Journal Description
Biology
Biology
is an international, peer-reviewed, open access journal of biological sciences published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) and Federation of European Laboratory Animal Science Associations (FELASA) are affiliated with Biology, and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q2 (Biology) / CiteScore - Q1 (General Agricultural and Biological Sciences)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 18.7 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
4.2 (2022);
5-Year Impact Factor:
4.4 (2022)
Latest Articles
α-Catenin and Piezo1 Mediate Cell Mechanical Communication via Cell Adhesions
Biology 2024, 13(5), 357; https://doi.org/10.3390/biology13050357 (registering DOI) - 19 May 2024
Abstract
Cell-to-cell distant mechanical communication has been demonstrated using in vitro and in vivo models. However, the molecular mechanisms underlying long-range cell mechanoresponsive interactions remain to be fully elucidated. This study further examined the roles of α-Catenin and Piezo1 in traction force-induced rapid branch
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Cell-to-cell distant mechanical communication has been demonstrated using in vitro and in vivo models. However, the molecular mechanisms underlying long-range cell mechanoresponsive interactions remain to be fully elucidated. This study further examined the roles of α-Catenin and Piezo1 in traction force-induced rapid branch assembly of airway smooth muscle (ASM) cells on a Matrigel hydrogel containing type I collagen. Our findings demonstrated that siRNA-mediated downregulation of α-Catenin or Piezo1 expression or chemical inhibition of Piezo1 activity significantly reduced both directional cell movement and branch assembly. Regarding the role of N-cadherin in regulating branch assembly but not directional migration, our results further confirmed that siRNA-mediated downregulation of α-Catenin expression caused a marked reduction in focal adhesion formation, as assessed by focal Paxillin and Integrin α5 localization. These observations imply that mechanosensitive α-Catenin is involved in both cell–cell and cell-matrix adhesions. Additionally, Piezo1 partially localized to Paxillin in focal adhesions, which was inhibited by siRNA-mediated downregulation of α-Catenin expression. This result provides insights into the Piezo1-mediated mechanosensing of traction force on a hydrogel. Collectively, our findings highlight the significance of α-Catenin in the regulation of cell-matrix interactions and provide a possible interpretation of Piezo1-mediated mechanosensing activity at focal adhesions during cell–cell distant mechanical communication.
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(This article belongs to the Section Cell Biology)
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Open AccessArticle
Carrabiitol®, a Novel Oligosaccharide Polyol Composition, Mitigates the Impact of Flooding, Drought, Salinity, and High Temperature in Tomato
by
Femida Yunus Patel, Kaushal Kishore Upreti, Ramanna Hunashikatti Laxman and Neil Jaykumar Shah
Biology 2024, 13(5), 356; https://doi.org/10.3390/biology13050356 (registering DOI) - 19 May 2024
Abstract
Abiotic stress results in various physiological and biochemical changes in plants. Osmolytes play a pivotal role in improving the tolerance to abiotic stress in plants. This study evaluated the effectiveness of a commercial formulation, Carrabiitol®, an oligosaccharide polyol composition, in alleviating
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Abiotic stress results in various physiological and biochemical changes in plants. Osmolytes play a pivotal role in improving the tolerance to abiotic stress in plants. This study evaluated the effectiveness of a commercial formulation, Carrabiitol®, an oligosaccharide polyol composition, in alleviating adverse impacts of abiotic stress in tomato (Solanum lycopersicum L. var. Arka Rakshak) plants. Plants were raised from seed and treated with 1 mL/L, 2 mL/L, and 3 mL/L of Carrabiitol®. The foliage of developing plants was treated at the 2–3 leaf stage (T2, T3, and T4) and at pre-flowering stage (T5, T6, and T7). Growth conditions were compared with those of plants developed from untreated seed (T1). Developing tomato plants were then exposed to flooding, salinity (50 mM NaCl), high temperature (41.1 °C), or drought at the flowering stage. Plants were evaluated for their dry weight, leaf water potential, stomatal conductance, transpiration rate, antioxidant potential, chlorophyll, carotenoid, glucose, sucrose, malondialdehyde, and proline contents. Pre-treated seed, which received a booster treatment at the 2–3 leaf stage (T4 = seed treatment and booster at the 2–3 leaf stage with 3 mL/L Carrabiitol®) and pre-flowering stages (T5, T6, and T7 = seed treatment and booster doses at the pre-flowering stage with 1, 2, and 3 mL/L Carrabiitol®, respectively), was effective in mitigating negative impacts on various growth parameters of stressed tomato plants (p < 0.05). Carrabiitol® may be an effective, sustainable, and bio-rational organic osmolyte formulation for reducing the effects of abiotic stress on plant growth and productivity.
Full article
(This article belongs to the Special Issue Uncovering the Mechanisms of Plant Salinity Stress Response and Tolerance)
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Open AccessArticle
Among Other Tissues, Short-Term Garlic Oral Treatment Incrementally Improves Indicants of Only Pancreatic Islets of Langerhans Histology and Insulin mRNA Transcription and Synthesis in Diabetic Rats
by
Amani M. Al-Adsani and Khaled K. Al-Qattan
Biology 2024, 13(5), 355; https://doi.org/10.3390/biology13050355 (registering DOI) - 18 May 2024
Abstract
Background: The source, mRNA transcription, and synthesis of insulin in the pancreas, in addition to the bile duct and liver, in streptozotocin (STZ)-induced diabetic rats (DR) in response to garlic oral treatment are not yet clear. Objective: This study investigated the accumulative effects
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Background: The source, mRNA transcription, and synthesis of insulin in the pancreas, in addition to the bile duct and liver, in streptozotocin (STZ)-induced diabetic rats (DR) in response to garlic oral treatment are not yet clear. Objective: This study investigated the accumulative effects of continued garlic oral treatment on changes in the pancreas, bile duct, and liver with regards to: 1—Insulin mRNA transcription, synthesis, and concentration in relation to changes in serum insulin (SI); 2—Insulinogenic cells insulin intensity and distribution, proliferation, and morphology. Method: Fasting blood glucose (FBG) and insulin concentration in serum and pancreas (PI) and sources and mRNA transcription in the pancreas, bile duct, and liver in normal rats given normal saline (NR-NS) and DR given either NS (DR-NS) or garlic extract (DR-GE) before and after 1, 4, and 8 weeks of oral treatment were examined. Results: Compared to NR-NS, DR-NS showed a significant increase in FBG and reductions in SI and PI and deterioration in islets histology, associated pancreatic insulin numerical intensities, and mRNA transcription. However, compared to DR-NS, the targeted biochemical, histological, and genetic variables of DR-GE were significantly and incrementally improved as garlic treatment continued. Insulin or its indicators were not detected either in the bile duct or the liver in DR-GE. Conclusions: 8 weeks of garlic oral treatment is enough to incrementally restore only pancreatic islets of Langerhans insulin intensity and insulinogenic cells proliferation, morphology, and distribution. These indices were associated with enhanced pancreatic insulin mRNA transcription and synthesis. Eight weeks of garlic treatment were not enough to stimulate insulinogenesis in either the bile duct or the liver.
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(This article belongs to the Special Issue Animal Models of Pancreatic Diseases)
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Open AccessArticle
Antibacterial and Antibiofilm Potential of Bacterial Cellulose Hydrogel Containing Vancomycin against Multidrug-Resistant Staphylococcus aureus and Staphylococcus epidermidis
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Ana Alice Venancio Correia, Luís André de Almeida Campos, Hanne Lazla Rafael de Queiroz Macêdo, Davi de Lacerda Coriolano, Maria Anndressa Alves Agreles, Danilo Elias Xavier, Rafaela de Siqueira Ferraz-Carvalho, José Lamartine de Andrade Aguiar and Isabella Macário Ferro Cavalcanti
Biology 2024, 13(5), 354; https://doi.org/10.3390/biology13050354 - 17 May 2024
Abstract
The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially,
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The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially, HYDROGEL was obtained from sugar cane molasses, and scanning electron microscopy (SEM) was performed to determine morphological characteristics. Then, VAN was incorporated into HYDROGEL (VAN-HYDROGEL). The antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was assessed using the broth microdilution method to determine the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) against methicillin-sensitive S. aureus (MSSA) ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 33591, S. epidermidis INCQS 00016 (ATCC 12228), five clinical isolates of MRSA, and nine clinical isolates of methicillin-resistant S. epidermidis, following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Additionally, the antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was studied using the time-kill assay. Subsequently, the antibiofilm activity of VAN, HYDROGEL, and VAN-HYDROGEL was evaluated using crystal violet and Congo red methods, as well as SEM analysis. VAN and VAN-HYDROGEL showed bacteriostatic and bactericidal activity against MRSA and methicillin-resistant S. epidermidis strains. HYDROGEL did not show any antibacterial activity. Analysis of the time-kill assay indicated that HYDROGEL maintained the antibacterial efficacy of VAN, highlighting its efficiency as a promising carrier. Regarding antibiofilm activity, VAN and HYDROGEL inhibited biofilm formation but did not demonstrate biofilm eradication activity against methicillin-resistant S. aureus and S. epidermidis strains. However, it was observed that the biofilm eradication potential of VAN was enhanced after incorporation into HYDROGEL, a result also proven through images obtained by SEM. From the methods carried out in this study, it was possible to observe that HYDROGEL preserved the antibacterial activity of vancomycin, aside from exhibiting antibiofilm activity and enhancing the antibiofilm effect of VAN. In conclusion, this study demonstrated the potential of HYDROGEL as a candidate and/or vehicle for antibiotics against MDR bacteria that cause wound infections.
Full article
(This article belongs to the Collection Feature Papers in Microbial Biology)
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Open AccessArticle
Effects of Seed Size and Frequency on Seed Dispersal and Predation by Small Mammals
by
Jiming Cheng, Min Zhang, Xingfu Yan, Chao Zhang, Jinfeng Zhang and Yonghong Luo
Biology 2024, 13(5), 353; https://doi.org/10.3390/biology13050353 - 16 May 2024
Abstract
Frequency-dependent predation is common in predator–prey interactions. Size is an important characteristic of seeds and is crucial in the regeneration stage of plant seeds. However, the frequency dependence of animal predation on seed size has not been reported. In this study, we conducted
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Frequency-dependent predation is common in predator–prey interactions. Size is an important characteristic of seeds and is crucial in the regeneration stage of plant seeds. However, the frequency dependence of animal predation on seed size has not been reported. In this study, we conducted a field experiment and used different sizes of Liaodong oak (Quercus wutaishanica) seeds to test the frequency dependence of intraspecific seed size selection in rodents. We used the number ratio of large to small seeds as the frequency. The results show that the rate of small seeds being eaten in situ was significantly higher than that of large seeds (p < 0.05). The rates of different-sized seeds being eaten after removal decreased with increasing frequencies, and there was no significant difference between frequencies except for 1:9 and 9:1. The rates of large seeds being scatter-hoarded were significantly higher than those of small seeds at different frequencies (p < 0.05). The eating distances after removal of large seeds were significantly longer than those of small seeds at the same frequencies (p < 0.05). Furthermore, the scatter-hoarding distances of large seeds were significantly longer than those of small seeds at three frequencies (1:9, 3:7, and 9:1) (p < 0.05). That is, rodents consumed more small seeds in situ, dispersed and scatter-hoarded more large seeds, and dispersed large seeds over longer distances. Rodents exhibited a negative frequency dependence for small seeds and a positive frequency dependence for large seeds on being eaten in situ. Moreover, rodents exhibited a negative frequency dependence for large seeds and a positive frequency dependence for small seeds on being eaten after removal and scatter-hoarding. These results reveal the frequency dependence of rodent selection on seed size and provide new insights into animal-mediated seed dispersal and the regeneration of plant populations.
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(This article belongs to the Section Ecology)
Open AccessReview
Associations between “Cancer Risk”, “Inflammation” and “Metabolic Syndrome”: A Scoping Review
by
Elsa Vitale, Alessandro Rizzo, Kazuki Santa and Emilio Jirillo
Biology 2024, 13(5), 352; https://doi.org/10.3390/biology13050352 - 16 May 2024
Abstract
Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk,
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Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk, inflammation, and metabolic syndrome. Methods: A search strategy was performed, mixing keywords and MeSH terms, such as “Cancer Risk”, “Inflammation”, “Metabolic Syndrome”, “Oncogenesis”, and “Oxidative Stress”, and matching them through Boolean operators. A total of 20 manuscripts were screened for the present study. Among the selected papers, we identified some associations with breast cancer, colorectal cancer, esophageal adenocarcinoma, hepatocellular carcinoma (HCC), and cancer in general. Conclusions: Cancer and its related progression may also depend also on a latent chronic inflammatory condition associated with other concomitant conditions, including type 2 diabetes mellitus, metabolic syndrome, and obesity. Therefore, prevention may potentially help individuals to protect themselves from cancer.
Full article
(This article belongs to the Special Issue Effects of Environmental Stress on the Metabolic Dysfunction and Its Mechanism)
Open AccessArticle
DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments
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Anna D. Katsiki, Pantelis E. Karatzas, Hector-Xavier De Lastic, Alexandros G. Georgakilas, Ourania Tsitsilonis and Constantinos E. Vorgias
Biology 2024, 13(5), 351; https://doi.org/10.3390/biology13050351 - 16 May 2024
Abstract
Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI’s GEO. Developed with R,
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Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI’s GEO. Developed with R, Shiny, and Bioconductor, DExplore integrates WebGestalt for functional enrichment analysis. It also provides visualization plots for enhanced result interpretation. With a Docker image for local execution, DExplore accommodates unpublished data. To illustrate its utility, we showcase two case studies on cancer cells treated with chemotherapeutic drugs. DExplore streamlines microarray data analysis, empowering molecular biologists to focus on genes of biological significance.
Full article
(This article belongs to the Special Issue Differential Gene Expression and Coexpression 2.0)
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Open AccessArticle
Paired Primary and Recurrent Rhabdoid Meningiomas: Cytogenetic Alterations, BAP1 Gene Expression Profile and Patient Outcome
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Patricia Alejandra Garrido Ruiz, Álvaro Otero Rodriguez, Luis Antonio Corchete, Victoria Zelaya Huerta, Alejandro Pasco Peña, Cristina Caballero Martínez, Joaquín González-Carreró Fojón, Inmaculada Catalina Fernández, Juan Carlos López Duque, Laura Zaldumbide Dueñas, Lorena Mosteiro González, María Aurora Astudillo, Aurelio Hernández-Laín, Emma Natalia Camacho Urkaray, María Amparo Viguri Diaz, Alberto Orfao and María Dolores Tabernero
Biology 2024, 13(5), 350; https://doi.org/10.3390/biology13050350 - 16 May 2024
Abstract
Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven
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Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven primary and 14 recurrent tumors) vs. non-recurrent RM (n = 8). Recurrent RM showed one (29%), two (29%) or three (42%) recurrences. BAP1 loss of expression was found in one third of all RM at diagnosis and increased to 100% in subsequent tumor recurrences. Despite both recurrent and non-recurrent RM shared chromosome 22 losses, non-recurrent tumors more frequently displayed extensive losses of chromosome 19p (62%) and/or 19q (50%), together with gains of chromosomes 20 and 21 (38%, respectively), whereas recurrent RM (at diagnosis) displayed more complex genotypic profiles with extensive losses of chromosomes 1p, 14q, 18p, 18q (67% each) and 21p (50%), together with focal gains at chromosome 17q22 (67%). Compared to paired primary tumors, recurrent RM samples revealed additional losses at chromosomes 16q and 19p (50% each), together with gains at chromosomes 1q and 17q in most recurrent tumors (67%, each). All deceased recurrent RM patients corresponded to women with chromosome 17q gains, although no statistical significant differences were found vs. the other RM patients.
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(This article belongs to the Special Issue New Sight in Cancer Genetics)
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Open AccessArticle
Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus
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Qinyue Min, Kaifeng Zheng, Tao Liu, Zitao Wang, Xiuhua Xue, Wanjie Li, Yuping Liu, Yanfen Zhang, Feng Qiao, Jinyuan Chen, Xu Su and Shengcheng Han
Biology 2024, 13(5), 349; https://doi.org/10.3390/biology13050349 - 16 May 2024
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may
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Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.
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(This article belongs to the Special Issue Biological Response of Plants to Environmental Changes)
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Open AccessArticle
Effects of Bacillus subtilis on Cucumber Seedling Growth and Photosynthetic System under Different Potassium Ion Levels
by
Chun Li, Qingpan Zeng, Yuzhu Han, Xiaofu Zhou and Hongwei Xu
Biology 2024, 13(5), 348; https://doi.org/10.3390/biology13050348 - 15 May 2024
Abstract
Potassium deficiency is one of the important factors restricting cucumber growth and development. This experiment mainly explored the effect of Bacillus subtilis (B. subtilis) on cucumber seedling growth and the photosynthetic system under different potassium levels, and the rhizosphere bacteria (PGPR)
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Potassium deficiency is one of the important factors restricting cucumber growth and development. This experiment mainly explored the effect of Bacillus subtilis (B. subtilis) on cucumber seedling growth and the photosynthetic system under different potassium levels, and the rhizosphere bacteria (PGPR) that promote plant growth were used to solubilize potassium in soil, providing theoretical support for a further investigation of the effect of biological bacteria fertilizer on cucumber growth and potassium absorption. “Xinjin No. 4” was used as the test material for the pot experiment, and a two-factor experiment was designed. The first factor was potassium application treatment, and the second factor was bacterial application treatment. The effects of different treatments on cucumber seedling growth, photosynthetic characteristics, root morphology, and chlorophyll fluorescence parameters were studied. The results showed that potassium and B. subtilis had obvious promotion effects on the cucumber seedling growth and the photosynthesis of leaves. Compared with the blank control, the B. subtilis treatment had obvious effects on the cucumber seedling height, stem diameter, leaf area, total root length, total root surface area, total root volume, branch number, crossing number, gs, WUE, Ci, and A; the dry weight of the shoot and root increased significantly (p ≤ 0.05). Potassium application could significantly promote cucumber growth, and the effect of B. subtilis and potassium application was greater than that of potassium application alone, and the best effect was when 0.2 g/pot and B. subtilis were applied. In conclusion, potassium combined with B. subtilis could enhance the photosynthesis of cucumber leaves and promote the growth of cucumber.
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(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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Open AccessArticle
New Discovery of Calamitaceae from the Cisuralian in Northwest China: Morphological Evolution of Strobilus
by
Xuelian Wang, Yunfa Miao, Yanzhao Ji and Bainian Sun
Biology 2024, 13(5), 347; https://doi.org/10.3390/biology13050347 - 15 May 2024
Abstract
Calamitaceae was the predominant arborescent element of the Late Paleozoic plant assemblages. However, there is currently controversy surrounding the evolutionary relationships of their four reproductive organs, and there is no unified understanding of the geographical distribution and species richness characteristics. This paper is
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Calamitaceae was the predominant arborescent element of the Late Paleozoic plant assemblages. However, there is currently controversy surrounding the evolutionary relationships of their four reproductive organs, and there is no unified understanding of the geographical distribution and species richness characteristics. This paper is based on the detailed description of the macro- and microstructures of Calamites and Macrostachya discovered in the Shanxi Formation of the Cisuralian in the eastern Hexi Corridor of northwestern China, and it discusses the evolutionary patterns of calamitean reproductive organs. The results indicate that the current specimens can be identified as the Calamites cistii and Macrostachya sp., and the in situ spores should exhibit distinct trilete marks, indicating that they belong to the Punctatisporites punctatus. The abundant fossil records suggest that the “Calamostachys” type should be considered as the ancestral type of strobili. Additionally, Calamitaceae was widely distributed in mid to low latitudes globally from the Pennsylvanian to the Cisuralian and coupled with paleogeographic distribution characteristics.
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(This article belongs to the Section Plant Science)
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Open AccessArticle
1,25-Dihydroxyvitamin D3 Suppresses Prognostic Survival Biomarkers Associated with Cell Cycle and Actin Organization in a Non-Malignant African American Prostate Cell Line
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Jabril R. Johnson, Rachel N. Martini, Yate-Ching Yuan, Leanne Woods-Burnham, Mya Walker, Greisha L. Ortiz-Hernandez, Firas Kobeissy, Dorothy Galloway, Amani Gaddy, Chidinma Oguejiofor, Blake Allen, Deyana Lewis, Melissa B. Davis, K. Sean Kimbro, Clayton C. Yates, Adam B. Murphy and Rick A. Kittles
Biology 2024, 13(5), 346; https://doi.org/10.3390/biology13050346 - 15 May 2024
Abstract
Vitamin D3 is a steroid hormone that confers anti-tumorigenic properties in prostate cells. Serum vitamin D3 deficiency has been associated with advanced prostate cancer (PCa), particularly affecting African American (AA) men. Therefore, elucidating the pleiotropic effects of vitamin D on signaling
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Vitamin D3 is a steroid hormone that confers anti-tumorigenic properties in prostate cells. Serum vitamin D3 deficiency has been associated with advanced prostate cancer (PCa), particularly affecting African American (AA) men. Therefore, elucidating the pleiotropic effects of vitamin D on signaling pathways, essential to maintaining non-malignancy, may provide additional drug targets to mitigate disparate outcomes for men with PCa, especially AA men. We conducted RNA sequencing on an AA non-malignant prostate cell line, RC-77N/E, comparing untreated cells to those treated with 10 nM of vitamin D3 metabolite, 1α,25(OH)2D3, at 24 h. Differential gene expression analysis revealed 1601 significant genes affected by 1α,25(OH)2D3 treatment. Pathway enrichment analysis predicted 1α,25(OH)2D3- mediated repression of prostate cancer, cell proliferation, actin cytoskeletal, and actin-related signaling pathways (p < 0.05). Prioritizing genes with vitamin D response elements and associating expression levels with overall survival (OS) in The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA PRAD) cohort, we identified ANLN (Anillin) and ECT2 (Epithelial Cell Transforming 2) as potential prognostic PCa biomarkers. Both genes were strongly correlated and significantly downregulated by 1α,25(OH)2D3 treatment, where low expression was statistically associated with better overall survival outcomes in the TCGA PRAD public cohort. Increased ANLN and ECT2 mRNA gene expression was significantly associated with PCa, and Gleason scores using both the TCGA cohort (p < 0.05) and an AA non-malignant/tumor-matched cohort. Our findings suggest 1α,25(OH)2D3 regulation of these biomarkers may be significant for PCa prevention. In addition, 1α,25(OH)2D3 could be used as an adjuvant treatment targeting actin cytoskeleton signaling and actin cytoskeleton-related signaling pathways, particularly among AA men.
Full article
(This article belongs to the Special Issue Cancer and Signalling: Targeting Cellular Pathways)
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Open AccessCommunication
Distinct Expression Profiles of Neuroblastoma-Associated mRNAs in Peripheral Blood and Bone Marrow of Non-High-Risk and High-Risk Neuroblastoma Patients
by
Naoko Nakatani, Kaung Htet Nay Win, Cho Yee Mon, Tomoko Fujikawa, Suguru Uemura, Atsuro Saito, Toshiaki Ishida, Takeshi Mori, Daiichiro Hasegawa, Yoshiyuki Kosaka, Shotaro Inoue, Akihiro Nishimura, Nanako Nino, Akihiro Tamura, Nobuyuki Yamamoto, Kandai Nozu and Noriyuki Nishimura
Biology 2024, 13(5), 345; https://doi.org/10.3390/biology13050345 - 15 May 2024
Abstract
Non-high-risk (non-HR) neuroblastoma (NB) patients have excellent outcomes, with more than a 90% survival rate, whereas HR NB patients expect less than a 50% survival rate. Metastatic disease is the principal cause of death among both non-HR and HR NB patients. Previous studies
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Non-high-risk (non-HR) neuroblastoma (NB) patients have excellent outcomes, with more than a 90% survival rate, whereas HR NB patients expect less than a 50% survival rate. Metastatic disease is the principal cause of death among both non-HR and HR NB patients. Previous studies have reported the significant but limited prognostic value of quantitative PCR (qPCR)-based assays, measuring overlapping but different sets of neuroblastoma-associated mRNAs (NB-mRNAs), to detect metastatic disease in both non-HR and HR patient samples. A droplet digital PCR (ddPCR)-based assay measuring seven NB-mRNAs (CRMP1, DBH, DDC, GAP43, ISL1, PHOX2B, and TH mRNAs) was recently developed and exhibited a better prognostic value for HR patient samples than qPCR-based assays. However, it remained to be tested on non-HR patient samples. In the present study, we employed the ddPCR-based assay to study peripheral blood (PB) and bone marrow (BM) samples collected at diagnosis from eight non-HR and eleven HR cases and characterized the expression profiles of NB-mRNAs. The most highly expressed NB-mRNAs in PB and BM differed between non-HR and HR cases, with the CRMP1 mRNA being predominant in non-HR cases and the GAP43 mRNA in HR cases. The levels of NB-mRNAs in PB and BM were 5 to 1000 times lower in non-HR cases than in HR cases. The PB to BM ratio of NB-mRNAs was 10 to 100 times higher in non-HR cases compared to HR cases. The present case series suggests that non-HR and HR NB patients have the distinct expression profiles of NB-mRNAs in their PB and BM.
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(This article belongs to the Section Cancer Biology)
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Open AccessArticle
Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis
by
Guozhong Du, Xue Yang, Zhengxiong Wu, Minghui Pan, Zhuoxu Dong, Yanyan Zhang, Wensheng Xiang and Shanshan Li
Biology 2024, 13(5), 344; https://doi.org/10.3390/biology13050344 - 15 May 2024
Abstract
Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of
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Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.
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(This article belongs to the Section Biotechnology)
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Examining the Influence of Cognitive Load and Environmental Conditions on Autonomic Nervous System Response in Military Aircrew: A Hypoxia–Normoxia Study
by
Harrison L. Wittels, S. Howard Wittels, Michael J. Wishon, Jonathan Vogl, Paul St. Onge, Samantha M. McDonald and Leonard A. Temme
Biology 2024, 13(5), 343; https://doi.org/10.3390/biology13050343 - 14 May 2024
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Executing flight operations demand that military personnel continuously perform tasks that utilize low- and high-order cognitive functions. The autonomic nervous system (ANS) is crucial for regulating the supply of oxygen (O2) to the brain, but it is unclear how sustained cognitive loads of
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Executing flight operations demand that military personnel continuously perform tasks that utilize low- and high-order cognitive functions. The autonomic nervous system (ANS) is crucial for regulating the supply of oxygen (O2) to the brain, but it is unclear how sustained cognitive loads of different complexities may affect this regulation. Therefore, in the current study, ANS responses to low and high cognitive loads in hypoxic and normoxic conditions were evaluated. The present analysis used data from a previously conducted, two-factor experimental design. Healthy subjects (n = 24) aged 19 to 45 years and located near Fort Novosel, AL, participated in the parent study. Over two, 2-h trials, subjects were exposed to hypoxic (14.0% O2) and normoxic (21.0% O2) air while simultaneously performing one, 15-min and one, 10-min simulation incorporating low- and high-cognitive aviation-related tasks, respectively. The tests were alternated across five, 27-min epochs; however, only epochs 2 through 4 were used in the analyses. Heart rate (HR), HR variability (HRV), and arterial O2 saturation were continuously measured using the Warfighter MonitorTM (Tiger Tech Solutions, Inc., Miami, FL, USA), a previously validated armband device equipped with electrocardiographic and pulse oximetry capabilities. Analysis of variance (ANOVA) regression models were performed to compare ANS responses between the low- and high-cognitive-load assessments under hypoxic and normoxic conditions. Pairwise comparisons corrected for familywise error were performed using Tukey’s test within and between high and low cognitive loads under each environmental condition. Across epochs 2 through 4, in both the hypoxic condition and the normoxic condition, the high-cognitive-load assessment (MATB-II) elicited heightened ANS activity, reflected by increased HR (+2.4 ± 6.9 bpm) and decreased HRV (−rMSSD: −0.4 ± 2.7 ms and SDNN: −13.6 ± 14.6 ms). Conversely, low cognitive load (ADVT) induced an improvement in ANS activity, with reduced HR (−2.6 ± 6.3 bpm) and increased HRV (rMSSD: +1.8 ± 6.0 ms and SDNN: vs. +0.7 ± 6.3 ms). Similar observations were found for the normoxic condition, albeit to a lower degree. These within-group ANS responses were significantly different between high and low cognitive loads (HR: +5.0 bpm, 95% CI: 2.1, 7.9, p < 0.0001; rMSSD: −2.2 ms, 95% CI: −4.2, −0.2, p = 0.03; SDNN: −14.3 ms, 95% CI: −18.4, −10.1, p < 0.0001) under the hypoxic condition. For normoxia, significant differences in ANS response were only observed for HR (+4.3 bpm, 95% CI: 1.2, 7.4, p = 0.002). Lastly, only high cognitive loads elicited significant differences between hypoxic and normoxic conditions but just for SDNN (−13.3 ms, 95% CI, −17.5, −8.9, p < 0.0001). Our study observations suggest that compared to low cognitive loads, performing high-cognitive-load tasks significantly alters ANS activity, especially under hypoxic conditions. Accounting for this response is critical, as military personnel during flight operations sustain exposure to high cognitive loads of unpredictable duration and frequency. Additionally, this is likely compounded by the increased ANS activity consequent to pre-flight activities and anticipation of combat-related outcomes.
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Open AccessSystematic Review
Enhancement of Vascularization and Ovarian Follicle Survival Using Stem Cells in Cryopreserved Ovarian Tissue Transplantation—A Systematic Review
by
Luca Zaninović, Marko Bašković, Davor Ježek, Dubravko Habek, Zenon Pogorelić, Ana Katušić Bojanac, Vesna Elveđi Gašparović and Lana Škrgatić
Biology 2024, 13(5), 342; https://doi.org/10.3390/biology13050342 - 14 May 2024
Abstract
The increase in cancer survival rates has put a focus on ensuring fertility preservation procedures for cancer patients. Ovarian tissue cryopreservation presents the only option for prepubertal girls and patients who require immediate start of treatment and, therefore, cannot undergo controlled ovarian stimulation.
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The increase in cancer survival rates has put a focus on ensuring fertility preservation procedures for cancer patients. Ovarian tissue cryopreservation presents the only option for prepubertal girls and patients who require immediate start of treatment and, therefore, cannot undergo controlled ovarian stimulation. We aimed to provide an assessment of stem cells’ impact on cryopreserved ovarian tissue grafts in regard to the expression of growth factors, angiogenesis promotion, tissue oxygenation, ovarian follicle survival and restoration of endocrine function. For this systematic review, we searched the Scopus and PubMed databases and included reports of trials using murine and/or human cryopreserved ovarian tissue for transplantation or in vitro culture in combination with mesenchymal stem cell administration to the grafting site. Of the 1201 articles identified, 10 met the criteria. The application of stem cells to the grafting site has been proven to support vascular promotion and thereby shorten the period of tissue hypoxia, which is reflected in the increased number of remaining viable follicles and faster recovery of ovarian endocrine function. Further research is needed before implementing the use of stem cells in OT cryopreservation and transplantation procedures in clinical practice. Complex ethical dilemmas make this process more difficult.
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(This article belongs to the Section Reproductive Biology)
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Applying a Random Encounter Model to Estimate the Asiatic Black Bear (Ursus thibetanus) Density from Camera Traps in the Hindu Raj Mountains, Pakistan
by
Faizan Ahmad, Tomoki Mori, Muhammad Rehan, Luciano Bosso and Muhammad Kabir
Biology 2024, 13(5), 341; https://doi.org/10.3390/biology13050341 - 14 May 2024
Abstract
Estimating the population density of vulnerable species, such as the elusive and nocturnal Asiatic black bear (Ursus thibetanus), is essential for wildlife conservation and management. We used camera traps and a Random Encounter Model (REM) to estimate the population density of
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Estimating the population density of vulnerable species, such as the elusive and nocturnal Asiatic black bear (Ursus thibetanus), is essential for wildlife conservation and management. We used camera traps and a Random Encounter Model (REM) to estimate the population density of U. thibetanus during the autumn and winter seasons in the Hindu Raj Mountains. We installed 23 camera traps from October to December 2020 and acquired 66 independent pictures of Asiatic black bears over 428 nights of capture. Our results showed that the bears preferred lowland areas with the presence of Quercus spp. We estimated, using the REM, a population density of U. thibetanus of 1.875 (standard error = 0.185) per square kilometer, which is significantly higher than that in other habitats. Our results showed that during autumn and winter, the bear population density tends to concentrate at lower elevations. Forest cover showed a positive correlation with the rates of bear encounters unlike the Euclidean distance to human settlements, altitude, and aspect variables. The approaches used here are cost-effective for estimating the population density of rare and vulnerable species such as U. thibetanus, and can be used to estimate their population density in Pakistan. Population density estimation can identify areas where the bears live and human–bear conflicts occurred and use this information in future wildlife management plans.
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(This article belongs to the Section Zoology)
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Spectroscopic Investigation of Tomato Seed Germination Stimulated by Trichoderma spp.
by
Igor Vukelić, Danka Radić, Ilinka Pećinar, Steva Lević, Daniela Djikanović, Ksenija Radotić and Dejana Panković
Biology 2024, 13(5), 340; https://doi.org/10.3390/biology13050340 - 13 May 2024
Abstract
Seed germination is a complex process that can be negatively affected by numerous stresses. Trichoderma spp. are known as effective biocontrol agents as well as plant growth and germination stimulators. However, understanding of the early interactions between seeds and Trichoderma spp. remains limited.
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Seed germination is a complex process that can be negatively affected by numerous stresses. Trichoderma spp. are known as effective biocontrol agents as well as plant growth and germination stimulators. However, understanding of the early interactions between seeds and Trichoderma spp. remains limited. In the present paper, Fourier-transform infrared spectroscopy (FTIR) and Raman spectroscopy were used to reveal the nature of tomato seed germination as stimulated by Trichoderma. A rapid response of tomato seeds to Trichoderma spp. was observed within 48 h on Murashige and Skoog medium (MS) substrate, preceding any physical contact. Raman analysis indicated that both Trichoderma species stimulated phenolic compound synthesis by triggering plant-specific responses in seed radicles. The impact of T. harzianum and T. brevicompactum on two tomato cultivars resulted in alterations to the middle lamella pectin, cellulose, and xyloglucan in the primary cell wall. The Raman spectra indicated increased xylan content in NA with T9 treatment as well as increased hemicelluloses in GZ with T4 treatment. Moreover, T4 treatment resulted in elevated conjugated aldehydes in lignin in GZ, whereas the trend was reversed in NA. Additionally, FTIR analysis revealed significant changes in total protein levels in Trichoderma spp.-treated tomato seed radicles, with simultaneous decreases in pectin and/or xyloglucan. Our results indicate that two complementary spectroscopic methods, FTIR and Raman spectroscopy, can give valuable information on rapid changes in the plant cell wall structure of tomato radicles during germination stimulated by Trichoderma spp.
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(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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Open AccessCommunication
Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135
by
Ekaterina Frantsuzova, Alexander Bogun, Olga Kopylova, Anna Vetrova, Inna Solyanikova, Rostislav Streletskii and Yanina Delegan
Biology 2024, 13(5), 339; https://doi.org/10.3390/biology13050339 - 13 May 2024
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds.
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The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the “panIGRome” of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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(This article belongs to the Special Issue Environmental Microbes: From Distribution Exploration to Biosignatures Analysis)
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Integrative Multi-Omics Analysis for Etiology Classification and Biomarker Discovery in Stroke: Advancing towards Precision Medicine
by
Alberto Labarga, Judith Martínez-Gonzalez and Miguel Barajas
Biology 2024, 13(5), 338; https://doi.org/10.3390/biology13050338 - 13 May 2024
Abstract
Recent advancements in high-throughput omics technologies have opened new avenues for investigating stroke at the molecular level and elucidating the intricate interactions among various molecular components. We present a novel approach for multi-omics data integration on knowledge graphs and have applied it to
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Recent advancements in high-throughput omics technologies have opened new avenues for investigating stroke at the molecular level and elucidating the intricate interactions among various molecular components. We present a novel approach for multi-omics data integration on knowledge graphs and have applied it to a stroke etiology classification task of 30 stroke patients through the integrative analysis of DNA methylation and mRNA, miRNA, and circRNA. This approach has demonstrated promising performance as compared to other existing single technology approaches.
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(This article belongs to the Special Issue Multi-omics Data Integration in Complex Diseases)
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