Biomedical subjects

K Gabriel

Publications and source records attributed to K Gabriel.

At least 19 recordsLinked to original sources

PubMed2006

Crohn's-like colitis, enterocolitis and perianal disease in Hermansky-Pudlak syndrome.

Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessively inherited disorder consisting of the triad of oculocutaneous tyrosinase-positive albinism, prolonged bleeding time secondary to platelet storage pool defect and ceroid depositions within the reticuloendothelial system. Some patients also reportedly have gastrointestinal (GI) complications related to chronic granulomatous colitis, enterocolitis and extensive granulomatous perianal disease, the later previously unreported in the literature. These observations suggest that the GI complications of HPS are due to the development of classical Crohn's disease. The implications for disease pathogenesis and surgical management are discussed.

Adult↗

PubMed2005

Alvimopan, a peripherally acting mu-opioid receptor antagonist, compared with placebo in postoperative ileus after major abdominal surgery: results of a randomized, double-blind, controlled study.

BACKGROUND: Alvimopan is a peripherally acting mu-opioid receptor (PAM-OR) antagonist for accelerating gastrointestinal recovery after surgery. METHODS: Patients undergoing open laparotomy (bowel resection, n = 418; hysterectomy, n = 197) were randomized to receive alvimopan 6 or 12 mg or placebo orally > or = 2 h before surgery and then b.i.d. until hospital discharge (up to 7 days). The primary efficacy endpoint was time to gastrointestinal (GI) recovery (measured by toleration of solid food and passage of flatus/stool; GI-3). Secondary endpoints included time to GI-2 recovery (toleration of solid food and passage of stool) and hospital discharge order written (DCO). RESULTS: Alvimopan did not significantly accelerate GI-3 compared with placebo [6 mg: hazard ratio (HR) = 1.20, p = 0.080; 12 mg: HR = 1.24, p = 0.038). However, after adjustment for significant covariates (sex/surgical duration), benefits were significant for both doses (6 mg: HR = 1.24, p = 0.037; 12 mg: HR = 1.26, p = 0.028). Alvimopan also significantly accelerated time to GI-2 (6 mg: HR = 1.37, p = 0.008; 12 mg: HR = 1.33, p = 0.018) and DCO (6 mg: HR = 1.31, p = 0.008; 12 mg: HR = 1.28, p = 0.015). Adverse events were similar between groups. CONCLUSIONS: Alvimopan (6 or 12 mg) accelerates GI recovery and is well tolerated in patients undergoing open laparotomy.

Abdomen↗

PubMed2002

Both paracetamol and ibuprofen are equally effective in managing flu-like symptoms in relapsing-remitting multiple sclerosis patients during interferon beta-1a (AVONEX) therapy.

Interferon beta-1a is an established therapy for patients with relapsing-remitting multiple sclerosis (MS). Adverse effects in the first weeks of treatment are common. This open-label, multicenter, randomized, prospective study compared treatment of flu-like symptoms (FLS) with paracetamol versus ibuprofen administered 48 h within interferon injection. The percentage of patients with FLS was comparable between both treatment groups and improved during the course of the study (baseline: paracetamol 92%, ibuprofen 90%; week 12: paracetamol 60%, ibuprofen 57%). More than 75% of patients receiving either paracetamol or ibuprofen reported no or only mild impairment of daily activities. There was no significant difference in general satisfaction or incidence of additional symptoms (weakness, nausea, headache; paracetamol 84.6% patients, ibuprofen 86.0% patients) between the two groups. A significant overall improvement from baseline to week 12 was observed for all parameters studied (paracetamol and ibuprofen groups were pooled). These results indicate that neither the paracetamol nor the ibuprofen treatment regimen is better.

Acetaminophen↗

PubMed2001

The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.

The 2.6 A resolution crystal structure of an inactive complex between yeast tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular details of a tRNA-induced mechanism that controls the specificity of the reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering the active site cleft of its subunit. However, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the terminal adenosine. The structure suggests that the acceptor stem regulates the loop movement through sugar phosphate backbone- protein interactions. Solution and cellular studies on mutant tRNAs confirm the crucial role of the tRNA three-dimensional structure versus a specific recognition of bases in the control mechanism.

Aspartate-tRNA Ligase↗

PubMed2001

Construction of an Escherichia coli knockout strain for functional analysis of tRNA(Asp).

The specific aminoacylation of tRNA is critical for translation of the genetic code. A molecular description of aminoacylation requires knowledge of the relevant three-dimensional structures, biochemical parameters and the structure-function relationship of the synthetase and its substrate tRNA. Extensive structural and biochemical data are available on the aspartic acid system of Escherichia coli, but there is a paucity of cellular functional data. We have developed a system to overcome this deficiency by engineering an E. coli knockout tRNA(Asp) strain, thereby allowing a penetrating analysis of tRNA(Asp) structure and function under conditions that prevail in the cell.

Acylation↗

PubMed2001

Plasmid systems to study RNA function in Escherichia coli.

Determining the functional activity of an essential RNA in vivo presents special challenges. We have devised an in vivo analysis of alternative forms of an essential tRNA gene in Escherichia coli knockout cells using either a plasmid switch or a regulated two-plasmid system. The model system is presented together with a description of the new plasmids and procedures necessary to effect these analyses. The system is readily adaptable to non-essential RNAs.

Arabinose↗

PubMed2001

The alpha and the beta: protein translocation across mitochondrial and plastid outer membranes.

In the evolution of mitochondria and plastids from endosymbiotic bacteria, most of the proteins that make up these organelles have become encoded by nuclear genes and must therefore be transported across the organellar membranes, following synthesis in the cytosol. The core component of the protein translocation machines in both the mitochondrial and plastid outer membranes appears to be a beta-barrel protein, perhaps a relic from their bacterial ancestry, distinguishing these translocases from the alpha-helical-based protein translocation pores found in all other eukaryotic membranes.

Bacterial Proteins↗

PubMed1999

The reliability of in vivo structure-function analysis of tRNA aminoacylation.

The G.U wobble base-pair in the acceptor helix of Escherichia coli tRNAAlais critical for aminoacylation by the alanine synthetase. Previous work by several groups probed the mechanism of enzyme recognition of G.U by a structure-function analysis of mutant tRNAs using either a cell assay (amber suppressor tRNA) or a test tube assay (phage T7 tRNA substrate and purified enzyme). However, the aminoacylation capacity of particular mutant tRNAs was about 10(4)-fold higher in the cell assay. This led us to scrutinize the cell assay to determine if any parameter exaggerates the extent of aminoacylation in mutants forming substantial amounts of alanyl-tRNAAla. In doing so, we have refined and developed experimental designs to analyze tRNA function. We examined the level of aminoacylation of amber suppressor tRNAAlawith respect to the method of isolating aminoacyl-tRNA, the rate of cell growth, the cellular levels of alanine synthetase and elongation factor TU (EF-Tu), the amount of tRNA and the characteristics of EF-Tu binding. Within the precision of our measurements, none of these parameters varied in a way that could significantly amplify cellular alanyl-tRNAAla. A key observation is that the extent of aminoacylation of tRNAAlawas independent of tRNAAlaconcentration over a 75-fold range. Therefore, the cellular assay of tRNAAlareflects the substrate quality of the molecule for formation of alanyl-tRNAAla. These experiments support the authenticity of the cellular assay and imply that a condition or factor present in the cell assay may be absent in the test tube assay.

Acylation↗

PubMed1999

A set of plasmids constitutively producing different RNA levels in Escherichia coli.

New plasmids were developed for the in vivo expression of RNA in Escherichia coli. These plasmids combine constitutive promoters of different strengths with different origins of replication to provide a 75-fold range of expression of amber suppressor tRNA. The plasmids are either pMB1, p15A or temperature-sensitive SC101 replicons, and can be used in two plasmid systems for studying RNA-protein interactions. The temperature-sensitive SC101 plasmids may be useful as gene replacement vectors. Another vector that is suitable for generating lethal mutations was constructed in a plasmid containing a regulatable phage T7 promoter.

Escherichia coli↗

PubMed1999

Functional compensation by particular nucleotide substitutions of a critical G*U wobble base-pair during aminoacylation of transfer RNA.

Expression of the genetic code depends on precise tRNA aminoacylation by cognate aminoacyl-tRNA synthetase enzymes. The G.U wobble base-pair in the acceptor helix of Escherichia coli alanine tRNA is the primary aminoacylation determinant of this molecule. Previous work on the process of synthetase recognition of the G.U pair showed that replacing G.U by a G.C Watson-Crick base-pair inactivates alanine acceptance by the tRNA, but that C.A and G.A wobble pair replacements preserve acceptance. Work by another group reported that the effects of a G.C replacement were reversed by a distal wobble base-pair in the anticodon helix. This result is potentially interesting because it suggests that distant regions in alanine tRNA are functionally coupled during synthetase recognition and more generally because recognition determinants of many other tRNAs lie in both the acceptor helix and anticodon helix region. Here, we have conducted an extensive in vivo analysis of the distal wobble pair in alanine tRNA and report that it does not behave like a compensating mutation. Restoration of alanine acceptance was not detected even when the synthetase enzyme was overproduced. We discuss the previous experimental evidence and suggest how the distal wobble pair was incorrectly analyzed. The available data indicate that all principal recognition determinants of alanine tRNA lie in the molecule's acceptor helix.

Acylation↗

PubMed1999

The relationship of thermodynamic stability at a G x U recognition site to tRNA aminoacylation specificity.

The G x U pair at the third position in the acceptor helix of Escherichia coli tRNA(Ala) is critical for aminoacylation. The features that allow G x U recognition are likely to include direct interaction of alanyl-tRNA synthetase with distinctive atomic groups and indirect recognition of the structural and stability information encoded in the sequence of G x U and its immediate context. The present work investigates the thermodynamic stability and acceptor activity for a comprehensive set of variant RNAs with substitutions of the G x U pair of E. coli tRNA(Ala). The four RNAs with Watson-Crick substitutions had a lower acceptor activity and a higher stability relative to the G x U RNA. On the other hand, the RNAs with mispair substitutions had a lower stability, but either a higher or a lower acceptor activity. Thus, the entire set of variant RNAs does not exhibit a correlation between thermodynamic stability of the free, unbound tRNA and its acceptor activity. The substantial acceptor activity of tRNAs with particular mispair substitutions may be explained by their ability to assume the conformational preferences of alanyl-tRNA synthetase. Moreover, the G x U pair may provide a point of deformability for the substrate tRNA to adapt to the enzyme's active site.

Base Pairing↗

PubMed1999

Human spinal cord retains substantial structural mass in chronic stages after injury.

In chronic stages of human spinal cord injury, atrophy of the cord has been reported in regions both at and distant to the injury site. Local cord atrophy results from the direct effects of bony impact and ischemia, whereas distant atrophy results from anterograde (Wallerian) and retrograde axonal degeneration. However, the actual extent of degenerative changes in the chronically injured human spinal cord both at and remote from the injury site has rarely been reported, and has not been rigorously quantified to date. In the present study, we quantified the extent of spinal cord atrophy in 12 humans with chronic injury (2-34 years posttrauma) utilizing quantitative stereological assessment of spinal cord magnetic resonance images, and compared the results to uninjured human spinal cords. Focal cystic atrophy of the cord, characterized by signal attenuation on T1-weighted images, was regularly present at the actual site of impact injury and replaced a mean longitudinal area equaling less than one spinal cord segment in length (2.01 +/- 0.60 cm2, or a loss of 89.3 +/- 17.4% of the longitudinal area of one spinal cord segment). Spinal cord segments immediately rostral to the zone of cystic degeneration showed atrophy of only 19.4 +/- 7.5% of normal cord longitudinal area, and spinal cord segments immediately caudal to the zone of cystic degeneration showed atrophy of 16.5 +/- 4.1% of normal cord longitudinal area. Extensive spinal cord atrophy extending beyond the region of injury occurred in two of twelve cases (16.7%), and both were caused by late syrinx formation. Thus, spinal cord atrophy after trauma remains primarily restricted to the original site of injury. Experimental neural repair strategies should take into account the importance of "bridging" relatively short zones of cystic atrophy, then promoting axonal regeneration through potentially long segments of remaining cord parenchyma.

Adult↗

PubMed1998

The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation.

We have identified six new aminoacylation determinants of Escherichia coli tRNAGln in a genetic and biochemical analysis of suppressor tRNA. The new determinants occupy the interior of the acceptor stem, the inside corner of the L shape, and the anticodon loop of the molecule. They supplement the primary determinants located in the anticodon and acceptor end of tRNAGln described previously. Remarkably, the three-dimensional structure of the complex between tRNAGln and glutaminyl-tRNA synthetase shows that the enzyme interacts with the phosphate-sugar backbone but not the base of every new determinant. Moreover, a small protein motif interacts with five of these determinants, and it binds proximal to the sixth. The motif also interacts with the middle base of the anticodon and with the backbones of six other nucleotides. Our results emphasize that synthetase recognition of tRNA is more elaborate than amino acid side chains of the enzyme interacting with nucleotide bases of the tRNA. Recognition also includes synthetase interaction with tRNA backbone functionalities whose distinctive locations in three-dimensional space are exquisitely determined by the tRNA sequence.

Acylation↗

PubMed1998

Fetal ethanol effects on benzodiazepine sensitivity measured by behavior on the elevated plus-maze.

Rodents prenatally exposed to ethanol demonstrate altered behavioral and hormonal responses to stressful environments. Prenatal ethanol exposure may also have long-term effects on the offspring's GABAergic system. Using the elevated plus-maze, the present study examined the sensitivity of adult Sprague-Dawley rat offspring from prenatal ethanol (E), pair-fed (PF) and ad lib-fed control (C) conditions to the effects of benzodiazepine (BZD) on plus-maze behavior and corticosterone (CORT) responses. At 60-90 days of age, E, PF, and C males and females were injected subcutaneously with either BZD or saline. Twenty minutes later animals were placed in an open field (OF) for a 5-min test and then on the plus-maze for a 5 min test; behaviors were recorded during testing and blood samples collected at the end of testing for CORT determinations. Overall, sex differences were observed in both OF and plus-maze behaviors. Females showed more ambulation and rearing in the OF than males, and exhibited increased exploratory behaviors and decreased fear-related behaviors compared to males on the plus-maze. Following BZD treatment, both males and females exhibited increased time on open arms, increased open arm entries, and decreased time on closed arms compared to saline-treated males and females, regardless of prenatal treatment. These differences did not appear to be due to altered activity levels, as BZD treatment had no effect on total ambulation in the OF. Importantly, although no significant differences in plus-maze behaviors were found among saline-injected E, PF, and C males or females. BZD treatment differentially affected E males and females compared to their PF and C counterparts. Both E males and females treated with BZD spent increased time on open arms and decreased time on closed arms compared to their PF and C counterparts, suggesting decreased fear. Further, BZD-treated E males exhibited decreased open and closed arm entries, spent significantly more time in the central area, and had lower CORT levels, another index of fear or stress, compared to BZD-treated PF and C males. These data support and extend previous work demonstrating that the plus-maze provides a reliable measure of anxiety/fear, and that plus-maze behavior is sensitive to anxiolytic agents such as BZD. Furthermore, these data suggest that prenatal ethanol exposure may alter sensitivity to the effects of BZD on plus-maze behavior and CORT responsiveness, and may do so differentially in male and females offspring.

Animals↗

PubMed1998

A randomized trial of an intervention to prevent lawnmower injuries in children.

The U.S. Consumer Product Safety Commission reports about 60,000 emergency room visits for lawnmower injuries annually with 20% to children under 15 years. Employing a randomized pre-post control group design, the current study evaluated a 20-minute video intervention to increase parents' (n = 80) safety awareness and preventive actions. The setting was an outpatient clinic at a Children's Hospital. Differences favoring the intervention group were found for four of six behavior outcomes. For example, the proportion reporting never allowing children near operating mowers increased from half to two-thirds with no change among comparison group parents. In addition, significant increases in severity beliefs were found. The results provide formative support for the video intervention which possesses the key advantages of ease of use and constancy of message.

Accidents, Home↗

PubMed1998

The hormonal effects of alcohol use on the mother and fetus.

During pregnancy, the hormonal systems of the mother and fetus are intricately interconnected to ensure normal fetal development. Accordingly, maternal alcohol consumption during pregnancy can interfere with fetal development, not only directly, through adverse effects exerted by alcohol that crosses the placenta and enters the fetal bloodstream, but also indirectly, by disturbing the functions and interactions of maternal and fetal hormones. In both the mother and the fetus, alcohol exposure can impair the functioning of the hypothalamic-pituitary-adrenal axis, which regulates the body's response to stress; the hypothalamic-pituitary-gonadal axis, which controls reproductive functions; and the hypothalamic-pituitary-thyroid axis, which regulates the metabolism of almost all tissues. In addition, alcohol can interfere with the activities of growth hormone and insulin-like growth factors, which promote body growth and activity. Some of the effects of maternal alcohol consumption on fetal hormone systems may contribute to the adverse effects observed in children with fetal alcohol syndrome and related disorders.

Alcohol Drinking↗

PubMed1997

Improving clinician acceptance and use of computerized documentation of coded diagnosis.

After the Northwest Division of Kaiser Permanente implemented EpicCare, a comprehensive electronic medical record, clinicians were required to directly document orders and diagnoses on this computerized system, a task they found difficult and time consuming. We analyzed the sources of this problem to improve the process and increase its acceptance by clinicians. One problem was the use of the International Classification of Diseases (ICD-9) as our coding scheme, even though ICD-9 is not a complete nomenclature of diseases and using it as such creates difficulties. In addition, the synonym list we used had some inaccurate associations, contributing to clinician frustration. Furthermore, the initial software program contained no adequate mechanism for adding qualifying comments or preferred terminology. We sought to address all these issues. Strategies included adjusting the available coding choices and descriptions and modifying the medical record software. In addition, the software vendor developed a utility that allows clinicians to replace the ICD-9 description with their own preferred terminology while preserving the ICD-9 code. We present an evaluation of this utility.

Abstracting and Indexing↗

PubMed1996

Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetase.

The structural features of the G.U wobble pair in Escherichia coli alanine transfer RNA (tRNA(Ala)) that are associated with aminoacylation by alanyl-tRNA synthetase (AlaRS) were investigated in vivo for wild-type tRNA(Ala) and mutant tRNAs with G.U substitutions. tRNA(Ala) with G.U, C.A, or G.A gave similar amounts of charged tRNA(Ala) and supported viability of E. coli lacking chromosomal tRNA(Ala) genes. tRNA(Ala) with G.C was inactive. Recognition of G.U by AlaRS thus requires more than the functional groups on G.U in a regular helix and may involve detection of a helical distortion.

Alanine-tRNA Ligase↗