Protist最新文献

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Protists and Society: A report on the 2024 autumn meeting of Protistology-UK, at the natural history museum, London 原生生物与社会：英国原生生物学2024年秋季会议报告，伦敦自然历史博物馆

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126072

David J.S. Montagnes

引用次数: 0

Integrative studies shed light on the pseudocryptic genus Crassohymena n. gen. (Protozoa, Ciliophora) 综合研究揭示了假隐属（原生动物，纤毛虫目）。

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126074

Atef Omar , Jiwon Jung , Gaeul Lee , Jae-Ho Jung

The morphology, morphogenesis, molecular phylogeny, and the resting cyst morphology of the freshwater ciliate, Crassohymena primicirrata (Berger and Foissner, 1987) n. gen., n. comb., found in samples collected from South Korea, were investigated. The Korean two populations observed are identical to each other and are highly similar to the type population showing only few and minor differences in the size and arrangement of cortical granules and the length of dorsal kinety 4. The new genus Crassohymena n. gen. is established and characterized by a number of morphological and ontogenetic features: the thick undulating membranes comprising three or four rows of kinetosomes and in Cyrtohymena pattern; the anteriorly distinctly displaced transverse cirri; the posteriorly set-off cirrus V/3; the opisthe's anlagen IV–VI originate from cirri IV/2, V/4, and V/3, respectively; the proter's anlagen IV–VI originate from cirrus IV/3; and the enormous anlage I in each daughter cell. Phylogenetic analyses based on 18S rRNA gene sequences show that Crassohymena primicirrata n. gen., n. comb. is separated from all other morphologically most similar taxa and forms an adelphotaxon to the clade containing sequences of the families Neokeronopsidae and Spirofilidae, and the two oxytrichid genera Australocirrus and Notohymena.

淡水纤毛虫Crassohymena primicirrata的形态、形态发生、分子系统发育和静息囊形态（Berger and Foissner, 1987） n. gen. n. comb。从韩国采集的样本中发现的。观察到的朝鲜两个种群彼此完全相同，与型种群高度相似，在皮质颗粒的大小和排列以及背部运动的长度上只有很少和微小的差异4。新属（Crassohymena n. geng .）被建立，并具有许多形态学和个体发生特征：由三或四行动体组成的厚波状膜和细胞膜模式；前面明显移位的横卷；后抵消卷云V/3；蛇的胶原IV- vi分别来源于cirri IV/2、V/4和V/3；蛋白原IV- vi源自IV/3型卷病毒；以及每个子细胞中巨大的细胞I。基于18S rRNA基因序列的系统发育分析表明，原膜虫属（Crassohymena primicirrata n. gen., n. comb.）；从所有其他形态上最相似的分类群中分离出来，形成了一个adelphotaxon，它的进化枝包含了Neokeronopsidae和Spirofilidae家族的序列，以及两个oxytrichid属australcirrus和Notohymena。

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引用次数: 0

Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina. 长读DNA测序揭示了早期分支甲藻Oxyrrhis marina线粒体基因组的组织结构。

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-11-22 DOI: 10.1016/j.protis.2024.126071

Ronie Haro , Nikita Walunjkar , Soham Jorapur , Claudio H. Slamovits

The mitochondrial genomes of dinoflagellate protists are remarkable for their highly fragmented and heterogeneous organization. Early attempts to determine their structure without ‘next-generation’ DNA sequencing failed to recover a defined genome. Still, it coincided in showing that the proteins coding genes, three in total, and parts of the ribosomal RNA genes were spread across a diffuse assortment of small linear fragments. In contrast, a recent study employed Illumina sequencing to assemble a 326 kbp long single-molecule, circular mitochondrial genome in the symbiotic dinoflagellate Breviolum minutum. Here, we used a combination of short- and long-read massively-parallel DNA sequencing to analyze further the mitochondrial DNA of the early-branching dinoflagellate Oxyrrhis marina. We found that the mitochondrial genome of O. marina consists of 3 linear chromosomes sized 15.9, 33.8 and 40.6 kbp for a total of 90.3 kbp. It contains the cox1, cox3 and cob genes, the same three proteins encoded in the mitochondrion of all myzozoans (Apicomplexa and Dinophyceae), some fragments of ribosomal RNA genes as well as many non-functional gene fragments and extensive noncoding DNA. Our analysis unveiled segments syntenic patterns and rearrangements encompassing coding and non-coding regions, suggesting that recombination is a pervasive process driving the evolution of these genomes.

甲藻原生动物的线粒体基因组因其高度分散和异质的组织结构而引人注目。在没有进行 "下一代 "DNA 测序的情况下，确定其结构的早期尝试未能恢复一个确定的基因组。尽管如此，它还是不约而同地显示，蛋白质编码基因（共三个）和部分核糖体 RNA 基因分布在各种小的线性片段中。与此相反，最近的一项研究利用 Illumina 测序技术在共生甲藻 Breviolum minutum 中组装了一个 326 kbp 长的单分子环形线粒体基因组。在这里，我们结合使用了短线程和长线程大规模平行DNA测序技术，进一步分析了早枝甲藻（Oxyrrhis marina）的线粒体DNA。我们发现，O. marina 的线粒体基因组由 3 条线性染色体组成，大小分别为 15.9、33.8 和 40.6 kbp，总计 90.3 kbp。基因组中包含 cox1、cox3 和 cob 基因，这三种蛋白在所有无脊椎动物（拟尾柱虫纲和鼎足目）的线粒体中都有编码，还包含一些核糖体 RNA 基因片段以及许多无功能基因片段和大量非编码 DNA。我们的分析揭示了包括编码区和非编码区的片段同源模式和重排，表明重组是推动这些基因组进化的一个普遍过程。

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引用次数: 0

Flagellar proteomic analysis of the brown alga Mutimo cylindricus revealed a novel calcium-binding protein abundantly localized in the anterior flagellum 褐藻 Mutimo cylindricus 的鞭毛蛋白质组分析发现了一种新型钙结合蛋白，该蛋白大量定位于前鞭毛中

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-10-26 DOI: 10.1016/j.protis.2024.126070

Nana Kinoshita-Terauchi , Kogiku Shiba , Makoto Terauchi , Hideki Noguchi , Kazuo Inaba

Mutimo cylindricus gametes have two flagella with different structures : an anterior and a posterior flagellum. Their flagellar waveforms are regulated by calcium ions through various mechanisms, however the factors involved in this regulation remain largely unknown To elucidate the molecular basis underlying the difference between the two flagella, we performed a flagellar proteomic analysis of male M. cylindricus gametes. We identified 848 proteins shared with Ectocarpus siliculosus, including 28 calcium-binding proteins. Among the EF-hand proteins, a 111 kDa protein showed predominant localization along the anterior flagellum. Immunogold localization suggested that this protein is associated with outer doublet microtubules. This is the first report to show heterogeneous localization of a calcium-binding protein between two flagellar axonemes and suggests that calcium-binding proteins are involved in the specific regulation of the anterior flagellum.

圆柱木配子有两种不同结构的鞭毛：前鞭毛和后鞭毛。为了阐明两种鞭毛差异的分子基础，我们对雄性圆筒木配子进行了鞭毛蛋白质组分析。我们发现了848个与硅外皮藻共有的蛋白质，其中包括28个钙结合蛋白。在EF-手蛋白中，一个111 kDa的蛋白主要沿前鞭毛定位。免疫金定位表明，该蛋白与外双微管有关。这是首次报道钙结合蛋白在两个鞭毛轴丝之间的异质性定位，表明钙结合蛋白参与了前鞭毛的特异性调控。

引用次数: 0

The protists of Ernst Haeckel’s Kunstformen der Natur 恩斯特-海克尔《自然形态学》中的原生生物

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-10-05 DOI: 10.1016/j.protis.2024.126069

John R. Dolan

Haeckel’s ’art book’, Kunstformen der Natur, is likely familiar to most protistologists as it is probably Haeckel’s best known work, and it prominently featured protists. No doubt many of us have used some of the images from it in our lectures. Most familiar are perhaps the often-reproduced images of nassularian radiolaria, but plates were also devoted to phaeodarians, acantharia, foraminifera, ciliates, diatoms, dinoflagellates and desmids. Despite the fame of Kunstformen der Natur, there are aspects of the work that have received little attention, and are of potential interest to protistologists. These include the overall importance of protists in the work, compared to other taxa, the surprisingly under appreciated role of Haeckel’s collaborator, Adolph Giltsch in creating the figures, the disputed fidelity of the illustrations of protists, and Haeckel’s discrete inclusion of many descriptions of new species of protists, forcing us to consider Kunstformen a scientific publication. Here these aspects, and the 20 plates featuring protists will be reviewed. The goal of this review is to familiarize protistologists with the most famous work featuring protists, and point out the many particular figures of protists we may wish to avoid showcasing, as the illustrations are questionable. A supplemental file is provided listing the currently accepted names of the protist taxa (for names found in a database), and the reasons for considering some illustrations as questionable.

大多数原生生物学家可能对海克尔的 "艺术书"《Kunstformen der Natur》并不陌生，因为这本书可能是海克尔最著名的作品，其中突出介绍了原生生物。毫无疑问，我们中的许多人都曾在讲座中使用过其中的一些图片。大家最熟悉的可能是经常被复制的纳氏放射虫的图片，但也有专门介绍辉石虫、棘皮动物、有孔虫、纤毛虫、硅藻、甲藻和脱壳虫的图版。尽管《Kunstformen der Natur》声名远播，但该作品的某些方面却鲜有人关注，而原生动物学家却可能对此感兴趣。这些方面包括：与其他类群相比，原生动物在该著作中的整体重要性；海克尔的合作者阿道夫-吉尔施（Adolph Giltsch）在绘制图像中发挥的作用出人意料地未得到充分重视；原生动物插图的真实性存在争议；海克尔单独纳入了许多原生动物新物种的描述，迫使我们将《Kunstformen》视为一份科学出版物。在此，我们将对这些方面以及 20 幅以原生动物为主题的图版进行回顾。这篇评论的目的是让原生生物学家熟悉这本以原生生物为主题的最著名作品，并指出我们可能希望避免展示的许多特定的原生生物形象，因为这些插图是有问题的。我们还提供了一份补充文件，列出了目前公认的原生生物类群名称（针对数据库中找到的名称），以及认为某些插图有问题的原因。

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引用次数: 0

Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans 利用单氮化丙啶（PMA）-定量 PCR 对原生生物的存活率进行死算；以周龄新巴拉米阿米巴为例进行研究

IF 1.9 3区生物学 Q4 MICROBIOLOGY

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

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.

区分有活力和无活力原生动物寄生虫的能力是改善人类和动物健康管理的核心。虽然概念上很简单，但在原位区分细胞活力的方法仍然具有挑战性。由周新巴拉米巴（Neoparamoeba perurans）引起的阿米巴鳃病是一种影响全球大西洋鲑水产养殖的寄生虫病。尽管商业淡水处理可减轻 AGD，但鳃上或使用过的处理水中仍残留着可存活的阿米巴。现有的基于 PCR 的检测方法能够量化 N. perurans 的数量，但无法区分阿米巴的存活率。我们研究了在实时 PCR 之前使用单氮化丙啶（PMA）来区分活细胞和死细胞的方法。我们证明，200 μM PMA 可显著降低未存活（异丙醇处理过的）培养阿米巴在至少三个对数的细胞浓度下的扩增。通过对有活力细胞和无活力细胞进行系列稀释，我们发现非 PMA PCR 可扩增有活力和无活力的变形虫，而 PMA 暴露可抑制（但不能完全抑制）无活力变形虫的扩增。使用 PMA-PCR 评估了淡水处理对 N. perurans 存活率的影响。暴露于 PMA 后，淡水处理变形虫的扩增率降低了约 94-97%。总之，这项研究表明，PMA 与传统的实时 PCR 相结合可以评估变形虫的存活率。

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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 Q4 MICROBIOLOGY

Protist

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

Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki

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.

自噬是一种细胞内降解机制，通过这种机制，细胞质物质被运送到溶酶体融合的自噬体（自溶酶体）中并在其中降解。内共生硅藻（即所谓的 "硅藻"）是真核生物光营养体通过内共生完全融入宿主控制的细胞器（即质体）的中间产物。开创性的研究系统地评估了宿主对内共生硅藻（ESD）中几种代谢途径的控制程度。然而，人们很少关注内共生生活方式对ESDs自噬的影响。在这项研究中，我们从Durinskia baltica和Kryptoperidinium foliaceum的RNA-seq数据中寻找了自噬体形成所需的ATG3、ATG4、ATG5、ATG7、ATG8、ATG10和ATG12。在系统进化分析中，我们在恐龙物种中发现了两组进化不同的 ATG 蛋白，一组与甲藻同源，另一组与硅藻同源。结果表明，被双鞭毛虫宿主吸收的硅藻后裔ATG蛋白持续用于自噬体的形成，并很可能用于自噬。

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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 Q4 MICROBIOLOGY

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 Q4 MICROBIOLOGY

Protist

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

Limin Jiang , Qianhui Sun , Xiaoxuan Zhu , Xiaozhong Hu

Prostomateans, as common inhabitants in diverse aquatic environments, are among the simplest ciliate lineages, and serve as trophic links in food webs. However, only a few members are well-known and thoroughly studied, and the diversity of this group remains elusive. The unique genus Plagiocampa has a long history of research, but few studies have been performed using up-to-date methods. In the present work, Plagiocampa longis Kahl, 1927 and Plagiocampa minima Kahl, 1927, collected from Chinese coastal habitats, were investigated based on microscopical observation, protargol staining, and SSU rRNA gene sequencing. Their ciliature and morphometric data as well as gene sequences are documented. Phylogenetic analyses revealed that the family Plagiocampidae is likely monophyletic and has a closer relationship with parasitic Cryptocaryon.

纤毛虫是各种水生环境中的常见居民，属于最简单的纤毛虫类群，是食物网中的营养环节。然而，只有少数成员为人所知并被深入研究，该类的多样性仍然难以捉摸。对独特的 Plagiocampa 属的研究由来已久，但采用最新方法进行的研究却寥寥无几。本研究通过显微镜观察、原色染色和 SSU rRNA 基因测序，对采集于中国沿海生境的 Plagiocampa longis Kahl, 1927 和 Plagiocampa minima Kahl, 1927 进行了研究。记录了它们的纤毛和形态数据以及基因序列。系统进化分析表明，栉水母科可能是单系的，与寄生隐杆线虫的关系更为密切。

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 Q4 MICROBIOLOGY

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

Iodamoeba is a single-celled intestinal parasite, which is common in humans in certain parts of the world, and also in pigs. For the first time, we provide DNA-based evidence of goat, dromedary, fallow deer, and donkey as hosts of Iodamoeba and show that Iodamoeba-specific nucleotide sequences from these four hosts do not appear to overlap with those of humans, unlike those from pigs. We moreover show that similar strains of Iodamoeba can be found in Madagascar, Western Sahara, and Ecuador and that intra-sample diversity is typically extensive across even small fragments of DNA in both human and non-human hosts.

碘阿米巴是一种单细胞肠道寄生虫，在世界某些地区常见于人类和猪。我们首次提供了山羊、单峰驼、矮鹿和驴作为碘阿米巴宿主的 DNA 证据，并表明这四种宿主的碘阿米巴特异性核苷酸序列似乎与人类的核苷酸序列并不重叠，这与猪的核苷酸序列不同。此外，我们还表明，在马达加斯加、西撒哈拉和厄瓜多尔也能发现类似的碘阿米巴菌株，而且在人类和非人类宿主中，即使是很小的 DNA 片段，样本内的多样性通常也很广泛。

引用次数: 0

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