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D Kahn

Publications and source records attributed to D Kahn.

At least 55 records · Page 3Linked to original sources
PubMed2000

InterPro--an integrated documentation resource for protein families, domains and functional sites.

MOTIVATION: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. RESULTS: Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc. Merged and individual entries (i.e. those that have no counterpart in the companion resources) are assigned unique accession numbers. Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).

Computational Biology↗
PubMed2000

Simple predictors of uvulopalatopharyngoplasty outcome in the treatment of obstructive sleep apnea.

STUDY OBJECTIVE: Our objective was to determine whether baseline polysomnography, cephalometry, and anthropometry data could predict uvulopalatopharyngoplasty (UPPP) success or failure. DESIGN: We retrospectively reviewed polysomnography, cephalometry, and anthropometry data from patients who underwent UPPP for obstructive sleep apnea (OSA). SETTING: A university medical center. PATIENTS: OSA was diagnosed by polysomnography in 46 patients who underwent UPPP surgery for their sleep disorder. INTERVENTIONS: UPPP surgery with/or without tonsillectomy. MEASUREMENTS AND RESULTS: The mean patient age was 43 years, and the mean body mass index was 32.5 kg/m(2). The mean presurgical apnea-hypopnea index (AHI) was 45, and the mean baseline nadir oxygen saturation was 81%. Successful surgery was defined as a reduction in AHI to < 10 or to < 20 with a 50% reduction from the patient's baseline AHI. Of the 46 patients, 16 were successfully treated and 30 did not respond to surgical treatment. A mandibular-hyoid distance (MP-H) > 20 mm was found to be significantly (p = 0.05) predictive of failure of UPPP. When stepwise regression analysis was performed utilizing postsurgical AHI as the dependent variable and presurgical AHI, age, body mass index, baseline nadir O(2) saturation, and five cephalometric measurements as independent variables, MP-H distance significantly (r = 0.524; p = 0.01) correlated positively with postsurgical AHI. The distance between the superior point of a line-constructed plane of the sphenoidale (parallel to Frankfort horizontal) and a point at the intersection of the palatal plane perpendicular to the hyoid correlated negatively with postsurgical AHI (r = 0.586; p = 0.05). By creating a logistic model of this data, an MP-H distance < 21 mm, an angle created by point A to the nasion to point B < 3 degrees, and the presence of a baseline AHI < 38 enhanced the predictability of UPPP success. CONCLUSIONS: The presence of a baseline AHI < 38 and an MP-H < or = 20 mm, and the absence of retrognathia are predictors of improvement after UPPP. Based on these findings, we would advocate the continued evaluation of cephalometric measurements and careful consideration of surgical treatment options for OSA.

Adult↗
PubMed2000

Ten years of liver transplantation at Groote Schuur Hospital.

INTRODUCTION: Liver transplantation has evolved from an experimental procedure to being the treatment of choice for many patients with end-stage liver disease, and is performed on a routine basis in most major centres throughout the world. However, certain situations peculiar to developing countries have a major impact on liver transplant programmes in these countries. We present the results of the liver transplant programme in Cape Town. PATIENTS AND METHODS: All patients undergoing orthotopic liver transplantation at Groote Schuur Hospital and Red Cross War Memorial Children's Hospital were included in this report. Standard surgical techniques were used for procuring the donor liver, the recipient hepatectomy and the subsequent implantation of the liver. All patients received standardised peri-operative management; in particular, the immunosuppressive protocol consisted of cyclosporin, steroids and azathioprine. Since October 1988, 83 patients have undergone 89 orthotopic liver transplants. There were 44 adults and 39 children, the age range being from 6 months to 56 years. The commonest indications for hepatic transplantation in adults included cryptogenic cirrhosis, auto-immune hepatitis and primary sclerosing cholangitis. In children biliary atresia was the commonest cause of liver failure. RESULTS: Of the 81 patients transplanted, 50 are alive and well with follow-up ranging from 2 months to 9.5 years. The cumulative graft survival rate was 72% at 1 year and 61% at 5 years. Six patients have undergone re-transplantation and 4 patients have had combined liver/kidney transplants. De novo hepatitis due to hepatitis B virus (HBV) has occurred in 8 patients following transplantation. Subsequent investigation has shown that 5 of the donors of these livers were hepatitis B core antibody (HBcAb)-positive, while information on the remaining 3 was not available. Tuberculosis (TB) has been a significant problem in 4 patients, with 2 deaths precipitated by anti-TB drug-induced hepatitis. Post-transplant lymphoproliferative disorder was also responsible for significant postoperative morbidity. CONCLUSION: Orthotopic liver transplantation has been established at Groote Schuur Hospital as the treatment of choice for selected patients with chronic end-stage liver disease. However, hepatitis B and TB appear to present a problem. The particularly high prevalence of HBV carrier status in our donor population may necessitate the use of living donors in the future.

Adolescent↗
PubMed2000

History of liver transplantation at the University of Cape Town and Groote Schuur Hospital.

The liver transplant programme at Groote Schuur Hospital was born out of a rich history of experimental liver transplantation and an active liver clinic. Professor John Terblanche has played a key role in the initiation and success of the programme. In the first 10 years since October 1988, 41 adults have undergone liver transplantation. The cumulative graft survival rates at 1 and 5 years were 74% and 62% respectively.

History, 20th Century↗
PubMed2000

Liver transplantation in children--the Red Cross War Memorial Children's Hospital experience.

Liver transplantation for infants and children has been available in South Africa for more than a decade. Current concerns have shifted from an initial target of early post-transplant survival to quality of life in the long term. Since 1985, 175 infants and children have been assessed, with 104 accepted for transplantation. Fifty have had orthotopic liver transplants (OLTx), 48 (3 retransplants) in Cape Town and 2 abroad. Biliary atresia was the most frequent diagnosis (52%) followed by acute liver failure (ALF) (16%). Waiting list mortality has remained high (15%), particularly for the ALF group (50%). Thirty-four patients survive 1 month--14 years post-transplant. Early post OLTx mortality was low (7%) but late morbidity and mortality (23%) were mainly due to viral infection: de novo hepatitis B (5 patients, 2 deaths), EBV-related post-transplantation lymphoproliferative disease (PTLPD) (6 patients, 4 deaths) and CMV disease (9 patients, 4 deaths). Tuberculosis prophylaxis, required in 6 cases, resulted in major morbidity in 1. Hypertension requiring medication along with some compromise of renal function has been present in all but 2 patients. However, all those of school-going age (20) attend school normally and remain in good health and only 3 of the survivors have abnormal liver function tests. Successful liver transplantation is possible in a developing country with limited resources. Scarcity of virus-free donors (HBV and HIV) leading to waiting list mortality and infrequent retransplantation along with long-term consequences of immunosuppression (infection, lymphoma and renal toxicity) remain problems.

Child↗
PubMed1999

Conformational changes induced by phosphorylation of the FixJ receiver domain.

BACKGROUND: A variety of bacterial adaptative cellular responses to environmental stimuli are mediated by two-component signal transduction pathways. In these phosphorelay cascades, histidine kinases transphosphorylate a conserved aspartate in the receiver domain, a conserved module in the response regulator superfamily. The main effect of this phosphorylation is to alter the conformation of the response regulator in order to modulate its biological function. The response regulator FixJ displays a typical modular arrangement, with a phosphorylatable N-terminal receiver domain and a C-terminal DNA-binding domain. In the symbiotic bacterium Sinorhizobium meliloti, phosphorylation of this response regulator activates transcription of nitrogen-fixation genes. RESULTS: The crystal structures of the phosphorylated and of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) were solved at 2.3 A and 2.4 A resolution, respectively. They reveal the environment of the phosphoaspartate in the active site and the specific conformational changes leading to activation of the response regulator. Phosphorylation of the conserved aspartate induces major structural changes in the beta 4-alpha 4 loop, and in the signaling surface alpha 4-beta 5 that mediates dimerization of the phosphorylated full-length response regulator. A site-directed mutant at this protein-protein interface decreases the affinity of the phosphorylated response regulator for the fixK promoter tenfold. CONCLUSIONS: The cascade of phosphorylation-induced conformational changes in FixJN illustrates the role of conserved residues in stabilizing the phosphoryl group in the active site, triggering the structural transition and achieving the post-phosphorylation signaling events. We propose that these phosphorylation-induced conformational changes underly the activation of response regulators in general.

Amino Acid Sequence↗
PubMed1999

Structural transitions in the FixJ receiver domain.

BACKGROUND: Two-component signal transduction pathways are sophisticated phosphorelay cascades widespread in prokaryotes and also found in fungi, molds and plants. FixL/FixJ is a prototypical system responsible for the regulation of nitrogen fixation in the symbiotic bacterium Sinorhizobium meliloti. In microaerobic conditions the membrane-bound kinase FixL uses ATP to transphosphorylate a histidine residue, and the response regulator FixJ transfers the phosphoryl group from the phosphohistidine to one of its own aspartate residues in a Mg(2+)-dependent mechanism. RESULTS: Seven X-ray structures of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) have been solved from two crystal forms soaked in different conditions. Three conformations of the protein were found. In the first case, the protein fold impairs metal binding in the active site and the structure reveals a receiver domain that is self-inhibited for catalysis. In the second conformation, the canonical geometry of the active site is attained, and subsequent metal binding to the protein induces minimal conformational changes. The third conformation illustrates a non-catalytic form of the protein where unwinding of the N terminus of helix alpha 1 has occurred. Interconversion of the canonical and self-inhibited conformations requires a large conformational change of the beta 3-alpha 3 loop region. CONCLUSIONS: These unphosphorylated structures of FixJN stress the importance of flexible peptide segments that delineate the active site. Their movements may act as molecular switches that define the functional status of the protein. Such observations are in line with structural and biochemical results obtained on other response regulator proteins and may illustrate general features that account for the specificity of protein-protein interactions.

Amino Acid Sequence↗
PubMed1999

Whole genome protein domain analysis using a new method for domain clustering.

We present the outcome of a systematic analysis of protein domain shuffling in 17 completed microbial genomes. This analysis has been performed using MKDOM Version 2, a completely new version of the domain clustering program MKDOM based on PSI-BLAST recursive homology searches. It allows to delineate the most frequent protein domain building blocks, which domains are found specifically in Bacteria, Archaea or yeast, and which domains are shared between two or all three domains of life. The latter are good candidates as the basic protein building blocks underlying all forms of cellular life. Statistics of multi-domain proteins indicate that some organisms such as Bacillus subtilis or Mycobacterium tuberculosis contain an abnormally high number of large multi-domain proteins. We also provide examples of highly shuffled or circularly permutated domains. A WWW graphical interface has been made available to interactively browse domain arrangements of proteins in all 17 genomes, at http:@www.toulouse.inra.fr/prodomCG.html.

Archaea↗
PubMed1999

Recent improvements of the ProDom database of protein domain families.

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).

Amino Acid Sequence↗
PubMed1999

One-stage total hepatectomy in the rat using microvascular anastomoses.

A method is described for one-stage total hepatectomy in the rat using microvascular techniques. The operation consists of creation of a side-to-side mesocaval shunt performed just distal to the renal veins, total removal of the liver with ligation of the portal vein, hepatic arteries, and the bile duct. The vena cava is reconstructed with a segment of vena cava taken from a donor animal. The procedure takes 32 +/- 5 min to complete. Blood glucose concentration was maintained by infusions of balanced salt solution containing from 0.625% to 2.5% dextrose. Mean survival time was 10.5 hr (range, 5.5 to 21.5 hr).

Anastomosis, Surgical↗
PubMed1999

Renal transplantation from a living related donor with a retrocaval ureter--a note of caution.

In our study we describe a renal transplant from a living related donor who was found to have a retrocaval ureter. The retrocaval ureter is a rare congenital anomaly resulting from a defect in the embryological development of the ureter and the inferior vena cava (IVC). The compression of the ureter between the IVC and the vertebrae can result in progressive hydronephrosis. The non-dilated segment of the ureter was used for the uretero-neocystostomy. The patient presented with ureteric obstruction in the immediate post-transplant period, and at surgical exploration the ureteroneocystostomy was revised using the dilated portion of the ureter. We recommend that when transplanting a kidney with a retrocaval ureter, caution should be exercised in using the non-dilated portion of the ureter, since either the blood supply may be compromised or the peristalsis may be interrupted.

Adult↗
PubMed1999

HLA-A and -B alleles in cornea donors as risk factors for graft rejection.

We determined the human leucocyte antigen (HLA)-A, -B and -DR allele frequencies in recipients and donors of 115 cornea transplants, for recipients who developed graft rejection and those who did not. No difference in HLA allele frequencies of the recipients was found. The frequencies of the HLA-A26, -B35 and -B44 alleles in cornea donors were increased in recipients who developed graft failure. The detrimental effect on corneal graft survival of these alleles was significant (p < 0.001). No such effect was observed in renal transplantation. Corneal graft survival was similar when one or two A26, B35 or B44 alleles were present on the donor cornea. The negative effect was similar in magnitude to the previously reported negative effect of an HLA-B locus match between donor and recipient. When both a B-locus match and an A26, B35 or B44 allele were present, the negative effect on graft survival was twice as strong, indicating that different immune mechanisms are responsible for these phenomena.

Alleles↗
PubMed1999

Tuberculosis isolated to the renal allograft.

Immunosuppressed patients after renal transplantation are at increased risk of developing infective complications, including tuberculosis. We describe four renal transplant patients who presented with tuberculosis isolated to the renal allograft. The three patients with adequate follow-up presented with a febrile illness 12-26 months after the transplant. The mycobacterial infection was found in the graft nephrectomy specimen in three patients. One patient with renal allograft dysfunction had a percutaneous biopsy that showed tuberculosis. The latter patient recovered renal allograft function after anti-tuberculous therapy. None of the patients had evidence of tuberculosis elsewhere. We conclude that tuberculosis isolated to the renal allograft, especially in an endemic area, may be the cause of renal dysfunction, and appropriate therapy could lead to salvage of the graft.

Adult↗
PubMed1999

Phosphorylation-induced dimerization of the FixJ receiver domain.

The 'two-component' transcriptional activator FixJ controls nitrogen fixation in Sinorhizobium meliloti. Phosphorylation of FixJ induces its dimerization, as evidenced by gel permeation chromatography and equilibrium sedimentation analysis. Phosphorylation-induced dimerization is an intrinsic property of the isolated receiver domain FixJN. Accordingly, chemical phosphorylation of both FixJ and FixJN are second-order reactions with respect to protein concentration. However, the second-order phosphorylation constant is 44-fold higher for FixJN than for FixJ. Therefore, the C-terminal transcriptional activator domain FixJC inhibits the chemical phosphorylation of the receiver domain FixJN. Conversely, FixJN has been shown previously to inhibit FixJC activity approximately 40-fold, reflecting the interaction between FixJN and FixJC. Therefore, we propose that modulation of FixJ activity involves both its dimerization and the disruption of the interface between FixJN and FixJC, resulting in the opening of the protein structure. Alanine scanning mutagenesis of FixJN indicated that the FixJ approximately P dimerization interface involves Val-91 and Lys-95 in helix alpha4. Dimerization was required for high-affinity binding to fixK promoter DNA.

Bacterial Proteins↗
PubMed1999

Measurement of circulating red cell volume using biotin-labeled red cells: validation against 51Cr-labeled red cells.

BACKGROUND: Anemia is a serious problem in the fetus and preterm infant. To investigate the physiology and pathophysiology of anemia and to assess responses to blood transfusions or erythropoietin therapy, measurement of circulating red cell volume would be useful. Because the standard 51Cr method exposes the subject to radiation, a method of measuring circulating red cell volume without radiation exposure, sufficiently sensitive for use in fetuses and infants, was developed. STUDY DESIGN AND METHODS: In 10 healthy adults whose body mass ranged from 56.8 to 115.9 kg, aliquots of autologous red cells were labeled with biotin or with 51Cr, mixed, and transfused intravenously. Circulating red cell volume was measured in posttransfusion blood by quantitating the in vivo dilution of biotinylated red cells. Biotinylated red cells were detected by two methods: 1) 125I-streptavidin and 2) fluorescein-labeled avidin with flow cytometry. RESULTS: Circulating red cell volume measured by 125I-streptavidin detection agreed well with that measured by 51Cr (slope = 1.07, y-intercept = -97, correlation = 0.987). Similarly, circulating red cell volume measured by flow cytometry agreed well with that measured by 51Cr (slope = 1.05, y-intercept = -20, correlation = 0.987). CONCLUSIONS: Circulating red cell volume measured by the use of biotin with either 125I-streptavidin or flow cytometry agrees with that measured by 51Cr. Each system provides a method of performing these studies without exposing the subject to radiation.

Adult↗