Biology-BaselPub Date : 2024-10-10DOI: 10.3390/biology13100809
Haocheng Xu, Xin Tian, Yuanxin Wang, Junjie Lin, Baishu Zhu, Chen Zhao, Bin Wang, Xin Zhang, Yu Sun, Nan Li, Xun Sun, Fanxi Zeng, Mingzhi Li, Xiquan Ya, Renqing Zhao
{"title":"Exercise Promotes Hippocampal Neurogenesis in T2DM Mice via Irisin/TLR4/MyD88/NF-κB-Mediated Neuroinflammation Pathway.","authors":"Haocheng Xu, Xin Tian, Yuanxin Wang, Junjie Lin, Baishu Zhu, Chen Zhao, Bin Wang, Xin Zhang, Yu Sun, Nan Li, Xun Sun, Fanxi Zeng, Mingzhi Li, Xiquan Ya, Renqing Zhao","doi":"10.3390/biology13100809","DOIUrl":"https://doi.org/10.3390/biology13100809","url":null,"abstract":"<p><p>Neuroinflammation is a major feature of type 2 diabetic mellitus (T2DM), adversely affecting hippocampal neurogenesis. However, the precise mechanism is not fully understood, and therapeutic approaches are currently lacking. Therefore, we determined the effects of exercise on neuroinflammation and hippocampal neurogenesis in T2DM mice, with a specific focus on understanding the role of the irisin and related cascade pathways in modulating the beneficial effects of exercise in these processes. Ten-week exercise significantly decreased T2DM-induced inflammation levels and markedly promoted hippocampal neurogenesis and memory function. However, these positive effects were reversed by 10 weeks of treatment with cyclo RGDyk, an inhibitor of irisin receptor signaling. Additionally, exercise helped reduce the M1 phenotype polarization of hippocampal microglia in diabetic mice; this effect could be reversed with cyclo RGDyk treatment. Moreover, exercise markedly increased the levels of fibronectin type III domain-containing protein 5 (FNDC5)/irisin protein while decreasing the expression of Toll-like receptor 4 (TLR4), myeloid differential protein-88 (MyD88), and nuclear factor kappa-B (NF-κB) in the hippocampus of T2DM mice. However, blocking irisin receptor signaling counteracted the down-regulation of TLR4/MyD88/NF-κB in diabetic mice undergoing exercise intervention. Conclusively, exercise appears to be effective in reducing neuroinflammation and enhancing hippocampal neurogenesis and memory in diabetes mice. The positive effects are involved in the participation of the irisin/TLR4/MyD88/NF-κB signaling pathway, highlighting the potential of exercise in the management of diabetic-induced cognitive decline.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510940","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}
Biology-BaselPub Date : 2024-10-10DOI: 10.3390/biology13100808
Chiara Fogliano, Rosa Carotenuto, Claudio Agnisola, Chiara Maria Motta, Bice Avallone
{"title":"Impact of Benzodiazepine Delorazepam on Growth and Behaviour of <i>Artemia salina</i> Nauplii.","authors":"Chiara Fogliano, Rosa Carotenuto, Claudio Agnisola, Chiara Maria Motta, Bice Avallone","doi":"10.3390/biology13100808","DOIUrl":"https://doi.org/10.3390/biology13100808","url":null,"abstract":"<p><p>Benzodiazepines, a significant group of newly recognised water contaminants, are psychotropic medications prescribed for common anxiety symptoms and sleep disorders. They resist efficient degradation during sewage treatment and endure in aquatic environments. Their presence in aquatic matrices is increasing, particularly after the recent pandemic period, which has led many people to systematically use benzodiazepines to manage anxiety. In previous studies, an important interference of this class of drugs on both the larval and adult stages of some aquatic species has been demonstrated, with effects on behaviour and embryonic development. This study examined the influence of delorazepam, a diazepam metabolite, on <i>Artemia salina</i> development to gain insight into responses in naupliar larvae. Results demonstrated that treatments (1, 5, and 10 µg/L) increase the hatching percentage and induce a desynchronisation in growth. Mortality was only slightly increased (close to 10% at six days post-hatching), but lipid reserve consumption was modified, with the persistence of lipid globules at the advanced naupliar stages. Locomotory activity significantly decreased only at 10 µg/L treatment. No teratogenic effects were observed, though modest damages were noticed in the posterior trunk and eyes, two targets of environmental toxicity. The negative impact of delorazepam on <i>Artemia salina</i> adds to those already reported in other species of invertebrates and vertebrates, which are not yet considered targets of these drugs. This study underscores the need for further research and immediate attention to this class of contaminants and the importance of monitoring their presence during environmental risk assessments.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510948","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}
Biology-BaselPub Date : 2024-10-09DOI: 10.3390/biology13100805
Sazada Siddiqui
{"title":"DNA Damage, Cell Death, and Alteration of Cell Proliferation Insights Caused by Copper Oxide Nanoparticles Using a Plant-Based Model.","authors":"Sazada Siddiqui","doi":"10.3390/biology13100805","DOIUrl":"https://doi.org/10.3390/biology13100805","url":null,"abstract":"<p><p>The speedy growth of copper oxide nanoparticle (CuO NP) manufacturing due to their wide application in industries has caused concerns due to their increased discharge into the environment from both purposeful and accidental sources. Their presence at an elevated concentration in the environment can cause potential hazards to the plant kingdom, specifically to staple food crops. However, limited research is available to determine the consequences of CuO NPs. The present study aimed to assess the morphological and cytological changes induced by CuO NPs on <i>Pisum sativum</i> L., a key staple food crop. Seeds of <i>Pisum sativum</i> were exposed to various concentrations of CuO NPs (0, 25, 50, 75, 100, and 125 ppm) for 2 h, and their effects on seed germination (SG), radicle length (RL), cell proliferation kinetics (CPK), mitotic index (MI), cell death (CD), micronucleus frequency (MNF), and chromosomal aberration frequency (CAF) were studied. The results indicate a significant reduction in SG, RL, CPK, and MI and a significant dose-dependent increase in CD, MNF, and CAF. CuO NP treatment has led to abnormal meiotic cell division, increased incidence of micronucleus frequency, and chromosomal aberration frequency. Additionally, the CuO NP-treated groups showed an increase in the percentage of aberrant meiotic cells such as laggard (LG), double bridge (DB), stickiness (STC), clumped nuclei (CNi), precocious separation (PS), single bridge (SB), and secondary association (SA). CuO NP treatment led to reductions in SG as follows: 55% at 24 h, 60.10% at 48 h, and 65% at 72 h; reductions in RL as follows: 0.55 ± 0.021 cm at 24 h, 0.67 ± 0.01 cm at 48 h, and 0.99 ± 0.02 cm at 72 h; reductions in CPK as follows: 34.98% at prophase, 7.90% at metaphase, 3.5% at anaphase, and 0.97% at telophase. It also led to a 57.45% increase in CD, a 39.87% reduction in MI, and a 60.77% increase in MNF at a higher concentration of 125 ppm. The findings of this study clearly show that CuO NPs have a genotoxic effect on the food crop plant <i>Pisum sativum.</i></p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510925","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}
Biology-BaselPub Date : 2024-10-09DOI: 10.3390/biology13100804
Lisbeth Herrera-Castillo, Germán Vallejo-Palma, Nuria Saiz, Abel Sánchez-Jiménez, Esther Isorna, Ignacio Ruiz-Jarabo, Nuria de Pedro
{"title":"Metabolic Rate of Goldfish (<i>Carassius auratus</i>) in the Face of Common Aquaculture Challenges.","authors":"Lisbeth Herrera-Castillo, Germán Vallejo-Palma, Nuria Saiz, Abel Sánchez-Jiménez, Esther Isorna, Ignacio Ruiz-Jarabo, Nuria de Pedro","doi":"10.3390/biology13100804","DOIUrl":"https://doi.org/10.3390/biology13100804","url":null,"abstract":"<p><p>This study examined the metabolic rate (MO<sub>2</sub>, oxygen consumption) of goldfish (<i>Carassius auratus</i>) under normal management conditions in aquaculture. Using an intermittent respirometry system, we assessed daily variations and the effects of feeding, handling, temperature increase, and anesthetics. MO<sub>2</sub> exhibited a daily rhythm, with higher values during day. Feeding to satiety produced a 35% increase in MO<sub>2</sub> compared to fasted animals, with a maximum peak after 3 h and returning to baseline after 7 h. Handling stress (5 min) produced a 140% MO<sub>2</sub> peak (from 180 to 252 mg O<sub>2</sub> kg<sup>-1</sup> h<sup>-1</sup>), returning to the routine MO<sub>2</sub> after 2.5 h. An increase in water temperature (+0.1 °C min<sup>-1</sup>) up to 30 °C caused MO<sub>2</sub> to peak at 200% after 2.5 h from the start of the temperature increase. The use of common anesthetics in aquaculture (MS-222, 2-phenoxyethanol and clove oil in deep anesthesia concentration) affects MO<sub>2</sub> during the first few minutes after anesthetic recovery, but also during the following 4 h. It can be concluded that the metabolic rate is a good indicator of the goldfish's response to aquaculture practices involving energy expenditure and stress. Thus, intermittent respirometry is a valuable non-invasive tool for understanding and improving fish welfare in aquaculture.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510954","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}
Biology-BaselPub Date : 2024-10-08DOI: 10.3390/biology13100803
Yanlong Zhang, Hua Yang, Aerguli Jiamahate, Honglan Yang, Liangming Cao, Yingqiao Dang, Zhaozhi Lu, Zhongqi Yang, Tohir A Bozorov, Xiaoyi Wang
{"title":"Potential Ecological Distribution of the Beetle <i>Agrilus mali</i> Matsumura (Coleoptera: Buprestidae) in China under Three Climate Change Scenarios, with Consequences for Commercial and Wild Apple Forests.","authors":"Yanlong Zhang, Hua Yang, Aerguli Jiamahate, Honglan Yang, Liangming Cao, Yingqiao Dang, Zhaozhi Lu, Zhongqi Yang, Tohir A Bozorov, Xiaoyi Wang","doi":"10.3390/biology13100803","DOIUrl":"https://doi.org/10.3390/biology13100803","url":null,"abstract":"<p><p>The apple jewel beetle (AJB), <i>Agrilus mali</i> Matsumura (Coleoptera: Buprestidae), is a dangerous pest of commercial apple orchards across China, the largest apple production country in the world, and has recently become invasive in the Xinjiang Uygur Autonomous Region (XUAR) of northwestern China, where wild apple forests also occur. This pest poses a serious threat to apple production and wild apple forests throughout the world. Global warming is expected to change the geographical distribution of <i>A. mali</i> in China, but the extent of this is unknown. Based on empirical data from 1951 to 2000, a MaxEnt model was used to forecast the ecological distribution of <i>A. mali</i> under three different climate scenarios projected in the fifth report of the Intergovernmental Panel on Climate Change. The results showed that the most important variables were the maximum temperature of November, precipitation in January, and minimum temperatures in April. Under all climate scenarios, the forecasted suitable regions for <i>A. mali</i> in China will expand northward in the 2050s and 2070s. The forecasted highly suitable regions will be 1.11-1.34 times larger than they are currently, and their central distributions will be 61.57-167.59 km further north. These findings suggest that the range and damage caused by <i>A. mali</i> in China will increase dramatically in the future. Monitoring and management measures should be implemented urgently to protect both the commercial apple industry and wild apple resources.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510966","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}
Biology-BaselPub Date : 2024-10-08DOI: 10.3390/biology13100802
Antonino Maniaci, Marilena Briglia, Fabio Allia, Giuseppe Montalbano, Giovanni Luca Romano, Mohamed Amine Zaouali, Dorra H'mida, Caterina Gagliano, Roberta Malaguarnera, Mario Lentini, Adriana Carol Eleonora Graziano, Giovanni Giurdanella
{"title":"The Role of Pericytes in Inner Ear Disorders: A Comprehensive Review.","authors":"Antonino Maniaci, Marilena Briglia, Fabio Allia, Giuseppe Montalbano, Giovanni Luca Romano, Mohamed Amine Zaouali, Dorra H'mida, Caterina Gagliano, Roberta Malaguarnera, Mario Lentini, Adriana Carol Eleonora Graziano, Giovanni Giurdanella","doi":"10.3390/biology13100802","DOIUrl":"https://doi.org/10.3390/biology13100802","url":null,"abstract":"<p><p>Inner ear disorders, including sensorineural hearing loss, Meniere's disease, and vestibular neuritis, are prevalent conditions that significantly impact the quality of life. Despite their high incidence, the underlying pathophysiology of these disorders remains elusive, and current treatment options are often inadequate. Emerging evidence suggests that pericytes, a type of vascular mural cell specialized to maintain the integrity and function of the microvasculature, may play a crucial role in the development and progression of inner ear disorders. The pericytes are present in the microvasculature of both the cochlea and the vestibular system, where they regulate blood flow, maintain the blood-labyrinth barrier, facilitate angiogenesis, and provide trophic support to neurons. Understanding their role in inner ear disorders may provide valuable insights into the pathophysiology of these conditions and lead to the development of novel diagnostic and therapeutic strategies, improving the standard of living. This comprehensive review aims to provide a detailed overview of the role of pericytes in inner ear disorders, highlighting the anatomy and physiology in the microvasculature, and analyzing the mechanisms that contribute to the development of the disorders. Furthermore, we explore the potential pericyte-targeted therapies, including antioxidant, anti-inflammatory, and angiogenic approaches, as well as gene therapy strategies.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510899","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}
Biology-BaselPub Date : 2024-10-07DOI: 10.3390/biology13100800
Salimat K Bidzhieva, Tatyana P Tourova, Vitaly V Kadnikov, Salima R Samigullina, Diyana S Sokolova, Andrey B Poltaraus, Alexander N Avtukh, Vera M Tereshina, Alexey V Beletsky, Andrey V Mardanov, Tamara N Nazina
{"title":"Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium <i>Pseudodesulfovibrio methanolicus</i> sp. nov. Isolated from a Petroleum Reservoir in Russia.","authors":"Salimat K Bidzhieva, Tatyana P Tourova, Vitaly V Kadnikov, Salima R Samigullina, Diyana S Sokolova, Andrey B Poltaraus, Alexander N Avtukh, Vera M Tereshina, Alexey V Beletsky, Andrey V Mardanov, Tamara N Nazina","doi":"10.3390/biology13100800","DOIUrl":"https://doi.org/10.3390/biology13100800","url":null,"abstract":"<p><p>The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69<sup>T</sup>. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0-4.0% (<i>w</i>/<i>v</i>) NaCl, at pH 6.5, and at 23-28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H<sub>2</sub> and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H<sub>2</sub>/CO<sub>2</sub>/acetate for sulfate reduction. The genome size of the type strain 5S69<sup>T</sup> was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69<sup>T</sup> ((VKM B-3653<sup>T</sup> = KCTC 25499<sup>T</sup>) to a new species within the genus <i>Pseudodesulfovibrio</i>, is suggested, with the proposed name <i>Pseudodesulfovibrio methanolicus</i> sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510961","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}
Biology-BaselPub Date : 2024-10-07DOI: 10.3390/biology13100801
Marina Shuklina, Liudmila Stepanova, Olga Ozhereleva, Anna Kovaleva, Inna Vidyaeva, Alexandr Korotkov, Liudmila Tsybalova
{"title":"Inserting CTL Epitopes of the Viral Nucleoprotein to Improve Immunogenicity and Protective Efficacy of Recombinant Protein against Influenza A Virus.","authors":"Marina Shuklina, Liudmila Stepanova, Olga Ozhereleva, Anna Kovaleva, Inna Vidyaeva, Alexandr Korotkov, Liudmila Tsybalova","doi":"10.3390/biology13100801","DOIUrl":"https://doi.org/10.3390/biology13100801","url":null,"abstract":"<p><p>Conserved influenza virus proteins, such as the hemagglutinin stem domain (HA2), nucleoprotein (NP), and matrix protein (M), are the main targets in the development of universal influenza vaccines. Previously, we constructed a recombinant vaccine protein Flg-HA2-2-4M2ehs containing the extracellular domain of the M2 protein (M2e) and the aa76-130 sequence of the second HA subunit as target antigens. It demonstrated immunogenicity and broad protection against influenza A viruses after intranasal and parenteral administration. This study shows that CD8+ epitopes of NP, inserted into a flagellin-fused protein carrying M2e and HA2, affect the post-vaccination immune humoral response to virus antigens without reducing protection. No differences were found between the two proteins in their ability to stimulate the formation of follicular Th in the spleen, which may contribute to a long-lasting antigen-specific humoral response. The data obtained on Balb/c mice suggest that the insertion of CTL NP epitopes into the flagellin-fused protein carrying M2e and HA2 reduces the antibody response to M2e and A/H3N2. In C57Bl6 mice, this stimulates the formation of NP-specific CD8+ Tem and virus-specific mono- and multifunctional CD4+ and CD8+ Tem in the spleen and completely protects mice from influenza virus subtypes A/H1N1pdm09 and A/H3N2.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510949","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}
Biology-BaselPub Date : 2024-10-07DOI: 10.3390/biology13100799
Jeong-Woon Park, Je-Keun Rhee
{"title":"Integrative Analysis of ATAC-Seq and RNA-Seq through Machine Learning Identifies 10 Signature Genes for Breast Cancer Intrinsic Subtypes.","authors":"Jeong-Woon Park, Je-Keun Rhee","doi":"10.3390/biology13100799","DOIUrl":"https://doi.org/10.3390/biology13100799","url":null,"abstract":"<p><p>Breast cancer is a heterogeneous disease composed of various biologically distinct subtypes, each characterized by unique molecular features. Its formation and progression involve a complex, multistep process that includes the accumulation of numerous genetic and epigenetic alterations. Although integrating RNA-seq transcriptome data with ATAC-seq epigenetic information provides a more comprehensive understanding of gene regulation and its impact across different conditions, no classification model has yet been developed for breast cancer intrinsic subtypes based on such integrative analyses. In this study, we employed machine learning algorithms to predict intrinsic subtypes through the integrative analysis of ATAC-seq and RNA-seq data. We identified 10 signature genes (<i>CDH3</i>, <i>ERBB2</i>, <i>TYMS</i>, <i>GREB1</i>, <i>OSR1</i>, <i>MYBL2</i>, <i>FAM83D</i>, <i>ESR1</i>, <i>FOXC1</i>, and <i>NAT1</i>) using recursive feature elimination with cross-validation (RFECV) and a support vector machine (SVM) based on SHAP (SHapley Additive exPlanations) feature importance. Furthermore, we found that these genes were primarily associated with immune responses, hormone signaling, cancer progression, and cellular proliferation.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510950","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":"Microbial Community Structure in the Taklimakan Desert: The Importance of Nutrient Levels in Medium and Culture Methods.","authors":"Feng Wen, Siyuan Wu, Xiaoxia Luo, Linquan Bai, Zhanfeng Xia","doi":"10.3390/biology13100797","DOIUrl":"https://doi.org/10.3390/biology13100797","url":null,"abstract":"<p><p>Although the Taklimakan Desert lacks the necessary nutrients and conditions to support an extensive ecosystem, it is a treasure trove of extremophile resources with special structures and functions. We analyzed the bacterial communities using oligotrophic medium and velvet cloth replicate combined with an extended culture duration. We isolated numerous uncultured microorganisms and rare microorganisms belonging to genera not often isolated or recently described, such as <i>Aliihoeflea</i>, <i>Halodurantibacterium</i>, and <i>Indioceanicola</i>. A total of 669 strains were isolated from the soil of the Taklimakan Desert, which were classified into 5 phyla, 7 classes, 25 orders, 42 families, 83 genera, and 379 species. Among them, 148 strains were potential new species. Our data show that even when working with samples from extreme environments, simple approaches are still useful for cultivating stubborn microbes. Through comparing the isolation effects of different nutrient levels on microbial diversity and abundance, the results show that reducing the nutrient level of the medium was more conducive to improving the culturability of microorganisms in low-nutrient environments, while the high-nutrient medium was more suitable for the isolation of dominant fast-growing strains. This study helps to better reflect the diversity of microbial resources and lays a foundation for the further research and utilization of soil microbial resources in the Taklimakan Desert.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"13 10","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510955","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}