Seasonal variation in non-volatile flavor substances of fresh tea leaves (Camellia sinensis) by integrated lipidomics and metabolomics using UHPLC-Q-Exactive mass spectrometry

Harvest season exerts great influence on tea quality. Herein, the variations in non-volatile flavor substances in spring and summer fresh tea leaves of four varieties were comprehensively investigated by integrating UHPLC-Q-Exactive based lipidomics and metabolomics. A total of 327 lipids and 99 metabolites were detected, among which, 221 and 58 molecules were significantly differential. The molecular species of phospholipids, glycolipids and acylglycerolipids showed most prominent and structure-dependent seasonal changes, relating to polar head, unsaturation and total acyl length. Particularly, spring tea contained higher amount in aroma precursors of highly unsaturated glycolipids and phosphatidic acids. The contents of umami-enhancing amino acids and phenolic acids, e.g., theanine, theogallin and gallotannins, were increased in spring. Besides, catechins, theaflavins, theasinensins and flavone/flavonol glycosides showed diverse changes. These phytochemical differences covered key aroma precursors, tastants and colorants, and may confer superior flavor of black tea processed using spring leaves, which was verified by sensory evaluation.

RG-I pectic polysaccharides and hesperidin synergistically modulate gut microbiota: An in vitro study targeting the proportional relationship

In this study, we investigated how different proportions blends of Rhamnogalacturonan-I pectic polysaccharides and hesperidin impact the gut microbiota and metabolites using an in vitro simulated digestion and fermentation model. The results indicated that both of them could modulate the gut microbiota and produce beneficial metabolites. However, their blends in particular proportions (such as 1:1) exhibited remarkable synergistic effects on modulating the intestinal microenvironment, surpassing the effects observed with individual components. Specifically, these blends could benefit the host by increasing short-chain fatty acids production (such as acetate), improving hesperidin bioavailability, producing more metabolites (such as hesperetin, phenolic acids), and promoting the growth of beneficial bacteria. This synergistic and additive effect was inseparable from the role of gut microbiota. Certain beneficial bacteria, such as Blautia, Faecalibacterium, and Prevotella, exhibited strong preferences for those blends, thereby contributing to host health through participating in carbohydrate and flavonoid metabolism.

The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus

One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.

Evaluation of amylose content: Structural and functional properties, analytical techniques, and future prospects

Amylose content (AC) is critical in evaluating starch properties, significantly influencing the food industry and human nutrition. Although amylose is not completely linear, its unique structure makes it a key research focus across various scientific fields. Understanding amylose's structural and functional properties is essential for its applications in medical, nutritional, and industrial sectors. Accurate determination of AC, from simple qualitative assessments to precise quantitative measurements, is vital for effectively processing and using starch-rich products. The choice of AC determination method depends on the specific application and the required accuracy and detail. This review summarizes amylose's structural and functional characteristics and recent advancements in qualitative and quantitative AC determination techniques. It also provides insights into future trends and prospects for these technologies, emphasizing the need for more rapid, convenient, accurate, and customizable methods. In conclusion, advancements in amylose determination should enhance accuracy, speed, and ease of use to improve quality control and applications across various sectors while expanding our understanding of amylose and its functionalities.

Transcriptome analysis of the medicinal mushroom Sanghuangporus vaninii in response to white light stress

Light is a vital environmental factor that promotes the growth and development of edible fungi mycelium. Under white light, the mycelium color of Sanghuangporus vaninii shifts during its growth stages. To investigate the impact of visible light on mycelial morphogenesis, a comparative transcriptomic analysis was conducted. This analysis revealed the molecular processes that underpin mycelial growth and development in S. vaninii when cultured in both darkness and light conditions. From the analysis, 13,643 genes were aligned using Illumina raw reads. Of these, 596 genes exhibited significant expression changes under white light exposure. Specifically, 226 genes were upregulated and 370 downregulated, spanning 55 different metabolic pathways. We further classified differentially expressed genes (DEGs), these genes play roles in photomorphogenesis, signal transduction, carbohydrate metabolism, and melanin production, among other processes. Some are also implicated in cell cycle regulation and the differential expression of respiratory functions. The validation of the differentially expressed transcripts using qRT-PCR showed complete agreement with RNA-Seq data for 9 transcripts. Meanwhile, the light had an inhibitory effect on the bioactive components in S. vaninii. These findings offer valuable insights into the transcriptional shifts and molecular mechanisms driving the color change in S. vaninii under light exposure, providing a basis for further research into mechanisms of light-response regulation.

Unlocking DOE potential by selecting the most appropriate design for rAAV optimization

Producing recombinant adeno-associated virus (rAAV) for gene therapy via triple transfection is an intricate process involving many cellular interactions. Each of the different elements encoded in the three required plasmids-pHelper, pRepCap, and pGOI-plays a distinct role, affecting different cellular pathways when producing rAAVs. The required expression balance emphasizes the critical need to fine-tune the concentration of all these different elements. The use of design of experiments (DOE) to find optimal ratios is a powerful method to streamline the process. However, the choice of the DOE method and design construction is crucial to avoid misleading results. In this work, we examined and compared four distinct DOE approaches: rotatable central composite design (RCCD), Box-Behnken design (BBD), face-centered central composite design (FCCD), and mixture design (MD). We compared the abilities of the different models to predict optimal ratios and interactions among the plasmids and the transfection reagent. Our findings revealed that blocking is essential to reduce the variability caused by uncontrolled random effects and that MD coupled with FCCD outperformed all other approaches, improving volumetric productivity 109-fold. These outcomes underscore the importance of selecting a model that can effectively account for the biological context, ultimately yielding superior results in optimizing rAAV production.

13-Week repeated-dose toxicity study of optimized aqueous extract of Moringa oleifera leaves in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Moringa oleifera (Moringaceae family), commonly known as horseradish or tree of life, is traditionally used for various diseases, such as diabetes, hypercholesterolemia, neurological disorders, among others.

AIM OF THE STUDY

To evaluate the toxicological profile of the oral use of an aqueous extract of Moringa oleifera leaves for 13 weeks in mice.

MATERIALS AND METHODS

Initially, a factorial design (23) was carried out to optimize aqueous extraction using as variables; the extraction method and proportion of drug. The 13-week repeated-dose toxicity trial used female and male mice, with oral administration of aqueous extract of Moringa oleifera leaves at doses of 250, 500, and 1000 mg/kg. The animals were evaluated for body weight, water and feed intake, biochemical and hematological parameters, urinalysis, ophthalmology and histopathology of the liver, spleen and kidneys.

RESULTS

The extraction efficiency was evidenced by the extraction by maceration at 5%, obtaining the optimized extract of Moringa oleifera (OEMo). The oral administration of OEMo did not promote significant difference (p > 0.05) in the weight gain, food and water consumption of the control animals and those treated with 250 and 500 mg/kg. However, treatment with 1000 mg/kg promoted a reduction (p < 0.05) in food intake and body weight from the 7th week onwards in male and female mice. No alterations were detected in the hematological and histological parameters in the concentrations tested for both sexes. The highest concentration treatment (1000 mg/kg) promoted an increase in transaminases in males and females. All concentrations promoted a significant decrease (p < 0.05) in the serum lipid profile of mice.

CONCLUSION

This study developed an optimized extract of Moringa oleifera leaves, which should be used with caution in preparations above 500 mg/kg for the long term because it leads to significant changes in liver enzymes. On the other hand, the extract proved to be a promising plant preparation for hyperlipidemia in mice.

Effect of antifungal proteins (AFPs) on the viability of heat-resistant fungi (HRFs) and the preservation of fruit juices

The control of heat-resistant fungi (HRFs), which cause spoilage of heat-treated fruit products, is considered a challenge for the fruit juice and beverage industry and requires new strategies for the development of antifungal compounds. In this study, four antifungal proteins (AFPs) from Penicillium digitatum (PdAfpB) and Penicillium expansum (PeAfpA, PeAfpB and PeAfpC), were evaluated against conidia from a representative collection of HRFs. A total of 19 strains from 16 different species belonging to the genera Aspergillus, Hamigera, Paecilomyces, Rasamsonia, Sarocladium, Talaromyces and Thermoascus were included in the study. PeAfpA and PdAfpB exhibited potent antifungal activity in synthetic media, completely inhibiting the growth of most of the fungi evaluated in the range of 0.5-32 μg/mL. The efficacy of the four AFPs was also tested in fruit juices against ascospores of five HRFs relevant to the food industry, including P. fulvus, P. niveus, P. variotii, A. fischeri and T. flavus. PdAfpB was the most effective protein in fruit juices, since it completely inhibited the growth of the five species tested in at least one of the fruit juices evaluated. This is the first study to demonstrate the activity of AFPs against fungal ascospores. Finally, a challenge test study showed that PdAfpB, at a concentration of 32 μg/mL, protected apple fruit juice artificially inoculated with ascospores of P. variotii for 17 days, highlighting the potential of the protein as a preservative in the fruit juice industry.

Phosphate solubilization and plant growth properties are promoted by a lactic acid bacterium in calcareous soil

On the basis of good phosphate solubilization ability of a lactic acid bacteria (LAB) strain Limosilactobacillus sp. LF-17, bacterial agent was prepared and applied to calcareous soil to solubilize phosphate and promote the growth of maize seedlings in this study. A pot experiment showed that the plant growth indicators, phosphorus content, and related enzyme activity of the maize rhizospheric soils in the LF treatment (treated with LAB) were the highest compared with those of the JP treatment (treated with phosphate solubilizing bacteria, PSB) and the blank control (CK). The types of organic acids in maize rhizospheric soil were determined through LC-MS, and 12 acids were detected in all the treatments. The abundant microbes belonged to the genera of Lysobacter, Massilia, Methylbacillus, Brevundimonas, and Limosilactobacillus, and they were beneficial to dissolving phosphate or secreting growth-promoting phytohormones, which were obviously higher in the LF and JP treatments than in CK as analyzed by high-throughput metagenomic sequencing methods. In addition, the abundance values of several enzymes, Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology, and Carbohydrate-Active Enzymes (CAZys), which were related to substrate assimilation and metabolism, were the highest in the LF treatment. Therefore, aside from phosphate-solubilizing microorganisms, LAB can be used as environmentally friendly crop growth promoters in agriculture and provide another viable option for microbial fertilizers. KEY POINTS: • The inoculation of LAB strain effectively promoted the growth and chlorophyll synthesis of maize seedlings. • The inoculation of LAB strain significantly increased the TP content of maize seedlings and the AP concentration of the rhizosphere soil. • The inoculation of LAB strain increased the abundances of the dominant beneficial functional microbes in the rhizosphere soil.

A bacteriocin-based coating strategy to prevent vancomycin-resistant Enterococcus faecium biofilm formation on materials of interest for indwelling medical devices

The ever-increasing use of exogenous materials as indwelling medical devices in modern medicine offers to pathogens new ways to gain access to human body and begin, in some cases, life threatening infections. Biofouling of such materials with bacteria or fungi is a major concern during surgeries, since this is often associated with biofilm formation and difficult to treat, recalcitrant infections. Intense research efforts have therefore developed several strategies to shield the medical devices' surface from colonization by pathogenic microorganisms. Here, we used dopamine as a coupling agent to coat four different materials of medical interest (plastic polyetheretherketone (PEEK), stainless steel, titanium and silicone catheter) with the bacteriocins, enterocin EJ97-short and the thiopeptide micrococcin P1. Water contact angle measurements and x-ray photoelectron spectroscopy were used to verify the effective coating of the materials. The effect of bacteriocins coated on these materials on the biofilm formation by a vancomycin resistant Enterococcus faecium (VRE) strain was studied by biofilm-oriented antimicrobial test (BOAT) and electron scanning microscopy. The in vitro biocompatibility of bacteriocin-modified biomaterials was tested on cultured human cells. The results demonstrated that the binding of the bacteriocins to the implant surfaces is achieved, and the two bacteriocins in combination could inhibit biofilm formation by E. faecium on all four materials. The modified implant showed no cytotoxicity to the human cells tested. Therefore, surface modification with the two bacteriocins may offer a novel and effective way to prevent biofilm formation on a wide range of implant materials.

Enhanced growth and metabolite production from a novel strain of Porphyridium sp

Microalgae are capable of generating numerous metabolites that possess notable biological activities and hold substantial promise for various industrial applications. Nevertheless, the taxonomic diversity of these photosynthetic microorganisms has not received thorough investigation. Using the 18S rRNA encoding gene, a recently discovered strain originating from the Tunisian coast (the governorate of Mahdia) was identified as a member of the Porphyridium genus. The growth response as well as the metabolite accumulation of Porphyridium sp. to different culture media (Pm, F/2, and Hemerick) was investigated over a period of 52 days. The highest biomass production was recorded with Pm medium (2 × 107 cell/mL). The apparent growth rates (µ) and the doubling time (Dt) were about 0.081 day-1 and 12.34 days, respectively. The highest chlorophyll a (0.678 ± 0.005 pg/cell), total carotenoids (0.18 ± 0.003 pg/cell), phycoerythrin (3.88 ± 0.003 pg/cell), and proteins (14.58 ± 0.35 pg/cell) contents were observed with F/2 medium. Cultivating Porphyridium sp. in both F/2 and Hemerick media yielded similar levels of starch accumulation. The Hemerick medium has proven to be the most suitable for the production of lipids (2.23% DW) and exopolysaccharides (5.41 ± 0.56 pg/cell).

Efficient expression of OUC-Sb-lip2 in Yarrowia lipolytica and its comprehensive utilization in the enrichment of DHA and EPA from fish oil

Lipases are widely used in the modification of functional lipids, particularly in the enrichment of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). In this study, a lipase named OUC-Sb-lip2 was expressed in Yarrowia lipolytica, achieving a promising enzyme activity of 472.6 U/mL by optimizing the culture medium, notably through olive oil supplementation. A significant proportion (58.8%) of the lipase activity was located in the cells, whereas 41.2% was secreted into the supernatant. Both whole-cell and immobilized OUC-Sb-lip2 were used to enrich DHA and EPA from fish oil. The whole-cell approach increased the DHA and EPA contents to 2.59 and 2.55 times that of the original oil, respectively. Similarly, the immobilized OUC-Sb-lip2 resulted in a 2.00-fold increase in DHA and an 1.99-fold increase in EPA after a 6-h hydrolysis period. Whole cell and the immobilized OUC-Sb-lip2 retained 48.7% and 52.7% of their activity after six cycles of reuse, respectively.

Multiplex competitive annealing mediated isothermal amplification with high fidelity DNA polymerase (HiFi-CAMP)

Various isothermal amplification methods have been developed for point-of-care testing (POCT) of various infectious diseases. Here, we proposed a novel isothermal amplification method, named as 5'-half complementary primers mediated isothermal amplification (HCPA). Because of the similarity of our method to the previous method competitive annealing mediated isothermal amplification (CAMP) in primer design, we also use the name CAMP for our method. We demonstrated that CAMP is mediated by both a linear isothermal amplification pattern and a loop-mediated isothermal amplification pattern. To improve the specificity and enable multiplex detection, we further developed HiFi-CAMP method that uses a small amount of high-fidelity DNA polymerase to cut HFman probe to release fluorescent signal. The HiFi-CAMP method was demonstrated to have a good specificity and sensitivity, and fast amplification speed in detection of three human respiratory viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus A (RSV-A) and influenza A viruses (IAV). When compared with gold standard RT-qPCR assays, the HiFi-CAMP assays showed sensitivities of 90.0 %, 71.4 % and 78.1 %, specificities of 100 %, 100 % and 95.5 %, and consistencies of 93.0 %, 93.3 % and 88.2 % for SARS-CoV-2, RSV-A and IAV, respectively. Furthermore, a duplex HiFi-CAMP assay was also developed to simultaneously detect RSV-A and SARS-CoV-2. The HiFi-CAMP will provide a promising candidate for POCT diagnosis in resource-limited settings.

A case of refractory onychomycosis caused by Kloeckera apiculata: Successful treatment with itraconazole

Here, we present the case of an otherwise healthy patient, without risk factors, who developed a refractory case of onychomycosis caused by Kloeckera apiculata, an uncommon human pathogen. The diagnosis was ultimately confirmed by fungal nail plate culture, histopathology, and PCR. Whereas prior treatments with topical 5 % tavaborole solution, oral terbinafine, and oral fluconazole were ineffective, complete clinical and mycological cure was achieved with a 3-month course of oral itraconazole.

Toxicity potential of a pyraclostrobin-based fungicide in plant and green microalgae models

Pyraclostrobin-based fungicides play an effective role in controlling fungal diseases and are extensively used in agriculture. However, there is concern regarding the potential adverse effects attributed to exposure to these fungicides on non-target organisms and consequent influence exerted on ecosystem functioning. Thus, it is essential to conduct studies with model organisms to determine the impacts of these fungicides on different groups of living organisms. The aim of this study was to examine the ecotoxicity associated with exposure to commercial fungicides containing pyraclostrobin. The focus of the analysis involved germination and initial development of seedlings of 4 plant models (Lactuca sativa, Raphanus sativus, Pennisetum glaucum and Triticum aestivum), in addition to determining the population growth rate and total carbohydrate content in microalga Raphidocelis subcapitata. The fungicide pyraclostrobin adversely influenced growth and development of the tested plants, indicating a toxic effect. The fungicide exerted a significant impact on the initial development of seedlings of all model species examined with T. aestivum plants displaying the greatest susceptibility to pyraclostrobin. Plants of this species exhibited inhibitory effects on both aerial parts and roots when treated with a concentration of 4.75 mg/L pyraclostrobin. In addition, the green microalga R. subcapitata was also significantly affected by the fungicide, especially at relatively high concentrations as evidenced by a reduction in total carbohydrate content. This commercial fungicide demonstrated potential phytotoxicity for the tested plant models and was also considered toxic to the selected microalgae, indicating an ecotoxic effect that might affect other organisms in aquatic environments.

Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.

Development of genetic markers in Yarrowia lipolytica

The oleaginous yeast Yarrowia lipolytica represents a potential microbial cell factory for the recombinant production of various valuable products. Currently, the commonly used selection markers for transformation in Y. lipolytica are limited, and successive genetic manipulations are often restricted by the number of available selection markers. In our study, we developed a dominant marker, dsdA, which encodes a D-serine deaminase for genetic manipulation in Y. lipolytica. In Y. lipolytica, this marker confers the ability to use D-serine as a nitrogen source. In addition, the selection conditions of several infrequently used dominant markers including bleoR (zeocin resistance), kanMX (G418 resistance), and guaB (mycophenolic acid resistance) were also analyzed. Our results demonstrated that these selection markers can be used for the genetic manipulation of Y. lipolytica and their selection conditions were different for various strains. Ultimately, the selection markers tested here will be useful to expand the genetic toolbox of Y. lipolytica. KEY POINTS: • The dsdA from Escherichia coli was developed as a dominant marker. • The applicability of several resistance markers in Y. lipolytica was determined. • We introduced the Cre/mutant lox system for marker recycling.

Advances in stress-tolerance elements for microbial cell factories

Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.

High-solid digestion - A comparison of completely stirred and plug-flow reactor systems

High-solid digestion (HSD) for biogas production is a resource-efficient and sustainable method to treat organic wastes with high total solids content and obtain renewable energy and an organic fertiliser, using a lower dilution rate than in the more common wet digestion process. This study examined the effect of reactor type on the performance of an HSD process, comparing plug-flow (PFR) type reactors developed for continuous HSD processes, and completely stirred-tank reactors (CSTRs) commonly used for wet digestion. The HSD process was operated in thermophilic conditions (52 °C), with a mixture of household waste, garden waste and agricultural residues (total solids content 27-28 %). The PFRs showed slightly better performance, with higher specific methane production and nitrogen mineralisation than the CSTRs, while the reduction of volatile solids was the same in both reactor types. Results from 16S rRNA gene sequencing showed a significant difference in the microbial population, potentially related to large differences in stirring speed between the reactor types (1 rpm in PFRs and 70-150 rpm in CSTRs, respectively). The bacterial community was dominated by the genus Defluviitoga in the PFRs and order MBA03 in the CSTRs. For the archaeal community, there was a predominance of the genus Methanoculleus in the PFRs, and of the genera Methanosarcina and Methanothermobacter in the CSTRs. Despite these shifts in microbiology, the results showed that stable digestion of substrates with high total solids content can be achieved in both reactor types, indicating flexibility in the choice of technique for HSD processes.

Discovery, development and optimisation of a novel frog antimicrobial peptide with combined mode of action against drug-resistant bacteria

Antimicrobial peptides (AMP) have emerged as promising candidates for addressing the clinical challenges posed by the rapid evolution of antibiotic-resistant microorganisms. Brevinins, a representative frog-derived AMP family, exhibited broad-spectrum antimicrobial activities, attacking great attentions in previous studies. However, their strong haemolytic activity and cytotoxicity, greatly limit their further development. In this work, we identified and characterised a novel brevinin-1 peptide, brevinin-1pl, from the skin secretions of the northern leopard frog, Rana pipiens. Like many brevinins, brevinin-1pl also displayed strong haemolytic activity, resulting in a lower therapeutic index. We employed several bioinformatics tools to analyse the structure and potential membrane interactions of brevinin-1pl, leading to a series of modifications. Among these analogues, des-Ala16-[Lys4]brevinin-1pl exhibited great enhanced therapeutic efficacy in both in vitro and in vivo tests, particularly against some antibiotics-resistant Escherichia coli strains. Mechanistic studies suggest that des-Ala16-[Lys4]brevinin-1pl may exert bactericidal effects through multiple mechanisms, including membrane disruption and DNA binding. Consequently, des-Ala16-[Lys4]brevinin-1pl holds promise as a candidate for the treatment of drug-resistant Escherichia coli infections.

Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress

Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.

Preparation of in vivo intermediate metabolites of soybean saponins with improved bioactivity by in vitro deacetylation and deglucosylation

Unlike natural soyasaponins and their aglycones formed by enzymatic hydrolysis in the human intestine, in vivo intermediate soyasaponin metabolites are difficult to prepare. Therefore, the pharmacological activities of in vivo intermediate soyasaponins remain uninvestigated. Herein, in vivo intermediate soyasaponins with purities of >90% were prepared by in vitro deacetylation (alkaline treatment) and deglucosylation (β-glucosidase treatment) of natural soyasaponins using preparative high-performance liquid chromatography. These compounds exhibited higher anti-inflammatory and antioxidant activities than natural soyasaponins in in vitro bioassays, suggesting that the intermediate soyasaponins can be used as improved bioactive food supplements. To the best of our knowledge, this is the first study reporting the in vitro preparation and bioassays of in vivo intermediate soyasaponin metabolites formed in the human intestine.

Characterization of pectin-zein nanoparticles encapsulating tanshinone: Antioxidant activity, controlled release properties, physicochemical stability to environmental stresses

Tanshinone compounds, natural antioxidants found in the roots of Salvia subg Perovskia plants, offer various health benefits and can serve as natural food additives, replacing synthetic antioxidants. In this study, the nanoparticles were created using the antisolvent method, which were then evaluated for their antioxidant and antibacterial properties, as well as their ability to release tanshinone and withstand environmental stress. The results of the study demonstrated a significant improvement in the antioxidant capabilities of tanshinone with the nanoparticle coating. The T/Z/P NPs exhibited enhanced tanshinone release under simulated gastrointestinal conditions compared to T/Z nanoparticles. These nanoparticles displayed remarkable stability against fluctuations in environmental pH and thermal conditions. The study also revealed that the critical flocculation concentration of the system was 0.5 M of salt. Furthermore, the T/Z/P NPs showed good stability during storage at 4°C for 30 days, making them an excellent candidate for use in various food products.

Ferulic acid-arabinoxylan conjugates: Synthesis, characterization and applications in antibacterial film formation

A novel antibacterial film based on arabinoxylan (AX) was prepared by introducing ferulic acid (FA) to AX through a laccase-catalyzed procedure. The ferulic acid-arabinoxylan conjugates (FA-AX conjugates) have been characterized. Results showed that FA was successfully grafted onto the AX chains by covalent linkages, likely through nucleophilic addition between O-Ph in the phenolic hydroxyl group of FA, or through Michael addition via O-quinone intermediates. FA-AX conjugates showed improved crystallinity, thermal stability, and rheological properties, as well as a distinct surface morphology, compared with those of native AX. Moreover, FA-AX conjugates exhibited enhanced antibacterial ability against Staphylococcus aureus, Escherichia coli, Shewanella sp., and Pseudomonas sp. Mechanistic studies revealed that the enhanced antibacterial ability was due to the penetration of bacterial membrane by the phenolic molecule and the steric effect of FA-AX conjugates. The study demonstrates that the laccase-induced grafting method was effective in producing FA-AX conjugates; we have demonstrated its antibacterial ability and great potential in prolonging the shelf life of fresh seafood products.

Novel reaction systems for catalytic synthesis of structured phospholipids

Phospholipids are distinctive, adaptable molecules that are crucial to numerous biological systems. Additionally, their various architectures and amphiphilic characteristics support their unrivaled crucial functions in scientific and industrial applications. Due to their enormous potential for use in the fields of medicine, food, cosmetics, and health, structured phospholipids, which are modified phospholipids, have garnered increased attention. Traditional extraction methods, however, are pricy, resource-intensive, and low-yielding. The process of enzyme-catalyzed conversion is effective for producing several types of structured phospholipase. However, most frequently employed catalytic procedures involve biphasic systems with organic solvents, which have a relatively large mass transfer resistance and are susceptible to solvent residues and environmental effects due to the hydrophobic nature of phospholipids. Therefore, the adoption of innovative, successful, and environmentally friendly enzyme-catalyzed conversion systems provides a new development route in the field of structured phospholipids processing. Several innovative catalytic reaction systems are discussed in this mini-review, including aqueous-solid system, mixed micelle system, water-in-oil microemulsion system, Pickering emulsion system, novel solvent system, three-liquid-phase system, and supercritical carbon dioxide solvent system. However, there is still a glaring need for a thorough examination of these systems for the enzymatic synthesis of structural phospholipids. In terms of the materials utilized, applicability, benefits and drawbacks, and comparative effectiveness of each system, this research establishes further conditions for the system's selection. To create more effective biocatalytic processes, it is still important to build green biocatalytic processes with improved performance. KEY POINTS: • The latest catalytic systems of phospholipase D are thoroughly summarized. • The various systems are contrasted, and their traits are enumerated. • Different catalytic systems' areas of applicability and limitations are discussed.

Characterization and stabilization of GluLm and its application to deglycosylate dietary flavonoids and lignans

This study describes the characterization of the recombinant GH3 aryl-β-glucosidase "GluLm" from Limosilactobacillus mucosae INIA P508, followed by its immobilization on an agarose support with the aim of developing an efficient application to increase the availability and concentration of flavonoid and lignan aglycones in a vegetal beverage. In previous studies, heterologous GluLm-producing strains demonstrated a great capacity to deglycosylate flavonoids. Nevertheless, the physicochemical properties and substrate spectrum of the enzyme remained unknown up to now. A high production of purified GluLm was achieved (14 mg L-1). GluLm exhibited optimal activity at broad ranges of pH (5.0-8.0) and temperature (25-60°C), as well as high affinity (Km of 0.10 mmol L-1) and specific constant (86554.0 mmol L-1 s-1) against p-nitrophenyl-β-D-glucopyranoside. Similar to other GH3 β-glucosidases described in lactic acid bacteria, GluLm exhibited β-xylosidase, β-galactosidase, and β-fucosidase activities. However, this study has revealed for the first time that a GH3 β-glucosidase is capable to hydrolyze different families of glycosylated phenolics such as flavonoids and secoiridoids. Although it exhibited low thermal stability, immobilization of GluLm improved its thermostability and allowed the development of a beverage based on soybeans and flaxseed extract with high concentration of bioactive isoflavone (daidzein, genistein), lignan (secoisolariciresinol, pinoresinol, and matairesinol), and other flavonoid aglycones. KEY POINTS: • Limosilactobacillus mucosae INIA P508 GluLm was purified and biochemically characterized • Immobilized GluLm efficiently deglycosylated flavonoids and lignans from a vegetal beverage • A viable application to produce vegetal beverages with a high content of aglycones is described.

Enzymatic synthesis of N-succinyl-L-phenylalanine and exploration of its potential as a novel taste enhancer

N-succinyl-L-phenylalanine (SP) has been identified as a taste-active contributor in an array of foods. Despite its recognized importance, the understanding of its synthesis and taste enhancement properties remains rudimentary. The study examined the enzymatic synthesis of SP with 45.58 ± 1.95% yield. This was achieved under optimized conditions: 0.3 mol/L L-phenylalanine, 0.9 mol/L succinic acid, 30,000 U/L of the AY 50C, pH 4 and 55 °C for 24 h. Sensory evaluation and electronic tongue revealed that the incorporation of a mere 1 mg/L SP substantially increased the kokumi, umami, and saltiness intensities, indicating the potential of SP as a potent taste enhancer. Moreover, time-intensity (TI) results demonstrated a significant increase of umami duration in samples containing 1 mg/L of SP (210.0 ± 0 s), a significant extension compared to the control group (150.0 ± 0 s). Notably, the intensity of umami and saltiness in the SP sample were consistently higher than that of control group. The sigmoid curve analysis further confirmed that SP exhibited a synergistic effect on umami and saltiness perceptions. Moreover, the study also illuminated interaction of SP with T1R1, T1R3, TMC4, TRPV1, and CaSR receptors, resulting in significant enhancement in umami, saltiness, and kokumi.

Global challenges and microbial biofilms: Identification of priority questions in biofilm research, innovation and policy

Priority question exercises are increasingly used to frame and set future research, innovation and development agendas. They can provide an important bridge between the discoveries, data and outputs generated by researchers, and the information required by policy makers and funders. Microbial biofilms present huge scientific, societal and economic opportunities and challenges. In order to identify key priorities that will help to advance the field, here we review questions from a pool submitted by the international biofilm research community and from practitioners working across industry, the environment and medicine. To avoid bias we used computational approaches to group questions and manage a voting and selection process. The outcome of the exercise is a set of 78 unique questions, categorized in six themes: (i) Biofilm control, disruption, prevention, management, treatment (13 questions); (ii) Resistance, persistence, tolerance, role of aggregation, immune interaction, relevance to infection (10 questions); (iii) Model systems, standards, regulatory, policy education, interdisciplinary approaches (15 questions); (iv) Polymicrobial, interactions, ecology, microbiome, phage (13 questions); (v) Clinical focus, chronic infection, detection, diagnostics (13 questions); and (vi) Matrix, lipids, capsule, metabolism, development, physiology, ecology, evolution environment, microbiome, community engineering (14 questions). The questions presented are intended to highlight opportunities, stimulate discussion and provide focus for researchers, funders and policy makers, informing future research, innovation and development strategy for biofilms and microbial communities.

Management of hypertension addressing hyperuricaemia: introduction of nano-based approaches

Uric acid (UA) levels in blood serum have been associated with hypertension, indicating a potential causal relationship between high serum UA levels and the progression of hypertension. Therefore, the reduction of serum UA level is considered a potential strategy for lowering and mitigating blood pressure. If an individual is at risk of developing or already manifesting elevated blood pressure, this intervention could be an integral part of a comprehensive treatment plan. By addressing hyperuricaemia, practitioners may subsidize the optimization of blood pressure regulation, which illustrates the importance of addressing UA levels as a valuable strategy within the broader context of hypertension management. In this analysis, we outlined the operational principles of effective xanthine oxidase inhibitors for the treatment of hyperuricaemia and hypertension, along with an exploration of the contribution of nanotechnology to this field.

Protein secretion and associated stress in industrially employed filamentous fungi

Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.

Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures

The thermostable α-amylase derived from Bacillus licheniformis (BLA) has multiple advantages, including enhancing the mass transfer rate and by reducing microbial contamination in starch hydrolysis. Nonetheless, the application of BLA is constrained by the accessibility and stability of enzymes capable of achieving high conversion rates at elevated temperatures. Moreover, the thermotolerance of BLA requires further enhancement. Here, we developed a computational strategy for constructing small and smart mutant libraries to identify variants with enhanced thermostability. Initially, molecular dynamics (MD) simulations were employed to identify the regions with high flexibility. Subsequently, FoldX, a computational design predictor, was used to design mutants by rigidifying highly flexible residues, whereas the simultaneous decrease in folding free energy assisted in improving thermostability. Through the utilization of MD and FoldX, residues K251, T277, N278, K319, and E336, situated at a distance of 5 Å from the catalytic triad, were chosen for mutation. Seventeen mutants were identified and characterized by evaluating enzymatic characteristics and kinetic parameters. The catalytic efficiency of the E271L/N278K mutant reached 184.1 g L-1 s-1, which is 1.88-fold larger than the corresponding value determined for the WT. Furthermore, the most thermostable mutant, E336S, exhibited a 1.43-fold improvement in half-life at 95 ℃, compared with that of the WT. This study, by combining computational simulation with experimental verification, establishes that potential sites can be computationally predicted to increase the activity and stability of BLA and thus provide a possible strategy by which to guide protein design.

Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis

Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.

Soy protein hydrolysates induce menaquinone-7 biosynthesis by enhancing the biofilm formation of Bacillus subtilis natto

Menaquinone-7 (MK-7) is a form of vitamin K2 with health-beneficial effects. A novel fermentation strategy based on combining soy protein hydrolysates (SPHs) with biofilm-based fermentation was investigated to enhance menaquinone-7 (MK-7) biosynthesis by Bacillus subtilis natto. Results showed the SPHs increased MK-7 yield by 199.4% in two-stage aeration fermentation as compared to the SP-based medium in submerged fermentation, which was related to the formation of robust biofilm with wrinkles and the enhancement of cell viability. Moreover, there was a significant correlation between key genes related to MK-7 and biofilm synthesis, and the quorum sensing (QS) related genes, Spo0A and SinR, were downregulated by 0.64-fold and 0.39-fold respectively, which promoted biofilm matrix synthesis. Meanwhile, SPHs also enhanced the MK-7 precursor, isoprene side chain, supply, and MK-7 assembly efficiency. Improved fermentation performances of bacterial cells during fermentation were attributed to abundant oligopeptides (Mw < 1 kDa) and moderate amino acids, particularly Arg, Asp, and Phe in SPHs. All these results revealed that SPHs were a potential and superior nitrogen source for MK-7 production by Bacillus subtilis natto.

Natural pigments in the food industry: Enhancing stability, nutritional benefits, and gut microbiome health

Natural pigments are increasingly favored in the food industry for their vibrant colors, fewer side effects and potential health benefits compared to synthetic pigments. However, their application in food industry is hindered by their instability under harsh environmental conditions. This review evaluates current strategies aimed at enhancing the stability and bioactivity of natural pigments. Advanced physicochemical methods have shown promise in enhancing the stability of natural pigments, enabling their incorporation into food products to enhance sensory attributes, texture, and bioactive properties. Moreover, recent studies demonstrated that most natural pigments offer health benefits. Importantly, they have been found to positively influence gut microbiota, in particular their regulation of the beneficial and harmful flora of the gut microbiome, the reduction of ecological dysbiosis through changes in the composition of the gut microbiome, and the alleviation of systemic inflammation caused by a high-fat diet in mice, suggesting a beneficial role in dietary interventions.

A study on the structure-functionality relationship of Solenaia oleivora protein under high-intensity ultrasonication processing

Solenaia oleivora is a valuable freshwater mussel endemic to China with a high content of high-quality proteins, but the lack of structural information and limited functionality of Solenaia oleivora proteins constrained their application in the food industry. This study investigates the changes in structural characteristics and functionality of Solenaia oleivora protein under ultrasound processing at power from 200 to 600 W. The ultrasound treatment caused increased contents of β-turn and α-helix, and the exposure of interior hydrophobic groups, resulting in the increased hydrophobicity by around 3 folds. The ultrasound treatment could significantly decrease particle size and increase surface charges of Solenaia oleivora proteins, facilitating the increase of hydrosolubility from 10.2% to 81.7%. These structural changes and increased hydrosolubility contributed to the enhancement of emulsifying and foaming properties, and in vitro digestibility. The results suggested that the ultrasound-treated Solenaia oleivora proteins possessed the potential as an alternative protein in food applications.

Plant-derived and dietary phenolic cinnamic acid derivatives: Anti-inflammatory properties

Cinnamic acids are aromatic acids primarily found in plants and plant-derived food. Phenolic cinnamic acids, with one or more hydroxyl groups in the aromatic ring, often contribute to the biological activities attributed to these compounds. The presence of hydroxyl groups and a carboxyl group makes cinnamic acids very hydrophilic, preventing them from crossing biological membranes and exerting their biological activities. To alleviate this condition, a panel of synthetic modifications have been made leading to a diverse set of phenolic cinnamic structures. In this review, an overview of the natural phenolic cinnamic acid derivatives and their plant sources (more than 200) is described. The synthetic approaches to obtain the referred derivatives (more than 200) namely esters and amides are reviewed. Further, their anti-inflammatory activity (more than 70 compounds) is scrutinized. Finally, future directions will be indicated to translate the research on phenolic cinnamic derivatives into potentially effective anti-inflammatory drugs.

Widely targeted metabolomic analysis reveals metabolite changes induced by incorporating black tea fermentation techniques in oolong tea processing for quality improvement

Oolong tea, a semi-fermented tea, has a prominent fruity and floral aroma, resembling green tea's astringency and pungency but lacking black tea's mellowness. Oolong tea incorporating black tea fermentation techniques (OT-IBTFT) not only retained its excellent floral and fruity aroma but also reduced astringency and enriched taste. However, metabolite changes remain unknown. In this study, widely targeted metabolomic analysis showed OT-IBTFT reduced prunin, gallocatechin, methyl gallate, and increased loliolide by changing the flavonoid biosynthesis and biosynthesis of secondary metabolites pathways, thereby reducing the astringency and increasing the mellow taste and richness to improve oolong tea quality. In addition, Wrap-rolling 5 times increased fermentation, improving the color and aroma of oolong tea by increasing theaflavic acid and 2-furoic acid, is more significant than wrap-rolling once. In conclusion, these findings provide a theoretical basis for the improvement of oolong tea processing techniques and flavor and quality control.

Establishment of an RNA-based transient expression system in the green alga Chlamydomonas reinhardtii

Chlamydomonas reinhardtii, a unicellular green alga, is a prominent model for green biotechnology and for studying organelles' function and biogenesis, such as chloroplasts and cilia. However, the stable expression of foreign genes from the nuclear genome in C. reinhardtii faces several limitations, including low expression levels and significant differences between clones due to genome position effects, epigenetic silencing, and time-consuming procedures. We developed a robust transient expression system in C. reinhardtii to overcome these limitations. We demonstrated efficient entry of in vitro-transcribed mRNA into wall-less cells and enzymatically dewalled wild-type cells via electroporation. The endogenous or exogenous elements can facilitate efficient transient expression of mRNA in C. reinhardtii, including the 5' UTR of PsaD and the well-characterized Kozak sequence derived from the Chromochloris zofingiensis. In the optimized system, mRNA expression was detectable in 120 h with a peak around 4 h after transformation. Fluorescently tagged proteins were successfully transiently expressed, enabling organelle labeling and real-time determination of protein sub-cellular localization. Remarkably, transiently expressed IFT46 compensated for the ift46-1 mutant phenotype, indicating the correct protein folding and function of IFT46 within the cells. Additionally, we demonstrated the feasibility of our system for studying protein-protein interactions in living cells using bimolecular fluorescence complementation. In summary, the established transient expression system provides a powerful tool for investigating protein localization, function, and interactions in C. reinhardtii within a relatively short timeframe, which will significantly facilitate the study of gene function, genome structure, and green biomanufacturing in C. reinhardtii and potentially in other algae.

Exploiting UPO versatility to transform rutin in more soluble and bioactive products

The discovery of unspecific peroxygenases (UPOs) completely changed the paradigm of enzyme-based oxyfunctionalization reactions, as these enzymes can transform a wide variety of substrates with a relatively simple reaction mechanism. The fact that UPO can exert both peroxygenative and peroxidative activity in either aromatic or aliphatic carbons, represents a great potential in the production of high value-added products from natural antioxidants. In this work, the flavonoid rutin has been considered as possible substrate for UPO from Agrocybe aegerita, and its peroxygenation or its peroxidation and successive oligomerization have been studied. Different experiments were performed in order to reduce the range of process variables involved and gaining insight on the behavior of this enzyme, leading to a multivariable optimization of UPO-based rutin modification. While trying to preserve enzyme activity this optimization aimed for maximizing the production of more soluble antioxidants. Reusability of the enzyme was evaluated recovering UPO using an enzymatic membrane reactor, revealing challenges in enzyme stability due to inactivation during the filtration stages. The influence of the radical scavenger ascorbic acid on product formation was investigated, revealing its role in directing the reaction towards hydroxylated rutin derivatives, hence indicating a shift towards more soluble and bioactive products.

Examining the crucial role of polysaccharide polymers in influencing soil hydraulic conductivity: A comprehensive review

This paper examines the impact of biopolymers on hydraulic conductivity of soils, representing a key parameter for many environmental and geotechnical applications. The complexity of this relationship is compounded by researchers employing diverse approaches and presentation formats, resulting in apparent inconsistencies. However, this review intends to address these challenges by identifying various categories of biopolymers that influence the hydraulic conductivity and discuss the recent research findings. By elucidating the diverse impacts of these biopolymers on hydraulic conductivity, this review offers valuable insights into the historical development and origins of soils treated with hydraulic conductivity modifying biopolymers. It not only traces the evolution and background of these treatments but also identifies areas of conflicting evidence and ongoing debate in the field. In the overall, this review is an essential resource for engineers and researchers working in the geotechnical field, by providing a nuanced understanding of the intricate dynamics between biopolymers and soil hydraulic conductivity. The newly developed multi-variable functions can be systematically utilized to predict the hydraulic conductivity of soils treated with biopolymers, commonly encountered in various geotechnical and environmental engineering applications.

Polyethylene and related hydrocarbon polymers ("plastics") are not biodegradable

Research on the biodegradation of polyethylene (PE), polystyrene (PS) and related polymers has become popular and the number of publications on this topic is rapidly increasing. However, there is no convincing evidence that the frequently claimed biodegradability of these so-called "plastics" really exists. Rather, a diffuse definition of the term "biodegradability" has led to the publication of reports showing either marginal weight losses of hydrocarbon polymers by the action of isolated bacterial strains or mechanical disintegration and polymer surface modification in case of hydrocarbon polymer-consuming insect larvae. Most of the data can be alternatively explained by the utilization of polymer impurities/additives, by the utilization of low molecular weight oligomers, and/or by physical fragmentation and subsequent loss of small fragments. Evidence for a (partial) biotic and/or abiotic oxidation of the amorphous polymer fraction and of surface-exposed hydrocarbon side chains is not sufficient to claim that PE is biodegradable. To the best of my knowledge, no report has been so far published in which substantial biodegradation and mineralization of PE or related (long chain length) hydrocarbon polymers to carbon dioxide has been convincingly demonstrated by the determination of the fate of carbon atoms in isotope-labeled polymers. It is disappointing that publications with a critical view on biodegradation of hydrocarbon polymers are not cited in most of these reports. The possibility should be considered that the rapidly expanding research field of hydrocarbon polymer biodegradation is chasing rainbows.

Genomic and transcriptomic analyses reveal insights into cadmium resistance mechanisms of Cupriavidus nantongensis strain E324

The cadmium-resistant Cupriavidus sp. strain E324 has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the strain E324 was most closely related to C. nantongensis X1T, indicating that the strain E324 should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. nantongensis strain E324, the transcriptional response of this strain to acute Cd exposure was assessed using RNA-seq-based transcriptome analysis, followed by validation through qRT-PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure. Among these, only the Zn pretreatment resulting in high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis strain E324 via the enhancement of metal-chelating and antioxidant capacities of the cells.

Occupational agents-mediated asthma: From the perspective of autophagy

Occupational asthma (OA) is a common occupational pulmonary disease that is frequently underdiagnosed and underreported. The complexity of diagnosing and treating OA creates a significant social and economic burden, making it an important public health issue. In addition to avoiding allergens, patients with OA require pharmacotherapy; however, new therapeutic targets and strategies need further investigation. Autophagy may be a promising intervention target, but there is a lack of relevant studies summarizing the role of autophagy in OA. In this review consolidates the current understanding of OA, detailing principal and novel agents responsible for its onset. Additionally, we summarize the mechanisms of autophagy in HMW and LMW agents induced OA, revealing that occupational allergens can induce autophagy disorders in lung epithelial cells, smooth muscle cells, and dendritic cells, ultimately leading to OA through involving inflammatory responses, oxidative stress, and cell death. Finally, we discuss the prospects of targeting autophagy as an effective strategy for managing OA and even steroid-resistant asthma, encompassing autophagy interventions focused on organoids, organ-on-a-chip systems, nanomaterials vehicle, and nanobubbles; developing combined exposure models, and the role of non-classical autophagy in occupational asthma. In briefly, this review summarizes the role of autophagy in occupational asthma, offers a theoretical foundation for OA interventions based on autophagy, and identifies directions and challenges for future research.

Valorization of seafood waste: a review of life cycle assessment studies in biorefinery applications

The escalating challenges posed by seafood waste generated by the fishing and aquaculture industries underscore the urgent need for innovative solutions that promote both environmental conservation and economic viability within the seafood sector. Seafood waste biorefinery emerges as a promising solution, offering the potential to transform waste materials into valuable products. However, it is essential to recognize that seafood waste biorefinery operations also entail environmental impacts that warrant careful consideration. Environmental assessment tools like Life Cycle Assessment (LCA) provide a valuable framework for assessing these impacts comprehensively. This review critically examines LCA studies in seafood waste biorefinery, focusing on key concepts, emerging technologies, and potential product avenues. Despite the growing body of research in this area, direct comparisons between published studies prove challenging due to discrepancies in feedstocks, processing techniques, value-added products, and LCA methodologies. Nevertheless, the findings consistently demonstrate significant reductions in environmental impacts achieved through seafood waste biorefinery processes. The selection of technologies significantly influences both product quality and sustainability measures. High energy consumption, including diesel fuel consumption in fishing vessels and electricity consumption in processing steps, should be carefully considered and reduced to mitigate associated environmental impacts. In conclusion, while seafood waste biorefinery processes hold significant promise for providing environmental and economic benefits, substantial challenges remain. This review provides invaluable insights for researchers, policymakers, and stakeholders, emphasizing the importance of continuous interdisciplinary collaboration and methodological standardization to advance sustainable waste management practices in the seafood industry.

Evolution of the biochemistry underpinning purine alkaloid metabolism in plants

Purine alkaloids are naturally occurring nitrogenous methylated derivatives of purine nucleotide degradation products, having essential roles in medicine, food and various other aspects of our daily lives. They are generated through convergent evolution in different plant species. The pivotal reaction steps within the purine alkaloid metabolic pathways have been largely elucidated, and the convergent evolution of purine alkaloids has been substantiated through bioinformatic, biochemical and other research perspectives within S-adenosyl-ʟ-methionine-dependent N-methyltransferases. Currently, the biological and ecological roles of purine alkaloids, further refinement of the purine alkaloid metabolic pathways and the investigation of purine alkaloid adaptive evolutionary mechanisms continue to attract widespread research interest. The exploration of the purine alkaloid metabolic pathways also enhances our comprehension of the biochemical mechanism, providing insights into inter-species interactions and adaptive evolution and offering potential value in drug development and agricultural applications. Here, we review the progress of research in the distribution, metabolic pathway elucidation and regulation, evolutionary mechanism and ecological roles of purine alkaloids in plants. The opportunities and challenges involved in elucidating the biochemical basis and evolutionary mechanisms of the purine alkaloid metabolic pathways, as well as other research aspects, are also discussed. This article is part of the theme issue 'The evolution of plant meta-bolism'.

Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in Arabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein-protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in Arabidopsis thaliana and Chlamydomonas reinhardtii unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in Arabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue 'The evolution of plant metabolism'.

Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue 'The evolution of plant metabolism'.

The evolution of flavonoid biosynthesis

The flavonoid pathway is characteristic of land plants and a central biosynthetic component enabling life in a terrestrial environment. Flavonoids provide tolerance to both abiotic and biotic stresses and facilitate beneficial relationships, such as signalling to symbiont microorganisms, or attracting pollinators and seed dispersal agents. The biosynthetic pathway shows great diversity across species, resulting principally from repeated biosynthetic gene duplication and neofunctionalization events during evolution. Such events may reflect a selection for new flavonoid structures with novel functions that enable occupancy of varied ecological niches. However, the biochemical and genetic diversity of the pathway also likely resulted from evolution along parallel trends across land plant lineages, producing variant compounds with similar biological functions. Analyses of the wide range of whole-plant genome sequences now available, particularly for archegoniate plants, have enabled proposals on which genes were ancestral to land plants and which arose within the land plant lineages. In this review, we discuss the emerging proposals for how the flavonoid pathway may have evolved and diversified. This article is part of the theme issue 'The evolution of plant metabolism'.

The use of water in wineries: A review

Water is essential at various stages of winemaking, from irrigation in the vineyard to cleaning equipment and facilities, controlling fermentation temperatures, and diluting grape juice if necessary. Additionally, water is used for sanitation purposes to ensure the quality and safety of the final product. This article provides an overview of the existing knowledge regarding the use of water in wineries throughout the winemaking process, water consumption values, effluent treatment, efficient use of water measures, and water reuse. Different assessment methods, including Water Footprint (WF) and Life Cycle Assessment(LCA), provide varied insights into water use impacts, emphasizing the importance of standardized methodologies for accurate assessment and sustainable practices. This research showed that the characterization of the vinification processes of each type of wine is fundamental for further analysis on the environmental impact of winemaking regarding water use. It was also observed that WF is affected by factors like climate, irrigation needs, and cleaning procedures. Thus, efficient water management in all the stages of wine production is crucial to reduce the overall WF. Water efficiency measures may involve the modification of the production processes, reusing and recycling water and the implementation of cleaner production practices and technological innovations, such as automated fermentation systems that reduce water needs. Furthermore, waste management in wineries emphasizes the importance of sustainable practices and technological innovations to mitigate environmental impacts and enhance resource efficiency.

Exploring industrial lignocellulosic waste: Sources, types, and potential as high-value molecules

Lignocellulosic biomass has a promising role in a circular bioeconomy and may be used to produce valuable molecules for green chemistry. Lignocellulosic biomass, such as food waste, agricultural waste, wood, paper or cardboard, corresponded to 15.7% of all waste produced in Europe in 2020, and has a high potential as a secondary raw material for industrial processes. This review first presents industrial lignocellulosic waste sources, in terms of their composition, quantities and types of lignocellulosic residues. Secondly, the possible high added-value chemicals obtained from transformation of lignocellulosic waste are detailed, as well as their potential for applications in the food industry, biomedical, energy or chemistry sectors, including as sources of polyphenols, enzymes, bioplastic precursors or biofuels. In a third part, various available transformation treatments, such as physical treatments with ultrasound or heat, chemical treatments with acids or bases, and biological treatments with enzymes or microorganisms, are presented. The last part discusses the perspectives of the use of lignocellulosic waste and the fact that decreasing the cost of transformation is one of the major issues for improving the use of lignocellulosic biomass in a circular economy and green chemistry approach, since it is currently often more expensive than petroleum-based counterparts.