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Feathers of Grace: The "After You" Gesture in Japanese Tits.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-16 DOI: 10.3390/biology14030297
Sergio Da Silva, Raul Matsushita
{"title":"Feathers of Grace: The \"After You\" Gesture in Japanese Tits.","authors":"Sergio Da Silva, Raul Matsushita","doi":"10.3390/biology14030297","DOIUrl":"10.3390/biology14030297","url":null,"abstract":"<p><p>A recent study found evidence of symbolic gesture use in Japanese tits (<i>Parus minor</i>). The study reveals how these birds use wing-fluttering movements to transmit an \"after you\" directive to their partners, implying a degree of cognitive skill previously thought to be unique to humans and great apes. If confirmed, this research contradicts long-held notions about animal communication by proving that Japanese tits not only participate in intricate vocal communications, which can comprise phrases with specific grammatical rules, but also use body language as a form of engagement. Here, we evaluate this claim by inspecting the data and utilizing bootstrapping to expand the sample size. We find a large variation in how frequently the \"after you\" gesture is employed in different bootstrap samples, suggesting that while the gesture is a consistent behavior, its frequency can vary significantly. Moreover, the timing of the male's response to the female's gesture can fluctuate, though the response itself appears to be a stable phenomenon. Beyond evaluating the bootstrapping technique, we employ causal inference to examine whether wing fluttering by female Japanese tits leads to a quicker response by males, entering the nest more swiftly. The analysis supports this hypothesis, suggesting that wing fluttering functions as an effective communicative gesture in this species, influencing male nesting behavior. However, because the frequency of the \"after you\" gesture varied greatly, especially in light of potential cognitive and other biases influencing the study, this bold claim should be taken with caution.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11939911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711762","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}
引用次数: 0
Tryptophan-2,3-Dioxygenase as a Therapeutic Target in Digestive System Diseases.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-15 DOI: 10.3390/biology14030295
Zhengsen Wang, Xianxian Xie, Yu Xue, Yixuan Chen
{"title":"Tryptophan-2,3-Dioxygenase as a Therapeutic Target in Digestive System Diseases.","authors":"Zhengsen Wang, Xianxian Xie, Yu Xue, Yixuan Chen","doi":"10.3390/biology14030295","DOIUrl":"10.3390/biology14030295","url":null,"abstract":"<p><p>Tryptophan (Trp) is an essential amino acid that must be acquired exclusively through dietary intake. The metabolism of tryptophan plays a critical role in maintaining immune homeostasis and tolerance, as well as in preventing excessive inflammatory responses. Tryptophan-2,3-dioxygenase (TDO2) is a tetrameric heme protein and serves as one of the pivotal rate-limiting enzymes in the first step of tryptophan metabolism. Dysregulation of TDO2 expression has been observed in various digestive system diseases, encompassing those related to the oral cavity, esophagus, liver, stomach, pancreas, and colon and rectum. Digestive system diseases are the most common clinical diseases, with complex clinical manifestations and interrelated symptoms, and have become a research hotspot in the field of medicine. Studies have demonstrated that aberrant TDO2 expression is closely associated with various clinical manifestations and disease outcomes in patients with digestive system disorders. Consequently, TDO2 has garnered increasing recognition as a promising therapeutic target for digestive system diseases in recent years, attracting growing attention. This article provides a brief overview of the role of TDO2 in the tryptophan pathway, emphasizing its significant involvement in diseases of the digestive system. Strategies targeting TDO2 through specific inhibitors suggest considerable promise in enhancing therapeutic outcomes for digestive diseases. Thus, this review concludes by discussing recent advancements in the development of TDO2 inhibitors. We believe that targeted inhibition of TDO2 combined with immunotherapy, the screening of a large number of natural products, and the assistance of artificial intelligence in drug design will be important directions for developing more effective TDO2 inhibitors and improving treatment outcomes in the future.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11939885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711884","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}
引用次数: 0
How to Define Spacing Among Forest Trees to Mitigate Competition: A Technical Note.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-15 DOI: 10.3390/biology14030296
Khodabakhsh Zabihi, Vivek Vikram Singh, Aleksei Trubin, Nataliya Korolyova, Rastislav Jakuš
{"title":"How to Define Spacing Among Forest Trees to Mitigate Competition: A Technical Note.","authors":"Khodabakhsh Zabihi, Vivek Vikram Singh, Aleksei Trubin, Nataliya Korolyova, Rastislav Jakuš","doi":"10.3390/biology14030296","DOIUrl":"10.3390/biology14030296","url":null,"abstract":"<p><p>Establishing an optimum range of inter-species spacing that reduces competition among trees and mitigates the effects of drought is a critical yet complex challenge in forest management. Stand density plays a crucial role in forest functioning by regulating resource allocation within individual trees. Higher stand densities have been shown to reduce sap velocities, indicating intensified competition for water and other resources. However, determining the precise spacing that minimizes competition while maintaining ecosystem balance remains unclear. In this study, conducted in temperate Norway spruce forests at an altitude range of 400-500 m in the Czech Republic, we propose a novel technique to define tree spacing that reduces competitive interactions. We used xylem sap flow residuals of an ordinary least square (OLS) regression model to filter out the effects of elevation and diameter at breast height (DBH) on field-measured sap flow for 101 planted Norway spruce trees with a DBH range of 40 ± 5 cm (≈90-100 years old). The model residuals allowed us to account for the most important driver of sap flow variability: tree density and its underlying effects on individual tree traits. To minimize the confounding effects of temporal and spatial variability, we used twelve consecutive daily measurements of sap flow (6 a.m. to 6 p.m.) taken at the start of the growing season. By constructing an experimental variogram, we quantified sap flow variability as a function of tree spacing. The results showed a steady sap flow pattern at tree densities of 12, 11, and 10 trees per 314 m<sup>2</sup> (equivalent to 350 ± 32 trees per hectare), corresponding to inter-tree spacing measurements of 5.12 m, 5.34 m, and 5.60 m, respectively. These findings suggest that when the <i>N</i> number of trees (median) per unit area (<i>A</i>) is in equilibrium with resource availability, increasing or decreasing the <i>n</i> number of trees may not significantly change competition levels (<i>A; f(A) = N ± n</i>). The size or deviation of <i>n</i> depends on the area to define the minimum and maximum thresholds or tolerance capacity for the number of trees allowed to be in the area. This technique-using a variogram of sap flow residuals to determine tree spacing-can be periodically applied, such as every 10-15 years, and adapted for different elevation gradients (e.g., within 100 m intervals). It offers a practical tool for forest managers and policymakers, guiding thinning and planting strategies to enhance forest resilience in the face of water-stress conditions.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711730","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}
引用次数: 0
Mucus Trail Proteins May Infer Reproductive Readiness for Land Snails.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-14 DOI: 10.3390/biology14030294
Kate R Ballard, Tomer Ventura, Tianfang Wang, Abigail Elizur, Scott F Cummins
{"title":"Mucus Trail Proteins May Infer Reproductive Readiness for Land Snails.","authors":"Kate R Ballard, Tomer Ventura, Tianfang Wang, Abigail Elizur, Scott F Cummins","doi":"10.3390/biology14030294","DOIUrl":"10.3390/biology14030294","url":null,"abstract":"<p><p>Mucus trails are defining features of the class Gastropoda, which includes snails and slugs. While several studies have shown that mucus trails are followed by conspecifics, the detectable elements in the mucus have not been clearly identified. This is particularly relevant during periods of reproduction, whereby conspecific cues are critical for mate finding. A better understanding of the mucus' molecular components, including proteins differentially represented between the reproductive and non-reproductive stages, could aid the development of novel eco-friendly biocontrol approaches. In this study, we investigated the mucus trails of the globally invasive land snail <i>Cernuella virgata</i>, which has become a significant pest to the grain industry. We conducted a comparative proteomic analysis of the non-reproductive- and reproductive-stage trail mucus, whereby 533 proteins were identified, including 191 and 226 stage-exclusive proteins, respectively. Subsequent comparative tissue transcriptomic analysis found that the albumen gland, which is the key gland for the preparation of fertilized eggs prior to egg laying, was the primary source of secreted proteins present in the reproductive stage trail mucus. This included leukocyte elastase inhibitors, achacin, perlucin, and other proteins without any known function (uncharacterized). In summary, our results strongly implicate the albumen gland as a source for snail trail mucus proteins deposited during the reproductive stage, suggesting a mechanism that could convey their reproductive status to conspecifics. Further research testing their bioactivity related to chemical communication is paramount and may assist in the development of a novel biocontrol strategy.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711754","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}
引用次数: 0
Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-14 DOI: 10.3390/biology14030293
Simona Pizzi, Angela Conti, Alessandra Di Canito, Debora Casagrande Pierantoni, Roberto Foschino, Mathabatha Evodia Setati, Ileana Vigentini
{"title":"Endophytic Diversity in <i>Vitis vinifera</i> with Different Vineyard Managements and <i>Vitis sylvestris</i> Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.","authors":"Simona Pizzi, Angela Conti, Alessandra Di Canito, Debora Casagrande Pierantoni, Roberto Foschino, Mathabatha Evodia Setati, Ileana Vigentini","doi":"10.3390/biology14030293","DOIUrl":"10.3390/biology14030293","url":null,"abstract":"<p><p>This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included <i>Aureobasidium pullulans</i>, <i>Alternaria alternata</i>, and <i>Cladosporium allicinum</i>, while predominant bacterial species were <i>Ralstonia pikettii</i>, <i>Nocardia niigatensis</i>, and <i>Sphingomonas echinoides</i>. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included <i>Halomonas</i> sp., <i>Sphingomonas</i> sp. and <i>Massilia</i> sp., whereas the fungal population was dominated by <i>Cladosporium</i> sp., <i>Malassezia</i> sp. and <i>Mucor</i> sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711689","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}
引用次数: 0
Editorial for the Special Issue "Neurobiology of Invertebrates Inaccessible from Mammalian Studies".
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-13 DOI: 10.3390/biology14030290
Etsuro Ito, Kengo Namiki
{"title":"Editorial for the Special Issue \"Neurobiology of Invertebrates Inaccessible from Mammalian Studies\".","authors":"Etsuro Ito, Kengo Namiki","doi":"10.3390/biology14030290","DOIUrl":"10.3390/biology14030290","url":null,"abstract":"<p><p>This Special Issue features five excellent papers on invertebrate neurobiology [...].</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711666","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}
引用次数: 0
Modulatory Effects of the Recombinant Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Spike S1 Subunit Protein on the Phenotype of Camel Monocyte-Derived Macrophages.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-13 DOI: 10.3390/biology14030292
Jamal Hussen, Abdullah I A Al-Mubarak, Turke Shawaf, Khulud Bukhari, Khaled R Alkharsah
{"title":"Modulatory Effects of the Recombinant Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Spike S1 Subunit Protein on the Phenotype of Camel Monocyte-Derived Macrophages.","authors":"Jamal Hussen, Abdullah I A Al-Mubarak, Turke Shawaf, Khulud Bukhari, Khaled R Alkharsah","doi":"10.3390/biology14030292","DOIUrl":"10.3390/biology14030292","url":null,"abstract":"<p><p>Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic pathogen with different pathogenesis in humans and camels. The mechanisms behind the higher tolerance of camels to MERS-CoV infection are still unknown. Monocytes are innate myeloid cells that are able, depending on the local stimulation in their microenvironment, to differentiate into different functional subtypes of macrophages with an impact on the adaptive immune response. Several in vitro protocols have been used to induce the differentiation of monocyte-derived macrophages (MDMs) in human and several veterinary species. Such protocols are not available for camel species. In the present study, monocytes were separated from camel blood and differentiated in vitro in the presence of different stimuli into MDM. Camel MDMs generated in the presence of a combined stimulation of monocytes with LPS and GM-CSF resulted in the development of an M1 macrophages phenotype with increased abundance of the antigen-presentation receptor MHCII molecules and a decreased expression of the scavenger receptor CD163. The expression pattern of the cell markers CD163, CD14, CD172a, CD44, and CD9 on MDM generated in the presence of the MERS-CoV S1 protein revealed similarity with M-CSF-induced MDM, suggesting the potential of the MERS-CoV S1 protein to induce an M2 macrophages phenotype. Similarly to the effect of M-CSF, MERS-CoV-S protein-induced MDMs showed enhanced phagocytosis activity compared to non-polarized or LPS/GM-CSF-polarized MDMs. Collectively, our study represents the first report on the in vitro generation of monocyte-derived macrophages (MDMs) in camels and the characterization of some phenotypic and functional properties of camel MDM under the effect of M1 and M2 polarizing stimuli. In addition, the results suggest a polarizing effect of the MERS-CoV S1 protein on camel MDMs, developing an M2-like phenotype with enhanced phagocytosis activity. To understand the clinical relevance of these in vitro findings on disease pathogenesis and camel immune response toward MERS-CoV infection, further studies are required.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711753","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}
引用次数: 0
Unraveling the Evolutionary Patterns of Genus Frontonia: An Integrative Approach with Morphological and Molecular Data.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-13 DOI: 10.3390/biology14030289
Ratih Kusuma Wardani, Ragib Ahsan, Mann Kyoon Shin
{"title":"Unraveling the Evolutionary Patterns of Genus <i>Frontonia</i>: An Integrative Approach with Morphological and Molecular Data.","authors":"Ratih Kusuma Wardani, Ragib Ahsan, Mann Kyoon Shin","doi":"10.3390/biology14030289","DOIUrl":"10.3390/biology14030289","url":null,"abstract":"<p><p>Ciliates of the genus <i>Frontonia</i> have been extensively studied to resolve their phylogenetic and evolutionary history, but challenges remain. This study used molecular analyses of SSU rRNA genes, phylogenetic tree reconstruction, molecular dating, and diversification analysis, together with ancestral state reconstruction of morphological traits and habitat preferences. Data included newly sequenced Korean species, GenBank records and published morphological information. Phylogenetic trees revealed paraphyly within <i>Frontonia</i>, identifying four groups that emerged in the Mesozoic era: Group I (~172 mya), Group II (~83 mya), Group III (~115 mya), and Group IV (~190 mya), with a common ancestor dating to ~420 mya in the Palaeozoic era. Diversification analysis revealed higher extinction rates (0.826 and 0.613 species/year) than speciation rates (0.011 and 0.016 species/year). Morphological evolution showed habitat adaptation and plasticity, with habitat transitions unrelated to contractile vacuolar traits. The SSU rRNA gene polymorphism likely contributed to the paraphyletic state of <i>Frontonia</i>. These results highlight the complex evolutionary patterns of the genus, shaped by genetic diversity, morphology, and environmental constraints.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711888","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}
引用次数: 0
Imbalance of Bile Acids Metabolism Mediated by Gut Microbiota Contributed to Metabolic Disorders in Diabetic Model Mice.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-13 DOI: 10.3390/biology14030291
Hongwang Dong, Xinguo Liu, Ge Song, Wenting Peng, Xihan Sun, Wei Fang, Wentao Qi
{"title":"Imbalance of Bile Acids Metabolism Mediated by Gut Microbiota Contributed to Metabolic Disorders in Diabetic Model Mice.","authors":"Hongwang Dong, Xinguo Liu, Ge Song, Wenting Peng, Xihan Sun, Wei Fang, Wentao Qi","doi":"10.3390/biology14030291","DOIUrl":"10.3390/biology14030291","url":null,"abstract":"<p><p>Type 2 diabetes (T2D) is a chronic disease prevalent in the world, accompanied by a variety of diseases, endangering human health and safety. Bile acids (BAs) play an important role in the regulation of host glucose and lipid metabolism homeostasis, and are strictly regulated by gut microbiota. However, the relationship between key BAs, BAs transporters and signaling, as well as gut microbiota, and host metabolism in T2D remains elusive. In this study, 9-week-old db/db mice were used as diabetes model (db/db group, <i>n</i> = 10), and their wild-type (wt) littermates of same age were used as the healthy control (CON group, <i>n</i> = 10). After 8 weeks of feeding, the BA profiles and microbial composition in the colon, and gene expression level of BA regulatory factors were analyzed in the db/db and CON groups to explore the underlying mechanisms of T2D. Compared with healthy mice, the body weight, blood glucose and lipid levels of db/db mice were significantly increased. The concentrations of total BAs, primary BAs, conjugated BAs and non-12α-hydroxylated BAs (non-12-OH BAs) were significantly decreased, while Deoxycholic acid (DCA) in secondary BAs was increased in db/db group. Compared with wt mice, the synthesis of BAs in the liver was transformed from the alternative pathway to the classical pathway, and hepatic BAs transporters (NTCP, BSEP, MRP2, OATP-1 and OSTβ) and receptors (FXR and TGR5) were significantly down-regulated in the db/db mice. In the colon, the mRNA level of FXR was up-regulated, while TGR5 was down-regulated. The diabetic (db/db) mice presented a changed gut microbiota composition, including an increased abundance of secondary BAs-producing bacteria, <i>Escherichia-Shigella</i>, and a decreased the abundance of <i>Akkermansia</i>, which are involved in the synthesis of non-12-OH BAs. We further found that the reduced BA types in db/db mice were negatively correlated with metabolic-disorder-related indicators, while an increased DCA level had the opposite correlation. Our results shed light into how the imbalance of BAs' metabolism mediated by intestinal flora may be potential mechanisms of T2D.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711802","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}
引用次数: 0
Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model.
IF 3.6 3区 生物学
Biology-Basel Pub Date : 2025-03-12 DOI: 10.3390/biology14030288
Ruoying Gao, Thomas N Ferraro, Liang Chen, Shaoqiang Zhang, Yong Chen
{"title":"Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model.","authors":"Ruoying Gao, Thomas N Ferraro, Liang Chen, Shaoqiang Zhang, Yong Chen","doi":"10.3390/biology14030288","DOIUrl":"10.3390/biology14030288","url":null,"abstract":"<p><p>The 3D organization of chromatin in the nucleus plays a critical role in regulating gene expression and maintaining cellular functions in eukaryotic cells. High-throughput chromosome conformation capture (Hi-C) and its derivative technologies have been developed to map genome-wide chromatin interactions at the population and single-cell levels. However, insufficient sequencing depth and high noise levels in bulk Hi-C data, particularly in single-cell Hi-C (scHi-C) data, result in low-resolution contact matrices, thereby limiting diverse downstream computational analyses in identifying complex chromosomal organizations. To address these challenges, we developed a transformer-based deep learning model, HiCENT, to impute and enhance both scHi-C and Hi-C contact matrices. Validation experiments on large-scale bulk Hi-C and scHi-C datasets demonstrated that HiCENT achieves superior enhancement effects compared to five popular methods. When applied to real Hi-C data from the GM12878 cell line, HiCENT effectively enhanced 3D structural features at the scales of topologically associated domains and chromosomal loops. Furthermore, when applied to scHi-C data from five human cell lines, it significantly improved clustering performance, outperforming five widely used methods. The adaptability of HiCENT across different datasets and its capacity to improve the quality of chromatin interaction data will facilitate diverse downstream computational analyses in 3D genome research, single-cell studies and other large-scale omics investigations.</p>","PeriodicalId":48624,"journal":{"name":"Biology-Basel","volume":"14 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11940666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711732","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}
引用次数: 0
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