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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu saleh a.al-Farraj Naomi A.Stover Feng Gao Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of ScienceKing Saud University Department of Biology Bradley University Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome a.alyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic a.alyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Phylogenetic position of three Condylostoma species (Protozoa, Ciliophora, Heterotrichea) inferred from the small subunit rRNA gene sequence

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Progress in Natural Science:Materials International 2008年第9期18卷 1089-1093页

作者： Khaled A.S.al-Rasheid saleh a.al-Farraj saleh a.al-Qurishy Zoology Department King Saud University Riyadh 11451 Saudi Arabia

The systematically poorly known ciliate genus Condylostoma was erected by Vincent in *** 10 morphotypes have been reported, but any molecular investigations concerning this group so far are *** this work, the small subunit ribosomal RNA (SS rRNA) gene of three marine Condylostoma species was sequenced, by which the phylogenetic trees were constructed by distance-matrix, maximum parsimony and Bayesian inference *** results show that (1) all the trees have similar topologies with high supports;(2) Condylostoma is mostly related to the genus Condylostentor;and (3) three Condylostoma species as well as Condylostentor auriculatus cluster together and form a sister group with other *** is moderately consistent with the assessment of phylo-genetic relationships of Condylostoma-related heterotrichs from the morphological *** phylogenetic relationship of some other related heterotrichs, Peritromus, Folliculina, Stentor and Blepharisma, has been also discussed.

关键词： Marine ciliates Condylostoma SS rRNA Phylogeny Heterotrichs

CO_(2)utilization in syngas conversion to dimethyl ether and aromatics:Roles and challenges of zeolites-based ca.alysts

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Journal of Energy Chemistry 2023年第4期79卷 418-449页

作者： ali a.al-Qadri Ga.al A.Nasser Haruna Adamu Oki Muraza Tawfik A.saleh Department of Chemical Engineering King Fahd University of Petroleum and MineralsDhahran 31261Saudi Arabia Interdisciplinary Research Center for Hydrogen and Energy Storage(IRC-HES) King Fahd University of Petroleum&MineralsDhahran 31261Saudi Arabia Department of Environmental Management Technology and Department of ChemistryAbubakar Tafawa Balewa UniversityBauchiNigeria Department of Chemistry King Fahd University of Petroleum and MineralsDhahran 31261Saudi Arabia

Several studies have proven a strong correlation between global warming and CO_(2)***,38 billion tons of CO_(2)are approximately emitted into the *** CO_(2)via chemical conversion to clean fuels and value-added aromatics can substantially contribute to controlling the *** the thermodynamic and environmental limitations of hydrogenation of CO_(2)alone to value-added aromatics and fuels,CO_(2)utilization has currently emerged as a promising and practical approach for the production of fuels and aromatics with simultaneous utilization of both CO and CO_(2)*** such,the approach is economically ***_(2)could be converted directly to fuels by the hydrogenation process or as a part of a syngas *** ether(DME)is a clean fuel with a higher energy density,which could be used as a substituent for several fuels such as *** the same vein,value-added aromatics such as benzene,toluene,and xylene(BTX)can be produced from a similar ***,we report a review that collects the most recent studies for the conversion of CO_(2)to DME and aromatics via zeolite-based bifunctional *** highlighted the main routes for producing DME and aromatics,as well as thoroughly discussed the conducted studies on CO_(2)hydrogenation and CO_(2)-rich syngas utilized as feedstock for conversion to DME and *** CO_(2)hydrogenation mostly occurs through the methanol-mediated reaction route but is most often limited by low selectivity and ca.alyst deactivation,particularly in the utilization of CO_(2)alone for the reduction *** review takes an overview of the progress made so far and concluded by identifying the roles and challenges of zeolite-based ca.alysts for CO_(2)utilization and conversion to DME and ***,despite the incredible growth the field received in the last couple of years,however,many research challenges and opportunities associated with this process are still abou

关键词： Clean fuel DME Aromatics Bifunctional ca.alyst CO_(2)mitigation

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Morphological and molecular examination of the ciliate family Lagynusidae(Protista,Ciliophora,Prostomatea)with descriptions of two new genera and two new species from China

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Marine Life Science & Technology 2023年第2期5卷 178-195页

作者： Limin Jiang Congcong Wang saleh a.al-Farraj Hunter N.Hines Xiaozhong Hu College of Fisheries and Key Laboratory of MaricultureMinistry of EducationOcean University of ChinaQingdao 266003China Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao 266003China Department of Zoology College of ScienceKing Saud UniversityRiyadh 11451Saudi Arabia Harbor Branch Oceanographic Institute Florida Atlantic UniversityFort PierceFL 34982USA

Ciliates in the class Prostomatea play an important role in the global microbial loop due to their signifcant abundances and broad feeding strategies at the foundation of food *** their importance in ecosystems,the taxonomy and systematics of this group of ciliates has long been poorly understood,with this being especially true for members of the family *** we examine four lagynusids collected from sandy beaches in China,using silver-staining and 18S rRNA gene sequencing *** investigations revealed two new genera and two new species and provided details for two little known forms:Penardella marina ***.,***.,Apolagynus cucumis(as reported by Penard.Études sur les infusoires d’eau *** and Cie,Genève,1922)***.,***.,Lagynus minutus ***.,and Lagynus elegans(Engelmann in Z Wiss Zool 11:347-393,1862)Quennerstedt(Acta Univ Lund 4:1-48,1867).Penardella *** be morphologically distinguished by having more than three dikinetidal perioral *** *** from the closely related genus Lagynus in the absence of a conspicuous neck-like *** ciliature of Apolagynus cucumis is revealed here for the frst time,which demonstrates the classifcation of this species within ***,Apolagynus binucleatus(Jiang et al.,2021)*** established according to the new *** results of our phylogenetic a.alyses based on the 18S rRNA gene support the establishment of two new genera and indicate that Lagynusidae is monophyletic,which further strengthens its valid taxonomic status.

关键词： Ciliate Morphology New genus New species Phylogeny 18S rRNA gene

Ontogenesis and systematic position of a new hypotrichous ciliate,Chaetospira sinica ***.,with an improved diagnosis of the poorly defined family Chaetospiridae Jankowski,1985(Protozoa,Ciliophora,Hypotrichia)

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Marine Life Science & Technology 2022年第4期4卷 513-526页

作者： Wenya Song Xiaotian Luo Yong Chi saleh a.al-Farraj Chen Shao Laboratory of Protozoological Biodiversity and Evolution in Wetland College of Life SciencesShaanxi Normal UniversityXi’an710119China Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao266003China Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of HydrobiologyChinese Academy of SciencesWuhan430072China Zoology Department College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia

Ciliates are unique single-celled organisms that play important roles in ecological,environmental,evolutionary,and ontogenetic *** the present study,phylogenetic a.alyses based on 18S rRNA gene sequence data reveal that Chaetospira sinica *** with Stichotricha aculeata with strong to full support(97%ML,1.00 BI),but is not closely related to members of Spirofilidae Gelei,1929 to which Chaetospira and Stichotricha have previously been *** a.alyses,together with morphological and morphogenetic data from Chaetospira sinica ***.,support the validity of family Chaetospiridae Jankowski,*** and Stichotricha are here assigned to the family Chaetospiridae,the improved diagnosis of which is as follows:non-dorsomarginalian Hypotrichia with flask-shaped body;oral region extending along narrow anterior neck region;lorica usually present;two ventral and two marginal cirral rows,all distinctly spiraled or obliquely curved;pretransverse and transverse cirri *** basic morphogenetic features in *** *** be summarized as:(1)the oral primordium for the opisthe develops de novo and the parental adoral zone is completely retained by the proter;(2)all ventral cirral anlagen and marginal anlagen developed intrakinetally;(3)three dorsal kineties anlagen formed intrakinetally in each daughter cell;and(4)macronuclear nodules fuse into a single *** cells were also isolated and their morphologic and molecular data are provided.

关键词： 18S rRNA gene Morphogenesis Phylogeny Spirofilidae-Stichotricha

Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical a.alyses of multiple molecular markers

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Chinese Journal of Oceanology and Limnology 2011年第1期29卷 96-102页

作者：胡晓燕胡晓钟 Khaled A.S.al-RASHEID saleh a.al-FARRAJ 宋微波 Laboratory of Protozoology Institute of Evolution and Marine BiodiversityOcean University of China Department of Zoology Natural History Museum Zoology Department King Saud University

The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and α-tubulin. a.alyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and α-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the α-tubulin a.alysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.

关键词： sporadotrichid ciliates phylogeny SSrRNA actin I alpha-tubulin amino acid sequences

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Applying Non-Local Means Filter on Seismic Exploration

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Computer Systems Science & Engineering 2022年第2期40卷 619-628页

作者： Mustafa Youldash saleh al-dossary Lama.alDaej Farah alOtaibi Asma.alDubaikil Noora.alBinali Maha.alGhamdi College of Computer Science and Information Technology Imam Abdulrahman Bin Faisal UniversityDammamP.O.1982Saudi Arabia Geophysical Application Division Exploration Application Services DepartmentSaudi AramcoDhahranSaudi Arabia

The seismic reflection method is one of the most important methods in geophysical *** are three stages in a seismic exploration survey:acquisition,processing,and *** paper focuses on a pre-processing tool,the Non-Local Means(NLM)filter algorithm,which is a powerful technique that can significantly suppress noise in seismic ***,the domain of the NLM algorithm is the whole dataset and 3D seismic data being very large,often exceeding one terabyte(TB),it is impossible to store all the data in Random Access Memory(RAM).Furthermore,the NLM filter would require a considerably long *** factors make a straightforward implementation of the NLM algorithm on real geophysical exploration data *** paper redesigned and implemented the NLM filter algorithm to fit the challenges of seismic *** optimized implementation of the NLM filter is capable of processing production-size seismic data on modern clusters and is 87 times faster than the straightforward implementation of NLM.

关键词： Seismic exploration pa.allel programming seismic processing optimizing methods

Molecular Phylogenetic Lineage of Plagiopogon and Askenasia(Protozoa, Ciliophora) Revealed by Their Gene Sequences

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Journal of Ocean University of China 2015年第4期14卷 724-730页

作者： LIU An YI Zhenzhen LIN Xiaofeng HU Xiaozhong saleh a.al-FARRAJ Khaled A.S.al-RASHEID Laboratory of Protozoology Institute of Evolution & Marine Biodiversity Ocean University of China Laboratory of Protozoology School of Life Science South China Normal University Zoology Department College of Science King Saud University

Prostomates and haptorians are two ba.al groups of ciliates with limited morphological characteristics available for tax- onomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene （hereafter SSU rDNA）, internal transcribed spacer region （ITS region）, and large subunit ribosomal RNA gene （LSU rDNA） were a.alyzed, 10 new sequences five species each. Our findings included 1） class Prostomatea and order Haptorida are multiphyletic; 2） it may not be appropriate to place order Cyclotriehiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3） genus Plagio- pogon branches consistently within a clade covering most prostomes and is ba.al of clade Colepidae, implying its close lineage to Prostomatea; and 4） Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.

关键词： Plagiopogon Askenasia multi-gene phylogeny SSU rDNA ITS region LSU rDNA

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Phylogeny of the anaerobic ciliate genus Sonderia(Protista:Ciliophora:Plagiopylea),including the description of three novel species and a brief revision of the genus

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Marine Life Science & Technology 2022年第4期4卷 493-512页

作者： Ran Li Wenbao Zhuang Xiaochen Feng saleh a.al-Farraj alan Warren Xiaozhong Hu College of Fisheries &Key Laboratory of MaricultureMinistry of EducationOcean University of ChinaQingdao266003China Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao266003China Zoology Department College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Department of Life Sciences Natural History MuseumLondonSW75BDUK

Anaerobic protists in general,and ciliates in particular,are important components of anoxic or hypoxic environments,however,their diversity remains *** is a poorly studied genus that is distributed worldwide and is commonly found in anaerobic *** the present study,the taxonomy and phylogeny of three new species,namely Sonderia aposinuata ***.,Sonderia paramacrochilus *** Sonderia steini ***.,collected from China,were investigated based on microscopic observations and SSU rRNA gene sequencing *** aposinuata *** diagnosed mainly by having a relatively large body size,a crescent-shaped oral opening,numerous slender extrusomes,one suture on the ventral side and two on the dorsal side,and a buccal cavity that occupies the anterior third of the *** paramacrochilus *** resembles *** but differs mainly by its oral opening being located closer to the anterior cell margin and its spindle-shaped *** steini *** a freshwater species that can be recognized by its shallow buccal cavity,sparsely distributed rod-shaped extrusomes,and having 68–79 monokinetidal somatic kineties that form sutures on both sides of the *** a.alyses based on small subunit ribosomal RNA(SSU rRNA)gene sequence data support the monophyly of the family Sonderiidae,however,Sonderia is *** genus Sonderia is briefly revised and a key to the identification of species belonging to this genus is supplied.

关键词： Anaerobic ciliates Ciliature New species SSU rRNA gene Taxonomy