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Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants
The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.
Journal Article
عبارات \غامضة\ عن الصين : مقالات في الجغرافيا البشرية
هذا الكتاب هو الجزء الأول من سلسلة كتب \"الحكمة الصينية\" ويأتي تحت عنوان (عبارات \"غامضة\" عن الصين : مقالات في الجغرافيا البشرية)، وجمع بين دفتيه ما مجموعة أربعة عشر مصطلحا متعلقا بالجغرافيا البشرية، ومن بينها \"الأقاليم التسعة\"، \"العالم\"، \"النهر الأصفر\"، \"سور الصين العظيم\"، \"المدينة\"، \"و\"العاصمة\"، وغيرها، ويتمثل الغرض الرئيسي للكتاب في تعريف الأطفال بالجغرافيا الصينية التقليدية، وتعميم معارف الجغرافيا البشرية في نفس الوقت، وهو الأمر الذي يترك الأطفال يستكشفون المعنى الثقافي وراء المصطلحات والمفردات الشائعة.
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WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and indole-3-acetic acid-conjugating genes and by inhibiting ammonium efflux in the root elongation zone
• Ammonium (NH₄⁺) is toxic to root growth in most plants, even at moderate concentrations. Transcriptional regulation is one of the most important mechanisms in the response of plants to NH₄⁺ toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear.
• Here, RNA-seq analysis was performed on Arabidopsis roots to screen for ammonium-responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH₄⁺, was selected. We defined the role of WRKY46 using mutation and overexpression assays, and characterized the regulation of NUDX9 and indole-3-acetic acid (IAA)-conjugating genes by WRKY46 via yeast one-hybrid and electrophoretic mobility shift assays and chromatin immunoprecipitation-quantitative real-time polymerase chain reaction (ChIP-qPCR).
• Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH₄⁺-suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA-conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and to inhibit their transcription, thus positively regulating free IAA content and stabilizing protein N-glycosylation, leading to an inhibition of NH₄⁺ efflux in the root elongation zone (EZ).
• We identify TF involvement in the regulation of NH₄⁺ efflux in the EZ, and show that WRKY46 inhibits NH₄⁺ efflux by negative regulation of NUDX9 and IAA-conjugating genes.
Journal Article
Emerging prospects of macro- and microalgae as prebiotic
Macro- and microalgae-based foods are becoming popular due to their high nutritious value. The algal biomass is enriched with polysaccharides, protein, polyunsaturated fatty acids, carotenoids, vitamins and minerals. However, the most promising fraction is polysaccharides (PS) or their derivatives (as dietary fibers) which are not entirely fermented by colonic bacteria hence act as potential prebiotic. Primarily, algae become famous as prominent protein sources. Recently, these are widely adopted as functional food (e.g., desserts, dairy products, oil-derivatives, pastas etc.) or animal feed (for poultry, cattle, fish etc.). Besides prebiotic and balanced amino acids source, algae derived compounds implied as therapeutics due to comprising bioactive properties to elicit immunomodulatory, antioxidative, anticancerous, anticoagulant, hepato-protective, and antihypertensive responses. Despite the above potentials, broader research determinations are inevitable to explore these algal compounds until microalgae become a business reality for broader and specific applications in all health domains. However, scale up of algal bioprocess remains a major challenge until commercial affordability is accomplished which can be possible by discovering their hidden potentials and increasing their value and application prospects. This review provides an overview of the significance of algae consumption for several health benefits in humans and animals mainly as prebiotics, however their functional food and animal feed potential are briefly covered. Moreover, their potential to develop an algal-based food industry to meet the people's requirements not only as a sustainable food solution with several health benefits but also as therapeutics is inevitable.
Journal Article
An Overview of the Mechanisms through Which Plants Regulate ROS Homeostasis under Cadmium Stress
Cadmium (Cd2+) is a non-essential and highly toxic element to all organic life forms, including plants and humans. In response to Cd stress, plants have evolved multiple protective mechanisms, such as Cd2+ chelation, vesicle sequestration, the regulation of Cd2+ uptake, and enhanced antioxidant defenses. When Cd2+ accumulates in plants to a certain level, it triggers a burst of reactive oxygen species (ROS), leading to chlorosis, growth retardation, and potentially death. To counteract this, plants utilize a complex network of enzymatic and non-enzymatic antioxidant systems to manage ROS and protect cells from oxidative damage. This review systematically summarizes how various elements, including nitrogen, phosphorus, calcium, iron, and zinc, as well as phytohormones such as abscisic acid, auxin, brassinosteroids, and ethylene, and signaling molecules like nitric oxide, hydrogen peroxide, and hydrogen sulfide, regulate the antioxidant system under Cd stress. Furthermore, it explores the mechanisms by which exogenous regulators can enhance the antioxidant capacity and mitigate Cd toxicity.
Journal Article
Agro-Industrial Food Waste as a Low-Cost Substrate for Sustainable Production of Industrial Enzymes: A Critical Review
The grave environmental, social, and economic concerns over the unprecedented exploitation of non-renewable energy resources have drawn the attention of policy makers and research organizations towards the sustainable use of agro-industrial food and crop wastes. Enzymes are versatile biocatalysts with immense potential to transform the food industry and lignocellulosic biorefineries. Microbial enzymes offer cleaner and greener solutions to produce fine chemicals and compounds. The production of industrially important enzymes from abundantly present agro-industrial food waste offers economic solutions for the commercial production of value-added chemicals. The recent developments in biocatalytic systems are designed to either increase the catalytic capability of the commercial enzymes or create new enzymes with distinctive properties. The limitations of low catalytic efficiency and enzyme denaturation in ambient conditions can be mitigated by employing diverse and inexpensive immobilization carriers, such as agro-food based materials, biopolymers, and nanomaterials. Moreover, revolutionary protein engineering tools help in designing and constructing tailored enzymes with improved substrate specificity, catalytic activity, stability, and reaction product inhibition. This review discusses the recent developments in the production of essential industrial enzymes from agro-industrial food trash and the application of low-cost immobilization and enzyme engineering approaches for sustainable development.
Journal Article
Dual-energy CT–based deep learning radiomics can improve lymph node metastasis risk prediction for gastric cancer
ObjectivesTo build a dual-energy CT (DECT)–based deep learning radiomics nomogram for lymph node metastasis (LNM) prediction in gastric cancer.Materials and methodsPreoperative DECT images were retrospectively collected from 204 pathologically confirmed cases of gastric adenocarcinoma (mean age, 58 years; range, 28–81 years; 157 men [mean age, 60 years; range, 28–81 years] and 47 women [mean age, 54 years; range, 28–79 years]) between November 2011 and October 2018, They were divided into training (n = 136) and test (n = 68) sets. Radiomics features were extracted from monochromatic images at arterial phase (AP) and venous phase (VP). Clinical information, CT parameters, and follow-up data were collected. A radiomics nomogram for LNM prediction was built using deep learning approach and evaluated in test set using ROC analysis. Its prognostic performance was determined with Harrell’s concordance index (C-index) based on patients’ outcomes.ResultsThe dual-energy CT radiomics signature was associated with LNM in two sets (Mann-Whitney U test, p < 0.001) and an achieved area under the ROC curve (AUC) of 0.71 for AP and 0.76 for VP in test set. The nomogram incorporated the two radiomics signatures and CT-reported lymph node status exhibited AUCs of 0.84 in the training set and 0.82 in the test set. The C-indices of the nomogram for progression-free survival and overall survival prediction were 0.64 (p = 0.004) and 0.67 (p = 0.002).ConclusionThe DECT-based deep learning radiomics nomogram showed good performance in predicting LNM in gastric cancer. Furthermore, it was significantly associated with patients’ prognosis.Key Points• This study investigated the value of deep learning dual-energy CT–based radiomics in predicting lymph node metastasis in gastric cancer.• The dual-energy CT–based radiomics nomogram outweighed the single-energy model and the clinical model.• The nomogram also exhibited a significant prognostic ability for patient survival and enriched radiomics studies.
Journal Article
A cyclic peptide-based PROTAC induces intracellular degradation of palmitoyltransferase and potently decreases PD-L1 expression in human cervical cancer cells
IntroductionOur previous research has found that degradation of palmitoyltransferase in tumor cells using a linear peptide PROTAC leads to a significant decrease in PD-L1 expression in tumors. However, this degradation is not a sustained and efficient process. Therefore, we designed a cyclic peptide PROTAC to achieve this efficient anti-PD-L1 effect.MethodsWe designed and synthesized an improvement in linear peptide PROTAC targeting palmitoyltransferase DHHC3, and used disulfide bonds to stabilize the continuous N- and C-termini of the peptides to maintain their structure. Cellular and molecular biology techniques were used to test the effect of this cyclic peptide on PD-L1.ResultsIn human cervical cancer cells, our cyclic peptide PROTAC can significantly downregulate palmitoyl transferase DHHC3 and PD-L1 expressions. This targeted degradation effect is enhanced with increasing doses and treatment duration, with a DC50 value much lower than that of linear peptides. Additionally, flow cytometry analysis of fluorescence intensity shows an increase in the amount of cyclic peptide entering the cell membrane with prolonged treatment time and higher concentrations. The Cellular Thermal Shift Assay (CETSA) method used in this study indicates effective binding between our novel cyclic peptide and DHHC3 protein, leading to a change in the thermal stability of the latter. The degradation of PD-L1 can be effectively blocked by the proteasome inhibitor MG132. Results from clone formation experiments illustrate that our cyclic peptide can enhance the proliferative inhibition effect of cisplatin on the C33A cell line. Furthermore, in the T cell-C33A co-culture system, cyclic peptides target the degradation of PD-L1, thereby blocking the interaction between PD-L1 and PD-1, and promoting the secretion of IFN-γ and TNF-α in the co-culture system supernatant.ConclusionOur results demonstrate that a disulfide-bridged cyclic peptide PROTAC targeting palmitoyltransferase can provide a stable and improved anti-PD-L1 activity in human tumor cells.
Journal Article