IF 1.9 3区生物学

Protist Pub Date : 2024-09-24 DOI: 10.1016/j.protis.2024.126068

James W. Wynne , Anca G. Rusu , Ben T. Maynard , Megan L. Rigby , Richard S. Taylor

{"title":"Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans","authors":"James W. Wynne , Anca G. Rusu , Ben T. Maynard , Megan L. Rigby , Richard S. Taylor","doi":"10.1016/j.protis.2024.126068","DOIUrl":"10.1016/j.protis.2024.126068","url":null,"abstract":"<div><div>The ability to distinguish between viable and non-viable protozoan parasites is central to improved human and animal health management. While conceptually simple, methods to differentiate cell viability in situ remain challenging. Amoebic gill disease, caused by Neoparamoeba perurans is a parasitic disease impacting Atlantic salmon aquaculture globally. Although commercial freshwater treatments alleviate AGD, viable amoebae remain on gills or in used treatment water. Existing PCR-based assays are able to quantify N. perurans abundance but cannot discriminate amoeba viability. We investigated the use of propidium monoazide (PMA) application, prior to real-time PCR, to distinguish between alive and dead cells. We demonstrate that 200 μM PMA can significantly reduce amplification from non-viable (isopropanol treated) cultured amoebae across at least three logs of cell concentrations. Using a serial dilution of viable and non-viable cells, we show that non-PMA PCR amplifies both viable and non-viable amoebae, while PMA exposure suppresses (but does not completely inhibit) amplification from non-viable amoebae. The effect of freshwater treatment on N. perurans viability was assessed using the PMA-PCR. Following PMA exposure, amplification from freshwater treated amoebae was reduced by approximately 94–97 %. Taken together this study demonstrates that PMA combined with traditional real-time PCR can estimate amoeba viability.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126068"},"PeriodicalIF":1.9,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142326407","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

Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems 恐龙在进化过程中拥有两种不同的自噬相关泛素类连接系统

IF 1.9 3区生物学

Protist Pub Date : 2024-09-21 DOI: 10.1016/j.protis.2024.126067

Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki

{"title":"Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems","authors":"Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki","doi":"10.1016/j.protis.2024.126067","DOIUrl":"10.1016/j.protis.2024.126067","url":null,"abstract":"<div><div>Autophagy is an intracellular degradation mechanism by which cytoplasmic materials are delivered to and degraded in the lysosome-fused autophagosome (autolysosome) and proposed to have been established at an early stage of eukaryotic evolution. Dinoflagellates harboring endosymbiotic diatoms (so-called “dinotoms”), which retain their own nuclei and mitochondria in addition to plastids, have been investigated as an intermediate toward the full integration of a eukaryotic phototroph into the host-controlled organelle (i.e., plastid) through endosymbiosis. Pioneering studies systematically evaluated the degree of host governance on several metabolic pathways in the endosymbiotic diatoms (ESDs). However, little attention has been paid to the impact of the endosymbiotic lifestyle on the autophagy operated in the ESDs. In this study, we searched for ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, and ATG12, which are required for autophagosome formation, in the RNA-seq data from dinotoms Durinskia baltica and Kryptoperidinium foliaceum. We detected two evolutionally distinct sets of the ATG proteins in the dinotom species, one affiliated with the dinoflagellate homologs and the other with the diatom homologs in phylogenetic analyses. The results suggest that the ATG proteins descended from the diatom taken up by the dinoflagellate host persist for autophagosome formation and, most likely, autophagy.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126067"},"PeriodicalIF":1.9,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142323616","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

Basic biology, ecology, and biotechnology of euglenids 八目鳗的基础生物学、生态学和生物技术

IF 1.9 3区生物学

Protist Pub Date : 2024-09-12 DOI: 10.1016/j.protis.2024.126066

Michael L. Ginger Guest Editor, Anna Karnkowska Guest Editor, Vladimír Hampl Guest Editor, Scott C. Farrow Guest Editor

引用次数: 0

Taxonomy and molecular phylogeny of genus Plagiocampa (Ciliophora, Prostomatea), with redescriptions of two poorly known species 纤毛虫属（Plagiocampa）的分类和分子系统发育，以及两个鲜为人知物种的重新描述

IF 1.9 3区生物学

Protist Pub Date : 2024-08-18 DOI: 10.1016/j.protis.2024.126059

Limin Jiang , Qianhui Sun , Xiaoxuan Zhu , Xiaozhong Hu

引用次数: 0

On the host specificity and genetic diversity of Iodamoeba bütschlii: Observations from short amplicon-based next-generation sequencing 关于 Bütschlii 碘阿米巴的宿主特异性和遗传多样性：基于短扩增片段的新一代测序观察结果

IF 1.9 3区生物学

Protist Pub Date : 2024-07-26 DOI: 10.1016/j.protis.2024.126058

Asma Guilane , Meriem Ali Zouaoui , Maria Trelis , Amina Boutellis , Christen Rune Stensvold

引用次数: 0

Dinoflagellate chloroplasts as a model for extreme genome reduction and fragmentation in organelles – The COCOA principle for gene retention 将甲藻叶绿体作为细胞器中基因组极度减少和破碎的模型--基因保留的 COCOA 原理

IF 1.9 3区生物学

Protist Pub Date : 2024-06-14 DOI: 10.1016/j.protis.2024.126048

Christopher J. Howe , Adrian C. Barbrook

{"title":"Dinoflagellate chloroplasts as a model for extreme genome reduction and fragmentation in organelles – The COCOA principle for gene retention","authors":"Christopher J. Howe , Adrian C. Barbrook","doi":"10.1016/j.protis.2024.126048","DOIUrl":"10.1016/j.protis.2024.126048","url":null,"abstract":"<div>The genomes of peridinin-containing dinoflagellate chloroplasts have a very unusual organisation. These genomes are highly fragmented and greatly reduced, with most of the usual complement of chloroplast genes relocated to the nucleus. Dinoflagellate chloroplasts highlight evolutionary changes that are found to varying extents in a number of other organelle genomes. These include the chloroplast genome of the green alga Boodlea and other Cladophorales, and the mitochondrial genomes of blood-sucking and chewing lice, the parasitic plant Rhopalocnemis phalloides, the red alga Rhodosorus marinus and other members of the Stylonematophyceae, diplonemid flagellates, and some Cnidaria. Consideration of the coding content of the remnant chloroplast genomes indicates that organelles may preferentially retain genes for proteins important in initiating assembly of complexes, and the same is largely true for mitochondria. We propose a new principle, of CO-location for COntrol of Assembly (COCOA), indicating the importance of retaining these genes in the organelle. This adds to, but does not invalidate, the existing hypotheses of the multisubunit completion principle, CO-location for Redox Regulation (CORR) and Control by Epistasy of Synthesis (CES).</div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 4","pages":"Article 126048"},"PeriodicalIF":1.9,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1434461024000403/pdfft?md5=18f463c69c8a8b489f34662fe907cefa&pid=1-s2.0-S1434461024000403-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141410457","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

New geographical records and molecular investigation of the ciliate Spirostomum 纤毛虫 Spirostomum 的新地理记录和分子研究。

IF 1.9 3区生物学

Protist Pub Date : 2024-05-31 DOI: 10.1016/j.protis.2024.126047

Sheng-Bo Zhou, Zhi-Yu Zhao, Ping Guan, Bo Qu

{"title":"New geographical records and molecular investigation of the ciliate Spirostomum","authors":"Sheng-Bo Zhou, Zhi-Yu Zhao, Ping Guan, Bo Qu","doi":"10.1016/j.protis.2024.126047","DOIUrl":"10.1016/j.protis.2024.126047","url":null,"abstract":"<div>Spirostomum is a genus of large ciliates, and its species are distributed worldwide. However, there has been limited research conducted on their geographical distribution and genomics. We obtained nine samples of ciliates from eight regions in Liaoning Province, China, and conducted a study on their geographical distribution and characteristics. Morphological and second-generation high-throughput sequencing methods were applied to identify the species, and a phylogenetic tree was established to gain a deeper understanding of the geographical distribution and evolutionary relationships of Spirostomum in Northeast China. The results identified Spirostomum yagiui and Spirostomum subtilis as a newly recorded species in Northeast China region. There are now five species of Spirostomum that have been recorded in China, and new details on the genomic characteristics of Spirostomum yagiui were provided. In addition, this study also identified the main branches of Spirostomum teres and Spirostomum minus in northern China, and provided a theoretical basis for the existence of hidden species. Spirostomum yagiui is the first species in the family Spirostomidae to have undergone mitochondrial genome sequencing.</div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 4","pages":"Article 126047"},"PeriodicalIF":1.9,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535140","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

Checklist of colourless euglenoids of the Czech Republic, with several taxonomic additions 捷克共和国无色曙红虫核对表及若干分类补充

IF 2.5 3区生物学

Protist Pub Date : 2024-05-25 DOI: 10.1016/j.protis.2024.126045

Jaroslav Kubín , Josef Juráň , Jan Kučera

{"title":"Checklist of colourless euglenoids of the Czech Republic, with several taxonomic additions","authors":"Jaroslav Kubín , Josef Juráň , Jan Kučera","doi":"10.1016/j.protis.2024.126045","DOIUrl":"https://doi.org/10.1016/j.protis.2024.126045","url":null,"abstract":"<div>This study presents the results of a complex survey of freshwater heterotrophic euglenoids in the Czech Republic, including both literature data and own field surveys of 469 sites visited in the course of three years. The checklist includes 189 taxa in 28 genera: Anisonema (10), Astasia (26), Atraktomonas (1), Calycimonas (2), Chasmostoma (1), Dinematomonas (3), Distigma (8), Dylakosoma (1), Entosiphon (4), Euglena (1), Gyropaigne (1), Heteronema (19), Jenningsia (11), Khawkinea (1), Lepocinclis (1), Menoidium (7), Neometanema (3), Notosolenus (18), Petalomonas (40), Phacus (1), Ploeotia (2), Pseudoperanema (7), Rhabdomonas (5), Scytomonas (1), Sphenomonas (5), Teloprocta (1) Tropidocyphus (1), Urceolus (4), and 4 species of uncertain identity. In addition, a general description of habitat types in which the taxa were found and a review of the current taxonomy and nomenclature of included taxa are provided. Several taxonomic and nomenclatural novelties are proposed, based on the review of morphological features, mostly applying to the genera Notosolenus and Jenningsia.</div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 4","pages":"Article 126045"},"PeriodicalIF":2.5,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292229","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

Nannostelium ampullaceum gen. et sp. nov., a tiny new member of the protosteloid amoeba of the Cavosteliida (Variosea, Amoebozoa) Nannostelium ampullaceum gen.

IF 2.5 3区生物学

Protist Pub Date : 2024-05-25 DOI: 10.1016/j.protis.2024.126046

Yoshiaki Iwamoto, Takeshi Nakayama

引用次数: 0

The biomolecules of Euglena gracilis: Harnessing biology for natural solutions to future problems 褐飞虱的生物大分子：利用生物学自然解决未来问题

IF 2.5 3区生物学

Protist Pub Date : 2024-05-23 DOI: 10.1016/j.protis.2024.126044

S. Bedard , E. Roxborough , E. O’Neill , V. Mangal

{"title":"The biomolecules of Euglena gracilis: Harnessing biology for natural solutions to future problems","authors":"S. Bedard , E. Roxborough , E. O’Neill , V. Mangal","doi":"10.1016/j.protis.2024.126044","DOIUrl":"10.1016/j.protis.2024.126044","url":null,"abstract":"<div>Over the past decade, the autotrophic and heterotrophic protist Euglena gracilis (E. gracilis) has gained popularity across the studies of environmental science, biosynthesis experiments, and nutritional substitutes. The unique physiology and versatile metabolism of E. gracilis have been a recent topic of interest to many researchers who continue to understand the complexity and possibilities of using E. gracilis biomolecule production. In this review, we present a comprehensive representation of recent literature outlining the various uses of biomolecules derived from E. gracilis across the fields of natural product biosynthesis, as a nutritional substitute, and as bioremediation tools. In addition, we highlight effective strategies for altering metabolite production using abiotic stressors and growth conditions. To better understand metabolite biosynthesis and its role in E. gracilis, integrated studies involving genomics, metabolomics, and proteomics should be considered. Together, we show how the ongoing advancements in E. gracilis related research continue to broaden applications in the biosynthetic sector and highlight future works that would strengthen our understanding of overall Euglena metabolism.</div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 4","pages":"Article 126044"},"PeriodicalIF":2.5,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1434461024000361/pdfft?md5=944edaf9331dedf9ead23841c8994821&pid=1-s2.0-S1434461024000361-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141145738","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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