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D M Cohen

Publications and source records attributed to D M Cohen.

At least 91 records · Page 5Linked to original sources
PubMed1994

Prediction of positional isotopomers of the citric acid cycle: the syntactic approach.

We propose a syntactic approach to modeling of biochemical fluxes that combines a rule-based description of atomic transfer in chemical reactions with a structurally oriented, stochastic model of chemical reaction kinetics. This approach avoids the use of differential equations to describe the production and disappearance of each molecule. The computer simulation predicts the changes over time in the abundance of each positional isotopomer of every metabolic intermediate in the citric acid cycle of heart cells, subsequent to administration of [2-13C]acetate (including natural abundance of 13C). (Positional isotopomers are isomers that differ in the positions of isotopes within the molecule.) The 32 positional isotopomers of glutamate fell into four groups with similar intragroup dynamics but with very different amplitudes. From the relative abundance of each isotopomer of glutamate, we calculate the relative area of multiplets of the nuclear magnetic resonance spectrum.

Acetates↗
PubMed1993

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases.

A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.

Adenine↗
PubMed1993

Urea induces Egr-1 and c-fos expression in renal epithelial cells.

The membrane-permeant solute urea, in concentrations present in the mammalian renal medulla, increased expression at the mRNA level of two immediate-early gene (IEG) transcription factors, Egr-1 and c-fos, in a time- and dose-dependent fashion in confluent growth-suppressed Madin-Darby canine kidney (MDCK) cells. This upregulation occurred in the absence of both cytotoxicity and an inhibition of protein synthesis, two potential nonspecific inducers of IEG expression. These findings were of interest because we have previously shown that hyperosmotic stress induced by the functionally membrane-impermeant solute NaCl increased expression of these IEG, whereas hyperosmotic stress induced by the membrane-permeant solute glycerol failed to do so. The urea-induced increase in Egr-1 mRNA expression was not secondary to enhanced message stability as determined by actinomycin D experiments and is therefore likely a consequence of urea-induced transcriptional activation. Augmented Egr-1 expression in response to urea treatment was also observed in another renal epithelial cell line, LLC-PK1, but not in other cell types examined. Therefore cells of renal epithelial origin may be uniquely capable of responding to hyperosmotic urea with increased expression of IEG transcription factors, and this increase is likely transcriptionally mediated.

Animals↗
PubMed1993

Urea selectively induces DNA synthesis in renal epithelial cells.

Hyperosmotic stress with the functionally impermeant solute NaCl has been shown by us and others to inhibit cell growth and DNA synthesis. Several lines of evidence suggest that urea, the other principal renal medullary solute, may exert a growth-promoting effect on renal epithelial cells. Among these is the finding that urea upregulates expression at the mRNA level of two growth-associated immediate-early genes, Egr-1 and c-fos. In the present study, urea, in concentrations characteristic of the renal medulla, increased [3H]thymidine incorporation approximately threefold in confluent, growth-suppressed Madin-Darby canine kidney (MDCK) cells, whereas another readily membrane-permeant solute, glycerol, did not. Urea also overcame the inhibitory effect of hyperosmotic NaCl on DNA synthesis. The urea-induced increase in [3H]thymidine incorporation was also evident in the renal epithelial LLC-PK1 cell line, but not in renal nonepithelial and epithelial nonrenal cell types examined. In addition, it was associated with a 15% increase in total DNA content measured fluorometrically at 24 h of treatment. There was, however, no associated increase in cell proliferation as measured by cell number, total protein content, or cell cycle distribution. Urea also failed to induce polyploidy or aneuploidy. Therefore cells of renal epithelial origin may be uniquely capable of responding to hyperosmotic urea with increased DNA synthesis through an undefined and potentially novel mechanism.

Animals↗
PubMed1993

Transmembrane segment prediction from protein sequence data.

We consider the automated identification of transmembrane domains in membrane protein sequences. 324 proteins (containing 1585 segments) were examined, representing every protein in the PIR database having the transmembrane domain feature annotation. Machine learning techniques were used to evaluate the efficacy of alternative hydrophobicity measures and windowing techniques. We describe a simpler measure of hydrophobicity and a new variable window size concept. We demonstrate that these techniques are superior to some previous techniques in minimizing the segment error rate. Using these new techniques, we describe an algorithm that has a 7.9% segment error rate on the sampled proteins, while classifying 16.7% of the amino acid residues as transmembrane.

Algorithms↗
PubMed1992

Expression of GLUT-2 cDNA in human B lymphocytes: analysis of glucose transport using flow cytometry.

The molecular characterization of transport proteins is often limited by transient functional expression or the need for a simple method to select functional cDNA clones. We used a mammalian expression system to obtain long-term expression of GLUT-2, an isoform of glucose permease. Rat GLUT-2 cDNA was ligated into an EBV vector (pLPP) and transfected into B lymphocytes which lack GLUT-2. Northern and Western analyses confirmed expression of GLUT-2 protein in membranes of transfected cells. Two functional assays using flow cytometry were developed to distinguish GLUT-2 transfectants from control/pLPP transfectants. Uptake of NBD-glucosamine, a fluorescent analogue of glucose, was increased in GLUT-2 transfectants. In addition, when exposed to hypertonic glucose medium, GLUT-2 transfectants and control/pLPP transfectants exhibited a difference in forward-angle light scatter (FALS), an index of cell volume, indicating a difference in glucose permeability. Independent measurements of glucose uptake (isotopic) and cell volume (video microscopy) confirmed the flow cytometry observations. This expression system used in combination with flow cytometry is useful for studying the functional properties of glucose and other solute transporters.

4-Chloro-7-nitrobenzofurazan↗
PubMed1992

Surgical management of congenital heart disease in the 1990s.

OBJECTIVE: To provide a broad overview of recent trends in surgical management of congenital heart disease. DESIGN: Review of recent literature. SETTING: Major centers for surgical management of congenital heart disease. SELECTION PROCEDURES: Analysis of important recent clinical publications. INTERVENTIONS: None. RESULTS AND CONCLUSIONS: Definitive, corrective surgery was previously reserved for children beyond infancy. Recognition of the complications associated with palliative operations as well as the realization that neonates and infants did not fare worse than older children during open heart surgery provided the impetus for primary corrective surgery at an earlier age. Advances in our understanding of perioperative care, improved diagnostic capability, and increasing experience with corrective surgery in association with several different congenital heart lesions has resulted in an established therapeutic approach to surgical management of congenital heart disease in neonates and infants.

General Surgery↗
PubMed1992

Primary malignant melanoma of the cervix and review of the literature.

Primary malignant melanoma of the cervix was diagnosed in a patient presenting with postmenopausal bleeding. A cervical lesion was biopsied, and diagnosis was established by electron microscopy and staining procedures. After failing radiotherapy, the patient was treated with simple hysterectomy and bilateral salpingo-oophorectomy. The cytology, histology, and electron microscopy of this lesion are presented in addition to a clinical discussion.

Aged↗
PubMed1991

N6-substituted adenosine receptor agonists: potential antihypertensive agents.

Adenosine is known to exert a wide range of pharmacological effects including hypotension. This effect of adenosine suggested that modified analogues of adenosine might provide useful antihypertensive agents. Thus, we prepared a series of novel N6-benzocycloalkyladenosines and studied their receptor binding and antihypertensive activity. The structure-activity relationship study shows that the adenosine analogues having the hydrophobic phenyl moiety one carbon away from the C6-nitrogen have modest affinity and selectivity for the A1 receptor, whereas those with the phenyl moiety two carbons away from the C6-nitrogen have excellent affinity and selectivity for the A1 receptor. Many of these analogues showed excellent antihypertensive activity with a wide range of effects on heart rate. There is no direct correlation between the receptor binding affinities and antihypertensive activity; however, it is more closely associated with A1 than A2 affinity. The bradycardic effect of these agonists seems to be due to the A1 affinity. From this set, compound 3 was further evaluated in secondary antihypertensive screens. It lowered the blood pressure dose dependently with effects lasting for over 20 h following administration of a 30 mg/kg dose. Compound 3 was also effective in lowering blood pressure in a renal hypertensive rat model. Thus, appropriately modified N6-substituted adenosines represent a novel class of antihypertensive agents.

Adenosine↗
PubMed1991

Immediate early gene and HSP70 expression in hyperosmotic stress in MDCK cells.

The early genetic response to hyperosmotic stress remains to be elucidated in eukaryotes. We observed that hyperosmotic NaCl in Madin-Darby canine kidney cells increased levels of mRNA encoding the immediate early gene (IEG) transcription factors Egr-1 and c-fos at 2 h of treatment by two- and threefold, respectively. Sham treatment and hyperosmotic glycerol, and ineffective osmole, had no effect. Hyperosmotic NaCl, but not glycerol, also increased the mRNA level of the stress protein HSP70 by four- to fivefold at 2, 6, and 24 h. These changes occurred despite inhibition of total RNA transcription rate and DNA synthesis rate by NaCl. Neither NaCl nor glycerol treatment manifested significant cytotoxicity. NaCl, and to a lesser extent glycerol, suppressed protein synthesis, a phenomenon previously correlated with IEG superinduction. Therefore, hyperosmotic stimuli with different physiological effects result in differential expression of IEGs and the stress protein HSP70; induction of the former may govern the ensuing program of gene expression that culminates in the osmolyte response, while the latter may serve as a temporizing protective measure.

Animals↗
PubMed1990

Randomness in the heparin polymer: computer simulations of alternative action patterns of heparin lyase.

Heparin is a mixture of linear polysaccharides of undetermined sequence. Both biosynthetic data and computer simulation studies have established that each heparin polymer chain is comprised of oligosaccharides of defined sequence, representing ordered domains. One such ordered domian is a pentasaccharide corresponding to heparin's antithrombin III binding site. Previous computer simulation studies, performed under the assumption that heparin lyase (heparinase, EC 4.2.2.7), has a random endolytic action pattern, suggested that certain of these ordered oligosaccharide domains may themselves be nonrandomly arranged in the heparin polymer. The present work presents computer simulations of alternative action patterns for heparin lyase while assuming a random distribution of these oligosaccharide units within the heparin polymer. We consider action patterns that are determined solely by the primary structure of the substrate molecules. Results of the simulations are compared to (1) the experimental measurements of product chains formed throughout the reaction and (2) the change in weight average molecular weight Mw as a function of reaction completion as determined by absorbance at 232 nm. From the simulation of 60 action patterns for heparin lyase, we infer that one of the following statements concerning heparin and heparin lyase is true: (1) Heparin is a random arrangement of a small number of structurally defined oligosaccharide units. Heparin lyase changes its action pattern during the depolymerization of heparin (perhaps influenced by the secondary structure of substrate). (2) Heparin contain clusters of oligosaccharide sequences that are present in low concentrations (overall) in the polymer. Heparin lyase has a specificity for cleaving glycosidic linkages either exolytically at the nonreducing terminus of a chain or (endolytically) at the reducing side of these rare oligosaccharide sequence.

Carbohydrate Conformation↗
PubMed1990

Episcleral radioactive plaque therapy: initial clinical experience with 56 patients.

Between 1983 and 1987, 56 patients with choroidal melanoma were treated at the University of Southern California with episcleral plaque (RPT). There were 29 female and 27 male patients, with a mean age of 59 years. Tumor stage at diagnosis was T2 in 18 (32%) and T3 in 38 (68%) patients. The tumor height ranged from 2.9 to 15 mm (mean 6.8 mm). Radial dimensions ranged from 5 to 25 mm (mean 13.2 mm), and circumference ranged from 7 to 23 mm (mean 12.3 mm). Most (77%) patients had posteriorly located tumors, including 18% that were juxtapapillary. Custom-designed gold plaques were utilized in this study. Radioactive isotopes used were 125I for 26 procedures or 192Ir for 31 procedures. A total of 56 patients were treated, with one patient having two procedures. Radiation doses at the tumor apex ranged from 29.8 to 165.4 Gy (mean 94.5 Gy), with the dose at 5-mm depth ranging from 70.5 to 430 Gy (mean 161.5 Gy). Follow-up ranged from 29 to 57 months (mean 39 months). The overall 4-year survival was 96%, with a 91% incidence of free-of-disease progression at 4 years. The majority (84%) of patients experienced a decrease in tumor height, with 27 (48%) patients having greater than 50% decrease. Increase in tumor height was noted in 5 (9%) and no change in 4 (7%) patients. Useful vision (greater than 5/200) was observed in 59% of patients, including 21% who had improved vision. Metastatic tumor occurred in 5 (9%) patients, with a mean time to metastases of 14 months. There was a good correlation between radial tumor dimension and metastatic disease, p less than 0.001. Treatment complications were observed in 34 (61%) patients, with cataract and retinopathy being the most common. Enucleation was performed in 11 (20%) patients, with a mean time to enucleation of 14.5 months. Causative factors for enucleation were treatment complications in 6 and tumor progression in 5 patients. Enucleations were required primarily in patients with tumors greater than 8 mm in height (p = 0.009). Improved RPT techniques with three-dimensional dosimetry are needed to reduce the overall incidence of treatment complications. Adjuvant hyperthermia is being investigated in an attempt to improve tumor control in patients with larger tumors.

Adult↗
PubMed1989

An artificial-intelligence technique for qualitatively deriving enzyme kinetic mechanisms from initial-velocity measurements and its application to hexokinase.

We have developed a computer method based on artificial-intelligence techniques for qualitatively analysing steady-state initial-velocity enzyme kinetic data. We have applied our system to experiments on hexokinase from a variety of sources: yeast, ascites and muscle. Our system accepts qualitative stylized descriptions of experimental data, infers constraints from the observed data behaviour and then compares the experimentally inferred constraints with corresponding theoretical model-based constraints. It is desirable to have large data sets which include the results of a variety of experiments. Human intervention is needed to interpret non-kinetic information, differences in conditions, etc. Different strategies were used by the several experimenters whose data was studied to formulate mechanisms for their enzyme preparations, including different methods (product inhibitors or alternate substrates), different experimental protocols (monitoring enzyme activity differently), or different experimental conditions (temperature, pH or ionic strength). The different ordered and rapid-equilibrium mechanisms proposed by these experimenters were generally consistent with their data. On comparing the constraints derived from the several experimental data sets, they are found to be in much less disagreement than the mechanisms published, and some of the disagreement can be ascribed to different experimental conditions (especially ionic strength).

Adenosine Triphosphate↗
PubMed1989

Nonrandom structural features in the heparin polymer.

Computer simulation studies were used to prepare an ensemble of heparin number chains. The polydispersity of these chains was simulated by introducing a specific "fraction of terminators", and it closely resembled the experimentally observed polydispersity of a porcine mucosal, glycosaminoglycan heparin. The same percentage of simulated chains contained antithrombin III (ATIII) binding site sequences as are typically found to contain ATIII binding sites using affinity chromatography. Heparin lyase action was then simulated by using Michaelis-Menten kinetics. In one model, heparin chains were constructed from the random assembly of monosaccharide units using the observed mole percentage of each. After simulated depolymerization, the final oligosaccharides formed were compared to the observed oligosaccharide products. The simulation which assumed a random distribution of monosaccharide units in heparin did not agree with experimental observations. In particular, no ATIII binding site sequences were found in the simulated number chains. The results of this simulation indicate that heparin is not simply a random assembly of monosaccharide units. These results are consistent with the known, ordered biosynthesis of heparin. In a second model, heparin chains were constructed from randomly assembled oligosaccharides at the mole percentage in which each is found in the final product mixture. The action of heparin lyase was then simulated, and the distribution of the oligosaccharide products was measured throughout the simulated time course of the depolymerization reaction. The simulated rate of formation and final concentration of a particular oligosaccharide which contains a portion of heparin's ATIII binding site were similar to those observed experimentally. These results are consistent with the random distribution of ATIII binding sites within glycosaminoglycan heparin.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbohydrate Conformation↗
PubMed1989

Maxillary metastasis of transitional cell carcinoma: report of a case.

Metastases to the maxilla are extremely rare, and only 64 cases of histologically proven maxillary metastases can be found in the English-language literature. This article reports the first case of metastatic transitional cell carcinoma of the urinary bladder to the maxilla. The distribution of proven cases of maxillary metastasis and the possible anatomic pathways for this metastasis are discussed.

Aged↗
PubMed1988

Concurrent anomalies: cheilitis glandularis and double lip. Report of a case.

Double lip and cheilitis glandularis are uncommon anomalies involving the minor salivary glands of the lip. A unique case of concurrent double lip and cheilitis glandularis is presented. The development, diagnosis, and treatment of both lesions are reviewed. Their concurrent development in this patient appears to be unrelated.

Aged↗