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Biology, Volume 12, Issue 12 (December 2023) – 84 articles

Cover Story (view full-size image): Dysfunctional gut microbiota lead to the activation of multiple pathways in the gut and in the liver that sustain hepatic inflammation and are involved in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Many studies have recently investigated the role of gut dysbiosis in MASLD, with the final aim of finding novel strategies to improve liver steatosis and hepatic function. Moreover, recent evidence underlines the role of adipose tissue in sustaining hepatic inflammation during MASLD development. In this review, we focus on the novel strategies proposed to improve the alteration of gut microbiota observed in MASLD patients, with a particular insight into those known to modulate gut microbiota-associated dysfunction and to affect the complex crosstalk between the gut, adipose tissue, and the liver. View this paper
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17 pages, 2276 KiB  
Article
Metal Interactions in the Ni Hyperaccumulating Population of Noccaea caerulescens Monte Prinzera
Biology 2023, 12(12), 1537; https://doi.org/10.3390/biology12121537 - 18 Dec 2023
Viewed by 1191
Abstract
Hyperaccumulation is a fascinating trait displayed by a few plant species able to accumulate large amounts of metal ions in above-ground tissues without symptoms of toxicity. Noccaea caerulescens is a recognized model system to study metal hyperaccumulation and hypertolerance. A N. caerulescens population [...] Read more.
Hyperaccumulation is a fascinating trait displayed by a few plant species able to accumulate large amounts of metal ions in above-ground tissues without symptoms of toxicity. Noccaea caerulescens is a recognized model system to study metal hyperaccumulation and hypertolerance. A N. caerulescens population naturally growing on a serpentine soil in the Italian Apennine Mountains, Monte Prinzera, was chosen for the study here reported. Plants were grown hydroponically and treated with different metals, in excess or limiting concentrations. Accumulated metals were quantified in shoots and roots by means of ICP-MS. By real-time PCR analysis, the expression of metal transporters and Fe deficiency-regulated genes was compared in the shoots and roots of treated plants. N. caerulescens Monte Prinzera confirmed its ability to hypertolerate and hyperaccumulate Ni but not Zn. Moreover, excess Ni does not induce Fe deficiency as in Ni-sensitive species and instead competes with Fe translocation rather than its uptake. Full article
(This article belongs to the Special Issue Toxicity and Detoxification of Heavy Metals in Plants)
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15 pages, 2026 KiB  
Article
The Enrichment of miRNA-Targeted mRNAs in Translationally Less Active over More Active Polysomes
Biology 2023, 12(12), 1536; https://doi.org/10.3390/biology12121536 - 18 Dec 2023
Viewed by 1595
Abstract
miRNAs moderately inhibit the translation and enhance the degradation of their target mRNAs via cognate binding sites located predominantly in the 3′-untranslated regions (UTR). Paradoxically, miRNA targets are also polysome-associated. We studied the polysome association by the comparative translationally less-active light- and more-active [...] Read more.
miRNAs moderately inhibit the translation and enhance the degradation of their target mRNAs via cognate binding sites located predominantly in the 3′-untranslated regions (UTR). Paradoxically, miRNA targets are also polysome-associated. We studied the polysome association by the comparative translationally less-active light- and more-active heavy-polysome profiling of a wild type (WT) human cell line and its isogenic mutant (MT) with a disrupted DICER1 gene and, thus, mature miRNA production. As expected, the open reading frame (ORF) length is a major determinant of light- to heavy-polysome mRNA abundance ratios, but is rendered less powerful in WT than in MT cells by miRNA-regulatory activities. We also observed that miRNAs tend to target mRNAs with longer ORFs, and that adjusting the mRNA abundance ratio with the ORF length improves its correlation with the 3′-UTR miRNA-binding-site count. In WT cells, miRNA-targeted mRNAs exhibit higher abundance in light relative to heavy polysomes, i.e., light-polysome enrichment. In MT cells, the DICER1 disruption not only significantly abrogated the light-polysome enrichment, but also narrowed the mRNA abundance ratio value range. Additionally, the abrogation of the enrichment due to the DICER1 gene disruption, i.e., the decreases of the ORF-length-adjusted mRNA abundance ratio from WT to MT cells, exhibits a nearly perfect linear correlation with the 3′-UTR binding-site count. Transcription factors and protein kinases are the top two most enriched mRNA groups. Taken together, the results provide evidence for the light-polysome enrichment of miRNA-targeted mRNAs to reconcile polysome association and moderate translation inhibition, and that ORF length is an important, though currently under-appreciated, transcriptome regulation parameter. Full article
(This article belongs to the Section Cancer Biology)
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13 pages, 1514 KiB  
Article
Citral-Enriched Fraction of Lemon Essential Oil Mitigates LPS-Induced Hepatocyte Injuries
Biology 2023, 12(12), 1535; https://doi.org/10.3390/biology12121535 - 17 Dec 2023
Viewed by 1098
Abstract
Lemon essential oil (LEO) is known for its aromatic and healthy properties; however, less consideration is given to the biological properties of the fractions obtained from LEO. This study aims to evaluate the ability of a citral-enriched fraction obtained from LEO (Cfr-LEO) to [...] Read more.
Lemon essential oil (LEO) is known for its aromatic and healthy properties; however, less consideration is given to the biological properties of the fractions obtained from LEO. This study aims to evaluate the ability of a citral-enriched fraction obtained from LEO (Cfr-LEO) to counteract lipopolysaccharide (LPS)-mediated inflammation, oxidative stress, and epithelial–mesenchymal transition (EMT) in healthy human hepatocytes. Human immortalized hepatocytes (THLE-2 cell line) were pretreated with Cfr-LEO and subsequently exposed to LPS at various time points. We report that the pretreatment with Cfr-LEO counteracts LPS-mediated effects by inhibiting inflammation, oxidative stress, and epithelial–mesenchymal transition in THLE-2. In particular, we found that pretreatment with Cfr-LEO reduced NF-κB activation and the subsequent proinflammatory cytokines release, ROS production, and NRF2 and p53 expression. Furthermore, the pretreatment with Cfr-LEO showed its beneficial effect in counteracting LPS-induced EMT. Taken together, these results support Cfr-LEO application in the nutraceutical research field not only for its organoleptic properties, conferred by citral enrichment, but also for its biological activity. Our study could lay the basis for the development of foods/drinks enriched with Cfr-LEO, aimed at preventing or alleviating chronic conditions associated with liver dysfunction. Full article
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18 pages, 765 KiB  
Review
Neuroprotective Action of Humanin and Humanin Analogues: Research Findings and Perspectives
Biology 2023, 12(12), 1534; https://doi.org/10.3390/biology12121534 - 16 Dec 2023
Viewed by 1047
Abstract
Humanin is a 24-mer peptide first reported in the early 2000s as a new neuroprotective/cytoprotective factor rescuing neuronal cells from death induced by various Alzheimer’s disease-associated insults. Nowadays it is known that humanin belongs to the novel class of the so-called mitochondrial-derived peptides [...] Read more.
Humanin is a 24-mer peptide first reported in the early 2000s as a new neuroprotective/cytoprotective factor rescuing neuronal cells from death induced by various Alzheimer’s disease-associated insults. Nowadays it is known that humanin belongs to the novel class of the so-called mitochondrial-derived peptides (which are encoded by mitochondrial DNA) and has been shown to exert beneficial cytoprotective effects in a series of in vitro and/or in vivo experimental models of human diseases, including not only neurodegenerative disorders but other human diseases as well (e.g., age-related macular degeneration, cardiovascular diseases, or diabetes mellitus). This review article is focused on the presentation of recent in vitro and in vivo research results associated with the neuroprotective action of humanin as well as of various, mainly synthetic, analogues of the peptide; moreover, the main mode(s)/mechanism(s) through which humanin and humanin analogues may exert in vitro and in vivo regarding neuroprotection have been reported. The prospects of humanin and humanin analogues to be further investigated in the frame of future research endeavors against neurodegenerative/neural diseases have also been briefly discussed. Full article
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16 pages, 2671 KiB  
Article
Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay
Biology 2023, 12(12), 1533; https://doi.org/10.3390/biology12121533 - 15 Dec 2023
Viewed by 1115
Abstract
Although ionizing radiation (IR) is widely used for therapeutic and research purposes, studies on low-dose ionizing radiation (LDIR) are limited compared with those on other IR approaches, such as high-dose gamma irradiation and ultraviolet irradiation. High-dose IR affects DNA damage response and nucleotide–protein [...] Read more.
Although ionizing radiation (IR) is widely used for therapeutic and research purposes, studies on low-dose ionizing radiation (LDIR) are limited compared with those on other IR approaches, such as high-dose gamma irradiation and ultraviolet irradiation. High-dose IR affects DNA damage response and nucleotide–protein crosslinking, among other processes; however, the molecular consequences of LDIR have been poorly investigated. Here, we developed a method to profile RNA species crosslinked to an RNA-binding protein, namely, human antigen R (HuR), using LDIR and high-throughput RNA sequencing. The RNA fragments isolated via LDIR-crosslinking and immunoprecipitation sequencing were crosslinked to HuR and protected from RNase-mediated digestion. Upon crosslinking HuR to target mRNAs such as PAX6, ZFP91, NR2F6, and CAND2, the transcripts degraded rapidly in human cell lines. Additionally, PAX6 and NR2F6 downregulation mediated the beneficial effects of LDIR on cell viability. Thus, our approach provides a method for investigating post-transcriptional gene regulation using LDIR. Full article
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20 pages, 3747 KiB  
Article
Risk for Seasonal Affective Disorder (SAD) Linked to Circadian Clock Gene Variants
Biology 2023, 12(12), 1532; https://doi.org/10.3390/biology12121532 - 15 Dec 2023
Viewed by 1117
Abstract
Molecular pathways affecting mood are associated with circadian clock gene variants and are influenced, in part, by the circadian clock, but the molecular mechanisms underlying this link are poorly understood. We use machine learning and statistical analyses to determine the circadian gene variants [...] Read more.
Molecular pathways affecting mood are associated with circadian clock gene variants and are influenced, in part, by the circadian clock, but the molecular mechanisms underlying this link are poorly understood. We use machine learning and statistical analyses to determine the circadian gene variants and clinical features most highly associated with symptoms of seasonality and seasonal affective disorder (SAD) in a deeply phenotyped population sample. We report sex-specific clock gene effects on seasonality and SAD symptoms; genotypic combinations of CLOCK3111/ZBTB20 and PER2/PER3B were significant genetic risk factors for males, and CRY2/PER3C and CRY2/PER3-VNTR were significant risk factors for females. Anxiety, eveningness, and increasing age were significant clinical risk factors for seasonality and SAD for females. Protective factors for SAD symptoms (in females only) included single gene variants: CRY1-GG and PER3-VNTR-4,5. Clock gene effects were partially or fully mediated by diurnal preference or chronotype, suggesting multiple indirect effects of clock genes on seasonality symptoms. Interestingly, protective effects of CRY1-GG, PER3-VNTR-4,5, and ZBTB20 genotypes on seasonality and depression were not mediated by chronotype, suggesting some clock variants have direct effects on depressive symptoms related to SAD. Our results support previous links between CRY2, PER2, and ZBTB20 genes and identify novel links for CLOCK and PER3 with symptoms of seasonality and SAD. Our findings reinforce the sex-specific nature of circadian clock influences on seasonality and SAD and underscore the multiple pathways by which clock variants affect downstream mood pathways via direct and indirect mechanisms. Full article
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14 pages, 2786 KiB  
Article
Influence of Breast Cancer Extracellular Vesicles on Immune Cell Activation: A Pilot Study
Biology 2023, 12(12), 1531; https://doi.org/10.3390/biology12121531 - 15 Dec 2023
Viewed by 1138
Abstract
Breast cancer is the leading cause of cancer-related death in women worldwide. It is well known that breast cancer shows significant alterations in the tumor microenvironment (TME), which is composed of a variety of immune cells, including natural killer (NK) cells, that have [...] Read more.
Breast cancer is the leading cause of cancer-related death in women worldwide. It is well known that breast cancer shows significant alterations in the tumor microenvironment (TME), which is composed of a variety of immune cells, including natural killer (NK) cells, that have a key role in tumor development or anti-tumor responses in breast cancer patients. Luminal B (BT474) and triple-negative breast cancer (HS578T) cell lines were cultured in 2D and 3D model systems. PMBCs from healthy donors were isolated and treated with extracellular vesicles (EVs) from monolayer and spheroids of BT474 and HS578T and analyzed using cytofluorimetric approaches. We observed that EVs can alter the activation and presence of CD335+/CD11b+ NK cells. EVs derived from BT474 and HS578T cells trigger the activation and, simultaneously, a reduction in the percentage of CD335+/CD11b+ NK cells. In addition, EVs derived from BT474 also significantly reduce CD39+ T-regulatory (T-reg) cells. Our preliminary data suggest that using EVs to treat tumors could potentially alter components of the immune system, which causes hyperactivation of specific cell types and can lead to aggressive growth. These data will guide the designing of new personalized diagnostic approaches based on in-depth study of the TME. Full article
(This article belongs to the Special Issue Advances in Biological Breast Cancer Research)
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13 pages, 2860 KiB  
Review
Vesicular Trafficking, a Mechanism Controlled by Cascade Activation of Rab Proteins: Focus on Rab27
Biology 2023, 12(12), 1530; https://doi.org/10.3390/biology12121530 - 15 Dec 2023
Viewed by 1188
Abstract
Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the [...] Read more.
Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the elimination of waste products or for the emission of intercellular communication vectors such as cytokines, chemokines and extracellular vesicles. Ras-related proteins (Rab) and their effector(s) are of crucial importance in all of these processes, and mutations/alterations to them have serious pathophysiological consequences. This review presents a non-exhaustive overview of the role of the major Rab involved in vesicular trafficking, with particular emphasis on their involvement in the biogenesis and secretion of extracellular vesicles, and on the role of Rab27 in various pathophysiological processes. Therefore, Rab and their effector(s) are central therapeutic targets, given their involvement in vesicular trafficking and their importance for cell physiology. Full article
(This article belongs to the Special Issue Cell Transport in Health and Disease)
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15 pages, 1073 KiB  
Review
The Impact of Apolipoprotein E (APOE) Epigenetics on Aging and Sporadic Alzheimer’s Disease
Biology 2023, 12(12), 1529; https://doi.org/10.3390/biology12121529 - 15 Dec 2023
Viewed by 2549
Abstract
Sporadic Alzheimer’s disease (AD) derives from an interplay among environmental factors and genetic variants, while epigenetic modifications have been expected to affect the onset and progression of its complex etiopathology. Carriers of one copy of the apolipoprotein E gene (APOE) ε4 [...] Read more.
Sporadic Alzheimer’s disease (AD) derives from an interplay among environmental factors and genetic variants, while epigenetic modifications have been expected to affect the onset and progression of its complex etiopathology. Carriers of one copy of the apolipoprotein E gene (APOE) ε4 allele have a 4-fold increased AD risk, while APOE ε4/ε4-carriers have a 12-fold increased risk of developing AD in comparison with the APOE ε3-carriers. The main longevity factor is the homozygous APOE ε3/ε3 genotype. In the present narrative review article, we summarized and described the role of APOE epigenetics in aging and AD pathophysiology. It is not fully understood how APOE variants may increase or decrease AD risk, but this gene may affect tau- and amyloid-mediated neurodegeneration directly or indirectly, also by affecting lipid metabolism and inflammation. For sporadic AD, epigenetic regulatory mechanisms may control and influence APOE expression in response to external insults. Diet, a major environmental factor, has been significantly associated with physical exercise, cognitive function, and the methylation level of several cytosine-phosphate-guanine (CpG) dinucleotide sites of APOE. Full article
(This article belongs to the Special Issue Epigenetic Modifications and Changes in Neurodegenerative Diseases)
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15 pages, 871 KiB  
Review
Immune Escape in Glioblastoma: Mechanisms of Action and Implications for Immune Checkpoint Inhibitors and CAR T-Cell Therapy
Biology 2023, 12(12), 1528; https://doi.org/10.3390/biology12121528 - 15 Dec 2023
Viewed by 1297
Abstract
Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with [...] Read more.
Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with glioblastoma. Understanding the mechanisms by which glioblastoma exerts tumor-mediated immune suppression in both the tumor microenvironment and the systemic immune landscape is a critical step towards developing effective immunotherapeutic strategies. In this review, we discuss the current understanding of immune escape mechanisms in glioblastoma that compromise the efficacy of immunotherapies, with an emphasis on immune checkpoint inhibitors and chimeric antigen receptor T-cell therapy. In parallel, we review data from preclinical studies that have identified additional therapeutic targets that may enhance overall treatment efficacy in glioblastoma when administered alongside existing immunotherapies. Full article
(This article belongs to the Special Issue Progression of the Immune Escape Mechanism in Tumors)
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12 pages, 5722 KiB  
Article
The Molecular Evolution, Structure, and Function of Coproporphyrinogen Oxidase and Protoporphyrinogen Oxidase in Prokaryotes
Biology 2023, 12(12), 1527; https://doi.org/10.3390/biology12121527 - 15 Dec 2023
Viewed by 1261
Abstract
Coproporphyrinogen oxidase (CgoX) and protoporphyrinogen oxidase (PgoX) catalyze the oxidation of the flexible cyclic tetrapyrrole of porphyrinogen compounds into fully conjugated, planar macrocyclic porphyrin compounds during heme biosynthesis. These enzymes are activated via different pathways. CgoX oxidizes coproporphyrinogen III to coproporphyrin III in [...] Read more.
Coproporphyrinogen oxidase (CgoX) and protoporphyrinogen oxidase (PgoX) catalyze the oxidation of the flexible cyclic tetrapyrrole of porphyrinogen compounds into fully conjugated, planar macrocyclic porphyrin compounds during heme biosynthesis. These enzymes are activated via different pathways. CgoX oxidizes coproporphyrinogen III to coproporphyrin III in the coproporphyrin-dependent pathway, whereas PgoX oxidizes protoporphyrinogen IX to protoporphyrin IX in the penultimate step of the protoporphyrin-dependent pathway. The phylogenetic analysis presented herein demonstrates a clear differentiation between the two enzyme classes, as evidenced by the clustering of sequences in distinct clades, and it shows that, at the origin of porphyrinogen-type oxidase evolution, PgoXs from cyanobacteria were found, which were noticeably separated from descendant PgoX representatives of Deltaproteobacteria and all later PgoX variants, leading to many eukaryotic clades. CgoX sequences originating from the monoderm Actinomycetota and Bacillota were well separated from the predecessor clades containing PgoX types and represent a peculiar type of gene speciation. The structural similarities and differences between these two oxidases are discussed based on their protein sequence alignment and a structural comparison. Full article
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13 pages, 1654 KiB  
Article
The Impact of Genetic Polymorphisms on Anterior Cruciate Ligament Injuries in Athletes: A Meta-Analytical Approach
Biology 2023, 12(12), 1526; https://doi.org/10.3390/biology12121526 - 15 Dec 2023
Viewed by 1038
Abstract
This meta-analysis aimed to investigate the association between genetic polymorphisms in Collagen type 1 alpha-1 (COL1A1), Collagen type 3 alpha-1 (COL3A1), Collagen type 5 alpha-1 (COL5A1), and Collagen type 12 alpha-1 (COL12A1) genes and anterior cruciate ligament (ACL) injuries in athletes. A systematic [...] Read more.
This meta-analysis aimed to investigate the association between genetic polymorphisms in Collagen type 1 alpha-1 (COL1A1), Collagen type 3 alpha-1 (COL3A1), Collagen type 5 alpha-1 (COL5A1), and Collagen type 12 alpha-1 (COL12A1) genes and anterior cruciate ligament (ACL) injuries in athletes. A systematic search was diligently conducted on the PubMed and Web of Science databases to identify relevant studies on 5–9 September 2023. Only case–control studies were included in the meta-analysis. A total of 19 studies were reviewed, involving the analysis of 3522 cases and 6399 control subjects. Data relevant to the study objectives were extracted from these chosen studies and subsequently analyzed using either a random-effects or fixed-effects model. It indicates that individuals carrying the G allele in the COL1A1 (rs1107946) gene have a decreased risk of anterior cruciate ligament injuries (OR: −0.27, 95% CI: −0.42 to −0.12, p < 0.001). A similar relationship was observed in the dominant model, but this relationship was reversed in the recessive model (OR: 0.69, 95% CI: 0.33 to 1.05, p < 0.001). However, no significant associations were found in the COL3A1 (rs1800255) and COL5A1 (rs12722) genes. In the COL12A1 (rs970547) gene, the A allele was associated with an increased risk of anterior cruciate ligament injuries (OR: 0.18, 95% CI: 0.01 to 0.36, p = 0.041). This meta-analysis suggests that genetic variants in COL1A1 (rs1107946) and COL12A1 (rs970547) may be associated with ACL injuries in athletes. However, COL3A1 rs1800255 and COL5A1 rs12722 gene variants do not appear to have a significant association with these injuries. Full article
(This article belongs to the Topic Human Anatomy and Pathophysiology, 2nd Volume)
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21 pages, 4067 KiB  
Article
Assessment of Drought and Zinc Stress Tolerance of Novel Miscanthus Hybrids and Arundo donax Clones Using Physiological, Biochemical, and Morphological Traits
Biology 2023, 12(12), 1525; https://doi.org/10.3390/biology12121525 - 14 Dec 2023
Viewed by 935
Abstract
High-yield potential perennial crops, such as Miscanthus spp. and Arundo donax are amongst the most promising sources of sustainable biomass for bioproducts and bioenergy. Although several studies assessed the agronomic performance of these species on diverse marginal lands, research to date on drought [...] Read more.
High-yield potential perennial crops, such as Miscanthus spp. and Arundo donax are amongst the most promising sources of sustainable biomass for bioproducts and bioenergy. Although several studies assessed the agronomic performance of these species on diverse marginal lands, research to date on drought and zinc (Zn) resistance is scarce. Thus, the objective of this study was to investigate the drought and Zn stress tolerance of seven novel Miscanthus hybrids and seven Arundo clones originating from different parts of Italy. We subjected both species to severe drought (less than 30%), and Zn stress (400 mg/kg−1 of ZnSO4) separately, after one month of growth. All plants were harvested after 28 days of stress, and the relative drought and Zn stress tolerance were determined by using a set of morpho-physio-biochemical and biomass attributes in relation to stress tolerance indices (STI). Principal component analysis (PCA), hierarchical clustering analysis (HCA) and stress tolerance indices (STI) were performed for each morpho-physio-biochemical and biomass parameters and showed significant relative differences among the seven genotypes of both crops. Heatmaps of these indices showed how the different genotypes clustered into four groups. Considering PCA ranking value, Miscanthus hybrid GRC10 (8.11) and Arundo clone PC1 (11.34) had the highest-ranking value under both stresses indicating these hybrids and clones are the most tolerant to drought and Zn stress. In contrast, hybrid GRC3 (−3.33 lowest ranking value) and clone CT2 (−5.84) were found to be the most sensitive to both drought and Zn stress. Full article
(This article belongs to the Special Issue Toxicity and Detoxification of Heavy Metals in Plants)
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15 pages, 9583 KiB  
Technical Note
A Method to Locally Irradiate Specific Organ in Model Organisms Using a Focused Heavy-Ion Microbeam
Biology 2023, 12(12), 1524; https://doi.org/10.3390/biology12121524 - 14 Dec 2023
Viewed by 957
Abstract
The functions of organisms are performed by various tissues composed of different cell types. Localized irradiation with heavy-ion microbeams, which inactivate only a portion of the constituent cells without destroying the physical intercellular connections of the tissue, is a practical approach for elucidating [...] Read more.
The functions of organisms are performed by various tissues composed of different cell types. Localized irradiation with heavy-ion microbeams, which inactivate only a portion of the constituent cells without destroying the physical intercellular connections of the tissue, is a practical approach for elucidating tissue functions. However, conventional collimated microbeams are limited in the shape of the area that can be irradiated. Therefore, using a focused heavy-ion microbeam that generates a highly precise beam spot, we developed a technology to uniformly irradiate specific tissues of an organism with a defined dose, which conventional methods cannot achieve. The performance of the developed paint irradiation technology was evaluated. By irradiating the CR-39 ion track detector, we confirmed that the new method, in which each ion hit position is placed uniformly in the irradiated area, makes it possible to uniformly paint the area at a specified dose. The targeted irradiation of the pharynx and gonads of living Caenorhabditis elegans demonstrated that the irradiated ions were distributed in the same shape as the targeted tissue observed under a microscope. This technology will elucidate biological mechanisms that are difficult to analyze with conventional collimated microbeam irradiation. Full article
(This article belongs to the Special Issue Microbeam Radiation Biology and Its State-of-the-Art Technology)
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18 pages, 2417 KiB  
Article
An Investigation on the Effects of Dietary Vitamin E on Juvenile Sea Urchin (Strongylocentrotus intermedius): Growth, Intestinal Microbiota, Immune Response, and Related Gene Expression
Biology 2023, 12(12), 1523; https://doi.org/10.3390/biology12121523 - 14 Dec 2023
Viewed by 1053
Abstract
A 90 d feeding experiment was conducted to investigate the effects of vitamin E (VE) on growth, intestinal microbiota, immune response, and related gene expression of juvenile sea urchin (Strongylocentrotus intermedius). Six dry feeds were made to contain graded levels of [...] Read more.
A 90 d feeding experiment was conducted to investigate the effects of vitamin E (VE) on growth, intestinal microbiota, immune response, and related gene expression of juvenile sea urchin (Strongylocentrotus intermedius). Six dry feeds were made to contain graded levels of VE (78, 105, 152, 235, 302, and 390 mg/kg); these were named E78, E105, E152, E235, E302, and E390, respectively. Dry feed E50 and fresh kelp (HD) were used as the control diets. There were six replicates of cages in each dietary group, and each cage held 20 sea urchins with an initial body weight of approximately 1.50 g. Results exhibited that weight gain rate and gonadosomatic index (GSI) of the sea urchins were not significantly affected by dietary VE ranging from 78 to 390 mg/kg. Sea urchins in the dry feed groups showed poorer growth performance, but significantly higher GSI than those in the fresh kelp groups. The pepsin and lipase activities were not significantly promoted by low or moderate VE, but were inhibited by a high level of VE (302–390 mg/kg), while amylase and cellulase activities were significantly increased by low or moderate VE, with the highest values observed in the E105 and E235 groups, respectively. VE addition at a low dosage (105–152 mg/kg) showed inhibitory effects on immune and antioxidant enzyme activities and expression of inflammation-related genes, but showed no beneficial effects at moderate or high dosage (235–390 mg/kg), while a moderate or relatively higher level of VE (235–302 mg/kg) significantly increased the expression of several immune-related genes. The relative abundance of Proteobacteria, Actinobacteria, Ruegeria, and Maliponia in the intestine of the sea urchins increased with the increase in VE in the dry feeds. On the contrary, the relative abundance of the Firmicutes, Bacteroidetes, Escherichia-Shigella, Bacteroides, and Clostridium sensu stricto 1 gradually decreased as VE content increased. These results indicated that a moderate level of VE (172.5–262.4) can achieve ideal digestive enzyme activities and growth performance, but a relatively higher level of VE (235–302 mg/kg) was beneficial for maintaining the immune and antioxidant capacity of juvenile S. intermedius by regulating the expression of inflammation- and immune-related genes and abundance of some bacteria to a healthy state. Full article
(This article belongs to the Special Issue Current Advances in Echinoderm Research)
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13 pages, 1780 KiB  
Article
Benefits of Harmonicity for Hearing in Noise Are Limited to Detection and Pitch-Related Discrimination Tasks
Biology 2023, 12(12), 1522; https://doi.org/10.3390/biology12121522 - 13 Dec 2023
Viewed by 913
Abstract
Harmonic complex tones are easier to detect in noise than inharmonic complex tones, providing a potential perceptual advantage in complex auditory environments. Here, we explored whether the harmonic advantage extends to other auditory tasks that are important for navigating a noisy auditory environment, [...] Read more.
Harmonic complex tones are easier to detect in noise than inharmonic complex tones, providing a potential perceptual advantage in complex auditory environments. Here, we explored whether the harmonic advantage extends to other auditory tasks that are important for navigating a noisy auditory environment, such as amplitude- and frequency-modulation detection. Sixty young normal-hearing listeners were tested, divided into two equal groups with and without musical training. Consistent with earlier studies, harmonic tones were easier to detect in noise than inharmonic tones, with a signal-to-noise ratio (SNR) advantage of about 2.5 dB, and the pitch discrimination of the harmonic tones was more accurate than that of inharmonic tones, even after differences in audibility were accounted for. In contrast, neither amplitude- nor frequency-modulation detection was superior with harmonic tones once differences in audibility were accounted for. Musical training was associated with better performance only in pitch-discrimination and frequency-modulation-detection tasks. The results confirm a detection and pitch-perception advantage for harmonic tones but reveal that the harmonic benefits do not extend to suprathreshold tasks that do not rely on extracting the fundamental frequency. A general theory is proposed that may account for the effects of both noise and memory on pitch-discrimination differences between harmonic and inharmonic tones. Full article
(This article belongs to the Special Issue Neural Correlates of Perception in Noise in the Auditory System)
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16 pages, 1731 KiB  
Article
Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species
Biology 2023, 12(12), 1521; https://doi.org/10.3390/biology12121521 - 13 Dec 2023
Cited by 1 | Viewed by 1098
Abstract
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated [...] Read more.
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated with sibling species in the hosts’ adaptation remains largely unexplored. In this study, we examined the composition and plasticity of the bacteriomes in two sibling intertidal gastropod species, Littorina fabalis and L. obtusata, which are sympatric but differ in microhabitats. We applied 16S rRNA gene metabarcoding and shotgun sequencing to describe associated microbial communities and their spatial and temporal variation. A significant drop in the intestinal bacteriome diversity was revealed during the cold season, which may reflect temperature-related metabolic shifts and changes in snail behavior. Importantly, there were significant interspecies differences in the gut bacteriome composition in summer but not in autumn. The genera Vibrio, Aliivibrio, Moritella and Planktotalea were found to be predominantly associated with L. fabalis, while Granulosicoccus, Octadecabacter, Colwellia, Pseudomonas, Pseudoalteromonas and Maribacter were found to be mostly associated with L. obtusata. Based on these preferential associations, we analyzed the metabolic pathways’ enrichment. We hypothesized that the L. obtusata gut bacteriome contributes to decomposing algae and detoxifying polyphenols produced by fucoids. Thus, differences in the sets of associated bacteria may equip their closely phylogenetically related hosts with a unique ability to occupy specific micro-niches. Full article
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21 pages, 26525 KiB  
Article
Transcriptomic Responses of a Lightly Calcified Echinoderm to Experimental Seawater Acidification and Warming during Early Development
Biology 2023, 12(12), 1520; https://doi.org/10.3390/biology12121520 - 13 Dec 2023
Viewed by 935
Abstract
Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised [...] Read more.
Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised under combinations of two temperatures (19 °C or 22 °C) and two pCO2 levels (400 or 1000 μatm) that reflect the current and end-of-21st-century projected ocean scenarios. The investigation focused on assessing larval development and identifying differences in gene expression patterns at four crucial embryo–larval stages (blastula, gastrula, auricularia, and doliolaria) of sea cucumbers, using RNA-seq. Results showed the detrimental effect of OA on the early development and body growth of A. japonicus larvae and a reduction in the expression of genes associated with biomineralization, skeletogenesis, and ion homeostasis. This effect was particularly pronounced during the doliolaria stage, indicating the presence of bottlenecks in larval development at this transition phase between the larval and megalopa stages in response to OA. OW accelerated the larval development across four stages of A. japonicus, especially at the blastula and doliolaria stages, but resulted in a widespread upregulation of genes related to heat shock proteins, antioxidant defense, and immune response. Significantly, the negative effects of elevated pCO2 on the developmental process of larvae appeared to be mitigated when accompanied by increased temperatures at the expense of reduced immune resilience and increased system fragility. These findings suggest that alterations in gene expression within the larvae of A. japonicus provide a mechanism to adapt to stressors arising from a rapidly changing oceanic environment. Full article
(This article belongs to the Section Marine Biology)
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28 pages, 2794 KiB  
Article
Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential
Biology 2023, 12(12), 1519; https://doi.org/10.3390/biology12121519 - 12 Dec 2023
Cited by 1 | Viewed by 1280
Abstract
The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work [...] Read more.
The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology. Full article
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14 pages, 2989 KiB  
Article
Comparative Transcriptome Analysis of the Response to Vibrio parahaemolyticus and Low-Salinity Stress in the Swimming Crab Portunus trituberculatus
Biology 2023, 12(12), 1518; https://doi.org/10.3390/biology12121518 - 12 Dec 2023
Viewed by 989
Abstract
Vibrio parahaemolyticus is one of the main pathogenic bacteria of Portunus trituberculatus and causes mass mortality of P. trituberculatus in aquaculture. In addition, low-salinity stimulation makes P. trituberculatus more susceptible to V. parahaemolyticus infections. In order to elucidate the molecular mechanism of resistance [...] Read more.
Vibrio parahaemolyticus is one of the main pathogenic bacteria of Portunus trituberculatus and causes mass mortality of P. trituberculatus in aquaculture. In addition, low-salinity stimulation makes P. trituberculatus more susceptible to V. parahaemolyticus infections. In order to elucidate the molecular mechanism of resistance to V. parahaemolyticus in P. trituberculatus, comparative transcriptomic analysis of blood cells stimulated by low salinity and V. parahaemolyticus was carried out in this study. Transcriptome sequencing of low-salinity stress and pathogen infection at different time points was completed using Illumina sequencing technology. A total of 5827, 6432, 5362 and 1784 differentially expressed genes (DEGs) involved in pathways related to ion transport and immunoregulation were found under low-salinity stress at 12, 24, 48 and 72 h compared with the control at 0 h. In contrast, 4854, 4814, 5535 and 6051 DEGs, which were significantly enriched in Toll and IMD signaling pathways, were found at 12, 24, 48 and 72 h compared with the control at 0 h under V. parahaemolyticus infection. Among them, 952 DEGs were shared in the two treatment groups, which were mainly involved in apoptosis and Hippo signaling pathway. Cluster analysis screened 103 genes that were differentially expressed in two factors that were negatively correlated, including immunoglobulin, leukocyte receptor cluster family, scavenger receptor, macroglobulin and other innate-immune-related genes. These results provide data support for the analysis of the mechanisms of immunity to V. parahaemolyticus under low-salinity stress in P. trituberculatus and help to elucidate the molecular mechanisms by which environmental factors affect immunity. Full article
(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)
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15 pages, 3432 KiB  
Article
In Search of the Elusive North: Evolutionary History of the Arctic Fox (Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data
Biology 2023, 12(12), 1517; https://doi.org/10.3390/biology12121517 - 12 Dec 2023
Viewed by 1880
Abstract
Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data [...] Read more.
Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking. Full article
(This article belongs to the Section Evolutionary Biology)
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20 pages, 572 KiB  
Review
Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei
Biology 2023, 12(12), 1516; https://doi.org/10.3390/biology12121516 - 12 Dec 2023
Viewed by 1284
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments [...] Read more.
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes. Full article
(This article belongs to the Special Issue Immune Response Regulation in Animals)
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2 pages, 180 KiB  
Editorial
Editorial for the Special Issue, ‘Secondary Metabolites from Microorganisms or Microorganism–Host Interaction?’
Biology 2023, 12(12), 1515; https://doi.org/10.3390/biology12121515 - 12 Dec 2023
Viewed by 921
Abstract
In this Special Issue, there are 13 published papers from over 10 countries [...] Full article
11 pages, 675 KiB  
Perspective
Immunopeptidomics in the Era of Single-Cell Proteomics
Biology 2023, 12(12), 1514; https://doi.org/10.3390/biology12121514 - 12 Dec 2023
Viewed by 2405
Abstract
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. [...] Read more.
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses. Full article
(This article belongs to the Special Issue Proteomics in Immunology and Cell Signaling)
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54 pages, 5510 KiB  
Review
Hypomagnetic Conditions and Their Biological Action (Review)
Biology 2023, 12(12), 1513; https://doi.org/10.3390/biology12121513 - 11 Dec 2023
Cited by 1 | Viewed by 1696
Abstract
The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic [...] Read more.
The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic field interaction with living systems. The applied significance is improving the training of astronauts for long-term space expeditions. This review describes the effects of HMC on animals and plants, manifested at the cellular and organismal levels. General information is given about the probable mechanisms of HMC and geomagnetic field action on living systems. The main experimental approaches are described. We attempted to systematize quantitative data from various studies and identify general dependencies of the magnetobiology effects’ value on HMC characteristics (induction, exposure duration) and the biological parameter under study. The most pronounced effects were found at the cellular level compared to the organismal level. Gene expression and protein activity appeared to be the most sensitive to HMC among the molecular cellular processes. The nervous system was found to be the most sensitive in the case of the organism level. The review may be of interest to biologists, physicians, physicists, and specialists in interdisciplinary fields. Full article
(This article belongs to the Special Issue The Rules of Life Rethought: Latest Progress in Quantum Biology)
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20 pages, 1659 KiB  
Article
The Oxygen–Ozone Adjunct Medical Treatment According to the Protocols from the Italian Scientific Society of Oxygen–Ozone Therapy: How Ozone Applications in the Blood Can Influence Clinical Therapy Success via the Modulation of Cell Biology and Immunity
Biology 2023, 12(12), 1512; https://doi.org/10.3390/biology12121512 - 11 Dec 2023
Cited by 1 | Viewed by 1661
Abstract
Background. Ozone is an allotrope of oxygen whose use in medicine has rapidly grown in recent years. Ozonated blood allows for the use of ozone in a safe modality, as plasma and blood cells are endowed with an antioxidant system able to quench [...] Read more.
Background. Ozone is an allotrope of oxygen whose use in medicine has rapidly grown in recent years. Ozonated blood allows for the use of ozone in a safe modality, as plasma and blood cells are endowed with an antioxidant system able to quench ozone’s pro-oxidant property and to elicit the Nrf2/Kwap1/ARE pathway. Methods. We present two clinical studies, a case-series (six patients) observational study adopting ozone as a major autohemotherapy and topical ozone to address infected post-surgical wounds with multi-drug resistant bacteria and an observational study (250 patients) using ozonated blood for treating knee osteoarthritis. Results. Ozonated blood via major autohemotherapy reduced the extent of infections in wounds, reduced the inflammatory biomarkers by more than 75% and improved patients’ QoL, whereas ozonated blood via minor autohemotherapy improved significantly (p < 0.001) WOMAC and Lequesne’s parameters in knee osteoarthritis. Conclusions. The models described, i.e., ozone autohemotherapy in wound antimicrobial treatment and ozonated blood in knee osteoarthrosis, following our protocols, share the outstanding ability of ozone to modulate the innate immune response and address bacterial clearance as well as inflammation and pain. Full article
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50 pages, 8349 KiB  
Review
Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression
Biology 2023, 12(12), 1511; https://doi.org/10.3390/biology12121511 - 11 Dec 2023
Viewed by 1382
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. [...] Read more.
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology. Full article
(This article belongs to the Special Issue Cancer and Signalling: Targeting Cellular Pathways)
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18 pages, 6275 KiB  
Article
microRNA-mRNA Analysis Reveals Tissue-Specific Regulation of microRNA in Mangrove Clam (Geloina erosa)
Biology 2023, 12(12), 1510; https://doi.org/10.3390/biology12121510 - 11 Dec 2023
Viewed by 944
Abstract
Geloina erosa is an important benthic animal in the mangrove, serving as an indicator organism for coastal environmental pollution. This study aimed to investigate the tissue-specific expression of miRNAs and their regulatory roles in predicted targets in G. erosa. Through miRNA sequencing [...] Read more.
Geloina erosa is an important benthic animal in the mangrove, serving as an indicator organism for coastal environmental pollution. This study aimed to investigate the tissue-specific expression of miRNAs and their regulatory roles in predicted targets in G. erosa. Through miRNA sequencing and co-expression network analysis, we extensively studied the miRNA expression in three tissues: gills, hepatopancreas, and muscle. The results revealed a total of 1412 miRNAs, comprising 1047 known miRNAs, and 365 newly predicted miRNAs. These miRNAs exhibited distinct tissue-specific expression patterns. In the miRNA target gene prediction, a total of 7404 potential predicted targets were identified, representing approximately 33% of all unique transcripts associated with miRNAs. Further co-expression network analysis revealed nine modules, each showing a positive correlation with specific tissues (gills, hepatopancreas, or muscle). The blue module showed a significant correlation with gills (r = 0.83, p-value = 0.006), the black module was significantly related to the hepatopancreas (r = 0.78, p-value = 0.01), and the purple module was significantly correlated with muscle (r = 0.83, p-value = 0.006). Within these modules, related miRNAs tended to cluster together, while their correlations with other modules were relatively weak. Functional enrichment analysis was performed on miRNAs and their predicted targets in each tissue. In the gills, miRNAs primarily regulate immune-related genes, substance transport, and cytoskeletal organization. In the hepatopancreas, miRNAs suppressed genes involved in shell formation and played a role in cellular motor activity and metabolism. In muscle, miRNAs participate in metabolism and photoreceptive processes, as well as immune regulation. In summary, this study provides valuable insights into the tissue-specific regulation of miRNAs in G. erosa, highlighting their potential roles in immune response, metabolism, and environmental adaptation. These findings offer important clues for understanding the molecular mechanisms and biological processes in G. erosa, laying the foundation for further validation and elucidation of these regulatory relationships. Full article
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40 pages, 14702 KiB  
Article
Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus
Biology 2023, 12(12), 1509; https://doi.org/10.3390/biology12121509 - 11 Dec 2023
Viewed by 1141
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this [...] Read more.
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski’s rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (−48.74 kcal/mol), dodecanedioc acid (−34.53 kcal/mol), and tetradecanedioc acid (−36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function. Full article
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29 pages, 10972 KiB  
Article
Germ Line/Multipotency Genes Show Differential Expression during Embryonic Development of the Annelid Enchytraeus coronatus
Biology 2023, 12(12), 1508; https://doi.org/10.3390/biology12121508 - 10 Dec 2023
Viewed by 1173
Abstract
Germ line development and the origin of the primordial germ cells (PGCs) are very variable and may occur across a range of developmental stages and in several developmental contexts. In establishing and maintaining germ line, a conserved set of genes is involved. On [...] Read more.
Germ line development and the origin of the primordial germ cells (PGCs) are very variable and may occur across a range of developmental stages and in several developmental contexts. In establishing and maintaining germ line, a conserved set of genes is involved. On the other hand, these genes are expressed in multipotent/pluripotent cells that may give rise to both somatic and germline cells. To begin elucidating mechanisms by which the germ line is specified in Enchytraeus coronatus embryos, we identified twenty germline/multipotency genes, homologs of Vasa, PL10, Piwi, Nanos, Myc, Pumilio, Tudor, Boule, and Bruno, using transcriptome analysis and gene cloning, and characterized their expression by whole-mount in situ hybridization. To answer the question of the possible origin of PGCs in this annelid, we carried out an additional description of the early embryogenesis. Our results suggest that PGCs derive from small cells originating at the first two divisions of the mesoteloblasts. PGCs form two cell clusters, undergo limited proliferation, and migrate to the developing gonadal segments. In embryos and juvenile E. coronatus, homologs of the germline/multipotency genes are differentially expressed in both germline and somatic tissue including the presumptive germ cell precursors, posterior growth zone, developing foregut, and nervous system. Full article
(This article belongs to the Section Developmental Biology)
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