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In vitro transcription and translation of proteins encoded by the BamHI-B genomic fragment of herpes simplex virus-1.

The BamHI-B DNA fragment of herpes simplex virus type-1 (HSV-1) is associated with intraperitoneal pathogenicity. Among the recently mapped RNA transcripts from this fragment (15), one was reported to be associated with latency. To relate the RNA transcripts to virus pathogenicity, the in vitro-transcribed RNAs from BamHI-B fragments of three HSV-1 strains--F (pathogenic), R19, and HFEM (apathogenic), were studied by in vitro translation. When the BamHI-HpaI (0.738-0.755 map units) DNA fragment from HSV-1 strain F was transcribed rightward and translated, three proteins of 70, 63, and 51 kD were detected. The 63 kD protein resembles in size and orientation the protein encoded by the ICP-27 (IE-2) gene (0.740-0.749 mu). The 51 kD polypeptide is assumed to be a prematurely terminated form of this protein. No proteins were obtained from RNA transcribed in the opposite direction. The SalI-NcoI (0.746-0.761 mu) fragment of the three HSV-1 strains yielded two proteins of 25 and approximately 15 kD when transcribed rightward and a 35 kD polypeptide from RNA transcribed in the opposite direction. As a result of the genomic deletion in HFEM, it was possible to obtain the 35 kD protein from the SalI-SalI DNA fragment (0.746-0.761 mu) as well. In vitro transcription and translation of the PstI-SalI (0.778-0.790 mu) DNA fragment (the right-hand side of HpaI-P) did not result in protein synthesis. The possibility that the UL56 gene is connected with the intraperitoneal pathogenicity of HSV-1 is discussed.

Animals↗

The generation effect in primed word-fragment completion reexamined.

Two experiments were designed to test a claim made by Gardiner (1988) that there are generation effects in implicit memory as measured by word-fragment completion. Subjects either read words at study or generated the words from fragments. As in previous research, fragments were completed to a greater extent if they were identical at study and test than if they differed. In Experiment 1 it was found that subjects could recognize explicitly the exact form of fragments that had been used for self-generation and distinguish these from other forms of fragments. An analysis of the contingency relations between recognition of fragments and fragment completion showed a high degree of dependence between the two tests. In Experiment 2 it was found that the match of surface features between study and test was a necessary, but not sufficient, condition to produce enhancement of priming. The results are interpreted as supporting the claim that generation does involve a data-driven component in addition to semantic elaboration.

Adolescent↗

Conformation of concanavalin A and its fragments in aqueous solution and organic solvent-water mixtures.

The conformations of concanavalin A (con A), an all-beta protein, and its three CNBr-cleaved fragments were studied by CD. Con A in buffer showed a 197 nm maximum and a 223 nm minimum, which were red-shifted by 6-7 nm from those of regular all-beta proteins and beta-sheet of (Lys)n. Fragment 1 (residue 1-42) resembled an unordered form with a CD maximum at 200 nm, but fragments 2 (residues 43-129) and 3 (residues 130-237) showed a regular CD spectrum with two extrema at 192-193 nm (+) and 214-216 nm (-). Equimolar mixture of the three fragments showed some degree of interaction, but did not reconstitute the conformation of native con A, probably because of the loss of bound Ca2+ and Mn2+ ions in the fragments. In ethanol-, methanol-, and dioxane-water mixed solvents, con A and its fragments remained as beta-sheet. In contrast, addition of trifluoroethanol and sodium dodecyl sulfate induced alpha-helix at the expense of beta-sheet for con A and its fragments in aqueous solution. In 80% trifluoroethanol, the induced helicities exceeded their sequence-predicted helix-potentials, but in 10 mM sodium dodecyl sulfate the helicities agreed well with corresponding predictions.

Buffers↗

Cell death due to ACNU-induced DNA fragmentation: inhibition by cycloheximide.

Several anticancer drugs have recently been shown to induce cell death in a manner similar to programmed cell death or apoptosis. The purpose of this study is to explore the mode of cell death caused by ACNU, a water-soluble nitrosourea. Exposure of rat glioma cell line KEG-1 to ACNU for 2 hours resulted in oligonucleosomal DNA fragmentation, creating a 'ladder' on agarose gel electrophoresis. DNA fragmentation began 18 hours after ACNU treatment, and preceded loss of membrane integrity as evaluated by the trypan blue exclusion test. The extent of DNA fragmentation increased in a dose-dependent manner, and the cell survival rate decreased reciprocally. A translational inhibitor, cycloheximide, suppressed this DNA fragmentation and enhanced cell survival rate with partial inhibition of protein synthesis. However, a transcriptional inhibitor, actinomycin D, failed to inhibit DNA fragmentation or enhance cell survival. Cycloheximide-inhibitable DNA fragmentation was also found in the KEG-1 implanted in vivo rat model following the administration of ACNU. These findings suggest that ACNU induces cell death associates with DNA fragmentation and partially with protein synthesis.

Animals↗

Effect of laser fragmentation of cholesterol and mixed gallstones on in vitro dissolution in methyl tert-butyl ether.

This study examined cholesterol and mixed gallstone dissolution in vitro by methyl-tert-butyl ether (MTBE) after gallstone fragmentation. Three morphologically identical gallstones were obtained from 42 patients. One stone from each patient was fragmented with laser energy at a wavelength of 504 nm delivered to the stone surface with a 320-microns quartz fiber. Intact and fragmented stones from the same patient were incubated without stirring in MTBE and dissolution was expressed as the percent of initial stone weight remaining after 2 hr. Stone composition did not correlate with the amount of laser energy required for stone fragmentation. Fragmented stones dissolved faster than intact stones in MTBE with 13.97% +/- 0.37% vs 31.0% +/- 0.51% respectively (mean +/- SEM) of initial stone weight remaining at 2 hr (P less than 0.0001). Initial stone weight and stone matrix content significantly predicted dissolution of intact (P = 0.0033 and P = 0.0483, respectively) and fragmented stones (P = 0.003 and P = 0.0001, respectively) in MTBE. These data suggest that the gallstone matrix may inhibit stone dissolution even after stone fragmentation.

Cholelithiasis↗

Stability of genomic DNA fragment patterns in methicillin resistant Staphylococcus aureus (MRSA) during the course of intra- and interhospital spread.

The analysis of genomic DNA fragment patterns has revealed as a powerful tool for strain discrimination in Staphylococcus aureus; for use as an epidemiological marker, stability during the course of an outbreak is an essential prerequisite. Genomic DNA fragment patterns (SmaI restriction, pulsed-field electrophoresis) of four different epidemic MRSA strains were compared along with intra- and interhospital and country-wide spread over more than 12 months in Germany. Strain I was isolated from infections in 8 hospitals. In one hospital a subclone arised which differed from the original strain by 4 fragments. Strain II was spread among 4 hospitals, isolates from three of these hospitals exhibited a variability of one to three fragments in the 150-200 kb range. Two hospitals in the Hannover-area were affected by strain III; in 17 isolates of this strain a variability up to three fragments was found in the 170-200 kb range. Strain IV was isolated from 19 cases of infections in 3 hospitals in Berlin. The fragment patterns were completely stable. When S. aureus strains are typed by genomic DNA fragment patterns, a variability in a definite range of molecular masses during the course of an epidemic should be taken into consideration.

Cross Infection↗

Cloning in Escherichia coli of a Bacillus subtilis arginine repressor gene through its ability to confer structural stability on a fragment carrying genes of arginine biosynthesis.

The structural stability of a previously isolated recombinant plasmid pUL720 was examined. pUL720 contains an insert in pBR322 of 23.8 kbp comprising 4 EcoR1 fragments of sizes 12 kbp and 6 kbp, both of which are homologous to the B. subtilis genome, and 5 kbp and 0.8 kbp (of unknown origin). The 12 kbp fragment, which encodes the arginine biosynthesis genes argA-F-cpa, cannot be cloned in isolation in a high copy vector in E. coli but can be inserted into a low copy vector pGV1106 to generate pUL800. Deletion analysis of pUL720 indicated that the 5 kbp and 0.8 kbp fragments were not necessary to maintain plasmid stability. The 6 kbp fragment, when cloned into the EcoR1 site in pACYC184 to generate pUL2030, permitted the cloning in trans in pBR322 of the 12 kbp fragment or subclones containing the instability region. The minimum inhibitory concentration of kanamycin determined in the B. subtilis argC-neo transcriptional fusion pUL730 and expression of the argF gene product, ornithine carbamoyltransferase (OCTase), in pUL800 were reduced by approximately 3 and 2 fold respectively under conditions of arginine excess and in the presence of pUL2030. B. subtilis partial diploids were constructed by transforming parental and arginine hydroxamate resistant (Ahr) mutants with pUL2100, a plasmid generated by inserting the 6 kbp fragment into the integration vector pJH101. The 6 kbp fragment complemented and restored parental type levels of OCTase in ahrC mutants.(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗

Cytokeratin 19 fragments in patients with acute lung injury: a preliminary observation.

OBJECTIVE: Cytokeratin 19 (CK19) is a specific cytoskeletal structure for alveolar epithelium. We hypothesized that the levels of CK19 fragments in bronchoalveolar lavage (BAL) fluid could serve as an index of epithelial injury and as a prognosis marker in patients with acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). The aims of our study were, in patients with ALI/ARDS: (1) to measure CK19 fragments concentrations in BAL fluid, (2) to assess its prognostic value, and (3) to identify the cellular source of CK19 in the alveolar space. DESIGN: Prospective preliminary study. SETTING: University hospital surgical ICU. PATIENTS: Twenty-two mechanically ventilated patients with ALI/ARDS and 10 non-ventilated control patients. Plasma samples were obtained for 11 ALI/ARDS patients. MEASUREMENTS AND RESULTS: The concentration of BAL CK19 fragments was higher in patients (median 4916 pg/ml, 25th-75th percentile 2717-10533) than in controls (2208 pg/ml. 767-3923; p =0.05), and higher in 10 non-survivors (7051 pg/ml, 4372-13371) than in 12 survivors (2888 pg/ml, 1315-5639; p =0.03 among ALI/ARDS patients). BAL CK19 fragment concentration did not correlate with simplified acute physiologic score, lung injury score or PaO(2)/FIO(2) ratio, but correlated positively with BAL albumin concentration (p =0.002) and with number of BAL macrophages (p=0.0001). Plasma CK19 fragment concentrations were 10 times lower than those in BAL. Immunohistochemical staining for CK19 showed a strong labelling of injured detached epithelial cells and hyperplastic epithelium in ALI/ARDS lung samples. CONCLUSION: CK19 fragment concentrations were found to be elevated in BAL fluid in ALI/ARDS patients compared with control subjects. High BAL CK19 fragment levels were associated with a poor prognosis.

Bronchoalveolar Lavage Fluid↗

The impact of the geometry of the lithotriptor aperture on fragmentation effect at extracorporeal shock wave lithotripsy treatment.

The aim of this study was to determine the impact of the aperture size of an electro-hydraulic lithotriptor on the fragmentation effect. We also wanted to investigate whether a potential change in the capacitance of the pulse forming network (PFN), at a certain energy level, might have an impact on fragmentation rate. Two different apertures with a diameter of 23 and 17 cm respectively were compared using two different values of total PFN capacitance: 50 nF and 80 nF. Model stones of similar size and weight were fragmented. The number of shots for complete fragmentation or the grade of fragmentation after a certain number of shots was measured. This study shows that for the shock wave system used, the 23-cm aperture seems to provide more effective fragmentation as function of the number of shots compared with the 17-cm aperture at the same energy level. Furthermore, a minor change in the PFN capacitance between reasonable limits does not affect the fragmentation efficiency. This article also highlights the fact that it is not relevant simply to compare the voltage level given in the shots in extracorporeal shock wave lithotripsy treatment between different lithotriptors.

Electric Conductivity↗

A DNA fragment from the cyanobacterium Synechocystis sp. PCC 6803 mediates gene expression inducible by osmotic stress in E. coli.

Fragments of Synechocystis-DNA driving salt-induced gene expression in E. coli were isolated with translational fusions to a 'lacZ gene. One fragment (fragment 19) showed a NaCl-dependent activation of betaGal expression with the maximum of a ninefold increase in enzyme activity. A similar induction was triggered by the nonionic osmolyte sucrose, indicating an osmotically dependent activation. On the contrary, transcriptional activity of the DNA fragment 19 was only slightly enhanced under salt stress conditions, suggesting a posttranscriptional mechanism of induction. Primer extension assay was performed to identify the transcription initiation site. Upstream regions share weak homology to the "-10" hexamer consensus of E. coli sigma70 promoters. The most thermodynamically stable secondary structure for the nontranslated part of the mRNA indicated that potential translation initiation sites might be blocked, leading to a low basal translation, whereas osmotic stress-induced changes of mRNA structure could be involved to increase translation. In order to analyze the function of fragment 19 in Synechocystis, promoter-probe plasmids were constructed allowing the stable integration of transcriptional and translational reporter gene fusions into the cyanobacterial chromosome. Quantitative assessment of reporter gene expression revealed a weak constitutive promoter activity of fragment 19 in Synechocystis. Sequence analysis showed that fragment 19 comprises 223 bp of the ORF sll0747 of the Synechocystis genome.

Base Sequence↗

Posterior epidural migration of a lumbar disc fragment causing cauda equina syndrome: case report and review of the relevant literature.

Posterior epidural migration (PEM) of free disc fragments is rare, and reported PEM patients usually presented with radicular signs. An uncommon case involving a patient with cauda equina syndrome due to PEM of a lumbar disc fragment is reported with a review of the literature. The patient described in this report presented with an acute cauda equina syndrome resulting from disc fragment migration at the L3-L4 level that occurred after traction therapy for his lower back pain. The radiological characteristics of the disc fragment were the posterior epidural location and the ring enhancement. A fenestration was performed and histologically confirmed sequestered disc material was removed. An early postoperative examination revealed that motor, sensory, urological, and sexual functions had been recovered. At late follow-up, the patient was doing well after 18 months. Sequestered disc fragments may occasionally migrate to the posterior epidural space of the dural sac. Definite diagnosis of posteriorly located disc fragments is difficult because the radiological images of disc fragments may mimic those of other more common posterior epidural lesions.

Diagnosis, Differential↗

Fragmented electrograms and continuous electrical activity in atrial flutter.

Multiple endocardial bipolar electrograms were recorded in 13 patients with atrial flutter (AF) to locate areas of fragmented electrical activity. Stable fragmentation patterns were found in each case, covering between 36% and 100% of the flutter cycle. Double or triple spike patterns were common. The direction of atrial activation was approximately defined in 11 patients, and in all of them at least part of the areas showing fragmentation was included in the circuit. In 1 patient an area of continuous electrical activity was found. AF circuits appeared to be included in the right atrium in 12 patients and in the left atrium in 1 patient. During atrial stimulation changes in fragmented electrograms coincided with changes in AF pattern before its interruption, while restoration of stable AF after stimulation was accompanied by reappearance of previous stable fragmented electrograms. In 6 patients electrograms were recorded after sinus rhythm was reestablished, and all showed marked decreases or disappearance of fragmentation. It is concluded that fragmented electrograms are often found in AF and may be related to abnormal local conduction in relation to the reentrant activation circuits.

Adult↗

Discriminatory 32P 3'-end labeling of restriction endonuclease co-digested DNA fragments.

We present an improved method for selectively labeling specific DNA fragments in a mixture of restriction fragments. lambda DNA, used to develop the procedure, was digested with a combination of restriction enzymes and treated, at various incubation temperatures, with reverse transcriptase and one or more [alpha-32P]dNTP molecules. The labeled fragments were subjected to agarose gel electrophoresis and detected by autoradiography. We were able to direct the 3'-end labeling to precise subpopulations of DNA fragments, generated by multiple restriction enzyme digestions. We also show that labeling selectivity of DNA restriction fragments, by reverse transcriptase, is affected by the incubation temperature used during the labeling reaction. This paper describes an approach to 3'-end label select DNA fragments with reverse transcriptase and [alpha-32P]dNTPs. The procedure permits the bypassing of time-consuming isolation and purification steps required, by conventional radiolabeling techniques, to radiolabel specific DNA fragments.

Autoradiography↗

A procedure for the construction of linear restriction fragment maps of a 50- to 100-kb DNA.

A simple and effective procedure for the construction of linear restriction fragment maps was developed. Using a two-enzyme digestion, two-dimensional (2-D) electrophoresis procedure, all the restriction fragments in a 50- to 100-kb DNA can be individually resolved and displayed on a 2-D plane. This 2-D gel pattern, with appropriate markers, provides a fixed set of x, y coordinates for each fragment obtained from the single and double digestion as well as the relationship between the two steps. A matrix is constructed from the 2-D pattern. The vertical column shows all the singly digested individual fragments and their sizes obtained from each restriction enzyme treatment, and the dividing horizontal row shows all the doubly digested DNA fragments and their sizes after treatment with two enzymes. The order of arrangement is always from the smallest to the largest fragments. Using this matrix, two linear DNA restriction maps for these two enzymes can be simultaneously constructed in a self-reconfirming manner. As examples for this procedure, we describe the construction of two linear restriction fragment maps, a combination of EcoRI and BamHI digestion as well as a combination of EcoRI and HindIII digestion of lambda-phage DNA.

Bacteriophage lambda↗

Random fragmentation of replicative DNA structures of eucaryotes.

The expectation values of the sizes of the different types of fragments containing replication forks obtained by random fragmentation of the DNA of growing mammalian cells have been derived. Fragments containing a single fork are expected to have, on the average, three branches of the length of a mean linear fragment thus exceeding the molecular weight of the latter by a factor 3. This factor is about 2 for fragments containing two forks very recently started from a common initiation point, and about 4 for fragments containing two forks meeting each other at the end of adjacent replication units. Only forks very close to one another are expected in these latter fragment types. Therefore, they should represent the earliest or the latest stages of replicon action.

DNA↗

Molecular fragments associated with non-genotoxic carcinogens, as detected using a software program based on graph theory: their usefulness to predict carcinogenicity.

We assembled 390 chemicals with a structure non-alerting to DNA-reactivity (145 carcinogens and 245 non-carcinogens) for which rodent carcinogenicity data were available. These non-alerting chemicals were defined by the absence in their molecules of DNA-reactive (directly or after metabolic activation) alerting structures, as described by Ashby and coworkers (Mutat. Res., 204 (1988) 17-115; Mutat. Res., 223 (1989) 73-103; Mutat. Res., 257 (1991) 209-227; Mutat. Res., 286 (1993) 3-74). Using our software program based on graph theory we analyzed the compounds in order to estimate the program's ability to predict nonalerting carcinogens. Our software fragmented the structural formula of the chemicals into all possible fragments of contiguous atoms with size between 2 and 8 (non-hydrogen) atoms and learned about statistically significant fragments from a training set of chemicals. These fragments were used to predict carcinogenicity or lack thereof in a verification set of compounds. For 390 runs of the software program we used (n - 1) of the chemicals as a training set, to predict the excluded chemical at each run (as a test set). Using two different probability thresholds to select significant fragments (P = 0.05 and P = 0.125 1-tailed according to binomial distribution), we performed two analyses: in the better one (P = 0.05) 19% of the molecules tested lacked significant fragments, for the remaining 81% the observed level of accuracy of the prediction was 66.0% against an expected level of accuracy of 51.7%. The difference was highly significant (P < 0.0001). We also examined the more significant activating fragments (biophores) and discussed at length both their biological plausibility and the working hypothesis that additional alerting structures for carcinogenicity (not only those related to genotoxicity) can be detected using this type of SAR approach. This new class of alerting structures could identify subfamilies of congeneric analogs active through mechanisms of receptor mediated carcinogenesis.

Carcinogens↗

Identification of EcoRV fragments spanning the N alpha-tubulin gene of Physarum.

The N alpha-tubulin gene of Physarum polycephalum has an EcoRV site at codons 252/253. EcoRV digestion of physarum DNA generated two EcoRV fragments per gene copy comprising both coding and flanking sequences. Hybridisation probes which included coding sequences upstream from the central EcoRV site cross-hybridised with another alpha-tubulin gene. Probes derived from either 5'- or 3'-flanking regions were gene-specific. These probes identified two EcoRV fragments in the haploid strain CLdAXE viz 5.4 kb (5'-fragment) and 6.2 kb (3'-fragment). The same two fragments were identified in EcoRV digests of DNA of the diploid strain M3CVIII, and a second form of the gene was also identified comprising two fragments viz 5.0 kb (5'-end) and 5.5 kb (3'-end). Both forms gave rise to an identical 4.65 kb HindIII fragment as judged by restriction mapping.

Deoxyribonucleases, Type II Site-Specific↗

Neither glycine-extended gastrin nor the 1-13 fragment of gastrin 17 influences gastric acid secretion in humans.

The effect on gastric acid secretion of two gastrin 17-related peptides without the carboxyamide, i.e., the glycine-extended 5-17 fragment and the 1-13 fragment of human gastrin 17, was examined in normal subjects. Acid secretion was stimulated by an intravenous infusion of 21 pmol/kg.h of gastrin 17 or by intragastric instillation of peptone; gastric acid output during simultaneous infusion of 325 pmol/kg.h of the glycine-extended 5-17 fragment or 319 pmol/kg.h of the 1-13 fragment was then compared with acid output during infusion of saline. Neither the glycine-extended 5-17 fragment nor the 1-13 fragment of gastrin 17 influenced gastric acid secretion. By gel and ion-exchange chromatography of serum drawn during infusion, the infused peptide was recovered at the position of the intact synthetic peptide. The disappearance curve of circulating glycine-extended gastrin could be described by two components with half-lives of 3.6 and 48 min. As the glycine-extended fragment was stable in serum or plasma in vitro for 1 h at 37 degrees C, the rapid elimination observed in vivo cannot be ascribed to circulating plasma enzymes.

Adult↗