Biology

18 pages, 19561 KiB

Open AccessArticle

Effectiveness of Sampling Techniques in Collecting the Polyp Stage of the Invasive Freshwater Hydrozoan Craspedacusta sowerbii

by Jonathan A. Zhu and Nadine C. Folino-Rorem

Biology 2024, 13(8), 645; https://doi.org/10.3390/biology13080645 - 22 Aug 2024

Viewed by 711

Abstract

Current sampling methods for detecting the presence of the invasive freshwater hydrozoan Craspedacusta sowerbii rely mainly on visual confirmation of the medusa stage. Confirming the presence of the polyp stage is equally important for observing medusae since typical late summer/early fall occurrences or [...] Read more.

Current sampling methods for detecting the presence of the invasive freshwater hydrozoan Craspedacusta sowerbii rely mainly on visual confirmation of the medusa stage. Confirming the presence of the polyp stage is equally important for observing medusae since typical late summer/early fall occurrences or observations of medusae are sporadic though are becoming more frequent. The polyp stage is important as it is the organism’s primary stage and is present throughout the year depending on water temperatures. Therefore, sampling methods for the polyp stage are, commonly, the collection of substrates such as rocks, plants, or pieces of wood in a given body of water, and these can be cumbersome to examine. Polyps are also small, transparent, and difficult to see on natural substrates. Based on a preliminary culturing of the polyp stage on glass and plastic microscope slides in the laboratory, we designed a sampling methodology based on submerging four substrate types (glass and plastic microscope slides, Hester-Dendy discs, and small glass Petri dishes) to confirm the presence of C. sowerbii polyps in the field. We tested this method in three lakes in the Illinois–Indiana region (USA). Two of the lakes have recorded sightings of medusae but the third has no record of polyps or medusae. The sampling method we designed was effective in that C. sowerbii polyps were found on both plastic and glass slides. While this method can be sufficient for detection of the polyp stage, it also shows potential for improvement; we highlight abiotic and biotic ecological parameters as significant factors influencing the collection of C. sowerbii polyps to be considered for future methodologies. Full article

(This article belongs to the Special Issue Ecological Characteristics and Genetic Population Structure of the Invasive Freshwater Jellyfish Craspedacusta sowerbii Species Complex)

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15 pages, 9514 KiB

Open AccessArticle

LncRNA495810 Promotes Proliferation and Migration of Hepatocellular Carcinoma Cells by Interacting with FABP5

by Haili Wu, Haiyan Yuan, Yiwei Duan, Guangjun Li, Jin’e Du, Panfeng Wang and Zhuoyu Li

Biology 2024, 13(8), 644; https://doi.org/10.3390/biology13080644 - 22 Aug 2024

Viewed by 701

Abstract

Hepatocellular carcinoma (HCC) is one of the malignant tumors with high morbidity and mortality. Long non-coding RNAs (lncRNAs) are frequently dysregulated in human cancers and play an important role in the initiation and progression of HCC. Here, we investigated the expression of a [...] Read more.

Hepatocellular carcinoma (HCC) is one of the malignant tumors with high morbidity and mortality. Long non-coding RNAs (lncRNAs) are frequently dysregulated in human cancers and play an important role in the initiation and progression of HCC. Here, we investigated the expression of a new reported lncRNA495810 in our previous study by analyzing the publicly available datasets and using RT-qPCR assay. The cell proliferation experiment, cell cycle and apoptosis assay, wound healing assay, cell migration assay were used to explore the biological function of lncRNA495810 in HCC. The western blot, RNA pull down and RNA immunoprecipitation (RIP) detection were used to investigate the potential molecular mechanisms of lncRNA495810. The results demonstrated that lncRNA495810 was significantly upregulated in hepatocellular carcinoma and associated with poor prognosis of hepatocellular carcinoma patients. Moreover, it proved that lncRNA495810 promotes the proliferation and metastasis of hepatoma cells by directly binding and upregulating the expression of fatty acid-binding protein 5. These results reveal the oncogenic roles of lncRNA495810 in HCC and provide a potential therapeutic target for HCC. Full article

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18 pages, 772 KiB

Open AccessReview

Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones

by Shangyu Wang, Lei Wu, Qianghui Zhu, Jiahao Wu, Shiyu Tang, Yifang Zhao, Yalin Cheng, Dezhi Zhang, Gexia Qiao, Runzhi Zhang and Fumin Lei

Biology 2024, 13(8), 643; https://doi.org/10.3390/biology13080643 - 22 Aug 2024

Viewed by 881

Abstract

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment [...] Read more.

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation. Full article

(This article belongs to the Special Issue Bird Biology and Conservation)

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21 pages, 4589 KiB

Open AccessArticle

Variation in the Health Status of the Mediterranean Gorgonian Forests: The Synergistic Effect of Marine Heat Waves and Fishing Activity

by Martina Canessa, Rosella Bertolotto, Federico Betti, Marzia Bo, Alessandro Dagnino, Francesco Enrichetti, Margherita Toma and Giorgio Bavestrello

Biology 2024, 13(8), 642; https://doi.org/10.3390/biology13080642 - 21 Aug 2024

Viewed by 881

Abstract

Over the past thirty years, the red gorgonian Paramuricea clavata in the Mediterranean Sea has faced increasing threats, including heat waves and human activities such as artisanal and recreational fishing. Epibiosis on damaged gorgonian colonies is generally used as an indirect indication of [...] Read more.

Over the past thirty years, the red gorgonian Paramuricea clavata in the Mediterranean Sea has faced increasing threats, including heat waves and human activities such as artisanal and recreational fishing. Epibiosis on damaged gorgonian colonies is generally used as an indirect indication of stressed conditions. The density and height of P. clavata and the percentage of colonies affected by epibiosis and entangled in lost fishing gear were monitored to investigate the phenomenon and its trend over time in the Ligurian Sea. Analyses were based on transects collected during ROV campaigns between 2015 and 2022 at depths of 33–90 m. A strong correlation was observed between fishing efforts in the study area and the level of epibiosis. Maximal percentages of colonies affected by epibiosis and entanglement were recorded at depths of 50–70 m. Temporally, marine heat waves before 2019 were identified as the primary cause of damage to P. clavata. The decrease in epibiosis percentages after 2019, despite the 2022 heat wave, may be due to a quick recovery ability of the populations and a reduction in fishing activities during the COVID-19 lockdown in 2020. Long-term monitoring programmes are essential to understand the changes in marine benthic communities exposed to different stressors. Full article

(This article belongs to the Special Issue Epibiosis in Aquatic Environments)

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14 pages, 2170 KiB

Open AccessReview

Effect of Probiotic Fermented Milk Supplementation on Glucose and Lipid Metabolism Parameters and Inflammatory Markers in Patients with Type 2 Diabetes Mellitus: A Meta-Analysis of Randomized Controlled Trials

by Hao Zhong, Lingmiao Wang, Fuhuai Jia, Yongqiu Yan, Feifei Xiong, Khemayanto Hidayat and Yunhong Li

Biology 2024, 13(8), 641; https://doi.org/10.3390/biology13080641 - 21 Aug 2024

Viewed by 1060

Abstract

Modulating gut microbiota composition through probiotic administration has been proposed as a novel therapy for type 2 diabetes mellitus (T2DM), and fermented milk is arguably the most common and ideal probiotic carrier. The present meta-analysis was performed to assess the effects of probiotic [...] Read more.

Modulating gut microbiota composition through probiotic administration has been proposed as a novel therapy for type 2 diabetes mellitus (T2DM), and fermented milk is arguably the most common and ideal probiotic carrier. The present meta-analysis was performed to assess the effects of probiotic fermented milk supplementation on glucose and lipid metabolism parameters and inflammatory markers in patients with T2DM using published data from randomized controlled trials (RCTs). The PubMed, Web of Science, and Cochrane Library databases were searched for relevant RCTs. A random-effects model was used to generate the weighted mean difference (WMD) and 95% confidence interval (95% CI). Probiotic fermented milk supplementation reduced the levels of fasting plasma glucose (MD = −17.01, 95% CI −26.43, −7.58 mg/dL; n = 7), hemoglobin A1c (MD = −0.47, 95% CI −0.74, −0.21%; n = 7), total cholesterol (MD = −5.15, 95% CI −9.52, −0.78 mg/dL; n = 7), and C-reactive protein (MD = −0.25, 95% CI −0.43, −0.08; n = 3) but did not significantly affect the levels of HOMA-IR (MD = −0.89, 95% CI −2.55, 0.78; n = 3), triglyceride (MD = −4.69, 95% CI −14.67, 5.30 mg/dL; n = 6), low-density lipoprotein cholesterol (MD = −4.25, 95% CI −8.63, 0.13 mg/dL; n = 7), high-density lipoprotein cholesterol (MD = 1.20, 95% CI −0.96, 3.36 mg/dL; n = 7), and tumor necrosis factor-alpha (MD: −0.58, 95% CI −1.47, 0.32 pg/mL; n = 2). In summary, the present findings provide a crude indication of the potential benefits of probiotic fermented milk supplementation in improving glucose and lipid metabolism and inflammation in patients with T2DM. However, more robust evidence is needed to determine the clinical significance of probiotic fermented milk in the management of T2DM. Full article

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

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16 pages, 9613 KiB

Open AccessArticle

Effects of Ocean Acidification and Temperature Coupling on Photosynthetic Activity and Physiological Properties of Ulva fasciata and Sargassum horneri

by Kai Wang, Xiang Tao, Shouyu Zhang and Xu Zhao

Biology 2024, 13(8), 640; https://doi.org/10.3390/biology13080640 - 21 Aug 2024

Viewed by 612

Abstract

To investigate the ecological impacts of macroalgae in the framework of shifting global CO₂ concentrations, we conducted a study utilizing Ulva fasciata and Sargassum horneri specimens sourced from the Ma’an Archipelago in Zhejiang Province on how ocean acidification (OA) and temperature changes [...] Read more.

To investigate the ecological impacts of macroalgae in the framework of shifting global CO₂ concentrations, we conducted a study utilizing Ulva fasciata and Sargassum horneri specimens sourced from the Ma’an Archipelago in Zhejiang Province on how ocean acidification (OA) and temperature changes interact to affect the photosynthetic physiological responses of macroalgae. The results of the study showed that OA reduced the tolerance of U. fasciata to bright light at 20 °C, resulting in more pronounced photoinhibition, while 15 °C caused significant inhibition of U. fasciata, reducing its growth and photosynthetic activity, but OA alleviated the inhibition and promoted the growth of the alga to a certain extent. The tolerance of S. horneri to bright light was also reduced at 20 °C; the inhibition was relieved at 15 °C, and the OA further improved the algal growth. The Relative Growth Rate (RGR), photosynthetic pigment content, and the release of the dissolved organic carbon (DOC) of U. fasciata were mainly affected by the change in temperature; the growth of the alga and the synthesis of metabolites were more favored by 20 °C. A similar temperature dependence was observed for S. horneri, with faster growth and high metabolism at 15 °C. Our results suggest that OA reduces the tolerance of macroalgae to high light at suitable growth temperatures; however, at unsuitable growth temperatures, OA effectively mitigates this inhibitory effect and promotes algal growth. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Aquatic Macrophytes)

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18 pages, 8531 KiB

Open AccessArticle

Pathological Role of High Sugar in Mitochondrial Respiratory Chain Defect-Augmented Mitochondrial Stress

by Ebrima D. Cham, Tsung-I Peng and Mei-Jie Jou

Biology 2024, 13(8), 639; https://doi.org/10.3390/biology13080639 - 21 Aug 2024

Viewed by 1095

Abstract

According to many research groups, high glucose induces the overproduction of superoxide anions, with reactive oxygen species (ROS) generally being considered the link between high glucose levels and the toxicity seen at cellular levels. Respiratory complex anomalies can lead to the production of [...] Read more.

According to many research groups, high glucose induces the overproduction of superoxide anions, with reactive oxygen species (ROS) generally being considered the link between high glucose levels and the toxicity seen at cellular levels. Respiratory complex anomalies can lead to the production of ROS. Calcium [Ca²⁺] at physiological levels serves as a second messenger in many physiological functions. Accordingly, mitochondrial calcium [Ca²⁺]_m overload leads to ROS production, which can be lethal to the mitochondria through various mechanisms. F1F0-ATPase (ATP synthase or complex V) is the enzyme responsible for catalyzing the final step of oxidative phosphorylation. This is achieved by F1F0-ATPase coupling the translocation of protons in the mitochondrial intermembrane space and shuttling them to the mitochondrial matrix for ATP synthesis to take place. Mitochondrial complex V T8993G mutation specifically blocks the translocation of protons across the intermembrane space, thereby blocking ATP synthesis and, in turn, leading to Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome. This study seeks to explore the possibility of [Ca²⁺]_m overload mediating the pathological roles of high glucose in defective respiratory chain-mediated mitochondrial stress. NARP cybrids are the in vitro experimental models of cells with F1FO-ATPase defects, with these cells harboring 98% of mtDNA T8993G mutations. Their counterparts, 143B osteosarcoma cell lines, are the parental cell lines used for comparison. We observed that NARP cells mediated and enhanced the death of cells (apoptosis) when incubated with hydrogen peroxide (H₂O₂) and high glucose, as depicted using the MTT assay of cell viability. Furthermore, using fluorescence probe-coupled laser scanning confocal imaging microscopy, NARP cells were found to significantly enable mitochondrial reactive oxygen species (mROS) formation and enhance the depolarization of the mitochondrial membrane potential (ΔΨm). Elucidating the mechanisms of sugar-enhanced toxicity on the mitochondria may, in the future, help to alleviate the symptoms of patients with NARP syndromes and other neurodegenerative diseases. Full article

(This article belongs to the Special Issue Unique Response of Pluripotent Stem Cells to External Stimuli and Stresses)

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27 pages, 2291 KiB

Open AccessReview

Deciphering Depression: Epigenetic Mechanisms and Treatment Strategies

by Alaa A. A. Aljabali, Almuthanna K. Alkaraki, Omar Gammoh, Murtaza M. Tambuwala, Vijay Mishra, Yachana Mishra, Sk. Sarif Hassan and Mohamed El-Tanani

Biology 2024, 13(8), 638; https://doi.org/10.3390/biology13080638 - 20 Aug 2024

Cited by 1 | Viewed by 2796

Abstract

Depression, a significant mental health disorder, is under intense research scrutiny to uncover its molecular foundations. Epigenetics, which focuses on controlling gene expression without altering DNA sequences, offers promising avenues for innovative treatment. This review explores the pivotal role of epigenetics in depression, [...] Read more.

Depression, a significant mental health disorder, is under intense research scrutiny to uncover its molecular foundations. Epigenetics, which focuses on controlling gene expression without altering DNA sequences, offers promising avenues for innovative treatment. This review explores the pivotal role of epigenetics in depression, emphasizing two key aspects: (I) identifying epigenetic targets for new antidepressants and (II) using personalized medicine based on distinct epigenetic profiles, highlighting potential epigenetic focal points such as DNA methylation, histone structure alterations, and non-coding RNA molecules such as miRNAs. Variations in DNA methylation in individuals with depression provide opportunities to target genes that are associated with neuroplasticity and synaptic activity. Aberrant histone acetylation may indicate that antidepressant strategies involve enzyme modifications. Modulating miRNA levels can reshape depression-linked gene expression. The second section discusses personalized medicine based on epigenetic profiles. Analyzing these patterns could identify biomarkers associated with treatment response and susceptibility to depression, facilitating tailored treatments and proactive mental health care. Addressing ethical concerns regarding epigenetic information, such as privacy and stigmatization, is crucial in understanding the biological basis of depression. Therefore, researchers must consider these issues when examining the role of epigenetics in mental health disorders. The importance of epigenetics in depression is a critical aspect of modern medical research. These findings hold great potential for novel antidepressant medications and personalized treatments, which would significantly improve patient outcomes, and transform psychiatry. As research progresses, it is expected to uncover more complex aspects of epigenetic processes associated with depression, enhance our comprehension, and increase the effectiveness of therapies. Full article

(This article belongs to the Special Issue Epigenetic Modifications and Changes in Neurodegenerative Diseases)

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23 pages, 16552 KiB

Open AccessArticle

Ablation of TrkB from Enkephalinergic Precursor-Derived Cerebellar Granule Cells Generates Ataxia

by Elena Eliseeva, Mohd Yaseen Malik and Liliana Minichiello

Biology 2024, 13(8), 637; https://doi.org/10.3390/biology13080637 - 20 Aug 2024

Viewed by 3381

Abstract

In ataxia disorders, motor incoordination (ataxia) is primarily linked to the dysfunction and degeneration of cerebellar Purkinje cells (PCs). In spinocerebellar ataxia 6 (SCA6), for example, decreased BDNF–TrkB signalling appears to contribute to PC dysfunction and ataxia. However, abnormal BDNF–TrkB signalling in granule [...] Read more.

In ataxia disorders, motor incoordination (ataxia) is primarily linked to the dysfunction and degeneration of cerebellar Purkinje cells (PCs). In spinocerebellar ataxia 6 (SCA6), for example, decreased BDNF–TrkB signalling appears to contribute to PC dysfunction and ataxia. However, abnormal BDNF–TrkB signalling in granule cells (GCs) may contribute to PC dysfunction and incoordination in ataxia disorders, as TrkB receptors are also present in GCs that provide extensive input to PCs. This study investigated whether dysfunctional BDNF–TrkB signalling restricted to a specific subset of cerebellar GCs can generate ataxia in mice. To address this question, our research focused on Trkb^Penk-KO mice, in which the TrkB receptor was removed from enkephalinergic precursor-derived cerebellar GCs. We found that deleting Ntrk2, encoding the TrkB receptor, eventually interfered with PC function, leading to ataxia symptoms in the Trkb^Penk-KO mice without affecting their cerebellar morphology or levels of selected synaptic markers. These findings suggest that dysfunctional BDNF–TrkB signalling in a subset of cerebellar GCs alone is sufficient to trigger ataxia symptoms and may contribute to motor incoordination in disorders like SCA6. Full article

(This article belongs to the Special Issue Roles and Functions of Neurotrophins and Their Receptors in the Brain)

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15 pages, 29814 KiB

Open AccessCase Report

Assessment of Extracellular Matrix Fibrous Elements in Male Dermal Aging: A Ten-Year Follow-Up Preliminary Case Study

by Bogusław Machaliński, Dorota Oszutowska-Mazurek, Przemyslaw Mazurek, Mirosław Parafiniuk, Paweł Szumilas, Alicja Zawiślak, Małgorzata Zaremba, Iwona Stecewicz, Piotr Zawodny and Barbara Wiszniewska

Biology 2024, 13(8), 636; https://doi.org/10.3390/biology13080636 - 20 Aug 2024

Cited by 1 | Viewed by 625

Abstract

Skin aging is a complex phenomenon influenced by multiple internal and external factors that can lead to significant changes in skin structure, particularly the degradation of key extracellular matrix (ECM) components such as collagen and elastic fibers in the dermis. In this study, [...] Read more.

Skin aging is a complex phenomenon influenced by multiple internal and external factors that can lead to significant changes in skin structure, particularly the degradation of key extracellular matrix (ECM) components such as collagen and elastic fibers in the dermis. In this study, we aimed to meticulously assess the morphological changes within these critical fibrous ECM elements in the dermis of the same volunteer at age 47 and 10 years later (2012 to 2022). Using advanced histological staining techniques, we examined the distribution and characteristics of ECM components, including type I collagen, type III collagen, and elastic fibers. Morphological analysis, facilitated by hematoxylin and eosin staining, allowed for an accurate assessment of fiber bundle thickness and a quantification of collagen and elastic fiber areas. In addition, we used the generalized Pareto distribution for histogram modeling to refine our statistical analyses. This research represents a pioneering effort to examine changes in ECM fiber material, specifically within the male dermis over a decade-long period. Our findings reveal substantial changes in the organization of type I collagen within the ECM, providing insight into the dynamic processes underlying skin aging. Full article

(This article belongs to the Section Cell Biology)

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12 pages, 2363 KiB

Open AccessArticle

Role of Cholecystokinin (cck) in Feeding Regulation of Largemouth Bass (Micropterus salmoides): Peptide Activation and Antagonist Inhibition

by Hualiang Liang, Haifeng Mi, Heng Yu, Dongyu Huang, Mingchun Ren, Lu Zhang and Tao Teng

Biology 2024, 13(8), 635; https://doi.org/10.3390/biology13080635 - 20 Aug 2024

Viewed by 686

Abstract

This study investigated the role of cholecystokinin (cck) in the feeding regulation of largemouth bass (Micropterus salmoides) via peptide activation and antagonist inhibition. The results show that the cck gene was expressed in various tissues, with the highest expression [...] Read more.

This study investigated the role of cholecystokinin (cck) in the feeding regulation of largemouth bass (Micropterus salmoides) via peptide activation and antagonist inhibition. The results show that the cck gene was expressed in various tissues, with the highest expression level occurring in the brain. Feeding, continuous feeding, and refeeding after fasting could significantly improve the mRNA levels of cck in the brain. Moreover, the activation of cck via injecting an exogenous CCK peptide could inhibit feed intake by regulating the mRNA levels of anorexigenic and feed-promoting factors in the brain and intestine. Furthermore, the CCK peptide reduced feed intake; however, the presence of an antagonist (Ly225910-CCK1R and devazepide-CCK2R) could reverse this effect through regulating the mRNA levels of anorexigenic and feed-promoting factors in the brain and intestine. Treatment with devazepide + CCK (CCK2R) reversed feed intake more effectively than Ly225910 + CCK (CCK1R) treatment. In summary, cck could regulate the feed intake of largemouth bass through regulating feeding-related genes in the brain and intestine. In addition, cck required binding with the receptor to inhibit feed intake more effectively in largemouth bass, and the binding effect of CCK1R was better than that of CCK2R. Full article

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14 pages, 4225 KiB

Open AccessArticle

Comparative Analysis of Angora Rabbit Colostrum and Mature Milk Using Quantitative Proteomics

by Dongwei Huang, Yuanlang Wang, Haisheng Ding and Huiling Zhao

Biology 2024, 13(8), 634; https://doi.org/10.3390/biology13080634 - 19 Aug 2024

Viewed by 847

Abstract

Colostrum intake is a crucial determinant of survival in newborn rabbits. Neonates rely entirely on passive immunity transfer from their mothers while suckling colostrum. The goal of this study was to explore the protein differences of rabbit milk during different lactation periods. Our [...] Read more.

Colostrum intake is a crucial determinant of survival in newborn rabbits. Neonates rely entirely on passive immunity transfer from their mothers while suckling colostrum. The goal of this study was to explore the protein differences of rabbit milk during different lactation periods. Our findings showed that the daily milk yield exhibited an increasing trend from the 2nd to the 21st day of lactation. A data-independent acquisition proteomics approach identified a total of 2011 proteins. Significantly, different abundances were found for 525 proteins in the colostrum and the mature milk samples. Eleven differentially abundant proteins (DAPs) were examined using parallel reaction monitoring, which verified the reliability of the proteomic data. Gene Ontology analysis revealed that these DAPs were primarily associated with glycosyltransferase activity, macromolecule transmembrane transporter activity, and regulation of acute inflammatory response. The dominant metabolic pathways of the DAPs involve the complement and coagulation cascades. A protein–protein interaction analysis identified apolipoprotein B, apolipoprotein A1, triose phosphate isomerase 1, and albumin as the hub proteins responsible for distinguishing differences between biological properties in rabbit colostrum and mature milk. These findings enhance our comprehension of the rabbit milk proteome, particularly in expanding our knowledge regarding the requirements of neonatal rabbits. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding 2.0)

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14 pages, 20836 KiB

Open AccessArticle

Identification of Clinical Value and Biological Effects of XIRP2 Mutation in Hepatocellular Carcinoma

by Dahuan Li, Xin Bao, Shan Lei, Wenpeng Cao, Zhirui Zeng and Tengxiang Chen

Biology 2024, 13(8), 633; https://doi.org/10.3390/biology13080633 - 19 Aug 2024

Viewed by 998

Abstract

Hepatocellular carcinoma (HCC) is a prevalent malignant digestive tumor. Numerous genetic mutations have been documented in HCC, yet the clinical significance of these mutations remains largely unexplored. The objective of this study is to ascertain the clinical value and biological effects of xin [...] Read more.

Hepatocellular carcinoma (HCC) is a prevalent malignant digestive tumor. Numerous genetic mutations have been documented in HCC, yet the clinical significance of these mutations remains largely unexplored. The objective of this study is to ascertain the clinical value and biological effects of xin actin binding repeat containing 2 (XIRP2) mutation in HCC. The gene mutation landscape of HCC was examined using data from the Cancer Genome Atlas and the International Cancer Genome Consortium databases. The prognostic significance of the XIRP2 mutation was assessed through KM plot analysis. The association between drug sensitivity and the XIRP2 mutation was investigated using the TIDE algorithm and CCK-8 experiments. The biological effects of the XIRP2 mutation were evaluated through qRT-PCR, protein stability experiments, and relevant biological experiments. The XIRP2 mutation is one of the high-frequency mutations in HCC, and is associated with poor prognosis. A total of 72 differentially expressed genes (DEGs) were observed in HCC tissues with the XIRP2 mutation as compared to those with the XIRP2 wildtype, and these DEGs were closely related to ion metabolic processes. The XIRP2 mutation was linked to alterations in the sensitivity of fludarabine, oxaliplatin, WEHI-539, and LCL-161. CCK-8 assays demonstrated that HCC cells carrying the XIRP2 mutation exhibited increased resistance to fludarabine and oxaliplatin, but enhanced sensitivity to WEHI-539 and LCL-161 as compared with those HCC cells with the XIRP2 wildtype. The XIRP2 mutation was found to have no impact on the mRNA levels of XIRP2 in tissues and cells, but it did enhance the stability of the XIRP2 protein. Mechanically, the inhibition of XIRP2 resulted in a significant increase in sensitivity to oxaliplatin through an elevation in zinc ions and a calcium ion overload. In conclusion, the XIRP2 mutation holds potential as a biomarker for predicting the prognosis and drug sensitivity of HCC and serves as a therapeutic target to enhance the efficacy of oxaliplatin. Full article

(This article belongs to the Topic Biomarkers and Therapeutic Targets Based on Bioinformatical Studies)

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32 pages, 6010 KiB

Open AccessArticle

Mutations and Differential Transcription of Mating-Type and Pheromone Receptor Genes in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungi Complex

by Xiu-Zhang Li, Meng-Jun Xiao, Yu-Ling Li, Ling Gao and Jia-Shi Zhu

Biology 2024, 13(8), 632; https://doi.org/10.3390/biology13080632 - 18 Aug 2024

Cited by 1 | Viewed by 923

Abstract

Sexual reproduction in ascomycetes is controlled by the mating-type (MAT) locus. (Pseudo)homothallic reproduction has been hypothesized on the basis of genetic data from Hirsutella sinensis (Genotype #1 of Ophiocordyceps sinensis). However, the differential occurrence and differential transcription of mating-type genes in the [...] Read more.

Sexual reproduction in ascomycetes is controlled by the mating-type (MAT) locus. (Pseudo)homothallic reproduction has been hypothesized on the basis of genetic data from Hirsutella sinensis (Genotype #1 of Ophiocordyceps sinensis). However, the differential occurrence and differential transcription of mating-type genes in the MAT1-1 and MAT1-2 idiomorphs were found in the genome and transcriptome assemblies of H. sinensis, and the introns of the MAT1-2-1 transcript were alternatively spliced with an unspliced intron I that contains stop codons. These findings reveal that O. sinensis reproduction is controlled at the genetic, transcriptional, and coupled transcriptional-translational levels. This study revealed that mutant mating proteins could potentially have various secondary structures. Differential occurrence and transcription of the a-/α-pheromone receptor genes were also found in H. sinensis. The data were inconsistent with self-fertilization under (pseudo)homothallism but suggest the self-sterility of H. sinensis and the requirement of mating partners to achieve O. sinensis sexual outcrossing under heterothallism or hybridization. Although consistent occurrence and transcription of the mating-type genes of both the MAT1-1 and MAT1-2 idiomorphs have been reported in natural and cultivated Cordyceps sinensis insect-fungi complexes, the mutant MAT1-1-1 and α-pheromone receptor transcripts in natural C. sinensis result in N-terminal or middle-truncated proteins with significantly altered overall hydrophobicity and secondary structures of the proteins, suggesting heterogeneous fungal source(s) of the proteins and hybridization reproduction because of the co-occurrence of multiple genomically independent genotypes of O. sinensis and >90 fungal species in natural C. sinensis. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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20 pages, 2182 KiB

Open AccessArticle

Auditory Noise Facilitates Lower Visual Reaction Times in Humans

by Argelia Pérez-Pacheco, Fernando Yael Rodríguez Morales, Khashayar Misaghian, Jocelyn Faubert and Jesus Eduardo Lugo Arce

Biology 2024, 13(8), 631; https://doi.org/10.3390/biology13080631 - 18 Aug 2024

Viewed by 1780

Abstract

Noise is commonly seen as a disturbance but can influence any system it interacts with. This influence may not always be desirable, but sometimes it can improve the system’s performance. For example, stochastic resonance is a phenomenon where adding the right amount of [...] Read more.

Noise is commonly seen as a disturbance but can influence any system it interacts with. This influence may not always be desirable, but sometimes it can improve the system’s performance. For example, stochastic resonance is a phenomenon where adding the right amount of noise to a weak signal makes it easier to detect. This is known as sub-threshold detection. This sub-threshold detection’s natural fingerprint is the fact that the threshold values follow an inverse U-shaped curve as the noise intensity increases. The minimum threshold value is the point of maximum sensitivity and represents the optimal point that divides the dynamics in two. Below that point, we can find the beneficial noise branch, where the noise can facilitate better detection. Above that point, the common detrimental noise concept can be found: adding noise hinders signal detection. The nervous system controls the movements and bodily functions in the human body. By reducing the sensory thresholds, we can improve the balance of these functions. Additionally, researchers have wondered if noise could be applied to different senses or motor mechanisms to enhance our abilities. In this work, noise is used to improve human reaction times. We tested the hypothesis that visual reaction times decrease significantly when the subject’s perception is in the beneficial noise branch and closer to the optimal point than outside of this condition. Auditory noise was introduced in 101 human subjects using an interface capable of searching for the right amount of noise to place the subject in the beneficial noise branch close to the optimal point. When comparing the results, the reaction times decreased when the subjects were at the optimal point compared to when the subjects were outside of such conditions. These results reveal the possibility of using this approach to enhance human performance in tasks requiring faster reaction times, such as sports. Full article

(This article belongs to the Special Issue Neurobiology and Biophysics of Sensory Systems)

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12 pages, 3795 KiB

Open AccessArticle

Corazonin Stimulates Ecdysteroid Synthesis during the Molting Process of the Swimming Crab, Portunus trituberculatus

by Xi Xie, Jun Zhang, Shisheng Tu, Qi Zhou and Dongfa Zhu

Biology 2024, 13(8), 630; https://doi.org/10.3390/biology13080630 - 18 Aug 2024

Viewed by 734

Abstract

The neuropeptide corazonin (Crz) exerts diverse physiological effects in insects, yet its role in crustaceans remains elusive. The abundant expression of Crz receptor (CrzR) in the Y-organs of several crustaceans suggests a potential involvement of Crz in regulating ecdysteroid synthesis. In this study, [...] Read more.

The neuropeptide corazonin (Crz) exerts diverse physiological effects in insects, yet its role in crustaceans remains elusive. The abundant expression of Crz receptor (CrzR) in the Y-organs of several crustaceans suggests a potential involvement of Crz in regulating ecdysteroid synthesis. In this study, we examined the effects of PtCrz on ecdysteroid synthesis during the molting period of Portunus trituberculatus through PtCrz treatments and PtCrzR silencing. Our results showed that PtCrz peptide stimulates ecdysteroid levels and the gene expression involved in ecdysteroidogenesis both in vitro and in vivo, whereas dsPtCrzR treatments had opposite effects on ecdysteroid levels and associated gene expression. Thus, our study suggests that PtCrz may modulate ecdysteroid synthesis via Y-organ-expressed PtCrzR. Furthermore, we also discovered the involvement of PtCrz/PtCrzR signaling in regulating PtETH expression. Notably, the inhibitory effect of dsPtCrzR on ecdysteroid synthesis or PtETH expression can be reversed by PtCrz treatment, suggesting the potential existence of multiple receptors for PtCrz. This study provides new insights into the function of crustacean Crz and, for the first time, elucidates the presence of a neuropeptide that can stimulate ecdysteroid synthesis in crustaceans. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)

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19 pages, 2111 KiB

Open AccessReview

Assembly, Activation, and Helicase Actions of MCM2-7: Transition from Inactive MCM2-7 Double Hexamers to Active Replication Forks

by Zhiying You and Hisao Masai

Biology 2024, 13(8), 629; https://doi.org/10.3390/biology13080629 - 17 Aug 2024

Viewed by 1214

Abstract

In this review, we summarize the processes of the assembly of multi-protein replisomes at the origins of replication. Replication licensing, the loading of inactive minichromosome maintenance double hexamers (dhMCM2-7) during the G1 phase, is followed by origin firing triggered by two serine–threonine kinases, [...] Read more.

In this review, we summarize the processes of the assembly of multi-protein replisomes at the origins of replication. Replication licensing, the loading of inactive minichromosome maintenance double hexamers (dhMCM2-7) during the G1 phase, is followed by origin firing triggered by two serine–threonine kinases, Cdc7 (DDK) and CDK, leading to the assembly and activation of Cdc45/MCM2-7/GINS (CMG) helicases at the entry into the S phase and the formation of replisomes for bidirectional DNA synthesis. Biochemical and structural analyses of the recruitment of initiation or firing factors to the dhMCM2-7 for the formation of an active helicase and those of origin melting and DNA unwinding support the steric exclusion unwinding model of the CMG helicase. Full article

(This article belongs to the Special Issue The Replication Licensing System)

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18 pages, 7633 KiB

Open AccessArticle

Dendrochronological Analysis of Pinus pinea in Central Chile and South Spain for Sustainable Forest Management

by Verónica Loewe-Muñoz, Antonio M. Cachinero-Vivar, Jesús Julio Camarero, Rodrigo Del Río, Claudia Delard and Rafael M. Navarro-Cerrillo

Biology 2024, 13(8), 628; https://doi.org/10.3390/biology13080628 - 17 Aug 2024

Viewed by 702

Abstract

Pinus pinea is an important Mediterranean species due to its adaptability and tolerance to aridity and its high-quality pine nuts. Different forest types located in Mediterranean native and non-native environments provide the opportunity to perform comparative studies on the species’ response to climate [...] Read more.

Pinus pinea is an important Mediterranean species due to its adaptability and tolerance to aridity and its high-quality pine nuts. Different forest types located in Mediterranean native and non-native environments provide the opportunity to perform comparative studies on the species’ response to climate change. The aims of this study were to elucidate growth patterns of the species growing in native and exotic habitats and to analyze its response to climatic fluctuations, particularly drought, in both geographical contexts. Understanding stone pine (Pinus pinea) growth responses to climate variability in native and exotic habitats by comparing natural stands and plantations may provide useful information to plan adequate management under climate change. By doing so, we enhance the understanding of P. pinea’s adaptability and provide practical approaches to its sustainable management. In this study, we reconstructed and compared the stem radial growth of seven stone pine stands, two in southern Spain and five in central–southern Chile, growing under different climatic conditions. We quantified the relationships between growth variability and climate variables (total rainfall, mean temperature, and SPEI drought index). Growth was positively correlated with autumn rainfall in plantations and with autumn–winter rainfall in natural stands. Growth was also enhanced by high autumn-to-spring rainfall in the driest Chilean plantation, whereas in the wettest and coolest plantation, such correlation was found in winter and summer. A negative impact of summer temperature was found only in one of the five Chilean plantations and in a Spanish site. The correlation between SPEI and tree-ring width indices showed different patterns between and within countries. Overall, exotic plantations showed lower sensitivity to climate variability than native stands. Therefore, stone pine plantations may be useful to assist in mitigating climate change. Full article

(This article belongs to the Special Issue Dendrochronology in Arid and Semiarid Regions)

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20 pages, 3496 KiB

Open AccessArticle

Neutralizing Oxidized Phosphatidylcholine Reduces Airway Inflammation and Hyperreactivity in a Murine Model of Allergic Asthma

by Jignesh Vaghasiya, Aruni Jha, Sujata Basu, Alaina Bagan, Siwon K. Jengsuksavat, Amir Ravandi, Christopher D. Pascoe and Andrew J. Halayko

Biology 2024, 13(8), 627; https://doi.org/10.3390/biology13080627 - 17 Aug 2024

Viewed by 1037

Abstract

Oxidative stress is associated with asthma pathobiology. We reported that oxidized phosphatidylcholines (OxPCs) are mediators of oxidative stress and accumulate in the lung in response to allergen challenge. The current study begins to unravel mechanisms for OxPC accumulation in the lung, providing the [...] Read more.

Oxidative stress is associated with asthma pathobiology. We reported that oxidized phosphatidylcholines (OxPCs) are mediators of oxidative stress and accumulate in the lung in response to allergen challenge. The current study begins to unravel mechanisms for OxPC accumulation in the lung, providing the first insights about how OxPCs underpin allergic airway pathophysiology, and pre-clinical testing of selective neutralization of OxPCs in a murine model of allergic asthma. We hypothesized that intranasal delivery of E06, a natural IgM antibody that neutralizes the biological activity of OxPCs, can ameliorate allergen-induced airway inflammation and airway hyperresponsiveness. Adult BALB/c mice were intranasally (i.n.) challenged with house dust mite (HDM) (25 μg/mouse, 2 weeks). Some animals also received E06 monoclonal antibody (mAb) (10 µg) i.n. 1 hr before each HDM challenge. HDM challenge reduced mRNA for anti-oxidant genes (SOD1, SOD2, HO-1, and NFE2L2) in the lung by several orders of magnitude (p < 0.05). Concomitantly, total immune cell number in bronchoalveolar lavage fluid (BALF) increased significantly (p < 0.001). E06 mAb treatment prevented allergen-induced BALF immune cell number by 43% (p < 0.01). This included a significant blockade of eosinophils (by 48%, p < 0.001), neutrophils (by 80%, p < 0.001), macrophages (by 80%, p < 0.05), and CD4 (by 30%, p < 0.05) and CD8 (by 42%, p < 0.01) lymphocytes. E06 effects correlated with a significant reduction in TNF (by 64%, p < 0.001) and IL-1β (by 75%, p < 0.05) and a trend to diminish accumulation of other cytokines (e.g., IL-4, -10, and -33, and IFN-γ). E06 mAb treatment also inhibited HDM exposure-induced increases in total respiratory resistance and small airway resistance by 24% and 26%, respectively. In conclusion, prophylactic treatment with an OxPC-neutralizing antibody significantly limits allergen-induced airway inflammation and airway hyperresponsiveness, suggesting that OxPCs are important mediators of oxidative stress-associated allergic lung pathophysiology. Full article

(This article belongs to the Special Issue Molecular Mechanisms and New Targets of Refractory Asthma)

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24 pages, 2619 KiB

Open AccessArticle

Rare Earth Element Content in Hair Samples of Children Living in the Vicinity of the Kola Peninsula Mining Site and Nervous System Diseases

by Natalia K. Belisheva and Svetlana V. Drogobuzhskaya

Biology 2024, 13(8), 626; https://doi.org/10.3390/biology13080626 - 17 Aug 2024

Viewed by 754

Abstract

The aim of this study is to assess the rare earth element (REE) content in hair samples of children living in Lovozero village, near an REE mining site, and the possible effects of REEs on the prevalence of nervous system diseases in Lovozersky [...] Read more.

The aim of this study is to assess the rare earth element (REE) content in hair samples of children living in Lovozero village, near an REE mining site, and the possible effects of REEs on the prevalence of nervous system diseases in Lovozersky District (Murmansk region, Kola Peninsula). Fifty-three school-age children were recruited for the analysis of REE content in hair samples. REE (Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) content was estimated by means of inductively coupled plasma mass spectrometry (ICP-MS). The analysis of REE content in the hair of children living in Russia, Kazakhstan, and China indicated REE intake from the environment. The possible contribution of REEs to nervous system disorders is supported by the link between the REE content in hair samples of children living near REE mining areas (China) and the manifestation of cognitive disorders in these children. It is also found that the prevalence of nervous system diseases in children aged 15–17 years is higher in Lovozersky District compared to the other districts of the Murmansk region. In this paper, the possible contribution of REEs to the prevalence of episodic paroxysmal disorders (G40–G47), cerebral palsy (G80–G83), and epilepsy and status epilepticus (G40–G41) is discussed. Full article

(This article belongs to the Section Medical Biology)

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21 pages, 4738 KiB

Open AccessReview

Germplasm Resources and Genetic Breeding of Huang-Qi (Astragali Radix): A Systematic Review

by Pengbin Dong, Lingjuan Wang, Yong Chen, Liyang Wang, Wei Liang, Hongyan Wang, Jiali Cheng, Yuan Chen and Fengxia Guo

Biology 2024, 13(8), 625; https://doi.org/10.3390/biology13080625 - 16 Aug 2024

Viewed by 862

Abstract

Huang-Qi (Astragali radix) is one of the most widely used herbs in traditional Chinese medicine, derived from the dried roots of Astragalus membranaceus or Astragalus membranaceus var. mongholicus. To date, more than 200 compounds have been reported to be isolated and identified [...] Read more.

Huang-Qi (Astragali radix) is one of the most widely used herbs in traditional Chinese medicine, derived from the dried roots of Astragalus membranaceus or Astragalus membranaceus var. mongholicus. To date, more than 200 compounds have been reported to be isolated and identified in Huang-Qi. However, information pertaining to Huang-Qi breeding is considerably fragmented, with fundamental gaps in knowledge, creating a bottleneck in effective breeding strategies. This review systematically introduces Huang-Qi germplasm resources, genetic diversity, and genetic breeding, including wild species and cultivars, and summarizes the breeding strategy for cultivars and the results thereof as well as recent progress in the functional characterization of the structural and regulatory genes related to horticultural traits. Perspectives about the resource protection and utilization, breeding, and industrialization of Huang-Qi in the future are also briefly discussed. Full article

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20 pages, 3131 KiB

Open AccessArticle

Soil Solarization Efficiently Reduces Fungal Soilborne Pathogen Populations, Promotes Lettuce Plant Growth, and Affects the Soil Bacterial Community

by George T. Tziros, Anastasios Samaras and George S. Karaoglanidis

Biology 2024, 13(8), 624; https://doi.org/10.3390/biology13080624 - 15 Aug 2024

Viewed by 869

Abstract

Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods [...] Read more.

Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods such as solarization, chemical disinfestation, and application of a biofungicide were evaluated in a commercial field that has been repeatedly used for lettuce cultivation. The populations of soilborne pathogens Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Fusarium equiseti were measured via qPCR before and after the implementation of the specific disinfestation methods. Although all the tested methods significantly reduced the population of the four soilborne pathogens, soil solarization was the most effective one. In addition, solarization reduced the number of lettuce plants affected by the pathogens R. solani and F. equiseti, and at the same time, significantly influenced the growth of lettuce plants. Amplicon sequence analysis of 16S rRNA-encoding genes used to study the soil bacterial community structure showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in soil samples. In general, solarization had positive effects on Firmicutes and negative effects on Proteobacteria and Actinobacteria; soil fumigation with dazomet increased the relative abundance of Firmicutes and Proteobacteria and reduced the corresponding values of Actinobacteria; and biofungicide had no significant effects on the three predominant bacterial phyla. The bacterial community composition and structure varied after the application of the soil disinfestation treatments since they imposed changes in the α- and β-diversity levels. The results of this study are expected to contribute towards implementing the most effective control method against the most common soilborne pathogens in intensively cultivated fields, such as those cultivated with leafy vegetables. Full article

(This article belongs to the Special Issue Biological Control of Vegetable Diseases and Bacterial Molecular Biology)

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22 pages, 7466 KiB

Open AccessArticle

High-Throughput Sequencing Analysis Revealed a Preference for Animal-Based Food in Purple Sea Urchins

by Zerui Liu, Yu Guo, Chuanxin Qin, Xiaohui Mu and Jia Zhang

Biology 2024, 13(8), 623; https://doi.org/10.3390/biology13080623 - 15 Aug 2024

Viewed by 986

Abstract

Sea urchins play an important role in marine ecosystems. Owing to limitations in previous research methods, there has been insufficient understanding of the food sources and ecological functional value of purple sea urchins, leading to considerable controversy regarding their functional positioning. We focused [...] Read more.

Sea urchins play an important role in marine ecosystems. Owing to limitations in previous research methods, there has been insufficient understanding of the food sources and ecological functional value of purple sea urchins, leading to considerable controversy regarding their functional positioning. We focused on Daya Bay as the research area, utilizing stable isotope technology and high-throughput sequencing of 16S rDNA and 18S rDNA to analyze sea urchins and their potential food sources in stone and algae areas. The results showed that the δ¹³C range of purple sea urchins in the stone area is −11.42~−8.17‰, and the δ¹⁵N range is 9.15~10.31‰. However, in the algal area, the δ¹³C range is −13.97~−12.44‰, and the δ¹⁵N range is 8.75~10.14‰. There was a significant difference in δ¹³C between the two areas (p < 0.05), but there was no significant difference in δ¹⁵N (p > 0.05). The main food source for purple sea urchins in both areas is sediment. The sequencing results of 18S rDNA revealed that, in the algal area, the highest proportion in the sea urchin gut was Molluska (57.37%). In the stone area, the highest proportion was Arthropoda (76.71%). The sequencing results of 16S rDNA revealed that, in the algal area, Bacteroidetes was the dominant group in the sea urchin gut (28.87%), whereas, in the stone area, Proteobacteria was the dominant group (37.83%). Diversity detection revealed a significant difference in the number of gut microbes and eukaryotes between the stone and algal areas (p < 0.05). The results revealed that the main food source of purple sea urchins in both areas is sediment, but the organic nutritional value is greater in the algal area, and the richness of microbiota and eukaryotes in the gut of purple sea urchins in the stone area is greater. These results indicated that purple sea urchins are likely omnivores and that the area where they occur impacts their growth and development. The results of this study provide a theoretical basis for the restoration of wild purple sea urchin resources and the selection of areas for restocking and release. Full article

(This article belongs to the Section Marine Biology)

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17 pages, 3655 KiB

Open AccessArticle

The Mechanism of the Development and Maintenance of Sexual Dimorphism in the Dioecious Mulberry Plant (Morus alba)

by Yisu Shi, Michael Ackah, Frank Kwarteng Amoako, Mengdi Zhao, Grace C. van der Puije and Weiguo Zhao

Biology 2024, 13(8), 622; https://doi.org/10.3390/biology13080622 - 15 Aug 2024

Viewed by 886

Abstract

Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex [...] Read more.

Intersexual differentiation is crucial for the speciation and maintenance of dioecious plants, but the underlying mechanisms, including the genes involved, are still poorly understood. Here, we focused on a typical dioicous plant Morus alba, to explore the molecular footprints relevant to sex evolution by revealing the differentially expressed genes (DEGs) between two sexes and the testing signals of selection for these DEGs. From the results, we found a total of 1543 DEGs. Interestingly, 333 and 66 genes expression were detected only in male and female inflorescences, respectively. Using comparative transcriptomics, the expression of 841 genes were found to be significantly higher in male than in female inflorescences and were mainly enriched in defense-related pathways including the biosynthesis of phenylpropanoids, cutin, suberine and waxes. Meanwhile, the expression of 702 genes was female-biased and largely enriched in pathways related to growth and development, such as carbohydrate metabolism, auxin signaling and cellular responses. In addition, 16.7% and 17.6% signals of selection were significantly detected in female- and male-biased genes, respectively, suggesting their non-negligible role in evolution. Our findings expanded the understanding of the molecular basis of intersexual differentiation and contribute to further research on sex evolution in dioecious plants. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)

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12 pages, 4445 KiB

Open AccessCommunication

The Morphological and Molecular Characterization of the Avian Trematodes Harrahium obscurum and Morishitium dollfusi (Digenea: Cyclocoelidae) from the Middle Volga Region (European Russia)

by Alexander A. Kirillov, Nadezhda Yu. Kirillova, Sergei V. Shchenkov, Alexei E. Knyazev and Victoria A. Vekhnik

Biology 2024, 13(8), 621; https://doi.org/10.3390/biology13080621 - 15 Aug 2024

Viewed by 839

Abstract

The taxonomic status of many species of the family Cyclocoelidae is still unclear. Two species of cyclocoelids, Harrahium obscurum and Morishitium dollfusi, were collected from the air sacs of birds (Turdus merula and Tringa ochropus) inhabiting the Middle Volga region [...] Read more.

The taxonomic status of many species of the family Cyclocoelidae is still unclear. Two species of cyclocoelids, Harrahium obscurum and Morishitium dollfusi, were collected from the air sacs of birds (Turdus merula and Tringa ochropus) inhabiting the Middle Volga region (European Russia). Here, we provide the first detailed morphological description of these cyclocoelids and combine it with the first molecular phylogenetic analysis of Cyclocoelidae from birds in Russia based on partial sequences of their 28s rDNA and coI mtDNA genes. Specimens of both flatworm species from different host individuals differ slightly in body shape and size, which probably reflects host-induced intraspecific variability. For the first time, we have shown that a stable morphological character such as the length of the vitelline fields in the studied digeneans is variable at the species level and cannot be used in their morphological diagnosis. Full article

(This article belongs to the Section Zoology)

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16 pages, 10683 KiB

Open AccessArticle

Activation of P2X7 Receptor Mediates the Abnormal Ovulation Induced by Chronic Restraint Stress and Chronic Cold Stress

by Xiang Fan, Jing Wang, Yinyin Ma, Dandan Chai, Suo Han, Chuyu Xiao, Yingtong Huang, Xiaojie Wang, Jianming Wang, Shimeng Wang, Li Xiao and Chunping Zhang

Biology 2024, 13(8), 620; https://doi.org/10.3390/biology13080620 - 15 Aug 2024

Viewed by 794

Abstract

Chronic stress has become a major problem that endangers people’s physical and mental health. Studies have shown that chronic stress impairs female reproduction. However, the related mechanism is not fully understood. P2X7 receptor (P2X7R) is involved in a variety of pathological changes induced [...] Read more.

Chronic stress has become a major problem that endangers people’s physical and mental health. Studies have shown that chronic stress impairs female reproduction. However, the related mechanism is not fully understood. P2X7 receptor (P2X7R) is involved in a variety of pathological changes induced by chronic stress. Whether P2X7R is involved in the effect of chronic stress on female reproduction has not been studied. In this study, we established a chronic restraint stress mouse model and chronic cold stress mouse model. We found that the number of corpora lutea was significantly reduced in the two chronic stress models. The number of corpora lutea indirectly reflects the ovulation, suggesting that chronic stress influences ovulation. P2X7R expression was significantly increased in ovaries of the two chronic stress models. A superovulation experiment showed that P2X7R inhibitor A-438079 HCL partially rescued the ovulation rate of the two chronic stress models. Further studies showed that activation of P2X7R signaling inhibited the cumulus expansion and promoted the expression of NPPC in granulosa cells, one key negative factor of cumulus expansion. Moreover, sirius red staining showed that the ovarian fibrosis was increased in the two chronic stress models. For the fibrosis-related factors, TGF-β1 was increased and MMP2 was decreased. In vitro studies also showed that activation of P2X7R signaling upregulated the expression of TGF-β1 and downregulated the expression of MMP2 in granulosa cells. In conclusion, P2X7R expression was increased in the ovaries of the chronic restraint-stress and chronic cold-stress mouse models. Activation of P2X7R signaling promoted NPPC expression and cumulus expansion disorder, which contributed to the abnormal ovulation of the chronic stress model. Activation of P2X7R signaling is also associated with the ovarian fibrosis changes in the chronic stress model. Full article

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14 pages, 2705 KiB

Open AccessArticle

Cloning, Expression, and Characterization of a Metalloprotease from Thermophilic Bacterium Streptomyces thermovulgaris

by Amna Mushtaq, Sibtain Ahmed, Tahir Mehmood, Jorge Cruz-Reyes, Amer Jamil and Shafaq Nawaz

Biology 2024, 13(8), 619; https://doi.org/10.3390/biology13080619 - 15 Aug 2024

Viewed by 961

Abstract

Proteases hydrolyze proteins and reduce them to smaller peptides or amino acids. Besides many biological processes, proteases play a crucial in different industrial applications. A 792 bp protease gene (nprB) from the thermophilic bacterium Streptomyces thermovulgaris was cloned and expressed in [...] Read more.

Proteases hydrolyze proteins and reduce them to smaller peptides or amino acids. Besides many biological processes, proteases play a crucial in different industrial applications. A 792 bp protease gene (nprB) from the thermophilic bacterium Streptomyces thermovulgaris was cloned and expressed in E. coli BL21 using pET 50b (+). Optimal recombinant protease expression was observed at 1 mM IPTG, 37 °C for 4 h. The resulting protease was observed in soluble form. The molecular mass estimated by SDS-PAGE and Western blot analysis of the protease (NprB) fused with His and Nus tag is ~70 KDa. The protease protein was purified by Ammonium sulfate precipitation and immobilized metal ion affinity chromatography. The optimum pH and temperature for protease activity using casein as substrate were 7.2 and 70 °C, respectively. The mature protease was active and retained 80% of its activity in a broad spectrum of pH 6–8 after 4 h of incubation. Also, the half-life of the protease at 70 °C was 4 h. EDTA (5 mM) completely inhibited the enzyme, proving the isolated protease was a metalloprotease. NprB activity was enhanced in the presence of Zn²⁺, Mn²⁺, Fe²⁺ and Ca²⁺, while Hg²⁺ and Ni²⁺ decreased its activity. Exposure to organic solvents did not affect the protease activity. The recombinant protease was stable in the presence of 10% organic solvents and surfactants. Further characterization showed that zinc-metalloprotease is promising for the detergent, laundry, leather, and pharmaceutical industries. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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20 pages, 7394 KiB

Open AccessArticle

Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming

by Lijun Wang, Xiaofei Lu, Zhikai Xing, Xindong Teng, Shuang Wang, Tianyi Liu, Li Zheng, Xumin Wang and Jiangyong Qu

Biology 2024, 13(8), 618; https://doi.org/10.3390/biology13080618 - 15 Aug 2024

Cited by 1 | Viewed by 838

Abstract

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are [...] Read more.

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism–environment–ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources. Full article

(This article belongs to the Section Microbiology)

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10 pages, 1535 KiB

Open AccessArticle

Generation of Two-Line Restorer Line with Low Chalkiness Using Knockout of Chalk5 through CRISPR/Cas9 Editing

by Gucheng Fan, Jiefeng Jiang, Yu Long, Run Wang, Famao Liang, Haiyang Liu, Junying Xu, Xianjin Qiu and Zhixin Li

Biology 2024, 13(8), 617; https://doi.org/10.3390/biology13080617 - 15 Aug 2024

Viewed by 823

Abstract

Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H⁺-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both [...] Read more.

Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H⁺-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions. Full article

(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)

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15 pages, 2740 KiB

Open AccessArticle

Spatial Pattern of Host Tree Size, Rather than of Host Tree Itself, Affects the Infection Likelihood of a Fungal Stem Disease

by Yanli Shi, Xinbo Gao, Yunxiao Jiang, Junsheng Zhang, Feng-Hui Qi and Tian-Zhong Jing

Biology 2024, 13(8), 616; https://doi.org/10.3390/biology13080616 - 14 Aug 2024

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Abstract

The spatial pattern of diseased forest trees is a product of the spatial pattern of host trees and the disease itself. Previous studies have focused on describing the spatial pattern of diseased host trees, and it remains largely unknown whether an antecedent spatial [...] Read more.

The spatial pattern of diseased forest trees is a product of the spatial pattern of host trees and the disease itself. Previous studies have focused on describing the spatial pattern of diseased host trees, and it remains largely unknown whether an antecedent spatial pattern of host/nonhost trees affects the infection pattern of a disease and how large the effect sizes of the spatial pattern of host/nonhost trees and host size are. The results from trivariate random labeling showed that the antecedent pattern of the host ash tree, Fraxinus mandshurica, but not of nonhost tree species, impacted the infection pattern of a stem fungal disease caused by Inonotus hispidus. To investigate the effect size of the spatial pattern of ash trees, we employed the SADIE (Spatial Analysis by Distance IndicEs) aggregation index and clustering index as predictors in the GLMs. Globally, the spatial pattern (v_i index) of ash trees did not affect the infection likelihood of the focal tree; however, the spatial pattern of DBH (diameter at breast height) of ash trees significantly affected the infection likelihood of the focal tree. We sampled a series of circular plots with different radii to investigate the spatial pattern effect of host size on the infection likelihood of the focal tree locally. The results showed that the location (patch/gap) of the DBH of the focal tree, rather than that of the focal tree itself, significantly affected its infection likelihood in most plots of the investigated sizes. A meta-analysis was employed to settle the discrepancy between plots of different sizes, which led to results consistent with those of global studies. The results from meta-regression showed that plot size had no significant effects. Full article

(This article belongs to the Special Issue Advances in Research on Diseases of Plants)

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