Journal of Plant Biochemistry and Biotechnology最新文献

In this study, we present an innovative binning approach for metagenomics data that combines Natural Language Processing (NLP) with a Deep Contrastive Convolutional Autoencoder (DCAE). We used NLP for feature extraction, specifically focusing on Tetra-nucleotide frequency (TNF) through CountVec and (Term Frequency -Inverse Document Frequency) TF-IDF, further enriched by integrating GC-Content into their respective feature matrices. The DCAE, equipped with advanced convolutional layers and a contrastive loss function, excels at capturing intricate patterns in the data, providing a sophisticated representation for binning. By applying k-means clustering to the latent representations obtained from the DCAE, our approach consistently achieves impressive results. To assess the performance of our method, we utilized three standard benchmark metagenomics datasets: 10s, 25s, and Sharon datasets. Across all datasets, we observed Silhouette Indices exceeding 0.6 and Rand Indices surpassing 0.8, demonstrating the superior performance of our proposed method. Compared to existing methodologies, our approach not only surpasses the Rand Index and Silhouette Index of current unsupervised methods but also performs on par with semi-supervised methods across datasets. This underscores the effectiveness and versatility of our approach in metagenomics analysis.

Anemone plants (Ranunculaceae) are perennial, low-growing herbs that have a long history of traditional medicinal use. However, the phylogenetic relationship of Anemone species and the comprehensive study of the tribe Anemoneae have not been thoroughly examined due to the lack of available molecular resources. In this study, we conducted a comprehensive sequencing and characterization of the complete chloroplast genomes of Anemone species. These genomes exhibited typical quadripartite structures, ranging in length from 156,659 to 162,991 bp. We also identified several highly divergent intergenic regions (trnQ-UUG–psbK, trnfM-CAU–psbC, trnT-GGU–trnC-GCA, trnG-UCC–trnL-UAA, ndhC–trnM-CAU, psbE–petL, trnW-CCA–rpl33, rps12–trnV-GAC, and trnL-UAG–ndhF) and genes (rps16, ndhD, and ycf1) that could potentially serve as phylogenetic markers. We conducted phylogenetic analyses on 125 species from the tribe Anemoneae using chloroplast genome sequences. We obtained consistent topological structures and strong support for the backbone of phylogenetic relationships by employing maximum likelihood and Bayesian inference methods. Our findings suggest that Hepatica forms a monophyletic group, while Anemone s.l. is paraphyletic, based on the phylogenetic trees. Furthermore, the Hepatica + Anemone clade and the Anemoclema + Clematis clade exhibit a sister relationship. Overall, these results provide valuable genetic resources for the identification and phylogenetic studies of Anemone species.

Serine proteases have been receiving special attention from the industrial point of view, due to their thermo-stable properties and activity over wide ranges of pH. In the present investigation, a serine protease (49.3 kDa) from jackfruit latex has been purified using chromatographic techniques. Fold purification of the serine protease in the final purification step was 92.41 with 24% yield. The protease is completely inhibited by PMSF, a serine protease-specific inhibitor at a minimal concentration (100 µM). The purified serine protease was immobilized with sodium alginate (2.5%) and calcium chloride (0.3 M) solution. The kinetic studies of immobilized enzyme showed stable activity up to pH 7, and can withstand temperatures up to 45 °C. The immobilization process improves the catalytic efficiency of the enzyme over purified soluble enzyme (for K_cat 1.4 times and for K_cat/K_m 1.21 times). Our results depicted that alginate mediated immobilization of serine protease greatly improves the pH and temperature optima which broadens the scope of usage of the enzyme further.

Cytokinins (CKs) not only promote the growth of female flowers in industrial hemp but also serve as plant hormones that influence leaf development and regulate various genes, including transcription factors. The molecular mechanism of cytokinin response in industrial hemp leaves remains unclear. In this study, industrial hemp Longma 5 was utilized, with 60 mg·L^− 1 and 120 mg·L^− 1 of 6-BA sprayed at the three-leaf stage, followed by transcriptome sequencing at the mature stage. 3244 DEGs were identified in the Ctrl (control) vs. B60 (60 mg·L^− 1 6-BA treatment) group, including 1714 upregulated genes and 1530 downregulated genes; 7818 DEGs were identified in the Ctrl vs. B120 (120 mg·L^− 1 6-BA treatment) group, including 3772 upregulated genes and 4046 downregulated genes. Further analysis showed that these DEGs were primarily enriched in pathways associated with metabolism and energy, including photosynthesis, photosynthesis-antenna protein, and phenylpropanoid biosynthesis. The CTK, auxin, ABA, GA, ETH and JA signaling pathways displayed differential gene expression under 6-BA treatment. A total of 283 transcription factors were categorized into 16 families, suggesting that CKs could enhance the growth and metabolism of industrial hemp. This study lays the groundwork for further exploring the molecular mechanisms of the CTK effect on industrial hemp.

Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).

The fatty acid profiling in chickpea remains unexplored and offers relevant knowledge for crop improvement program. In the present work, the metabolite approach has been utilized with mass spectral analysis to metabolite changes in twelve varieties of kabuli as well as desi cultivars (twenty four totals) for fatty acid profiling. The total oil was extracted and found to be higher in all cultivars of kabuli chickpea (3.6–5.3%) as compared to all desi chickpea (3.2–4.6%) cultivars. However, no difference in the refractive indices of desi (1.4755–1.4773) and kabuli (1.4739–1.476) cultivars has been observed. Polyunsaturated fatty acids (PUFAs) were reported to be predominant (kabuli; 50–68.6%, desi; 61.5–72.5%) and monounsaturated (MUFA) (kabuli; 19.9–38.4%, desi; 16.7–26.4%) and saturated fatty acids (SFA) (kabuli; 11–14.9%, desi; 10–11.9%) were relatively low in the oil of all selected cultivars. Among fatty acids, linoleic acid (C18:2), followed by oleic acid (C18:1), was most prevalent in all selected chickpea cultivars. The volatile organic compounds, 9,12-octadecadienoic acid, 9-octadecenoic acid, and hexadecanoic acid have also been detected comparatively high. Similarly, oil contents also detected terpenoids including b-tocopherol, fucosterol, stigmasterol, and stigmata-5, 22-dien-3-ol. This work could offer comprehensive understanding of fatty acid composition in chickpea that could be used further for crop improvement to assess their nutritional importance in human diet and help to draft strategy for improving self-life during storage of flour of chickpea. This key insight of this work could be further harness to identify potential biochemical biomarkers for improving fatty acid content in chickpea seeds for crop improvement.

Antioxidant responses play a crucial role in combating free radical damage induced by drought stress. In guar plants, the antioxidant mechanism is crucial for stress tolerance; however, the specific antioxidant response in individual guar genotypes remains unclear. This study investigates the physiological, biochemical, and transcriptional responses of four guar genotypes to drought stress by maintaining soil moisture content (SMC) at varying levels: control (100% FC), medium (60% FC), and severe (20% FC). Among the genotypes examined, HG-563 and HG-365 exhibit higher leaf relative water content (RWC) and total chlorophyll/carotenoid content, indicating lesser inhibition under drought stress compared to HG-75 and RGC-936. Notably, HG-563 and HG-365 demonstrate a significant increase in activities of key antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), ascorbate (AsA), and glutathione (GSH) during medium and severe drought stress conditions. This observation is further supported by in-gel activity assays revealing a notable upregulation of Cu/ZnSOD and POD isozymes, which is consistent with higher expression levels of Cu/ZnSOD and POD genes at the transcriptional level. Consequently, these results highlight the comparatively higher drought tolerance of HG-563 and HG-365 genotypes. The findings shed light on the activation of antioxidant responses in drought-tolerant guar genotypes under stress conditions, emphasizing the crucial role of antioxidant enzymes in the drought tolerance mechanism of guar plants.

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This study investigated the activity and thermostability of α-amylase in green malt across a diverse panel of 54 barley genotypes, comprising 20 mutants, 19 hulled, 4 hulless, and 11 wild types, using starch as a substrate. The primary objective was to assess the variability in α-amylase activity among these genotypes and identify those with superior enzymatic activity and thermostability. Given that α-amylase is the most thermostable enzyme among the diastatic power enzymes yet exhibits significant activity reduction above 72.5 °C, a threshold frequently exceeded in industrial kilning and mashing. This research is therefore crucial for identifying genotypes that could enhance starch hydrolysis efficiency during mashing, a process critically dependent on sufficient enzymatic activity. We reported α-amylase activity and thermostability across a temperature range of 37 to 85 °C. The findings indicated that optimal temperature for α-amylase activity in barley malting lies between 65 and 75 °C. Interestingly, wild barley genotypes demonstrated the highest mean α-amylase activity, while hulless varieties exhibited the lowest. These results were validated by a significant negative correlation between α-amylase activity and the content of starch. Among the 54 genotypes, 11 displayed high α-amylase activity at 65 °C. Furthermore, one mutant (BL2105) and one wild genotype (WS230) exhibited high activity and thermostability at 75 °C, and another wild genotype (WS236) retained 30% of its original activity after heat treatment at 85 °C. These genotypes with enhanced α-amylase activity and thermostability could be strategically exploited in breeding programs to develop superior malt varieties. Such advancements could significantly enhance both malt quality and efficiency in beer production industry.

MADS-box genes play a vital role in the vegetative and reproductive growth of plants. In this study, a MiAGL1 gene was cloned and identified from mango (Mangifera indica L.). The DNA sequence of AGAMOUS-LIKE1 (MiAGL1) was 8741 bp in length, including a 723 bp open reading frame and encoding 241 amino acids. MiAGL1 belongs to the MADS-box family. This gene was expressed not only in vegetative tissues but also in floral organs, and the highest expression level was found in flowers. MiAGL1 was expressed in leaves at different floral developmental stages, but the peak appeared at the floral organ differentiation stage. MiAGL1 was present in the cell membrane and nucleus. Ectopic expression of MiAGL1 in Arabidopsis resulted in significant early flowering under long-day conditions. Overexpression of MiAGL1 resulted in abnormal flowering and silique morphology, such as a decrease or absence of petals, smaller petals, and shorter, bent or distorted capsules. The endogenous Arabidopsis thaliana flowering-related genes FT, AP1, and SEP were significantly upregulated, and AtSVP was downregulated in the transgenic lines. Therefore, our data showed that the MiAGL1 gene may play a crucial role in flowering time regulation and floral organ identity.

This study investigates the antimicrobial, antioxidant, and phytochemical properties of banana extracts from both ripe and unripe pulp and peel, using various solvents, including ethanol, methanol, hexane, and aqueous solutions. Antimicrobial test reveals the effectiveness of unripe pulp aqueous extract against Staphylococcus aureus, while the unripe pulp ethanol extract against Bacillus subtilis among gram-positive bacteria. For gram negative bacteria, unripe pulp ethanol extract was most effective against Acinetobacter baumannii, and unripe pulp aqueous extract against Pseudomonas aeruginosa. In antifungal tests, ethanol extract of ripe banana pulp (1.8 ± 0.081) and aqueous extract of unripe pulp (2.5 ± 0.081) show effectiveness against Fusarium oxysporum. However, for Alternaria alternata, the aqueous extract of unripe pulp (1.8 ± 0.081) and methanolic extracts showed stronger inhibition compared to other samples. Phytochemical analysis detected secondary metabolites, including saponins, terpenoids, tannins and phytosterols. The highest polyphenol content was found in the ethanol extract of unripe peel (1.35 ± 0.01 mg GAE/g), and the highest flavonoid content in unripe peel ethanol extract (1.358 ± 0.03 mg QE/g). In contrast, carotenoid levels showed variation among extracts with no direct correlation to fruit maturity. Gas Chromatography–Mass Spectrometry analysis identified 14 bioactive compounds that were found to be common among all the solvent extracts of banana samples. Furthermore, the study reveals a decrease in free radical scavenging capacity with fruit maturity and solvent choice. The study suggests that both the banana fruit pulp and peel can result in a valuable source of natural antimicrobial and antioxidant agents for potential health and medicine applications.