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At least 739 records · Page 41Linked to original sources
PubMed1993

A technique for the high-speed characterization of ultrasonic transducer insertion loss performance.

A characterization technique has been developed to address the problems associated with calibrating very-high frequency (i.e., > 50 MHz) ultrasound transducers. The technique is based on using a pc-controlled network analyzer to acquire the through-transmission voltage transfer function spectrum from a pair of ultrasound transducers which are closely spaced in water. This spectrum, which includes electrical feed-through noise and multiple reflection artifacts, is then corrected for the water's attenuation and the transfer response of the electronics system. An inverse Fourier transform is then performed, to produce the time domain response of the transducers. The portion of the response which corresponds to the first acoustic arrival is then gated out of this response, and a Fourier transform is performed to compute the transducers' true transfer function (insertion loss) spectrum. A pc-controlled automated calibration system based on this technique has been developed and numerous transducer pairs have been tested. Excellent agreement has been shown between this method and the conventional tone-burst technique for accurately characterizing insertion loss spectra. In this paper, a detailed description of the technique, actual transducer test results, and comparisons with the conventional tone-burst method are presented in detail.

Calibration↗
PubMed1995

Characterization of a novel zinc finger gene (ZNF165) mapping to 6p21 that is expressed specifically in testis.

Clone ZF388 was identified during the course of expressed sequence tag analysis of human adult testis cDNAs as being a member of the C2H2 zinc finger gene family. Northern blot analysis of a range of 16 different human tissues has shown that clone ZF388 detects a single 2.2-kb transcript and that the expression of this mRNA species is strictly specific to the testis. Sequence analysis of ZF388 and other clones isolated by rescreening a testis cDNA library has defined a transcript with an extensive N-terminal acidic domain containing 17% aspartic and glutamic acid residues and a C-terminal domain composed of five zinc finger motifs linked through the highly conserved sequence TGE-KPYE. This gene has been designated ZNF165. Analysis of somatic cell hybrids containing single human chromosomes shows that ZNF165 maps to chromosome 6. Fluorescence in situ hybridization of cDNA insert probes to male metaphase spreads shows that the ZNF165 transcript maps to 6p21 close to the human MHC region. Human 6p21 is homologous with the distal inversion of the mouse t-complex, which has been shown to contain a cluster of genes expressed specifically in the testis.

Adult↗
PubMed2004

Functional prediction of a T-DNA tagged gene of Arabidopsis thaliana by in silico analysis.

We have employed a gene-knockout approach using T-DNA tagging and in vivo gene fusion in Arabidopsis thaliana for identification and isolation of specific plant genes. Screening of about 3,000 T-DNA tagged lines resulted in identification of a mutant line (no. 197) exhibiting a significant delay in flowering. From this line a 600-bp plant DNA fragment downstream of the left T-DNA junction was cloned by inverse PCR. BLAST searching in the A. thaliana genomic database indicated a putative gene, frf (flowering regulating factor), with unknown function downstream of the T-DNA insert. Bioinformatic tools were used to predict possible protein structure and function. The protein structure predicted by fold recognition indicates that frf is a transcriptional regulator, a ligand-binding receptor responsive to steroids and hormones. Analyzing the predicted results and the phenotype of the T-DNA tagged plant we hypothesized that FRF might be involved in hormone response in A. thaliana. For verification of this hypothesis we exposed the plants of line no. 197 to gibberellic acid (GA3), a potential growth regulator in higher plants. This treatment resulted in an earlier onset of flowering, almost similar to that in wild type control plants.

Amino Acid Sequence↗
PubMed2003

Diffusion-weighted imaging in kainic acid-induced complex partial status epilepticus in dogs.

OBJECTIVE: To investigate diffusion-weighted imaging (DWI) in status epilepticus, a canine model of kainic acid (KA)-induced complex partial status epilepticus (CPSE) was produced. In order to validate its usefulness, MR imaging was carried out at various times following onset of CPSE followed by histopathology. MATERIAL AND METHODS: Six normal dogs were used in this study. In each dog, a cannula was stereotactically inserted into the left amygdala. One week after surgery, all dogs were imaged at MRI. Pre-injection imaging consisted of T2 weighted (T2W) imaging, fluid attenuated inversion recovery (FLAIR), and DWI. Two weeks after surgery, five dogs received intraamygdaloid KA microinjections. One dog was used as a control. MRI was carried out at 3, 6, 12, 24 and 48 h after onset of CPSE. Animals were euthanized immediately after MRI for histopathological evaluation. The average of each apparent diffusion coefficient (ADC) in the regions of interest was calculated from each DWI. RESULTS: At 3 and 6 h, DWI hyperintensity and low ADC were found in the injected amygdala, without any T2W and FLAIR imaging changes. At 12 and 24 h, all imaging showed hyperintensity with higher ADC in the amygdala and the hippocampus. At 48 h, all imaging techniques showed continued hyperintensity, but ADC showed a trend towards normalization. This increasing hyperintensity in DWIs were in agreement with the degree of histopathology during CPSE. SUMMARY: This study suggests that DWI is a useful imaging method for finding the epileptic focus or for examining potential epileptic brain damage in status epilepticus.

Algorithms↗
PubMed1990

Upstream regulatory sequence for transcriptional activator XylR in the first operon of xylene metabolism on the TOL plasmid.

Transcription of the first operon coding for m-xylene-degrading enzymes on the TOL plasmid of Pseudomonas putida is activated by the xylR gene product in the presence of m-xylene. The operon has the consensus sequence of the ntr/nif promoters at -24 and -12 regions, and the transcription is dependent on an RNA polymerase containing a sigma factor NtrA (RpoN or sigma 54). Deletion derivatives of the upstream sequence of the operon promoter were made in vitro and connected with the xylE gene on a plasmid. Their promoter activities were analyzed in Escherichia coli by monitoring catechol 2,3-dioxygenase activity, the xylE gene product. A cis-acting DNA element was identified, which is required for activation of the operon promoter by XylR protein in the presence of the inducer. This regulatory sequence of about 40 base-pairs in length was located 150 base-pairs upstream from the transcription start site. Analysis of the mutants containing insertions between the upstream regulatory sequence and the promoter sequence demonstrated strong dependence of the activation upon helical periodicity of DNA. The regulatory sequence functioned in the inverse orientation or at a distance of more than 1 x 10(3) base-pairs upstream from the promoter though less efficient. These results indicated that this upstream regulatory sequence might be the binding site for XylR protein. DNA-loop formation through protein-protein interaction between XylR protein attached to the upstream sequence and the NtrA-containing RNA polymerase bound by the promoter sequence was suggested for activation of the operon transcription. A sequence similar to the regulatory sequence of the first operon of xylene metabolism was found in the upstream region of the xylS gene, which is also activated by XylR protein in the presence of m-xylene.

Base Sequence↗
PubMed2003

Site-specific cassette exchange and germline transmission with mouse ES cells expressing phiC31 integrase.

Currently two site-specific recombinases are available for engineering the mouse genome: Cre from P1 phage and Flp from yeast. Both enzymes catalyze recombination between two 34-base pair recognition sites, lox and FRT, respectively, resulting in excision, inversion, or translocation of DNA sequences depending upon the location and the orientation of the recognition sites. Furthermore, strategies have been designed to achieve site-specific insertion or cassette exchange. The problem with both recombinase systems is that when they insert a circular DNA into the genome (trans event), two cis-positioned recognition sites are created, which are immediate substrates for excision. To stabilize the trans event, functional mutant recognition sites had to be identified. None of the systems, however, allowed efficient selection-free identification of insertion or cassette exchange. Recently, an integrase from Streptomyces phage phiC31 has been shown to function in Schizosaccharomyces pombe and mammalian cells. This enzyme recombines between two heterotypic sites: attB and attP. The product sites of the recombination event (attL and attR) are not substrates for the integrase. Therefore, the phiC31 integrase is ideal to facilitate site-specific insertions into the mammalian genome.

Animals↗
PubMed2002

New approaches to the development of live attenuated rabies vaccines.

In the United States, extensive reservoirs of the rabies virus exist in many diverse wild animal species, which continue to pose a serious risk of lethal infection of humans and cause an economic burden exceeding $1 billion annually. Previous experience with rabies control in foxes in Europe has clearly demonstrated that oral immunization with live vaccines is the only practical approach to eradicate rabies in free-ranging animals. However, unlike Europe where vulpine rabies was the only major reservoir, the Americas harbor a variety of species including raccoons, skunks, coyotes, and bats that serve as the primary reservoirs of rabies. Each of these animal reservoirs carries an antigenically distinct virus variant. The currently available modified-live rabies virus vaccines have either safety problems or do not induce sufficient protective immunity in particular wildlife species. Therefore, there is a need for the development of new live rabies virus vaccines that are very safe and highly effective in particular wildlife species. Based on previous observations indicating that the potency of a vaccine is significantly increased if the G protein of the vaccine strain is identical to that of the target virus, we have used a reverse genetics approach to engineer viruses that contain G proteins from virus strains associated with relevant wildlife species. Furthermore, because our recent data also indicate that the pathogenicity of a particular rabies virus strain is inversely proportional to its ability to induce apoptosis and that low-level apoptosis-inducing ability is associated with low anti-viral immune responses, we inserted genes encoding pro-apoptotic proteins to stimulate immunity or otherwise interfere with viral pathogenesis into these recombinant viruses to enhance their efficacy and safety.

Animals↗
PubMed1993

TTAA serves as the target site for TFP3 lepidopteran transposon insertions in both nuclear polyhedrosis virus and Trichoplusia ni genomes.

We have analysed TFP3 transposable elements from five independently isolated FP mutants of the Autographa californica nuclear polyhderosis virus (AcMNPV). We also analysed genomic copies of TFP3 elements amplified from the DNAs of the Trichoplusia ni cell line (TN-368) and T. ni larvae using the polymerase chain reaction (PCR). The sequences of all the newly isolated TFP3 elements closely resemble the previously described TFP3/1 element. Each of the transposons isolated from the virus mutants duplicated a TTAA tetranucleotide target site upon insertion into the viral genome. Four of these TFP3 elements transposed into three different 'TTAA' target sites within the 25 K gene (FP locus, map units 36-37 of AcMNPV). The fifth TFP3 element inserted at a 'TTAA' site within the AcMNPV Hin dIII-E fragment. One genomic TFP3 element, amplified from the TN-368 cell line DNA by an inverse PCR method, duplicated a 'TTAA' tetranucleotide target site that is present only once in the homologous larval DNA sequence. These data suggest that mobilization of TFP3 into both viral and cellular sites is identical in specificity and mechanism.

Animals↗
PubMed2004

Translation of duck hepatitis B virus reverse transcriptase by ribosomal shunting.

The duck hepatitis B virus (DHBV) polymerase (P) is translated by de novo initiation from a downstream open reading frame (ORF) that partially overlaps the core (C) ORF on the bicistronic pregenomic RNA (pgRNA). The DHBV P AUG is in a poor context for translational initiation and is preceded by 14 AUGs that could intercept scanning ribosomes, yet P translation is unanticipatedly rapid. Therefore, we assessed C and P translation in the context of the pgRNA. Mutating the upstream C ORF revealed that P translation was inversely related to C translation, primarily due to occlusion of P translation by ribosomes translating C. Translation of the pgRNA was found to be cap dependent, because inserting a stem-loop (BamHI-SL) that blocked >90% of scanning ribosomes at the 5' end of the pgRNA greatly inhibited C and P synthesis. Neither mutating AUGs between the C and P start sites in contexts similar to that of the P AUG nor blocking ribosomal scanning by inserting the BamHI-SL between the C and P start codons greatly altered P translation, indicating that most ribosomes that translate P do not scan through these sequences. Finally, optimizing the P AUG context did not increase P translation. Therefore, the majority of the ribosomes that translate P are shunted from a donor region near the 5' end of the pgRNA to an acceptor site at or near the P AUG, and the shunt acceptor sequences may augment initiation at the P AUG.

DNA-Directed RNA Polymerases↗
PubMed2003

Reptiles: a group of transition in the evolution of genome size and of the nucleotypic effect.

A comparison between genome size and some phenotypic parameters, such as developmental length and metabolic rate, showed in reptiles a nucleotypic correlation similar to the one observed in birds and mammals. Indeed, like homeotherms, reptiles exhibit a highly significant, inverse correlation of genome size with metabolic rate but unlike amphibians, no relationship with developmental length. Several lines of evidence suggest that these nucleotypic correlations are influenced by body temperature, which also affects the guanine + cytosine nuclear percentage, and that they play an important role in the adaptation of these amniotes. However, the reptilian suborders exhibit differences in the quantitative and compositional characters of the genome that do not completely correspond to differences in the phenotypic parameters commonly involved in the nucleotypic effect. Thus, additional factors could have influenced genome size in this class. These data could be explained with the model of Hartl and Petrov, who observed an inverse correlation between genome size, non-coding portion of the genome and rate of DNA loss and hypothesized a strong role for different spectra of spontaneous insertions and deletions (indels) in the variations of genome size. It is thus reasonable to surmise that variations in the reptilian genome were initially influenced by different indels spectra typical of the diverse lineages, possibly related to different chromosome compartmentalizations. The consequent size increases or decreases would have influenced various morphological and functional cell parameters, and through these some phenotypic characteristics of the whole organism, especially the metabolic rate, very important for environmental adaptation and thus subject to natural selection. Through this "nucleotypic" bond, natural selection would also have controlled genome size variations.

Adaptation, Physiological↗
PubMed1990

Somatic mosaicism in a patient with bilateral retinoblastoma.

We describe two cell lines with different deletions of the retinoblastoma gene in a patient with bilateral retinoblastoma. This patient has transmitted the mutation less frequent in his lymphocytes to two affected children. We cloned, mapped, and sequenced the junction fragments of the two deletions and found that they share one breakpoint but extend into opposite directions. An insertion of 4 bp of unknown origin is present between the breakpoints in one of the deletions. The second deletion shows a more complex rearrangement, including an inversion at the 5' end. Short regions of homology were found at the breakpoints and flanking the inversion. These results support the notion that bilateral retinoblastoma may not only be due to a germ-line mutation but also to a postzygotic mutation leading to somatic mosaicism.

Base Sequence↗
PubMed1996

Generation of Campylobacter fetus S-layer protein diversity utilizes a single promoter on an invertible DNA segment.

Wild-type strains of Campylobacter fetus contain a monomolecular array of surface layer proteins (SLPs) and vary the antigenicity of the predominant SLP expressed. Reciprocal recombination events among the eight genomic SLP gene cassettes, which encode 97- to 149 kDa SLPs, permit this variation. To explore whether SLP expression utilizes a single promoter, we created mutant bacterial strains using insertional mutagenesis by rescue of a marker from plasmids. Experimental analysis of the mutants created clearly indicates that SLP expression solely utilizes the single sapA promoter, and that for variation C. fetus uses a mechanism of DNA rearrangement involving inversion of a 6.2 kb segment of DNA containing this promoter. This DNA inversion positions the sapA promoter immediately upstream of one of two oppositely oriented SLP gene cassettes, leading to its expression. Additionally, a second mechanism of DNA rearrangement occurs to replace at least one of the two SLP gene cassettes bracketing the invertible element. As previously reported promoter inversions in prokaryotes, yeasts and viruses involve alternate expression of at most two structural genes, the ability of C. fetus to use this phenomenon to express one of multiple cassettes is novel.

Bacterial Outer Membrane Proteins↗
PubMed2000

Increased renal production of C-type natriuretic peptide (CNP) in patients with cirrhosis and functional renal failure.

BACKGROUND/AIMS: C-type natriuretic peptide (CNP), the third member of the natriuretic peptide family, is considered to be involved in the regulation of vascular tone. Furthermore, the recent demonstration of CNP in human kidney and urine may indicate a role for CNP in fluid and electrolyte homeostasis. Therefore, the aim of the present study was to investigate the possible role of CNP in renal function disturbances in patients with cirrhosis of the liver. METHODS: Peripheral venous and urinary concentrations of CNP were determined in samples from 11 healthy controls, 20 cirrhotic patients with normal renal function (creatinine clearance 117 (8) ml/min), and 20 cirrhotic patients with impaired renal function (creatinine clearance 35 (4) ml/min). In a second protocol, arterial and renal venous plasma concentrations of CNP were determined in 37 patients with cirrhosis of the liver to estimate renal extraction ratios of CNP. A sensitive and specific radioimmunoassay was applied after solid phase extraction of samples. RESULTS: Plasma CNP was lower in cirrhotic patients with normal and impaired renal function than in controls (3.0 (0.4) and 2.7 (0.2) v. 4.2 (0.4) pg/ml, respectively; p<0.05; mean (SEM)). In contrast, urinary CNP was higher in patients with impaired renal function compared with those with normal renal function and healthy controls (47.2 (7.4) v. 20.8 (1.9) and 17.0 (3.0) ng CNP/g creatinine, respectively; p<0.05). Urinary CNP was found to be inversely related to urinary sodium excretion in cirrhotic patients (r=-0.56; p<0.01). No differences were observed between arterial and renal venous concentrations of CNP in cirrhosis (2.4 (0.2) v. 2.4 (0.2) pg/ml). In cirrhotic patients with hepatorenal syndrome or refractory ascites (n=5), urinary CNP decreased from 132 (59) to 38 (7) ng/g creatinine (p<0.05) one week after either ornipressin infusion or insertion of a transjugular intrahepatic portosystemic shunt together with an increase in urinary sodium excretion from 27 (17) to 90 (34) mmol/24 hours. CONCLUSIONS: Increased urinary CNP in cirrhotic patients in the absence of renal arteriovenous concentration gradients suggests enhanced renal CNP production in cirrhosis. Furthermore, an inverse relation between urinary CNP and urinary sodium excretion suggests a role for this peptide in renal sodium handling in patients with cirrhosis.

Analysis of Variance↗
PubMed2000

Spontaneous variability of cardiac output in ventilated critically ill patients.

OBJECTIVE: To define the magnitude of spontaneous cardiac output variability over time in sedated medical intensive care unit patients attached to a continuous cardiac output monitor, and to determine whether high level positive end-expiratory pressure or inverse inspiratory-to-expiratory (I:E) ratio ventilation resulted in greater variability over time than low positive end-expiratory pressure with conventional I:E ratio ventilation. DESIGN: Prospective study. SETTING: Medical intensive care unit in a tertiary medical center. PATIENTS: A total of 22 hemodynamically stable acute respiratory failure patients with a pulmonary artery catheter inserted for hemodynamic monitoring INTERVENTIONS: After being sedated, patients were randomized ultimately to receive pressure control ventilation first at setting A (high positive end-expiratory pressure [15 cm H2O] with conventional I:E ratio [1:2]) and then at setting B (low positive end-expiratory pressure [5 cm H2O] with inverse I:E ratio [2:1]), or vice versa, and then at setting C (low positive end-expiratory pressure [5 cm H2O] with conventional I:E ratio [1:2]). Each ventilation setting period lasted 1 hr. MEASUREMENTS AND MAIN RESULTS: Cardiac output (CO) was measured continuously. The continuous CO value displayed was updated every 30-60 secs. The updated value reflected an average of the previous 3-6 mins. The coefficient of variation (CV) of CO for each setting in each patient was calculated to represent the spontaneous variability. The mean CO+/-SD and CV of each setting was 5.7+/-1.8 L/min and 4.4% for setting A, 5.6+/-1.5 L/min and 4.6% for setting B, and 5.9+/-1.7 L/min and 4.8% for setting C. Analysis of variance revealed no significant differences between the CVs of the three settings. The 95% confidence interval for the COs for each setting was approximately the mean CO+/-0.1 x mean CO measured. CONCLUSIONS: In critically ill sedated medical intensive care unit patients with stable hemodynamics, the spontaneous variability of cardiac output over time was not significant. High positive end-expiratory pressure (15 cm H2O) and inverse ratio ventilation (2:1) did not contribute to increased spontaneous variability of cardiac output.

APACHE↗
PubMed1991

Molecular analysis of the Bg-rbg transposable element system of Zea mays L.

The two components of the Bg-rbg transposable element system of maize have been cloned. The Bg element, isolated from the mutable allele wx-m32:: Bg is inserted in the intron of the Waxy (Wx) gene between exons 12 and 13. The length of the element is of 4869 bp. Bg has 5 bp terminal inverted repeats, and generates upon insertion an 8 bp direct duplication of the target sequence. Both ends of the Bg element contain a 76 bp direct repeat adjacent to the terminal inverted repeats. The hexamer motif TATCGGC is here repeated several times in direct or inverse orientation. The rbg element was isolated from the mutable allele o2m(r) where it is located in the promoter region of the Opaque-2 (O2) gene. rbg is approximately 4.5 kb in length, has terminal inverted repeats identical to those of the Bg element, and is also flanked by an 8 bp direct duplication at the target site. Like Bg, rbg carries the 76 bp direct repeats. Restriction enzyme analysis reveals that, compared to Bg, the receptor element is distinguishable by small deletion and insertion events. Sequence data indicate that not more than 75% homology exists at the DNA level between the rbg element and the autonomous Bg element.

Alleles↗
PubMedDate not supplied

A DNA insertion in the apolipoprotein A-I gene of patients with premature atherosclerosis.

Apolipoprotein A-I (apo A-I) is the major protein constituent of high-density lipoprotein (HDL). The study of the apo A-I gene is of interest because plasma levels of HDL have been inversely correlated with the development of coronary artery disease and because polymorphisms related to this gene have been associated with hypertriglyceridaemia and premature atherosclerosis. We have recently isolated and characterized the human apo A-I gene and have shown that apo A-I and apolipoprotein C-III (apo C-III) genes are physically linked and that a polymorphism (of unknown frequency in the general population) of the apo A-I gene is inherited as a mendelian trait linked to premature atherosclerosis in an affected family (not the same polymorphism as has previously been reported to be associated with hypertriglyceridaemia). Here we report that this polymorphism is due an at least 6.5-kilobase (kb) DNA insertion in the coding region of the apo A-I gene and that there is no detectable alteration (as determined by limited genomic blotting analysis) of the apo C-III gene of these patients.

Apolipoprotein A-I↗
PubMed2001

Cholesterol, a modulator of membrane-associated Abeta-fibrillogenesis and neurotoxicity.

Recent studies have suggested that cholesterol, an important determinant of the physical state of biological membranes, plays a significant role in the development of Alzheimer's disease. We have employed in situ scanning probe microscopy, fluorescence anisotropy, and electron microscopy to investigate how cholesterol levels within total brain lipid bilayers effect amyloid beta-peptide (Abeta)-assembly. Fluorescence anisotropy measurements revealed that the relative fluidity of the total brain lipid membranes was influenced by the level of cholesterol and the addition of Abeta40 resulted in a decrease in the overall vesicle fluidity. In situ scanning probe microscopy performed on supported planar bilayers of total brain lipid revealed a correlation between membrane fluidity, as influenced by cholesterol level, and the extent of Abeta-insertion and subsequent fibrillogenesis. These observations were consistent with fluorescence microscopy studies of PC-12 and SH-SY5Y cell lines exposed to exogenous Abeta, which revealed an inverse correlation between membrane cholesterol level, and Abeta-cell surface binding and subsequent cell death. These results collectively suggest that Abeta-cell surface interactions are mediated by cellular cholesterol levels, the distribution of cholesterol throughout the cell, and membrane fluidity.

Alzheimer Disease↗