Open Biology最新文献

A comprehensive toolkit for protein localization and functional analysis in trypanosomatids.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1098/rsob.240361

Athina Paterou, Julia Sáez Conde, Jiří Týč, Jack Daniel Sunter, Sue Vaughan, Keith Gull, Samuel Dean

{"title":"A comprehensive toolkit for protein localization and functional analysis in trypanosomatids.","authors":"Athina Paterou, Julia Sáez Conde, Jiří Týč, Jack Daniel Sunter, Sue Vaughan, Keith Gull, Samuel Dean","doi":"10.1098/rsob.240361","DOIUrl":"10.1098/rsob.240361","url":null,"abstract":"African trypanosomes are medically important parasites that cause sleeping sickness in humans and nagana in animals. In addition to their pathogenic role, they have emerged as valuable model organisms for studying fundamental biological processes. Protein tagging is a powerful tool for investigating protein localization and function. In a previous study, we developed two plasmids for rapid and reproducible polymerase chain reaction-based protein tagging in trypanosomes, which enabled the subcellular mapping of 89% of the trypanosome proteome. However, the limited selection of fluorescent protein tags and selectable markers restricted the flexibility of this approach. Here, we present an extended set of >100 plasmids that incorporate universal primer annealing sequences, enabling protein tagging with a range of fluorescent, biochemical and epitope tags, using five different selection markers. We evaluated the suitability of various fluorescent proteins for live and fixed cell imaging, fluorescent movies, and we demonstrate the use of tagging plasmids encoding tandem epitope tags to support expansion microscopy approaches. We show that this series of plasmids is functional in other trypanosomatid parasites, significantly increasing its value. Finally, we developed a new plasmid for tagging glycosylphosphatidylinositol-anchored proteins. We anticipate that this will be an important toolset for investigating trypanosomatid protein localization and function.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240361"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764463","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

Mild activation of the mitochondrial unfolded protein response increases lifespan without increasing resistance to stress. 线粒体未折叠蛋白反应的轻度激活会延长寿命，但不会增强对压力的抵抗力。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1098/rsob.240358

Alexa Di Pede, Bokang Ko, Abdelrahman AlOkda, Aura A Tamez González, Shusen Zhu, Jeremy M Van Raamsdonk

{"title":"Mild activation of the mitochondrial unfolded protein response increases lifespan without increasing resistance to stress.","authors":"Alexa Di Pede, Bokang Ko, Abdelrahman AlOkda, Aura A Tamez González, Shusen Zhu, Jeremy M Van Raamsdonk","doi":"10.1098/rsob.240358","DOIUrl":"10.1098/rsob.240358","url":null,"abstract":"The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway that responds to mitochondrial insults by altering gene expression to recover mitochondrial homeostasis. The mitoUPR is mediated by the stress-activated transcription factor ATFS-1 (activating transcription factor associated with stress 1). Constitutive activation of ATFS-1 increases resistance to exogenous stressors but paradoxically decreases lifespan. In this work, we determined the optimal levels of expression of activated ATFS-1 with respect to lifespan and resistance to stress by treating constitutively active atfs-1(et17) worms with different concentrations of RNA interference (RNAi) bacteria targeting atfs-1. We observed the maximum lifespan of atfs-1(et17) worms at full-strength atfs-1 RNAi, which was significantly longer than wild-type lifespan. Under the conditions of maximum lifespan, atfs-1(et17) worms did not show enhanced resistance to stress, suggesting a trade-off between stress resistance and longevity. The maximum resistance to stress in atfs-1(et17) worms occurred on empty vector. Under these conditions, atfs-1(et17) worms are short-lived. This indicates that constitutive activation of ATFS-1 can increase lifespan or enhance resistance to stress but not both, at the same time. Overall, these results demonstrate that constitutively active ATFS-1 can extend lifespan when expressed at low levels and that this lifespan extension is not dependent on the ability of ATFS-1 to enhance resistance to stress.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 4","pages":"240358"},"PeriodicalIF":4.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764467","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

Footprints in the Sno: investigating the cellular and molecular mechanisms of SNORD116.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-19 DOI: 10.1098/rsob.240371

Terri L Holmes, Alzbeta Chabronova, Chris Denning, Victoria James, Mandy J Peffers, James G W Smith

引用次数: 0

C-terminal glycosylation of type IX secretion system cargo proteins in Prevotella intermedia with both short and long secretion signals.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-26 DOI: 10.1098/rsob.240335

Xi Ye, Nabil Bin Rustam, Dhana Gorasia, Eric Reynolds, Debnath Ghosal, Paul Veith

{"title":"C-terminal glycosylation of type IX secretion system cargo proteins in Prevotella intermedia with both short and long secretion signals.","authors":"Xi Ye, Nabil Bin Rustam, Dhana Gorasia, Eric Reynolds, Debnath Ghosal, Paul Veith","doi":"10.1098/rsob.240335","DOIUrl":"10.1098/rsob.240335","url":null,"abstract":"Prevotella intermedia is a Gram-negative bacterium that is associated with periodontitis and acute necrotizing ulcerative gingivitis. P. intermedia utilizes the type IX secretion system (T9SS) to secrete and anchor virulence factors to the cell surface, presumably via C-terminal glycosylation. The identity of the linking sugar and the sites of modification on the cargo are unknown. Here, we employed hidden Markov models to predict cargo proteins in P. intermedia and conducted LC-MS/MS analyses of partially deglycosylated fractions to characterize the C-terminal glycosylation. A total of 80 cargo proteins were predicted based on the presence of a T9SS C-terminal domain (CTD) signal, and these were divided into 48 short CTDs and 32 long CTDs. Cleavage sites for five short and four long CTDs were experimentally determined, and glycosylation was observed at the mature C-terminus of six cargo. Two glycans were identified of delta masses 419.198 and 433.185 Da, corresponding to novel C-terminal amide linkages to N-alanyl dHex-HexNAc and N-alanyl (Me-dHex)-HexNAc, respectively. This indicated that both short and long CTDs supported cleavage and glycosylation. AlphaFold multimer modelling predicted that both kinds of CTDs could bind to the PorV shuttle protein in the same manner, with the conserved CTD motifs interacting with the same sites in PorV.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240335"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11969387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710681","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

Polycomb-mediated transgenerational epigenetic inheritance of Drosophila eye colour is independent of small RNAs.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-12 DOI: 10.1098/rsob.240298

Maximilian Fitz-James, Poppy Sparrow, Christopher Paton, Peter Sarkies

{"title":"Polycomb-mediated transgenerational epigenetic inheritance of Drosophila eye colour is independent of small RNAs.","authors":"Maximilian Fitz-James, Poppy Sparrow, Christopher Paton, Peter Sarkies","doi":"10.1098/rsob.240298","DOIUrl":"10.1098/rsob.240298","url":null,"abstract":"Transgenerational epigenetic inheritance (TEI) describes the process whereby distinct epigenetic states are transmitted between generations, resulting in heritable gene expression and phenotypic differences that are independent of DNA sequence variation. Chromatin modifications have been demonstrated to be important in TEI; however, the extent to which they require other signals to establish and maintain epigenetic states is still unclear. Here we investigate whether small non-coding RNAs contribute to different epigenetic states of the Fab2L transgene in Drosophila triggered by transient long-range chromosomal contacts, which requires Polycomb complex activity to deposit the H3K27me3 modification for long-term TEI. By analysing mutants deficient in small non-coding RNAs, high-throughput sequencing data, long-range chromosomal contacts and gene expression, we demonstrate that small non-coding RNAs do not contribute directly to initiation or maintenance of silencing. However, we uncover an indirect role for microRNA expression in transgene silencing through effects on the Polycomb group gene Pleiohomeotic. Additionally, we show that a commonly used marker gene, Stubble (Sb), affects Pleiohomeotic expression, which may be important in interpreting experiments assaying Polycomb function in Drosophila development. By ruling out a plausible candidate for TEI at the Fab2L transgene, our work highlights the variability in different modes of TEI across species.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240298"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605731","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

Simple, streamlined, cost-effective cDNA synthesis method from cell cultures.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-12 DOI: 10.1098/rsob.240226

Daniel Stránský, Monika Šteigerová, Markéta Kuklová, Veronika Hanzíková, Nikolina Canová, Jiří Novotný, Ladislav Šenolt, Ondřej Slanař

{"title":"Simple, streamlined, cost-effective cDNA synthesis method from cell cultures.","authors":"Daniel Stránský, Monika Šteigerová, Markéta Kuklová, Veronika Hanzíková, Nikolina Canová, Jiří Novotný, Ladislav Šenolt, Ondřej Slanař","doi":"10.1098/rsob.240226","DOIUrl":"10.1098/rsob.240226","url":null,"abstract":"Applications like drug development need simple and streamlined methods to process samples from 96-well cell culture plates for gene expression measurements. Unfortunately, current options are expensive for such processing. Therefore, our aim was to develop a method that would allow streamlined analysis of mRNA from 96-well cell culture plates while being relatively cheap and simple. We developed a method based on the qPCR 'Cells-to-cDNA' approach and validated it against commercially available kits using the same approach or spin columns-based RNA purification. For this purpose, we conducted a series of comparisons of gene expression from peripheral blood mononuclear cells, SK-HEP-1 and U-87 cell cultures in 96-well plates. Our final method involved lysing cells with 25-100 µl solution of 0.5% SDS, 10 mM DTT, 1 mg ml-1 proteinase K dissolved in water, 1 h incubation at 50°C, followed by proteinase K inactivation at 90°C for 5 min and lysate neutralization with 1 : 1 dilution by 20% Tween 20 solution. Reverse transcription and qPCR were carried out using standard methods. This method showed a mean reduction of Ct ± s.d. value by 2.4 ± 1.3 compared with the 'Cells-to-cDNA' kit and by 1.4 ± 0.5 compared with the RNA purification kit with lower variability.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240226"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605733","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

Genetic regulation and variation of fetal plasma metabolome in the context of sex, paternal breeds and variable fetal weight.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-05 DOI: 10.1098/rsob.240285

Siriluck Ponsuksili, Eduard Murani, Beate Fuchs, Christina E Galuska, Henry Reyer, Muhammad Arsalan Iqbal, Shuaichen Li, Michael Oster, Klaus Wimmers

{"title":"Genetic regulation and variation of fetal plasma metabolome in the context of sex, paternal breeds and variable fetal weight.","authors":"Siriluck Ponsuksili, Eduard Murani, Beate Fuchs, Christina E Galuska, Henry Reyer, Muhammad Arsalan Iqbal, Shuaichen Li, Michael Oster, Klaus Wimmers","doi":"10.1098/rsob.240285","DOIUrl":"https://doi.org/10.1098/rsob.240285","url":null,"abstract":"Metabolic processes in fetuses can significantly influence piglet weight at birth. Understanding the genetic determinants of systemic metabolism is crucial for uncovering how genetic and molecular pathways impact biological mechanisms, particularly during the fetal phase. We present data on 1112 plasma metabolites using untargeted ultra-high performance liquid chromatography-tandem mass spectrometry methods, of 260 backcross (BC) fetuses from two sires' breeds at 63 days post-conception. Eight chemical superclasses have been identified, with lipids accounting for the majority of metabolites. Genomic heritability (h²) was estimated for each metabolite, revealing that 50% had h² values below 0.2, with a higher average in the amino acid class compared with the lipid. We annotated 448 significant metabolite quantitative trait loci associated with 10 metabolites, primarily lipids, indicating strong genetic regulation. Additionally, metabolite associations with sex, fetal weight and sire's breed were explored, revealing significant associations for 354 metabolites. Fetal weight influenced the largest number of metabolites, particularly glycerophospholipids and sphingolipids, emphasizing the genetic and metabolic complexity underlying fetal development. These findings enhance our understanding of the genetic regulation of metabolite levels and their associations with key phenotypic traits in fetuses, providing insights into metabolic pathways, potential biomarkers and serving as a baseline dataset for metabolomics studies of fetuses.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240285"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-05 DOI: 10.1098/rsob.240242

Soumi Dutta, Lars Hering, Milena M Grollmann, Niklas Metzendorf, Vladimir Gross, Kazuharu Arakawa, Susanne Neupert, Monika Stengl, Friedrich W Herberg, Georg Mayer

{"title":"Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades.","authors":"Soumi Dutta, Lars Hering, Milena M Grollmann, Niklas Metzendorf, Vladimir Gross, Kazuharu Arakawa, Susanne Neupert, Monika Stengl, Friedrich W Herberg, Georg Mayer","doi":"10.1098/rsob.240242","DOIUrl":"10.1098/rsob.240242","url":null,"abstract":"Pigment-dispersing factors (PDFs) are neuropeptides that play key roles in controlling the circadian rhythms in various insects, whereas their function remains elusive in other protostomes including tardigrades (water bears). Here we show that the three PDFs of the tardigrade Hypsibius exemplaris are co-localized in two pairs of inner lobe cells in the brain, whereas only one PDF occurs in four additional cerebral and two extracerebral cells. The axons of the inner lobe cells pass through the contralateral brain hemisphere, descend to the ventral nerve cord and terminate in two pairs of potential release sites in the posteriormost trunk ganglion. Using in vitro assays, we demonstrate that all three PDFs and their deorphanized receptor (PDFR) are functional. Widespread localization of PDFR suggests that tardigrade PDFs may act as multifunctional hormones and neuromodulators that control major functions including light detection, neural processing, locomotion, feeding, digestion, osmoregulation, growth, embryonic development and oogenesis/reproduction.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240242"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557482","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

Limitations of sequence dissimilarity as a predictor of prokaryotic lineage. 序列异质性作为原核生物血统预测指标的局限性

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-19 DOI: 10.1098/rsob.240302

Alvar A Lavin, Juan Rivas-Santisteban

引用次数: 0

Schwann cells in regeneration and cancer: an epithelial-mesenchymal transition perspective.

IF 4.5 3区生物学

Open Biology Pub Date : 2025-03-01 Epub Date: 2025-03-05 DOI: 10.1098/rsob.240337

Francisco Gracia, Berta Sanchez-Laorden, Jose A Gomez-Sanchez

{"title":"Schwann cells in regeneration and cancer: an epithelial-mesenchymal transition perspective.","authors":"Francisco Gracia, Berta Sanchez-Laorden, Jose A Gomez-Sanchez","doi":"10.1098/rsob.240337","DOIUrl":"https://doi.org/10.1098/rsob.240337","url":null,"abstract":"In the peripheral nervous system, glial cells, known as Schwann cells (SCs), are responsible for supporting and maintaining nerves. One of the most important characteristics of SCs is their remarkable plasticity. In various injury contexts, SCs undergo a reprogramming process that generates specialized cells to promote tissue regeneration and repair. However, in pathological conditions, this same plasticity and regenerative potential can be hijacked. Different studies highlight the activation of the epithelial-mesenchymal transition (EMT) as a driver of SC phenotypic plasticity. Although SCs are not epithelial, their neural crest origin makes EMT activation crucial for their ability to adopt repair phenotypes, mirroring the plasticity observed during development. These adaptive processes are essential for regeneration. However, EMT activation in SCs-derived tumours enhances cancer progression and aggressiveness. Furthermore, in the tumour microenvironment (TME), SCs also acquire activated phenotypes that contribute to tumour migration and invasion by activating EMT in cancer cells. In this review, we will discuss how EMT impacts SC plasticity and function from development and tissue regeneration to pathological conditions, such as cancer.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 3","pages":"240337"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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