Lysosomal dysfunction and overload of nucleosides in thymidine phosphorylase deficiency of MNGIE.

Inherited deficiency of thymidine phosphorylase (TP), encoded by TYMP, leads to a rare disease with multiple mitochondrial DNA (mtDNA) abnormalities, mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). However, the impact of TP deficiency on lysosomes remains unclear, which are important for mitochondrial quality control and nucleic acid metabolism. Muscle biopsy tissue and skin fibroblasts from MNGIE patients, patients with m.3243 A > G mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) and healthy controls (HC) were collected to perform mitochondrial and lysosomal functional analyses. In addition to mtDNA abnormalities, compared to controls distinctively reduced expression of LAMP1 and increased mitochondrial content were detected in the muscle tissue of MNGIE patients. Skin fibroblasts from MNGIE patients showed decreased expression of LAMP2, lowered lysosomal acidity, reduced enzyme activity and impaired protein degradation ability. TYMP knockout or TP inhibition in cells can also induce the similar lysosomal dysfunction. Using lysosome immunoprecipitation (Lyso- IP), increased mitochondrial proteins, decreased vesicular proteins and V-ATPase enzymes, and accumulation of various nucleosides were detected in lysosomes with TP deficiency. Treatment of cells with high concentrations of dThd and dUrd also triggers lysosomal dysfunction and disruption of mitochondrial homeostasis. Therefore, the results provided evidence that TP deficiency leads to nucleoside accumulation in lysosomes and lysosomal dysfunction, revealing the widespread disruption of organelles underlying MNGIE.

Six2 Is a Coordinator of LiCl-Induced Cell Proliferation and Apoptosis.

The metanephric mesenchyme (MM) cells are a subset of kidney progenitor cells and play an essential role in mesenchymal-epithelial transition (MET), the key step of nephron generation. Six2, a biological marker related to Wnt signaling pathway, promotes the proliferation, inhibits the apoptosis and maintains the un-differentiation of MM cells. Besides, LiCl is an activator of Wnt signaling pathway. However, the role of LiCl in cellular regulation of MM cells remains unclear, and the relationship between LiCl and Six2 in this process is also little known. Here, we performed EdU assay and flow cytometry assay to, respectively, detect the proliferation and apoptosis of MM cells treated with LiCl of increasing dosages. In addition, reverse transcription-PCR (RT-PCR) and Western-blot were conducted to measure the expression of Six2 and some maker genes of Wnt and bone-morphogenetic-protein (BMP) signaling pathway. Furthermore, luciferase assay was also carried out to detect the transcriptional regulation of Six2. Then we found LiCl promoted MM cell proliferation at low-concentration (10, 20, 30, and 40 mM). The expression of Six2 was dose-dependently increased in low-concentration (10, 20, 30, and 40 mM) at both mRNA and protein level. In addition, both of cell proliferation and Six2 expression in MM cells declined when dosage reached high-concentration (50 mM). However, Six2 knock-down converted the proliferation reduction at 50 mM. Furthermore, Six2 deficiency increased the apoptosis of MM cells, compared with negative control cells at relative LiCl concentration. However, the abnormal rise of apoptosis at 30 mM of LiCl concentration implies that it might be the reduction of GSK3ß that increased cell apoptosis. Together, these demonstrate that LiCl can induce the proliferation and apoptosis of MM cells coordinating with Six2.

Splicing Factor PQBP1 Curtails BAX Expression to Promote Ovarian Cancer Progression.

Splicing factor polyglutamine binding protein-1 (PQBP1) is abundantly expressed in the central nervous system during development, and mutations in the gene cause intellectual disability. However, the roles of PQBP1 in cancer progression remain largely unknown. Here, it is shown that PQBP1 overexpression promotes tumor progression and indicates worse prognosis in ovarian cancer. Integrative analysis of spyCLIP-seq and RNA-seq data reveals that PQBP1 preferentially binds to exon regions and modulates exon skipping. Mechanistically, it is shown that PQBP1 regulates the splicing of genes related to the apoptotic signaling pathway, including BAX. PQBP1 promotes BAX exon 2 skipping to generate a truncated isoform that undergoes degradation by nonsense-mediated mRNA decay, thus making cancer cells resistant to apoptosis. In contrast, PQBP1 depletion or splice-switching antisense oligonucleotides promote exon 2 inclusion and thus increase BAX expression, leading to inhibition of tumor growth. Together, the results demonstrate an oncogenic role of PQBP1 in ovarian cancer and suggest that targeting the aberrant splicing mediated by PQBP1 has therapeutic potential in cancer treatment.

Morphology and phylogenies of two hypotrichous brackish-water ciliates from China, Neourostylopsis orientalis n. sp. and Protogastrostyla sterkii (Wallengren, 1900) n. comb., with establishment of a new genus Neourostylopsis n. gen. (Protista, Ciliophora, Hypotrichia).

This paper investigates the morphology, infraciliature and small-subunit (SSU) rRNA gene sequences of two hypotrichous ciliates, Neourostylopsis orientalis n. sp., and Protogastrostyla sterkii (Wallengren, 1900) n. comb. (basionym Gastrostyla sterkii), collected from coastal waters in southern China. Neourostylopsis orientalis n. sp. is diagnosed mainly by the arrangement of brownish cortical granules, the numbers of adoral membranelles and frontal and transverse cirri and the characteristics of its midventral cirral pairs. The SSU rRNA gene phylogeny strongly supports the establishment of the new genus Neourostylopsis n. gen., which is characterized mainly by the following features: frontal and transverse cirri clearly differentiated, buccal cirri present, two frontoterminal cirri, midventral complex composed of midventral pairs only and not exceeding the halfway point of the cell, more than one row of marginal cirri on each side which derive from individual anlagen within each parental row, caudal cirri lacking. Thus, two new combinations are required: Neourostylopsis songi (Lei et al., 2005) n. comb., and Neourostylopsis flavicana (Wang et al., 2011) n. comb. Additionally, improved diagnoses for both Metaurostylopsis and Apourostylopsis are supplied in this study. Protogastrostyla sterkii (Wallengren, 1900) n. comb. differs from the similar congener Protogastrostyla pulchra mainly in body shape, ratio of buccal field to body length in vivo and molecular data. Based on the present studies, we conclude that the estuarine population of P. pulchra collected by J. Gong and others [Gong et al., J Eukaryot Microbiol (2007) 54, 468-478] is a population of P. sterkii.

Distinctive metabolic remodeling in TYMP deficiency beyond mitochondrial dysfunction.

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in the TYMP gene, which encodes thymidine phosphorylase (TP). As a cytosolic metabolic enzyme, TP defects affect biological processes that are thought to not be limited to the abnormal replication of mitochondrial DNA. This study aimed to elucidate the characteristic metabolic alterations and associated homeostatic regulation caused by TYMP deficiency. The pathogenicity of novel TYMP variants was evaluated in terms of clinical features, genetic analysis, and structural instability. We analyzed plasma samples from three patients with MNGIE; three patients with m.3243A > G mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS); and four healthy controls (HC) using both targeted and untargeted metabolomics techniques. Transcriptomics analysis and bioenergetic studies were performed on skin fibroblasts from participants in these three groups. A TYMP overexpression experiment was conducted to rescue the observed changes. Compared with controls, specific alterations in nucleosides, bile acids, and steroid metabolites were identified in the plasma of MNGIE patients. Comparable mitochondrial dysfunction was present in fibroblasts from patients with TYMP deficiency and in those from patients with the m.3243A > G mutation. Distinctively decreased sterol regulatory element binding protein (SREBP) regulated cholesterol metabolism and fatty acid (FA) biosynthesis as well as reduced FA degradation were revealed in fibroblasts with TYMP deficiency. The restoration of thymidine phosphorylase activity rescued the observed changes in MNGIE fibroblasts. Our findings indicated that more widespread metabolic disturbance may be caused by TYMP deficiency in addition to mitochondrial dysfunction, which expands our knowledge of the biochemical outcome of TYMP deficiency. KEY MESSAGES: Distinct metabolic profiles in patients with TYMP deficiency compared to those with m.3243A > G mutation. TYMP deficiency leads to a global disruption of nucleoside metabolism. Cholesterol and fatty acid metabolism are inhibited in individuals with MNGIE. TYMP is functionally related to SREBP-regulated pathways. Potential metabolite biomarkers that could be valuable clinical tools to improve the diagnosis of MNGIE.

A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus.

Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.

Medical Education Systems in China: Development, Status, and Evaluation.

Since 1949, China has made many changes to develop its medical education system and now has a complex array of medical degrees. The current system comprises a 3-year junior college medical program, 5-year medical bachelor's degree program, "5 + 3" medical master's degree program, and 8-year medical doctoral degree program; these programs each provide a different path to earning a medical degree. The advantages and drawbacks of such complexity are open to discussion. Since the government set a strategic goal of "Healthy China" in 2019, it has sought to increase the training capacity of its medical education system to establish a high-quality health service system. This article reviews medical education reform in China, discusses the current medical education system, and presents evaluations of medical education programs based on assessments by 1,025 participants (medical students and doctors) recruited from 31 provinces of China. These assessments were compiled via a multicenter self-reported questionnaire administered July 1 to 5, 2021. Participants were training for a medical degree or practicing doctors trained in the 5-year program, "5 + 3" program, 8-year program, or "4 + 4" program. The authors assessed the medical education system to which each of the participants belong and their career stage and career satisfaction, and they requested that participants name the 3 most promising programs. The 8-year program ranked first in work satisfaction (7.92/10), education program satisfaction (7.78/10), and potential (1.91/2). Scores of the 5-year program and "5 + 3" programs were 7.25 and 7.17 for system satisfaction, respectively, and the "4 + 4" program (7.00/10) ranked the next highest. The innovations that have occurred in the Chinese medical education system have offered opportunities to meet the needs of more patients, but the lack of consistency has also posed challenges. Currently, Chinese medical education is becoming more uniform and standardized.

Immune and inflammation: related factor alterations as biomarkers for predicting prognosis and responsiveness to PD-1 monoclonal antibodies in cervical cancer.

PURPOSE: We aimed to elucidate the potential mechanisms of effective responsiveness to PD-1 monoclonal antibody and evaluate more reliable biomarkers to improve the ability to predict the populations of cervical cancer (CC) suitable for immunotherapy. METHODS: Peripheral blood samples of CC patients undergoing anti-PD-1 therapy were collected before and after treatment. Differentially expressed genes (DEGs) were analyzed between partial response (PR) and progressive disease (PD) patients. A novel prognostic inflammation and immune-related response gene (IRRG) model was constructed and its prognostic role, correlation with tumor immunity and tumor mutation were evaluated. RESULTS: DEGs in PR patient after treatment could predict the response to PD-1 monoclonal antibodies. Among PR-specific pathways, tumor immunity, leukocyte migration, and cytokine activities were prominently enriched. Additionally, an IRRG signature comprising CTLA4, AZU1, C5, LAT, CXCL2, GDF7, MPL, PPARG and CELA1 was established and validated to predict the prognosis of CC with great accuracy and specificity. This signature could reflect the tumor microenvironment (TME) and tumor mutational burden (TMB). We also found stimulated adaptive immunity and downregulated inflammation at baseline in patients with sensitive responses to PD-1 monoclonal antibody. CONCLUSION: We developed an IRRG signature and verified that it was an independent prognostic factor for predicting survival and could reflect a sensitive response to PD-1 monoclonal antibody, which plays a nonnegligible role in the TME of CC. Further investigations are warranted to confirm that patients with stimulated adaptive immunity and downregulated inflammation at baseline could achieve a better survival benefit from PD-1 monoclonal antibody.

Environmental impact and recovery of the Bohai Sea following the 2011 oil spill.

The 2011 spill at platforms B and C of the Penglai 19-3 oil field in the Bohai Sea has been the worst oil spill accident in China. To assess long-term effects, a comprehensive monitoring program of chemical and biological variables (within a 2.2 km radius of the spill site) was conducted five years after the spill. Comparison of nutrient, Chl-a and oil concentrations in seawater, TOC, PAHs, heavy metals concentrations within the sediments, and the abundance and biomass of macrobenthic organisms to values obtained before and after the oil spill in previous studies indicate habitat recovery has occurred within the Bohai Sea following the episodic oil release. Observed elevated oil concentration in the water column and higher concentrations of two heavy metals, five PAHs, TOC, TOC/TN and lower values of δ13C, together with a reduction in macrobenthic biomass in near-field samples, suggest the influence of contaminants from chronic releases of oil and operational waste discharges within the vicinity of the oil platforms.

Effect of Tumor Size on Long-Term Survival After Resection for Solitary Intrahepatic Cholangiocarcinoma.

BACKGROUND: The relationship between tumor size and survival in intrahepatic cholangiocarcinoma (ICC) is still controversial. This study aimed to evaluate the prognostic ability of tumor size for solitary ICC after resection and explore optimal cut-off values in different subgroups. METHODS: Patients with solitary ICC who underwent liver resection from the Surveillance, Epidemiology, and End Results Program and Shandong Provincial Hospital were retrospectively analyzed. Kaplan-Meier and Cox regression analysis were used to assess the prognostic ability of tumor size. The log-rank test was used to determine the optimal cut-off values, and a minimum P was regarded as the optimal one in different subgroups. RESULTS: Large tumor size groups had worse overall survival (OS) than small tumor size groups. Cox regression analysis suggested that tumor size was an independent prognostic factor for OS for solitary ICC after resection. Subgroup analysis showed tumor size was associated with OS for both solitary ICC with and without vascular invasion (VI). Furthermore, the optimal cut-off values for solitary ICC with and without VI were found to be 8 and 3 cm, respectively, which could divide the patients into two groups with significant differences in OS. CONCLUSION: Tumor size was an independent prognostic factor for solitary ICC after resection. The existing American Joint Committee on Cancer (AJCC) staging system could be improved if the cut-off value of the T1 stage was changed to 8 cm and if the T2 stage incorporated a tumor size with a cut-off value of 3 cm. Further studies with more cases are needed to validate these findings.

Diagnostic and Prognostic Values of MANF Expression in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, and its prognosis is still poor. Mesencephalic astrocyte-derived neurotrophic factor (MANF) plays a key role in endoplasmic reticulum stress. ER stress plays a key role in HCC carcinogenesis. To confirm the clinical and prognostic value of MANF in HCC, we investigated the expression level of MANF in HCC as recorded in databases, and the results were verified by experiment. Survival analysis was probed by the Kaplan-Meier method. Cox regression models were used to ascertain the prognostic value of MANF in HCC tissue microarray. The diagnostic value of MANF in HCC was evaluated by receiver operating characteristic curve analysis. Potential correlation between MANF and selected genes was also analyzed. Results showed that MANF was overexpressed in HCC. Patients with high MANF expression levels had a worse prognosis and higher risk of tumor recurrence. Furthermore, the expression level of MANF had good diagnostic power. Correlation analysis revealed potential regulatory networks of MANF in HCC, laying a foundation for further study of the role of MANF in tumorigenesis. In conclusion, MANF was overexpressed in HCC and related to the occurrence and development of HCC. It is a potential diagnostic and prognostic indicator of HCC.

Mesencephalic Astrocyte-Derived Neurotrophic Factor, a Prognostic Factor of Cholangiocarcinoma, Affects Sorafenib Sensitivity of Cholangiocarcinoma Cells by Deteriorating ER Stress.

PURPOSE: Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignant tumor characterized by high malignancy and poor prognosis. Although the efficacy of sorafenib against cholangiocarcinoma cell lines has been demonstrated in vivo and in vitro, limited clinical data are available on the efficacy of sorafenib in patients with cholangiocarcinoma. Sorafenib can enhance endoplasmic reticulum (ER) stress-mediated apoptosis, and ER stress and unfolded protein response are also the mechanisms by which cancer cells resist drug therapy. Mesencephalic astrocyte-derived neurotrophic factor (MANF), initially identified as a neurotrophic factor, can be regulated by ER stress activation. There are no available studies on the diagnostic value and therapeutic significance of MANF in ICC. Hence, the purpose of this study was to evaluate the role of MANF in cholangiocarcinoma, investigating the possibility of whether sorafenib could become a reliable strategy for cholangiocarcinoma therapy. METHODS: In this study, the expression level of MANF in ICC patients was investigated by bioinformatic analysis and the results were verified by tissue microarray assay. Cholangiocarcinoma cell lines were also used to determine how MANF regulates the therapeutic effect of sorafenib and to identify the underlying mechanisms. RESULTS: The results showed that MANF was correlated with poor prognosis and MANF knockdown could facilitate sorafenib-mediated apoptosis and increase the sensitivity of sorafenib treatment by activating excessive ER stress. CONCLUSION: MANF is a prognostic marker of cholangiocarcinoma. MANF knockdown increases sorafenib-mediated ER stress and apoptosis in the cholangiocarcinoma cell lines. This mechanism may lead to a new therapeutic strategy in cholangiocarcinoma.

Clinicopathological characteristics and surgical outcomes of sarcomatoid hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is the sixth most common type of cancer and the fourth leading cause of cancer-related death worldwide. Sarcomatoid HCC, which contains poorly differentiated carcinomatous and sarcomatous components, is a rare histological subtype of HCC that differs from conventional HCC. It is highly aggressive and has a poor prognosis. Its clinicopathological characteristics, surgical outcomes and underlying mechanisms of its highly aggressive nature have not been fully elucidated. AIM: To examine the clinicopathological characteristics and surgical outcomes of sarcomatoid HCC and explore the histogenesis of sarcomatoid HCC. METHODS: In total, 196 patients [41 sarcomatoid HCC and 155 high-grade (Edmondson-Steiner grade III or IV) HCC] who underwent surgical resection between 2007 and 2017 were retrospectively reviewed. The characteristics and surgical outcomes of sarcomatoid HCC were compared with those of patients with high-grade HCC. The histological composition of invasive and metastatic sarcomatoid HCCs was evaluated. RESULTS: Sarcomatoid HCC was more frequently diagnosed at an advanced stage with a larger tumor and higher rates of nonspecific symptom, adjacent organ invasion and lymph node metastasis than high-grade HCC (all P < 0.05). Compared with high-grade HCC patients, sarcomatoid HCC patients are less likely to have typical dynamic imaging features of HCC (44.4% vs 72.7%, P = 0.001) and elevated serum alpha-fetoprotein levels (> 20 ng/mL; 36.6% vs 78.7%, P < 0.001). The sarcomatoid group had a significantly shorter median recurrence-free survival (5.6 mo vs 16.4 mo, log-rank P < 0.0001) and overall survival (10.5 mo vs 48.1 mo, log-rank P < 0.0001) than the high-grade group. After controlling for confounding factors, the sarcomatoid subtype was identified as an independent predictor of poor prognosis. Pathological analyses indicated that invasive and metastatic lesions were mainly composed of carcinomatous components. CONCLUSION: Sarcomatoid HCC was associated with a more advanced stage, atypical dynamic imaging, lower serum alpha-fetoprotein levels and a worse prognosis. The highly aggressive nature of sarcomatoid HCC is perhaps mediated by carcinomatous components.

Temporal and spatial variations and impact factors of nutrients in Bohai Bay, China.

The temporal and spatial distributions of dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP), and dissolved silicate (DSi), and their long-term changes were investigated in Bohai Bay (BHB) in spring, summer, and autumn (2013-2014). The high DIN values were consistently distributed in the western inshore waters, mainly determined by terrestrial factors, e.g., riverine input, while DIP and DSi were mostly distributed in the southern coastal waters, the central BHB, or near the sea port Caofeidian in northern BHB, largely related to non-terrestrial factors, e.g., sediment release. Based on the nutrient distribution, BHB could be partitioned into western and eastern parts, with -15 m depth as the separation. The long-term variations of nutrients since 2000 showed an increase in DIN and decreases in DIP and DSi. Relatively slow changes in DIN and DIP and a rapid decrease in DSi were exhibited in summer, which was associated with precipitation and sediment release.

Efficacy and safety of laparoscopic splenectomy and esophagogastric devascularization for portal hypertension: A single-center experience.

Many patients in China have portal hypertension secondary to liver cirrhosis. Splenectomy and devascularization have become an efficacious surgical procedure for portal hypertension, and has been recommended in China as the first choice for the treatment of portal hypertension for a long time. As a result of advances in laparoscopic equipment and techniques, splenectomy and esophagogastric devascularization have been carried out with laparoscope.From January 2012 to December 2017, 453 patients who were diagnosed with portal hypertension and serious gastroesophageal varices received surgical management in our institution. 250 patients chose laparoscopic splenectomy and esophagogastric devascularization and 203 underwent open splenectomy and esophagogastric devascularization.We retrospectively analyzed the perioperative data and follow-up data of these patients. The operation time of laparoscopic group was longer than open group (P ≤ .001). Intraoperative blood loss was less (P ≤ .001), the passing of flatus was earlier (P = .042), and postoperative hospital stay was shorter (P = .001) in the laparoscopic group. During postoperative follow-up of 4 to 75 months, the incidence of esophagogastric variceal rebleeding, encephalopathy, and secondary liver cancer showed no significant differences.Laparoscopic splenectomy and esophagogastric devascularization were safe and more effective than open surgery for portal hypertension and gastroesophageal varices.

Variations and evolution of polyubiquitin genes from ciliates.

Polyubiquitin genes from seven ciliate species were amplified, cloned and sequenced. It is estimated that Strombidium sulcatum, Euplotes vannus, E. rariseta and Anteholosticha manca have a polyubiquitin gene of 3 repeats, and A. parawarreni, Paramecium caudatum and Pseudokeronopsis flava 4 repeats. The newly obtained ubiquitins mostly differ from that of humans by 1-5 residues in amino acid sequences. A neighbor-joining tree constructed based on monomeric ubiquitin genes supports the monophyly of an assemblage comprising the litostomateans and some oligohymenophoreans, but not the class Spirotrichea. The monomers from the same species are generally placed together and highly supported for the class Litostomatea, the genera Paramecium and Ichthyophthirius, but not for other species. The non-synonymous/synonymous rate ratio (dN/dS) at the protein level are less than 1, and the synonymous nucleotide differences per synonymous site (p(S)) from intraspecific comparisons are fairly high (0.02-0.72). These results indicate that ciliates have not only the conserved, but also some quite divergent, polyubiquitin genes and confirm that the polyubiquitin genes in ciliates evolve according to the birth-and-death mode of evolution under strong purifying selection.

Extremely high copy numbers and polymorphisms of the rDNA operon estimated from single cell analysis of oligotrich and peritrich ciliates.

The copy number and sequence variation of the ribosomal DNA (rDNA) operon are of functional significance in evolution and ecology of organisms. However, the relationship between copy number and sequence variation of rDNA in protists has been rarely studied. Here we quantified rDNA copy numbers of oligotrich and peritrich ciliate species using single-cell quantitative PCR. We also examined the rDNA sequence variation by using single-cell PCR, cloning, and sequencing of multiple clones. We found that the rDNA copy numbers per cell were extremely high and different among even congeners, with the highest record of about 310,000. There was substantial intraindividual haplotype diversity and nucleotide diversity for the rDNA markers, with sequence differences primarily characterized by single nucleotide polymorphisms. Haplotype and nucleotide diversity was positively correlated to the rDNA copy number. Our findings provide evidence that: (1) ciliates generally have much higher rDNA copy numbers than other protists and fungi, which could lead to overestimation of the relative abundance of ciliates in environmental samples when rDNA sequence-based methodologies are used; and that (2) the rDNA might not always evolve in a strictly concerted manner in ciliates, which may raise problems in rDNA-based inference of species richness and phylogeny.

Revealing the diversity and quantity of peritrich ciliates in environmental samples using specific primer-based PCR and quantitative PCR.

Peritrichs are a diverse, ecologically important ciliate group usually with a complex life cycle. To date, the community of the peritrichs has been investigated by using morphology-based methods such as living observation and silver staining. Here we show a molecular approach for characterizing the diversity and quantity of free-living peritrichs in environmental samples. We newly designed four peritrich-specific primers targeting 18S rRNA genes that allow clone library construction, screening and analysis. A quantitative real-time PCR (qPCR) assay was developed to quantify peritrichs in environmental samples by using rDNA copy number as an indicator. DNA extracted from four water samples of contrasting environmental gradients was analysed. The results showed that the peritrich community was differentiated among these samples, and that the diversity decreased with the increase of water salinity. The qPCR results are consistent with the library sequence analysis in terms of quantity variations from sample to sample. The development of peritrich-specific primers, for the first time, for conventional PCR and qPCR assays, provides useful molecular tools for revealing the diversity and quantity of peritrich ciliates in environmental samples. Also, our study illustrates the potential of these molecular tools to ecological studies of other ciliate groups in diverse environments.