Biology Open最新文献

Morphlight theory inspired by raptor: musculoskeletal modeling and muscle control in Falco peregrinus wing flapping.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-25 DOI: 10.1242/bio.061859

Di Tang, Kai Chem, Yanbin Dai, Yang Liu, Yibo Zhao, Kunpeng Wang, Siyu Wang, Zhongyong Fan

{"title":"Morphlight theory inspired by raptor: musculoskeletal modeling and muscle control in Falco peregrinus wing flapping.","authors":"Di Tang, Kai Chem, Yanbin Dai, Yang Liu, Yibo Zhao, Kunpeng Wang, Siyu Wang, Zhongyong Fan","doi":"10.1242/bio.061859","DOIUrl":"https://doi.org/10.1242/bio.061859","url":null,"abstract":"Falco peregrinus can achieve highly maneuverable flight through their morphing wing structure, which has significant research value. However, there has been limited research on the Falco Peregrinus wing musculoskeletal system. In this study, musculoskeletal modeling, flapping movement, and muscle function of Falco Peregrinus wing were studied through computer modeling and simulation to better understand the biomechanics of Falco peregrinus wing flapping. Using anatomical data and the musculoskeletal modeling method based on OPENSIM, a three-dimensional model of the Falco peregrinus wing was developed. Based on the experimental data, the flapping movements were reconstructed, muscle movements during different stages of flapping were simulated, and the function of muscles in the flapping process was analyzed. While this study provides valuable insights into the muscle function of Falco peregrinus wing during flapping, it also highlights certain limitations, such as the simplification of musculoskeletal structures and joints in the modeling approach and deviations from actual Falco peregrinus wing movements. This study provides both experimental and analytical methods for raptor wing flapping research, potentially reducing the need for live experiments and offering valuable insights into the mechanisms of raptor flapping.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into Octopus maya cathepsins from metatranscriptome and genome: structure evolutionary relationships and functional role prediction in digestive processes.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-19 DOI: 10.1242/bio.061778

Daisy Pineda-Suazo, Francisco Guillén-Chable, Wendy Itzel Escobedo-Hinojosa, Clara E Galindo-Sánchez, Carlos Rosas

{"title":"Insights into Octopus maya cathepsins from metatranscriptome and genome: structure evolutionary relationships and functional role prediction in digestive processes.","authors":"Daisy Pineda-Suazo, Francisco Guillén-Chable, Wendy Itzel Escobedo-Hinojosa, Clara E Galindo-Sánchez, Carlos Rosas","doi":"10.1242/bio.061778","DOIUrl":"https://doi.org/10.1242/bio.061778","url":null,"abstract":"Physiological response to feeding is crucial for various production factors as feed catabolism and growth. Despite growing significance in red Octopus maya aquaculture, large-scale commercial production is limited by not sufficiently knowing its nutritional needs, especially digestive physiology. Since this species is carnivorous, one of the main feeding aspects is directed to protein digestion, but its enzymatic digestive repertoire has not been studied yet at genomic and transcriptomic levels. This study searched for protease enzymes encoded in O. maya genome and expressed in the transcriptome, allowing an initial annotation of genes involved in protein catabolism; 117 amino acid sequences related to \"octopus digestive enzymes\" were retrieved from 66-species available genomes in NCBI database coding for cathepsins, papilins, and metalloproteases. Homology analysis identified 36 homologous sequences from O. maya transcriptome and three from its genome. Phylogenetic analysis grouped 37 of 39 sequences into 11 of 14 main clades, offering new insights into the evolutionary relationships and functional roles of these proteases. Phylogenetic and motif analyses resulted in selecting 19 amino acid O. maya sequences using multiple sequence alignment that were used to generate three-dimensional protein models. The obtained models revealed a diverse structure architecture among 16 modelled cathepsins; remains determining their catalytic potential to fully clarify their role in protein hydrolysis and cellular processes. Foundational data provides insights into biochemistry and physiology behind O. maya protein digestion. Further complementation of these results with enzymatic characterization of the identified proteases should allow improved diet formulation to foster this species aquaculture.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptive evolution of cytochrome b in songbirds. 鸣禽细胞色素 b 的适应性进化。

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-19 DOI: 10.1242/bio.061908

Hagai Rottenberg

{"title":"Adaptive evolution of cytochrome b in songbirds.","authors":"Hagai Rottenberg","doi":"10.1242/bio.061908","DOIUrl":"https://doi.org/10.1242/bio.061908","url":null,"abstract":"The mitochondrial bc1 complex catalyzes the oxidation of ubiquinol by reducing cytochrome c. Cytochrome b, the catalytic core of bc1, generates superoxide during the oxidation of ubiquinol. Excessive superoxide production is known to accelerate aging and neurodegeneration. Songbirds (oscine, Passeri) exhibit lower production of mitochondrial ROS and greatly accelerated evolution of cytochrome b, relative to all other modern birds, suggesting adaptive selection for lower generation of ROS. Here we identified songbirds-specific substitutions in modern bird's cytochrome b amino-acids sequences and examined the high-resolution structures of the chicken bc1 complex in an effort to predict the effect of these substitutions on the function of bc1. Many of the songbirds-specific substitution cluster around sites that are critical for the function of bc1. One cluster of substitutions interacts with heme BH. A second cluster of substitutions interacts with residues in the ubiquinone reduction site, Qi. Both groups of substitution may affect the rate of reduction of ubiquinone at the Qi site. Another cluster of cytochrome b substitutions interacts with the hinge region of the Rieske protein that transfers electron from cytochrome b to cytochrome c1. These songbirds-specific substitutions appear to be selected to modulate the rate of both ubiquinol oxidation at the Qo site and ubiquinone reduction at the Qi site thereby modulating the rate of superoxide production. These findings are compatible with the hypothesis that cytochrome b evolution in songbirds was driven by selection of substitutions that reduce the rate of superoxide production thereby increasing songbird lifespan and cognitive abilities.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GSK3 coordinately regulates mitochondrial activity and nucleotide metabolism in quiescent oocytes.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-24 DOI: 10.1242/bio.061815

Leah Eller, Lei Wang, Mehmet Oguz Gok, Helin Hocaoglu, Shenlu Qin, Parul Gupta, Matthew H Sieber

{"title":"GSK3 coordinately regulates mitochondrial activity and nucleotide metabolism in quiescent oocytes.","authors":"Leah Eller, Lei Wang, Mehmet Oguz Gok, Helin Hocaoglu, Shenlu Qin, Parul Gupta, Matthew H Sieber","doi":"10.1242/bio.061815","DOIUrl":"10.1242/bio.061815","url":null,"abstract":"As cells transition between periods of growth and quiescence, their metabolic demands change. During this transition, cells must coordinate changes in mitochondrial function with the induction of biosynthetic processes. Mitochondrial metabolism and nucleotide biosynthesis are key rate-limiting factors in regulating early growth. However, it remains unclear what coordinates these mechanisms in developmental systems. Here, we show that during quiescence, as mitochondrial activity drops, nucleotide breakdown increases. However, at fertilization, mitochondrial oxidative metabolism and nucleotide biosynthesis are coordinately activated to support early embryogenesis. We have found that the serine/threonine kinase GSK3 is a key factor in coordinating mitochondrial metabolism with nucleotide biosynthesis during transitions between quiescence and growth. Silencing GSK3 in quiescent oocytes causes increased levels of mitochondrial activity and a shift in the levels of several redox metabolites. Interestingly, silencing GSK3 in quiescent oocytes also leads to a precocious induction of nucleotide biosynthesis in quiescent oocytes. Taken together, these data indicate that GSK3 functions to suppress mitochondrial oxidative metabolism and prevent the premature onset of nucleotide biosynthesis in quiescent eggs. These data reveal a key mechanism that coordinates mitochondrial function and nucleotide synthesis with fertilization.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of silver and gold nanoparticles green synthesis by Artemisia annua hairy root extracts. 黄花蒿毛根提取物绿色合成银纳米粒子和金纳米粒子的比较。

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-19 DOI: 10.1242/bio.061739

Taisa Bohdanovych, Pavlo Kuzema, Viktor Anishchenko, Volodymyr Duplij, Maksym Kharchuk, Viktoriia Lyzhniuk, Anatolij Shakhovsky, Nadiia Matvieieva

{"title":"Comparison of silver and gold nanoparticles green synthesis by Artemisia annua hairy root extracts.","authors":"Taisa Bohdanovych, Pavlo Kuzema, Viktor Anishchenko, Volodymyr Duplij, Maksym Kharchuk, Viktoriia Lyzhniuk, Anatolij Shakhovsky, Nadiia Matvieieva","doi":"10.1242/bio.061739","DOIUrl":"10.1242/bio.061739","url":null,"abstract":"The green synthesis of metal nanoparticles (NPs) has garnered significant attention due to its simplicity, cost-effectiveness, and environmental sustainability. Gold NPs (AuNPs) and silver NPs (AgNPs) are widely employed across various industries, agriculture, and medicine owing to their unique physicochemical properties. This study explores the feasibility of synthesizing metal NPs through green methods using ethanolic (70%) extracts from Artemisia annua hairy roots. These extracts were found to contain reducing agents, primarily phenolic compounds, as identified by HPLC and MALDI-MS analyses. The phenolic compounds included hydroxybenzoic acids (e.g. p-coumaric and gallic acids) and hydroxycinnamic acids (e.g. caffeic acid and its derivatives such as chlorogenic, dicaffeoylquinic, and rosmarinic acids). The synthesis and structural characteristics of AuNPs and AgNPs were systematically compared. AgNPs formed a stable colloidal solution over extended periods, while AuNPs exhibited instability due to significant NP aggregation and precipitation. Furthermore, the photocatalytic activities of these NPs in the degradation of Methylene Blue were evaluated. AuNPs demonstrated substantial photocatalytic activity, whereas AgNPs exhibited negligible catalytic effects. This study highlights the potential and limitations of A. annua hairy root extracts in the biosynthesis of AuNPs and AgNPs, providing insights into their structural and functional differences.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Science under siege: protecting scientific progress in turbulent times.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-13 DOI: 10.1242/bio.061972

James Briscoe, Craig E Franklin, Daniel A Gorelick, E Elizabeth Patton, Michael Way

引用次数: 0

Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-20 DOI: 10.1242/bio.061901

Lorenzo Latini, Gioia Burini, Valeria Mazza, Giacomo Grignani, Riccardo De Donno, Eleonora Bello, Elena Tricarico, Stefano Malavasi, Giuseppe Nascetti, Daniele Canestrelli, Claudio Carere

{"title":"Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).","authors":"Lorenzo Latini, Gioia Burini, Valeria Mazza, Giacomo Grignani, Riccardo De Donno, Eleonora Bello, Elena Tricarico, Stefano Malavasi, Giuseppe Nascetti, Daniele Canestrelli, Claudio Carere","doi":"10.1242/bio.061901","DOIUrl":"10.1242/bio.061901","url":null,"abstract":"Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g. substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alveolar epithelial paxillin in postnatal lung alveolar development. 肺泡上皮 paxillin 在出生后肺泡发育过程中的作用

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-20 DOI: 10.1242/bio.061939

Mikaela Scheer, Priscilla Kyi, Tadanori Mammoto, Akiko Mammoto

引用次数: 0

Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-07 DOI: 10.1242/bio.061819

Carly Guiltinan, Ramon C Botigelli, Juliana I Candelaria, Justin M Smith, Rachel B Arcanjo, Anna C Denicol

{"title":"Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics.","authors":"Carly Guiltinan, Ramon C Botigelli, Juliana I Candelaria, Justin M Smith, Rachel B Arcanjo, Anna C Denicol","doi":"10.1242/bio.061819","DOIUrl":"10.1242/bio.061819","url":null,"abstract":"In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). Regardless of original blastocyst stage, bESC lines had a similar phenotype, including differentiation capacity, stable karyotype, and pluripotency marker expression over feeder-free transition and long-term culture. Transcriptome and functional analyses indicated that eBL- and BL-derived lines were in primed pluripotency. We additionally compared RNA-sequencing data from our lines to bovine embryos and stem cells from other recent reports, finding that base medium was the predominant source of variation among cell lines. In conclusion, our results show that indistinguishable bESC lines can be readily derived from eBL and BL, widening the pool of embryos available for bESC establishment. Finally, our investigation points to sources of variation in cell phenotype among recently reported bESC conditions, opening the door to future studies investigating the impact of factors aside from signaling molecules on ESC derivation, maintenance, and performance.","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11911636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Fast & Fair peer review: a bold experiment in scientific publishing.

IF 1.8 4区生物学

Biology Open Pub Date : 2025-03-15 Epub Date: 2025-03-25 DOI: 10.1242/bio.061982

Daniel A Gorelick, Alejandra Clark

引用次数: 0