Biology

11 pages, 1895 KiB

Open AccessArticle

Comparison of Adenine-Induced Rat Models for Vascular Calcification in Chronic Kidney Disease

by Ho Won Kang, Ji Hye Kim, A Ro Yoon, Jahyung Kim, Joonhee Kim, Min Gyu Kyung and Dong Yeon Lee

Biology 2025, 14(7), 814; https://doi.org/10.3390/biology14070814 (registering DOI) - 4 Jul 2025

Abstract

Vascular calcification significantly contributes to cardiovascular complications and limb loss in chronic kidney disease (CKD). To establish an optimal rat model for vascular calcification, we tested varying adenine concentrations and feeding durations in Sprague–Dawley rats (n = 72), divided into six groups (n [...] Read more.

Vascular calcification significantly contributes to cardiovascular complications and limb loss in chronic kidney disease (CKD). To establish an optimal rat model for vascular calcification, we tested varying adenine concentrations and feeding durations in Sprague–Dawley rats (n = 72), divided into six groups (n = 12 each). The control group received a standard diet for 18 weeks. Group 1 was given 0.5% adenine for 4 weeks, followed by a standard diet. Group 2 received 0.5% adenine for 4 weeks, then 0.25% for 14 weeks. Group 3A received 0.5% adenine for 12 weeks and then standard diet; group 3B received 0.5% adenine for 12 weeks, followed by 0.25% for 6 weeks; group 3C received 0.5% adenine for 18 weeks. At week 18, vascular calcification was absent in the control and group 1. Groups 2 and 3A showed low incidence (12.5%), while groups 3B and 3C showed high incidence (66.7%). However, survival rates differed: 75.0% in 3B and 50.0% in 3C after 12 wk. Thus, 0.5% adenine for 12 weeks followed by 0.25% for 6 weeks effectively induced vascular calcification while maintaining acceptable survival, providing a practical model for studying CKD-related vascular pathology. Full article

(This article belongs to the Section Medical Biology)

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15 pages, 1244 KiB

Open AccessArticle

ScnR1-Mediated Competitive DNA Binding and Feedback Inhibition Regulate Guvermectin Biosynthesis in Streptomyces caniferus

by Haoran Shi, Jiabin Wang, Xuedong Zhang, Na Zhou, Xiangjing Wang, Wensheng Xiang, Shanshan Li and Yanyan Zhang

Biology 2025, 14(7), 813; https://doi.org/10.3390/biology14070813 (registering DOI) - 4 Jul 2025

Abstract

Guvermectin, a Streptomyces-derived purine nucleoside compound, exhibits dual bioactivities as a plant growth regulator and an antibacterial agent. While its biosynthetic gene cluster (BGC) is regulated by the cluster-situated activator GvmR and the adjacent repressor GvmR2, the role of distal transcriptional regulators [...] Read more.

Guvermectin, a Streptomyces-derived purine nucleoside compound, exhibits dual bioactivities as a plant growth regulator and an antibacterial agent. While its biosynthetic gene cluster (BGC) is regulated by the cluster-situated activator GvmR and the adjacent repressor GvmR2, the role of distal transcriptional regulators (TRs) in guvermectin biosynthesis remains unexplored. Here, we identified ScnR1, a highly conserved LacI-family TR located far from the guvermectin BGC, which is directly activated by GvmR. Overexpression of scnR1 significantly suppressed guvermectin biosynthesis. Further investigations revealed that ScnR1 competitively binds to the gvmR, gvmA, and O1 promoters (overlapping with the GvmR-binding sites), thereby inhibiting the guvermectin BGC transcription. Moreover, ScnR1 formed a reciprocal feedback loop with the adjacent repressor GvmR2, where each repressor inhibits the other’s expression. These findings reveal a multi-layered regulatory mechanism wherein LacI-family TRs fine-tune guvermectin biosynthesis through competitive DNA binding and reciprocal feedback control. This study offers new perspectives on the hierarchical control of secondary metabolism in Streptomyces and provides valuable theoretical guidance for the engineering of strains with enhanced natural product production. Full article

(This article belongs to the Section Microbiology)

29 pages, 4734 KiB

Open AccessReview

The Cytochrome CYP4 in Breast and Other Cancers

by Gloria M. Calaf, Leodan A. Crispin, Felipe Ossandon-Acosta, Summer Perez-Tapia and Luis N. Ardiles

Biology 2025, 14(7), 812; https://doi.org/10.3390/biology14070812 (registering DOI) - 4 Jul 2025

Abstract

Breast cancer has emerged as the leading cause of death among females worldwide. The CYPs play a crucial role in carcinogenesis. The role of the CYP enzyme family, particularly the CYP4 family, in cancer biology has attracted significant attention in recent years. Bioinformatics [...] Read more.

Breast cancer has emerged as the leading cause of death among females worldwide. The CYPs play a crucial role in carcinogenesis. The role of the CYP enzyme family, particularly the CYP4 family, in cancer biology has attracted significant attention in recent years. Bioinformatics indicated that breast cancer is influenced by genes like CYP4B1, CYP4F12, and CYP4F3. CYP4B1 has a non-significant correlation with BRCA1 and BRCA2, but a positive correlation with ESR1 in the basal subtype. CYP4F12 has a significant positive correlation with BRCA1 in the Luminal B subtype, but not with BRCA2, and a positive correlation with ESR1 in the basal subtype. CYP4F3 has a significant positive correlation with BRCA1 in the Luminal A and Luminal B subtypes and with BRCA2 in Her2, Luminal A, and Luminal B subtypes, and a positive correlation with ESR1 in the basal subtype and Luminal B patients. This article aims to emphasize the functional importance of CYP4, highlighting the complex interplay between CYP enzymes and estrogen receptors in breast cancer, and indicating new avenues for future research and potential therapeutic interventions. In addition, their expression profiles and alterations were examined across various organs and cancer types. These findings underscore the potential relevance of these genes as predictive biomarkers and prospective therapeutic targets in specific cancer settings. Full article

(This article belongs to the Section Cancer Biology)

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20 pages, 5864 KiB

Open AccessArticle

Immune Dysregulation and Trophoblastic Dysfunction as a Potential Cause of Idiopathic Recurrent Pregnancy Loss

by Sara Vasconcelos, Ana Costa Braga, Ioannis Moustakas, Bruno Cavadas, Mariana Santos, Carla Caniçais, Carla Ramalho, Susana M. Chuva de Sousa Lopes, Cristina Joana Marques and Sofia Dória

Biology 2025, 14(7), 811; https://doi.org/10.3390/biology14070811 (registering DOI) - 4 Jul 2025

Abstract

Recurrent pregnancy loss (RPL) is a multifactorial condition affecting 1–5% of couples, often with unclear etiology. Idiopathic pregnancy losses (iPLs) are particularly challenging due to unknown molecular mechanisms. This study investigates the transcriptomic profiles of first-trimester products of conception (POC) from iPLs to [...] Read more.

Recurrent pregnancy loss (RPL) is a multifactorial condition affecting 1–5% of couples, often with unclear etiology. Idiopathic pregnancy losses (iPLs) are particularly challenging due to unknown molecular mechanisms. This study investigates the transcriptomic profiles of first-trimester products of conception (POC) from iPLs to uncover underlying molecular pathways. We performed RNA-sequencing on nine POC samples, identifying two distinct clusters enriched in trophoblast and decidual cells. Deconvolution analysis revealed reduced syncytiotrophoblast (STB) cells, with increased cytotrophoblast (CTB) and extravillous trophoblast (EVT) cells in iPLs. Gene Set Enrichment Analysis highlighted immune pathways enrichment in both villous trophoblasts and decidua. Gene ontology (GO) analysis of downregulated genes implicated hormonal and endocrine processes, consistent with STB reduction, while upregulated genes were associated with MHC protein complex and immune system processes, aligning with EVT increases. Histological analysis showed chronic histiocytic intervillositis (CHI) in iPL samples, supporting maternal immune dysregulation in unexplained RPL. Together, transcriptomic and histological analyses indicate that immune signaling dysregulation and impaired trophoblast differentiation may underlie unexplained iPLs. These findings bridge molecular and histopathological evidence, underscoring the interplay between trophoblast dysfunction and immune imbalance. Our results provide insights into iPL pathogenesis, highlighting potential biomarkers that may contribute to improved diagnosis and future research. Full article

(This article belongs to the Special Issue Pregnancy Health and Complications: Molecular Processes and Mechanisms)

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17 pages, 889 KiB

Open AccessReview

Functions of Intrinsically Disordered Regions

by Linhu Xiao and Kun Xia

Biology 2025, 14(7), 810; https://doi.org/10.3390/biology14070810 - 4 Jul 2025

Abstract

Intrinsically disordered regions (IDRs), defined as protein segments lacking stable tertiary structures, are ubiquitously present in the human proteome and enriched with disease-associated mutations. IDRs harbor molecular recognition features (MoRFs) and post-translational modification sites (e.g., phosphorylation), enabling dynamic intermolecular interactions through conformational plasticity. [...] Read more.

Intrinsically disordered regions (IDRs), defined as protein segments lacking stable tertiary structures, are ubiquitously present in the human proteome and enriched with disease-associated mutations. IDRs harbor molecular recognition features (MoRFs) and post-translational modification sites (e.g., phosphorylation), enabling dynamic intermolecular interactions through conformational plasticity. Furthermore, IDRs drive liquid–liquid phase separation (LLPS) of biomacromolecules via multivalent interactions such as electrostatic attraction and pi–pi interactions, generating biomolecular condensates that are essential throughout the cellular lifecycle. These condensates separate intracellular space, forming a physical barrier to avoid interference between other molecules, thereby improving reaction specificity and efficiency. As a dynamically equilibrated process, LLPS formation and maintenance are regulated by multiple factors, endowing the condensates with rapid responsiveness to environmental cues and functional versatility in modulating diverse signaling cascades. Consequently, disruption of LLPS homeostasis can derail its associated biological processes, ultimately contributing to disease pathogenesis. Moreover, precisely because liquid–liquid phase separation (LLPS) is co-regulated by multiple factors, it may provide novel insights into the pathogenic mechanisms of disorders such as autism spectrum disorder (ASD), which result from the cumulative effects of multiple etiological factors. Full article

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22 pages, 4262 KiB

Open AccessArticle

Transcriptomic Changes of Telencephalon and Hypothalamus in Largemouth Bass (Micropterus salmoides) Under Crowding Stress

by Meijia Li, Leshan Yang and Ying Liu

Biology 2025, 14(7), 809; https://doi.org/10.3390/biology14070809 - 3 Jul 2025

Abstract

Crowding stress is an inevitable stressor in intensive farming, yet its underlying mechanisms are still obscure, severely hindering the aquaculture industry’s healthy development. As the primary sensory and regulatory organ for stressors, the brain plays a crucial role in stress responses. In this [...] Read more.

Crowding stress is an inevitable stressor in intensive farming, yet its underlying mechanisms are still obscure, severely hindering the aquaculture industry’s healthy development. As the primary sensory and regulatory organ for stressors, the brain plays a crucial role in stress responses. In this study, the effect of crowding stress on the telencephalon (Tel) and hypothalamus (Hy) has been explored using RNA sequencing. After four weeks of crowding stress, neuroinflammation-related genes were significantly induced in both the Tel and Hy. Additionally, cell fate-related processes were markedly altered. Neurogenesis-related pathways, including the Wnt and Hedgehog signaling pathways, were significantly enriched in both regions. The apoptosis-related genes (caspase3, p53) were predominantly downregulated in the Tel (log₂Fold Change: −1.27 and −0.71, respectively), while ferroptosis-related genes (ho1, ncoa4) were specifically activated in the Hy (log₂Fold Change: 1.15 and 0.73, respectively). The synaptic plasticity-related genes (prkcg, cacna1d) were significantly downregulated in both the Tel (log₂Fold Change: −1.78 and −0.88) and Hy (log₂Fold Change: −1.99 and −1.52). Furthermore, neurotransmitter synthesis (γ-aminobutyric acid (GABA) and serotonin (5-HT)) was disrupted in the Tel, whereas growth-related hormone gene expression was markedly altered in the Hy. These findings provide novel insights into the neurobiological mechanisms of chronic crowding stress in fish, laying a foundation for developing brain-targeted strategies to enhance welfare and mitigate stress in intensive largemouth bass farming. Full article

(This article belongs to the Special Issue Metabolic and Stress Responses in Aquatic Animals)

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18 pages, 2415 KiB

Open AccessArticle

Population Estimation and Demographic Characteristics of Free-Roaming Dogs on Kasetsart University Kamphaeng Saen Campus, Thailand: Implications for Rabies Control

by Tita Phiriyaphokhai, Thitiwan Patanasatienkul, Tipsarp Kittisiam, Suwicha Kasemsuwan and Kansuda Leelahapongsathon

Biology 2025, 14(7), 808; https://doi.org/10.3390/biology14070808 - 3 Jul 2025

Abstract

Free-roaming dogs (FRDs) pose significant public health and animal welfare challenges globally, particularly in developing nations, where they serve as major reservoirs for zoonotic diseases, especially rabies. Determining the population size of FRDs, their demographic characteristics, and the factors influencing population size is [...] Read more.

Free-roaming dogs (FRDs) pose significant public health and animal welfare challenges globally, particularly in developing nations, where they serve as major reservoirs for zoonotic diseases, especially rabies. Determining the population size of FRDs, their demographic characteristics, and the factors influencing population size is essential for effective dog population management, which constitutes a critical component of rabies control programs. This study aimed to estimate the size and describe the characteristics of the FRD population and evaluate temporal and spatial variations in FRD sightings on the Kasetsart University Kamphaeng Saen Campus, Thailand. Factors influencing population size were assessed using a negative binomial regression model. The campus area was divided into 52 accessible blocks for dog-counting purposes. In 2018 and 2019, each block was surveyed once annually for a comprehensive census. In 2021, each block was surveyed on six occasions, three in the morning and three in the evening, using a photographic recapture method. Dogs sighted were photographed, and their characteristics and spatial coordinates were recorded. The total population sizes of FRDs on campus were documented as 529, 577, and 531 in 2018, 2019, and 2021, respectively. Intact female dogs predominantly constituted the majority of the FRD population. Regression analysis indicated a significant association between the number of FRDs within a block and the number of intact adult female dogs. The percentage of dogs sighted per occasion was significantly higher during evening surveys compared to morning surveys. This study proposes a practical census approach that combines total block counts with photographic recapture to estimate the population of FRDs. The findings offer valuable insights for developing effective dog population management strategies and planning rabies vaccination campaigns. Full article

(This article belongs to the Special Issue Large Animal Experimental and Epidemiological Models for Diseases)

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15 pages, 2921 KiB

Open AccessArticle

Effects of Different Ecological Floating Bed Plant Assemblages on Water Purification and Phytoplankton Community Structure in Shallow Eutrophic Lakes: A Case Study in Lake Taihu

by Yidong Liang, Ting Zhang, Wei Cui, Zhen Kuang and Dongpo Xu

Biology 2025, 14(7), 807; https://doi.org/10.3390/biology14070807 - 3 Jul 2025

Abstract

To explore the effects of different plant combinations in ecological floating beds on water quality purification and phytoplankton community structure in shallow eutrophic lakes, we conducted a survey of phytoplankton communities within ecological floating beds featuring distinct plant combinations in Meiliang Bay, Lake [...] Read more.

To explore the effects of different plant combinations in ecological floating beds on water quality purification and phytoplankton community structure in shallow eutrophic lakes, we conducted a survey of phytoplankton communities within ecological floating beds featuring distinct plant combinations in Meiliang Bay, Lake Taihu, during June and August 2021. The study focuses on two combinations: EA (Canna indica + Acorus calamus + Phragmites australis) and ES (Canna indica + Oenanthe javanica + Sagittaria sagittifolia). Results indicated that ecological floating beds significantly improved water quality, with the strongest restoration effects observed in the EA area. Specifically, turbidity was reduced by 47–89%, while chlorophyll a (Chl-a) concentration inhibition rates reached 82% in June and 54% in August. The comprehensive trophic state index (TLI) remained stable at levels indicating slight eutrophication (≤58.6). Phytoplankton community structure shifted from dominance by eutrophic functional groups (primarily FG M) toward greater diversity. In the EA area, the number of dominant functional groups increased from five (control) to six, and the abundance of the key cyanobacteria group (FG M) declined from 18.29% (control) to 7.86%. Redundancy analysis (RDA) revealed temporal changes in driving factors: nutrients were primary in June (explanation rate: 64.7%), while physical factors dominated in August (explanation rate: 51.2%). This study demonstrates that installing ecological floating beds with diverse plant combinations in shallow eutrophic lakes can effectively alter phytoplankton community structure and enhance in situ water restoration. Among the tested combinations, EA (Canna indica + Acorus calamus + Phragmites australis) exhibited the optimal restoration effect. These findings provide a scientific basis for water environment protection and aquatic biological resource restoration in shallow eutrophic lakes. Full article

(This article belongs to the Special Issue Global Fisheries Resources, Fisheries, and Carbon-Sink Fisheries)

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26 pages, 8290 KiB

Open AccessArticle

Genome-Wide Identification, Evolutionary Expansion, and Expression Analyses of Aux/IAA Gene Family in Castanea mollissima During Seed Kernel Development

by Yujuan Tian, Jingmiao Huang, Jinxin Wang, Dongsheng Wang, Ruimin Huang, Xia Liu, Haie Zhang, Jingzheng Zhang, Xiangyu Wang and Liyang Yu

Biology 2025, 14(7), 806; https://doi.org/10.3390/biology14070806 - 3 Jul 2025

Abstract

Auxin/induced-3-acetic acid (Aux/IAA) serves as a key regulator in the auxin signaling pathway of plants, which exhibits crucial functions in the development of plants. However, the Aux/IAA gene family has not yet been characterized in the genome of Castanea mollissima, an important [...] Read more.

Auxin/induced-3-acetic acid (Aux/IAA) serves as a key regulator in the auxin signaling pathway of plants, which exhibits crucial functions in the development of plants. However, the Aux/IAA gene family has not yet been characterized in the genome of Castanea mollissima, an important food source in the Northern Hemisphere. During this research, 23 Aux/IAA genes were identified in the C. mollissima genome, which were unevenly distributed across seven chromosomes. CmAux/IAA genes were assigned to four subfamilies by phylogenetic analysis, and members of the same subfamily exhibited similar molecular characteristics. Collinear analysis revealed that the expansion of CmAux/IAA genes was primarily driven by whole-genome duplication (WGD) and purifying selection. The promoter regions of CmAux/IAA genes were enriched with development-related and hormone-related cis-acting elements, suggesting their crucial functions in the growth and hormonal regulation of C. mollissima. Upon the maturation of the seed kernels, the size and starch content exhibited a significant increasing trend, alongside notable changes in hormone levels. Given the connections between expression levels and physiological indicators, as well as weighted gene co-expression network analysis (WGCNA) analysis, CmIAA27a, CmIAA27b, and CmIAA27c were identified as potential regulators involved in the development of C. mollissima seed kernels. Furthermore, the reliability of the transcriptomic data was further confirmed by RT-qPCR experiments. Overall, this study provides a theoretical basis for the evolutionary expansion of the Aux/IAA gene family in C. mollissima, alongside its potential functions in seed kernel development. Full article

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26 pages, 6233 KiB

Open AccessReview

Colonic Aging and Colorectal Cancer: An Unignorable Interplay and Its Translational Implications

by Qiyan Yin, Fen Qin, Fangliu Gan, Guangxi Zhao, Ronghua Chen, Yue Wen, Xueyang Hua, Fugui Zeng, Yuezheng Zhang, Yuliang Xiao, Wenbing Xie and Yong Tao

Biology 2025, 14(7), 805; https://doi.org/10.3390/biology14070805 - 3 Jul 2025

Abstract

Colorectal cancer (CRC) incidence increases markedly with age, yet chronological age is an inadequate proxy for the complex biological processes involved. Colon aging, the intrinsic biological aging of the colonic tissue, is emerging as a crucial, active driver of CRC development. This review [...] Read more.

Colorectal cancer (CRC) incidence increases markedly with age, yet chronological age is an inadequate proxy for the complex biological processes involved. Colon aging, the intrinsic biological aging of the colonic tissue, is emerging as a crucial, active driver of CRC development. This review comprehensively analyzes the interplay between colon aging and CRC pathogenesis by examining fundamental hallmarks of aging—such as altered tissue homeostasis, epigenetic dysregulation, and microenvironmental shifts including chronic inflammation (inflammaging), gut microbiome dysbiosis, and extracellular matrix remodeling—manifest specifically within the aging colon to synergistically foster a pro-tumorigenic environment. Key findings synthesized from the literature highlight the critical roles of impaired colonic stem cell function, epithelial barrier disruption (“leaky gut”), persistent low-grade inflammation, and altered microbial communities and their metabolites in promoting CRC initiation and progression. Translating this mechanistic understanding holds significant promise: insights from colon aging research can inform novel biomarkers for improved early detection and risk stratification, guide the development of personalized preventative strategies and therapeutic interventions targeting aging pathways, and underpin public health initiatives focused on healthy colon aging. Ultimately, recognizing colon aging as a modifiable contributor to CRC offers a powerful avenue to potentially reduce CRC incidence and enhance patient outcomes, particularly in the vulnerable aging population. Full article

(This article belongs to the Section Cancer Biology)

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15 pages, 2135 KiB

Open AccessArticle

Pollination Strategies of Eranthis stellata (Ranunculaceae), a Spring Ephemeral with Elaborate Petals

by Jiudong Zhang, Jie Sui, Lin Wang, Xianhua Tian, Xiaohui Zhang, Jing Xu and Tianpeng Gao

Biology 2025, 14(7), 804; https://doi.org/10.3390/biology14070804 - 3 Jul 2025

Abstract

Spring ephemerals have different pollination strategies to avoid the rareness and/or low activity of insect pollinators caused by low temperature in early spring. However, limited research has been conducted on the effects of elaborate petals and the pseudonectaries on petals on pollinator attraction. [...] Read more.

Spring ephemerals have different pollination strategies to avoid the rareness and/or low activity of insect pollinators caused by low temperature in early spring. However, limited research has been conducted on the effects of elaborate petals and the pseudonectaries on petals on pollinator attraction. We examined the role of the elaborate petals and the pseudonectaries in pollinator attractions of the spring ephemeral Eranthis stellata (Ranunculaceae) using a combination of observational and experimental approaches. The results indicated that the color contrast created by the yellow pseudonectaries that did not secrete nectar on the white petals, was more attractive to both bees and flies as nectar guides, but only bees with relatively longer tongues could access nectar at the base of the petal tubes. Also, the pseudonectaries were food deception for fly visitors. Food deception as a mechanism to increase the efficiency of pollination has not been reported for Ranunculaceae or other basal eudicots. Full article

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32 pages, 6839 KiB

Open AccessArticle

Identification of Novel Molecular Panel as Potential Biomarkers of PAN-Gastrointestinal Cancer Screening: Bioinformatics and Experimental Analysis

by Fatemeh Hajibabaie, Parisa Mohamadynejad, Laleh Shariati, Kamran Safavi and Navid Abedpoor

Biology 2025, 14(7), 803; https://doi.org/10.3390/biology14070803 - 2 Jul 2025

Abstract

PAN-gastrointestinal cancers (PAN-GI cancers), including the oral, esophageal, gastric, hepatocellular, pancreatic=, and colorectal cancers, are the leading cause of cancer-related mortality. Despite recent advances in identifying the molecular mechanisms driving these malignancies, the high incidence and recurrence of the PAN-gastrointestinal cancers and the [...] Read more.

PAN-gastrointestinal cancers (PAN-GI cancers), including the oral, esophageal, gastric, hepatocellular, pancreatic=, and colorectal cancers, are the leading cause of cancer-related mortality. Despite recent advances in identifying the molecular mechanisms driving these malignancies, the high incidence and recurrence of the PAN-gastrointestinal cancers and the low survival rates of patients indicate the need to introduce biomarkers for early diagnosis to improve diagnostic and therapeutic approaches. In the present study, using integrated transcriptomics, RNA-Seq and microarray data, from the TCGA and GEO databases, respectively, were combined to discover and validate a global biomarker panel for PAN-gastrointestinal cancers. In order to validate the bioinformatics data, the expression levels of genes in the molecular panel were evaluated using real-time quantitative polymerase chain reaction (qPCR) in tumor tissues of 21 patients with early diagnosis of gastric cancer and colorectal cancer (Stage I and II). By examining the transcriptomic profiles of six types of PAN-gastrointestinal cancers, a network of closely related hub genes (n = 167) with biomarker potential (p value < 0.05) was identified. Also, using ROC curve analysis and the Youden index, a molecular panel consisting of AURKA, CEP55, DTL, and TTK was presented (95% confidence interval and p value < 0.05), which showed exceptional sensitivity and specificity in differentiating malignant tissue from normal tissue (AUC > 80%). The diagnostic efficacy of these markers was confirmed by further validation using qPCR in colorectal and gastric tumor samples (p value < 0.05). In conclusion, a novel molecular signature panel including the AURKA, CEP55, DTL, and TTK genes could improve early cancer detection and diagnostic accuracy, and it may contribute to the treatment outcomes of PAN-gastrointestinal cancer patients. Full article

(This article belongs to the Special Issue Application of Bioinformatics to Unravel the Molecular Mechanisms of Cancer Biology)

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26 pages, 2006 KiB

Open AccessReview

Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota–Bile Acid Axis

by Jin Jiang, Huange Zhang, Muhammad Hussain, Abdullah, Fengqin Feng, Rongfa Guan and Hao Zhong

Biology 2025, 14(7), 802; https://doi.org/10.3390/biology14070802 - 2 Jul 2025

Abstract

Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)–gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs [...] Read more.

Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)–gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs into bioactive secondary BAs, which function as endocrine signaling molecules by activating the nuclear farnesoid X receptor (FXR) and G protein-coupled membrane receptor (TGR5), forming a communication network essential for metabolic homeostasis. BAs also reciprocally modulate gut microbiota composition. This BA–gut microbiota co-metabolism has emerged as a promising therapeutic target for lipid metabolism disorders. This comprehensive review examines the bidirectional interplay between gut microbiota and BA metabolism, focusing on microbial transformation of BAs, host–microbial co-regulatory pathways and mechanisms of BA metabolism, and the therapeutic implications of modulating the gut microbiota–BA axis in addressing glucose and lipid metabolism disorders. The synthesis of current evidence aims to elucidate the intricate crosstalk between microbial ecology and host metabolism mediated by BA signaling pathways, thereby exploring novel therapeutic intervention strategies. Full article

(This article belongs to the Special Issue Gut Microbiome in Health and Disease (2nd Edition))

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43 pages, 1231 KiB

Open AccessReview

Climate Adaptation Strategies for Maintaining Rice Grain Quality in Temperate Regions

by Yvonne Fernando, Ben Ovenden, Nese Sreenivasulu and Vito Butardo, Jr.

Biology 2025, 14(7), 801; https://doi.org/10.3390/biology14070801 - 2 Jul 2025

Abstract

Climate change poses significant challenges to temperate rice production, particularly affecting grain quality and market acceptance. This review synthesizes current knowledge of climate-induced quality changes, with a focus on the Australian rice industry as a case study with comparisons to other temperate regions. [...] Read more.

Climate change poses significant challenges to temperate rice production, particularly affecting grain quality and market acceptance. This review synthesizes current knowledge of climate-induced quality changes, with a focus on the Australian rice industry as a case study with comparisons to other temperate regions. Environmental stressors such as extreme temperatures, variable rainfall, elevated CO₂, and salinity disrupt biochemical pathways during grain development, altering physicochemical, textural, and aromatic traits. Different rice classes exhibit distinct vulnerabilities: medium-grain japonica varieties show reduced amylose under heat stress, aromatic varieties experience disrupted aroma synthesis under drought, and long-grain types suffer kernel damage under combined stresses. Temperature is a key driver, with quality deterioration occurring above 35 °C and below 15 °C. Systems biology analyses reveal complex signalling networks underpinning these stress responses, although experimental validation remains limited. The Australian industry has responded by developing cold-tolerant cultivars, precision agriculture, and water-saving practices, yet projected climate variability demands more integrated strategies. Priorities include breeding for stress-resilient quality traits, refining water management, and deploying advanced phenotyping tools. Emerging technologies like hyperspectral imaging and machine learning offer promise for rapid quality assessment and adaptive management. Sustaining high-quality rice in temperate zones requires innovation linking physiology with practical adaptation. Full article

(This article belongs to the Special Issue The Impact of Climate Change on Quality, Yield, and Nutritional Properties of Cereals, Legumes, and Oilseeds)

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14 pages, 308 KiB

Open AccessReview

Biomarkers in Venous Thrombosis: Diagnostic Potential and Limitations

by Yijin Chang, Jiahao Lu and Changsheng Chen

Biology 2025, 14(7), 800; https://doi.org/10.3390/biology14070800 - 1 Jul 2025

Abstract

Venous thromboembolism (VTE), comprising deep vein thrombosis (DVT) and pulmonary embolism (PE), is a life-threatening vascular disorder associated with significant morbidity and mortality. Prompt diagnosis is crucial for preventing fatal complications. Current clinical VTE diagnosis predominantly relies on imaging modalities such as compression [...] Read more.

Venous thromboembolism (VTE), comprising deep vein thrombosis (DVT) and pulmonary embolism (PE), is a life-threatening vascular disorder associated with significant morbidity and mortality. Prompt diagnosis is crucial for preventing fatal complications. Current clinical VTE diagnosis predominantly relies on imaging modalities such as compression ultrasound, computed tomography angiography (CTA), and magnetic resonance imaging (MRI). However, these techniques are resource-intensive, time-consuming, and may expose patients to radiation risks. Consequently, the development of highly sensitive and specific biomarkers is imperative to enhance early detection and guide therapeutic interventions. This review examines established and emerging biomarkers in venous thrombosis, evaluates current challenges, and outlines promising future directions for biomarker research in VTE. Full article

(This article belongs to the Special Issue Advances in Thrombosis and Vascular Biology)

13 pages, 956 KiB

Open AccessArticle

Timing and Amplitude of Light Exposure, Not Photoperiod, Predict Blood Lipids in Arctic Residents: A Circadian Light Hypothesis

by Denis Gubin, Sergey Kolomeichuk, Konstantin Danilenko, Oliver Stefani, Alexander Markov, Ivan Petrov, Kirill Voronin, Marina Mezhakova, Mikhail Borisenkov, Aislu Shigabaeva, Julia Boldyreva, Julianna Petrova, Larisa Alkhimova, Dietmar Weinert and Germaine Cornelissen

Biology 2025, 14(7), 799; https://doi.org/10.3390/biology14070799 - 1 Jul 2025

Abstract

In Arctic residents, blood lipids fluctuate seasonally in response to changes in light exposure (LE) patterns. This study investigates which aspects of LE (timing, dynamic range, and duration) are related to lipid profiles. We analyzed actigraphy data measuring LE and blue light exposure [...] Read more.

In Arctic residents, blood lipids fluctuate seasonally in response to changes in light exposure (LE) patterns. This study investigates which aspects of LE (timing, dynamic range, and duration) are related to lipid profiles. We analyzed actigraphy data measuring LE and blue light exposure (BLE) along with blood determinations from 27 residents across different seasons. We assessed circadian parameters of melatonin in a subset of participants. We found that features of BLE and melatonin significantly predicted lipids: An earlier BLE acrophase was associated with higher HDL-C (β = −0.246, p = 0.013). Nighttime BLE was positively associated with TC (β = 0.290, p = 0.008) and LDL-C (β = 0.253, p = 0.025). The normalized circadian amplitude of BLE was inversely associated with the TG/HDL ratio (β = −0.384, p < 0.001). Finally, earlier melatonin was associated with lower TG/HDL (β = 0.464, p = 0.007). Results remained significant after adjusting for co-factors of photoperiod duration, age, sex, and indigeneity. These findings suggest that patterns of LE (circadian light hygiene) could be a way to improve cardiovascular health. Full article

(This article belongs to the Special Issue Biological Rhythms and Molecular Clockworks in Physiology and Pathology)

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17 pages, 2818 KiB

Open AccessReview

Metabolic Responses, Uptake, and Export of Copper in Cyanobacteria

by Jean Coutinho Oder, Thamires Emidio Sateles, Laila Barros de Souza, Adriano Nunes-Nesi, Wagner L. Araújo and Luna Alvarenga-Lucius

Biology 2025, 14(7), 798; https://doi.org/10.3390/biology14070798 - 1 Jul 2025

Abstract

Copper (Cu) is an essential micronutrient for cyanobacteria, where it functions as a cofactor in key proteins involved in photosynthesis and antioxidant defense. However, at elevated concentrations, Cu becomes toxic, exhibiting algicidal effects by disrupting metal homeostasis and competing for metal-binding sites on [...] Read more.

Copper (Cu) is an essential micronutrient for cyanobacteria, where it functions as a cofactor in key proteins involved in photosynthesis and antioxidant defense. However, at elevated concentrations, Cu becomes toxic, exhibiting algicidal effects by disrupting metal homeostasis and competing for metal-binding sites on critical cellular proteins. Due to the considerable morphological and physiological diversity within the phylum Cyanobacteria, the thresholds for Cu deficiency or toxicity vary considerably among strains. Maintaining Cu homeostasis in cyanobacterial cells is a complex process involving multiple layers of regulation. It begins at the extracellular polysaccharide layer, involves specialized membrane-bound proteins (in the outer, plasma, and thylakoid membranes), and results in transcriptional regulation in response to intracellular Cu status. This review summarizes the current understanding of Cu uptake and efflux pathways in cyanobacteria and explores how these mechanisms contribute to maintaining cellular Cu balance. The knowledge gained may contribute to the application of cyanobacteria in bioremediation strategies and/or the targeted use of Cu in the control of harmful cyanobacterial blooms. Full article

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29 pages, 1116 KiB

Open AccessReview

The Impact of Oncogenic Viruses on Cancer Development: A Narrative Review

by Maria Karoliny da Silva Torres, Gabriel dos Santos Pereira Neto, Izaura Maria Vieira Cayres Vallinoto, Leonardo Oliveira Reis and Antonio Carlos Rosário Vallinoto

Biology 2025, 14(7), 797; https://doi.org/10.3390/biology14070797 - 1 Jul 2025

Abstract

Oncogenic viruses are infectious agents that can cause cancer in humans and animals. They are estimated to be responsible for approximately 12% of human cancers worldwide. These viruses trigger a series of mechanisms that allow them to insert their genetic material into host [...] Read more.

Oncogenic viruses are infectious agents that can cause cancer in humans and animals. They are estimated to be responsible for approximately 12% of human cancers worldwide. These viruses trigger a series of mechanisms that allow them to insert their genetic material into host cells, disrupting normal cellular processes and leading to uncontrolled growth and tumor formation. This article reviews the literature on the main oncogenic viruses and reports on newly identified viruses potentially associated with cancer development, addressing the mechanisms of oncogenesis and the types of cancers associated. In addition, the article brings together the evidence for preventive strategies, such as vaccination, and therapeutic advances in combating oncogenic viral infections. This review discusses the role of early detection and treatment in managing virus-related cancers globally. This article reviews current prevention and treatment strategies, including HPV and HBV vaccines and antiviral therapies, and mentions future approaches like immunotherapies and CRISPR/Cas9. Therefore, this article underscores the importance of studying the dynamics of co-infection and the role of human microbiota in viral persistence and carcinogenesis, which opens new possibilities for combination therapies and microbiome-based interventions to slow the progression of viral-related tumors. Full article

(This article belongs to the Special Issue Unraveling the Tumor-Immune Microenvironment Using Transcriptomics)

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20 pages, 1406 KiB

Open AccessArticle

Responses of Fish Zeta Diversity (ζ) to Human Pressure and Cumulative Effects: A Feasibility Study of Fishing Ban Measures in the Pearl River Basin, China

by Jiayang He, Hao Liu, Xianda Bi and Zhiqiang Wu

Biology 2025, 14(7), 796; https://doi.org/10.3390/biology14070796 - 30 Jun 2025

Abstract

Amid declining fish diversity and human pressures in freshwater ecosystems, robust basin-scale assessments are vital for effective fisheries management. This study collated nearly four decades of fishery yields from the Pearl and Yangtze Rivers to identify conservation priorities in the Pearl River Basin. [...] Read more.

Amid declining fish diversity and human pressures in freshwater ecosystems, robust basin-scale assessments are vital for effective fisheries management. This study collated nearly four decades of fishery yields from the Pearl and Yangtze Rivers to identify conservation priorities in the Pearl River Basin. It introduced a novel cumulative effect indicator based on zeta diversity—a biodiversity pattern metric—integrated with cumulative effects analysis for management decision-making. The research employed a multi-site generalized dissimilarity model to examine the non-linear relationships between fish species composition (ζ_n) and human pressures, environmental factors, and geospatial variations across elevation gradients. The cumulative effect indicator, reflecting responses to anthropogenic stress when assessing ζ₂ (related to β diversity), helped evaluate basins for conservation or restoration needs based on their unique or homogenized biotic communities. The results suggest that ζ diversity in low-elevation sub-basins has a stronger filtering effect on ζ by human pressures than in mid- to high-elevation sub-basins, where community aggregation is more random. The impact varied with diversity aspects (nestedness vs. turnover) and zeta order. A negative correlation between cumulative effects and community uniqueness validated the novel cumulative effect indicator’s effectiveness for guiding restoration in the Pearl River Delta, potential fishing bans, and karst conservation. This approach offers a theoretical basis for prioritizing areas for freshwater fish diversity conservation and fishing restrictions in the Pearl River Basin. Full article

(This article belongs to the Special Issue Advances in Wildlife Conservation and Habitat Management in the Anthropocene)

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