Biology-Basel最新文献

{"title":"Wildfire-Driven Shifts in Bird and Red Fox Activity: A Case Study from Biebrza National Park.","authors":"Jakub Gryz, Dagny Krauze-Gryz, Michał Brach","doi":"10.3390/biology14060685","DOIUrl":"10.3390/biology14060685","url":null,"abstract":"<p><p>Fires of natural or anthropogenic origin shape some ecosystems on Earth; this disturbance can maintain the landscape and influence many processes like vegetation structure, carbon, and hydrological cycle, climate, and others [...].</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Based on the Spatial Multi-Scale Habitat Model, the Response of Habitat Suitability of Purpleback Flying Squid (<i>Sthenoteuthis oualaniensis</i>) to Sea Surface Temperature Variations in the Nansha Offshore Area, South China Sea.","authors":"Xue Feng, Xiaofan Hong, Zuozhi Chen, Jiangtao Fan","doi":"10.3390/biology14060684","DOIUrl":"10.3390/biology14060684","url":null,"abstract":"<p><p>Overfishing and climate change have led to the depletion of fishery resources in the offshore South China Sea. The purpleback flying squid (<i>Sthenoteuthis oualaniensis</i>) has emerged as a promising alternative due to its ecological and economic value. However, information on its preferred habitat conditions remains scarce. This study integrates geostatistical and fisheries oceanographic approaches to explore optimal spatial-temporal scales for habitat modeling and to assess habitat changes under warming scenarios. Utilizing fishery data from 2013 to 2017, environmental variables including SST, sea surface temperature anomaly (SSTA), and chlorophyll-a concentration (CHL) were analyzed. Fishing effort data revealed significant seasonal differences, with the highest vessel numbers in summer and the lowest in autumn. Among the six modeling schemes, the combination of 0.5° × 0.5° spatial resolution and seasonal temporal resolution yielded the highest HSI model accuracy (84.02%). Optimal environmental ranges varied by season. Simulations of SST deviations (±0.2 °C, ±0.5 °C, and ±1 °C) showed that extreme warming or cooling could eliminate suitable habitats. These findings highlight the vulnerability of squid habitats to thermal shifts and support adaptive fishery strategies in the South China Sea.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Methylation of <i>Igf2r</i> Promoter CpG Island 2 Governs <i>Cis</i>-Acting Inheritance and Gene Dosage in Equine Hybrids.","authors":"Xisheng Wang, Yingchao Shen, Hong Ren, Minna Yi, Gerelchimeg Bou","doi":"10.3390/biology14060678","DOIUrl":"10.3390/biology14060678","url":null,"abstract":"<p><p>Genomic imprinting is critical for mammalian development, but its regulation varies across species. The insulin-like growth factor 2 receptor (IGF2R), which is a maternally expressed imprinted gene critical for cell proliferation and differentiation, as well as embryonic and placental development, is classically regulated by differentially methylated regions (DMRs) and lncRNA-<i>Airn</i> in mice. However, studies on this in equus are scarce, especially in terms of mechanistic studies. In the present study, heart, liver, spleen, lung, kidney, brain, and muscle samples were obtained from horses, donkeys, and hybrids, and gene expression and imprinting state were tested to investigate the imprinting regulation of <i>Igf2r</i> in these animals. Bisulfite sequencing combined with an allele-specific expression analysis revealed a tissue-specific loss of imprinting in the mule liver and hybrid brain tissues. Strikingly, we found that the maternal-specific expression of equine <i>Igf2r</i> did not rely on the canonical DMRs or lncRNA-<i>Airn</i>. Surprisingly, DNA methylation of a specific region called CpG island 2 (CpGI2) in the <i>Igf2r</i> promoter showed <i>cis</i>-acting inheritance, meaning that the DNA methylation patterns of the parental alleles are retained in hybrid tissues. Notably, the DNA methylation of CpGI2 correlated negatively with <i>Igf2r</i> expression in the spleen (R² = 0.8797, <i>p</i> = 6.46 × 10^-6), lung (R² = 0.8569, <i>p</i> = 1.57 × 10^-5), and kidney (R² = 0.8650, <i>p</i> = 3.85 × 10^-6). Our findings suggest that imprinting may work differently in other species. This study provides a framework for understanding imprinting diversity in hybrids and shows that equine hybrids can be used to study how epigenetic inheritance works.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Single-Cell Transcriptomics and Network Modeling Reveal Modular Regulators of Sheep Zygotic Genome Activation.","authors":"Xiaopeng Li, Peng Niu, Kai Hu, Xueyan Wang, Fei Huang, Pengyan Song, Qinghua Gao, Di Fang","doi":"10.3390/biology14060676","DOIUrl":"10.3390/biology14060676","url":null,"abstract":"<p><p>Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA sequencing (Smart-seq2) to in vivo- and in vitro-derived sheep embryos at the 8-, 16-, and 32-cell stages. Differential expression analysis revealed 114, 1628, and 1465 genes altered in the 8- vs. 16-, 16- vs. 32-, and 8- vs. 32-cell transitions, respectively, with the core pluripotency factors <i>SOX2</i>, <i>NANOG</i>, <i>POU5F1</i>, and <i>KLF4</i> upregulated during major ZGA. To uncover coordinated regulatory modules, we constructed a weighted gene co-expression network using WGCNA, identifying the MEred module as most tightly correlated with developmental progression (r = 0.48, <i>p</i> = 8.6 × 10^-14). The integration of MERed genes into the STRING v11 protein-protein interaction network furnished a high-confidence scaffold for community detection. Louvain partitioning delineated two discrete communities: Community 0 was enriched in ER-Golgi vesicle-mediated transport, transmembrane transport, and cytoskeletal dynamics, suggesting roles in membrane protein processing, secretion, and early signaling; Community 1 was enriched in G2/M cell-cycle transition and RNA splicing/processing, indicating a coordinated network for accurate post-ZGA cell division and transcript maturation. Together, these integrated analyses reveal a modular regulatory architecture underlying sheep ZGA and provide a framework for dissecting early embryonic development in this species.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Genes to Fisheries: A Synthesis of Current Research in Crustacean Biology and Management.","authors":"Yafei Duan, Lutz Auerswald, Xianliang Meng","doi":"10.3390/biology14060677","DOIUrl":"10.3390/biology14060677","url":null,"abstract":"<p><p>Crustaceans represent an extraordinarily diverse group of arthropods, occupying a vast array of aquatic and terrestrial habitats worldwide [...].</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stray Dogs as Reservoirs and Sources of Infectious and Parasitic Diseases in the Environment of the City of Uralsk in Western Kazakhstan.","authors":"Askar Nametov, Rashid Karmaliyev, Bekzhassar Sidikhov, Kenzhebek Murzabayev, Kanat Orynkhanov, Bakytkanym Kadraliyeva, Balaussa Yertleuova, Dosmukan Gabdullin, Zulkyya Abilova, Laura Dushayeva","doi":"10.3390/biology14060683","DOIUrl":"10.3390/biology14060683","url":null,"abstract":"<p><p>The increasing number of owned and stray dogs in large cities is becoming a pressing issue due to rising population densities, urban conditions, and poor control over animal reproduction. This situation poses serious epidemiological risks, as dogs can act as reservoirs and transmitters of infectious and parasitic diseases dangerous to humans. This study aimed <b>to</b> investigate the prevalence and carriage of infectious and parasitic diseases in stray dogs in the city of Uralsk as a factor of epidemiological risk. In 2024, 1213 stray dogs were captured from different city districts and examined at the veterinary clinic and laboratory of Zhangir Khan University. Biological samples (blood, urine, feces) from 10% of the animals were analyzed using molecular (PCR), serological (ELISA), and helminthological methods. Serological and molecular analyses revealed the widespread circulation of bacterial pathogens. Antibodies to additional bacterial agents, including <i>Pasteurella multocida</i>, <i>Mycobacterium</i> spp., <i>Listeria monocytogenes</i>, and <i>Leptospira</i> spp., were detected in the samples, indicating an unfavorable sanitary and epidemiological situation in the urban environment. An enzyme-linked immunosorbent assay (ELISA) identified antibodies against <i>Toxocara canis</i> in 50.9% of the dogs and against <i>Echinococcus granulosus</i> in 76.4%, reflecting both active and past infections. The polymerase chain reaction (PCR) results showed the presence of <i>Brucella canis</i> DNA in blood and urine samples, while antibodies to <i>Brucella</i> spp. were detected in 57.8% of the examined dogs, underscoring the significant zooanthroponotic importance of this pathogen and its potential threat to human health. Additionally, <i>T. canis</i> DNA was found in 39.2% of the samples and <i>E. granulosus</i> DNA in 16.6%. A helminthological examination using the Fülleborn method revealed a high rate of helminth infection: <i>Ancylostoma caninum</i>-35.3%, <i>T. canis</i>-32.3%, and <i>Toxascaris leonina</i>-29.4%. The obtained results highlight the significant role of stray dogs as epizootiological and epidemiological reservoirs of zooanthroponotic infections. This poses a serious threat to public health and necessitates the implementation of effective control and prevention measures for infectious and parasitic diseases within urban fauna.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Halfway Through Ex Situ Population Genetic Lifespan: The Case of <i>Cochlearia polonica</i>.","authors":"Anna Rucińska, Katarzyna Joanna Chwedorzewska, Piotr Tomasz Bednarek, Maja Boczkowska, Jerzy Puchalski, Piotr Androsiuk, Ewa Czaplicka","doi":"10.3390/biology14060681","DOIUrl":"10.3390/biology14060681","url":null,"abstract":"<p><p>Although the usage of genetic data for the conservation management of threatened species is growing rapidly, the assessment of the trajectory and persistence of ex situ and in situ populations suffers from a lack of monitoring of genetic indicators. To fill this gap, we conducted a comparative analysis of the genetic structure ex situ and its source population of <i>Cochlearia polonica</i> to improve conservation outcomes for this species. <i>C. polonica</i>, as a range-restricted endemic species in Poland, exists in the wild in a single reintroduced population, which was the source for establishing an ex situ population in the botanical garden, and both populations have been well studied in abundance time series until the extinction of artificial populations due to genetic constraints. We collected AFLP data from individuals sampled after the peak recovery phase following the founder effect in the ex situ population, as well as from the source population, to assess the genetic consequences of long-term cultivation. The genetic profile of both populations suggested their strong differentiation. The genetic variation in the ex situ population expressed by Shannon's Information Index and expected heterozygosity (He) was approximately half that of the source population. While ex situ population growth was high, the gene pool was homogenised, and genetic diversity waned, leading to its extinction across merely 5-6 generations. Thus, the only reintroduced population of <i>C. polonica</i> left in the wild is more threatened with extinction than previously thought, and conservation action should be taken immediately.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"scRL: Utilizing Reinforcement Learning to Evaluate Fate Decisions in Single-Cell Data.","authors":"Zeyu Fu, Chunlin Chen, Song Wang, Junping Wang, Shilei Chen","doi":"10.3390/biology14060679","DOIUrl":"10.3390/biology14060679","url":null,"abstract":"<p><p>Single-cell RNA sequencing now profiles whole transcriptomes for hundreds of thousands of cells, yet existing trajectory-inference tools rarely pinpoint where and when fate decisions are made. We present single-cell reinforcement learning (scRL), an actor-critic framework that recasts differentiation as a sequential decision process on an interpretable latent manifold derived with Latent Dirichlet Allocation. The critic learns state-value functions that quantify fate intensity for each cell, while the actor traces optimal developmental routes across the manifold. Benchmarks on hematopoiesis, mouse endocrinogenesis, acute myeloid leukemia, and gene-knockout and irradiation datasets show that scRL surpasses fifteen state-of-the-art methods in five independent evaluation dimensions, recovering early decision states that precede overt lineage commitment and revealing regulators such as <i>Dapp1</i>. Beyond fate decisions, the same framework produces competitive measures of lineage-contribution intensity without requiring ground-truth probabilities, providing a unified and extensible approach for decoding developmental logic from single-cell data.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beta Diversity of Tenebrionid Beetles (Coleoptera, Tenebrionidae) in Ningxia Grasslands and Their Driving Factors.","authors":"Changyu Xiong, Ziyu Cao, Haixiang Zhang, Ying Wang, Wei Sun, Chun Shi, Yifan Cui, Rong Zhang, Shuhua Wei","doi":"10.3390/biology14060680","DOIUrl":"10.3390/biology14060680","url":null,"abstract":"<p><p>This study explored the beta diversity patterns of tenebrionid beetles and their driving factors across four grassland types in Ningxia. A total of 32 monitoring sites were surveyed, capturing 5328 individuals from 47 tenebrionid species. Permutation multivariate dispersion (PERMDISP) and non-metric multidimensional scaling (NMDS) revealed significant differences in community composition among the four grassland types (Stress = 0.091). Beta diversity decomposition indicated that species replacement primarily drives beta diversity among four temperate grassland types. Canonical Correspondence Analysis (CCA) showed that mean temperature, field water holding capacity, total soil phosphorus, biomass of Asteraceae, biomass of Leguminosae, and frequency of Leguminosae significantly explained variations in dominant species abundance (<i>p</i> < 0.05). Mantel tests revealed that beta diversity was positively correlated with differences in mean temperature, field water holding capacity, total soil phosphorus, and Asteraceae biomass (<i>p</i> < 0.01), but negatively correlated with Leguminosae frequency (<i>p</i> < 0.05). Overall, daily mean temperature was the primary driver of diversity, with synergistic effects from climate, elevation, soil, and vegetation. This study provides a comprehensive analysis of environmental factors influencing tenebrionid diversity, offering insights for grassland biodiversity conservation.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12189152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined Ionizing Radiation Caused Cognition and Non-Cognition Behavior Benefits and Modulated Microglial Activity in Wild-Type and Alzheimer's-like Transgenic Mice.","authors":"Viktor S Kokhan, Anna I Levashova, Maxim S Nesterov, Vladimir A Pikalov, Maria M Chicheva","doi":"10.3390/biology14060682","DOIUrl":"10.3390/biology14060682","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is one of the primary causes of disability and dependency among aging populations worldwide. Neuroinflammation may be a potential therapeutic target in AD. Moreover, ionizing radiation may be a tool for modulating neuroinflammation. Here, we used three mouse lines-C57Bl/6 and the transgenic AD models 5xFAD and Tau P301S-to investigate the effects of combined ionizing radiation (γ-rays and carbon-12 nuclei) on emotional state, cognitive abilities, and markers of microglial activation. The obtained data show that combined irradiation results in enhanced exploratory behavior and spatial learning in the C57Bl/6 mice. The same changes, as well as a decrease in anxiety, were found in the Tau P301S mice. Irradiation of the 5xFAD mice resulted in improved welfare and ability to discriminate odors. At the same time, irradiation led to an increase in the level of pro- and anti-inflammatory cytokines in the prefrontal cortex and, to a lesser extent, in the hippocampus of the C57Bl/6 and Tau P301S mice. An increase in macrophage inflammatory protein-1α in the prefrontal cortex and a decrease in interleukin 2β in the hippocampus were found in the 5xFAD mice. Taken together, our data indicate that ionizing radiation exposure is an adequate tool to modulate microglial activity in the brain and may provide cognitive and non-cognitive behavioral benefits in neurodegenerative disease conditions.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 6","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}