrocytes of LC stage II 5 min after probe insertion and was significantly reduced in stage III LC in comparison to control. RSSI in samples both stage of patients prior to and after washing of erythrocytes was on average 1.5-fold higher than that of control. Conclusions. It was established that the LC patient’s endogenous intoxication is characterized by excessive accumulation of the total pool of MWM both in blood plasma and glycocalyx of erythrocytes, activation of catabolic processes in plasma, redistribution of MWM between the pool of erythrocyte proteins, which corresponds to the second stage of endotoxicosis. The reduction of the SCEM is shown, which is a manifestation of pathological changes in the surface functional activity of erythrocyte membranes. The effectiveness of AdTEMPO for the eva­luation of microviscosity of erythrocyte membranes in patients with LC was confirmed.

Demyelinating Events Following Initiation of Anti-TNFα Therapy in the British Society for Rheumatology Biologics Registry in Rheumatoid Arthritis

ObjectiveTo establish the incidence of demyelination in patients who have received anti–tumor necrosis factor alpha (anti-TNFα) therapy, through analysis of adverse events reported in a prospective cohort of patients receiving biological therapies.MethodsA cohort study was performed on prospectively acquired data via the British Society for Rheumatology Biologics Register in Rheumatoid Arthritis. All potential demyelinating events during follow-up were extracted and classified as definite, probable, or possible blinded to treatment data. The point of starting an anti-TNF therapy in individuals with no prior reported demyelination was the time of exposure. Crude rates of demyelination and standardized incident rates (SIRs) compared with the general UK population were calculated.ResultsThirty-five individuals with demyelinating events were identified from a total pool of 13,489. The median age at study entry was 44 years, and the median disease duration was 8 years; 71% were female. Events occurred a median of 3 (interquartile range 1–5) years from the start of the first anti-TNF therapy. Twenty-six events occurred in individuals still taking anti-TNFα therapy; of the other 9, 6 were within 90 days of drug withdrawal. The raw incidence of demyelination was 19.7/100,000 patient-years (95% CI 13.7–27.3). The SIR in the whole population was 1.38 (95% CI 0.96–1.92) and 0.83 (0.51–1.26) limited to definite/probable cases.ConclusionsDemyelination following anti-TNF therapy is uncommon. Patients receiving anti-TNFα therapy show a marginally increased SIR; this is lost in sensitivity analyses. Patients concerned about anti–TNFα-associated demyelination can be relatively reassured by these data.

Phytoremediation of CYN, MC-LR and ANTX-a from Water by the Submerged Macrophyte Lemna trisulca

Cyanotoxins are harmful to aquatic and water-related organisms. In this study, Lemna trisulca was tested as a phytoremediation agent for three common cyanotoxins produced by bloom-forming cyanobacteria. Cocultivation of L. trisulca with Dolichospermum flos-aquae in BG11 medium caused a release of the intracellular pool of anatoxin-a into the medium and the adsorption of 92% of the toxin by the plant—after 14 days, the total amount of toxin decreased 3.17 times. Cocultivation with Raphidopsis raciborskii caused a 2.77-time reduction in the concentration of cylindrospermopsin (CYN) in comparison to the control (62% of the total pool of CYN was associated with the plant). The greatest toxin limitation was noted for cocultivation with Microcystis aeruginosa. After two weeks, the microcystin-LR (MC-LR) concentration decreased more than 310 times. The macrophyte also influenced the growth and development of cyanobacteria cells. Overall, 14 days of cocultivation reduced the biomass of D. flos-aquae, M. aeruginosa, and R. raciborskii by 8, 12, and 3 times, and chlorophyll a concentration in comparison to the control decreased by 17.5, 4.3, and 32.6 times, respectively. Additionally, the macrophyte stabilized the electrical conductivity (EC) and pH values of the water and affected the even uptake of cations and anions from the medium. The obtained results indicate the biotechnological potential of L. trisulca for limiting the development of harmful cyanobacterial blooms and their toxicity.

Is There a FADS2-Modulated Link between Long-Chain Polyunsaturated Fatty Acids in Plasma Phospholipids and Polyphenol Intake in Adult Subjects Who Are Overweight?

Dietary polyphenols promote cardiometabolic health and are linked with long-chain polyunsaturated fatty acids in plasma phospholipids (LC-PUFA). The FADS2 polymorphisms are associated with LC-PUFA metabolism and overweight/obesity. This 4-week study examined the link between polyphenol intake, FADS2 variants (rs174593, rs174616, rs174576) and obesity in 62 overweight adults (BMI ≥ 25), allocated to consume 100 mL daily of either: Aronia juice, a rich source of polyphenols, with 1177.11 mg polyphenols (expressed as gallic acid equivalents)/100 mL (AJ, n = 22), Aronia juice with 294.28 mg polyphenols/100 mL (MJ, n = 20), or nutritionally matched polyphenol-lacking placebo as a control (PLB, n = 20). We analyzed LC-PUFA (% of total pool) by gas chromatography and FADS2 variants by real-time PCR. Four-week changes in LC-PUFA, BMI, and body weight were included in statistical models, controlling for gender and PUFA intake. Only upon AJ and MJ, the presence of FADS2 variant alleles affected changes in linoleic, arachidonic, and eicosapentaenoic acid (EPA). Upon MJ treatment, changes in EPA were inversely linked with changes in BMI (β= −0.73, p = 0.029) and weight gain (β= −2.17, p = 0.024). Only in subjects drinking AJ, the link between changes in EPA and anthropometric indices was modified by the rs174576 variant allele. Our results indicate the interaction between FADS2, fatty acid metabolism, and polyphenol intake in overweight subjects.

Spermidine and Rapamycin Reveal Distinct Autophagy Flux Response and Cargo Receptor Clearance Profile

Autophagy flux is the rate at which cytoplasmic components are degraded through the entire autophagy pathway and is often measured by monitoring the clearance rate of autophagosomes. The specific means by which autophagy targets specific cargo has recently gained major attention due to the role of autophagy in human pathologies, where specific proteinaceous cargo is insufficiently recruited to the autophagosome compartment, albeit functional autophagy activity. In this context, the dynamic interplay between receptor proteins such as p62/Sequestosome-1 and neighbour of BRCA1 gene 1 (NBR1) has gained attention. However, the extent of receptor protein recruitment and subsequent clearance alongside autophagosomes under different autophagy activities remains unclear. Here, we dissect the concentration-dependent and temporal impact of rapamycin and spermidine exposure on receptor recruitment, clearance and autophagosome turnover over time, employing micropatterning. Our results reveal a distinct autophagy activity response profile, where the extent of autophagosome and receptor co-localisation does not involve the total pool of either entities and does not operate in similar fashion. These results suggest that autophagosome turnover and specific cargo clearance are distinct entities with inherent properties, distinctively contributing towards total functional autophagy activity. These findings are of significance for future studies where disease specific protein aggregates require clearance to preserve cellular proteostasis and viability and highlight the need of discerning and better tuning autophagy machinery activity and cargo clearance.