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At least 199 records · Page 11Linked to original sources
PubMed2002

Extravascular necrotizing palisaded granulomas as the presenting skin sign of systemic lupus erythematosus.

We recently examined a patient who presented clinically with tender, erythematous papules associated with a febrile illness and polyarthralgias. Histopathological examination revealed extravascular palisaded neutrophilic granulomas, a skin reaction pattern originally described in Churg-Strauss disease but subsequently observed in a variety of other systemic disorders characterized by immune complex generation. A diagnosis of systemic lupus erythematosus (SLE) was established. To our knowledge, this is the first report of extravascular necrotizing palisaded granulomas as the presenting skin sign of SLE.

Adult↗
PubMed2005

An Eulerian path approach to local multiple alignment for DNA sequences.

Expensive computation in handling a large number of sequences limits the application of local multiple sequence alignment. We present an Eulerian path approach to local multiple alignment for DNA sequences. The computational time and memory usage of this approach is approximately linear to the total size of sequences analyzed; hence, it can handle thousands of sequences or millions of letters simultaneously. By constructing a De Bruijn graph, most of the conserved segments are amplified as heavy Eulerian paths in the graph, and the original patterns distributed in sequences are recovered even if they do not exist in any single sequence. This approach can accurately detect unknown conserved regions, for both short and long, conserved and degenerate patterns. We further present a Poisson heuristic to estimate the significance of a local multiple alignment. The performance of our method is demonstrated by finding Alu repeats in the human genome. We compare the results with Alus marked by repeatmasker, where the two programs are in good agreement. Our method is robust under various conditions and superior to other methods in terms of efficiency and accuracy.

Base Sequence↗
PubMed1975

Isolation of Escherichia coli mutants defective in enzymes of membrane lipid synthesis.

A new method has been developed which permits the rapid screening of E. coli colonies for mutants with defective enzymes of phospholipid metabolism. In this procedure, a disc of filter paper is pressed down on an agar plate containing several hundred colonies of mutagen-treated cells, after which the paper is lifted off. In the process the colonies are transferred to the paper, giving rise to a replica print of the master plate. The few cells from each colony left on the master keep growing in the original pattern. The pattern of colonies is also retained on the filter paper, even after the cells are rendered permeable with lysozyme and EDTA. Colonies treated in this manner remain absorbed to the paper, where they can convert sn-(U-14-C)glycero-3-P to phosphatidyl(U-14-C)glycerophosphate, dependent on added CDP-diglyceride. Unrelated reactions of sn-(U-14-C)glycero-3-P that may obscure the synthesis of phosphatidyl-glycerophosphate are inhibited by the addition of reagents poisoning energy generation. The radioactive phospholipid that forms around each colony on the paper is precipitated in situ with trichloroacetic acid, and unreacted sn-(U-14-C)glycero-3-P is washed away. After autoradiography, the colonies on the filter paper are stained with Coomassie blue. When the autoradiogram is superimposed on the strained paper, mutants are identified as blue colonies lacking a black halo. With this method, 20,000 colonies were screened in several days. Four mutants were identified with low levels of CDP-diglyceride:snglycero-3-P phosphatidyl transferase (EC 2.7.8.5, GLYCEROL-PHOSPHATE PHOSPHATIDYLTRANSFERASE, PHOSPHATIDYLGLYCEROPHOSPHATE SYNTHETASE) IN EXTRACTS. With a similar assay, 10,000 additional colonies were screened for mutants with altered CDP-diglyceride:L-serine O-phosphatidyltransferase (EC 2.7.8.8, phosphatidylserine synthetase), and four strains were found in which the enzyme is thermolabile. The screening technique described here is termed replica printing and should be applicable not only to studies of phospholipid metabolism but also to nucleic acid and protein synthesis.

Autoradiography↗
PubMed1996

Purification and characterization of the Ca2+-ATPase of Flavobacterium odoratum.

The P-type Ca2+-ATPase from Flavobacterium odoratum has been purified to homogeneity and characterized. Inside-out membrane vesicles were extracted with C12E8, followed by ammonium sulfate fractionation, centrifugation through two successive 32-48% glycerol gradients, and DE52 ion exchange chromatography. The purified Ca2+-ATPase consists of a single polypeptide. It migrates electrophoretically with an apparent molecular mass of 60,000 Da, consistent with the phosphorylation pattern originally reported in membrane vesicles. This single polypeptide is functional and capable of calcium-dependent vanadate-sensitive ATP hydrolysis and of forward and reverse phosphorylation. Maximum hydrolysis activity occurs at pH 8.0, with a specific activity of approximately 75 micromol of ATP hydrolyzed min-1 mg-1 protein. The purified Ca2+-ATPase has an apparent Km for calcium of 1.5 microM and for ATP of 90 microM. Vanadate strongly inhibits the activity with an IC50 of 0.6 microM. The prokaryotic Ca2+-ATPase is insensitive to the SR Ca2+-ATPase inhibitors fluorescein isothiocyanate, thapsigargin, and cyclopiazonic acid. It is rapidly phosphorylated by [gamma-32P]ATP in a calcium-dependent vanadate-inhibited manner and can be phosphorylated by Pi in both the presence and absence of calcium.

Adenosine Triphosphate↗
PubMed1996

Discord between the phylogenies inferred from molecular versus functional data: uneven rates of functional evolution or low levels of gene flow?

According to measures of molecular divergence, the three species of the Drosophila simulans clade are closely related to and essentially equidistant from each other. We introgressed 10% of the D. sechellia X chromosome into a pure D. simulans genetic background and found that males carrying this introgressed region were consistently fertile; in contrast, males carrying the same segment from D. mauritiana are sterile and suffer from incompatibilities at a minimum of four loci. Together with other recent results, these data suggest that D. simulans and D. sechellia are much more closely related to each other than either is to D. mauritiana. How can we reconcile the phylogeny inferred from the density of hybrid sterility genes with that inferred from molecular divergence? If the molecular phylogeny is correct, the discrepancy might be explained by uneven rates of functional evolution, resulting in the uneven accumulation of substitutions with corresponding negative effects in hybrids. If the functional phylogeny is correct, then low levels of gene flow across nascent species boundaries, particularly for loci not tightly linked to a hybrid sterility gene, may have erased the original pattern of lineage splitting. We propose tests that will allow us to discriminate between these hypotheses.

Animals↗
PubMed1999

Gestational choriocarcinoma whose responsible pregnancy was a complete hydatidiform mole identified by PCR analysis with new sequence tagged site primers.

We report a case where the pregnancy responsible for a gestational choriocarcinoma was not the antecedent pregnancy or the second normal term delivery, but a complete hydatidiform mole that had advanced to clinically invasive mole. This responsible pregnancy was identified by polymerase chain reaction analysis (PCR). PCR analysis was performed by using five new sets of sequence-tagged site (STS) primers on four chromosomes (chr. 1, D1S225; chr. 3, D3S1744; chr. 12, D12S1090; chr. 18, D18S849 and D18S877). The constitution of alleles of choriocarcinoma was shown to be almost identical with that of the husband on every marker. The allele patterns of choriocarcinoma on D3S1744 and D12S1090 were not observed with DNA from the patient. The band pattern originating from molar DNA was also identical with those of the husband and choriocarcinomas on D18S849 and D1S225.

Choriocarcinoma↗
PubMed1983

Modulation of RNA polymerase activities in the intestine of adult rats by dietary sucrose.

The effect of sucrose feeding on endogenous intestinal RNA polymerase activities and on chromatin structure was studied in rats. Adult rats were given a 70% sucrose solution for 15 hours following a 48-hour starvation period. Comparison was made with rats starved for 63 hours and with ad libitum nourished animals. Chromatin-bound RNA polymerase I activity was significantly reduced by starvation. Sucrose feeding provoked a significant rise in the activity, but the level found in the nourished rats was not reached. The free poly[d(A-T)]-dependent RNA polymerase I activity of the sucrose-fed rats exceeded that of the starved and the nourished animals. Chromatin-bound RNA polymerase II activity was enhanced most markedly by sucrose feeding. The balance between the chromatin-bound and free enzymes was shifted towards the chromatin-bound state when compared to the starved and nourished rats. Starvation caused a reduction in the size of oligonucleosomes but sucrose feeding restored almost entirely the original pattern obtained in the nourished animals. These results reflect modifications in the structure of chromatin after sucrose feeding. The present report demonstrates that the adaptive processes triggered in the intestine by dietary sucrose are associated with changes in gene expression.

Animals↗
PubMed1996

Anatomic studies and clinical experience with fasciocutaneous flap closure of large myelomeningoceles.

Thirteen patients have undergone reconstruction of large lumbosacral myelomeningoceles with bilateral paralumbar fasciocutaneous flaps. Fasciocutaneous flap closure is supported by a rich vascular network with three main dominant vascular territories. In the middle third of the flaps, a prominent transverse segmental vascular pattern originating from the muscular perforators and lateral cutaneous branches of the costal groove segment of the lower intercostal arteries was noted. The parascapular and scapular fascial branches of the circumflex scapular artery supplied the upper lateral portion of the flaps. Prominent lateral extensions of the superficial circumflex iliac arterial system formed the dominant fascial vasculature of the lower lateral flap, richly arborizing with the middle segmental intercostal extensions. All 13 patients tolerated the procedure without blood transfusion and without perioperative complications. Stable, durable cutaneous coverage was achieved in all patients. Two postmortem neonate humans with large lumbosacral myelomeningoceles were studied angiographically. Radiopaque silicone-rubber-lead-chrome matrix (Microfil) was infused under physiologic pressures in a 7-day neonate after successful defect closure with bilateral fasciocutaneous flaps. The flaps were reevaluated postmortem, and high-contrast, digitally enhanced computed radiographic imaging confirmed the rich vascular support of the bilateral fasciocutaneous flaps, identifying the dominant vascular pedicles. Rich vascularity was further documented by photographing the orange opaque Microfil cast vessels through the reelevated flaps. A second postmortem (stillborn) myelomeningocele specimen was studied with barium infusion with particular emphasis on the anomalous lumbar aorta. Angiographic studies provide a new understanding of the unique vascular anatomy of both the anomaly and the paralumbar fasciocutaneous flap.

Aorta↗
PubMedDate not supplied

Diffuse choroidal thickening detected by ultrasonography in various ocular disorders.

Diffusely thickened choroid was detected ultrasonically in 207 eyes in various conditions, including: following intraocular surgery (108 eyes), trauma (8 eyes), phthisis bulbi (52 eyes), endophthalmitis (12 eyes), and nanophthalmos (27 eyes). Diffusely thickened choroid was seen by A-scan as a widening of the echo pattern originating from the posterior coats of the eye and by B-scan as a curvilinear echo giving a double contour to the globe. Although B-scan characteristics of thickened choroid consisted of a smooth curvilinear echo in 196 eyes, this echo was irregular with multiple angulations in 11 eyes that had phthisis bulbi. The mechanisms suspected of choroidal thickening were ocular hypotony (sudden or chronic, 154 eyes), impaired drainage in the vortex system (41 eyes), and severe intraocular inflammation (12 eyes).

Adolescent↗
PubMed1986

The effect of lowering the pH on the composition and metabolism of a community of nine oral bacteria grown in a chemostat.

Nine oral bacteria, associated with both healthy and diseased sites in the mouth, were grown at D = 0.05 h-1 (mean generation time 13.9 h) in a glucose-limited chemostat. After an initial period of steady-state growth at pH 7.0, pH control was discontinued. The pH then decreased until it stabilized at pH 4.1 after 9 d (16 generations), while the Eh rose from -165 mV to +160 mV. The lowering in pH resulted in the composition and metabolism of the flora being altered and in increased bacterial aggregation. At pH 7.0, 'Streptococcus mitior', Veillonella alcalescens and S. sanguis were most numerous while at pH 4.1 the counts of all bacteria fell except for Lactobacillus casei, which became predominant. The proportions of S. mutans within the community also increased while S. sanguis was recovered only occasionally and Bacteroides intermedius was not detected below pH 4.6. The survival at pH 4.1 of several other species would not have been predicted from earlier pure culture studies. Relative to pH 7.0, the community growing at pH 4.1 produced more lactic acid, washed cells had a greater glycolytic activity over a wider pH range but amino acid metabolism decreased. In general, when pH control was restored, so were the original patterns of metabolism and bacterial counts, except for B. intermedius, which was still not detected. The inverse relationship between S. sanguis and S. mutans, and the increase in proportions of L. casei and S. mutans during growth in a low pH environment parallel observations made in vivo and suggest that the chemostat can be used as a model for microbial behaviour in dental plaque.

Actinomyces↗
PubMed2003

Discovering novel cis-regulatory motifs using functional networks.

We combined functional information such as protein-protein interactions or metabolic networks with genome information in Saccharomyces cerevisiae to predict cis-regulatory motifs in the upstream region of genes. We developed a new scoring metric combining these two information sources and used this metric in motif discovery. To estimate the statistical significance of this metric, we used brute-force randomization, which shows a consistent well-behaved trend. In contrast, real data showed complex nonrandom behavior. With conservative parameters we were able to find 42 degenerate motifs (that touch 40% of yeast genes) based on 647 original patterns, five of which are well known. Some of these motifs also show limited spatial position in the promoter, indicative of a true motif. We also tested the metric on other known motifs and show that this metric is a good discriminator of real motifs. As well as a pragmatic motif discovery method, with many applications beyond this work, these results also show that interacting proteins are often coordinated at the level of transcription, even in the absence of obvious coregulation in gene expression data sets.

Amino Acid Motifs↗
PubMed2000

Interatomic coulombic decay in van der waals clusters and impact of nuclear motion

It is demonstrated that excited van der Waals systems can relax by electron emission via a novel interatomic mechanism. The process is analyzed by means of extensive ab initio calculations of potential energy surfaces and electronic decay rates. The electronic emission, taking place on the same time scale as the motion of the atomic nuclei, is accompanied by interesting dynamical effects amenable to experimental observations. These effects arise as a consequence of the weak chemical bond in van der Waals clusters and the Coulomb repulsion pattern originating from electron emission.

Journal Article↗
PubMed2001

Aqua(benzene-1,3-dicarboxylato)zinc(II).

The title compound, poly[[aquazinc(II)]-mu-benzene-1,3-dicarboxylato-O1:O1':O2], [Zn(C8H4O4)(H2O)]n, forms a metal-organic coordination network that consists of tetrahedral Zn atoms bonded to one water molecule and three carboxylate groups. Isophthalate groups bridge the four-coordinate Zn centers to generate two-dimensional architectures in the ac plane. These planar zinc isophthalate motifs are linked by infinite C=O...H-O-H interactions along the a axis to form a chiral framework. The observed polar structural pattern originates due to the distorted tetrahedral Zn centers [O-Zn-O 100.7 (2)-136.0 (1) degrees ] and the alignment of the water molecules. Bridging isophthalate groups align to form approximate centrosymmetric motifs.

Journal Article↗
PubMed2004

Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach.

Practical applications of structured illumination microscopy (SIM) often suffer from various artefacts that result from imprecise instrumental hardware and certain bleaching properties of the sample. These artefacts can be observed as residual stripe patterns originating from the illumination grating. We investigated some significant causes of these artefacts and developed a correction approach that can be applied to images after acquisition. Most of the artefacts can be attributed to changes in illumination and detection intensities during acquisition. The proposed correction algorithm has been shown to be functional on noisy image data, and produces exceptional, artefact-free results in everyday laboratory work.

Actins↗
PubMed1995

Treatment of enuresis risoria in children by self-administered electric and imaginary shock.

OBJECTIVE: To treat enuresis risoria (giggle micturition) by a self-administered electric and imaginary shock and to evaluate the outcome after behavioural therapy. PATIENTS AND METHODS: Six boys and three girls with enuresis risoria were evaluated and treated. The mean age at referral was 10.4 years (range 5.7-14.2). All children had episodes of involuntary complete bladder emptying triggered by hearty laughter or giggling. The frequency ranged from four times per day to twice a week. No other voiding problems were noted. Five patients (four boys and one girl, mean age 10.2 years, range 5.7-14.2) received conditioning training which consisted largely of the self-administration of a harmless, painless electric shock to the back of one hand, at the moment when micturition was induced by laughter, leading to inhibition of the voiding reflex. Later, the electric shock was replaced by an imaginary shock. Training was undertaken on an outpatient basis. A mean of eight sessions, each of 45 min duration, was necessary to train the children. The mean follow-up was 26 months (range 12-51). RESULTS: The frequency of wetting was reduced by a mean of 89% in all children 1 year after the successful completion of the training. In three children, followed for 2 years, this result stabilized at that proportion. One of these children, followed for > 3 years, gradually reverted to the original pattern of daily wetting and another patient, with a follow-up of > 4 years, maintained an 86% reduction of wetting incidents. CONCLUSION: Until now, there was no specific treatment for enuresis risoria and not all patients outgrow the problem; this experimental conditioning programme shows promise in diminishing wetting incidents. However, the programme needs further testing in a prospective study.

Adolescent↗
PubMed1995

Restoration of brain protein synthesis in mature and aged rats by a DA agonist, piribedil.

Brain ageing affects numerous cerebral metabolic pathways such as cerebral glucose consumption or protein synthesis rate. The pharmacological effect of a mixed D1-D2 dopaminergic agonist, piribedil, on this last metabolism is reported. Cerebral Protein Synthesis Rate (CPSR) was measured by the [35S]L-methionine autoradiographic procedure in 38 main brain regions of 11 and 26-month-old Wistar rats after a 2-month treatment per os at 9 and 30 mg/kg/day with piribedil. Mean decrease of CPSR was -21% during the 15-month ageing we followed, with important local variations. Mean CPSR increased with the two treatments, +25% in mature and +35% in aged rats. Treatments restored CPSR of aged rats to the exact mature subjects levels in quite all the brain regions. No dose-effect or asymetrical modification was statistically revealed for the two treatments. Metabolic increases involved particularly central brain gray structures, especially some DA-targeted brain nuclei concerned with behaviour and learning. This effect argued for a general metabotrophic effect of D1-D2 dopamine stimulation of the brain. The original pattern of local ageing of brain protein synthesis in rat was also incidentally reported. This was the first direct report of a wide and effective metabolic activation of CPSR in the brain during ageing by a curative dopaminergic agonist treatment.

Aging↗
PubMed1996

Molecular evidence supporting the existence of two major groups in uropathogenic Escherichia coli.

Molecular methods allow an extremely fine strain typing that can be used to establish the population structure of bacterial species. This methodology has been used to characterize a collection of 74 uropathogenic Escherichia coli obtained from three hospitals located in geographically distant towns in Spain, some representatives of the ECOR collection and other reference strains. Genomic DNA was analyzed by RAPD (Random Amplified Polymorphic DNA) that can characterize a bacterial strain to the level of defining individual clones. The 16S rDNA-23S rDNA spacers were amplified by PCR and submitted to restriction analysis. Finally, the presence or absence of G adhesins in Escherichia coli as well as the type of adhesin (three types are known) have been shown by PCR amplification followed by digestion with restriction enzymes. As expected a wide diversity was shown by RAPD and identical patterns were only found in the case of strains isolated from the same individual, an obvious case of relapse. Analysis of the spacers' restriction patterns showed the presence of two markedly differentiated clusters that we have named alpha and beta. Both RAPD and spacer restriction patterns originated similar clusters of strains showing a consistency in the evolution of the global genome with the sequence variation of the ribosomal spacers. Furthermore, most of the strains having G-adhesin, with only a few exceptions, corresponded to the alpha rRNA spacer group. The two spacer types detected were also consistent with some phenotypic markers such as sucrose and raffinose utilization. The alpha and beta clusters could be intraspecific groups produced by partial sexual isolation or other barriers that are originating a divergent evolution.

Adhesins, Bacterial↗
PubMed2002

The effects of volatile microbial secondary metabolites on protein synthesis in Serpula lacrymans.

The effects of volatile secondary metabolites produced by Trichoderma pseudokoningii, Trichoderma viride and Trichoderma aureoviride on growth rate and protein synthesis in two Serpula lacrymans isolates were investigated. Mycelial growth was affected to differing degrees, depending on the specific interactive microbial couplet involved. Protein synthesis by both S. lacrymans (Forfar) and S. lacrymans (H28) was affected by the volatile secondary metabolites of T. aureoviride and T. viride, but not by those of T. pseudokoningii. Mycelial growth and the original pattern of protein synthesis resumed when the antagonists were removed. It is probable that volatile secondary metabolites have played an important role during the evolution of microorganisms in the context of community, population and functional dynamics.

Basidiomycota↗