Search Results (5,311)

The premature senescence of red raspberry leaves severely affects plant growth. In this study, the double-season red raspberry cultivar ‘Polka’ was used, with N₁₅₀ (0.10 g N·kg⁻¹) selected as the treatment group (T150) and N₀ (0 g N·kg⁻¹) set as the control (CK). This study systematically investigated the mechanism of premature senescence in red raspberry leaves under different nitrogen application levels by measuring physiological parameters and conducting a combined multi-omics analysis of transcriptomics and metabolomics. Results showed that T150 plants had 8.34 cm greater height and 1.45 cm greater ground diameter than CK. The chlorophyll, carotenoid, soluble protein, and sugar contents in all leaf parts of T150 were significantly higher than those in CK, whereas soluble starch contents were lower. Malondialdehyde (MDA) content and superoxide anion (O₂⁻) generation rate in the lower leaves of T150 were significantly lower than those in CK. Superoxide sismutase (SOD) and peroxidase (POD) activities in the middle and lower functional leaves of T150 were higher than in CK, while catalase (CAT) activity was lower. Transcriptomic analysis identified 4350 significantly differentially expressed genes, including 2062 upregulated and 2288 downregulated genes. Metabolomic analysis identified 135 differential metabolites, out of which 60 were upregulated and 75 were downregulated. Integrated transcriptomic and metabolomic analysis showed enrichment in the phenylpropanoid biosynthesis (ko00940) and flavonoid biosynthesis (ko00941) pathways, with the former acting as an upstream pathway of the latter. A premature senescence pathway was established, and two key metabolites were identified: chlorogenic acid content decreased, and naringenin chalcone content increased in early senescent leaves, suggesting their pivotal roles in the early senescence of red raspberry leaves. Modulating chlorogenic acid and naringenin chalcone levels could delay premature senescence. Optimizing fertilization strategies may thus reduce senescence risk and enhance the productivity, profitability, and sustainability of the red raspberry industry. Full article

Fistulina hepatica (Schaeff.) With. and Clitocybe nuda (Bull.) H.E. Bigelow & A.H. Sm. are wild edible mushrooms with nutritional and functional potential that remain insufficiently characterized. This study provides the first comparative assessment of their nutritional profiles, phenolic composition, and antioxidant activity, using specimens collected from Montesinho Natural Park (Portugal). Proximate composition, organic and phenolic acids, free sugars, and fatty acids were analyzed by chromatographic methods, and antioxidant capacity was assessed through OxHLIA and TBARS assays. F. hepatica showed higher carbohydrates (9.3 ± 0.2 g/100 g fw) and estimated energy values (43 ± 1 kcal/100 g fw), increased phenolic acids content (2.7 ± 0.1 mg/g extract), and the exclusive presence of p-coumaric and cinnamic acids, along with OxHLIA activity (IC₅₀ = 126 ± 5 µg/mL at Δt = 60 min). C. nuda displayed higher protein (2.5 ± 0.1 g/100 g dw) and quinic acid contents (4.13 ± 0.02 mg/g extract), a PUFA-rich profile, and greater TBARS inhibition (EC₅₀ = 303 ± 17 µg/mL). These findings highlight distinct and complementary bioactive traits, supporting their valorization as natural functional ingredients. Their compositional features offer promising applications in sustainable food systems and nutraceutical development, encouraging further investigations into safety, bioaccessibility, and formulation strategies. Notably, F. hepatica is best consumed at a young developmental stage, as its sensory properties tend to decline with maturity. Full article

Urban expansion fragments once-contiguous forest patches, generating pronounced edge gradients that modulate soil physicochemical properties and biodiversity. We quantified how fragmentation reshaped the soil microbiome continuum and its implications for soil carbon storage in a temperate urban mixed deciduous forest. A total of 18 plots were considered in this study, with six plots for each fragment type. Intact interior forest (F), internal forest path fragment (IF), and external forest path fragment (EF) soils were sampled at 0–15, 15–30, and 30–45 cm depths and profiled through phospholipid-derived fatty acid (PLFA) chemotyping and amino sugar proxies for living microbiome and microbial-derived necromass assessment, respectively. Carbon fractionation was performed through the chemical oxidation method. Diversity indices (Shannon–Wiener, Pielou evenness, Margalef richness, and Simpson dominance) were calculated based on the determined fatty acids derived from the phospholipid fraction. The microbial biomass ranged from 85.1 to 214.6 nmol g⁻¹ dry soil, with the surface layers of F exhibiting the highest values (p < 0.01). Shannon diversity declined systematically from F > IF > EF. The microbial necromass varied from 11.3 to 23.2 g⋅kg⁻¹. Fragmentation intensified the stratification of carbon pools, with organic carbon decreasing by approximately 14% from F to EF. Our results show that EFs possess a declining microbiome continuum that weakens their carbon sequestration capacity in urban forests. Full article

Membrane transporters play a crucial role in any cell. Identifying the substrates they translocate across membranes is important for many fields of research, such as metabolomics, pharmacology, and biotechnology. In this study, we leverage recent advances in deep learning, such as amino acid sequence embeddings with protein language models (pLMs), highly accurate 3D structure predictions with AlphaFold 2, and structure-encoding 3Di sequences from FoldSeek, for predicting substrates of membrane transporters. We test new deep learning features derived from both sequence and structure, and compare them to the previously best-performing protein encodings, which were made up of amino acid k-mer frequencies and evolutionary information from PSSMs. Furthermore, we compare the performance of these features either using a previously developed SVM model, or with a regularized feedforward neural network (FNN). When evaluating these models on sugar and amino acid carriers in A. thaliana, as well as on three types of ion channels in human, we found that both the DL-based features and the FNN model led to a better and more consistent classification performance compared to previous methods. Direct encodings of 3D structures with Foldseek, as well as structural embeddings with ProstT5, matched the performance of state-of-the-art amino acid sequence embeddings calculated with the ProtT5-XL model when used as input for the FNN classifier. Full article

Background/Objectives: Nitrogen (N) is an essential macronutrient that strongly influences maize growth and metabolism. While many studies have focused on nitrogen responses during later developmental stages, early-stage physiological and metabolic responses remain less explored. This study investigated the effect of different nitrogen-deficient levels on maize seedling growth and primary metabolite profiles. Methods: Seedlings were treated with N-modified nutrient solution, which contained 0% to 120% of the standard nitrogen level (8.5 mM). Results: Nitrogen starvation (N0) significantly reduced plant height (by 11–14%), shoot fresh weight (over 30%) compared to the optimal N supply (N100). Total leaf nitrogen content under N0–N20 was less than half of that in N100, whereas moderate N deficiency resulted in moderate reductions in growth and nitrogen content. Metabolite analysis revealed that N deficiency induced the accumulation of soluble sugars and organic acids (up to threefold), while sufficient N promoted the synthesis of amino acids related to nitrogen assimilation and protein biosynthesis. Statistical analyses (PCA and ANOVA) showed that both genotypes (MB and TYC) and tissue type (upper vs. lower leaves) influenced the metabolic response to nitrogen, with MB displaying more consistent shifts and TYC exhibiting greater variability under moderate stress. Conclusions: These findings highlight the sensitivity of maize seedlings to early nitrogen deficiency, with severity influenced by nitrogen level, tissue-specific position, and genotype; thus underscore the close coordination between physiological growth and primary metabolic pathways in response to nitrogen availability. These findings expand current knowledge of nitrogen response mechanisms and offer practical insights for improving nitrogen use efficiency in maize cultivation. Full article

The aim of this study was to isolate Weizmannia spp. that produce lactic acid from xylose and use an experimental design to optimize the production of the metabolite. After isolation, the experiments were conducted in xylose-yeast extract-peptone medium. The identification of isolates was performed using the 16S rDNA PCR technique, followed by sequencing. A central composite rotatable design (CCRD) was used to optimize the concentrations of the carbon source (xylose), nitrogen source (yeast extract and peptone), and sodium acetate. Two strains were considered promising for lactic acid production, with W. coagulans BLMI achieving greater lactic acid production under anaerobic conditions (21.93 ± 0.9 g.L⁻¹) and a yield of 69.18 %, while the strain W. ginsengihumi BMI was able to produce 19.79 ± 0.8 g.L⁻¹, with a yield of 70.46 %. CCRD was used with the W. ginsengihumi strain due to the lack of records in the literature on its use for lactic acid production. The carbon and nitrogen sources influenced the response, but the interactions of the variables were nonsignificant (p < 0.05). The response surface analysis indicated that the optimal concentrations of carbon and nitrogen sources were 32.5 and 3.0 g.L⁻¹, respectively, without the need to add sodium acetate to the culture medium, leading to the production of 20.02 ± 0.19 g.L⁻¹, productivity of 0.55 g/L/h after 36 hours of fermentation, and a residual sugar concentration of 12.59 ± 0.51 g.L⁻¹. These results demonstrate the potential of W. ginsengihumi BMI for the production of lactic acid by xylose fermentation since it is carried out at 50 °C, indicating a path for future studies Full article

Koshu wine, produced from the indigenous Japanese grape Vitis vinifera L. cv. Koshu exhibits a lower pH than other white wines, hindering malolactic fermentation (MLF) by lactic acid bacteria (LAB). Here, we aimed to isolate LAB strains capable of performing MLF under these challenging conditions to improve wine quality. Sixty-four Oenococcus oeni and one Lactobacillus hilgardii strain were isolated from Koshu grapes and wines that had undergone spontaneous MLF. MLF activity was assessed under varying pH, SO₂, and ethanol conditions in modified basal medium (BM) and Koshu model wine media. Expression of stress-related genes was analyzed using real-time PCR. Carbon source utilization was evaluated via API 50CH assays. All isolates degraded malic acid and produced lactic acid at 15 °C and pH 3.2 in BM without reducing sugars. Seven strains, all identified as O. oeni, demonstrated MLF activity at pH 3.0 in modified BM lacking added reducing sugars or tomato juice. Six wine-derived strains tolerated up to 12% ethanol, whereas the grape-derived strain was inhibited at 10%. In a synthetic Koshu wine model (13% ethanol, pH 3.0), wine-derived isolates exhibited higher MLF activity than commercial starter strains. In high-performing strains, mleA was upregulated, and most isolates preferred fructose, arabinose, and ribose over glucose. These findings suggest that indigenous O. oeni strains from Koshu wine possess unique stress tolerance and metabolic traits, making them promising candidates for region-specific MLF starter cultures that could enhance Koshu wine quality and terroir expression. Full article

This study investigates the metabolic responses of the model diatom Phaeodactylum tricornutum under different growth conditions, comparing benthic (adherent) and planktonic states. Using a multiblock metabolomics approach combining LC-HRMS², NMR, and GC-MS techniques, we compared the metabolome of P. tricornutum cultivated on three laboratory substrates (glass, polystyrene, and polydimethylsiloxane) and under planktonic conditions. Our results revealed metabolic differences between adherent and planktonic cultures, particularly concerning the lipid and carbohydrate contents. Adherent cultures showed a metabolic profile with an increase in betaine lipids (DGTA/S), fatty acids (tetradecanoic and octadecenoic acids), and sugars (myo-inositol and ribose), suggesting modifications in membrane composition and lipid remodeling, which play a potential role in adhesion. In contrast, planktonic cultures displayed a higher content of cellobiose, specialized metabolites such as dihydroactinidiolide, quinic acid, catechol, and terpenes like phytol, confirming different membrane composition, energy storage capacity, osmoregulation, and stress adaptation. The adaptative strategies do not only concern adherent and planktonic states, but also different adherent culture conditions, with variations in lipid, amino acid, terpene, and carbohydrate contents depending on the physical properties of the support. Our results highlight the importance of metabolic adaptation in adhesion, which could explain the fouling process. Full article

In recent years, great attention has been paid to second-generation (from agricultural and industrial wastes) lactic acid (LA) production. In the present study, the possibility of two Lactiplantibacillus plantarum strains, namely 53 and 2HS, to produce LA from waste materials was investigated. Distiller’s dried grains with solubles (DDGS), spent coffee grounds (SCG), wood chips, and cheese whey were used as substrates after pretreatment, and the results were compared with those with lactose as a carbon source. Both strains were capable of assimilating sugars from all waste materials. Nearly 20 g/L LA from 23 g/L reducing sugars (RS) obtained from DDGS, 22 g/L LA from 21 g/L RS from SCG, and 22 g/L LA from 21 g/L whey lactose were produced compared to 22 g/L LA obtained from 22 g/L lactose monohydrate in the fermentation broth. The wood chip hydrolysate (WH) contains only 10 g/L RS, and its fermentation resulted in the production of 5 g/L LA. This amount is twice as low as that produced from 11 g/L lactose monohydrate. A mathematical model was constructed based on the Compertz and Luedeking–Piret equations. Full article

Petit Manseng is a variety of Vitis vinifera gaining popularity in Virginia, USA because it consistently produces high quality grapes under variable growing conditions. However, its high sugar and acid levels complicate dry wine production. The goal of this study was to characterize Petit Manseng ripening kinetics from veraison to harvest to identify optimal harvest timing for producing dry white wines, using Chardonnay as a comparator because of its popularity in Virginia, well-known ripening kinetics, and ability to produce high quality dry white wines. A total of 74 samples of Petit Manseng and Chardonnay grapes were collected from five commercial sites over 2 years and evaluated for berry weight, pH, titratable acidity (TA), malic acid, total soluble solids (TSS), glucose, and fructose, with ripening kinetics modeled using segmented regressions. Results indicated that harvest timing and grape variety were the primary factors influencing ripening kinetics. In contrast, growing location and vintage had limited impact. In Chardonnay grapes, TA declined from 21 to 7.1 g/L and TSS increased from 6.1 to 19.5 g/L. In Petit Manseng, TA declined from 25 to 10.8 g/L and TSS increased from 8.0 to 23.6 g/L. Acid depletion plateaued ~2 weeks after sugar accumulation plateaued in Petit Manseng grapes, though the plateaus were similar in Chardonnay grapes. Linear discriminant analysis (LDA) completely separated grapes based on pH or TA vs. sugars, but not malic acid vs. sugars, suggesting that tartaric acid is driving acidity differences between cultivars. These data indicate that regardless of when grapes are harvested, winemakers may need to employ targeted acid management strategies with Petit Manseng because of its ripening kinetics. Full article

Dialium guineense (velvet tamarind), Parkia biglobosa Jacq. (African locust bean) and Adanosonia digitata L. (baobab) are fruits from African plants whose nutritional potential remains poorly characterised. As such, their pulps and seeds were analysed for colour (CIELab system), moisture, ash, protein, fat, soluble and insoluble dietary fibre, free sugars (HPLC-RI), organic acids (HPLC-PDA), macro and microelements (XRF analyser) and amygdalin (HPLC-PDA). The colours of their pulps differed considerable (ΔE > 38 between the velvet tamarind and African locust bean) and the moisture content was lower in seeds (about 7%) compared to pulps (9–13%). Seeds were more concentrated in protein (20–28%) and fat (5–22%), whereas pulps were richer in sugar (1–12%). African locust bean pulp was the sweetest (39% total sugar), while baobab pulp contained the highest soluble fibre (>30%) and citric acid (3.2%), and velvet tamarind pulp was distinguished by its tartaric acid content (3.4%). Seeds of the African fruits presented higher Ca, P, S and Fe contents, whereas pulps had higher K content. No amygdalin (<6.34 mg per 100 g of dry weight) or toxic heavy metal contents were detected. The PCA segregated samples by pulp and seed and the PC1 explains the sugar and moisture of the pulps, while protein, fat and minerals are associated with the seeds. These data confirm that African fruit pulps and seeds have distinct functional profiles, are safe for food use and can be consumed, which is important for efforts to promote the conservation of these tropical plant species. Full article

Lactic acid (LA) is a high-value chemical with growing demand for the production of polymers and plastics and in the food and pharmaceutical industries. However, production costs remain a significant constraint when using conventional food-grade substrates. This study investigates Ivorian sugarcane molasses, an abundant agro-industrial by-product, as a low-cost carbon source for LA production via batch fermentation with Limosilactobacillus fermentum ATCC 9338. Molasses was pretreated by acid hydrolysis to improve fermentability, increasing glucose and fructose concentrations. Comparative fermentations using raw and pretreated molasses showed a 75% increase in LA production (32.4 ± 0.03 g/L) after pretreatment. Optimisation using Box–Behnken design revealed that the initial sugar concentration, inoculation rate, and stirring speed significantly influenced lactic acid production. Under optimal conditions, a maximum LA concentration of 52.4 ± 0.49 g/L was achieved with a yield of 0.95 g/g and productivity of 0.73 g/L·h. Kinetic analysis confirmed efficient sugar utilisation under the optimised conditions, and polarimetry revealed a near-racemic lactic acid. A simplified cost analysis showed that molasses could reduce carbon source costs by over 70% compared to refined sugars, supporting its economic viability. This work demonstrates the potential of pretreated molasses under robust fermentation conditions as a sustainable and cost-effective substrate for LA production in resource-limited contexts. The approach aligns with circular bioeconomy principles and presents a replicable model for decentralised bioproduction in a developing country like Côte d’Ivoire. Full article

The transition to sustainable energy sources has intensified interest in lignocellulosic biomass (LCB) as a feedstock for second-generation biofuels. However, the inherent structural recalcitrance of LCB requires the utilization of an effective pretreatment to enhance enzymatic hydrolysis and subsequent fermentation yields. This manuscript presents a novel, single-step, and optimized nitrogen explosive decompression system (NED 3.0) designed to address the critical limitations of earlier NED versions by enabling the in situ removal of inhibitory compounds from biomass slurry and fermentation inefficiency at elevated temperatures, thereby reducing or eliminating the need for post-treatment detoxification. Aspen wood (Populus tremula) was pretreated by NED 3.0 at 200 °C, followed by enzymatic hydrolysis and fermentation. The analytical results confirmed substantial reductions in common fermentation inhibitors, such as acetic acid (up to 2.18 g/100 g dry biomass) and furfural (0.18 g/100 g dry biomass), during early filtrate recovery. Hydrolysate analysis revealed a glucose yield of 26.41 g/100 g dry biomass, corresponding to a hydrolysis efficiency of 41.3%. Fermentation yielded up to 8.05 g ethanol/100 g dry biomass and achieved a fermentation efficiency of 59.8%. Inhibitor concentrations in both hydrolysate and fermentation broth remained within tolerable limits, allowing for effective glucose release and sustained fermentation performance. Compared with earlier NED configurations, the optimized system improved sugar recovery and ethanol production. These findings confirm the operational advantages of NED 3.0, including reduced inhibitory stress, simplified process integration, and chemical-free operation, underscoring its potential for scalability in line with the EU Green Deal for bioethanol production from woody biomass. Full article

The sensory and physicochemical properties of three different recipes for apple cream filling were investigated, focusing on their potential to enhance consumer appeal in pastry applications. Two of the recipes incorporate dried apple cubes (AP1, 48% and AP2, 38% w/w, respectively), while the third recipe (PD) features a cube-free formulation with higher quantities of sugar, potato starch, xanthan gum, dextrose, cinnamon and malic acid. The study evaluated the impact of ingredient composition and processing techniques on sensory attributes. The results indicate that AP1 and AP2 resulted in higher moisture, ash and fiber content but lower viscosity, pH values and emulsion stability compared to PD. All samples exhibited pseudoplastic behavior. The AP2 sample exhibited the most hydrophilic behavior. FT-IR spectra have shown three main peaks, i.e., O-H (3300–3320 cm⁻¹), C=O (1640–1730 cm⁻¹) and C-O (1025–1030 cm⁻¹) stretching vibrations. AP1 and AP2 significantly enhanced hardness and cohesion, providing a more engaging sensory experience. PD offers a smoother, creamier texture with lower inhomogeneity compared to AP1 and AP2 samples, making it ideal for consumers who prefer a uniform mouthfeel. This research demonstrates the critical role of formulation choices in tailoring sensory and physicochemical properties of apple cream fillings to meet diverse consumer preferences. Full article

This study investigates the roles of grapevine berry inner necrosis virus (GINV) and grapevine yellow speckle viroid 1 (GYSVd1) in regulating the soluble sugar and organic acid metabolism of grape berries and wine. The contents of soluble sugar and organic acid components and the activity and expression levels of critical enzymes of the soluble sugar acid metabolism pathway were measured in ‘Welschriesling’ grape berries and wine carrying the virus GINV, the viroid GYSVd1, and a mixed infection of both GINV and GYSVd1 (GINV + GYSVd1), respectively. The results show that the virus GINV and the viroid GYSVd1 decreased the soluble sugar and increased the organic acid in berries and wine. GINV decreased glucose content and increased malic acid content by regulating AI, NADP-IDH, PEPC, and NAD-MDH activity, as well as VvHT4, VvSWEET10, VvPEPC, and VvMDH expression levels. GYSVd1 decreased glucose content and increased malic acid content by regulating AI and CS activity and VvHT4, VvSWEET15, and VvPEPC expression. The results suggest that the viroid GYSVd1 negatively impacts berries and wine more than the virus GINV. Moreover, in the mixed infection with GINV + GYSVd1, the negative effects of GINV and GYSVd1 on soluble sugars do not seem to be observed. Full article