Biology最新文献

{"title":"The Evolution of Three Schizothoracinae Species from Two Major River Systems in Northwest China Based on Otolith Morphology and Skeletal Structure","authors":"Chengxin Wang, Linghui Hu, Yong Song, Haoyang Xie, Liting Yang, Gulden Serekbol, Bin Huo, Shengao Chen","doi":"10.3390/biology13070517","DOIUrl":"https://doi.org/10.3390/biology13070517","url":null,"abstract":"Schizothoracinae species are the largest group of Cypriniformes that readily adapt to the natural conditions of the Qinghai-Tibet Plateau. This group has habitat characteristics and distribution patterns centered on the Qinghai-Tibet Plateau. To study the evolution of three Schizothoracinae species in Northwest China, the evolutionary characteristics of these species were explored based on differences in otolith morphology and skeletal morphology. From 2020 to 2022, 138 samples (63 Aspiorhynchus laticeps, 35 Diptychus maculatus and 40 Schizothorax pseudaksaiensis) were collected from the Tarim River and Ili River, 6 basic morphological parameters of otoliths were measured and converted into 6 morphological factors and 7 morphological indices. A total of 77 Fourier transform coefficients of each otolith were selected The first three principal components accounted for 92.834% of the total variation in 13 otolith morphological indices of the three Schizothoracinae species, and the overall discrimination rate was 94.20%. According to the principal component analysis of 77 Fourier harmonic values of otoliths, the first 20 principal components explained 97.233% of the total variation, and the overall discrimination rate was 100%. The results of the cluster analysis directly reflected the relationships between related species. The differences in the bone morphology of the three Schizothoracinae species were particularly reflected in the number of whiskers, pharyngeal teeth and vertebrae, and there were also significant differences in the shapes of the sphenotic (SP), pterotic (PTE), preoperculum (PO), branchiostegal ray (BRA) and basibranchial (BB) bones. Their unique morphological and skeletal characteristics are closely related to geological changes and water system evolutionary trends. This study contributes to the understanding of species identification and the evolutionary status of plateau fishes, provides a reference for further evolutionary classification and for assessing the evolutionary mechanisms of plateau fishes, and provides a scientific basis for phylogeny and germplasm resource protection.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"83 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141657869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Organic Xenobiotics on Tenebrio molitor Larvae and Their Parasite Gregarina polymorpha","authors":"Viktoriia Lazurska, V. Brygadyrenko","doi":"10.3390/biology13070513","DOIUrl":"https://doi.org/10.3390/biology13070513","url":null,"abstract":"Environmental contamination with xenobiotics affects organisms and the symbiotic relations between them. A convenient object to study relationships between parasites and their hosts is the host–parasite system “Tenebrio molitor Linnaeus, 1758 (Coleoptera, Tenebrionidae)—Gregarina polymorpha (Hammerschmidt, 1838) Stein, 1848 (Eugregarinorida, Gregarinidae)”. For this experiment, we took 390 T. molitor larvae and 24 organic compounds. Groups of mealworms, 15 in each, were subjected to those compounds for 10 days. Then, we recorded the vitality of both the larvae of T. molitor and G. polymorpha. To assess how G. polymorpha had affected the hosts’ wellbeing, we looked for changes in the larvae’s body mass and compared them to the number of gregarines in their intestines. The vitality of the larvae was inhibited by cyclopentanol and 2-naphthol. The intensity of gregarine invasion was reduced by diphenyl ether, benzyl alcohol, catechol, and 3-aminobenzoic acid. No effect on the number of gregarines was produced by 3,4,5-trihydroxybenzoic acid, cyclohexanemethanol, phenol, benzalkonium chloride, maleic anhydride, cyclohexanol, resorcin, benzoic acid, 2-methylfuran, terpinen-4-ol, 1-phenylethylamine, dibutyl phthalate, 3-furancarboxylic acid, 5-methyl furfural, 6-aminohexanoic acid, succinic anhydride, o-xylene, and benzaldehyde. In the infected T. molitor individuals, the mean number of G. polymorpha equaled 45 specimens per host. The groups of smaller mealworms had fewer gregarines. Positive correlation was seen between growth rates of T. molitor larvae and the intensity of invasion by gregarines.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"26 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141659495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regional Changes in Brain Biomolecular Markers in a Collagen-Induced Arthritis Rat Model","authors":"A. Millen, Tshiamo T. Maluleke, Leandrie Pienaar, Farhanah N. Sallie, Radhini Veerappan, P. Andren, S. Baijnath","doi":"10.3390/biology13070516","DOIUrl":"https://doi.org/10.3390/biology13070516","url":null,"abstract":"Background: The effects of collagen-induced arthritis (CIA), a model of systemic inflammation, on brain regional molecular markers associated with neurological disorders are uncertain. Objective: This study investigated the brain regional molecular changes in markers associated with inflammation and neuronal dysfunction in a CIA model. Methods: Fourteen male Sprague Dawley rats were divided into control (n = 5) or CIA (n = 9) groups. 10 weeks after CIA induction, brain tissue was collected. Brain regional mRNA expression of inflammatory markers (IL-1β and IL-6), apoptotic markers (BAX and Bcl2) and neurotrophic factors (BDNF, CREB and TrkB) was determined. Monoamine distribution and abundance in different brain regions were determine by mass spectrometry imaging (MSI). Results: Neuroinflammation was confirmed in the CIA group by increased IL-β mRNA expression, concurrent with an increased BAX/Bcl2 ratio. The mRNA expression of CREB was increased in the midbrain and hippocampus while BDNF was increased and TrkB was decreased across all brain regions in CIA compared to control animals. Serotonin was decreased in the midbrain and hippocampus while dopamine was decreased in the striatum of CIA rats, compared to controls. Conclusion: CIA resulted in neuroinflammation concurrent with an apoptotic state and aberrant expression of neurotrophic factors and monoamines in the brain, suggestive of neurodegeneration.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"21 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141661245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping the Future: Revealing Habitat Preferences and Patterns of the Endangered Chilean Dolphin in Seno Skyring, Patagonia","authors":"Liliana Perez, Yenny Cuellar, Jorge Gibbons, Elias Pinilla Matamala, Simon Demers, Juan Capella","doi":"10.3390/biology13070514","DOIUrl":"https://doi.org/10.3390/biology13070514","url":null,"abstract":"Species distribution modeling helps understand how environmental factors influence species distribution, creating profiles to predict presence in unexplored areas and assess ecological impacts. This study examined the habitat use and population ecology of the Chilean dolphin in Seno Skyring, Chilean Patagonia. We used three models—random forest (RF), generalized linear model (GLM), and artificial neural network (ANN)—to predict dolphin distribution based on environmental and biotic data like water temperature, salinity, and fish farm density. Our research has determined that the RF model is the most precise tool for predicting the habitat preferences of Chilean dolphins. The results indicate that these dolphins are primarily located within six kilometers of the coast, strongly correlating with areas featuring numerous fish farms, sheltered waters close to the shore with river inputs, and shallow productive zones. This suggests a potential association between dolphin presence and fish-farming activities. These findings can guide targeted conservation measures, such as regulating fish-farming practices and protecting vital coastal areas to improve the survival prospects of the Chilean dolphin. Given the extensive fish-farming industry in Chile, this research highlights the need for greater knowledge and comprehensive conservation efforts to ensure the species’ long-term survival. By understanding and mitigating the impacts of fish farming and other human activities, we can better protect the habitat and well-being of Chilean dolphins.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"37 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141661756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Stable Isotope Techniques to Analyze the Trophic Relationship between Argentine Hake (Merluccius hubbsi) and Anisakidae","authors":"Yue Shu, Feiyu Wu, Zhou Fang","doi":"10.3390/biology13070515","DOIUrl":"https://doi.org/10.3390/biology13070515","url":null,"abstract":"The Argentine hake (Merluccius hubbsi) is a vital fishery species in the Southwest Atlantic, recognized for its substantial economic importance. Previous studies have identified Anisakidae larvae as common parasites of M. hubbsi. However, the nutritional relationships between these parasites and their host remain poorly understood. This study employs stable isotope techniques to investigate the specific nutritional relationships between Anisakidae larvae and different tissues of M. hubbsi. The findings reveal notable differences in δ13C and δ15N compositions between the parasites and their host. The lower δ13C values in parasites compared to host tissues indicate the utilization of different carbon sources. The δ15N values of the parasites partially overlap with those of the host’s stomach, indicating that the parasites primarily derive nutrients from the host’s stomach. Nutritional niche indicators show that parasites have a broad carbon range (CR) and nitrogen range (NR), suggesting a high diversity in nutritional sources. The trophic discrimination factor (ΔTDF), which represents the difference in stable isotope values between host tissues and parasites, was analyzed for both δ13C and δ15N. The ΔTDFδ13C between the host liver and the parasites showed the greatest variation, indicating a strong dependence of the parasites on the liver’s carbon sources. In contrast, variations in ΔTDFδ15N between host tissues and parasites were minimal. Analyzing ΔTDF across different stages of gonadal maturity in the host fish indicates that, as the gonads of the host fish mature, ΔTDFδ13C between host tissues and parasites significantly decreases (p < 0.01). The Kruskal–Wallis test showed significant differences in ΔTDFδ13C values among different parasite infection levels in muscle, liver, and stomach tissues, while no significant differences were found for ΔTDFδ15N values. These findings offer valuable insights into the nutritional relationships between parasites and hosts, aiding in a better understanding of the growth conditions and habitats of M. hubbsi.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"36 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141661889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diffusion on PCA-UMAP Manifold: The Impact of Data Structure Preservation to Denoise High-Dimensional Single-Cell RNA Sequencing Data","authors":"Padron-Manrique Cristian, Vázquez-Jiménez Aarón, Esquivel-Hernandez Diego Armando, Martínez-López Yoscelina Estrella, Neri-Rosario Daniel, Girón-Villalobos David, Mixcoha Edgar, Sánchez-Castañeda Jean Paul, Resendis-Antonio Osbaldo","doi":"10.3390/biology13070512","DOIUrl":"https://doi.org/10.3390/biology13070512","url":null,"abstract":"Single-cell transcriptomics (scRNA-seq) is revolutionizing biological research, yet it faces challenges such as inefficient transcript capture and noise. To address these challenges, methods like neighbor averaging or graph diffusion are used. These methods often rely on k-nearest neighbor graphs from low-dimensional manifolds. However, scRNA-seq data suffer from the ‘curse of dimensionality’, leading to the over-smoothing of data when using imputation methods. To overcome this, sc-PHENIX employs a PCA-UMAP diffusion method, which enhances the preservation of data structures and allows for a refined use of PCA dimensions and diffusion parameters (e.g., k-nearest neighbors, exponentiation of the Markov matrix) to minimize noise introduction. This approach enables a more accurate construction of the exponentiated Markov matrix (cell neighborhood graph), surpassing methods like MAGIC. sc-PHENIX significantly mitigates over-smoothing, as validated through various scRNA-seq datasets, demonstrating improved cell phenotype representation. Applied to a multicellular tumor spheroid dataset, sc-PHENIX identified known extreme phenotype states, showcasing its effectiveness. sc-PHENIX is open-source and available for use and modification.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"52 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141663405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic Profiling Changes Induced by Fermented Blackberries in High-Fat-Diet-Fed Mice utilizing Gas Chromatography–Mass Spectrometry Analysis","authors":"Jae Young Park, Ha-Rim Kim, Seung-Hyeon Lee, Sang-Wang Lee, H. Sin, Seon-Young Kim, Mi Hee Park","doi":"10.3390/biology13070511","DOIUrl":"https://doi.org/10.3390/biology13070511","url":null,"abstract":"The aim of this study was to investigate the metabolic changes associated with the anti-obesity effects of fermented blackberry extracts in the liver tissues of high-fat-diet-fed mice using mass spectrometry-based metabolomics analysis. C57BL/6J mice were divided into eight groups: normal-diet-fed mice, high-fat-diet-fed mice, high-fat diet treated with blackberry extract, high-fat-diet mice treated with blackberry fermented by L. plantarum, and high-fat diet with blackberry fermented by L. brevis. After 12 weeks, the high-fat-diet group exhibited a greater increase in liver weight compared to the control group, and among the groups, the group administered with blackberry fermented with L. plantarum showed the most pronounced reduction in liver weight. As the primary organ responsible for amino acid metabolism, the liver is crucial for maintaining amino acid homeostasis. In our study, we observed that the levels of several essential amino acids, including isoleucine and valine, were decreased by the high-fat diet, and were recovered by administration of blackberry extract fermented with L. plantarum. Our results demonstrated the potential of blackberry extract fermented with L. plantarum as a functional material for metabolic disorders by restoring some of the amino acid metabolism disturbances induced by a high-fat diet.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"36 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141663877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reverse Vaccinology Approach to Identify Novel and Immunogenic Targets against Streptococcus gordonii","authors":"Aneeqa Abid, Badr Alzahrani, S. Naz, Amina Basheer, S. Bakhtiar, Fahad Al-Asmari, Syed Babar Jamal, Muhammad Faheem","doi":"10.3390/biology13070510","DOIUrl":"https://doi.org/10.3390/biology13070510","url":null,"abstract":"Streptococcus gordonii is a gram-positive, mutualistic bacterium found in the human body. It is found in the oral cavity, upper respiratory tract, and intestines, and presents a serious clinical problem because it can lead to opportunistic infections in individuals with weakened immune systems. Streptococci are the most prevalent inhabitants of oral microbial communities, and are typical oral commensals found in the human oral cavity. These streptococci, along with many other oral microbes, produce multispecies biofilms that can attach to salivary pellicle components and other oral bacteria via adhesin proteins expressed on the cell surface. Antibiotics are effective against this bacterium, but resistance against antibodies is increasing. Therefore, a more effective treatment is needed. Vaccines offer a promising method for preventing this issue. This study generated a multi-epitope vaccine against Streptococcus gordonii by targeting the completely sequenced proteomes of five strains. The vaccine targets are identified using a pangenome and subtractive proteomic approach. In the present study, 13 complete strains out of 91 strains of S. gordonii are selected. The pangenomics results revealed that out of 2835 pan genes, 1225 are core genes. Out of these 1225 core genes, 643 identified as non-homologous proteins by subtractive proteomics. A total of 20 essential proteins are predicted from non-homologous proteins. Among these 20 essential proteins, only five are identified as surface proteins. The vaccine construct is designed based on selected B- and T-cell epitopes of the antigenic proteins with the help of linkers and adjuvants. The designed vaccine is docked against TLR2. The expression of the protein is determined using in silico gene cloning. Findings concluded that Vaccine I with adjuvant shows higher interactions with TLR2, suggesting that the vaccine has the ability to induce a humoral and cell-mediated response to treat and prevent infection; this makes it promising as a vaccine against infectious diseases caused by S. gordonii. Furthermore, validation of the vaccine construct is required by in vitro and in vivo trials to check its actual potency and safety for use to prevent infectious diseases caused by S. gordonii.","PeriodicalId":504576,"journal":{"name":"Biology","volume":"125 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141665602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pan-Evo: The Evolution of Information and Biology’s Part in This","authors":"William B. Sherwin","doi":"10.3390/biology13070507","DOIUrl":"https://doi.org/10.3390/biology13070507","url":null,"abstract":"Many people wonder whether biology, including humans, will benefit or experience harm from new developments in information such as artificial intelligence (AI). Here, it is proposed that biological and non-biological information might be components of a unified process, ‘Panevolution’ or ‘Pan-Evo’, based on four basic operations—innovation, transmission, adaptation, and movement. Pan-Evo contains many types of variable objects, from molecules to ecosystems. Biological innovation includes mutations and behavioural changes; non-biological innovation includes naturally occurring physical innovations and innovation in software. Replication is commonplace in and outside biology, including autocatalytic chemicals and autonomous software replication. Adaptation includes biological selection, autocatalytic chemicals, and ‘evolutionary programming’, which is used in AI. The extension of biological speciation to non-biological information creates a concept called ‘Panspeciation’. Panevolution might benefit or harm biology, but the harm might be minimal if AI and humans behave intelligently because humans and the machines in which an AI resides might split into vastly different environments that suit them. That is a possible example of Panspeciation and would be the first speciation event involving humans for thousands of years. This event will not be particularly hostile to humans if humans learn to evaluate information and cooperate better to minimise both human stupidity and artificial simulated stupidity (ASS—a failure of AI).","PeriodicalId":504576,"journal":{"name":"Biology","volume":"101 38","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141667210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neural Delays in Processing Speech in Background Noise Minimized after Short-Term Auditory Training","authors":"E. Skoe, Nina Kraus","doi":"10.3390/biology13070509","DOIUrl":"https://doi.org/10.3390/biology13070509","url":null,"abstract":"Background noise disrupts the neural processing of sound, resulting in delayed and diminished far-field auditory-evoked responses. In young adults, we previously provided evidence that cognitively based short-term auditory training can ameliorate the impact of background noise on the frequency-following response (FFR), leading to greater neural synchrony to the speech fundamental frequency(F0) in noisy listening conditions. In this same dataset (55 healthy young adults), we now examine whether training-related changes extend to the latency of the FFR, with the prediction of faster neural timing after training. FFRs were measured on two days separated by ~8 weeks. FFRs were elicited by the syllable “da” presented at a signal-to-noise ratio (SNR) of +10 dB SPL relative to a background of multi-talker noise. Half of the participants participated in 20 sessions of computerized training (Listening and Communication Enhancement Program, LACE) between test sessions, while the other half served as Controls. In both groups, half of the participants were non-native speakers of English. In the Control Group, response latencies were unchanged at retest, but for the training group, response latencies were earlier. Findings suggest that auditory training can improve how the adult nervous system responds in noisy listening conditions, as demonstrated by decreased response latencies.","PeriodicalId":504576,"journal":{"name":"Biology","volume":" 895","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141669062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}