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PubMed2003

Ionization chamber dosimetry of small photon fields: a Monte Carlo study on stopping-power ratios for radiosurgery and IMRT beams.

Absolute dosimetry with ionization chambers of the narrow photon fields used in stereotactic techniques and IMRT beamlets is constrained by lack of electron equilibrium in the radiation field. It is questionable that stopping-power ratio in dosimetry protocols, obtained for broad photon beams and quasi-electron equilibrium conditions, can be used in the dosimetry of narrow fields while keeping the uncertainty at the same level as for the broad beams used in accelerator calibrations. Monte Carlo simulations have been performed for two 6 MV clinical accelerators (Elekta SL-18 and Siemens Mevatron Primus), equipped with radiosurgery applicators and MLC. Narrow circular and Z-shaped on-axis and off-axis fields, as well as broad IMRT configured beams, have been simulated together with reference 10 x 10 cm2 beams. Phase-space data have been used to generate 3D dose distributions which have been compared satisfactorily with experimental profiles (ion chamber, diodes and film). Photon and electron spectra at various depths in water have been calculated, followed by Spencer-Attix (delta = 10 keV) stopping-power ratio calculations which have been compared to those used in the IAEA TRS-398 code of practice. For water/air and PMMA/air stopping-power ratios, agreements within 0.1% have been obtained for the 10 x 10 cm2 fields. For radiosurgery applicators and narrow MLC beams, the calculated s(w,air) values agree with the reference within +/-0.3%, well within the estimated standard uncertainty of the reference stopping-power ratios (0.5%). Ionization chamber dosimetry of narrow beams at the photon qualities used in this work (6 MV) can therefore be based on stopping-power ratios data in dosimetry protocols. For a modulated 6 MV broad beam used in clinical IMRT, s(w,air) agrees within 0.1% with the value for 10 x 10 cm2, confirming that at low energies IMRT absolute dosimetry can also be based on data for open reference fields. At higher energies (24 MV) the difference in s(w,air) was up to 1.1%, indicating that the use of protocol data for narrow beams in such cases is less accurate than at low energies, and detailed calculations of the dosimetry parameters involved should be performed if similar accuracy to that of 6 MV is sought.

Algorithms↗
PubMed1991

Transcripts from amplified sequences of an inherited homogeneously staining region in chromosome 1 of the house mouse (Mus musculus).

Several populations of the house mouse, Mus musculus, are polymorphic for the presence or absence of an inherited homogeneously staining region (HSR) in chromosome 1. The HSR consists of highly amplified DNA sequences, present in low copy numbers in the HSR- genome. A cloned HSR-derived genomic sequence detected transcripts of about 1.3 and 4.5 kb on blots of poly(A)+ RNA from liver of HSR+ mice but not from that of HSR- mice. A cDNA library was established from RNA of HSR+ mice and screened with the HSR-derived genomic clone. Positive clones were isolated and shown to be complementary to the 1.3-kb RNA species and to amplified DNA sequences in the HSR+ genome. The combined sequence of four overlapping cloned cDNAs is 959 nucleotides long and includes an open reading frame encoding a putative protein of 208 amino acids. The pertinent gene is unidentified. No homologous sequence is stored in the EMBL data base. A stretch of 109 nucleotides at the 3' end of the 1.3-kb RNA homology region in the same genomic fragment, as indicated by hybridization data and sequence motifs resembling promoter elements. Thus, our data suggest that at least two genes or gene families are encoded in the HSR.

Amino Acid Sequence↗
PubMed1995

Molecular and biochemical characterization of a protective 40-kilodalton antigen from Corynebacterium pseudotuberculosis.

A 40-kDa protein from Corynebacterium pseudotuberculosis has been previously identified as a protective antigen against ovine caseous lymphadenitis. From genomic DNA libraries of C. pseudotuberculosis, we have cloned and sequenced the 40-kDa protein gene, which was found to contain an open reading frame of 1,137 bp encoding a protein of 379 amino acids. No significant homology with previously published DNA or amino acid sequence data was found in databases, suggesting that this is a novel protein. Recombinant 40-kDa protein was overexpressed as a fusion protein to 15% of total cell proteins in Escherichia coli. Biochemical analysis of native and recombinant 40-kDa proteins has revealed associated proteolytic activity, which was shown to be of the serine protease type through the use of specific inhibitors. We suggest that this novel protective antigen be termed corynebacterial protease 40 (CP40).

Amino Acid Sequence↗
PubMed1998

Nucleotide sequences of glycoprotein I and E genes of equine herpesvirus type 4.

The nucleotide sequences of the glycoprotein I (gI) and E (gE) genes of equine herpesvirus type 4 (EHV-4) strain TH20 were determined. The predicted region encoding the EHV-4 gI gene is 1,263 nucleotides, corresponding to a polypeptide of 420 amino acids in length. The predicted region encoding the EHV-4 gE gene is 1,647 nucleotides, corresponding to a polypeptide of 548 amino acids in length. The EHV-4 gI and gE genes show 74% and 85% identity at the amino acid level with those of equine herpesvirus type 1 (EHV-1), respectively. Furthermore, we have found an open reading frame homologous to the EHV-1 gene 75, which overlaps in part with the 3' end of EHV-4 gE gene. These sequence data will be useful for development of a modified live vaccine against equine herpesvirus type 1 and 4 infections.

Amino Acid Sequence↗
PubMed1991

[Electronic data processing assisted documentation of tumor after care in an ambulatory setting--a simplification of daily routine].

A data collection system on microcomputer was developed for patients with malignant diseases in ambulant aftercare. At the same time when patient data are collected to be sent to a central medicostatistical plotting station, as it is usual in Austrian hospitals, a file for further aftercare is opened. By data transfer to other software products, statistical data evaluation is possible. Patients can also be called to hospital for different reasons.

Aftercare↗
PubMed2000

Mitochondria and cell death.

Mitochondria play a central role in both apoptosis and necrosis through the opening of the mitochondrial permeability transition pore (MPTP). This is thought to be formed through a Ca(2+)-triggered conformational change of the adenine nucleotide translocase (ANT) bound to matrix cyclophilin-D and we have now demonstrated this directly by reconstitution of the pure components. Opening of the MPTP causes swelling and uncoupling of mitochondria which, unrestrained, leads to necrosis. In ischaemia/reperfusion injury of the heart we have shown MPTP opening directly. Recovery of hearts correlates with subsequent closure, and agents that prevent opening or enhance closure protect from injury. Transient MPTP opening may also be involved in apoptosis by initially causing swelling and rupture of the outer membrane to release cytochrome c (cyt c), which then activates the caspase cascade and sets apoptosis in motion. Subsequent MPTP closure allows ATP levels to be maintained, ensuring that cell death remains apoptotic rather than necrotic. Apoptosis in the hippocampus that occurs after a hypoglycaemic or ischaemic insult is triggered by this means. Other apoptotic stimuli such as cytokines or removal of growth factors also involve mitochondrial cyt c release, but here there is controversy over whether the MPTP is involved. In many cases cyt c release is seen without any mitochondrial depolarization, suggesting that the MPTP does not open. Recent data of our own and others have revealed a specific outer-membrane cyt c-release pathway involving porin that does not release other intermembrane proteins such as adenylate kinase. This is opened by pro-apoptotic members of the Bcl-2 family such as BAX and prevented by anti-apoptotic members such as Bcl-X(L). Our own data suggest that this pathway may interact directly with the ANT in the inner membrane at contact sites.

Animals↗
PubMed1978

Fenestrations in endothelium of rat liver sinusoids revisited by freeze-fracture.

The freeze-fracture appearance of fenestrations of sinusoidal endothelial cells has been reassessed in perfusion-fixed rat liver. Fenestrations, limited to the attenuated portions of the endothelial cell cytoplasm are usually round or oval in shape, with diameters ranging from 40-600 nm. Within a given fenestrated region, they are disposed in clusters forming sieve plates. In addition, the presence of wide, irregularly shape openings suggest that adjacent fenestrations may coalesce and result in the larger openings. Our data thus confirm the existence of both small and large fenestrae in the endothelial wall, in contradistinction to previous studies showing only regular, medium sized (100 nm) openings.

Animals↗
PubMed1995

Sequence and functional analysis of a 7.2 kb fragment of Saccharomyces cerevisiae chromosome II including GAL7 and GAL10 and a new essential open reading frame.

The nucleotide sequence of a fragment of 7200 base pairs of Saccharomyces cerevisiae chromosome II has been determined. The sequence contains three open reading frames (ORFs). Two genes for galactose metabolism, GAL7 and part of the GAL10 coding region, are localized on the fragment. Comparison to the previously published sequence data showed several differences, leading to changes in the amino acid sequences of GAL7 and GAL10. One new ORF, YBR0224, was detected, coding for a protein with 918 amino acids. Comparison to the DNA and protein data bases showed no significant homologies. The protein has some interesting features pointing to a function involved in transcription regulation: a leucine zipper motif, a highly acidic region, possibly involved in transcription activation and a putative nuclear localization signal. Deletion analysis showed that the gene is essential when deleted in strain W303. Spores could germinate and form microcolonies, but efforts to propagate the colonies failed. Deletion of this gene in a different genetic background (strain M5) led to very poor-growing mutant strains with cells showing aberrant cellular morphologies.

Amino Acid Sequence↗
PubMed1991

Isolation and characterization of a cDNA encoding a chicken beta thyroid hormone receptor.

We have isolated and characterized a cDNA encoding a chicken beta homolog of c-erbA, or thyroid hormone receptor (TR). Chicken liver cDNA libraries were screened with a rat TR beta-1 cDNA probe, and several cDNA inserts were isolated and characterized. The sequence of one cDNA predicts a 369-amino-acid open reading frame (ORF), with a protein sequence that possesses 96% identity with that of rat TR beta-1, but only 88% identity with chicken TR alpha. These data indicate that the cDNA likely encodes a beta form of TR that has the expected putative DNA and T3 binding domains. The chicken TR beta (chTR beta) in vitro translated protein binds T3 with high affinity, and binds both the thyroid hormone response element (TRE) from the rat growth hormone gene and the Xenopus vitellogenin A2 gene estrogen response element (ERE), similarly to that of the rat TR beta-1. Northern blot analysis revealed the expression of a 7.0-kb RNA in several tissues including cerebellum, pituitary, kidney, and liver. This chicken liver TR beta cDNA sequence varies in both the 5' and 3' untranslated regions from the chicken kidney TR beta cDNA sequence recently reported (Forrest et al., 1990). The 5' untranslated cDNA sequence divergence occurs near a potential splice site junction of the human TR beta gene, suggesting that this chicken liver cDNA may represent an alternatively spliced RNA product of the chicken TR beta gene.

Amino Acid Sequence↗
PubMed1991

Nucleotide sequence of the DNA packaging and capsid synthesis genes of bacteriophage P2.

Overlapping DNA fragments containing the DNA packaging and capsid synthesis gene region of bacteriophage P2 were cloned and sequenced. In this report we present the complete nucleotide sequence of this 6550 bp region. Each of six open reading frames found in the interval was assigned to one of the essential genes (Q, P, O, N, M and L) by correlating genetic, physical and mutational data with DNA and protein sequence information. Polypeptides predicted were: a capsid completion protein, gpL; the major capsid precursor, gpN; the presumed capsid scaffolding protein; gpO; the ATPase and proposed endonuclease subunits of terminase, gpP and gpM, respectively; and a candidate for the portal protein, gpQ. These gene and protein sequences exhibited no homology to analogous genes or proteins of other bacteriophages. Expression of gene Q in E. coli from a plasmid caused production of a Mr 39,000 Da protein that restored Qam34 growth. This sequence analysis found only genes previously known from analysis of conditional-lethal mutations. No new capsid genes were found.

Adenosine Triphosphatases↗
PubMed2001

Laparoscopic bilateral synchronous nephrectomy for autosomal dominant polycystic kidney disease: the initial experience.

PURPOSE: We report our experience with laparoscopic bilateral synchronous nephrectomy for giant symptomatic autosomal dominant polycystic kidney disease (ADPKD) and compare outcome data with open bilateral nephrectomy. MATERIALS AND METHODS: Since March 1998, 10 patients underwent bilateral synchronous laparoscopic nephrectomy for giant symptomatic ADPKD. A 3 port retroperitoneal laparoscopic approach was used to secure the renal hilum and mobilize the kidney. Intact specimen extraction was performed through a midline infraumbilical extraperitoneal incision. The patient was then repositioned for the contralateral retroperitoneoscopic nephrectomy, with the second specimen also delivered through the same infraumbilical incision. Data were retrospectively compared with 10 patients who had undergone bilateral synchronous open nephrectomy for ADPKD between 1981 and 1992. RESULTS: Patients in the laparoscopic and open groups were comparable in regard to age (53 versus 47 years, p = 0.54) and Anesthesiologist Society of America class (3 versus 3, p = 0.84) but patients in the laparoscopic group were significantly more obese (body mass index 35.9 versus 23.8, p = 0.02). For comparable total specimen weights (3 versus 3 kg, p = 0.69) surgical time was longer in the laparoscopic group (4.4 versus 3.8 hours, p = 0.007). However, the laparoscopic group was superior in regard to blood loss (150 versus 325 cc, p = 0.05), postoperative requirement of nasogastric tube (10% versus 100%, p = 0.0001), narcotic analgesics (34.2 versus 120.4 mg. morphine sulfate equivalent, p = 0.03) and hospital stay (1.5 versus 9 days, p = 0.004). Complications occurred in 5 patients (50%) in the laparoscopic group and 4 (40%) in the open group (p = 0.66). No laparoscopic case was converted to open surgery. CONCLUSIONS: Synchronous bilateral retroperitoneal laparoscopic nephrectomy for giant symptomatic adult polycystic kidney disease is feasible, safe and efficacious, and can be performed either before or after renal transplantation. Compared to open surgery, the laparoscopic approach results in significantly shorter hospital stay, decreased morbidity and quicker recovery. Laparoscopy is currently our technique of choice in this setting.

Adult↗
PubMed1993

Cloning and sequencing of the gene encoding the [2Fe-2S] ferredoxin from Clostridium pasteurianum.

A 1348 basepair EcoRI fragment of genomic DNA containing the [2Fe-2S] ferredoxin gene from Clostridium pasteurianum has been cloned and sequenced. The translated protein sequence is identical to the sequence of the protein as previously determined by Edman chemistry. Two potential open reading frames occur upstream and downstream of the ferredoxin gene. However, the features surrounding the latter gene strongly suggest that it constitutes a separate transcriptional unit. The sequence data provide no evidence that this ferredoxin is involved in nitrogen fixation.

Amino Acid Sequence↗
PubMed1991

The broad-host-range plasmid pTF-FC2 requires a primase-like protein for autonomous replication in Escherichia coli.

A 3202-bp fragment of plasmid pTF-FC2, cloned into PUC19, had previously been identified as the minimum region required for replication in either Pseudomonas aeruginosa or Escherichia coli polA- mutants. During the course of experiments to construct broad-host-range cloning vectors based on the pTF-FC2 replicon, it was found that the 3202-bp fragment had an absolute requirement for some function of the pUC19 vector. This requirement was eliminated in the presence of co-resident pTF-FC2 derivatives. An additional 1239-bp fragment from pTF-FC2, immediately adjacent to the 3202-bp fragment, was identified which restored the ability of the pTF-FC2 replicon to replicate autonomously. Sequence analysis of the region revealed a single open reading frame encoding a 40-kDa polypeptide, which was synthesised in an in vitro transcription/translation system. A comparison of the amino acid sequence of this protein with sequence data banks revealed limited homology with the RepB' primase of the IncQ plasmid, RSF1010. An M13 delta lac 110 replication-deficient phage system was used to demonstrate that the 40-kDa protein did function as a primase with respect to replication at the origin of replication (vegetative) of pTF-FC2.

Amino Acid Sequence↗
PubMed1997

ord1, an oxidoreductase gene responsible for conversion of O-methylsterigmatocystin to aflatoxin in Aspergillus flavus.

Among the enzymatic steps in the aflatoxin biosynthetic pathway, the conversion of O-methylsterigmatocystin to aflatoxin has been proposed to be catalyzed by an oxidoreductase. Transformants of Aspergillus flavus 649WAF2 containing a 3.3-kb genomic DNA fragment and the aflatoxin biosynthesis regulatory gene aflR converted exogenously supplied O-methylsterigmatocystin to aflatoxin B1. A gene, ord1, corresponding to a transcript of about 2 kb was identified within the 3.3-kb DNA fragment. The promoter region presented a putative AFLR binding site and a TATA sequence. The nucleotide sequence of the gene revealed an open reading frame encoding a protein of 528 amino acids with a deduced molecular mass of 60.2 kDa. The gene contained six introns and seven exons. Heterologous expression of the ord1 open reading frame under the transcriptional control of the Saccharomyces cerevisiae galactose-inducible gal1 promoter results in the ability to convert O-methylsterigmatocystin to aflatoxin B1. The data indicate that ord1 is sufficient to accomplish the last step of the aflatoxin biosynthetic pathway. A search of various databases for similarity indicated that ord1 encodes a cytochrome P-450-type monooxygenase, and the gene has been assigned to a new P-450 gene family named CYP64.

Aflatoxins↗