Biology

Research

Jump to: Review

20 pages, 18498 KB

Open AccessArticle

Metabolomics and Transcriptomics Analyses Uncover the Potential of Flavonoids in Response to Saline–Alkali Stress in Codonopsis pilosula

by Jinhua Liu, Yongqing Wan, Xiaowei Sun, Wenting Su and Kaixia Li

Biology 2025, 14(12), 1759; https://doi.org/10.3390/biology14121759 - 9 Dec 2025

Abstract

Codonopsis pilosula (CP) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline–alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline–alkali stress response mechanism of CP’s flavonoids is unknown. This study [...] Read more.

Codonopsis pilosula (CP) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline–alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline–alkali stress response mechanism of CP’s flavonoids is unknown. This study carried out saline–alkali stress treatments in CP, collected samples from roots, stems, and leaves, and conducted physiological, biochemical, transcriptomic, and metabolomic tests. Phenotypic observations showed varying degrees of saline–alkali stress effects on different organs of CP. Physiological tests revealed inconsistent antioxidant indicator changes across organs. Transcriptomic and metabolomic analyses revealed that, compared to roots and stems, leaves contained the highest number of flavonoids, reaching up to 23, and harbored the most differentially expressed flavonoid-related genes, with up to 54; the roots treated with NaHCO₃ contained up to 14 types of differentially accumulated metabolites (DAMs) related to flavonoids, while the leaves treated with NaHCO₃ contained up to 20 types of differentially expressed flavonoid-related genes; additionally, flavonoid pathway genes, including CHS, CHI, and bHLH transcription factors, might have responded to saline–alkali stress by modulating the production of flavonoid compounds such as Cyanidin and Galangin. This study preliminarily elucidates the molecular mechanisms of flavonoid response to saline–alkali stress in CP, providing a theoretical basis for flavonoid exploitation, molecular breeding, and cultivation area expansion. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

12 pages, 1395 KB

Open AccessArticle

Possible Involvement of Leptin in Pathogenesis of Periodontal Disease

by Małgorzata Kozak, Agata Poniewierska-Baran, Michał Czerewaty, Karolina Łuczkowska, Małgorzata Mazurek-Mochol, Bogusław Machaliński and Andrzej Pawlik

Biology 2025, 14(10), 1454; https://doi.org/10.3390/biology14101454 - 20 Oct 2025

Viewed by 470

Abstract

Periodontitis is a chronic inflammatory condition of the periodontal tissues, ultimately leading to their destruction. The periodontal ligament is a key structure that not only secures the teeth within the alveolus but can also act as a source of numerous mediators involved in [...] Read more.

Periodontitis is a chronic inflammatory condition of the periodontal tissues, ultimately leading to their destruction. The periodontal ligament is a key structure that not only secures the teeth within the alveolus but can also act as a source of numerous mediators involved in the development of inflammation in periodontal tissues. The aim of this study was to investigate the effect of leptin on periodontal ligament cells and their secretion of selected pro-inflammatory mediators that may contribute to the pathogenesis of periodontal disease. The study was conducted on cultured periodontal ligament cells stimulated with leptin. The effect of leptin was assessed on the expression of selected cytokines implicated in the pathogenesis of periodontal disease (IL-1, IL-6, IL-8, IL-10, IL-17, IL-18, and tumour necrosis factor-alpha [TNF-α]) at the mRNA level, as well as on the protein concentrations of these cytokines in culture supernatants. Assessments were carried out after 12, 24, and 48 h of leptin stimulation. The results showed a statistically significant effect of leptin on IL-6 and IL-8 expression at both the mRNA and protein levels. For IL-1, a transient increase in mRNA expression and protein concentration was observed, persisting up to 24 h. A decrease in IL-10 mRNA expression was noted after 48 h of leptin stimulation, with no corresponding effect on IL-10 protein concentration. No significant effect of leptin was found on IL-17 or IL-18 protein concentrations in periodontal ligament cell cultures. These findings suggest that leptin may contribute to the pathogenesis of periodontitis by modulating the expression of certain pro-inflammatory cytokines in periodontal ligament cells. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

17 pages, 3988 KB

Open AccessArticle

NLRP3 Inflammasome Activation Restricts Viral Replication by Inducing Pyroptosis in Chicken HD11 Cells During Infectious Bronchitis Virus Infection

by Xiaoxiao Han, Xin Yang, Xingjing Yang, Tingting Liu and Wenjun He

Biology 2025, 14(8), 1049; https://doi.org/10.3390/biology14081049 - 14 Aug 2025

Viewed by 824

Abstract

IBV is a key pathogenic agent in poultry, causing significant respiratory and renal diseases. This study investigated NLRP3 inflammasome and pyroptosis involvement in IBV-infected chicken macrophage HD11 cells. IBV infection triggered a time-dependent increase in the release of IL-1β/IL-18, along with the upregulation [...] Read more.

IBV is a key pathogenic agent in poultry, causing significant respiratory and renal diseases. This study investigated NLRP3 inflammasome and pyroptosis involvement in IBV-infected chicken macrophage HD11 cells. IBV infection triggered a time-dependent increase in the release of IL-1β/IL-18, along with the upregulation of inflammasome-related genes. MCC950 treatment, an NLRP3 inhibitor, notably decreased inflammatory markers while enhancing viral replication, highlighting the NLRP3 inflammasome’s function in restricting viral proliferation and mediating immunopathology. Experiments with UV-inactivated IBV demonstrated that active viral replication was essential for inflammasome activation. Pyroptosis was confirmed in IBV-infected HD11 cells through increased LDH release, characteristic ultrastructural damage, and upregulation of pyroptosis-related genes. Additionally, transfection with the IBV nucleocapsid (N) gene alone induced inflammasome activation and pyroptosis, indicating that the N protein is a key viral factor in this process. Our study offers a new understanding of IBV pathogenesis mechanisms and indicates that targeting the NLRP3 inflammasome may serve as a therapeutic approach. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

13 pages, 1279 KB

Open AccessArticle

Transcriptome Sequencing-Based Analysis of Premature Fruiting in Amomum villosum Lour.

by Yating Zhu, Shuang Li, Hongyou Zhao, Qianxia Li, Yanfang Wang, Chunyong Yang, Ge Li, Yanqian Wang and Lixia Zhang

Biology 2025, 14(7), 883; https://doi.org/10.3390/biology14070883 - 18 Jul 2025

Viewed by 741

Abstract

Amomum villosum Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s [...] Read more.

Amomum villosum Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s sustainable development. Our research team observed a distinct premature fruiting phenomenon in A. villosum. We investigated the regulatory mechanisms underlying premature fruiting in A. villosum by identifying the key differentially expressed genes (DEGs) and metabolic pathways governing the premature fruiting (Precocious) and typical plants (CK) of the ‘Yunsha No.8’ cultivar. Transcriptomic sequencing (RNA-seq) and bioinformatic analyses were performed using the DNBSEQ^TM platform. The sequencing generated 29.0 gigabases (Gb) of clean data, and 115,965 unigenes were identified, with an average length of 1368 bp. Based on the sequencing results, 1545 DEGs were identified. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were annotated for these DEGs. This study identifies phytohormone signaling, carbohydrate and lipid metabolism, and polysaccharide degradation as critical pathways controlling premature fruiting in A. villosum. Six randomly selected DEGs were validated using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), and the results corroborated the transcriptome data, confirming their reliability. This study lays the foundation for the elucidation of the molecular mechanisms and metabolic pathways driving premature fruiting in A. villosum. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

18 pages, 3993 KB

Open AccessArticle

New Insights into the Geometry and Topology of DNA Replication Intermediates

by Victor Martínez, Edith Ruiz-Díaz, Delia Cardozo, Cristian Cappo, Christian E. Schaerer, Jorge Cebrián, Dora B. Krimer and María José Fernández-Nestosa

Biology 2025, 14(5), 478; https://doi.org/10.3390/biology14050478 - 26 Apr 2025

Viewed by 1742

Abstract

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present [...] Read more.

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present the first molecular dynamics simulations of partially replicated circular DNA molecules, with stalled replication forks at both early and late stages of DNA replication. These simulations allowed us to map the distribution of superhelical stress after deproteinization. We propose a five-component model that determines the linking number difference of replication intermediates. At a thermodynamic equilibrium, the contribution of these five components was correlated to the progress of the replication forks. Additionally, we identified four types of segment collision events in replication intermediates, characterized by their geometric properties, including chirality and topological sign. The distribution of these collision events between the early and late stages of DNA replication provides new insights into the coordinated function of topoisomerases, warranting further discussion. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Graphical abstract

13 pages, 4655 KB

Open AccessArticle

Cloning, Expression, and Bioinformatics Analysis of the AvFD1 Gene in Amomum villosum Lour

by Duo Wang, Yating Zhu, Shuang Li, Hongyou Zhao, Chongnan Wang, Qianxia Li, Yanfang Wang, Chunyong Yang, Ge Li, Yanqian Wang and Lixia Zhang

Biology 2025, 14(5), 457; https://doi.org/10.3390/biology14050457 - 24 Apr 2025

Viewed by 717

Abstract

As a perennial medicinal plant in the Zingiber genus, Amomum villosum Lour. faces agricultural challenges due to its prolonged vegetative and reproductive growth phases, which hinder efficient pollination and delay fruiting. To address this limitation, the present study aimed to identify the FD [...] Read more.

As a perennial medicinal plant in the Zingiber genus, Amomum villosum Lour. faces agricultural challenges due to its prolonged vegetative and reproductive growth phases, which hinder efficient pollination and delay fruiting. To address this limitation, the present study aimed to identify the FD gene involved in regulating flowering in A. villosum to provide a basis for research on the molecular mechanisms of early fruiting cultivars. Based on the differentially expressed gene AvFD1 obtained from the transcriptome database of early fruiting plants and controls, specific primers were designed for PCR to clone the full-length sequence of AvFD1. The characteristics of the cloned AvFD1 gene were analyzed using online bioinformatics software. The expression profiles of AvFD1 in various tissues and in 1- and 2-year bearing A. villosum varieties were investigated by quantitative real-time PCR. This study successfully cloned the FD1 gene sequence of A. villosum, marking the first reported characterization of this gene in the species. Tissue-specific expression analysis revealed significantly elevated AvFD1 expression levels in stolon tips and flower buds compared to tender leaves, suggesting its potential role as a positive regulator of flowering initiation. The obtained sequence establishes essential molecular data for subsequent functional validation of AvFD1 in A. villosum. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Graphical abstract

12 pages, 854 KB

Open AccessArticle

Effect of Adiponectin on the Expression of Selected Cytokines in Periodontal Ligament Cells

by Małgorzata Kozak, Agata Poniewierska-Baran, Michał Czerewaty, Karolina Łuczkowska, Krzysztof Safranow, Małgorzata Mazurek-Mochol, Bogusław Machaliński and Andrzej Pawlik

Biology 2025, 14(4), 321; https://doi.org/10.3390/biology14040321 - 21 Mar 2025

Cited by 2 | Viewed by 804

Abstract

Periodontitis is a disease caused by a bacterial infection that causes chronic inflammation. The pathogenesis of periodontitis is mediated by several mediators, including chemokines, cytokines, metalloproteinases, and adipokines. Adiponectin is an adipokine that influences several metabolic processes and numerous immunological processes. In this [...] Read more.

Periodontitis is a disease caused by a bacterial infection that causes chronic inflammation. The pathogenesis of periodontitis is mediated by several mediators, including chemokines, cytokines, metalloproteinases, and adipokines. Adiponectin is an adipokine that influences several metabolic processes and numerous immunological processes. In this study, we investigated the effect of adiponectin on the expression in the periodontal ligament of selected cytokines involved in the pathogenesis of periodontitis. Human periodontal ligament cells (hPDLCs) were stimulated with adiponectin and then analyzed for expression (TNF-α, IL-1, IL-6, IL-8, IL-10, IL-17, and IL-18) in cell cultures at the mRNA level and in supernatants at the protein level. The samples were analyzed after 12, 24, and 48 h of adiponectin stimulation. We found no significant effect of adipokine on TNF-α gene expression after 12, 24, and 48 h of stimulation. For IL-1, a statistically significant increase in IL-1 gene expression was found after 12 h of adiponectin stimulation, while the differences were not statistically significant after 24 and 48 h. Adiponectin caused a statistically significant increase in IL-6 gene expression after 12, 24, and 48 h of stimulation. Stimulating periodontal ligament cells with adiponectin significantly increased TNF-α, IL-6, and IL-8 protein levels in supernatants after 12, 24, and 48 h. The levels of IL-1 were statistically significantly increased after 12 and 24 h of adiponectin stimulation. There was no statistically significant effect of adiponectin on IL-10, IL-17, and IL-18 levels. The results of our study suggest that adiponectin may significantly increase the expression of selected cytokines in periodontal ligament cells. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

Review

Jump to: Research

18 pages, 538 KB

Open AccessReview

Critical Understanding of the Influence of Cellular Aging Biomarkers on Host–Parasite Relationships Serving as a Key Platform for Malaria Eradication

by Dorathy Olo Anzaku and Israel Sunmola Afolabi

Biology 2025, 14(10), 1458; https://doi.org/10.3390/biology14101458 - 21 Oct 2025

Viewed by 610

Abstract

Plasmodium parasites are the causative agents of malaria and can infect humans and other vertebrates, impacting socioeconomic development and causing significant health issues globally. Plasmodium falciparum causes the most severe type of infection, which can lead to chronic morbidity and other severe complications [...] Read more.

Plasmodium parasites are the causative agents of malaria and can infect humans and other vertebrates, impacting socioeconomic development and causing significant health issues globally. Plasmodium falciparum causes the most severe type of infection, which can lead to chronic morbidity and other severe complications like anemia and cerebral malaria. The onset of infection is marked by the injection of sporozoites into the skin through the bite of a female Anopheles mosquito. This triggers a cascade of reactions elicited both by the host immune system in response to infection and by the parasite in a bid to evade the host immune system, survive, and replicate. The dynamics of this host–parasite relationship have prompted extensive research in an attempt to understand and exploit it in the fight against malaria. Thus, understanding the temporal and spatial dimensions of adaptation in host–parasite relationships is critical for forecasting parasite evolution and spread within and between host populations. One such relationship is the complex interplay between malaria and cellular aging processes. Understanding this dynamic will provide novel insights into the pathophysiology of the disease. This comprehensive review takes us on that journey by providing an overview of the interaction between the Plasmodium parasite and its host and the interplay between infection mechanisms, host immune response, and parasite evasion strategies, narrowing it down to how it affects cellular aging biomarkers and how this can be explored as a platform in the fight against the disease. Full article

(This article belongs to the Special Issue Young Investigators in Biochemistry and Molecular Biology)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Young Investigators in Biochemistry and Molecular Biology

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (8 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI