From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms

One of the most diverse clades of ciliated protozoa,the class Spirotrichea,displays a series of unique characters in terms of eukaryotic macronuclear(MAC)genome,including high fragmentation that produces nanochromosomes.However,the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood.In this study,we assemble the MAC genome of a representative euplotid(a new model organism in Spirotrichea)species,Euplotes aediculatus.Our results indicate that:(a)the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb,and contains 13,145 complete nanochromosomes and 43,194 predicted genes,with the majority of these nanochromosomes containing tiny introns and harboring only one gene;(b)genomic comparisons between E.aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecifc variation,and chromosome breaking sites(CBSs)might be lost during evolution,resulting in the increase of multi-gene nanochromosome;(c)gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E.aediculatus,suggesting their potential roles in environment adaptation and survival strategies of E.aediculatus;and(d)a programmed ribosomal frameshift(PRF)with a conservative motif 5′-AAATAR-3′tends to occur in longer genes with more exons,and PRF genes play an important role in many cellular regulation processes.

近年来出现的几类新概念动物疫苗

动物疫病流行广泛、传播迅速,严重危害养殖业的发展。疫苗接种是预防和控制动物传染病最有效的策略之一。目前,随着生物技术的发展和疫病防控的需要,安全、高效、广谱、用量少、具有标记特征的新型疫苗成为研发重点。文中就近年来出现的黏膜疫苗、长效与速效疫苗、嵌合疫苗、纳米颗粒疫苗等新概念动物疫苗的发展、应用及优缺点进行了评述,并提出了其发展方向,以期为动物疫苗的研发提供借鉴。

钢纤维形状对高性能混凝土性能的影响

试验研究了6种长径比较小且直径较粗的钢纤维(SF)(短直形、长直线形、圆弧形、闭合三角形、闭合矩形、闭合圆环形)对高性能混凝土性能的影响。通过改变SF体积分数从而改变其形成的环域个数和面积,探究二者对混凝土流动性、抗拉及抗折强度的影响,并通过研究破坏界面分析混凝土破坏形式和机制。结果表明:闭合区域个数及纤维的环域面积对混凝土流动起主要影响;闭合SF中圆环形SF对混凝土抗折及抗压强度的提升效果优于其他形状的闭合SF。短直形SF与圆环形SF混杂试验中,圆环形SF体积分数为1vol%、短直形SF体积分数为0.5vol%时,SF/混凝土抗压强度和抗折强度提升的综合效果最佳。

A paradox： rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata(Protista, Ciliophora)

Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains(i.e. cryptic species). Three main results are:(i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata;(ii) in contrast, the germlinelimited regions are highly divergent in sequence and length among the cryptic species;(iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.

New contributions to the phylogeny of the ciliate class Heterotrichea(Protista,Ciliophora):analyses at family-genus level and new evolutionary hypotheses

Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology,regenerative biology,and toxicology.In the present study,we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea.The main results include:(1)96 new ribosomal DNA sequences from 36 populations,representing eight families and 13 genera,including three poorly annotated genera,Folliculinopsis,Ampullofolliculina and Linostomella;(2)the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree,but the family Peritromidae probably represents the basal lineage based on its possession of many"primitive"morphological characters;(3)some findings in molecular trees are not supported by morphological evidence,such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close;(4)the systematic positions of Condylostomatidae,Climacostomidae,and Gruberiidae remain uncertain based either on morphological or molecular data;and(5)the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees,except for Blepharisma in the SSU r DNA tree and Folliculina in the ITS1-5.8 S-ITS2 tree.

Integrative studies on the taxonomy and molecular phylogeny of four new Pleuronema species(Protozoa,Ciliophora,Scuticociliatia)

The ciliate genus Pleuronema comprises approximately 30 nominal species and has been reported in freshwater,brackish water,and marine habitats.Nevertheless,recent studies have indicated that there might be a large undiscovered species diversity.In the present work,four new Pleuronema species,namely P.foissneri sp.nov.,P.parasmalli sp.nov.,P.parasalmastra sp.nov.,and P.paraorientale sp.nov.,collected from Shenzhen,southern China,was investigated using taxonomic methods.The diagnosis,description,comparisons with morphologically related species and detailed morphometric data are supplied for each.The small subunit ribosomal RNA(SSU rRNA)gene of the four new species is sequenced and their molecular phylogeny is analyzed.The SSU rRNA gene tree shows that Pleuronema is polyphyletic comprising several separate clades.All four new species cluster consistently with P.orientale KF206429,P.puytoraci KF840520 and P.setigerum FJ848874 within the core Pleuronematidae+Peniculistomatidae clade.Phylogenies of Pleuronematidae-related taxa are also discussed.

CD1d^(hi)CD5^(+)B cells differentiate into antibody-secreting cells under the stimulation with calreticulin fragment

Calreticulin(CRT)is a multifunctional molecule in both intracellular and extracellular environment.We have previ-ously found that a recombinant CRT fragment(rCRT/39-272)could modulate T cell-mediated immunity in mice via activation and expansion of CD1dhiCD5+B cells as well as induction of CRT-specifi c regulatory antibodies.Anti-body secreting cells(ASCs)are terminally differentiated B cells responsible for producing antibodies to participate in positive immune response as well as immune regula-tion.In this study,we demonstrate that rCRT/39-272 dif-ferentiates murine CD1dhiCD5+B cells into ASCs mark-ed by increased expression of plasma cell-associated transcription factors and production of polyreactive antibodies against DNA and CRT in vitro.Intraperitoneal administration of rCRT/39-272 augmented differentiation of CD1dhiCD5+B cells into ASCs in naïve mice or mice with experimental autoimmune encephalomyelitis.Thus,we propose that ASC differentiation and subsequent an-tibody production of CD1dhiCD5+B cells are key steps in CRT-mediated immunoregulation on infl ammatory T cell responses.

Immune Checkpoint Inhibitor-induced Immune-mediated Hepatitis in A Lung Cancer Patient Undergoing Long-term Immunotherapy:A Case Report

Immune-mediated hepatitis(IMH)induced by immune checkpoint inhibitors(ICIs)is an immune-related adverse event(irAE).IMH usually occurs 8-12 weeks after the first dose of ICI therapy.We report an unusual case of a lung cancer patient who developed IMH 2 years after initial ICI treatment and relapsed during corticosteroid therapy.A 55-year-old male with stageⅣB lung cancer received ICIs(for over 2 years)and chemotherapy as a second-line therapy.Grade 4 IMH occurred 2 years after initial immunotherapy and was diagnosed as hepatitis via laboratory and imaging tests with the simultaneous exclusion of other causes.The patient responded well to the corticosteroids;however,he decided to discontinue treatment prematurely,meaning that the total treatment period was less than 4 weeks.This led to IMH reoccurrence and the need to readminister corticosteroids at a higher dose than before.Ultimately,the patient's IMH was controlled and did not reoccur.This case illustrates that immune-related toxicity needs to be monitored in patients undergoing long-term ICI therapy.Improving patient education is also essential for the management and treatment of irAEs.

A new hypotrich ciliate,Oxytricha xianica sp.nov.,with notes on the morphology and phylogeny of a Chinese population of Oxytricha auripunctata Blatterer&Foissner,1988(Ciliophora,Oxytrichidae)

The morphology and infraciliature of the new hypotrichous ciliate,Oxytricha xianica sp.nov.,and a Chinese population of Oxytricha auripunctata Blatterer&Foissner,1988,are investigated using live observation and protargol staining.Oxytricha xianica sp.nov.is defined by the body size 85-130µm×30-50µm in vivo,the typical oxytrichid 18 frontoventral-transverse cirri,cortical granules absent,undulating membranes reduced or absent,three caudal cirri,dorsal kineties in Oxytricha pattern,and two ellipsoidal macronuclear nodules.The Chinese population of O.auripunctata differs slightly from other populations in the arrangement and color of cortical granules and position of anterior end of dorsal kinety 4.Phylogenetic analyses based on SSU-rDNA sequences support the assertion that O.auripunctata belongs to Oxytricha and Oxytrichidae.