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PubMed1987

Rapid cytophotometry and its application to diagnostic pathology.

Computer processing of microscopic imagery of cervical lesions can provide novel quantitative diagnostic information. Interpretation of this information, from the level of the image itself to that of diagnostic truth, calls for the use of appropriate data structures. The resolution of the problems of diagnostic consensus and truth may be furthered by the use of these techniques in conjunction with diagnostic expert systems. The impact of our expanded ability to differentiate and to extract diagnostic and prognostic information will lead to changes in the way we practice clinical pathology. Technologic advances have now made it possible to perform quantitative measurements in a very rapid fashion as a practical part of routine clinical pathology activity.

Carcinoma↗
PubMed1973

Experimental lung injury. I. Bacterial pneumonia: ultrastructural, autoradiographic and histochemical observations.

Proteus infection in the rat produces an acute bacterial pneumonia which resolves without necrosis or significant organization within 2 weeks. Ultrastructural changes included widespread damage to type 2 cells and endothelial cells and rapid proliferation of the alveolar epithelial cells, which were the predominant site of labeling with tritiated thymidine. Histochemical staining for lysosomal enzymes showed an initial reduction in type 2 cell reactivity. The majority of proliferating epithelial cells were also unreactive until the normal pattern of staining and morphology returned at 8 to 12 days after infection. The acute inflammatory exudate was reactive, but there was only minimal to moderate staining in the subsequent clusters of alveolar macrophages. These data suggest that resolution with the preservation of the normal architecture of the peripheral airspaces may be correlated with superficial injury and limited reactivity for digestive enzymes.

Acid Phosphatase↗
PubMed1984

Heterologous radioimmunoassay of monkey luteinizing hormone: a critical assessment.

Available reagents for the immunoassay (RIA) of luteinizing hormone (LH) in monkeys, including a cynomolgus (cynLH) tracer, an antiserum against human chorionic gonadotropin (hCG), and a rhesus standard (rhLH), were assessed using an in vitro bioassay and the RIA in connection with fractionation by high-resolution isoelectrofocusing. The data presented indicate that the RIA system represents a significant improvement over the ovine-antiovine system. Since, however, the sensitivity of the RIA is some 50 times less than that of the in vitro bioassay, and since the rhLH standard is heavily contaminated with FSH, it is felt that until the advent of a homologous RIA, the in vitro bioassay is the method of choice.

Animals↗
PubMedDate not supplied

[Hydratation of the rubredoxin polypeptide chain from data on the spatial structure].

The hydration water distribution around the main chain protein rubredoxin has been analysed using the crystal data at high resolution obtained earlier. The analysis was based on the consideration of all nearest neighbour atoms around the N and O atoms of peptide groups. The atoms which can form hydrogen binds were the subject of final analysis. The nitrogen atom of a peptide NH group has only one vacancy for neighbours. The oxygen atom of a peptide CO group has one, two or more neighbours, some of them are oxygen-water atoms. About 27% of NH and 53% of CO peptide groups are hydrated, that corresponds to 0.12 H2O per gram of protein. A detailed analysis shows that NH and CO groups of the main chain are hydrated according to the principle of maximum possible in situ saturation of hydrogen bonds. Thus the peptide groups incorporated in the peptide hydrogen bond network were not hydrated as a rule. Consequently, for rubredoxin a pleated sheet region, some regions for the large and small main chain loops, and Fe-containing pocket are not hydrated. A method for evaluation of the main chain hydration is proposed when the coordinates of protein atoms are available.

Crystallization↗
PubMed1982

Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase.

Horse liver alcohol dehydrogenase was crystallized from an equilibrium mixture containing predominantly NAD+ and p-bromobenzyl alcohol. X-ray diffractometer data to a resolution of 2.9 A were collected and used to compute electron density maps with phases calculated from the isomorphous enzyme . NADH . dimethyl sulfoxide complex, which has been refined to an R value of 25.6%. The electron density maps were readily interpreted in a graphics display system. Both subunits of the dimer bind coenzyme and alcohol in essentially the same manner; there is no evidence of asymmetry between subunits. The bromophenyl group is accommodated in a large hydrophobic pocket that has the side chain of Leu-116 rotated into a different position than in the complex with dimethyl sulfoxide. The alcohol oxygen is directly ligated to the catalytic zinc atom. The zinc is tetracoordinate and there is no room for a water molecule to make the zinc pentacoordinate. A hydrogen-bonded system formed with the hydroxyl groups of the alcohol, Ser-48 and nicotinamide ribose (2'), and the imidazole of His-51 may provide a proton relay system that links the buried alcohol to solvent. The insertion of the coenzyme's hydroxyl group into this system appears to install the catalytically active species. The observed structure has the pro-R hydrogen on C1 of the alcohol pointing away from C4 of the nicotinamide ring. This is probably a nonproductive complex that easily becomes productive by a rapid rotation of the alcohol to put the pro-R hydrogen within 3 A of C4 of the nicotinamide ring and in position for a direct transfer of hydrogen. A model of the productive complex readily explains the stereospecificity of hydride transfer observed for ethanol.

Alcohol Dehydrogenase↗
PubMed1982

[Azotobacter chroococcum, a producer of a new antifungal antibiotic].

Strain 92 of Azotobacter chroococcum was obtained as result of natural selection. It produces an antibiotic active against phytopathogenic fungi. The antibiotic was isolated from the bacterial mass of the culture with ethanol extraction followed by column and thin-layer chromatography on silica gel. The pure antibiotic is a viscous oily substance of a yellowish colour, readily soluble in the majority of the organic solvents, not soluble in water, readily oxidized by air oxygen. The UV absorption spectrum of the antibiotic ethanol solution had bonds characteristic of the conjugated tetraene system. The presence of ketone and enol groups in the antibiotic molecule was shown with the colour reactions. It was confirmed by the data of the antibiotic IR spectrum investigation. According to the data of high resolution mass spectroscopy the empirical formula of the antibiotic is C20H30O4, the molecular weight is 334. It is suggested that the antibiotic is an ester of aliphatic tetraenic acid differing from the known antibiotics produced by Azotobacter.

Antifungal Agents↗
PubMed1994

Occipital condyle fractures: clinical presentation and radiologic detection.

PURPOSE: To describe the CT findings in occipital condyle fractures in patients suffering craniocervical trauma. METHODS: Six occipital condyle fractures in five patients were analyzed. Because of clinical or plain-film findings, the craniocervical junction in each patient was imaged using thin-section, high-resolution CT. Axial data were reformatted in the coronal plane or in both coronal and sagittal planes. Clinical and radiologic findings associated with occipital condyle fractures reported in the English medical literature were correlated with our cases to determine conclusive predictive features indicating condylar injury. RESULTS: Two avulsion (type III) fractures in two patients, two compression (type I) fractures in one patient, and two compression fractures in two patients were diagnosed by CT. Specific predictive features indicating occipital condyle fracture could not be confirmed. CONCLUSIONS: CT greatly facilitates diagnosing and typing of occipital condyle fractures. Nonspecific parameters promoting CT after trauma are unexplained persistent upper-neck pain with normal plain-film findings, lower cranial nerve palsies, spasmodic torticollis, retropharyngeal or prevertebral soft-tissue swelling, and fractures of the atlas or axis.

Cervical Vertebrae↗
PubMed1994

[Nuclear medicine for evaluation of liver functions].

The clinical usefulness of colloid liver scintigraphy to detect space occupying lesions in the liver has been reduced by X-ray CT and ultrasonography. However, scintigraphic examinations have potentials for characteristic diagnosis of liver tumors, such as 99mTc RBC SPECT for hepatic hemangioma, 99mTc PMT for positive imaging of hepatocellular carcinoma and its extrahepatic metastasis, and radioimmunoscintigraphy for metastatic tumors. Moreover, prediction of the prognosis and monitoring therapeutic effect to liver cancer can be made by the use of nuclear medicine techniques. Recently, 99mTc galactosyl serum albumin (GSA), a newly developed radiotracer to evaluate hepatocyte function, has become commercially available. Quantitative parameters of liver functions can be obtained by analysis of time-activity curve in blood and liver after 99mTc-GSA administration. In several cases, 99mTc-GSA study showed intrahepatic unevenness of function, which could not be depicted by other imaging examinations. Positron emission tomography (PET) with 18F-fluoro-2-deoxy glucose (FDG) is useful to detect malignant tumors in the liver. Since PET can provide absolutely quantitative data in better resolution, it is expected that regional true metabolic functions in the liver may be able to be quantitatively evaluated with PET in near future.

Carcinoma, Hepatocellular↗
PubMed1975

[The primary structure of a crystalline monoclonal immunoglobulin kappa-type L-chain, subgroup I (Bence-Jones protein Rei.); isolation and characterization of the tryptic peptides; the complete amino acid sequence of the protein; a contribution to the elucidation of the three-dimensional structure of antibodies, in particular their combining site (author's transl)].

Bence-Jones protein Rei. was isolated from the urine of a plasmacytoma patient by precipitation with ammonium sulfate and purified by ion exchange chromatography. The determination of the molecular weight showed that the protein was present in its monomeric form. The preparation cotained a minor fraction, which consisted of the dimer of the variable parts and was characterized by its ability to crystallize. X-ray data with a resolution on the atomic level could be achieved and allowed, together with the known primary structure, the construction of a three-dimensional model, which also gave an insight into the antigen binding site. It consists of the hypervariable regions, which form a pocket 15 A in diameter lying between the two monomers at the ends of the molecules. Sequence studies were performed with tryptic peptides which were purified by chromatographic procedures and aligned in homology to other kappa-chains. The protein belongs to subgroup I on the basis of its characteristic amino acid sequence and follows a highly regular pattern of amino acid exchanges. Its sequence is in agreement with an evolutionary origin of antibody variability.

Amino Acid Sequence↗
PubMed1994

Intramolecular interactions in muscarinic acetylcholine receptors studied with chimeric m2/m5 receptors.

Current models of the three-dimensional structures of muscarinic acetylcholine receptors and other G protein-coupled receptors are based primarily on high-resolution electron diffraction data obtained with bacteriorhodopsin, the molecular structure of which is characterized by the presence of seven alpha-helical transmembrane domains (TM I-VII). However, bacteriorhodopsin does not couple to G proteins and its primary sequence lacks a series of amino acids that are conserved among virtually all G protein-coupled receptors. Therefore, it remains to be shown experimentally whether the molecular structures of these functionally different proteins are in fact identical. To address this question, we have analyzed the pharmacological properties of a series of hybrid human m2/m5 muscarinic receptors. Initially, we identified several chimeric constructs that, upon transient expression in COS-7 cells, were unable to bind significant amounts of the muscarinic antagonists N-[3H]methylscopolamine and [3H]quinuclidinyl benzilate. A common structural feature of these constructs was the presence of m2 receptor sequence in TM VII and of m5 receptor sequence in TM I. The ligand-binding activity of these "pharmacologically inactive" hybrid receptors could be restored by replacing TM I (consisting of m5 receptor sequence) with the corresponding m2 receptor domain. These data provide the first direct experimental evidence that the molecular architecture of muscarinic receptors (and, most likely, that of other G protein-coupled receptors) resembles that of bacteriorhodopsin, in that the seven TM helices are arranged in a ring-like fashion such that TM I lies directly adjacent to TM VII.

Amino Acid Sequence↗
PubMed1997

[Diagnostic accuracy of teleradiology in thoracic and abdominal diseases].

For one year now, teleradiology has linked the "S. Marcello" Hospital to the Department of Radiology of "Del Ceppo." Hospital in Pistoia, 30 kilometers away. Plain films are digitized (Lumiscan 50, Philips), transmitted over a dedicated standard telephone line and displayed at 1024 x 1024 x 8 bits. To study the diagnostic accuracy of teleradiology in chest and abdominal conditions, we digitized and transmitted to the Pistoia Dept. of Radiology, a sample of 156 (96 chest and 60 abdominal) emergency examinations made in "S. Marcello" Hospital from January through November, 1995. The patients were 81 women (mean age: 69 years) and 75 men (mean age: 66 years); the age range was 17-93 years. Three radiologists independently reviewed the images in the Pistoia Dept. of Radiology on a digital workstation enabled to manipulate images. They filled in some given forms specific for chest and abdominal radiography, which were compared with the same forms filled in by the radiologist in "S. Marcello" Hospital who reviewed plain films. The differences were never clinically important; they concerned emphysema (4 false positives and 2 false negatives), congestion of the hila (2 false positives and 2 false negatives) and abnormal air in small bowel and colon (2 false positives and 2 false negatives). We believe these differences to be related to interobserver variability. The diagnostic accuracy of monitor image interpretation by the three radiologists who reviewed digitized radiographs exceeded 96% for both chest and abdominal examinations, which figure compares with literature data on high resolution workstations.

Adolescent↗
PubMed1998

From amplification to gene in thyroid cancer: a high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization.

Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. We now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. We used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3-6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKCepsilon), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKCepsilon as a previously unmapped candidate gene involved in thyroid tumorigenesis.

Adenocarcinoma, Follicular↗
PubMed1996

Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.

The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

Journal Article↗
PubMed1996

Experiments in microgravity: a comparison of crystals of a carbohydrate-binding fab grown on the ground, on space shuttle Discovery and on space station Mir.

The Fab fragment of the hybridoma antibody (YsT9.1) specific to Brucella abortus has been crystallized on earth using both Linbro plates and ground-based models of the flight hardware, as well as in microgravity on board the space shuttle Discovery and the space station Mir. Large-scale experiments using Linbro plates gave two different crystal morphologies, pyramidal and rhomboid, depending on conditions. The pyramidal crystals proved to scatter X-rays to higher resolution, and conditions within the ground-based flight hardware for both Discovery and Mir were adjusted to produce crystals with this morphology. The experiment on Discovery produced large crystals in each of ten chambers. The experiment on Mir produced crystals in only one of the five assigned chambers, despite the fact that the simultaneous ground-based experiment produced large crystals in every corresponding chamber. Data collection was attempted for crystals from both space and ground-based experiments. Higher resolution data was obtained from crystals grown on Discovery than from either Mir or ground-based crystals, even though the crystals obtained from Discovery were smaller and forced to grow over a much shorter period of time because of the shorter length of the shuttle mission.

Journal Article↗
PubMed1997

Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing.

The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recording of three data sets (f'-minimum: 7125 eV, f"-maximum: 7138 eV and reference for scaling: 10,077 eV) resulted in an initial electron density of very high quality at 2.1 A, which was readily interpretable for model building. The model was refined to an R value of 19.1% (Rfree=22.4%) at 1.28 A resolution using a fourth data set collected at a photon energy of 11,810 eV. Comparison of this thermophilic cytochrome with its mesophilic mitochondrial or bacterial counterparts reveals significant structural differences which are discussed with respect to their importance for thermostability and binding between this cytochrome and its corresponding ba3-oxidase. Amino acid sequence similarities to other class I cytochromes are very weak and entirely limited to the region around the CXXCH motif close to the N terminus. The N-terminal two-thirds of cytochrome-c552 cover spatial regions around the heme prosthetic group that are similar to those observed for other cytochromes. The actual secondary structural elements that are responsible for that shielding do not, however, correlate well to other structures. Only the N-terminal helix (containing the heme binding cysteine residues) aligns reasonably well with other class I cytochromes. The most striking differences that distinguish the present structure from all other class I cytochromes is the C-terminal one-third of the molecule that wraps around the remainder of the structure as a stabilizing clamp, the existence of an extended beta-sheet covering one edge of the heme and the lack of any internal water molecule.

Bacterial Proteins↗
PubMed2001

[Multi-resolution blending rendering of the medical structure].

This paper presents a new medical data visualization method called multi-resolution blending rendering which has been developed for visualizing the large medical volume data sets. Different from those multi-resolution rendering methods which simplify the structures by polygon mesh optimization technique, the new method uses different resolution levels to represent different parts of a structure at the same time. So, it can preserve the integrality of the structure and emphasize the important part of the structure when simplifying the structure. The new method also takes advantage of the good qualities of the wavelet transform and constructs the multi-resolution blending model of the structure by orthogonal wavelet transform and transition operator. The experiment proves that our method can effectively simplify the model of the structure, enormously reduce the number of the triangle of the structure and speed up the structure rendering. It is especially suitable for interactive observations on a complex medical structure.

Algorithms↗
PubMed2000

ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.

Succinyl-CoA synthetase (SCS) catalyzes the following reversible reaction via a phosphorylated histidine intermediate (His 246alpha): succinyl-CoA + P(i) + NDP <--> succinate + CoA + NTP (N denotes adenosine or guanosine). To determine the structure of the enzyme with nucleotide bound, crystals of phosphorylated Escherichia coli SCS were soaked in successive experiments adopting progressive strategies. In the first experiment, 1 mM ADP (>15 x K(d)) was added; Mg(2+) ions were omitted to preclude the formation of an insoluble precipitate with the phosphate and ammonium ions. X-ray crystallography revealed that the enzyme was dephosphorylated, but the nucleotide did not remain bound to the enzyme (R(working) = 17.2%, R(free) = 22.8% for data to 2.9 A resolution). Catalysis requires Mg(2+) ions; hence, the "true" nucleotide substrate is probably an ADP-Mg(2+) complex. In the successful experiment, the phosphate buffer was exchanged with MOPS, the concentration of sulfate ions was lowered, and the concentrations of ADP and Mg(2+) ions were increased to 10.5 and 50 mM, respectively. X-ray diffraction data revealed an ADP-Mg(2+) complex bound in the ATP-grasp fold of the N-terminal domain of each beta-subunit (R(working) = 19.1%, R(free) = 24.7% for data to 3.3 A resolution). We describe the specific interactions of the nucleotide-Mg(2+) complex with SCS, compare these results with those for other proteins containing the ATP-grasp fold, and present a hypothetical model of the histidine-containing loop in the "down" position where it can interact with the nucleotide approximately 35 A from where His 246alpha is seen in both phosphorylated and dephosphorylated SCS.

Adenosine Diphosphate↗
PubMed1996

Refinement and structural analysis of bovine cytochrome b5 at 1.5 A resolution.

The structure of bovine liver cytochrome b(5), a soluble 93-residue proteolytic fragment of a 16 kDa membrane-bound hemoprotein, initially solved at 2.0 A resolution, has been refined at 1.5 A using data collected on a diffractometer. Refinement to 2.0 A resolution used the Hendrickson-Konnert procedure PROLSQ and was then extended to 1.5 A resolution using the program PROFFT. Only residues 3-87 could be identified in the model and these residues together with 93 water molecules gave an agreement factor of R = 0.161 for data in the resolution range 1.5-5 A. The structure was finally refined using the program X-PLOR, which enabled alternate conformers to be modelled for several surface side chains. Residues 1 and 2 at the amino terminus of the protein and residue 88 near the carboxyl terminus could be identified from these electron-density maps. However the remaining disordered carboxy-terminal residues could not successfully be included in the model. A total of 117 solvent molecules were included in the final refinement to give R = 0.164 for the data between 1.5 and 10 A.

Journal Article↗