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
New Methods in Digital Wood Anatomy: The Use of Pixel-Contrast Densitometry with Example of Angiosperm Shrubs in Southern Siberia
Biology 2024, 13(4), 223; https://doi.org/10.3390/biology13040223 - 28 Mar 2024
Abstract
This methodological study describes the adaptation of a new method in digital wood anatomy, pixel-contrast densitometry, for angiosperm species. The new method was tested on eight species of shrubs and small trees in Southern Siberia, whose wood structure varies from ring-porous to diffuse-porous,
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This methodological study describes the adaptation of a new method in digital wood anatomy, pixel-contrast densitometry, for angiosperm species. The new method was tested on eight species of shrubs and small trees in Southern Siberia, whose wood structure varies from ring-porous to diffuse-porous, with different spatial organizations of vessels. A two-step transformation of wood cross-section photographs by smoothing and Otsu’s classification algorithm was proposed to separate images into cell wall areas and empty spaces within (lumen) and between cells. Good synchronicity between measurements within the ring allowed us to create profiles of wood porosity (proportion of empty spaces) describing the growth ring structure and capturing inter-annual differences between rings. For longer-lived species, 14–32-year series from at least ten specimens were measured. Their analysis revealed that maximum (for all wood types), mean, and minimum porosity (for diffuse-porous wood) in the ring have common external signals, mostly independent of ring width, i.e., they can be used as ecological indicators. Further research directions include a comparison of this method with other approaches in densitometry, clarification of sample processing, and the extraction of ecologically meaningful data from wood structures.
Full article
(This article belongs to the Section Plant Science)
Open AccessArticle
Physio-Biochemical Insights into the Cold Resistance Variations among Nectarine (Prunus persica (L.) Batsch var. nectarina) Cultivars
by
Guojie Qin, Yifan Liu, Jianzi Liu, Gefang Bian, Shikai Zhang, Yi Liu, Lixiang Zuo and Chunzhen Cheng
Biology 2024, 13(4), 222; https://doi.org/10.3390/biology13040222 - 28 Mar 2024
Abstract
Cold stress occurs in late winter and early spring threatens greatly the nectarine industry. In this study, the semi-lethal low temperature (LT50) and thirteen cold resistance related parameters of five nectarine cultivars, including ‘Nonglehong little princess’ (LP), ‘Luyou No. 5’ (LY),
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Cold stress occurs in late winter and early spring threatens greatly the nectarine industry. In this study, the semi-lethal low temperature (LT50) and thirteen cold resistance related parameters of five nectarine cultivars, including ‘Nonglehong little princess’ (LP), ‘Luyou No. 5’ (LY), ‘Nonglehong No. 6’ (NL), ‘Zhongyou No. 20’ (ZY) and ‘Qiuhongzhu’ (QH), were determined. Based on these parameters, they were categorized into high—(HR, including NL and LP), moderate—(MR, including QH) and low-cold resistant (LR, including ZY and LY) groups. The relative water (RW), proline (PRO), soluble sucrose (SS) and soluble protein (SP) contents, and superoxide dismutase (SOD) and peroxidase (POD) activities of HR cultivars were higher while their relative electronic conductivity (RE), malondialdehyde (MDA) and gibberellin acid (GA3) contents and catalase (CAT) activity were lower than other cultivars during natural overwintering. Redundancy analysis revealed that the lowest temperature in a day (LT) and LT50 significantly explains 69.8% and 10.9% of these physiological variables, respectively. Moreover, GA3 and indoleacetic acid (IAA) contents and CAT activity were positively correlated, while PRO, SS, ABA and RW contents were negatively correlated with both LT and LT50. Our study will be helpful in understanding the cold resistance variations of nectarine germplasm resources.
Full article
(This article belongs to the Section Plant Science)
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Open AccessArticle
Engineering a Microphysiological Model for Regenerative Endodontic Studies
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Diana Sanz-Serrano, Montse Mercade, Francesc Ventura and Cristina Sánchez-de-Diego
Biology 2024, 13(4), 221; https://doi.org/10.3390/biology13040221 - 28 Mar 2024
Abstract
Dental pulp infections are common buccal diseases. When this happens, endodontic treatments are needed to disinfect and prepare the root canal for subsequent procedures. However, the lack of suitable in vitro models representing the anatomy of an immature root canal hinders research on
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Dental pulp infections are common buccal diseases. When this happens, endodontic treatments are needed to disinfect and prepare the root canal for subsequent procedures. However, the lack of suitable in vitro models representing the anatomy of an immature root canal hinders research on regenerative events crucial in endodontics, such as regenerative procedures. This study aimed to develop a 3D microphysiological system (MPS) to mimic an immature root canal and assess the cytotoxicity of various irrigating solutions on stem cells. Utilizing the Dental Stem Cells SV40 (DSCS) cell line derived from human apical papilla stem cells, we analyzed the effects of different irrigants, including etidronic acid. The results indicated that irrigating solutions diminished cell viability in 2D cultures and influenced cell adhesion within the microphysiological device. Notably, in our 3D studies in the MPS, 17% EDTA and 9% 1-hydroxyethylidene-1, 1-bisphosphonate (HEBP) irrigating solutions demonstrated superior outcomes in terms of DSCS viability and adherence compared to the control. This study highlights the utility of the developed MPS for translational studies in root canal treatments and suggests comparable efficacy between 9% HEBP and 17% EDTA irrigating solutions, offering potential alternatives for clinical applications.
Full article
(This article belongs to the Section Cell Biology)
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Open AccessReview
Neuroarchitecture: How the Perception of Our Surroundings Impacts the Brain
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Sarah Abbas, Nathalie Okdeh, Rabih Roufayel, Hervé Kovacic, Jean-Marc Sabatier, Ziad Fajloun and Ziad Abi Khattar
Biology 2024, 13(4), 220; https://doi.org/10.3390/biology13040220 - 28 Mar 2024
Abstract
The study of neuroarchitecture is concerned with the significant effects of architecture on human behavior, emotions and thought processes. This review explores the intricate relationship between the brain and perceived environments, focusing on the roles of the anterior cingulate cortex (ACC) and parahippocampal
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The study of neuroarchitecture is concerned with the significant effects of architecture on human behavior, emotions and thought processes. This review explores the intricate relationship between the brain and perceived environments, focusing on the roles of the anterior cingulate cortex (ACC) and parahippocampal place area (PPA) in processing architectural stimuli. It highlights the importance of mirror neurons in generating empathetic responses to our surroundings and discusses how architectural elements like lighting, color, and space layout significantly impact emotional and cognitive experiences. The review also presents insights into the concept of cognitive maps and spatial navigation, emphasizing the role of architecture in facilitating wayfinding and orientation. Additionally, it addresses how neuroarchitecture can be applied to enhance learning and healing environments, drawing upon principles from the Reggio Emilia approach and considerations for designing spaces for the elderly and those with cognitive impairments. Overall, this review offers a neuroscientific basis for understanding how human cognition, emotions, spatial navigation, and well-being are influenced by architectural design.
Full article
(This article belongs to the Special Issue The Convergence of Neuroscience and ICT: From Data to Insights)
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Open AccessArticle
Nanoparticles and Chemical Inducers: A Sustainable Shield against Onion White Rot
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Ahmed Mohammed Elenany, Mahmoud Mohammed Mohammed Atia, Entsar E. A. Abbas, Mahmoud Moustafa, Mohammed O. Alshaharni, Sally Negm and Ahmed Saeed Mohammed Ali Elnahal
Biology 2024, 13(4), 219; https://doi.org/10.3390/biology13040219 - 27 Mar 2024
Abstract
This study investigated the effectiveness of nanoparticles and chemical inducers in managing onion white rot caused by Sclerotium cepivorum. The pathogen severely threatens onion cultivation, resulting in significant yield losses and economic setbacks. Traditional fungicides, though effective, raise environmental concerns, prompting a
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This study investigated the effectiveness of nanoparticles and chemical inducers in managing onion white rot caused by Sclerotium cepivorum. The pathogen severely threatens onion cultivation, resulting in significant yield losses and economic setbacks. Traditional fungicides, though effective, raise environmental concerns, prompting a shift toward eco-friendly alternatives. In this study, four S. cepivorum isolates were utilized, each exhibiting varying degrees of pathogenicity, with the third isolate from Abu-Hamad demonstrating the highest potency. During the in vitro studies, three nanoparticles (NPs) were investigated, including Fe3O4 NPs, Cu NPs, and ZnO NPs, which demonstrated the potential to inhibit mycelial growth, with salicylic acid and Fe3O4 NPs exhibiting synergistic effects. In vivo, these nanoparticles reduced the disease incidence and severity, with Fe3O4 NPs at 1000–1400 ppm resulting in 65.0–80.0% incidence and 80.0–90.0% severity. ZnO NPs had the most positive impact on the chlorophyll content, while Cu NPs had minimal effects. At 1000 ppm, Fe3O4 NPs had variable effects on the phenolic compounds (total: 6.28, free: 4.81, related: 2.59), while ZnO NPs caused minor fluctuations (total: 3.60, free: 1.82, related: 1.73). For the chemical inducers, salicylic acid reduced the disease (10.0% incidence, 25.0% to 10.0% severity) and promoted growth, and it elevated the chlorophyll values and enhanced the phenolic compounds in infected onions. Potassium phosphate dibasic (PDP) had mixed effects, and ascorbic acid showed limited efficacy toward disease reduction. However, PDP at 1400 ppm and ascorbic acid at 1000 ppm elevated the chlorophyll values and enhanced the phenolic compounds. Furthermore, this study extended to traditional fungicides, highlighting their inhibitory effects on S. cepivorum. This research provides a comprehensive comparative analysis of these approaches, emphasizing their potential in eco-friendly onion white rot management.
Full article
(This article belongs to the Section Plant Science)
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Open AccessArticle
Reproductive Ability Disparity in the Pacific Whiteleg Shrimp (Penaeus vannamei): Insights from Ovarian Cellular and Molecular Levels
by
Jianchun Zhang, Jie Kong, Jiawang Cao, Ping Dai, Baolong Chen, Jian Tan, Xianhong Meng, Kun Luo, Qiang Fu, Peiming Wei, Sheng Luan and Juan Sui
Biology 2024, 13(4), 218; https://doi.org/10.3390/biology13040218 - 27 Mar 2024
Abstract
The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the
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The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the inability to spawn, while others undergo multiple maturations and contribute to the majority of larval supply. Despite numerous studies that have been conducted on the regulatory mechanisms of ovarian development in shrimp, the factors contributing to the differences in reproductive capacity among females remain unclear. To elucidate the underlying mechanisms, this study examined the differences in the ovarian characteristics between high and low reproductive bulks at different maturity stages, focusing on the cellular and molecular levels. Transmission electron microscopy analysis revealed that the abundance of the endoplasmic reticulum, ribosomes, mitochondria, and mitochondrial cristae in oocytes of high reproductive bulk was significantly higher than that of the low reproductive bulk in the early stages of ovarian maturation (stages I and II). As the ovaries progressed to late-stage maturation (stages III and IV), differences in the internal structures of oocytes between females with different reproductive capacities gradually diminished. Transcriptome analysis identified differentially expressed genes (DEGs) related to the mitochondria between two groups, suggesting that energy production processes might play a crucial role in the observed variations in ovary development. The expression levels of the ETS homology factor (EHF) and PRDI-BF1 and RIZ homology domain containing 9 (PRDM9), which were significantly different between the two groups, were compared using qRT-PCR in individuals at different stages of ovarian maturation. The results showed a significantly higher expression of the EHF gene in the ovaries of high reproductive bulk at the II and IV maturity stages compared to the low reproductive bulk, while almost no expression was detected in the eyestalk tissue of the high reproductive bulk. The PRDM9 gene was exclusively expressed in ovarian tissue, with significantly higher expression in the ovaries of the high reproductive bulk at the four maturity stages compared to the low reproductive bulk. Fluorescence in situ hybridization further compared the expression patterns of EHF and PRDM9 in the ovaries of individuals with different fertility levels, with both genes showing stronger positive signals in the high reproductive bulk at the four ovarian stages. These findings not only contribute to our understanding of the regulatory mechanisms involved in shrimp ovarian development, but also provide valuable insights for the cultivation of new varieties aimed at improving shrimp fecundity.
Full article
Open AccessArticle
A Preliminary Study on Quantitative Analysis of Collagen and Apoptosis Related Protein on 1064 nm Laser-Induced Skin Injury
by
Qiong Ma, Yingwei Fan, Yufang Cui, Zhenkun Luo and Hongxiang Kang
Biology 2024, 13(4), 217; https://doi.org/10.3390/biology13040217 - 27 Mar 2024
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To investigate the associated factors concerning collagen and the expression of apoptosis-related proteins in porcine skin injuries induced by laser exposure, live pig skin was irradiated at multiple spots one time, using a grid-array method with a 1064 nm laser at different power
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To investigate the associated factors concerning collagen and the expression of apoptosis-related proteins in porcine skin injuries induced by laser exposure, live pig skin was irradiated at multiple spots one time, using a grid-array method with a 1064 nm laser at different power outputs. The healing process of the laser-treated areas, alterations in collagen structure, and changes in apoptosis were continuously observed and analyzed from 6 h to 28 days post-irradiation. On the 28th day following exposure, wound contraction and recovery were notably sluggish in the medium-high dose group, displaying more premature and delicate type III collagen within the newly regenerated tissues. The collagen density in these groups was roughly 37–58% of that in the normal group. Between days 14 and 28 after irradiation, there was a substantial rise in apoptotic cell count in the forming epidermis and granulation tissue of the medium-high dose group, in contrast to the normal group. Notably, the expression of proapoptotic proteins Bax, caspase-3, and caspase-9 surged significantly 14 days after irradiation in the medium-high dose group and persisted at elevated levels on the 28th day. During the later stage of wound healing, augmented apoptotic cell population and insufficient collagen generation in the newly generated skin tissue of the medium-high dose group were closely associated with delayed wound recovery.
Full article
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Open AccessArticle
PRMT5 Mediated HIF1α Signaling and Ras-Related Nuclear Protein as Promising Biomarker in Hepatocellular Carcinoma
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Wafaa Abumustafa, Darko Castven, Fatemeh Saheb Sharif-Askari, Batoul Abi Zamer, Mawieh Hamad, Jens-Uwe Marquardt and Jibran Sualeh Muhammad
Biology 2024, 13(4), 216; https://doi.org/10.3390/biology13040216 - 27 Mar 2024
Abstract
Protein arginine N-methyltransferase 5 (PRMT5) has been identified as a potential therapeutic target for various cancer types. However, its role in regulating the hepatocellular carcinoma (HCC) transcriptome remains poorly understood. In this study, publicly available databases were employed to investigate PRMT5 expression, its
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Protein arginine N-methyltransferase 5 (PRMT5) has been identified as a potential therapeutic target for various cancer types. However, its role in regulating the hepatocellular carcinoma (HCC) transcriptome remains poorly understood. In this study, publicly available databases were employed to investigate PRMT5 expression, its correlation with overall survival, targeted pathways, and genes of interest in HCC. Additionally, we utilized in-house generated NGS data to explore PRMT5 expression in dysplastic nodules compared to hepatocellular carcinoma. Our findings revealed that PRMT5 is significantly overexpressed in HCC compared to normal liver, and elevated expression correlates with poor overall survival. To gain insights into the mechanism driving PRMT5 overexpression in HCC, we analyzed promoter CpG islands and methylation status in HCC compared to normal tissues. Pathway analysis of PRMT5 knockdown in the HCC cells revealed a connection between PRMT5 expression and genes related to the HIF1α pathway. Additionally, by filtering PRMT5-correlated genes within the HIF1α pathway and selecting up/downregulated genes in HCC patients, we identified Ras-related nuclear protein (RAN) as a target associated with overall survival. For the first time, we report that PRMT5 is implicated in the regulation of HIF1A and RAN genes, suggesting the potential prognostic utility of PRMT5 in HCC.
Full article
(This article belongs to the Topic Biomarkers and Therapeutic Targets Based on Bioinformatical Studies)
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Open AccessArticle
Increased Vulnerability to Ferroptosis in FUS-ALS
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Muhammad Ismail, Dajana Großmann and Andreas Hermann
Biology 2024, 13(4), 215; https://doi.org/10.3390/biology13040215 - 26 Mar 2024
Abstract
Ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxide accumulation, plays a pivotal role in various pathological conditions, including neurodegenerative diseases. While reasonable evidence for ferroptosis exists, e.g., in Parkinson’s disease or Alzheimer’s disease, there are only a few reports
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Ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxide accumulation, plays a pivotal role in various pathological conditions, including neurodegenerative diseases. While reasonable evidence for ferroptosis exists, e.g., in Parkinson’s disease or Alzheimer’s disease, there are only a few reports on amyotrophic lateral sclerosis (ALS), a fast progressive and incurable neurodegenerative disease characterized by progressive motor neuron degeneration. Interestingly, initial studies have suggested that ferroptosis might be significantly involved in ALS. Key features of ferroptosis include oxidative stress, glutathione depletion, and alterations in mitochondrial morphology and function, mediated by proteins such as GPX4, xCT, ACSL4 FSP1, Nrf2, and TfR1. Induction of ferroptosis involves small molecule compounds like erastin and RSL3, which disrupt system Xc− and GPX4 activity, respectively, resulting in lipid peroxidation and cellular demise. Mutations in fused in sarcoma (FUS) are associated with familial ALS. Pathophysiological hallmarks of FUS-ALS involve mitochondrial dysfunction and oxidative damage, implicating ferroptosis as a putative cell-death pathway in motor neuron demise. However, a mechanistic understanding of ferroptosis in ALS, particularly FUS-ALS, remains limited. Here, we investigated the vulnerability to ferroptosis in FUS-ALS cell models, revealing mitochondrial disturbances and increased susceptibility to ferroptosis in cells harboring ALS-causing FUS mutations. This was accompanied by an altered expression of ferroptosis-associated proteins, particularly by a reduction in xCT expression, leading to cellular imbalance in the redox system and increased lipid peroxidation. Iron chelation with deferoxamine, as well as inhibition of the mitochondrial calcium uniporter (MCU), significantly alleviated ferroptotic cell death and lipid peroxidation. These findings suggest a link between ferroptosis and FUS-ALS, offering potential new therapeutic targets.
Full article
(This article belongs to the Special Issue Ferroptosis: Mechanisms and Human Disease)
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Open AccessArticle
Comparative Transcriptomics Analysis Reveals Unique Immune Response to Grass Carp Reovirus Infection in Barbel Chub (Squaliobarbus curriculus)
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Yuhong Huang, Xiaodong Wang, Zhao Lv, Xudong Hu, Baohong Xu, Hong Yang, Tiaoyi Xiao and Qiaolin Liu
Biology 2024, 13(4), 214; https://doi.org/10.3390/biology13040214 - 25 Mar 2024
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Grass carp (Ctenopharyngodon idella) and barbel chub (Squaliobarbus curriculus)—both Leuciscinae subfamily species—demonstrate differences in grass carp reovirus (GCRV) infection resistance. We infected barbel chubs with type II GCRV and subjected their liver, spleen, head kidney, and trunk kidney samples
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Grass carp (Ctenopharyngodon idella) and barbel chub (Squaliobarbus curriculus)—both Leuciscinae subfamily species—demonstrate differences in grass carp reovirus (GCRV) infection resistance. We infected barbel chubs with type II GCRV and subjected their liver, spleen, head kidney, and trunk kidney samples to investigate anti-GCRV immune mechanisms via RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). We identified 139, 970, 867, and 2374 differentially expressed genes (DEGs) in the liver, spleen, head kidney, and trunk kidney, respectively. Across all four tissues, gene ontology analysis revealed significant immune response-related DEG enrichment, and the Kyoto Encyclopedia of Genes and Genomes analysis revealed pattern recognition receptor (PRR) and cytokine-related pathway enrichment. We noted autophagy pathway enrichment in the spleen, head kidney, and trunk kidney; apoptosis pathway enrichment in the spleen and trunk kidney; and complement- and coagulation-cascade pathway enrichment in only the spleen. Comparative transcriptome analysis between GCRV-infected barbel chubs and uninfected barbel chubs comprehensively revealed that PRR, cytokine-related, complement- and coagulation-cascade, apoptosis, and autophagy pathways are potential key factors influencing barbel chub resistance to GCRV infection. qRT-PCR validation of 11 immune-related DEGs confirmed our RNA-seq data’s accuracy. These findings provide a theoretical foundation and empirical evidence for the understanding of GCRV infection resistance in barbel chub and hybrid grass carp–barbel chub breeding.
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Open AccessArticle
Enhanced TfR1 Recognition of Myocardial Injury after Acute Myocardial Infarction with Cardiac Fibrosis via Pre-Degrading Excess Fibrotic Collagen
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Wenwen Yang, Yueqi Wang, Hongzheng Li, Feifei Liao, Yuxuan Peng, Aimei Lu, Ling Tan, Hua Qu, Linzi Long and Changgeng Fu
Biology 2024, 13(4), 213; https://doi.org/10.3390/biology13040213 - 25 Mar 2024
Abstract
The fibrosis process after myocardial infarction (MI) results in a decline in cardiac function due to fibrotic collagen deposition and contrast agents’ metabolic disorders, posing a significant challenge to conventional imaging strategies in making heart damage clear in the fibrosis microenvironment. To address
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The fibrosis process after myocardial infarction (MI) results in a decline in cardiac function due to fibrotic collagen deposition and contrast agents’ metabolic disorders, posing a significant challenge to conventional imaging strategies in making heart damage clear in the fibrosis microenvironment. To address this issue, we developed an imaging strategy. Specifically, we pretreated myocardial fibrotic collagen with collagenase I combined with human serum albumin (HSA-C) and subsequently visualized the site of cardiac injury by near-infrared (NIR) fluorescence imaging using an optical contrast agent (CI, CRT-indocyanine green) targeting transferrin receptor 1 peptides (CRT). The key point of this strategy is that pretreatment with HSA-C can reduce background signal interference in the fibrotic tissue while enhancing CI uptake at the heart lesion site, making the boundary between the injured heart tissue and the normal myocardium clearer. Our results showed that compared to that in the untargeted group, the normalized fluorescence intensity of cardiac damage detected by NIR in the targeted group increased 1.28-fold. The normalized fluorescence intensity increased 1.21-fold in the pretreatment group of the targeted groups. These data demonstrate the feasibility of applying pretreated fibrotic collagen and NIR contrast agents targeting TfR1 to identify ferroptosis at sites of cardiac injury, and its clinical value in the management of patients with MI needs further study.
Full article
(This article belongs to the Special Issue Development of New Optical Techniques and Methods for Basic Biology and Biomedical Applications)
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Open AccessArticle
Evidence for Selection on Mitochondrial OXPHOS Genes in the Mediterranean Killifish Aphanius fasciatus Valenciennes, 1821
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Anna Maria Pappalardo, Giada Santa Calogero, Radek Šanda, Marta Giuga and Venera Ferrito
Biology 2024, 13(4), 212; https://doi.org/10.3390/biology13040212 - 25 Mar 2024
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) genes are a system subject to selection under determined environmental constraints despite a neutral evolution model that has long been hypothesized for the mitochondrial genome. In this study, the sequences of ND1, Cytb, and COI OXPHOS genes
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Mitochondrial oxidative phosphorylation (OXPHOS) genes are a system subject to selection under determined environmental constraints despite a neutral evolution model that has long been hypothesized for the mitochondrial genome. In this study, the sequences of ND1, Cytb, and COI OXPHOS genes were analyzed in six populations of the eurythermal and euryhaline killifish A. fasciatus, to detect non-synonymous mutations leading to amino acid changes and to check whether selection acted on them using tests of recombination and selection. The results indicate a high COI and Cytb gene diversity and a high percentage of private haplotypes in all populations. In the Greek population, non-synonymous nucleotide substitutions were observed in the N-terminal region of COI and Cytb. Positively selected sites were also found. The information we obtained from the mitochondrial DNA sequences of A. fasciatus adds to the growing data on selective pressure acting on mitochondrial DNA in non-model species. These results should be explored from the perspective of the local adaptation of eurythermal and euryhaline species and supported using experimental evidence to better understand the interplay between historical climatic events and local adaptation and how each of them contributes to shaping the genetic structure of this species.
Full article
(This article belongs to the Special Issue Mitochondria: The Signaling Organelle)
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Open AccessArticle
Comparative Metabolomics and Transcriptome Studies of Two Forms of Rhododendron chrysanthum Pall. under UV-B Stress
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Wang Yu, Fushuai Gong, Xiangru Zhou, Hongwei Xu, Jie Lyu and Xiaofu Zhou
Biology 2024, 13(4), 211; https://doi.org/10.3390/biology13040211 - 24 Mar 2024
Abstract
Rhododendron chrysanthum Pall. (R. chrysanthum), a plant with UV-B resistance mechanisms that can adapt to alpine environments, has gained attention as an important plant resource with the ability to cope with UV-B stress. In this experiment, R. chrysanthums derived from the
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Rhododendron chrysanthum Pall. (R. chrysanthum), a plant with UV-B resistance mechanisms that can adapt to alpine environments, has gained attention as an important plant resource with the ability to cope with UV-B stress. In this experiment, R. chrysanthums derived from the same origin were migrated to different culture environments (artificial climate chamber and intelligent artificial incubator) to obtain two forms of R. chrysanthum. After UV-B irradiation, 404 metabolites and 93,034 unigenes were detected. Twenty-six of these different metabolites were classified as UV-B-responsive metabolites. Glyceric acid is used as a potential UV-B stress biomarker. The domesticated Rhododendron chrysanthum Pall. had high amino acid and SOD contents. The study shows that the domesticated Rhododendron chrysanthum Pall. has significant UV-B resistance. The transcriptomics results show that the trends of DEGs after UV-B radiation were similar for both forms of R. chrysanthum: cellular process and metabolic process accounted for a higher proportion in biological processes, cellular anatomical entity accounted for the highest proportion in the cellular component, and catalytic activity and binding accounted for the highest proportion in the molecular function category. Through comparative study, the forms of metabolites resistant to UV-B stress in plants can be reflected, and UV-B radiation absorption complexes can be screened for application in future specific practices. Moreover, by comparing the differences in response to UV-B stress between the two forms of R. chrysanthum, references can be provided for cultivating domesticated plants with UV-B stress resistance characteristics. Research on the complex mechanism of plant adaptation to UV-B will be aided by these results.
Full article
(This article belongs to the Collection Abiotic Stress in Plants and Resilience: Recent Advances)
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Open AccessArticle
Immunohistochemical Characterization of Langerhans Cells in the Skin of Three Amphibian Species
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Giorgia Pia Lombardo, Anthea Miller, Marialuisa Aragona, Emmanuele Messina, Angelo Fumia, Michał Kuciel, Alessio Alesci, Simona Pergolizzi and Eugenia Rita Lauriano
Biology 2024, 13(4), 210; https://doi.org/10.3390/biology13040210 - 23 Mar 2024
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The amphibian taxon includes three orders that present different morphological characteristics: Anura, Caudata, and Apoda. Their skin has a crucial role: it acts as an immune organ constituting a physical, chemical, immunological, and microbiological barrier to pathogen insult and conducts essential physiological processes.
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The amphibian taxon includes three orders that present different morphological characteristics: Anura, Caudata, and Apoda. Their skin has a crucial role: it acts as an immune organ constituting a physical, chemical, immunological, and microbiological barrier to pathogen insult and conducts essential physiological processes. Amphibians have developed specialized features to protect the vulnerable skin barrier, including a glandular network beneath the skin surface that can produce antimicrobial and toxic substances, thus contributing to the defense against pathogens and predators. This study aims to characterize Langerhans cells in the skin of Lithobates catesbeianus (order: Anura; Shaw, 1802), Amphiuma means (order: Caudata; Garden, 1821), and Typhlonectes natans (order: Apoda; Fischer, 1880) with the following antibodies: Langerin/CD207 (c-type lectin), Major Histocompatibility Complex (MHC)II, and Toll-like receptor (TLR)2 (expressed by different types of DCs). Our results showed Langerhans cells positive for Langerin CD/207 in the epidermis of the three species; moreover, some antigen-presenting cells (APCs) in the connective tissue expressed TLR2 and MHCII. The distribution of the Langerhans cells is very similar in the three amphibians examined, despite their different habitats. A greater knowledge of the amphibian immune system could be useful to better understand the phylogeny of vertebrates and to safeguard amphibians from population declines. Furthermore, the similarities between amphibians’ and human skin concerning immunological features may be useful in both biology and translational medicine.
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Open AccessSystematic Review
Zebrafish Feed Intake: A Systematic Review for Standardizing Feeding Management in Laboratory Conditions
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Rosario Licitra, Baldassare Fronte, Tiziano Verri, Maria Marchese, Chiara Sangiacomo and Filippo Maria Santorelli
Biology 2024, 13(4), 209; https://doi.org/10.3390/biology13040209 - 23 Mar 2024
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Zebrafish are one of the most used animal models in biological research and a cost-effective alternative to rodents. Despite this, nutritional requirements and standardized feeding protocols have not yet been established for this species. This is important to avoid nutritional effects on experimental
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Zebrafish are one of the most used animal models in biological research and a cost-effective alternative to rodents. Despite this, nutritional requirements and standardized feeding protocols have not yet been established for this species. This is important to avoid nutritional effects on experimental outcomes, and especially when zebrafish models are used in preclinical studies, as many diseases have nutritional confounding factors. A key aspect of zebrafish nutrition is related to feed intake, the amount of feed ingested by each fish daily. With the goal of standardizing feeding protocols among the zebrafish community, this paper systematically reviews the available data from 73 studies on zebrafish feed intake, feeding regimes (levels), and diet composition. Great variability was observed regarding diet composition, especially regarding crude protein (mean 44.98 ± 9.87%) and lipid content (9.91 ± 5.40%). Interestingly, the gross energy levels of the zebrafish diets were similar across the reviewed studies (20.39 ± 2.10 kilojoules/g of feed). In most of the reviewed papers, fish received a predetermined quantity of feed (feed supplied). The authors fed the fish according to the voluntary intake and then calculated feed intake (FI) in only 17 papers. From a quantitative point of view, FI was higher than when a fixed quantity (pre-defined) of feed was supplied. Also, the literature showed that many biotic and abiotic factors may affect zebrafish FI. Finally, based on the FI data gathered from the literature, a new feeding protocol is proposed. In summary, a daily feeding rate of 9–10% of body weight is proposed for larvae, whereas these values are equal to 6–8% for juveniles and 5% for adults when a dry feed with a proper protein and energy content is used.
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Open AccessReview
Assessment of Human Health Impacts from Invasive Pufferfish (Attacks, Poisonings and Fatalities) across the Eastern Mediterranean
by
Aylin Ulman, Abdel Fattah Nazmi Abd Rabou, Sara Al Mabruk, Michel Bariche, Murat Bilecenoğlu, Nazli Demirel, Bella S. Galil, Mehmet Fatih Hüseyinoğlu, Carlos Jimenez, Louis Hadjioannou, Ali Rıza Kosker, Panagiota Peristeraki, Adib Saad, Ziad Samaha, Maria Th. Stoumboudi, Tarek A. Temraz and Paraskevi K. Karachle
Biology 2024, 13(4), 208; https://doi.org/10.3390/biology13040208 - 23 Mar 2024
Abstract
The silver-cheeked toadfish Lagocephalus sceleratus (Gmelin 1789), and to a lesser degree the orange spotted toadfish Torquigener hypselogeneion (Bleeker, 1852), pose threats to human health from physical attacks and poisonings in the Eastern Mediterranean Sea. This study reviewed human health-related impacts resulting from
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The silver-cheeked toadfish Lagocephalus sceleratus (Gmelin 1789), and to a lesser degree the orange spotted toadfish Torquigener hypselogeneion (Bleeker, 1852), pose threats to human health from physical attacks and poisonings in the Eastern Mediterranean Sea. This study reviewed human health-related impacts resulting from these pufferfish, compiling and assessing records from online sources, the peer-reviewed literature, medical records, personal interviews, and observations across the Eastern Mediterranean in the years 2004 to 2023. A total of 198 events impacting human health were documented: 28 records of physical attacks, at least 144 non-lethal poisoning episodes, and 27 human fatalities resulting from consumption. The majority of the reported incidences occurred in Syria, Türkiye, and Lebanon. Most physical attacks occurred in summer, while most poisoning events occurred during winter. The number of recorded incidents greatly increased after 2019, especially with regard to poisonings, yet whether this is related to greater media attention, or to increased fish abundance is unclear. This is the first comprehensive study to collate findings on attacks, poisonings and fatalities caused by these pufferfish in the Mediterranean Sea, and may help in improving national health policies. We urge the continuation of national campaigns to caution residents and tourists of these species’ high toxicities and potential aggressiveness.
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(This article belongs to the Special Issue Aquatic Alien Invasions and Their Impact on Biodiversity and Ecosystem Services (Volume II))
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Open AccessArticle
Influence of Mutations and N-Glycosylation Sites in the Receptor-Binding Domain (RBD) and the Membrane Protein of SARS-CoV-2 Variants of Concern on Antibody Binding in ELISA
by
Mandy Schwarze, Daniela Volke, Juan Camilo Rojas Echeverri, Robin Schick, Nicole Lakowa, Thomas Grünewald, Johannes Wolf, Stephan Borte, Markus Scholz, Andor Krizsan and Ralf Hoffmann
Biology 2024, 13(4), 207; https://doi.org/10.3390/biology13040207 - 23 Mar 2024
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect human cells by first attaching to the ACE-2 receptor via its receptor-binding domain (RBD) in the spike protein. Here, we report the influence of N-glycosylation sites of the RBD and the membrane (M) protein
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect human cells by first attaching to the ACE-2 receptor via its receptor-binding domain (RBD) in the spike protein. Here, we report the influence of N-glycosylation sites of the RBD and the membrane (M) protein on IgG antibody binding in serum samples from patients infected with the original SARS-CoV-2 strain in Germany. The RBDs of the wildtype, alpha, beta, gamma, and kappa variants expressed in HEK293S GnTI− cells were all N-glycosylated at Asn331, Asn334, Asn343, and Asn360 or Asn370, whereas the M-protein was glycosylated at Asn5. An ELISA using a coated RBD and probed with anti-RBD IgG antibodies gave a sensitivity of 96.3% and a specificity of 100% for the wildtype RBD, while the sensitivity decreased by 5% to 10% for the variants of concern, essentially in the order of appearance. Deglycosylation of the wildtype RBD strongly reduced antibody recognition by ~20%, considering the mean of the absorbances recorded for the ELISA. This effect was even stronger for the unglycosylated RBD expressed in Escherichia coli, suggesting structural changes affecting epitope recognition. Interestingly, the N-glycosylated M-protein expressed in HEK293S GnTI− cells gave good sensitivity (95%), which also decreased to 65% after deglycosylation, and selectivity (100%). In conclusion, N-glycosylation of the M-protein, the RBD, and most likely the spike protein are important for proper antibody binding and immunological assays, whereas the type of N-glycosylation is less relevant.
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(This article belongs to the Special Issue SARS-CoV-2 and Immunology)
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Modular Hub Genes in DNA Microarray Suggest Potential Signaling Pathway Interconnectivity in Various Glioma Grades
by
Marco A. Orda, Peter Matthew Paul T. Fowler and Lemmuel L. Tayo
Biology 2024, 13(4), 206; https://doi.org/10.3390/biology13040206 - 23 Mar 2024
Abstract
Gliomas have displayed significant challenges in oncology due to their high degree of invasiveness, recurrence, and resistance to treatment strategies. In this work, the key hub genes mainly associated with different grades of glioma, which were represented by pilocytic astrocytoma (PA), oligodendroglioma (OG),
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Gliomas have displayed significant challenges in oncology due to their high degree of invasiveness, recurrence, and resistance to treatment strategies. In this work, the key hub genes mainly associated with different grades of glioma, which were represented by pilocytic astrocytoma (PA), oligodendroglioma (OG), anaplastic astrocytoma (AA), and glioblastoma multiforme (GBM), were identified through weighted gene co-expression network analysis (WGCNA) of microarray datasets retrieved from the Gene Expression Omnibus (GEO) database. Through this, four highly correlated modules were observed to be present across the PA (GSE50161), OG (GSE4290), AA (GSE43378), and GBM (GSE36245) datasets. The functional annotation and pathway enrichment analysis done through the Database for Annotation, Visualization, and Integrated Discovery (DAVID) showed that the modules and hub genes identified were mainly involved in signal transduction, transcription regulation, and protein binding, which collectively deregulate several signaling pathways, mainly PI3K/Akt and metabolic pathways. The involvement of several hub genes primarily linked to other signaling pathways, including the cAMP, MAPK/ERK, Wnt/β-catenin, and calcium signaling pathways, indicates potential interconnectivity and influence on the PI3K/Akt pathway and, subsequently, glioma severity. The Drug Repurposing Encyclopedia (DRE) was used to screen for potential drugs based on the up- and downregulated hub genes, wherein the synthetic progestin hormones norgestimate and ethisterone were the top drug candidates. This shows the potential neuroprotective effect of progesterone against glioma due to its influence on EGFR expression and other signaling pathways. Aside from these, several experimental and approved drug candidates were also identified, which include an adrenergic receptor antagonist, a PPAR-γ receptor agonist, a CDK inhibitor, a sodium channel blocker, a bradykinin receptor antagonist, and a dopamine receptor agonist, which further highlights the gene network as a potential therapeutic avenue for glioma.
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(This article belongs to the Section Biochemistry and Molecular Biology)
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Open AccessCommunication
Ovotestis Isolation and Cryopreservation of Nesiohelix samarangae (Oriental Snail) as a Snail Model for Conserving Other Endangered Snail Species
by
Jukyeong Jeong, Seungki Lee and Jung Kyu Choi
Biology 2024, 13(4), 205; https://doi.org/10.3390/biology13040205 - 22 Mar 2024
Abstract
This study aimed to develop a cryopreservation system for the reproductive organs of Nesiohelix samarangae (oriental snail) to support the conservation of their species. The reproductive glands of N. samarangae are divided into numerous acini by acinar boundaries. Within each acinus, the presence
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This study aimed to develop a cryopreservation system for the reproductive organs of Nesiohelix samarangae (oriental snail) to support the conservation of their species. The reproductive glands of N. samarangae are divided into numerous acini by acinar boundaries. Within each acinus, the presence of spermatogonia, spermatocytes, spermatids, and sperm were observed, indicating various stages of sperm development. The spermatocytes were irregular in shape and possessed large nuclei. Spermatids, on the other hand, were predominantly located within the lumen of the tissue and exhibited densely packed nuclei. Furthermore, sperm with tails attached were observed within the tissue. In order to preserve the oriental snail species, we utilized the vitrification method to freeze the reproductive organs. Comparing the two methods, it was observed that cryopreservation of ovotestis using 2% alginate encapsulation exhibited superior viability following thawing, surpassing the viability achieved with the non-encapsulated approach. In this study, the establishment of a cryopreservation system for the reproductive organs of the oriental snail not only contributes to the genetic conservation of the endangered snail species but also plays a role in maintaining genetic resources and diversity.
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(This article belongs to the Special Issue Conservation Genetics as a Management Tool for Endangered, Vulnerable, and Threatened Species)
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Open AccessReview
Inhibitors against DNA Polymerase I Family of Enzymes: Novel Targets and Opportunities
by
Saathvik Kannan, Samuel W. Gillespie, Wendy L. Picking, William D. Picking, Christian L. Lorson and Kamal Singh
Biology 2024, 13(4), 204; https://doi.org/10.3390/biology13040204 - 22 Mar 2024
Abstract
DNA polymerases replicate cellular genomes and/or participate in the maintenance of genome integrity. DNA polymerases sharing high sequence homology with E. coli DNA polymerase I (pol I) have been grouped in Family A. Pol I participates in Okazaki fragment maturation and in bacterial
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DNA polymerases replicate cellular genomes and/or participate in the maintenance of genome integrity. DNA polymerases sharing high sequence homology with E. coli DNA polymerase I (pol I) have been grouped in Family A. Pol I participates in Okazaki fragment maturation and in bacterial genome repair. Since its discovery in 1956, pol I has been extensively studied, primarily to gain deeper insights into the mechanism of DNA replication. As research on DNA polymerases advances, many novel functions of this group of polymerases are being uncovered. For example, human DNA polymerase θ (a Family A DNA pol) has been shown to synthesize DNA using RNA as a template, a function typically attributed to retroviral reverse transcriptase. Increased interest in drug discovery against pol θ has emerged due to its roles in cancer. Likewise, Pol I family enzymes also appear attractive as drug-development targets against microbial infections. Development of antimalarial compounds targeting apicoplast apPOL, an ortholog of Pol I, further extends the targeting of this family of enzymes. Here, we summarize reported drug-development efforts against Family A polymerases and future perspective regarding these enzymes as antibiotic targets. Recently developed techniques, such as artificial intelligence, can be used to facilitate the development of new drugs.
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(This article belongs to the Section Medical Biology)
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