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Biology
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Young Investigators in Biochemistry and Molecular Biology
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Young Investigators in Biochemistry and Molecular Biology

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1530

Special Issue Editor

Dr. Wuqiang Zhu

E-Mail Website
Guest Editor
Mayo Clinic Arizona, Scottsdale, AZ 85259, USA
Interests: cardiomyocyte; cell cycle; regeneration; cardiotoxicity; nanoparticle
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In this Special Issue, we will feature early-career researchers in the field of biochemistry and molecular biology. The senior authors of the contributions should be a) the first or last author in addition to the corresponding author and b) either within 10 years of completing their PhD (or equivalent) or an assistant professor/on tenure track. We invite submissions from all sub-disciplines of biochemistry and molecular biology.

Articles submitted for this Special Issue should meet all the standard requirements of individual Biology articles (regarding quality, novelty, and significance) and be relevant to a broad international and interdisciplinary readership.

Authors featured in this Special Issue will have the opportunity to be nominated for next year's Young Investigator Award. They will receive a cash prize and subsequent free publication of an article in Biology. In addition, a few Article Processing Charge waivers are available for the best scholars who contribute to this Special Issue; waiver requests, accompanied by the manuscript title, author list and abstract, should be sent to biology@mdpi.com.

Dr. Wuqiang Zhu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein structure and function
  • DNA Methylation
  • apoptosis
  • computational biology
  • molecular development biology
  • molecular enzymology
  • molecular evolution
  • molecular immunology
  • molecular virology
  • systems biology
  • proteins and nucleic acids
  • protein trafficking
  • proteomics
  • structural and functional genomics
  • transcriptomics
  • signaling

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

18 pages, 3993 KiB  
Article
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 627
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)
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13 pages, 4655 KiB  
Article
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 225
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)
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12 pages, 854 KiB  
Article
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
Viewed by 277
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)
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