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For a Colorful Life: Recent Advances in Anthocyanin Biosynthesis during Leaf Senescence
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Advances in Mammary Tumor Spheroid Models
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Immune Indicators Related to Phagocytosis May Be Used for Selection of Disease-Resistant Sea Urchins
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Fire-Induced Changes in Soil Properties and Bacterial Communities in Rotational Shifting Cultivation
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Advances in Drug Treatments for Companion Animal Obesity
Journal Description
Biology
Biology
is an international, peer-reviewed, open access journal of biological sciences published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) and Federation of European Laboratory Animal Science Associations (FELASA) are affiliated with Biology, and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q1 (Biology) / CiteScore - Q1 (General Agricultural and Biological Sciences )
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the first half of 2024).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
3.6 (2023);
5-Year Impact Factor:
3.8 (2023)
Latest Articles
Comparative Analysis of Angora Rabbit Colostrum and Mature Milk Using Quantitative Proteomics
Biology 2024, 13(8), 634; https://doi.org/10.3390/biology13080634 - 19 Aug 2024
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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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
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
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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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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
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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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
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
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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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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
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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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
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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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
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
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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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Open AccessArticle
Neutralizing Oxidized Phosphatidylcholine Reduces Airway Inflammation and Hyperreactivity in a Murine Model of Allergic Asthma
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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
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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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
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
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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.
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(This article belongs to the Section Medical Biology)
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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
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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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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
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
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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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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
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
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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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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
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
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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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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 (registering DOI) - 15 Aug 2024
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
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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.
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(This article belongs to the Section Zoology)
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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
Abstract
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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
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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.
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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
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
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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.
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(This article belongs to the Section Biochemistry and Molecular Biology)
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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
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
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(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.
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(This article belongs to the Section Microbiology)
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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
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
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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.
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(This article belongs to the Special Issue Mining Favorable Alleles for Crop Yield, Biotic and Abiotic Stress Tolerance)
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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
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
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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 (vi 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.
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(This article belongs to the Special Issue Advances in Research on Diseases of Plants)
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Open AccessArticle
Methanogenic Community Characteristics and Its Influencing Factors in Reservoir Sediments on the Northeastern Qinghai Plateau
by
Zebi Liu, Xufeng Mao, Yi Wu, Liang Xia, Hongyan Yu, Wenjia Tang, Yanhong Qi, Ziping Zhang, Feng Xiao and Haichuan Ji
Biology 2024, 13(8), 615; https://doi.org/10.3390/biology13080615 - 14 Aug 2024
Abstract
Reservoirs are a hotspot for methane emissions, a potent greenhouse gas. However, the microbial basis for methane production in the Qinghai Plateau reservoirs remains unclear. To explore the characteristics of methanogenic communities in reservoir sediments on the northeastern Qinghai Plateau, sediment samples were
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Reservoirs are a hotspot for methane emissions, a potent greenhouse gas. However, the microbial basis for methane production in the Qinghai Plateau reservoirs remains unclear. To explore the characteristics of methanogenic communities in reservoir sediments on the northeastern Qinghai Plateau, sediment samples were collected from 18 reservoirs in the Yellow River basin during May 2023 (dry season) and August 2023 (wet season). High-throughput sequencing technology was employed to analyze the community composition, diversity, and co-occurrence network of methanogens. Furthermore, FAPROTAX and Mantel analysis were used to assess the metabolic functions of methanogens and their influencing factors. The results showed that (1) the predominant genera of methanogens were Methanobacterium (28.87%) and Methanosarcina (21.67%). Hydrogenotrophic methanogenesis was the main pathway in the sediments. (2) Significant spatiotemporal differences were observed in the diversity of methanogenic communities (p < 0.05). The composition and diversity of these communities were found to be significantly influenced by temperature, pH, altitude, organic carbon, and total nitrogen (p < 0.05). (3) Methanosarcina, Methanobacterium, and Methanospirillum play crucial roles in maintaining the stability of methanogenic community networks. The co-occurrence network nodes are predominantly positively correlated (99.82%). These results provide data for further studies on carbon cycling in the Qinghai Plateau reservoirs.
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(This article belongs to the Special Issue Wetland Ecosystems (2nd Edition))
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