Search Results (178)

The rapid evolution of deep learning (DL) has fundamentally transformed the paradigm for detecting special components in agricultural products, addressing critical challenges in food safety, quality control, and precision agriculture. This comprehensive review systematically analyzes many seminal studies to evaluate cutting-edge DL applications across three core domains: contaminant surveillance (heavy metals, pesticides, and mycotoxins), nutritional component quantification (soluble solids, polyphenols, and pigments), and structural/biomarker assessment (disease symptoms, gel properties, and physiological traits). Emerging hybrid architectures—including attention-enhanced convolutional neural networks (CNNs) for lesion localization, wavelet-coupled autoencoders for spectral denoising, and multi-task learning frameworks for joint parameter prediction—demonstrate unprecedented accuracy in decoding complex agricultural matrices. Particularly noteworthy are sensor fusion strategies integrating hyperspectral imaging (HSI), Raman spectroscopy, and microwave detection with deep feature extraction, achieving industrial-grade performance ($RPD$ > 3.0) while reducing detection time by 30–100× versus conventional methods. Nevertheless, persistent barriers in the “black-box” nature of complex models, severe lack of standardized data and protocols, computational inefficiency, and poor field robustness hinder the reliable deployment and adoption of DL for detecting special components in agricultural products. This review provides an essential foundation and roadmap for future research to bridge the gap between laboratory DL models and their effective, trusted application in real-world agricultural settings. Full article

Annually, more than 10,000 synthetic dyes are produced worldwide, generating around 280,000 tons of waste, posing risks to human and aquatic life, and potentially creating even more toxic products than the dyes themselves. This study aims to immobilize organic dyes, forming hybrid pigments using ZnO as support obtained through starch combustion. ZnO was obtained by starch (sago) combustion and characterized by XRD, SEM and the BET method. It was then used for the adsorption of orange and green textile dyes, evaluating the adsorbent dosage, initial dye concentration, contact time, and selectivity with copper ions. The removal studies indicated up to 100% removal of both dyes at low concentrations. The co-adsorption system showed excellent performance, with removal percentages exceeding 90% for both textile dyes and Cu (II) ions. Hybrid pigments were assessed for solvent resistance and durability under extended white light exposure. ZnO immobilized the dyes, showing resistance to organic solvents and good stability under prolonged white light exposure. Full article

Phalaenopsis pulcherrima are known for their captivating floral morphology and diverse colors, demonstrate exceptional resilience to adverse environmental conditions, and exhibit significant potential for hybrid breeding. However, current research on flower coloration is still limited. The data from this study indicates that variations in anthocyanin levels are the primary determinants of the difference between white and purple colors. Through RNA-seq, we identified 469 genes that were differentially expressed. Furthermore, our bioinformatics exploration uncovered two potential transcription factors, PpMYB1 and PpbHLH1, which play regulatory roles in anthocyanin accumulation. Y2H assays demonstrated that these two TFs could form heterodimers and interact with each other. Afterwards, transient expression assays were conducted for the first time in P. pulcherrima flowers, revealing that overexpression of PpMYB1 alone or in combination with PpbHLH1 resulted in purple petal pigmentation. Overexpressing PpMYB1 in tobacco resulted in more purple-colored corollas, stamens, pistils, and pods compared to control plants. Y1H and dual-luciferase assays provided further evidence that PpMYB1 and PpbHLH1 interact with the promoters of the structural genes PpF3H, PpDFR, and PpANS in the anthocyanin biosynthesis pathway, thereby driving their robust expression. This study not only enhances our understanding of the molecular mechanisms underlying anthocyanin synthesis but also holds significant practical implications for advancing plant hybrid breeding and genetic engineering applications in flower color regulation. Full article

The control of gene expression by cis-regulatory DNA sequences is a conserved genomic feature. The maize booster1 gene (b1) is a naturally occurring locus that serves as a mechanistic model for the control of gene expression from a distal cis element and a form of allelic interactions called paramutation. Two epi-alleles of b1 produce distinct pigmentation phenotypes correlated with transcriptional enhancement and the silencing of b1. These transcriptional dynamics depend on a hepta-tandem repeat sequence located 100 kb upstream of the b1 locus. In the heterozygous condition, the B′ epi-allele paramutates B-I, heritably converting the B-I epi-allele to the epigenetic state and expression level of B′, producing lightly pigmented plants. To identify b1TR-associated proteins, we used a targeted chromatin immunoprecipitation approach with a stably integrated transgenic b1TR locus. Applying a conservative filtering strategy, we detected several expected factors, including RNA Polymerase II, as well as the novel putative DNA-binding proteins ZAG4 and DDT4. ZAG4 and DDT4 activated GAL expression using b1TR as bait in yeast one-hybrid, supporting their potential interaction with this sequence. The identification of proteins uniquely associated with the UAS::b1TR chromatin provides insight into potential b1 regulatory factors and offers a foundation for future studies to investigate their roles in gene regulation. Full article

Three isolates of a novel, rapidly growing, non-pigmented Mycobacterium species were recovered from the water and runoff of a public fountain in a rural village in central Portugal, formerly used by the local population as a source of drinking water and not accessible to animals. High-quality draft genome sequencing, in silico DNA–DNA hybridization, and phylogenetic analyses confirmed that isolates 21AC1^T, 21AC14, and 21AC21 represent a previously undescribed species within the genus Mycobacterium, forming a distinct phylogenetic lineage closely related to Mycobacterium wolinskyi, Mycobacterium goodii and Mycobacterium smegmatis. MALDI-TOF MS analysis of the type strain 21AC1^T revealed a unique spectral profile. A comprehensive polyphasic characterization was performed, including chemotaxonomic analyses of fatty acid and mycolic acid composition, as well as an extensive biochemical characterization. Their susceptibility to 12 antimicrobials was also assessed. The identification and characterization of novel nontuberculous mycobacteria species are of increasing environmental and clinical relevance, as infections by these opportunistic pathogens are on the rise globally. Based on our findings, we propose that isolates 21AC1^T, 21AC14, and 21AC21 represent a novel species, for which we propose the name Mycobacterium appelbergii sp. nov., with the type strain designated as 21AC1^T (=BCCM/ITM 501212 = DSM 113570) and the additional two strains as 21AC14 (=BCCM/ITM 501447 = DSM 118402) and 21AC21 (=BCCM/ITM 501448 = DSM 118403). Full article

Meeting the rising demand for staple grains now requires cultivars that combine high yield, enhanced nutritional value, and strong chemical resilience. Blue-kernel landraces from central Mexico are rich in anthocyanins yet remain highly susceptible to post-emergence herbicides, whereas modern hybrids detoxify these compounds through cytochrome P450 (CYP450) enzymes. We crossed the anthocyanin-rich variety Polimaize with a CYP450-tolerant hybrid and evaluated the two parents and their F₁ segregants (designated “White” and “Yellow”) under greenhouse applications of mesotrione (75 g a.i. ha⁻¹), nicosulfuron (30 g a.i. ha⁻¹), and their mixture. Across 160 plants, the hybrid retained 95% of control dry matter and showed ≤7% foliar injury under all treatments, whereas Polimaize lost 28% biomass and exhibited 36% injury after nicosulfuron. The Yellow class matched hybrid performance while maintaining a blue pericarp and a β-carotene-rich endosperm, demonstrating that nutritional and agronomic traits can be stacked. The White class displayed heterosis-driven compensatory growth, exceeding its untreated biomass by 60% with nicosulfuron and by 82% with the mixture despite transient bleaching. Chlorophyll and carotenoid fluorescence revealed rapid, zeaxanthin-linked photoprotection in all tolerant genotypes, consistent with accelerated CYP450-mediated detoxification. These findings show that broad-spectrum herbicide tolerance can be introgressed into pigment-rich germplasm through conventional breeding, providing a non-transgenic path to herbicide-ready, anthocyanin-rich maize. The strategy preserves local biodiversity while delivering cultivars suited to intensive, weed-competitive agriculture and offers a template for integrating metabolic resilience into other native crops. Full article

The WRKY gene family is essential for controlling a variety of plant physiological functions, yet the involvement of specific WRKY members in pigment biosynthesis and accumulation in Camellia chekiangoleosa remains unexplored, particularly in anthocyanins and carotenoids, which play crucial roles in the pigmentation of C. chekiangoleosa. This study systematically identified 87 WRKY genes across 15 chromosomes in C. chekiangoleosa through bioinformatic approaches. Further structural and phylogenetic analyses of these TFs enabled their classification into six different subgroups. WRKY family expansion was shown to be mostly driven by tandem duplication. W-box elements, which can be binding sites for WRKY transcription factors, were present in a number of biosynthetic genes in the pigment production pathway. Yeast one-hybrid assay confirmed that five WRKY transcription factors (CchWRKY15/24/33/47/76) directly bind to the promoter regions of two key biosynthetic genes, CchPSY1 and Cch4CL1. Intriguingly, among the five WRKYs tested, the expression levels of CchWRKY15, CchWRKY33, and CchWRKY47 showed the strongest positive associations with flavonoid accumulation (p < 0.05, Pearson correlation analysis).These findings provide novel insights into the evolutionary patterns, transcriptional regulation, and functional characteristics of CchWRKYs, while elucidating their possible regulatory mechanisms in the fruit coloration of C. chekiangoleosa. Full article

The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. A Gram-positive, pink-pigmented Streptomyces strain designated HC307^T was isolated from a soil sample collected in Xizang (Tibet), China. The exploration of Streptomyces from extreme environments presents a particularly compelling avenue for novel compound discovery. In this study, the 16S rRNA sequence of strain HC307^T exhibited the highest similarity with Streptomyces prasinosporus NRRL B-12431^T (97.5%) and Streptomyces chromofuscus DSM 40273^T (97.3%), which were below 98.7%. The draft genome of the bacteria was 10.0 Mb, with a G+C content of 70.0 mol%. The average nucleotide identity (ANI) values of strain HC307^T and similar type strains ranged from 78.3% to 87.5% (<95%). The digital DNA-DNA hybridization (dDDH) values ranged from 22.6% to 33.9% (<70%), which was consistent with the results obtained from phylogenetic tree analysis. Phenotypically, this bacterium grew within the temperature range of 25–40 °C, at a pH range of 5 to 9, and in NaCl concentrations from 0% to 6% (w/v). The polar lipid profile of strain HC307^T was diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The analysis of 32 biosynthetic gene clusters (BGCs) indicated the strain’s capacity to synthesize diverse compounds. Phylogenetic and phenotypic analyses demonstrated that strain HC307^T represented a novel species within the genus Streptomyces, and proposed the name Streptomyces flavusporus sp. nov., with strain HC307^T (=DSM 35222^T=CGMCC 32047^T). The strain was deposited in Deutsche Sammlung von Mikroorganismen und Zellkulturen and the China General Microbiological Culture Collection Center for patent procedures under the Budapest Treaty. Full article

The psychrophilic aerobic heterotrophic bacterium, strain 1639^T, was isolated from the low-temperature Lake Untersee in Antarctica. The bacterium was Gram-positive, non-motile, yellow–green-pigmented, non-spore-forming, and a pleomorphic rod. Growth was observed at temperatures of 0–25 °C with an optimum at 10 °C. The strain used urea as a nitrogen source. The major fatty acids were i-C_16:0 (49.69%), ai-C_15:0 (17.59%), and C_16:1 branched (12.03%). Identified polar lipids were phosphatidylglycerols and a glycolipid. The respiratory quinone was determined to be MK-10. The genomic DNA G+C content was 68.03 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1639^T was a member of the genus Cryobacterium, with the highest sequence similarity to C. arcticum SK1^T (98.4%), C. soli GCJ02^T (98.4%), C. lactosi Sr59^T (98.3%), C. zongtaii TMN-42^T (98.2%), and C. adonitolivorans RHLS22-1^T (98.1%). The ANI and the DNA–DNA hybridization estimate values between strain 1639^T and all type strains of species of the genus Cryobacterium were in the range of 84.3–87.8% and 20.5–40.3%, respectively. The combined genotypic and phenotypic data indicate that strain 1639^T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium inferilacus sp. nov. is proposed with the type strain 1639^T (=KCTC 59142^T, =VKM Ac-2907^T, UQM 41460^T). Full article

Anthocyanins are key metabolites that determine red pigmentation in pear skin (Pyrus spp.) and their biosynthesis is controlled by multiple transcription factors. Although phytochrome-interacting factors (PIFs) of the bHLH family have been shown to regulate anthocyanin biosynthesis in Arabidopsis thaliana, their genome-wide identification and regulatory mechanisms in pear (Pyrus spp.) anthocyanin synthesis remain unclear. Here, we characterized PIFs family in pear, identifying eight PbPIF proteins. Promoter cis-elements and expression patterns analysis suggested that PbPIF3a and PbPIF4 might be involved in anthocyanin biosynthesis. Subcellular localization confirmed nuclear enrichment of PbPIF3a and PbPIF4. Functional studies demonstrated that overexpression of PbPIF3a and PbPIF4 significantly suppressed anthocyanin accumulation in fruit skins, downregulating key biosynthetic genes such as PbDFR and PbUFGT. In contrast, the silencing of related genes led to an enhancement of anthocyanin accumulation. Dual-luciferase reporter assays and yeast one-hybrid assays confirmed that PbPIF3a directly bound to the promoters of PbDFR and PbUFGT and repressed their transcriptional activation, while PbPIF4 specifically inhibited the activity of the PbDFR promoter. Taken together, we demonstrated that PbPIF3a and PbPIF4 negatively regulated pear fruit coloration by directly repressing the transcriptional activity of key anthocyanin biosynthesis genes, providing novel insights into PIF-mediated regulation of anthocyanin biosynthesis. Full article

This study focuses on the development and characterization of biodegradable polymer composites consisting of a polypropylene (PP) matrix, carbon black pigment, and hybrid fillers. The fillers incorporated into these composites consisted of a blend of fibers and particles derived from natural, biodegradable materials, such as flax fibers (FFs) and wood flour (WF) particles. The compositions of polymer material were expressed as PP/FF/WF weight ratios of 100/0/0, 70/5/25, and 70/10/20. The polymer materials were prepared using conventional plastic processing methods like extrusion to produce composite mixtures, followed by melt injection to manufacture the samples needed for characterization. The structural characterization of the polymer materials was conducted using optical microscopy and X-ray diffraction (XRD) analyses, while thermal, mechanical, and dielectric properties were also evaluated. Additionally, their biodegradation behavior under mold exposure was assessed over six months. The results were analyzed comparatively, and the optimal composition was identified as the polymer composite containing the highest flax fiber content, namely PP + 10 wt.% flax fiber + 20 wt.% wood flour. Full article

Salinity significantly impacts maize production globally, requiring a deeper understanding of maize response mechanisms to salt stress. This study assessed the response of two Egyptian maize hybrids, SC-10 and TWC-321, under salt stress (200 mM NaCl) and non-stressed conditions to identify traits and mechanisms linked to enhanced salinity tolerance. Both hybrids accumulated similar Na⁺ levels in leaves, but TWC-321 exhibited better ion regulation, with lower Na⁺ concentrations and Na⁺ to K⁺ ratio in roots. While SC-10 showed a reduction in leaf K⁺ levels, TWC-321 maintained stable K⁺ levels, highlighting its superior salinity tolerance. TWC-321 also demonstrated better oxidative stress management, as evidenced by lower malondialdehyde levels and significantly higher total chlorophyll content, relative water content, and stomatal conductance. Proline accumulation was more pronounced in TWC-321, and it showed higher antioxidant enzyme activities (SOD, CAT, and POD) compared to SC-10, which exhibited lower SOD and POD activities. Gene expression analysis demonstrated distinct responses to salt stress between the hybrids. Although zmHKT1;5 was similarly induced in both hybrids, TWC-321 exhibited higher expression levels of zmHKT2 (1.96-fold compared to 1.42-fold in SC-10) and upregulated zmNHX1 (1.92-fold), whereas zmNHX1 expression was slightly reduced in SC-10 (0.8-fold). Additionally, TWC-321 achieved a greater total dry weight than SC-10 under salinity stress, highlighting its superior performance and resilience. These findings indicate that enhanced Na⁺ exclusion and sequestration mechanisms mediate the salinity tolerance of TWC-321. Correlation analysis under salinity stress identified key indicators of salinity tolerance, including increased activity of CAT and SOD, elevated proline accumulation, and higher K⁺ content. Consequently, the salinity tolerance of TWC-321 can be attributed to its effective ion regulation, stable photosynthetic pigment levels, improved osmotic adjustment, enhanced water retention, and potent antioxidant defense system. These insights are highly valuable for breeding programs focused on developing salt-tolerant maize hybrids. Full article

Background: The dark green coloration of bunching onion leaf blades is a key determinant of market value, nutritional quality, and visual appeal. This trait is regulated by a complex network of pigment interactions, which not only determine coloration but also serve as critical indicators of plant growth dynamics and stress responses. This study aimed to elucidate the mechanisms regulating the dark green trait and develop a predictive model for accurately assessing pigment composition. These advancements enable the efficient selection of dark green varieties and facilitate the establishment of optimal growth environments through plant growth monitoring. Methods: Seven varieties and lines of heat-tolerant bunching onions were analyzed, including two commercial ${\mathrm{F}}_1$ cultivars, along with two purebred varieties and three ${\mathrm{F}}_1$ hybrid lines bred in Yamaguchi Prefecture. The analysis was conducted on visible spectral reflectance data (400–700 nm at 20 nm intervals) and pigment compounds (chlorophyll a, chlorophyll b and pheophytin a, lutein, and $\beta$-carotene), whereas primary and secondary metabolites were assessed by using widely targeted metabolomics. In addition, a random forest regression model was constructed by using spectral reflectance data and pigment compound contents. Results: Principal component analysis based on spectral reflectance data and the comparative profiling of 186 metabolites revealed characteristic metabolite accumulation associated with each green color pattern. The “green” group showed greater accumulation of sugars, the “gray green” group was characterized by the accumulation of phenolic compounds, and the “dark green” group exhibited accumulation of cyanidins. These metabolites are suggested to accumulate in response to environmental stress, and these differences are likely to influence green coloration traits. Furthermore, among the regression models for estimating pigment compound contents, the one for chlorophyll a content achieved high accuracy, with an $R^2$ value of 0.88 in the test dataset and 0.78 in Leave-One-Out Cross-Validation, demonstrating its potential for practical application in trait evaluation. However, since the regression model developed in this study is based on data obtained from greenhouse conditions, it is necessary to incorporate field trial results and reconstruct the model to enhance its adaptability. Conclusions: This study revealed that cyanidin is involved in the characteristics of dark green varieties. Additionally, it was demonstrated that chlorophyll a can be predicted using visible spectral reflectance. These findings suggest the potential for developing markers for the dark green trait, selecting high-pigment-accumulating varieties, and facilitating the simple real-time diagnosis of plant growth conditions and stress status, thereby enabling the establishment of optimal environmental conditions. Future studies will aim to elucidate the genetic factors regulating pigment accumulation, facilitating the breeding of dark green varieties with enhanced coloration traits for summer cultivation. Full article

This study investigated the phytochemical profiles and bioactivities of two edible boletes from Southwestern China, Phlebopus portentosus and Butyriboletus roseoflavus. A total of 33 secondary metabolites, comprising 15 alkaloids, 4 pulvinic acid derivative pigments, and 14 ergosterols, were isolated and identified. To our best knowledge, boletesine A (1), boletesine B (2), and cis-xerocomic acid (16) were previously undescribed compounds. The new structures were established by extensive spectroscopic methods and chemical calculations. Compound 1 features a hitherto unknown hybrid skeleton formed between a 2-formylpyrrole-alkaloid and a dopacetic acid (DOPAC) via a Michael addition reaction. Bioactivity assays revealed the neuroprotective effects of compounds 18 and 19 against Aβ_25–35- or H₂O₂-induced toxicity. In a cytotoxic assay against a small panel of cancer cell lines, compound 9 exhibited significant activity against HeLa cells (IC₅₀ = 10.76 µM), while 33 demonstrated broad-spectrum cytotoxicity against Hela229, SGC7901, PC-3, and BEL7402 cells (IC_50s in the range of 20~30 µM). Of particular note is the anti-influenza virus activities against A/H3N2 and B/Victoria strains of compounds 22 and 26 (EC₅₀ values ranging from 3.6 to 9.6 µM). Along with these, compound 29 showed a moderate antiviral effect against coxsackievirus B3. These findings underscore the therapeutic potential of the two edible boletes in addressing neurodegenerative diseases, cancer, and viral infections, paving the way for their prospective applications in the development of functional foods and pharmaceuticals. Full article

A Gram-negative aerobic, motile bacterium KMM 10153^T was isolated from bottom sediment sampled from the Sea of Japan at a depth of 256 m, Russia. Strain KMM 10153^T grew in 0–12% NaCl at temperatures ranging from 4 to 42 °C and produced brown diffusible pigments. Based on the 16S rRNA gene and whole genome sequences analyses, novel bacterium KMM 10153^T was affiliated with the genus Oceanisphaera (phylum Pseudomonadota) showing the highest 16S rRNA gene sequence similarities of 98.94% to Oceanisphaera arctica KCTC 23013^T, 98.15% to Oceanisphaera donghaensis BL1^T, and similarity values of <98% to other validly described Oceanisphaera species. The pairwise Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values between the novel strain KMM 10153^T and the three closest type strains Oceanishaera arctica KCTC 23013^T, Oceanisphaera litoralis DSM 15406^T and Oceanisphaera sediminis JCM 17329^T were 89.4%, 89.1%, 87.41%, and 90.7%, 89.8%, 89.7%, respectively. The values of digital DNA–DNA hybridization (dDDH) were below 39.3%. The size of the KMM 10153^T draft genome was 3,558,569 bp, and the GC content was 57.5%. The genome of KMM 10153^T harbors 343 unique genes with the most abundant functional classes consisting of transcription, mobilome, amino acid metabolism, and transport. Strain KMM 10153^T contained Q-8 as the predominant ubiquinone and C_16:1ω7c, C_16:0, and C_18:1ω7c as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidic acid. Based on the distinctive phenotypic characteristics and the results of phylogenetic and genomic analyses, the marine bacterium KMM 10153^T could be classified as a novel Oceanisphaera submarina sp. nov. The type strain of the species is strain KMM 10153^T (=KCTC 8836^T). Full article