Navneet Thakur, Vidhi Raturi, Aparna Sreeprakash
et al.
Abstract Background Temperature fluctuations beyond optimal limits such as heat or cold severely impair plant growth and productivity. Biostimulants are emerging as sustainable tools to enhance plant resilience under stress. Methyl salicylate (MeSA), a known defense modulator, holds promise as a biostimulant; however, its volatility and poor aqueous solubility limit its applications. To overcome these drawbacks, we have developed methyl-β-cyclodextrin (M-β-CD) based inclusion complex (IC) of MeSA. This study evaluated MeSA/M-β-CD-IC for improving temperature tolerance in Arabidopsis thaliana, offering a novel and environmentally compatible strategy for stress mitigation. Results Phase solubility analysis revealed that modified β-cyclodextrin (M-β-CD) enhanced MeSA solubility 4.41-fold, with a 1:1 inclusion stoichiometry. Spectroscopic, morphological and thermal analysis (FTIR, NMR, SEM and TGA) confirmed successful complexation and improved thermal stability. The in vitro release profile of MeSA/M-β-CD-IC indicated ~ 91% cumulative MeSA release at 120 min, validating enhanced aqueous release. Biologically, MeSA inhibited seed germination at ≥ 2.5 mM, whereas M-β-CD promoted germination at low concentrations. Notably, the MeSA/M-β-CD-IC alleviated MeSA-induced inhibition, enabling successful germination across all concentrations. Under cold and heat stress, plants treated with M-β-CD showed robust growth and biomass, while the MeSA/M-β-CD-IC treatment achieved intermediate yet significant protection compared with MeSA alone. Photosynthetic efficiency (Φmax, Fv/Fm, NPQ) and pigment contents were improved in IC-treated plants, reflecting enhanced photoprotection. Cold stress induced higher oxidative damage than heat, but MeSA/M-β-CD-IC markedly reduced reactive oxygen species and malondialdehyde accumulation. Molecularly, MeSA/M-β-CD-IC pre-priming enhanced the expression of cold-responsive (CBF, COR) and heat-responsive (HSFA, HSP) genes, along with major antioxidant genes (APX, CAT, GR, POD, SOD), indicating coordinated activation of stress signaling and tolerance pathways. Conclusions Encapsulation of MeSA within M-β-CD substantially improves its aqueous solubility and biological efficacy. The inclusion complex strengthens Arabidopsis tolerance to cold and heat through activation of antioxidant and thermoprotective mechanisms. This work highlights cyclodextrin-based encapsulation as a sustainable, scalable approach for delivering volatile biostimulants to enhance crop resilience under climate stress. Graphical abstract
Mohamed Awad Abd Allah, Ghada Khiralla, Hesham Elhariry
Abstract Refrigerated and frozen ready-to-eat cooked vegetables are becoming increasingly popular with consumers and catering services. Simulating digestion is essential for accurately assessing the nutritional value of ready-to-eat vegetables, as raw composition data alone may overestimate their health benefits. Therefore, this study evaluated the bioaccessibility of bioactive compounds in broccoli after heat treatment, storage, and in vitro gastrointestinal digestion. Fresh broccoli (FB) and heat-treated (boiled or steamed) broccoli were subjected to refrigerated (RBB, RSB) or frozen (FBB, FSB) storage. FB exhibited high phenol (610 mg GAE/100 g) and flavonoid (295 mg QE/100 g) contents. Thermal treatment significantly decreased the phenolic content to 503, 515, 368, and 393 mg GAE/100 g in RBB, RSB, FBB, and FSB, respectively. Total phenols, flavonoids, vitamin C, antioxidant capacity, dietary fibers, and phenolic profiles were analyzed before and after in vitro gastrointestinal digestion. After in vitro gastrointestinal digestion, phenol, flavonoid, and vitamin C contents decreased significantly compared to those after digestion with FB (DFB). No significant changes in total, soluble (SDF), or insoluble (IDF) dietary fiber were observed between heat-treated broccoli and FBs. However, in vitro, gastrointestinal digestion of FB decreased SDF from 1.84 to 1.59% and increased IDF from 1.02 to 1.3%. HPLC analysis revealed substantial phenolic compound losses after in vitro gastrointestinal digestion, ranging from 64.9% in DFB to 88% in DFBB. After digestion, the recovery of bioactive compounds decreased, particularly for vitamin C and phenolics. These findings emphasize the importance of simulating digestion when evaluating the nutritional value of processed vegetables, as relying solely on raw composition data may overestimate health-promoting compound intake. Therefore, dietary recommendations should consider cooking methods and the loss of bioactive substances during digestion. Further research is needed to gain deeper insights into the bioaccessibility of antioxidant compounds after the digestion of cooked and preserved vegetables.
Nevin Belder, Sulgun Charyyeva, Edibe Ece Abaci Oruc
et al.
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide, necessitating accurate and robust predictive approaches to assist oncologists with prognosis prediction and therapeutic decision-making in clinical practice. Here, we aimed to identify key genes involved in colorectal cancer pathology and develop a model for prognosis prediction and guide therapeutic decisions in CRC patients. We profiled 49 matched tumour and normal formalin-fixed paraffin-embedded (FFPE) samples using Affymetrix HGU133-X3P arrays and identified 845 differentially expressed genes (FDR ≤ 0.001, fold change ≥2), predominantly enriched in the extracellular matrix (ECM)-receptor interaction pathway. The integrative analysis of our data with publicly available mRNA and miRNA datasets, including their differentially expressed gene analyses, identified four overexpressed genes in the ECM-receptor interaction pathway as key regulators of human CRC development and progression. These four genes were independently validated for their differential expression and association with prognosis in a newly collected CRC cohort and publicly available datasets. A prognostic risk score was developed using these genes, with patient stages weighted by multivariate Cox regression coefficients to stratify patients into low-risk and high-risk groups, showing significantly poorer overall survival (OS) in the high-risk group. In conclusion, our risk assessment model exhibits strong potential for predicting poor survival and unfavorable clinicopathological features in CRC patients, offering valuable insights for personalised management strategies.
Previous studies showed that interplay between liver and adipose tissue was important for animals to adapt to high-fat diets (HFDs). While the mechanisms of adaptation to HFD are not fully understood in fish, we hypothesize that interaction between these key tissues will be crucial. The present study evaluated the physiological and biochemical characteristics and gene expression profiles of hepatopancreas and adipose tissue of Nile tilapia (Oreochromus niloticus; initial weight, 20.01 ± 0.01 g) fed diets containing either 6% lipid (normal-fat diet [NFD]) or 12% lipid (HFD) for up to 10 weeks. While growth was not affected, serum and hepatopancreatic lipid contents increased significantly in tilapia fed HFD compared to fish fed NFD at 6 weeks (p <0.05). In addition, feeding HFD for 6 weeks induced hepatopancreatic injury as shown by increased alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities in serum and higher expression of genes related to inflammation (tnfβ and il-1β) and malondialdehyde (MDA) content in hepatopancreas (p <0.05). However, after feeding HFD for 10 weeks, serum and hepatopancreatic lipid contents and injury indices decreased, whereas mesenteric fat index (MFI) and expression of genes related to glucose (GLU) metabolism (pfk, g6pd, and glut2) in hepatopancreas increased significantly compared to the NFD group (p <0.05). Significant expansion of mesenteric adipose tissue was observed in tilapia fed HFD, due mainly to adipocyte hypertrophy at 6 and 8 weeks and hyperplasia at 10 weeks. With the expansion of mesenteric adipose tissue, the expression of genes related to lipid metabolism and inflammation increased at 8 weeks, but decreased at 10 weeks. The data indicated that excess dietary lipid accumulated initially in hepatopancreas of tilapia consuming HFD, but prolonged intake promoted mesenteric adipose tissue development, potentially mitigating hepatopancreas damage caused by excess lipid deposition. Additionally, enhanced hepatopancreatic glycolysis may contribute to the adaptation of tilapia to HFD intake.
Tagreed Al-Subhi, Muhammad Yasir, Samar A. Badreddine
et al.
Background: The microbiome of the respiratory system functions as a gatekeeper of respiratory health and is influenced by respiratory diseases. The aim of this study was to identify changes in the respiratory bacterial community composition associated with respiratory infections and to explore their relationship with specific bacterial pathogens in the Saudi Arabian population. Methods: Nasopharyngeal samples were screened from 73 individuals, including 34 symptomatic respiratory tract infection patients, 10 asymptomatic participants, and 29 healthy controls. Respiratory pathogens were detected using real-time PCR, and the microbiota were characterized through 16S rRNA gene amplicon sequencing. Results: Alpha diversity analysis revealed a slight decrease in bacterial richness in patients and asymptomatic individuals compared to healthy controls. In beta diversity analysis, healthy controls clustered together, while most symptomatic patients clustered separately. Actinobacteria, known for maintaining microbial homeostasis and preventing pathogenic colonization, were abundant in asymptomatic and healthy controls (> 30 %) but were substantially reduced to < 20 % relative abundance in symptomatic patients. Several bacterial genera, including Abiotrophia, Capnocytophaga, Megasphaera, Campylobacter, Peptostreptococcus, Veillonella, Streptococcus, and Bulleidia, were positively correlated with respiratory infections. Corynebacterium, Dolosigranulum, and Lawsonella were more abundantly found in healthy and asymptomatic individuals. Patients harboring Streptococcus pneumoniae or methicillin-resistant Staphylococcus aureus (MRSA) exhibited distinct bacterial profiles. Genera such as Staphylococcus, Pseudomonas, and Peptoniphilus were correlated with MRSA infection, while samples positive for S. pneumoniae exhibited a relatively higher abundance of Neisseria and Prevotella. Notably, a substantial number of symptomatic patients tested negative for any of the screened pathogens by real-time PCR but still showed alterations in bacterial community composition. Conclusions: Specific bacterial taxa showed significant differences between healthy controls and symptomatically infected patients, suggesting that bacterial community structures and groups of taxa, rather than individual bacterial taxa, may play a role in regulating respiratory infections.
Infectious and parasitic diseases, Public aspects of medicine
Abstract Background Loss of the transcription factor GLI-Similar 3 (GLIS3) function causes congenital hypothyroidism (CH) in both humans and mice due to decreased expression of several thyroid hormone (TH) biosynthetic genes in thyroid follicular cells. Whether and to what extent, GLIS3 regulates thyroid gene transcription in coordination with other thyroid transcriptional factors (TFs), such as PAX8, NKX2.1 and FOXE1, is poorly understood. Methods PAX8, NKX2.1, and FOXE1 ChIP-Seq analysis with mouse thyroid glands and rat thyrocyte PCCl3 cells was performed and compared to that of GLIS3 to analyze the co-regulation of gene transcription in thyroid follicular cells by these TFs. Results Analysis of the PAX8, NKX2.1, and FOXE1 cistromes identified extensive overlaps between these TF binding loci and those of GLIS3 indicating that GLIS3 shares many of the same regulatory regions with PAX8, NKX2.1, and FOXE1, particularly in genes associated with TH biosynthesis, induced by thyroid stimulating hormone (TSH), and suppressed in Glis3KO thyroid glands, including Slc5a5 (Nis), Slc26a4, Cdh16, and Adm2. ChIP-QPCR analysis showed that loss of GLIS3 did not significantly affect PAX8 or NKX2.1 binding and did not cause major alterations in H3K4me3 and H3K27me3 epigenetic signals. Conclusions Our study indicates that GLIS3 regulates transcription of TH biosynthetic and TSH-inducible genes in thyroid follicular cells in coordination with PAX8, NKX2.1, and FOXE1 by binding within the same regulatory hub. GLIS3 does not cause major changes in chromatin structure at these common regulatory regions. GLIS3 may induce transcriptional activation by enhancing the interaction of these regulatory regions with other enhancers and/or RNA Polymerase II (Pol II) complexes.
Plants are a natural source of phytochemicals, many of which have favorable bioactive properties for human health and are therefore used in ethnomedicine for preventing and treating a variety of diseases [...]
Yashpal Ramakrishnaiah, Adam P. Morris, Jasbir Dhaliwal
et al.
Long non-coding RNAs (lncRNAs), comprising a significant portion of the human transcriptome, serve as vital regulators of cellular processes and potential disease biomarkers. However, the function of most lncRNAs remains unknown, and furthermore, existing approaches have focused on gene-level investigation. Our work emphasizes the importance of transcript-level annotation to uncover the roles of specific transcript isoforms. We propose that understanding the mechanisms of lncRNA in pathological processes requires solving their structural motifs and interactomes. A complete lncRNA annotation first involves discriminating them from their coding counterparts and then predicting their functional motifs and target bio-molecules. Current in silico methods mainly perform primary-sequence-based discrimination using a reference model, limiting their comprehensiveness and generalizability. We demonstrate that integrating secondary structure and interactome information, in addition to using transcript sequence, enables a comprehensive functional annotation. Annotating lncRNA for newly sequenced species is challenging due to inconsistencies in functional annotations, specialized computational techniques, limited accessibility to source code, and the shortcomings of reference-based methods for cross-species predictions. To address these challenges, we developed a pipeline for identifying and annotating transcript sequences at the isoform level. We demonstrate the effectiveness of the pipeline by comprehensively annotating the lncRNA associated with two specific disease groups. The source code of our pipeline is available under the MIT licensefor local use by researchers to make new predictions using the pre-trained models or to re-train models on new sequence datasets. Non-technical users can access the pipeline through a web server setup.
Daniela Lazaro-Pacheco, Mina Mohseni, Samuel Rudd
et al.
Low back pain is the leading cause of disability, producing a substantial socio-economic burden on healthcare systems worldwide. Intervertebral disc (IVD) degeneration is a primary cause of lower back pain, and while regenerative therapies aimed at full functional recovery of the disc have been developed in recent years, no commercially available, approved devices or therapies for the regeneration of the IVD currently exist. In the development of these new approaches, numerous models for mechanical stimulation and preclinical assessment, including in vitro cell studies using microfluidics, ex vivo organ studies coupled with bioreactors and mechanical testing rigs, and in vivo testing in a variety of large and small animals, have emerged. These approaches have provided different capabilities, certainly improving the preclinical evaluation of these regenerative therapies, but challenges within the research environment, and compromises relating to non-representative mechanical stimulation and unrealistic test conditions, remain to be resolved. In this review, insights into the ideal characteristics of a disc model for the testing of IVD regenerative approaches are first assessed. Key learnings from in vivo, ex vivo, and in vitro IVD models under mechanical loading stimulation to date are presented alongside the merits and limitations of each model based on the physiological resemblance to the human IVD environment (biological and mechanical) as well as the possible feedback and output measurements for each approach. When moving from simplified in vitro models to ex vivo and in vivo approaches, the complexity increases resulting in less controllable models but providing a better representation of the physiological environment. Although cost, time, and ethical constraints are dependent on each approach, they escalate with the model complexity. These constraints are discussed and weighted as part of the characteristics of each model.
Ioannis A. Tsolakis, Isidora Christopoulou, Erofili Papadopoulou
et al.
Background: Biotechnology shows a promising future in bridging the gap between biomedical basic sciences and clinical craniofacial practice. The purpose of the present review is to investigate the applications of biotechnology in the craniofacial complex. Methods: This critical review was conducted by using the following keywords in the search strategy: “biotechnology”, “bioengineering”, “craniofacial”, “stem cells”, “scaffolds”, “biomarkers”, and ”tissue regeneration”. The databases used for the electronic search were the Cochrane Library, Medline (PubMed), and Scopus. The search was conducted for studies published before June 2022. Results: The applications of biotechnology are numerous and provide clinicians with the great benefit of understanding the etiology of dentofacial deformities, as well as treating the defected areas. Research has been focused on craniofacial tissue regeneration with the use of stem cells and scaffolds, as well as in bioinformatics with the investigation of growth factors and biomarkers capable of providing evidence for craniofacial growth and development. This review presents the biotechnological opportunities in the fields related to the craniofacial complex and attempts to answer a series of questions that may be of interest to the reader. Conclusions: Biotechnology seems to offer a bright future ahead, improving and modernizing the clinical management of cranio-dento-facial diseases. Extensive research is needed as human studies on this subject are few and have controversial results.
Zhong-Yuan Lyu, Zhong-Yuan Lyu, Qing-Ting Bu
et al.
Daptomycin is a cyclic lipopeptide antibiotic with a significant antibacterial action against antibiotic-resistant Gram-positive bacteria. Despite numerous attempts to enhance daptomycin yield throughout the years, the production remains unsatisfactory. This study reports the application of multilevel metabolic engineering strategies in Streptomyces roseosporus to reconstruct high-quality daptomycin overproducing strain L2797-VHb, including precursor engineering (i.e., refactoring kynurenine pathway), regulatory pathway reconstruction (i.e., knocking out negative regulatory genes arpA and phaR), byproduct engineering (i.e., removing pigment), multicopy biosynthetic gene cluster (BGC), and fermentation process engineering (i.e., enhancing O2 supply). The daptomycin titer of L2797-VHb arrived at 113 mg/l with 565% higher comparing the starting strain L2790 (17 mg/l) in shake flasks and was further increased to 786 mg/l in 15 L fermenter. This multilevel metabolic engineering method not only effectively increases daptomycin production, but can also be applied to enhance antibiotic production in other industrial strains.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current global COVID-19 pandemic, in which millions of lives have been lost. Understanding the zoonotic evolution of the coronavirus may provide insights for developing effective vaccines, monitoring the transmission trends, and preventing new zoonotic infections. Homopolymeric nucleotide repeats (HP), the most simple tandem repeats, are a ubiquitous feature of eukaryotic genomes. Yet the HP distributions and roles in coronavirus genome evolution are poorly investigated. In this study, we characterize the HP distributions and trends in the genomes of bat and human coronaviruses and SARS-CoV-2 variants. The results show that the SARS-CoV-2 genome is abundant in HPs, and has augmented HP contents during evolution. Especially, the disparity of HP poly-(A/T) and ploy-(C/G) of coronaviruses increases during the evolution in human hosts. The disparity of HP poly-(A/T) and ploy-(C/G) is correlated to host adaptation and the virulence level of the coronaviruses. Therefore, we propose that the HP disparity can be a quantitative measure for the zoonotic evolution levels of coronaviruses. Peculiarly, the HP disparity measure infers that SARS-CoV-2 Omicron variants have a high disparity of HP poly-(A/T) and ploy-(C/G), suggesting a high adaption to the human hosts.
Stefania Momi, Jessica Canino, Mauro Vismara
et al.
Deep vein thrombosis results from the cooperative action of leukocytes, platelets, and endothelial cells. The proline-rich tyrosine kinase Pyk2 regulates platelet activation and supports arterial thrombosis. In this study, we combined pharmacological and genetic approaches to unravel the role of Pyk2 in venous thrombosis. We found that mice lacking Pyk2 almost completely failed to develop deep venous thrombi upon partial ligation of the inferior vena cava. Pyk2-deficient platelets displayed impaired exposure of phosphatidylserine and tissue factor expression by endothelial cells and monocytes was completely prevented by inhibition of Pyk2. In human umbilical vein endothelial cells (HUVEC), inhibition of Pyk2 hampered IL-1b-induced expression of VCAM and P-selectin, and von Willebrand factor release. Pyk2-deficient platelets showed defective adhesion on von Willebrand factor and reduced ability to bind activated HUVEC under flow. Moreover, inhibition of Pyk2 in HUVEC strongly reduced platelet adhesion. Similarly, Pyk2-deficient neutrophils were unable to efficiently roll and adhere to immobilized endothelial cells under venous flow conditions. Moreover, platelets and neutrophils from Pyk2- knockout mice showed defective ability to form heterogeneous aggregates upon stimulation, while platelet monocyte interaction occurred normally. Consequently, platelet neutrophil aggregates, abundant in blood of wild-type mice upon inferior vena cava ligation, were virtually undetectable in Pyk2-knockout mice. Finally, we found that expression of Pyk2 was required for NETosis induced by activated platelets. Altogether our results demonstrate a critical role of Pyk2 in the regulation of the coordinated thromboinflammatory responses of endothelial cells, leukocytes and platelets leading to venous thrombosis. Pyk2 may represent a novel promising target in the treatment of deep vein thrombosis.
Ling Li,1,2,* Yaoyao Du,1,* Yang Wang,3 Ning He,2 Bing Wang,1,4 Tong Zhang1 1School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China; 2School of Pharmacy, Anhui University of Chinese Medicine, Hefei, People’s Republic of China; 3Metabo-Profile Biotechnology (Shanghai) Co. Ltd, Shanghai, People’s Republic of China; 4Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Shanghai, People’s Republic of China*These authors contributed equally to this workCorrespondence: Bing Wang; Tong Zhang, Email bwang@simm.ac.cn; zhangtdmj@hotmail.comBackground: Gastric ulcer (GU) is the most common multifactor gastrointestinal disorder affecting millions of people worldwide. There is evidence that gut microbiota is closely related to the development of GU. Atractylone (ATR) has been reported to possess potential biological activities, but research on ATR alleviating GU injury is unprecedented.Methods: Helicobacter pylori (H. pylori)-induced GU model in zebrafish and ethanol-induced acute GU model in rat were established to evaluate the anti-inflammatory and ulcer inhibitory effects of ATR. Then, 16S rRNA sequencing and metabolomics analysis were performed to investigate the effect of ATR on the microbiota and metabolites in rat feces and their correlation.Results: Therapeutically, ATR inhibited H. pylori-induced gastric mucosal injury in zebrafish. In the ulceration model of rat, ATR mitigated the gastric lesions damage caused by ethanol, decreased the ulcer area, and reduced the production of inflammatory factors. Additionally, ATR alleviated the gastric oxidative stress injury by increasing the activity of superoxide dismutase (SOD) and decreasing the level of malondialdehyde (MDA). Furthermore, ATR played a positive role in relieving ulcer through reshaping gut microbiota composition including Parabacteroides and Bacteroides and regulating the levels of metabolites including amino acids, short-chain fatty acids (SCFAs), and bile acids.Conclusion: Our work sheded light on the mechanism of ATR treating GU from the perspective of the gut microbiota and explored the correlation between gut microbiota, metabolites, and host phenotype.Keywords: atractylone, gastric ulcer, inflammation, oxidative stress, gut microbiota, metabolomics