Detection and Quantification of Two Parasitic CiliatesBoveria labialisandBoveria subcylindrica(Ciliophora: Scuticociliatia) by Fluorescence in situ Hybridization

Re-discovery and novel contributions to morphology and multigene phylogeny of Protospirella mazurica (Raabe, 1968) Aescht, 2001 (Ciliophora: Pleuronematida), an obligate symbiont of the river nerite Theodoxus fluviatilis Linnaeus, 1758 (Mollusca: Gastropoda)

Although the river nerite Theodoxus fluviatilis (Gastropoda: Neritimorpha) has an exceptionally broad geographical and ecological distribution, it carries only four ciliate species: Hypocomella quatuor, Protospirella mazurica, Scyphidia sp., and Trichodina baltica. After more than a half-century gap, we re-discovered P. mazurica in a Danubian population of T. fluviatilis (haplotypes F31 and F34) and characterized it using an integrative morpho-molecular approach. Protospirella mazurica is distinguished by (i) a small, elongate-ellipsoidal to ovoidal body, (ii) a broadly ellipsoidal macronucleus accompanied by a single globular micronucleus, (iii) a subterminal contractile vacuole, (iv) about 24 somatic kineties, (v) thigmotactic ciliature composed of about 10 kineties shortened posteriorly to form a parenthetical system, and (vi) a long inverted J-shaped paroral membrane associated with three unequally long membranelles. According to the present phylogenetic analyses of two mitochondrial and three nuclear markers, P. mazurica robustly clusters within the order Pleuronematida (Oligohymenophorea: Scuticociliatia) along with other symbiotic members of the families Hemispeiridae and Thigmophryidae as well as free-living representatives of the paraphyletic family Cyclidiidae. In light of the present phylogenetic analyses, we consider the family Ancistridae to be a junior synonym of the family Hemispeiridae, which collates 14 genera in our classification framework.

FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates

Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.

Application of Fluorescence In Situ Hybridization Assisted by Fluorescence Microscope in Detection of Her2 Gene in Breast Cancer Patients

In order to study the important factors for evaluating the prognosis of breast cancer patients, a fluorescence microscopy-assisted fluorescence in situ hybridization technique was proposed. Compared with other detection techniques, fluorescence in situ hybridization (FISH) technology assisted by a fluorescence microscope has gradually gained favor in related fields due to its advantages of high detection specificity, high sensitivity, and strong experimental period. Combined with the basic overview of fluorescence microscopy and FISH technology, the advantages and application points of FISH technology assisted by fluorescence microscopy in the detection of the Her2 gene in breast cancer patients were studied and discussed. The results show that IHC can be used as the primary screening for HER2 gene status detection; IHC (2+) and IHC (3+) have false positives, which are related to chromosome 17 polysomy, so FISH should be done to confirm the diagnosis.

Study on Analysis of Several Molecular Identification Methods for Ciliates of Colpodea (Protista, Ciliophora)

The application of molecular techniques to accurately identify protozoan species can correct previous misidentifications based on traditional morphological identification. Colpodea ciliates have many toxicological and cytological applications, but their subtle morphological differences and small body size hinder species delineation. Herein, we used Cox I and β-tubulin genes, alongside fluorescence in situ hybridization (FISH), to evaluate each method in delineating Colpodea species. For this analysis, Colpoda harbinensis n. sp., C. reniformis, two populations of C. inflata, Colpoda compare grandis, and five populations of Paracolpoda steinii, from the soil in northeastern China, were used. We determined that (1) the Cox I gene was more suitable than the β-tubulin gene as a molecular marker for defining intra- and interspecific level relationships of Colpoda. (2) FISH probes designed for Colpoda sp., C. inflata, Colpoda compare grandis, and Paracolpoda steinii, provided rapid interspecific differentiation of Colpodea species. (3) Colpoda harbinensis n. sp. was established and mainly characterized by its size in vivo (approximately $80\times 60\mu \text{m}$ ), a reniform body in outline, one macronucleus, its spherical shape, a sometimes nonexistent micronucleus, 11–15 somatic kineties, and five or six postoral kineties. In conclusion, combining oligonucleotide probes, DNA barcoding, and morphology for the first time, we have greatly improved the delineation of Colpodea and confirmed that Cox I gene was a promising DNA barcoding marker for species of Colpodea, and FISH could provide useful morphological information as complementing traditional techniques such as silver carbonate.

Macroevolutionary analyses of ciliates associated with hosts support high diversification rates

Ciliophora is a phylum that is comprised of extremely diverse microorganisms with regard to their morphology and ecology. They may be found in various environments, as free-living organisms or associated with metazoans. Such associations range from relationships with low metabolic dependence such as epibiosis, to more intimate relationships such as mutualism and parasitism. We know that symbiotic relationships occur along the whole phylogeny of the group, however, little is known about their evolution. Theoretical studies show that there are two routes for the development of parasitism, yet few authors have investigated the evolution of these characteristics using molecular tools. In the present study, we inferred a wide dated molecular phylogeny, based on the 18S rDNA gene, for the entire Ciliophora phylum, mapped life habits throughout the evolutionary time, and evaluated whether symbiotic relationships were linked to the variation in diversification rates and to the mode of evolution of ciliates. Our results showed that the last common ancestor for Ciliophora was likely a free-living organism, and that parasitism is a recent adaptation in ciliates, emerging more than once and independently via two distinct routes: (i) a free-living ciliate evolved into a mutualistic organism and, later, into a parasitic organism, and (ii) a free-living ciliate evolved directly into a parasitic organism. Furthermore, we have found a significant increase in the diversification rate of parasitic and mutualistic ciliates compared with their free-living conspecifics. The evolutionary success in different lineages of symbiont ciliates may be associated with many factors including type and colonization placement on their host, as well as physical and physiological conditions made available by the hosts.