Biology subjects

Gomes, E.

Publications and source records attributed to Gomes, E..

6 recordsLinked to original sources

bioRxiv2026

From definition to discovery: metabolite markers of high temperature in green grape berries

Understanding how plants respond to high temperature is critical under global warming. Metabolite markers can provide insights into stress-responsive mechanisms and help guide strategies to maintain crop quality. However, heat-associated metabolite markers in grape berries remain poorly defined, particularly at the green stage, a critical phase of berry development during which early metabolic perturbations can influence subsequent ripening and ultimately determine berry composition and quality. Here, we applied berry-scale heat treatments of eight durations of two major wine cultivars, Cabernet Sauvignon and Merlot. Untargeted LC-MS profiling revealed both conserved and cultivar-dependent responses to heat. Based on these patterns, three time points were selected for targeted GC-MS analysis, and subsequent statistical analyses identified robust "cultivar-common heat markers": glycine decreased, whereas galactinol increased consistently across time points and cultivars. "Cultivar-dependent heat markers" were identified: xylose, lyxose, citrulline, quinic acid, and glutamine, that consistently distinguished CS and Merlot fruits under heat stress. Notably, xylose, lyxose, citrulline, and quinic acid also differentiated the two cultivars under ambient conditions, underscoring their potential as stable cultivar-discriminating metabolites. Together, these results reveal dynamic metabolic remodeling in grape berries under heat stress, particularly in amino acid, nitrogen, central carbon metabolism, raffinose family oligosaccharides pathway and the glutathione-ascorbate cycle.

plant biology↗

bioRxiv2023

Development of a Plasmodium vivax biobank for functional ex vivo assays

BackgroundPlasmodium vivax is the second most prevalent cause of malaria yet remains challenging to study due to the lack of a continuous in vitro culture system, highlighting the need to establish a biobank of clinical isolates with multiple freezes per sample for use in functional assays. Different methods for cryopreserving parasite isolates were compared and subsequently the most promising one was validated. Enrichment of early- and late-stage parasites and parasite maturation were quantified to facilitate assay planning. MethodsIn order to compare cryopreservation protocols, nine clinical P. vivax isolates were frozen with four glycerolyte-based mixtures. Parasite recovery post thaw, post KCl-Percoll enrichment and in short-term in vitro culture was measured via slide microscopy. Enrichment of late-stage parasites by magnetic activated cell sorting (MACS) was measured. Short and long-term storage of parasites at either -80{degrees}C or liquid nitrogen were also compared. ResultsOf the four cryopreservation mixtures, one mixture (glycerolyte:serum:RBC at a 2.5:1.5:1 ratio) resulted in improved parasite recovery and statistically significant (P<0.05) enhancement in parasite survival in short-term in vitro culture. A parasite biobank was subsequently generated using this protocol resulting in a collection with 106 clinical isolates, each with 8 vials. The quality of the biobank was validated by measuring several factors from 47 thaws: the average reduction in parasitemia post-thaw (25.3%); the average fold enrichment post KCl-Percoll (6.65-fold); and the average percent recovery of parasites (22.0%, measured from 30 isolates). During short-term in vitro culture, robust maturation of ring stage parasites to later stages (>20% trophozoites, schizonts and gametocytes) was observed in 60.0% of isolates by 48 hours. Enrichment of mature parasite stages via MACS showed good reproducibility, with an average 30.0% post-MACS parasitemia and an average 5.30 x 105 parasites/vial. Finally, the effect of storage temperature was tested, and no large impacts from short-term (7 day) or long term (7 - 10 year) storage at -80{degrees}C on parasite recovery, enrichment or viability was observed. ConclusionsHere, an optimized freezing method for P. vivax clinical isolates is demonstrated as a template for the generation and validation of a parasite biobank for use in functional assays.

microbiology↗

bioRxiv2023

Foraging at night under artificial light: consequences on reproductive senescence and lifetime reproductive success for a diurnal insect

O_LIThe increasing use of artificial light at night (ALAN) is currently a major anthropogenic disturbance, with largely unappreciated eco-evolutionary consequences for nocturnal but also diurnal organisms. It has been hypothesized that light pollution could create new opportunities for the latter to forage and reproduce at night, which is called the night-light niche, with fitness consequences still scarcely explored. C_LIO_LIWe exposed diurnal parasitoid wasps (Venturia canescens) to one of three light-at-night conditions: control (0 lux), low intensity (0.7 lux) or high intensity (20 lux) throughout their lives. We then monitored changes in both behavioural and life-history traits, namely daytime and nighttime feeding and egg-laying activity, reproductive senescence, lifespan and lifetime reproductive success. C_LIO_LILight pollution influenced the nighttime activity of wasps. The proportion of wasps feeding and laying eggs at night increased, and we also detected a tendency for a higher nighttime reproductive success under a high intensity of light pollution. Surprisingly, high intensity of light pollution also increased the wasps lifespan. Such changes did not affect the lifetime reproductive success of the wasps, but influenced the distribution of ovipositions between day and night. C_LIO_LIReproductive senescence occurs in V. canescens, evidenced by the linear decline in daily reproductive success with age regardless of the light condition. ALAN conditions, in interaction with mother age, affected developmental time in offspring, highlighting an effect on reproductive senescence. C_LIO_LIWe demonstrated that light pollution induced the use of the night-light niche in a diurnal insect, with a shift in the distribution of egg-laying events between day and night. While we did not observe strong consequences on individual fitness, such changes in the dynamics of parasitism behaviour may nevertheless have major consequences for population dynamics, especially in natural conditions. C_LI

animal behavior and cognition↗

bioRxiv2020

Therapeutic genetic variation revealed in diverse Hsp104 homologs

The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. We have engineered potentiated Hsp104 variants to antagonize proteotoxic misfolding linked to human neurodegenerative diseases. However, these Hsp104 variants can exhibit off-target toxicity, which may limit their therapeutic utility. Hsp104 is conserved among all nonmetazoan eukaryotes, which raises the possibility that natural variants might exist with enhanced, selective activity against neurodegenerative disease substrates. To assess this possibility, we screened a cross-kingdom collection of Hsp104 homologs in several yeast proteotoxicity models. We uncovered therapeutic genetic variation among several Hsp104 homologs that specifically antagonize TDP-43 or -synuclein condensate formation and toxicity in yeast, human cells, and C. elegans. Surprisingly, this variation manifested as increased passive chaperone activity, distinct from disaggregase activity, which neutralizes proteotoxicity of specific substrates. Thus, by exploring natural tuning of passive chaperone activity we elucidated enhanced, substrate-specific agents to counter proteotoxicity underlying neurodegenerative disease.

biochemistry↗

bioRxiv2019

Differences in berry primary and secondary metabolisms identified by transcriptomic and metabolic profiling of two table grape color somatic variants

Anthocyanins are flavonoids responsible for the color of berries in skin-pigmented grapevine (Vitis vinifera L.). Due to the widely adopted vegetative propagation of this species, somatic mutations occurring in meristematic cell layers can be fixed and passed into the rest of the plant when cloned. In this study we focused on the transcriptomic and metabolic differences between two color somatic variants. Using microscopic, metabolic and mRNA profiling analyses we compared the table grape cultivar (cv.) Red Globe (RG, with purplish berry skin) and cv. Chimenti Globe (CG, with a contrasting reddish berry skin color). As expected, significant differences were found in the composition of flavonoids and other phenylpropanoids, but also in their upstream precursors shikimate and phenylalanine. Among primary metabolites, sugar phosphates related with sucrose biosynthesis were less accumulated in cv. CG. The red-skinned cv. CG only contained di-hydroxylated anthocyanins (i.e. peonidin and cyanidin) while the tri-hydroxylated derivatives malvidin, delphinidin and petunidin were absent, in correlation to the reddish cv. CG skin coloration. Transcriptomic analysis showed alteration in flavonoid metabolism and terpenoid pathways and in primary metabolism such as sugar content. Eleven flavonoid 35-hydroxylase gene copies were down-regulated in cv. CG. This family of cytochrome P450 oxidoreductases are key in the biosynthesis of tri-hydroxylated anthocyanins. Many transcription factors appeared down-regulated in cv. CG in correlation to the metabolic and transcriptomic changes observed. The use of molecular markers and its confirmation with our RNA-seq data showed the exclusive presence of the null MYBA2 white allele (i.e. homozygous in both L1 and L2 layers) in the two somatic variants. Therefore, the differences in MYBA1 expression seem sufficient for the skin pigmentation differences and the changes in MYBA target gene expression in cv. Chimenti Globe.

plant biology↗

bioRxiv2019

Proteomic and metabolomic profiling underlines the stage- and time-dependent effects of high temperature on grape berry metabolism

Climate change scenarios predict an increase in mean air temperatures and in the frequency, intensity, and length of extreme temperature events in many wine-growing regions worldwide. Because elevated temperature has detrimental effects on the berry growth and composition, it threatens the economic and environmental sustainability of wine production. Using Cabernet Sauvignon fruit-bearing cuttings, we investigated the effects of high temperature (HT) on grapevine berries through a label-free shotgun proteomic analysis coupled to a complementary metabolomic study. Among the 2279 proteins identified, 592 differentially abundant proteins were found in berries exposed to HT. The gene ontology categories \"Stress\", \"Protein\", \"Secondary metabolism\" and \"Cell wall\" were predominantly altered under HT. High temperatures strongly impaired carbohydrate and energy metabolism, and the effects depended on the stage of development and duration of treatment. Transcript amounts correlated poorly with protein expression levels in HT berries, highlighting the value of proteomic studies in the context of heat stress. Furthermore, this work reveals that HT alters key proteins driving berry development and ripening. Finally, we provide a list of differentially abundant proteins that can be considered as potential markers for developing or selecting grape varieties that are better adapted to warmer climates or extreme heat waves.

plant biology↗