An automated imaging system for radiation biodosimetry.

We describe here an automated imaging system developed at the Center for High Throughput Minimally Invasive Radiation Biodosimetry. The imaging system is built around a fast, sensitive sCMOS camera and rapid switchable LED light source. It features complete automation of all the steps of the imaging process and contains built-in feedback loops to ensure proper operation. The imaging system is intended as a back end to the RABiT-a robotic platform for radiation biodosimetry. It is intended to automate image acquisition and analysis for four biodosimetry assays for which we have developed automated protocols: The Cytokinesis Blocked Micronucleus assay, the γ-H2AX assay, the Dicentric assay (using PNA or FISH probes) and the RABiT-BAND assay.

From molecules to morphology: cellular organization of Tetrahymena thermophila.

Tetrahymena thermophila is both a cell and an organism, which combines great intracellular complexity with a remarkable accessibility to investigation using many different approaches. In this review, we start with a description of the elaborate cortical organization of the Tetrahymena cell, and then proceed inward to consider the mitochondria and then the nuclei. For each of these cellular organelles and organelle-systems, first we familiarize the reader with its location in the cell and its structure and ultrastructure, and then we analyze the molecular mechanisms associated with organelle assembly, function, and subdivision. This analysis includes a molecular inventory of the organelle or organelle system, as well as a review of the consequences of modification, disruption or overexpression of important molecular components of each structure or system. Relevant comparisons to results obtained with other well-studied organisms, from Paramecium to Homo sapiens, are also included. Our goal is to provide investigators, in particular those who are new to this organism, both the background and the motivation to work with this model system and achieve further insight into its organization and dynamics.

Tetrahymena in the laboratory: strain resources, methods for culture, maintenance, and storage.

The ciliated protozoan Tetrahymena thermophila has been an important model system for biological research for many years. During that time, a variety of useful strains, including highly inbred stocks, a collection of diverse mutant strains, and wild cultivars from a variety of geographical locations have been identified. In addition, thanks to the efforts of many different laboratories, optimal conditions for growth, maintenance, and storage of Tetrahymena have been worked out. To facilitate the efficient use of Tetrahymena, especially by those new to the system, this chapter presents a brief description of many available Tetrahymena strains and lists possible resources for obtaining viable cultures of T. thermophila and other Tetrahymena species. Descriptions of commonly used media, methods for cell culture and maintenance, and protocols for short- and long-term storage are also presented.

Tetrahymena thermophila genetics: concepts and applications.

The differentiation of germline and somatic genomes in Tetrahymena thermophila results in two independent systems of genetic transmission. One is the conserved, sexual Mendelian genetics system of the germline genome. The other is a random genetic assortment mechanism, which operates in the somatic genome during asexual propagation. This chapter describes both systems, their interplay, and how they are exploited to construct useful biological reagents and powerful tools, which can be used to answer a variety of experimental questions.

Evolution of germline-limited sequences in two populations of the ciliate Chilodonella uncinata.

Ciliates are microbial eukaryotes that separate their nuclear functions into a germline micronucleus and a somatic macronucleus. During development of the macronucleus the genome undergoes a series of reorganization events that includes the precise excision of intervening DNA. Here, we determine the architecture of four loci in the micronuclear and macronuclear genomes of the ciliate Chilodonella uncinata and compare the levels of variation in micronuclear-limited sequences to macronuclear destined sequences at two of these loci. We find that within a population, germline-limited sequences are evolving at the same rate as other putatively neutral sites, but between populations germline-limited sequences are accumulating mutations at a much faster rate than other sites. We also find evidence of macronuclear recombination and incomplete elimination of intervening DNA, which result in increased diversity in the macronuclear genome. Our results support the assertion that the unusual genomic features of ciliates can result in rapid and unpredicted patterns of diversification.

Micronucleus in cervical intraepithelial lesions and carcinoma.

AIMS AND OBJECTIVES: To score and compare micronucleus (MN) in the whole spectrum of cervical lesions including normal, inflammatory, abnormal squamous cell of undetermined significance (ASC-US), low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL) and invasive cancer (IC) and to evaluate the role of MN as a biomarker in different pre-neoplastic and neoplastic lesions. MATERIALS AND METHODS: A total of 224 slides, comprised of normal (40), inflammatory (40), ASC-US (30), LSIL (38), HSIL (30) and IC (46), were studied. All the cases of HSIL, IC and ASC-US had histopathology. The LSIL, normal and inflammatory smears were again reviewed by 2 experienced cytopathologists independently. Two observers separately and independently counted the number of micronucleated cells per 1,000 of epithelial cells in oil immersion magnification (×100 objective) which was expressed as MN score per 1,000 cells. RESULTS: The mean MN scores±SD in normal, inflammatory, ASC-US, LSIL, HSIL and IC cases of cervical lesions were 1.02±1.59, 0.4250±0.71208, 2.87±2.21, 4.7368±5.62179, 21.30±17.18 and 18.50±9.54, respectively. MN scores of IC and HSIL were significantly high compared to the normal (p<0.000), the inflammatory (p<0.000), the ASC-US (p<0.000) and to the LSIL (p<0.000) group (analysis of variance test). LSIL showed significant difference with the normal (p=0.043), the inflammatory (p=0.019), the HSIL (p<0.000) and the IC (p<0.000) group but not with the ASC-US (p=0.342) group. CONCLUSIONS: MN scoring on the epithelial cells of cervix could be used as a biomarker in cancer screening. This is an easy, simple, reliable, reproducible and objective test which can be performed on routinely stained smears.

Micronuclear and macronuclear forms of beta-tubulin genes in the ciliate Chilodonella uncinata reveal insights into genome processing and protein evolution.

Chilodonella uncinata, like all ciliates, contains two distinct nuclei in every cell: a germline micronucleus and a somatic macronucleus. During development of the macronucleus from a zygotic nucleus, the genome is processed in several ways, including elimination of internal sequences. In this study, we analyze micronuclear and macronuclear copies of beta-tubulin in C. uncinata and find at least four divergent paralogs of beta-tubulin in the macronucleus. We characterize the micronuclear version of one paralog and compare its internally eliminated sequences (IESs) with previously described IESs in this species. These comparisons reveal the presence of a conserved sequence motif within IESs. In addition, we compare the sequences of beta-tubulin from C. uncinata with other ciliates and to other alveolates in order to test the hypothesis that the mode of molecular evolution in ciliates obscures phylogenetic signal in protein-coding genes. We find that heterogeneous rates of substitution in beta-tubulin across ciliates result in unstable genealogies that are inconsistent with phylogenies based on small subunit rDNA genes and on ultrastructure. We discuss the implications of our findings for genome processing and protein evolution in ciliates.

Differentiation of chromatin during DNA elimination in Euplotes crassus.

In Euplotes crassus, most of the micronuclear genome is eliminated during formation of a transcriptionally active macronucleus. To understand how this is mediated throughout the genome, we have examined the chromatin structure of the macronucleus-destined sequences and Tec transposons, which are dispersed in 15,000 copies in the micronuclear genome and completely eliminated during formation of the macronuclear genome. Whereas the macronucleus-destined sequences show a typical pattern of nucleosomal repeats in micrococcal nuclease digests, the Tec element chromatin structure digests to a nucleosome-like repeat pattern that is not typical: the minimum digestion products are approximately 300-600 base pairs, or "subnucleosomal," in size. In addition, the excised, circular forms of the Tec elements are exceedingly resistant to nucleases. Nevertheless, an underlying nucleosomal structure of the Tec elements can be demonstrated from the size differences between repeats in partial micrococcal nuclease digests and by trypsin treatment of nuclei, which results in mononucleosome-sized products. Characterization of the most micrococcal nuclease-resistant DNA indicates that micronuclear telomeres are organized into a chromatin structure with digestion properties identical to those of the Tec elements in the developing macronucleus. Thus, these major repetitive sequence components of the micronuclear genome differ in their chromatin structure from the macronuclear-destined sequences during DNA elimination. The potential role of developmental stage-specific histone variants in this chromatin differentiation is discussed.

Pdd1p, a novel chromodomain-containing protein, links heterochromatin assembly and DNA elimination in Tetrahymena.

During Tetrahymena conjugation, programmed DNA degradation occurs in two separate nuclei. Thousands of germline-specific deletion elements are removed from the genome of the developing somatic macronucleus, and the old parental macronucleus is degraded by an apoptotic mechanism. An abundant polypeptide, Pdd1p (formerly p65), localizes to both of these nuclei at the time of DNA degradation. Here we report that, in developing macronuclei, Pdd1p localizes to electron-dense, heterochromatic structures that contain germline-specific deletion elements. Pdd1p also associates with parental macronuclei during terminal stages of apoptosis. Sequencing of the PDD1 gene reveals it to be a member of the chromodomain family, suggesting a molecular link between heterochromatin assembly and programmed DNA degradation.

Gamma-tubulin is permanently associated with basal bodies in ciliates.

Ciliates are of special interest owing to the multiplicity and diversity of their microtubule organizing centers (MTOCs). The subcellular localization of gamma-tubulin in these protozoa has not been extensively studied. The cloning of a gamma-tubulin gene in Euplotes (Liang, A., K. Heckmann, Gene 136, 319-322 (1993) led us to examine the localization of this protein. We used three polyclonal antibodies, JH46, R58 and R70. They had been raised against peptides common to mammalian and Aspergillus gamma-tubulins. These regions had 69%, 95%, and 75% identity with the corresponding regions of Euplotes gamma-tubulin. Immunoblotting (R70) revealed a polypeptide corresponding to the molecular mass of Euplotes gamma-tubulin. In Euplotes octocarinatus, gamma-tubulin was detected by immunofluorescence (R70) in the basal bodies, the micronucleus and the macronucleus throughout the cell cycle. The presence of gamma-tubulin in basal bodies and micronuclei was confirmed with the other two antibodies JH46 and R58. The permanent association of gamma-tubulin with basal bodies was also observed in Tetrahymena thermophila and Paramecium tetraurelia, two ciliates distantly related to Euplotes. These results not only extend to ciliates the finding that gamma-tubulin is permanently associated with ciliary basal bodies, but also demonstrate that gamma-tubulin is present in unconventional MTOCs.

[A cytophotometric study of the amount of DNA in the macro- and micronuclei of the infusorian Nyctotherus cordiformis from the gut of tadpoles and juveniles of the common frog]. / Tsitofotometricheskoe issledovanie kolichestva DNK v makro- i mikronukleusakh infuzorii Nyctotherus cordiformis iz kishechnika golovastikov i segoletok travianoi liagushki.

The investigations of DNA amounts in the nuclei of the ciliate Nyctotherus cordiformis was continued. The measured ciliates were collected from guts of tadpoles and the most small frogs just from the water. The DNA content was measured (in arbitrary units--a.u.) in the nuclei of cysts, precysts, vegetative ciliates and small frogs. This paper is the second part of the investigation. The first part dealt with DNA amounts of the nuclei of the vegetative ciliates tested in spring, autumn and winter. The amount of the Feulgen-DNA complex was measured with a two-wave microcytophotometer MCFU-1. The average content of the DNA ranged from 1.7 +/- 2 a.u. in the Mi of cysts to 2.6 +/- 0.1 a.u. in the Mi of the youngest frogs. The DNA content of the Ma ranged from 275 +/- 21 a.u. in cysts to 479 +/- 25 a.u. in vegetative ciliates. The DNA content in presynthetic Mi (G1) is supposed to be approximately 1.3 and approximately 2.6 a.u. in postsynthetic (G2) Mi. Using nuclei of erythrocytes of Rana temporaria as internal standard, the DNA content of a 2 c Mi from tadpoles of N. cordiformis is supposed to amount to 0.57 pg or approximately 350 gDa. The DNA amount in Ma of N. cordiformis is at average 140-220 times as that of Mi.

Linker histones are not essential and affect chromatin condensation in vivo.

We have (separately) disrupted all of the expressed macronuclear copies of the HHO gene encoding macronuclear histone H1 and of the micronuclear linker histone (MLH) gene encoding the protein MicLH in Tetrahymena thermophila. These disruptions are shown to eliminate completely the expression of each protein. Strains without either linker histone grow at normal rates and reach near-normal cell densities, demonstrating that linker histones are not essential for cell survival. Histone H1 knockout (delta H1) cells have enlarged DAPI-stained macronuclei and normal-sized micronuclei, while MicLH knockout (delta MicLH) cells have enlarged micronuclei and normal-sized macronuclei. delta MicLH cells undergo mitosis normally. However, the micronuclear mitotic chromosome structure is less condensed. These studies provide evidence that linker histones are nonessential and are involved in chromatin packaging and condensation in vivo.