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PubMed2006

Sperm nuclear DNA damage: update on the mechanism, diagnosis and treatment.

Previous studies have shown that repeated intracytoplasmic sperm injection failures can be associated with sperm DNA damage. This paper reviews the current understanding of the mechanism of sperm DNA damage, discusses different diagnostic methods and their threshold values to discriminate between good- and poor-prognosis patients, and outlines the currently available treatment options. A rational approach to the interpretation of sperm DNA fragmentation data and to the choice of the optimal treatment method is suggested.

Antioxidants↗

PubMed1996

Development of a Comprehensive Surgical Information System at Madigan Army Medical Center.

The Operative Registry (DA Form 4108) has been the information source for surgical data supporting quality assurance and utilization review efforts at Madigan Army Medical Center. Recently, Madigan's requirements for data and reporting changed. Like other government medical facilities, Madigan began pervasive quality-improvement efforts. This resulted in new ideas to measure hospital performance. Consequently, requirements for surgical data required to support quality and resource management reporting, utilization review, residency review reporting, research and credentialing changed. This article details Madigan's approach to addressing these requirements via development of a comprehensive computing solution. It discusses Madigan's fragmented data environment before system development, and gives the reader perspective on the decision-making process that led to system development rather than purchasing a commercial product. Finally, the article describes how a strong partnership between staff and developers was key to providing a solution that exceeded established goals.

Hospitals, Military↗

PubMed1986

DIGICALC: a restriction fragment analysis program.

DIGICALC is a program designed to aid in the acquisition, storage, and analysis of nucleic acid restriction fragment data. The chief considerations during program design were (i) ease of use for people with varying degrees of computer experience, (ii) minimal hardware requirements (e.g. an IBM PC), (iii) portability and ease of modification, and (iv) improved functionality in sizing and comparing restriction fragments over manual methods. The program accepts manual or digitizer input of nucleic acid fragment mobility, calculates the fragments' sizes, and provides the means to search the fragment database and to produce charts of fragment sizes.

Base Sequence↗

PubMed2006

Electrospray ionization and triple quadrupole tandem mass spectrometry study of some biologically relevant homo- and heterodimeric cadmium thiolate conjugates.

A series of 19 compounds of general formula R1S-Cd-SR2, R1, and R2, being some biologically relevant thiol amino acids and peptides, were prepared by direct reaction of cadmium(II) ions and thiols in water at millimolar concentration. The obtained products were characterized by electrospray ionization and triple quadrupole tandem mass spectrometry. The source spectra of stoichiometric 1:2 Cd-thiol systems containing either an individual thiol or equimolar mixtures of two different thiols featured several Cd-containing signals, although at much lesser intensity than in the previously reported experiments with mercury(II) (J. Am. Soc. Mass Spectrom. 2004, 15, 288-300). Also, the relative intensity of the homo- and heterodimeric thiolates were significantly different from the theoretically expected 1:2:1 ratio, thus pointing at some degree of discrimination between the different thiols. In particular, homo-cysteine showed much less reactivity than cysteine, and penicillamine and cysteine methyl ester much less than the free amino acid. The fragment spectra show structure-specific ions for the different ligands bound to the metal ion and allow a stand-alone determination of the connectivity also of isomeric pairs. The fragmentation pathways are similar to those observed for the corresponding mercury(II) analogues, with the addition of further intense and specific fragments, one formally carrying a Cd-bound OH ligand and one connected as a five-membered oxazolone carrying a cadmium-bis-thiolate side chain, both formed with a high intensity. Energy-resolved fragmentation data show that metal-free ions can be generated from cysteine but not from glutathione conjugates and point to the possibility of unveiling differences in the biochemical behavior of the conjugates of different heavy metals through the detailed study of their mass spectrometric fragmentation.

Algorithms↗

PubMed2005

Identification of flavonoids of Rhodiola rosea by liquid chromatography-tandem mass spectrometry.

Phenolic compounds from the aerial parts of medicinal plant Rhodiola rosea were identified using LC/MS experiments with time-of-flight and triple quadrupole instruments, providing accurate mass and CID fragmentation data about the compounds. Supercritical fluid extraction (SFE) was used to remove non-polar compounds from the samples, followed by liquid extraction of the flavonoids. Flavonoids were the main constituents in aerial parts of the plant, and no phenylpropanoids were detected. In addition to usual fragment ions providing the size of the attached glycosides in flavonoids, ions due to radical cleavage of glycosides were observed in the negative ion mode with relatively high collision energies. Use of these ions for elucidating the glycosylation site in the aglycone part was evaluated and was found to give some tentative information, but their use in unambiguous identification of unknown flavonoids is not recommended. Fifteen flavonoids, of which 10 were previously unreported from the plant, were identified.

Chromatography, High Pressure Liquid↗

PubMed2005

Multi-parameter investigation of tandem mass spectrometry in a linear ion trap using response surface modelling.

The feasibility of experimental design in combination with subsequent response surface modelling was illustrated for the prediction and interpretation of tandem mass spectrometric (MS/MS) fragmentation data using a linear quadrupole ion trap under various experimental conditions. The instrumental parameters included were (i) the pressure of the collision gas, (ii) the collision energy, (iii) the fill time of the linear ion trap and (iv) the scan rate. The spectral intensity and width of five fragment ions of the doubly charged neuro-active peptide bombesin were used for evaluation, and all experiments were performed so as to resemble the results obtained from a liquid chromatographic peak. The reported results show how fairly simple mathematical tools can be utilized successfully to describe fundamental mechanisms associated with multiple collisional activation and collision-induced dissociation processes without an extensively controlled experimental environment. Most beneficial, using the suggested approach, is the ability to study interaction (synergistic) effects between various parameters. As was realized from the results, many interaction effects are indeed significant. For example, the effect on the signal intensity of different collision gas pressure settings is strongly dependent on the settings of the other parameters. The described approach can easily be adopted for optimization purposes of any MS/MS experiment.

Journal Article↗

PubMed1986

Gas chromatography-mass spectrometry of isobutyl ester trimethylsilyl ether derivatives of bile acids and application to the study of bile sterol and bile acid biosynthesis in rat liver epithelial cell lines.

The derivatization of bile acids into trimethylsilyl ether isobutyl ester (IBTMS) and of neutral sterols into trimethylsilyl ether (TMS) allowed the separation on an OV-1 capillary gas chromatography column of 15 bile steroids as follows: cholesterol, 7 alpha-hydroxycholesterol, 6 beta-hydroxycholesterol, 6 alpha-hydroxycholesterol, 7 beta-hydroxycholesterol, lithocholate, deoxycholate, 25-hydroxycholesterol, chenodeoxycholate, cholate, murocholate, hyodeoxycholate, ursodeoxycholate, hyocholate, and beta-muricholate. Fragmentation data of the coupled gas chromatographic-mass spectrometric (GC-MS) analysis of these nine bile acids as IBTMS derivatives under electron impact and chemical ionizations (methane, isobutane, and ammonia) are given. The ammonia chemical ionization appears to be the best mode for compound identification and quantitation due to fragmentations into high mass ions. The comparison of methylene units of the five sterols as TMS derivatives and of each type of methyl, TMS, or isobutyl ester of the nine bile acids as TMS ethers showed that isobutyl esterification increased dramatically the retention time of the bile acids, allowing their separation after the neutral sterols. Different methods of GC-MS analysis were applied to the study of bile steroid secretion in long-term rat liver epithelial cell lines, either serum-supplemented cell lines or serum-free cell lines, growing in serum-free medium since the primary explanation or after adaptation of serum-supplemented lines to this medium. It is demonstrated for the first time that liver epithelial cell lines maintain the metabolic pathway leading from synthesized cholesterol to dioxygenated sterols and the two normal main primary bile acids of the liver, chenodeoxycholic acid and cholic acid, up to 32-47% of the in vivo daily rate, and in addition the production of alpha-muricholic acid, the bile acid marker of murine liver.

Animals↗

PubMed1989

Intracellular cleavage of newly synthesized low affinity Fc epsilon receptor (Fc epsilon R2) provides a second pathway for the generation of the 28-kDa soluble Fc epsilon R2 fragment.

It has been reported that the 45-kDa low affinity Fc epsilon R (Fc epsilon R2) on B cells is cleaved spontaneously from the cell surface to release a 28-kDa soluble fragment (sFc epsilon R2). This study demonstrates an additional mechanism by which B cells generate this fragment. Data from 35S methionine pulse-chase experiments with the Fc epsilon R2 bearing human B lymphoblastoid cell line, RPMI 8866, and immunoprecipitations of cell lysates and culture supernatants with an Fc epsilon R2 specific mAb, mAb 25, demonstrates the existence of a cell-associated 28-kDa Fc epsilon R2 fragment. This fragment was shown by partial amino(NH2)-terminal sequence analysis to be identical to the previously described 28-kDa sFc epsilon R2. The resistance to cell treatment with trypsin indicated that it was located intracellularly. Its appearance early in the biosynthesis of the Fc epsilon R2 (within a 10-min pulse), before the Fc epsilon R2 reached the cell surface, suggested that some of this fragment was generated intracellularly. Neutralization of acidic organelles with NH4Cl inhibited the formation of this intracellular fragment, strongly suggesting that it was a produce of intracellular cleavage of the Fc epsilon R2. Finally, this 28-kDa intracellular fragment was shown to be released into the culture supernatant, suggesting an intracellular mechanism by which the cells generate sFc epsilon R2.

Antigens, Differentiation, B-Lymphocyte↗

PubMed2001

Informatics and multiplexing of intact protein identification in bacteria and the archaea.

Although direct fragmentation of protein ions in a mass spectrometer is far more efficient than exhaustive mapping of 1-3 kDa peptides for complete characterization of primary structures predicted from sequenced genomes, the development of this approach is still in its infancy. Here we describe a statistical model (good to within approximately 5%) that shows that the database search specificity of this method requires only three of four fragment ions to match (at +/-0.1 Da) for a 99.8% probability of being correct in a database of 5,000 protein forms. Software developed for automated processing of protein ion fragmentation data and for probability-based retrieval of whole proteins is illustrated by identification of 18 archaeal and bacterial proteins with simultaneous mass-spectrometric (MS) mapping of their entire primary structures. Dissociation of two or three proteins at once for such identifications in parallel is also demonstrated, along with retention and exact localization of a phosphorylated serine residue through the fragmentation process. These conceptual and technical advances should assist future processing of whole proteins in a higher throughput format for more robust detection of co- and post-translational modifications.

Algorithms↗

PubMed1989

[DNA fingerprinting of Rattus norvegicus: a new approach in genetic analysis].

Recent finding in highly effective DNA probes for RFLP testing (of hypervariable minisatellite DNA type) has led to the invention of DNA fingerprinting--the new technique of great value for identification of individuals, establishing biological kinship and studies in population genetics. We anticipate that DNA fingerprinting procedure with M13 phage DNA as a probe which we have developed earlier, makes it possible to apply new approach in genetic analysis--establishing, whether or not a particular locus is associated with the inheritance of genetic disease, by comparing the whole restriction fragment data from affected and unaffected animals. In this work, using the method described we characterized the Kroushynsky-Molodkina rat strain with hereditary disposition for epileptic attacks and performed comparative fingerprint analysis of these defective and normal rat genomes. The data obtained may hold some promises for further seeking the particular defective gene.

Animals↗

PubMed1986

Intracellular proteolytic systems may function as secondary antioxidant defenses: an hypothesis.

In recent years it has become clear that various free radicals and related oxidants can cause serious damage to intracellular enzymes and other proteins. Several investigators have shown that in extreme cases this can result in an accumulation of oxidatively damaged proteins as useless cellular debris. In other instances, proteins may undergo scission reactions with certain radicals/oxidants, resulting in the direct formation of potentially toxic peptide fragments. Data has also been gathered (recently) demonstrating that various intracellular proteolytic enzymes or systems can recognize, and preferentially degrade, oxidatively damaged proteins (to amino acids). In this hypothesis paper I present evidence to suggest that proteolytic systems (of proteinases, proteases, and peptidases) may function to prevent the formation or accumulation of oxidatively damaged protein aggregates. Proteolytic systems can also preferentially degrade peptide fragments and may thus prevent a wide variety of potentially toxic consequences. I propose that many proteolytic enzymes may be important components of overall antioxidant defenses because they can act to ameliorate the consequences of oxidative damage. A modified terminology is suggested in which the primary antioxidants are such agents as vitamin E, beta-carotene, and uric acid and such enzymes as superoxide dismutase, glutathione peroxidase, and DT-diaphorase. In this classification scheme, proteolytic systems, DNA repair systems, and certain lipolytic enzymes would be considered as secondary antioxidant defenses. As secondary antioxidant defenses, proteolytic systems may be particularly important in times of high oxidative stress, during periods of (primary) antioxidant insufficiency, or with advancing age.

Adenosine Triphosphate↗

PubMed2006

Approximate cost functions for solid waste treatment facilities.

Cost estimation is a basic requirement for planning municipal solid waste management systems. The variety of organizational, financial and management schemes and the continuously developing technological advancements render the economic analysis a complex task, made more complex by the scarcity of real cost data. The objectives of this paper were: (1) to explore the problems arising in getting cost estimates from scattered and limited published data; (2) to suggest a procedure for generating cost functions relating initial set-up cost and operating cost with facility size; and (3) to present such cost functions, relevant to European states, for selected types of solid waste treatment and disposal facilities. Regarding the problems of available scarce data, one needs to deal with cost figures which correspond to facilities with variations in size, technology, year of construction, working conditions, level of technological automation, environmental impacts, social acceptance, capacity utilization rate, composition of inflowing waste, waste management policies, degree of compliance with quality standards, etc. The paper addresses this issue and discusses the proper use of statistical analyses in such cases of fragmented data; moreover, it points out some usual misuses of statistics by analysts and the danger of getting erroneous results. The suggested process for generating cost functions acceptable to the decision-makers is pivoted around the question of acceptable approximation level. Finally, approximate cost curves are suggested for waste-to-energy facilities, landfilling facilities, anaerobic digestion facilities and composting facilities.

Conservation of Natural Resources↗

PubMed1999

Taxonomy and phylogeny of some Eimeria (Apicomplexa:Eimeriidae) species of rodents as determined by polymerase chain reaction/restriction-fragment-length polymorphism analysis of 18S rDNA.

The 18S rDNA genes of 10 Eimeria species from rodents (E. albigulae, E. arizonensis, E. falciformis, E. langebarteli, E. nieschulzi, E. onychomysis, E. papillata, E. reedi, E. separata, E. sevilletensis) were polymerase-chain-reaction (PCR)-amplified, digested with 12 restriction endonucleases, and electophoresed in agarose gels. The resulting fragment patterns (riboprints) distinguished all species except E. sevilletensis from E. falciformis, and E. arizonensis from E. albigulae; the sporulated oocysts of the latter two species and of E. onychomysis are often indistinguishable morphologically. When the restriction fragment data were analyzed using distance and parsimony phylogenetic methods a clade was found consistently, which contained E. arizonensis, E. albigulae, E. onychomysis, E. reedi, and E. papillata. This finding and other results of the phylogenetic analyses agreed and supplemented previous phylogenetic work on the Eimeria of rodents. Riboprinting appears to provide useful data for taxonomic and phylogenetic studies on the genus Eimeria and may be especially practical when samples do not contain enough oocysts for other molecular-based methods.

Animals↗

PubMed1983

Carbodiimide inactivation of Escherichia coli RNA polymerase promoters on supercoiled simian virus 40 and ColE1 DNAs occurs by a one-hit process at salt concentrations in the physiological range.

A previous study (Hale, P., Woodward, R. W., and Lebowitz, J. (1980) Nature 284, 640-644) showed that Escherichia coli RNA polymerase promoters on superhelical SV40 DNA are highly selective targets for chemical modification by the water-soluble carbodiimide, N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethyl carbodiimide (CMC). To extend the inactivation analysis of supercoiled DNAs, we determined the number and location of RNA polymerase binding sites on the supercoiled and linear forms of ColE1 DNA. We also determined the site distribution of [3H] CMC on the superhelical form. This information, coupled with per cent inhibition of transcription versus CMC-bound curves, allowed a test of the specificity of the CMC inactivation by the Poisson equation. Curves were obtained for supercoiled SV40 DNA modified at 0 and 100 mM NaCl (2 mM NaPi, pH 7.0) and for supercoiled ColE1 DNA modified at 0, 100, and 320 mM NaCl. For supercoiled SV40 DNA, these data, coupled to our knowledge of the number of RNA polymerase binding sites from the study cited above, revealed an excellent fit to a one-hit inactivation by the Poisson equation for DNA modified at 100 mM NaCl. For ColE1 DNA, we obtained an excellent fit to a Poisson distribution when supercoiled DNA was modified at 320 mM NaCl. The Poisson distribution can be applied to [3H] CMC restriction fragment data with equivalent results. These results suggest that promoter sites can be forced into different structural conformations with variable degrees of unpairing.

Affinity Labels↗

PubMed1990

Binding of a monoclonal antibody and its Fab fragment to supported phospholipid monolayers measured by total internal reflection fluorescence microscopy.

The association of an anti-dinitrophenyl monoclonal antibody and its Fab fragment with supported phospholipid monolayers composed of a mixture of dipalmitoylphosphatidylcholine and dinitrophenyl-conjugated dipalmitoylphosphatidylethanolamine has been characterized with total internal reflection fluorescence microscopy. The surface densities of bound antibodies were measured as a function of the antibody and Fab solution concentrations, and as a function of the solution concentration of dinitrophenylglycine. The apparent association constant of Fab fragments with surface-associated haptens was approximately 10-fold lower than the association constant for haptens in solution, and the apparent surface association constant for intact antibodies was only approximately 10-fold higher than the constant for Fab fragments. Data analysis with simple theoretical models indicated that, at most antibody surface densities, 50-90% of membrane-associated intact antibodies were attached to the surface by two antigen binding sites.

Antibodies, Monoclonal↗

PubMed2000

Caspase-dependent cleavage of the retinoblastoma protein is an early step in neuronal apoptosis.

Rb-deficient embryos (Rb-/-) show abnormal degeneration of neurons and die at mid-gestation, suggesting that RB may protect against apoptosis. Having previously shown that cyclin D1 accumulates during K+-induced apoptosis of granule neurons, we chose to investigate the role of RB under these conditions. We show that RB is cleaved in its C-terminus during the onset of neuronal apoptosis. Caspase 3-like activity increases following K+ deprivation and the time course correlates with RB cleavage and apoptosis. Although the use of a specific caspase 3-like inhibitor (z-DEBD.fmk) delays RB cleavage and reduces DNA fragmentation, data implicate other caspases in these processes. However, K+ deprivation induces a gradual production of the active p20 subunit of caspase 3 (CPP32) that coincides with RB disappearance at the cellular level. Nuclear detection of a transfected HA-tagged caspase cleavage-resistant RB mutant (DEAG/D to DEAA/D) revealed a significant decrease in apoptosis of neurons expressing the RB mutant (less than 5%) relative to the wild type form of RB (40%) during K+ deprivation. Taken together, these data show that caspase-dependent cleavage of RB is an early permissive step of the apoptosis-inducing signaling pathway in neurons. They indicate a major role of RB in neuronal protection.

Amino Acid Chloromethyl Ketones↗

PubMed1997

Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis.

Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.

Alligators and Crocodiles↗

PubMed1999

Molecular characterization of Drosophila C virus isolates.

Reverse transcription coupled with polymerase chain reaction and restriction enzyme analysis was used to characterize 12 Drosophila C virus isolates from geographically different regions. A 1.2-kb fragment was amplified from cDNA and profiles from digestion with 20 restriction enzymes were generated. Analysis of the restriction fragment data gave estimates of nucleotide divergence of 0-10% between isolates. The isolates were grouped on the basis of genetic distance estimates derived from the restriction data. For the isolates from which a single genotype could be purified, a geographical pattern in the distribution of viral genotypes was identified. The 4 Moroccan isolates were very closely related to each other, differing in only 1 restriction profile. The 2 Australian isolates were each other's closest relatives, as were the 2 isolates first recovered in France. The PCR-RFLP technique used in this study has provided us with a simple procedure which can be used to characterize DCV isolates. A single enzyme, Taq I, generated 5 distinct and diagnostic restriction fragment patterns, which allowed easy assignment of isolates to one of the five viral genotypes identified in this study.

Animals↗