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R Kriz

Publications and source records attributed to R Kriz.

At least 19 recordsLinked to original sources
PubMed2000

Applications of simulator computed tomography number for photon dose calculations during radiotherapy treatment planning.

PURPOSE: To study the variation of computed tomography (CT) number from a simulator-based scanner and the effect of this variation on photon-dose calculations. METHOD AND MATERIALS: CT images of a cylindrical phantom with multiple inserts were obtained using a commercially-available simulator-CT (Ximatron: Varian, Palo Alto, CA). The linear correlation coefficient and Chi-square methods were used to determine the X-ray effective energy in a phantom. CT numbers in Hounsfield units (HU) were measured as a function of phantom size, orientation, field of view (FOV), distance from the center, and time for various inserts. The change of dose calculations due to the CT number variations was then determined using the equivalent path-length (EPL) and collapsed cone convolution methods. RESULTS AND DISCUSSION: A significant beam-hardening effect was observed for the simulator-CT. Consequently, the CT number from the sim-CT was more sensitive to the size of the phantom than those from a conventional CT. The sim-CT number is not sensitive to the locations within the phantom and is stable over a 6-week period. It is important to use the proper FOV for sim-CT studies; scanning a small polystyrene phantom using a large FOV may result in an increase of l20 HU in CT number at the center of the field. However, the dose-calculation variations, due to the CT number uncertainty, do not exceed 2-3% for 6-18 MV photon beams. CONCLUSION: The simulator CT images were acquired with patients in the treatment position, and these CT numbers are useful for CT-based dose calculations.

Algorithms↗
PubMed1998

Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro.

We have cloned the cDNA encoding human GDP-mannose 4,6-dehydratase, the first enzyme in the pathway converting GDP-mannose to GDP-fucose. The message is expressed in all tissues and cell lines examined, and the cDNA complements Lec13, a Chinese Hamster Ovary cell line deficient in GDP-mannose 4,6-dehydratase activity. The human GDP-mannose 4,6-dehydratase polypeptide shares 61% identity with the enzyme from Escherichia coli, suggesting broad evolutionary conservation. Purified recombinant enzyme utilizes NADP+ as a cofactor and, like its E. coli counterpart, is inhibited by GDP-fucose, suggesting that this aspect of regulation is also conserved. We have isolated the product of the dehydratase reaction, GDP-4-keto-6-deoxymannose, and confirmed its structure by electrospray ionization-mass spectrometry and high field NMR. Using purified recombinant human GDP-mannose 4,6-dehydratase and FX protein (GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase), we show that the two proteins alone are sufficient to convert GDP-mannose to GDP-fucose in vitro. This unequivocally demonstrates that the epimerase and reductase activities are on a single polypeptide. Finally, we show that the two homologous enzymes from E. coli are sufficient to carry out the same enzymatic pathway in bacteria.

Amino Acid Sequence↗
PubMed1997

A genetic selection for isolating cDNAs encoding secreted proteins.

We describe a simple, rapid technique for simultaneously isolating large numbers of cDNAs encoding secreted proteins. The technique makes use of a facile genetic selection performed in a strain of Saccharomyces cerevisiae deleted for its endogenous invertase gene. A cDNA cloning vector which carries a modified invertase gene lacking its leader sequence is used in conjunction with this strain. Heterologous secreted genes fused appropriately upstream of this defective invertase provide the necessary signals to restore secretion, allowing the yeast to grow on sugars such as sucrose or raffinose. This microbial growth selection facilitates scanning cDNA libraries containing millions of clones, enabling the wholesale identification of novel secreted proteins without the need for specific bioassays. The technique is similar to one previously described (Klein et al. (1996) Proc. Natl. Acad. Sci. USA 93, 7108-7113). We describe results using a cDNA library derived from activated human peripheral blood mononuclear cells (PBMC). Genes identified from this library encoded signal sequences of proteins of diverse structure, function, and cellular location such as cytokines, type 1 and type 2 transmembrane proteins, and proteins found in intracellular organelles. In addition, a number of novel secreted proteins were identified, including a chemokine and a novel G-protein-coupled receptor. Since signal sequences possess features conserved throughout evolution, the procedure can be used to isolate genes encoding secreted proteins from both eukaryotes and prokaryotes.

Amino Acid Sequence↗
PubMed1994

The cloning of CD70 and its identification as the ligand for CD27.

CD70 is a surface Ag found on activated but not resting T and B lymphocytes. The biologic activity of this Ab-defined cell surface molecule on lymphocytes has not been established. Therefore, in an effort to understand the function of the CD70 protein, a mAb defining the CD70 Ag was used to isolate by expression cloning the cDNA responsible for the CD70 molecule. The predicted protein product is a type II transmembrane protein. Bioassays demonstrated that the CD70 cDNA clone expressed in African green monkey kidney cells would induce the proliferation of PHA-costimulated T cells. Comparison with known sequences indicates identity with the CD27 ligand. Therefore the molecule defining the CD70 Ag is identical to the recently defined ligand for CD27.

Amino Acid Sequence↗
PubMed1993

Molecular cloning of murine FLT and FLT4.

A wide range of growth and differentiation processes are regulated by the signalling of receptor tyrosine kinases (RTKs). We have developed a nested polymerase chain reaction (PCR) procedure with degenerate primers, and used it to identify RTKs expressed in murine fetal thymus. A novel RTK, called FLT4, and the murine homologue of FLT were found, and their PCR fragment sequences were used to isolate larger cDNA clones spanning the complete coding regions of these receptors. FLT4 was found to contain an extracellular region similar to the corresponding sequences of FLT and Flk-1, containing seven immunoglobulin domains.

Amino Acid Sequence↗
PubMed1992

Cloning, sequencing, expression, and Gq-independent activation of phospholipase C-beta 2.

cDNAs corresponding to a previously uncharacterized phospholipase C were isolated from an HL-60 cell cDNA library. The cDNAs encodes a putative polypeptide of 1181 amino acids with a calculated molecular mass of 133,700 daltons. Comparison of the amino acid sequence of the predicted protein with those of five mammalian phospholipase C isoforms (PLC-beta 1, PLC-gamma 1, PLC-gamma 2, PLC-delta 1, and PLC-delta 2) revealed that the new enzyme is most closely related to PLC-beta 1 with an overall amino acid sequence identity of 48%. Thus, the new phospholipase C was named PLC-beta 2. The least similarity between PLC-beta 1 and PLC-beta 2 is apparent in the carboxyl-terminal 450 amino acids. Both PLC-beta 1 and PLC-beta 2 were purified from extracts of HeLa cells that had been transfected with vaccinia virus containing the corresponding cDNAs. Like other mammalian PLC isoforms, including PLC-beta 1, the catalytic activity of PLC-beta 2 was entirely dependent on Ca2+, and PLC-beta 2 preferred phosphatidyl-inositol 4,5-bisphosphate to phosphatidylinositol as substrate. Recently, the alpha subunit of the pertussis toxin-insensitive G-protein alpha q has been shown to activate PLC-beta 1 but not PLC-gamma 1 and PLC-delta 1. When alpha q purified from bovine brain was reconstituted with PLC-beta 1 or PLC-beta 2, no stimulation of PLC-beta 2 was observed in the presence of either AlF4- or guanosine 5-O-(3-thiotriphosphate) (GTP gamma S), whereas PLC-beta 1 activity was enhanced markedly in the presence of AlF4- and less markedly but significantly in the presence of GTP gamma S. These results suggest that the receptor-dependent stimulation of PLC-beta 1 and that of PLC-beta 2 may require different G-protein alpha subunits. (see also accompanying article (Lee, C. H., Park, D., Wu, D., Rhee, S. G., and Simon, M. I. (1992) J. Biol. Chem. 267, 16044-16047).

Amino Acid Sequence↗
PubMed1992

Molecular cloning of the cDNA encoding a receptor tyrosine kinase-related molecule with a catalytic region homologous to c-met.

Receptor tyrosine kinases mediate a range of growth and differentiation processes in multiple biological systems. In this work, we report the identification of a novel tyrosine kinase-related molecule, nyk-r, and the molecular cloning of its complete cDNA. Its extra-cellular domain bears no apparent homology with other receptor families, but its intracellular kinase-related region has considerable similarity with members of the insulin-receptor family such as c-met and trk B. Also, the nyk-r gene is expressed in a wide range of tissues and cell lines.

Amino Acid Sequence↗
PubMed1991

Molecular cloning and characterization of a complete Chinese hamster provirus related to intracisternal A particle genomes.

We report here the nucleotide sequence of a full-length Chinese hamster genomic proviral element, CHIAP34. CHIAP34 is 6,403 bp long with long terminal repeats of 311 bp at each end. The genetic organization of CHIAP34 was determined by comparison with intracisternal A particle (IAP) genetic elements from the mouse and Syrian hamster. Extensive homology at the nucleotide and deduced amino acid sequence levels was observed between CHIAP34 and the mouse and Syrian hamster IAP elements. CHIAP34 may represent a defective Chinese hamster IAP genetic element. The gag gene consists of 837 codons, of which 558 codons are in a single long open reading frame followed by several frameshifts. The pol gene begins with a -1 frameshift and consists of a long open reading frame of 753 codons followed by a short open reading frame of 103 codons. The putative env region contains multiple termination codons in all reading frames. CHIAP34 is representative of the predominant retroviral elements in the Chinese hamster ovary cell genome present at around 80 copies per haploid genome.

Amino Acid Sequence↗
PubMed1990

Phospholipase C isozymes: structural and functional similarities.

Phospholipase C (PLC) is shown to comprise at least nine isoforms. These isoforms can be separated into three structurally related classes. Within a class the isozymes have similar enzymological properties. In the case of the PLC gamma class, both isoforms may be regulated by tyrosine phosphorylation. For PLC gamma 1 we show that the tyrosine phosphorylation sites are contained within the SH2/SH3 region or 'modulatory domain'. The overexpression of PLC gamma 1 in Rat-2 cells results in increased phosphatidylinositol breakdown in response to PDGF treatment, demonstrating that PLC gamma 1 mediates this response. We note that thrombin activates PLC gamma 1 in addition to other PLC isoforms.

Animals↗
PubMed1989

Unique substrate specificity and regulatory properties of PKC-epsilon: a rationale for diversity.

PKC-epsilon was isolated from a murine brain cDNA library. The clone, lambda 61PKC-epsilon, encoded a polypeptide of 737 amino acids that is homologous to other PKCs. Northern analysis showed that the 7 kb mRNA for this cDNA is widely expressed. The protein when expressed in COS-1 cells displayed phorbol ester-binding activity. However in order to detect the kinase activity of PKC-epsilon, it was necessary to employ a synthetic peptide substrate based upon the pseudosubstrate site. Subsequent analysis demonstrated that PKC-epsilon, while showing certain properties characteristic of the PKC family, has a quite distinct substrate specificity and is independent of Ca2+.

Amino Acid Sequence↗
PubMed1988

Stimulation of murine hemopoietic colony formation by human IL-6.

A novel hemopoietic CSF has been identified in the medium conditioned by lectin-stimulated human T cells. The cDNA clone encoding this factor, isolated by functional expression cloning in monkey cos-1 cells, proved to be identical with the cDNA encoding the cytokine B cell stimulatory factor-2/IFN-beta 2, a factor now known as IL-6. In the murine system, IL-6 indirectly supports the formation of several different types of hemopoietic colonies, including those derived from early blast cells, and directly supports the proliferation of granulocyte/macrophage progenitors. These results expand the range of known target cells of IL-6 to include hemopoietic progenitors in addition to B cells, T cells, and fibroblasts and provide further evidence that this cytokine plays an important role within a network of interacting cytokines that regulates many different biologic responses.

Animals↗
PubMed1988

Direct sagittal CT in the evaluation of temporal bone disease.

The human temporal bone is an extremely complex structure. Direct axial and coronal CT sections are quite satisfactory for imaging the anatomy of the temporal bone; however, many relationships of the normal and pathologic anatomic detail of the temporal bone are better seen with direct sagittal CT sections. The sagittal projection is of interest to surgeons, as it has the advantage of following the plane of surgical approach. This article describes the advantages of using direct sagittal sections for studying various diseases of the temporal bone. The CT sections were obtained with the aid of a new head holder added to our GE CT 9800 scanner. The direct sagittal projection was found to be extremely useful for evaluating diseases involving the vertical segment of the facial nerve canal, vestibular aqueduct, tegmen tympani, sigmoid sinus plate, sinodural angle, carotid canal, jugular fossa, external auditory canal, middle ear cavity, infra- and supralabyrinthine air cells, and temporomandibular joint.

Adolescent↗
PubMed1988

The human genes for GM-CSF and IL 3 are closely linked in tandem on chromosome 5.

As demonstrated by long-range mapping of restriction endonuclease recognition sequences and genomic cloning, we found that the human genes encoding interleukin 3 (IL 3) and granulocyte/macrophage colony-stimulating factor (GM-CSF) are tandemly arrayed on the long arm of chromosome 5, separated by 9 kilobases (kb) of DNA. This close physical linkage of genes with similar structure and biologic function suggests that these cytokines may have evolved from a common ancestral gene. This linkage in evolution of two relatively divergent genes further implies that some of the other lymphokine and cytokine genes that appear to share as much or more sequence similarity than do IL 3 and GM-CSF may be distantly related members of a cytokine gene family.

Chromosome Mapping↗
PubMed1987

Isolation of a cDNA clone encoding a high molecular weight precursor to a 6-kDa pulmonary surfactant-associated protein.

Mammalian surfactant is an incompletely defined mixture of lipids and associated proteins of molecular mass 35,000 Da and approximately 6,000 Da. Surfactant preparations which are highly effective in treating respiratory distress syndrome in premature infants lack the 35-kDa proteins, but contain the 6-kDa proteins. We isolated and partially sequenced one of these low molecular weight proteins from the lung lavage material of an alveolar proteinosis patient. Oligonucleotides deduced from the sequence were used as probes to isolate a human cDNA clone. The clone codes for a 42-kDa protein which contains the sequence of the 6-kDa protein. Messenger RNA coding for the 42-kDa protein was identified in human lung RNA by in vitro translation and immunoprecipitation of the translation products with an antiserum against purified bovine surfactant 6-kDa proteins. Immunoprecipitation of the 42-kDa primary translation product is inhibited by the presence of the bovine 6-kDa protein. These observations suggest a precursor-product relationship of the 42-kDa protein to one of the 6-kDa proteins.

Amino Acid Sequence↗
PubMed1987

Human CSF-1: molecular cloning and expression of 4-kb cDNA encoding the human urinary protein.

A 4-kilobase complementary DNA (cDNA) encoding human macrophage-specific colony-stimulating factor (CSF-1) was isolated. When introduced into mammalian cells, this cDNA directs the expression of CSF-1 that is structurally and functionally indistinguishable from the natural human urinary CSF-1. Direct structural analysis of both the recombinant CSF-1 and the purified human urinary protein revealed that these species contain a sequence of at least 40 amino acids at their carboxyl termini which are not found in the coding region of a 1.6-kilobase CSF-1 cDNA that was previously described. These results demonstrate that the human CSF-1 gene can be expressed to yield at least two different messenger RNA species that encode distinct but related forms of CSF-1.

Amino Acid Sequence↗
PubMed1987

Structure and expression of the murine L-myc gene.

We have isolated a 12 kb clone from the murine genome which we show by DNA transfection studies to contain an entire functional L-myc gene and the transcriptional promoter sequences necessary for its expression. We have also isolated a 3.1 kb cDNA sequence from a murine brain cDNA library which corresponds to most of the L-myc mRNA. We have identified the L-myc coding region within the genomic clone by a combination of S1 nuclease analyses. Northern blotting analyses and comparative nucleotide sequence analyses with the cDNA clone. The L-myc gene appears to be organized similarly to the other well-characterized myc-family genes, c-myc and N-myc. The predicted amino acid coding sequence of the L-myc gene indicates that the L-myc protein is significantly smaller than c- and N-myc, but is highly related. In particular, comparison of the N- and c-myc protein sequences reveals seven relatively conserved regions interspersed among non-conserved regions; the L-myc gene retains five of these conserved regions but lacks two others. In addition, a portion of one highly conserved region is encoded within a different region of the L-myc gene but, due to changes in the size of L-myc exons relative to those of N- and c-myc, maintains its overall position in the peptide backbone with respect to other conserved regions. We discuss these findings in the context of potential functional domains and the possibility of overlapping and distinct activities of myc-family proteins.

Amino Acid Sequence↗
PubMed1987

The nucleotide sequence encoding the hamster 78-kDa glucose-regulated protein (GRP78) and its conservation between hamster and rat.

The complete nucleotide (nt) sequence encoding the hamster 78-kDa glucose-regulated protein has been determined using a cDNA plasmid p3C5. Comparison of the nucleotide sequences from rat and hamster showed a strong conservation in the coding region as well as 5'- and 3'-untranslated regions (UTRs). The relatively long (206 nt for rat) 5'UTR shares 72% sequence homology between rat and hamster in the 142 nt upstream from the ATG start codon. This conserved region contained an imperfect inverted-repeat sequence. The long 5'UTR region is capable of forming stable dyad structures. The homology within the rat and hamster protein-coding region is 93.7%, with most of the differences resulting in silent site mutations. Out of the 654 amino acids, only four changes are detected, two of which are located in the signal peptide. While the sizes of the 3'UTR are different between the two species compared, strong sequence homologies (95%) were observed throughout the entire UTRs. Also, the 3'UTR was not rich in A + T residues as found in other eukaryotic mRNAs.

Animals↗