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At least 595 records · Page 33Linked to original sources
PubMed2000

Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1.

With the completion of many genome projects, a shift is now occurring from the acquisition of gene sequence to understanding the role and context of gene products within the genome. The opportunistic pathogen Pseudomonas aeruginosa is one organism for which a genome sequence is now available, including the annotation of open reading frames (ORFs). However, approximately one third of the ORFs are as yet undefined in function. Proteomics can complement genomics, by characterising gene products and their response to a variety of biological and environmental influences. In this study we have established the first two-dimensional gel electrophoresis reference map of proteins from the membrane fraction of P. aeruginosa strain PA01. A total of 189 proteins have been identified and correlated with 104 genes from the P. aeruginosa genome. Annotated membrane proteins could be grouped into three distinct categories: (i) those with functions previously characterised in P. aeruginosa (38%); (ii) those with significant sequence similarity to proteins with assigned function or hypothetical proteins in other organisms (46%); and (iii) those with unknown function (16%). Transmembrane prediction algorithms showed that each identified protein sequence contained at least one membrane-spanning region. Furthermore, the current methodology used to isolate the membrane fraction was shown to be highly specific since no contaminating cytosolic proteins were characterised. Preliminary analysis showed that at least 15 gel spots may be glycosylated in vivo, including three proteins that have not previously been functionally characterised. The reference map of membrane proteins from this organism is now the basis for determining surface molecules associated with antibiotic resistance and efflux, cell-cell signalling and pathogen-host interactions in a variety of P. aeruginosa strains.

Bacterial Proteins↗
PubMed1999

Slow information processing after very severe closed head injury: impaired access to declarative knowledge and intact application and acquisition of procedural knowledge.

As an explanation of the pattern of slow information processing after closed head injury (CHI), hypotheses of impaired access to declarative memory and intact application and acquisition of procedural memory after CHI are presented. These two hypotheses were tested by means of four cognitive reaction-time tasks, a semantic memory task, a memory comparison task, a mental rotation task and a mirror reading task. These tasks were administered on two different days to 12 survivors of a CHI tested more than 5 years after injury and a healthy control group of comparable age and education. In three tasks the difficulty of access to declarative knowledge was varied and it was expected that this would slow the CHI group more than the controls. In two tasks opportunities for procedural learning were provided by repeatedly presenting the same cognitive tasks and in one task, the difficulty of access to procedural memory was varied. It was expected that the CHI group would profit as much from this as would the control group. Both hypotheses were supported.

Adolescent↗
PubMed2001

GPMAW--a software tool for analyzing proteins and peptides.

General Protein/Mass Analysis for Windows (GPMAW) is a valuable piece of software for any molecular biologist, biochemist or mass spectrometrist wishing to analyze protein or peptide sequences. All steps from the acquisition of protein sequence from a built-in web interface, to proteolytic digests, theoretical peptide fragmentation, detailed annotation of sequences and secondary structure prediction, can be performed rapidly and intuitively without first having to spend days reading manuals.

Amino Acid Sequence↗
PubMed2002

HCV serotypes in Brazilian patients.

OBJECTIVE: To investigate the prevalence of the different types of hepatitis C virus (HCV) in a population of chronic HCV carriers using the Murex HCV serotyping 1-6 assay. METHODS: All serum samples from these patients had a positive nested PCR HCV reaction. The sera were submitted to ELISA, modified, for the identification of antibodies against HCV serotypes 1, 2, 3, 4, 5 and 6 (Murex HCV serotyping 1-6 assay). RESULTS: The viral serotype was identified in 166 (75.8%) of the 219 patients, 108 (65.11%) males and 58 (34.9%) females. Patient age ranged from 12 to 73 years, with a mean of 41.1 years. The form of acquisition of the disease most frequently reported was blood transfusion. The results showed a predominance of type 1 (70.0%), followed by type 3 (22.3%) and type 2 (4.2%). CONCLUSION: Samples presenting low and very close optical density readings may lead to discrepant diagnoses concerning HCV serotypes and should be confirmed by genotyping. The serotyping can be useful in clinical practice and can be of help in establishing the prognosis of the disease, also favoring epidemiologic studies independently of the technology required for genotyping tests.

Adolescent↗
PubMed2003

Early brain injury in children: development and reorganization of cognitive function.

Children who sustain congenital or acquired brain injury typically experience a diffuse insult that impacts many areas of the brain. Yet research has only recently begun to examine the development of these children, who often provide excellent examples of the presence or absence of neural plasticity. Development and recovery after such injuries reflects both restoration and reorganization of cognitive functions. To understand these processes, research should focus on questions and assessment paradigms oriented toward the acquisition (rather than the recovery) of cognitive functions. Outcomes may appear similar across types of insults, even when the sources of difficulties and their neural correlates are different. Comparisons of outcomes involving intellectual functions, memory and learning, reading, and language/discourse in children who sustain congenital injury (spina bifida meningomyelocele) and acquired injury (traumatic brain injury) illustrate these principles and the value of research on diffuse brain injury in children.

Brain Injuries↗
PubMed2003

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.

The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.

Adhesins, Bacterial↗
PubMed1987

Application of decision analysis to drug selection for formulary addition.

Decision analysis (DA) is a quantitative method for making decisions, incorporating both probabilistic data and value judgments, and clinical and economic outcomes. The P & T Committee at the Mary Hitchcock Memorial Hospital used this technique to aid in selection of a third-generation cephalosporin for formulary addition. Cost-specific data from this hospital, together with clinical data derived from the medical literature, and a panel of infectious disease specialists were used to compare costs associated with antibiotic regimens of three infections. Results show that ceftizoxime is the least costly treatment for hospital-acquired pneumonia and sepsis of unknown origin, whereas metronidazole plus gentamicin is the least costly regimen for intra-abdominal infections. This demonstrates that drugs with higher acquisition costs can, in some cases, be less expensive than drugs with lower acquisition costs when the total cost of drug therapy is considered.

Cephalosporins↗
PubMed2002

Late plasticity for language in a child's non-dominant hemisphere: a pre- and post-surgery fMRI study.

The ability of the right hemisphere to sustain the acquisition or the recovery of language after extensive damage to the left hemisphere has been essentially related to the age at the time of injury. Better language abilities are acquired when the insult occurs in early childhood (perinatal insults) compared with later occurrence. However, while previous studies have described the neuropsychological pattern of language development in typical cases, the neural bases of such plasticity remain unexplored. Non-invasive functional MRI (fMRI) is a unique tool to assess the neural correlates of brain plasticity through repeated studies, but the technique has not been widely used in children because of methodological limitations. Plasticity of language was studied in a boy who developed intractable epilepsy related to Rasmussen's syndrome of the left hemisphere at age 5 years 6 months, after normal language acquisition. The first fMRI study at age 6 years 10 months showed left lateralization of language networks during a word fluency task. After left hemispherotomy at age 9 years, the child experienced profound aphasia and alexia, with rapid recovery of receptive language but slower and incomplete recovery of expressive language and reading. Postoperative fMRI at age 10 years 6 months showed a shift of language-related networks to the right during expressive and receptive tasks. Right activation was seen mainly in regions that could not be detected preoperatively, but mirrored those previously found in the left hemisphere (inferior frontal, temporal and parietal cortex), suggesting reorganization in a pre-existing bilateral network. In addition, neuropsychological data of this case support the hypothesis of innately more bilateral distribution of receptive than expressive language. This first serial fMRI study illustrates the great plasticity of the child's brain and the ability of the right hemisphere to take over some expressive language functions, even at a relatively late age. It also suggests a limit for removal of the dominant hemisphere beyond the age of 6 years, a classical limit for the critical period of language acquisition.

Brain↗
PubMed1996

Cloning of a DNA fragment encoding a heme-repressible hemoglobin-binding outer membrane protein from Haemophilus influenzae.

Haemophilus influenzae is able to use hemoglobin as a sole source of heme, and heme-repressible hemoglobin binding to the cell surface has been demonstrated. Using an affinity purification methodology, a hemoglobin-binding protein of approximately 120 kDa was isolated from H. influenzae type b strain HI689 grown in heme-restricted but not in heme-replete conditions. The isolated protein was subjected to N-terminal amino acid sequencing, and the derived amino acid sequence was used to design corresponding oligonucleotides. The oligonucleotides were used to probe a Southern blot of EcoRI-digested HI689 genomic DNA. A hybridizing band of approximately 4.2 kb was successfully cloned into pUC19. Using a 1.9-kb internal BglII fragment of the 4.2-kb clone as a probe, hybridization was seen in both typeable and nontypeable H. influenzae but not in other bacterial species tested. Following partial nucleotide sequencing of the 4.2-kb insert, a putative open reading frame was subcloned into an expression vector. The host Escherichia coli strain in which the cloned fragment was expressed bound biotinylated human hemoglobin, whereas binding of hemoglobin was not detected in E. coli with the vector alone. In conclusion, we hypothesize that the DNA fragment encoding an approximately 120-kDa heme-repressible hemoglobin-binding protein mediates one step in the acquisition of hemoglobin by H. influenzae in vivo.

Amino Acid Sequence↗
PubMed1999

[The role of electron beam CT in the diagnosis of acute pulmonary embolism--presenting a new examination protocol].

PURPOSE: To evaluate electron beam tomography in the detection of acute pulmonary embolism using a new acquisition protocol. MATERIALS AND METHODS: 65 patients underwent electron beam tomography (EBT) and v./p. scintigraphy. According to the inclusion criteria 46 patients participated in the study. Contrast enhancement and detectability of pulmonary arteries were scored on a 4 step scale for image quality. The results of prospective detection of pulmonary embolism were compared for both modalities (blinded reading). "Embolism", "questionable embolism" and "no embolism" were used as categories. RESULTS: 22/46 patients (48%) showed acute pulmonary embolism. EBT and scintigraphy were discordant in 24% of patients. In EBT 1 false positive and 1 false negative case occurred, scintigraphy demonstrated 2 false negative and 3 false positive cases. 6/9 patients with questionable findings in scintigraphy were correctly classified by EBT to a category "embolism" or "no embolism" as "suspected embolism", EBT displayed a sensitivity of 96.3% and a specificity of 94.7%. Scintigraphy evidenced a sensitivity of 93.7% and a specificity of 84.4%. CONCLUSIONS: EBT shows better results than scintigraphy for the detection of acute pulmonary emboli. The evaluated new acquisition protocol for EBT seems to be well suited. High vessel contrast and thin slices allow a reliable detection of segmental and subsegmental pulmonary arteries.

Acute Disease↗
PubMed2000

Skill acquisition in music performance: relations between planning and temporal control.

We investigated the acquisition of music performance skills in novice and expert pianists. Temporal disruptions in novice performances coincided with constraints in planning capacities. Child and adult pianists ranging in age (9-26 years), training (3-15 years) and sight-reading ability learned to perform a novel musical piece in eleven practice trials. Computer-detected pitch and timing errors revealed: (1) gradual improvements in performance tempo and pitch accuracy with skill level and practice, generally fitting a power function; (2) a relative-timing/pitch accuracy trade-off and high incidence of simultaneous pitch/time errors; (3) improvements in relative timing (temporal continuity, underlying beat, metrical structure) with skill and practice; and (4) increased anticipatory behavior and a greater range of planning with skill and practice. A strong positive relationship between the mastery of temporal constraints and planning abilities within performance suggests that these two cognitive indicators are closely related and may arise from segmentation processes during performance. Examination of sequence timing may explicate planning abilities that underlie many complex skills.

Adolescent↗
PubMed1998

Development of a MicroStrip Gas Chamber as a Time-Resolved Area Detector.

A two-dimensional microstrip gas chamber (MSGC) has been developed with a 10 cm-square detection area and an ultrafast read-out system. The MSGC was made using multi-chip module (MCM) technology, and has a very thin substrate of 17 micro m and many anodes and back strips, both with 200 micro m pitches. The new read-out system, in which the hit addresses of the electrodes were sequentially encoded to the hit positions by a synchronous clock, handles data rates of up to 10(7) events s(-1) from MSGCs. This enables the acquisition of fast and sequential digital images. Furthermore, since the MSGC is a real photon-counting detector, the timing of the photons, to an accuracy of a few tens of nanoseconds, and energy can be recorded. Here, the performance of the MSGC system as a real-time area detector is reported, and the abilities of this system are discussed.

Journal Article↗
PubMed2002

Adaptation of aequorin functional assay to high throughput screening.

AequoScreen, a cellular aequorin-based functional assay, has been optimized for luminescent high-throughput screening (HTS) of G protein-coupled receptor (GPCRs). AequoScreen is a homogeneous assay in which the cells are loaded with the apoaequorin cofactor coelenterazine, diluted in assay buffer, and injected into plates containing the samples to be tested. A flash of light is emitted following the calcium increase resulting from the activation of the GPCR by the sample. Here we have validated a new plate reader, the Hamamatsu Photonics FDSS6000, for HTS in 96- and 384-well plates with CHO-K1 cells stably coexpressing mitochondrial apoaequorin and different GPCRs (AequoScreen cell lines). The acquisition time, plate type, and cell number per well have been optimized to obtain concentration-response curves with 4000 cells/well in 384-well plates and a high signal:background ratio. The FDSS6000 and AequoScreen cell lines allow reading of twenty 96- or 384-well plates in 1 h with Z' values of 0.71 and 0.78, respectively. These results bring new insights to functional assays, and therefore reinforce the interest in aequorin-based assays in a HTS environment.

Aequorin↗
PubMed2006

Three-dimensional ultrasonography navigation in spinal cord tumor surgery. Technical note.

The authors describe the technical application of three-dimensional (3D) ultrasonography navigation in spinal cord tumor surgery. The spinal cord is a complex neurological structure in which there is the potential for causing neurological morbidity during tumor resection. Standard neuronavigation systems based on computed tomography or C-arm images are not adapted to tumor surgery in the spinal cord. Since 2004 the authors have been using a 3D ultrasonography-based neuronavigation system. During surgery, two-dimensional ultrasound images were acquired and reconstructed into 3D image data to assist in tumor resection. The navigation cameras read the position of a patient reference frame attached to a spinous process, the ultrasonography probe, and surgical instruments. Five- and 10-MHz phased-array ultrasonography probes equipped with optical tracking frames were used for image data acquisition. Spinal cord tumors were visualized using ultrasonography, and 3D ultrasonography-guided tumor biopsy sampling and resection were performed. The practice of attaching the reference frame to a spinous process adjacent to the spinal cord tumor, as well as performing image acquisition just before starting the resection, reduced the possible sources of inaccuracy. The technical application of a navigation system based on intraoperative 3D ultrasound image reconstruction seems feasible and may have the potential of improving functional outcome in association with spinal cord tumor surgery.

Adult↗
PubMed2000

Pediatric nuclear medicine, Part I: Developmental cues.

OBJECTIVE: Children provide a continuous challenge for the nuclear medicine technologist. The task of successfully completing a nuclear medicine procedure varies little among a 20-y-old, a 40-y-old and a 60-y-old patient. Successful completion of a procedure varies much more among a 2-y-old, a 4-y-old and a 6-y-old. Successfully completing a pediatric nuclear medicine procedure includes quick acquisitions, technically acceptable images or calculations, and satisfied patients and parents. Understanding your patient is crucial, and it provides the parents with a greater sense of comfort and confidence about the nuclear medicine technologist and the procedure. After reading this article the nuclear medicine technologist should be able to: (a) discuss the developmental stages of children according to several major theories; (b) identify the physical and mental expectations for each age group; (c) explain applications for incorporating this information into common pediatric nuclear medicine practice; and (d) discuss the common realities surrounding the behavior of children and their parents. A second article will feature tips, indications and populations for common pediatric procedures.

Adolescent↗
PubMed2004

Pack-MULE transposable elements mediate gene evolution in plants.

Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3,000 Pack-MULEs in rice containing fragments derived from more than 1,000 cellular genes. Pack-MULEs frequently contain fragments from multiple chromosomal loci that are fused to form new open reading frames, some of which are expressed as chimaeric transcripts. About 5% of the Pack-MULEs are represented in collections of complementary DNA. Functional analysis of amino acid sequences and proteomic data indicate that some captured gene fragments might be functional. Comparison of the cellular genes and Pack-MULE counterparts indicates that fragments of genomic DNA have been captured, rearranged and amplified over millions of years. Given the abundance of Pack-MULEs in rice and the widespread occurrence of MULEs in all characterized plant genomes, gene fragment acquisition by Pack-MULEs might represent an important new mechanism for the evolution of genes in higher plants.

Base Sequence↗
PubMed2000

The Legionella pneumophila iraAB locus is required for iron assimilation, intracellular infection, and virulence.

Legionella pneumophila, a facultative intracellular parasite of human alveolar macrophages and protozoa, causes Legionnaires' disease. Using mini-Tn10 mutagenesis, we previously isolated a L. pneumophila mutant that was hypersensitive to iron chelators. This mutant, NU216, and its allelic equivalent, NU216R, were also defective for intracellular infection, particularly in iron-deficient host cells. To determine whether NU216R was attenuated for virulence, we assessed its ability to cause disease in guinea pigs following intratracheal inoculation. NU216R-infected animals yielded 1,000-fold fewer bacteria from their lungs and spleen compared to wild-type-130b-infected animals that had received a 50-fold-lower dose. Moreover, NU216R-infected animals subsequently cleared the bacteria from these sites. While infection with 130b resulted in high fever, weight loss, and ruffled fur, inoculation with NU216R did not elicit any signs of disease. DNA sequence analysis revealed that the transposon insertion in NU216R lies in the first open reading frame of a two-gene operon. This open reading frame (iraA) encodes a 272-amino-acid protein that shows sequence similarity to methyltransferases. The second open reading frame (iraB) encodes a 501-amino-acid protein that is highly similar to di- and tripeptide transporters from both prokaryotes and eukaryotes. Southern hybridization analyses determined that the iraAB locus was largely limited to strains of L. pneumophila, the most pathogenic of the Legionella species. A newly derived mutant containing a targeted disruption of iraB showed reduced ability to grow under iron-depleted extracellular conditions, but it did not have an infectivity defect in the macrophage-like U937 cells. These data suggest that iraA is critical for virulence of L. pneumophila while iraB is involved in a novel method of iron acquisition which may utilize iron-loaded peptides.

Amino Acid Sequence↗