A family of developmentally excised DNA elements in Tetrahymena is under selective pressure to maintain an open reading frame encoding an integrase-like protein.

Tlr1 is a member of a family of approximately 20-30 DNA elements that undergo developmentally regulated excision during formation of the macronucleus in the ciliated protozoan TETRAHYMENA: Analysis of sequence internal to the right boundary of Tlr1 revealed the presence of a 2 kb open reading frame (ORF) encoding a deduced protein with similarity to retrotransposon integrases. The ORFs of five unique clones were sequenced. The ORFs have 98% sequence conservation and align without frameshifts, although one has an additional trinucleotide at codon 561. Nucleotide changes among the five clones are highly non-random with respect to the position in the codon and 93% of the nucleotide changes among the five clones encode identical or similar amino acids, suggesting that the ORF has evolved under selective pressure to preserve a functional protein. Nineteen T/C transitions in T/CAA and T/CAG codons suggest selection has occurred in the context of the TETRAHYMENA: genome, where TAA and TAG encode Gln. Similarities between the ORF and those encoding retrotransposon integrases suggest that the Tlr family of elements may encode a polynucleotide transferase. Possible roles for the protein in transposition of the elements within the micronuclear genome and/or their developmentally regulated excision from the macronucleus are discussed.

A developmentally regulated deletion element with long terminal repeats has cis-acting sequences in the flanking DNA.

Approximately 6000 specific DNA deletion events occur during development of the somatic macro-nucleus of the ciliate Tetrahymena. The eliminated Tlr1 element is 13 kb or more in length and has an 825 bp inverted repeat near the rearrangement junctions. A functional analysis of the cis -acting sequences required for Tlr1 rearrangement was performed. A construct consisting of the entire inverted repeat and several hundred base pairs of flanking DNA on each side was rearranged accurately in vivo and displayed junctional variability similar to the chromosomal Tlr1 rearrangement. Thus, 11 kb or more of internal element DNA is not required in cis for DNA rearrangement. A second construct with only 51 bp of Tetra-hymena DNA flanking the right junction underwent aberrant rearrangement. Thus, a signal for determination of the Tlr1 junction is located in the flanking DNA, 51 bp or more from the right junction. Within the Tlr1 inverted repeat are 19 bp tandem repeats. A construct with the 19mer repeat region deleted from the right half of the inverted repeat utilized normal rearrangement junctions. Thus, despite its transposon-like structure, Tlr1 is similar to other DNA rearrangements in Tetrahymena in possessing cis -acting sequences outside the deleted DNA.

Nucleosome positioning is independent of histone H1 in vivo.

Nucleosome positioning in the somatic macronuclear genome of the ciliated protozoan Tetrahymena thermophila was analyzed by indirect end labeling. Nucleosomes were positioned nonrandomly in three different regions of the Tetrahymena genome. Nucleosome repeat length varied between adjacent nucleosomes. Nucleosome positioning in a histone H1 knockout strain was indistinguishable from that in a strain with wild type histone H1.

Analysis of genomic G + C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila.

In recent years, the amount of molecular sequencing data from Tetrahymena thermophila has dramatically increased. We analyzed G + C content, codon usage, initiator codon context and stop codon sites in the extremely A + T rich genome of this ciliate. Average G + C content was 38% for protein coding regions, 21% for 5' non-coding sequences, 19% for 3' non-coding sequences, 15% for introns, 19% for micronuclear limited sequences and 17% for macronuclear retained sequences flanking micronuclear specific regions. The 75 available T. thermophila protein coding sequences favored codons ending in T and, where possible, avoided those with G in the third position. Highly expressed genes were relatively G + C-rich and exhibited an extremely biased pattern of codon usage while developmentally regulated genes were more A + T-rich and showed less codon usage bias. Regions immediately preceding Tetrahymena translation initiator codons were generally A-rich. For the 60 stop codons examined, the frequency of G in the end + 1 site was much higher than expected whereas C never occupied this position.

Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila.

Approximately 0.8% of the adenine residues in the macronuclear DNA of the ciliated protozoan Tetrahymena thermophila are modified to N 6-methyladenine. DNA methylation is site specific and the pattern of methylation is constant between clonal cell lines. In vivo, modification of adenine residues appears to occur exclusively in the sequence 5'-NAT-3', but no consensus sequence for modified sites has been found. In this study, DNA fragments containing a site that is uniformly methylated on the 50 copies of the macronuclear chromosome were cloned into the extrachromosomal rDNA. In the novel location on the rDNA minichromosome, the site was unmethylated. The result was the same whether the sequences were introduced in a methylated or unmethylated state and regardless of the orientation of the sequence with respect to the origin of DNA replication. The data show that sequence is insufficient to account for site-specific methylation in Tetrahymena and argue that other factors determine the pattern of DNA methylation.

Alternate junctions and microheterogeneity of Tlr1, a developmentally regulated DNA rearrangement in Tetrahymena thermophila.

A large number of developmentally regulated DNA rearrangements occur during the development of the macronucleus in Tetrahymena thermophila. Tlr1 is a deletion element which has large inverted repeats near the rearrangement junctions and deletes more than 13 kbp of internal DNA. Previous analysis of caryonidal lines revealed alternate left junctions for the Tlr1 rearrangement in B strain cells. We show here that C2 strain Tetrahymena also use alternate rearrangement junctions. We have mapped and sequenced two additional rearrangement variants and find that both the left and right junctions can vary over a range of approximately 200 bp. We also demonstrate the presence of sequence microheterogeneity in the most commonly found Tlr1 rearrangement product.

Position effect for adenine methylation in the macronuclear DNA of Tetrahymena.

The macronucleus of the ciliate Tetrahymena contains about 45 copies of the genome. The fraction of the molecules on which an adenine residue is modified to N6-methyladenine is characteristic of the specific site, and consistent between clones. A fragment of DNA containing a site that is uniformly methylated on the macronuclear chromosome was moved to a new location on the extrachromosomal rDNA. The methylation pattern of the fragment on the rDNA was different from that on the chromosome. The data suggest that DNA sequence is not sufficient to determine the level of methylation.

Surgery for cure followed by chemotherapy in small cell carcinoma of the lung. For the ISC-Lung Cancer Study Group.

The Lung Cancer Study Group of the International Society of Chemotherapy (ISC-LCSG) organized multinational, cooperative, prospective and randomized trials for the cure of patients with small cell lung cancer at early stages (T1,2N0M0). Surgery for cure was used first, followed by postoperative chemotherapy, and thereafter by prophylactic cranial irradiation. Eight cycles of standard chemotherapy (CAV-cyclophosphamide-doxorubicin-vincristine) or 6 intermittent cycles of alternating chemotherapy, using 3 different drug combinations, were administered 1-2 weeks postoperatively for 6 months after randomization. A total of 183 evaluable patients received surgery for cure at 23 cooperating hospitals. The preliminary evaluation of ISC-studies I and II per May 1993 resulted in the 30-month total survival of 63% from 68 patients after complete resection at TN0M0R0-stages and 37% from 27 patients after such resections at TN2M0R0-stages. Their incidence of local recurrence as first relapse was quite similar (11/47:8/39). The related 4-year recurrence-free survival (57%, 37%), indicating a plateau-like curve of long-term survivors. These promising results have to be confirmed by larger studies. We conclude that the indication for surgery as the first treatment step for SCLC should be the same as for the other non-small subtypes of lung cancers.

A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.

Surgery in SCLC as first step of multimodality treatment.

186 patients received surgery for cure followed by aggressive randomized chemotherapy and PCI. After a median follow-up time of about 60 months the observed 4-year overall survival rate for patients completely resected was: 58% for 68 patients with pT1-3N0M0, and 33% for 27 patients with pT1-3 pN2M0 stages of SCLC. These promising results have to be confirmed by larger cooperative studies to support the recommendation to initiate surgery without delay, i.e. without preoperative chemotherapy for SCLC as well as for the non-SCLCs. From 148 patients in ISC study III after preoperative (neoadjuvant) chemotherapy only 12 received surgery for pT1-3N2M0 but only one of them survived 36 months and none 48 months p.o.

Two distinct gene subfamilies within the family of cysteine protease genes.

A cDNA clone for a physiologically regulated Tetrahymena cysteine protease gene was sequenced. The nucleotide sequence predicts that the clone encodes a 336-amino acid protein composed of a 19-residue N-terminal signal sequence followed by a 107-residue propeptide and a 210-residue mature protein. Comparison of the deduced amino acid sequence of the protein with those of other cysteine proteases revealed a highly conserved interspersed amino acid motif in the propeptide region of the protein, the ERFNIN motif. The motif was present in all of the cysteine proteases in the data base with the exception of the cathepsin B-like proteins, which have shorter propeptides. Differences in the propeptides and in conserved amino acids of the mature proteins suggest that the ERFNIN proteases and the cathepsin B-like proteases constitute two distinct subfamilies within the cysteine proteases.

The impact of surgery on the multidisciplinary treatment of bronchogenic small cell carcinoma (updated review including ongoing studies).

Recent results of studies on patients with SCLC treated by surgery with curative intent followed by adjuvant chemotherapy demonstrate a definite progress in comparison to non-surgical-treatment programs for patients with comparable stage of disease. Of 186 randomized patients enrolled for the multicenter cooperative ISC-Study I and II, 76 patients with stage pT1-3N0M0 received surgery for cure followed by chemotherapy and selective radiotherapy to the brain. The projected 4 year crude survival rate by September 1991 was 57%. In 27 of 43 patients with stage pT1-3N2M0, the tumors were completely resected, resulting in a 4 year survival rate of 32%. The survival curve for both groups of patients shows a sharp bent at 27 months postoperatively, whereafter the survival curves take a plateau-like course. These promising results were confirmed by several other groups. They are in favour of initial surgery for resectable tumors, followed by postoperative chemotherapy, while patients on preoperative chemotherapy followed by adjuvant surgery showed less favourable results.

Multimodality treatment for small cell bronchial carcinoma. Preliminary results of a prospective, multicenter trial. The ISC-Lung Cancer Study Group.

Preliminary results of the 1984 ISC (International Society of Chemotherapy) lung cancer studies I and II as of June 1990 are based on 146 patients with small cell bronchial carcinoma from 23 departments of thoracic surgery. All patients received surgery for cure in cTNM stages I and II followed by randomization for two different types of chemotherapy. For disease-free patients after completion of postoperative chemotherapy, prophylactic cranial irradiation (PCI) was administered. For the two different chemotherapeutic regimens, no statistically significant differences in survival (SVR) could be observed. Each patient was classified by the pTNM system. There were 63 patients with stage I, 44 patients with stage II and 38 patients with stage III disease. Four years after surgery, 63 patients with N0 disease had a SVR of 50%, 51 patients with N1 disease 31%, and 32 patients with N2 disease, 23%. No prolongation of brain-metastasis-free time for 62 patients receiving PCI was shown. It is concluded that initial surgical resection for small cell lung cancer in stages I and II followed by intensive chemotherapy is an appropriate therapeutic approach.

Transcriptional regulation of gene expression in Tetrahymena thermophila.

The only well-characterized study of gene expression in Tetrahymena thermophila (1) demonstrates that the temperature dependent expression of the Ser H3 gene is regulated at the level of mRNA stability. A run-on transcription assay was developed to determine if regulation of RNA stability was a major mechanism regulating gene expression in Tetrahymena or if transcriptional regulation dominates. The relative transcriptional activities of 14 Tetrahymena genes were determined in different physiological/developmental states (growing, starved and conjugating) in which many of the genes showed striking differences in RNA abundance. In every case except Ser H3, changes in transcription accompanied changes in RNA abundance. Thus differential transcription, not differential RNA degradation, is the major mechanism regulating RNA abundance in Tetrahymena.

Constancy of adenine methylation in Tetrahymena macronuclear DNA.

Macronuclear DNA from Tetrahymena was examined in order to determine whether the pattern of adenine methylation changed with the transcriptional activity of nearby genes. The DNA from growing, starved and conjugating cells was digested with six restriction enzymes which are sensitive to methylation of adenine within their recognition site. Southern blots of the restricted DNAs were probed with seven cDNA clones and one genomic clone which are homologous to polyA+ RNAs, whose transcriptional activity varies with the physiological state of the cell. One of the cDNA clones, BC11, had not been described previously. It hybridized to a 1.3 kb transcript which was present in populations of starved and conjugating, but not in growing cells. On Southern blots of genomic DNA it hybridized to a complex pattern of bands which was highly polymorphic between the DNAs of closely related strains. It was estimated that between 137 and 272 sites were assayed for changes in methylation, including at least 27 sites which were known to be methylated. No differences were seen in the size of restriction fragments from cells in different physiological states. The data suggested that the methylation pattern, which is determined during macronuclear development, does not vary with the physiological state of the cell.

The role of chemotherapy including ifosfamide for ovarian carcinoma. Austrian Collab. Ovarian Cancer Study Group.

On the basis of the results of earlier studies, 30 departments of gynecology have been cooperating nationwide in Austria since 1980 to promote the use of adjuvant chemotherapy after surgery for cure of ovarian carcinoma in early stages and the role of lymph node dissection and of second-look operation. Results recorded in more than 160 patients treated with adjuvant chemotherapy after so-called radical surgery performed in disease stages I and II demonstrate that only highly differentiated tumours in stage Ia can be cured by surgery only with no further adjuvant treatment. This underlines the necessity for staging. More than 200 patients with TNM stages III and IV were randomized after debulking surgery to receive treatment with different kinds of drug combinations to compare the therapeutic efficacy of a sequential alternating drug regimen consisting of Adriamycin-cisplatin + vincristine-cyclophosphamide + high-dose methotrexate with that of the combination of Adriamycin-cyclophosphamide and that of Adriamycin-cisplatin. High-dosed ifosfamide was also used in pilot studies.