Biomedical subjects

A Lim

Publications and source records attributed to A Lim.

At least 37 records · Page 2Linked to original sources

PubMed2001

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.

The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. Close to 75,000 cases of O157:H7 infection are now estimated to occur annually in the United States. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of E. coli O157:H7 (ref. 4). Here we have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for pathogenesis, to develop better methods of strain detection and to advance our understanding of the evolution of E. coli, through comparison with the genome of the non-pathogenic laboratory strain E. coli K-12 (ref. 5). We find that lateral gene transfer is far more extensive than previously anticipated. In fact, 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance.

Base Sequence↗

PubMed2001

egc, a highly prevalent operon of enterotoxin gene, forms a putative nursery of superantigens in Staphylococcus aureus.

The recently described staphylococcal enterotoxins (SE) G and I were originally identified in two separate strains of Staphylococcus aureus. We have previously shown that the corresponding genes seg and sei are present in S. aureus in tandem orientation, on a 3.2-kb DNA fragment (Jarraud, J. et al. 1999. J. Clin. Microbiol. 37:2446-2449). Sequence analysis of seg-sei intergenic DNA and flanking regions revealed three enterotoxin-like open reading frames related to seg and sei, designated sek, sel, and sem, and two pseudogenes, psi ent1 and psi ent2. RT-PCR analysis showed that all these genes, including seg and sei, belong to an operon, designated the enterotoxin gene cluster (egc). Recombinant SEG, SEI, SEK, SEL, and SEM showed superantigen activity, each with a specific V beta pattern. Distribution studies of genes encoding superantigens in clinical S. aureus isolates showed that most strains harbored such genes and in particular the enterotoxin gene cluster, whatever the disease they caused. Phylogenetic analysis of enterotoxin genes indicated that they all potentially derived from this cluster, identifying egc as a putative nursery of enterotoxin genes.

3' Untranslated Regions↗

PubMed2001

Use of an arterialized venous flap for resurfacing a circumferential soft tissue defect of a digit.

Circumferential defects of digit are uncommon but present a challenging problem to the clinician. The use of simple skin grafts tends to cause tendon adhesions and can limit digital range of motion. The use of local skin flaps, such as a cross-finger flap, is limited by the considerable skin loss in a defect that is circumferential in nature. Other options have included the use of reversed forearm flap or some free tissue transfer. We report a case in which the circumferential defect of an index finger, measuring 6 cm around the digit and 3 cm long, is resurfaced by the use of a free arterialized venous flap raised from the volar forearm skin.

Accidents, Occupational↗

PubMed2001

Intraoperative single-shot "3-in-1" femoral nerve block with ropivacaine 0.25%, ropivacaine 0.5% or bupivacaine 0.25% provides comparable 48-hr analgesia after unilateral total knee replacement.

PURPOSE: To compare analgesia after intraoperative single shot "3-in-1" femoral nerve block (FNB) in combination with general anesthesia using ropivacaine 0.25%, ropivacaine 0.5% with bupivacaine 0.25% for total knee replacement (TKR). METHODS: We performed a randomized, double-blind study in 48 patients for elective TKR under general anesthesia. Patients were randomized to one of four groups (C: sham block, R1: "3-in-1" FNB using 30 mL of ropivacaine 0.25%, R2: "3-in-1" FNB using 30 mL of ropivacaine 0.5%, B: "3-in-1" FNB using 30 mL of bupivacaine 0.25%). Verbal pain score (VPS) both at rest and movement were assessed for 48 hr after TKR (0=none; 1=mild; 2=moderate; 3=severe). Total morphine consumption and its associated side effects, duration of hospitalization after operation were also compared. RESULTS: There were no differences in patients' physical characteristics, intraoperative morphine usage, operation time, tourniquet time or length of hospitalization between the four groups. When compared with group C, the VPS was significantly lower in groups R1, R2 and B at one, four, eight, 24 and 48 hr after TKR (P <0.05). The morphine requirement of groups R1, R2 and B were also significantly lower when comparing with group C up to 48 hr postoperatively (P <0.05). There were no significant differences in VPS and postoperative morphine requirement at any time between groups R1, R2 and B. CONCLUSION: "3-in-1" FNB with ropivacaine provided analgesia that was clinically comparable to that of bupivacaine up to 48 hr after TKR. Increasing the concentration of ropivacaine from 0.25% to 0.5% failed to improve the postoperative analgesia of "3-in-1" FNB.

Adult↗

PubMed2001

Post-traumatic arachnoiditis: an unusual cause of Brown-Sequard syndrome.

Brown-Sequard syndrome (BSS) is a unilateral cord injury characterised by an ipsilateral motor deficit with contralateral pain and temperature hypoaesthesia. Although there are a variety of causes, the majority of cases are generally of neoplastic origin or are traumatic in origin. We describe a rare cause of Brown-Sequard syndrome as a result of post-traumatic arachnoiditis. Magnetic resonance imaging with the use of thin-slice high-resolution constructive interference in steady state (CISS) and T2-weighted spin-echo sequence were used to demonstrate the cause and appearance of the lesion in the spinal canal and was useful in the assessment and management of the patient. This case illustrates the usefulness of the CISS sequence in MRI for elucidating arachnoiditis.

Adult↗

PubMed2001

Dorso-ulnar osteocutaneous reverse flow flap of the thumb.

Three cases of distal thumb reconstruction with a reverse pedicled osteocutaneous flap taken from the dorso-ulnar aspect of the first metacarpal are presented. Even though the indications are rare, this flap is useful for the reconstruction of distal osteocutaneous defects of the thumb where more complex procedures are not feasible or considered as excessive.

Adult↗

PubMed2001

Ten years of experience with the submental flap.

This article describes the authors' experience with the submental flap over the past 10 years. A brief review of the key points and some refinements in the operative technique are discussed. The results concern 31 patients with a mean age of 57 years. All flaps were pedicled except two. One case of composite flap with bone was used. The mean size of the flap was 11.8 x 5.5 cm, and the mean postoperative stay was 11.1 days. Complications encountered were one case of temporary palsy of the marginal mandibular branch of the facial nerve, one hematoma at the recipient site, and two cases of partial flap loss. Color and texture match were good. The authors believe this flap to have great clinical potential and to be a worthwhile addition to the existing surgical armamentarium.

Adult↗

PubMed2001

Shotgun optical maps of the whole Escherichia coli O157:H7 genome.

We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.

Contig Mapping↗

PubMed2001

Perturbation and proinflammatory type activation of V delta 1(+) gamma delta T cells in African children with Plasmodium falciparum malaria.

gamma delta T cells have variously been implicated in the protection against, and the pathogenesis of, malaria, but few studies have examined the gamma delta T-cell response to malaria in African children, who suffer the large majority of malaria-associated morbidity and mortality. This is unfortunate, since available data suggest that simple extrapolation of conclusions drawn from studies of nonimmune adults ex vivo and in vitro is not always possible. Here we show that both the frequencies and the absolute numbers of gamma delta T cells are transiently increased following treatment of Plasmodium falciparum malaria in Ghanaian children and they can constitute 30 to 50% of all T cells shortly after initiation of antimalarial chemotherapy. The bulk of the gamma delta T cells involved in this perturbation expressed V delta 1 and had a highly activated phenotype. Analysis of the T-cell receptors (TCR) of the V delta 1(+) cell population at the peak of their increase showed that all expressed V gamma chains were used, and CDR3 length polymorphism indicated that the expanded V delta 1 population was highly polyclonal. A very high proportion of the V delta 1(+) T cells produced gamma interferon, while fewer V delta 1(+) cells than the average proportion of all CD3(+) cells produced tumor necrosis factor alpha. No interleukin 10 production was detected among TCR-gamma delta(+) cells in general or V delta 1(+) cells in particular. Taken together, our data point to an immunoregulatory role of the expanded V delta 1(+) T-cell population in this group of semi-immune P. falciparum malaria patients.

CD3 Complex↗

PubMed2001

Generation of a humanized, high affinity anti-tissue factor antibody for use as a novel antithrombotic therapeutic.

Blocking the cofactor function of human tissue factor may be beneficial in various coagulation-mediated diseases. The murine antibody D3 binds to the membrane proximal substrate interaction region of human tissue factor and blocks tissue factor function even in the presence of bound factor VIIa. The cloned murine D3 antibody was humanized and affinity matured by exchanging amino acids in the complementarity determining regions as well as in the antibody framework. The humanized antibody, D3H44, bound to tissue factor with a 100-fold increased affinity (KD 0.1 nM) as compared to the original murine and chimeric versions. Depending on the particular disease, different pharmacokinetic properties of the antibody may be required and, therefore, several antibody variants-- F(ab), F(ab')2, IgG2, IgG4 and IgG4b-were generated. In vitro, the humanized D3 antibodies displayed potent inhibition of plasma clotting and tissue factor: factor VIIa-mediated activation of factors IX and X (e.g. D3H44-F(ab')2, IC50(F.X) 47 pM). In addition, D3H44-F(ab')2 completely prevented fibrin deposition in a human ex vivo thrombosis model under venous blood flow conditions (IC50 37 nM). The humanized D3 antibodies may be utilized for treatment of cardiovascular diseases which involve tissue factor activity, e.g. acute coronary syndrome and venous thrombosis.

Amino Acid Sequence↗

PubMed2001

[Technological advances in immuno-oncology: from fundamental concepts to patient immunological monitoring].

Over the past decade, cancer immunology has known several advances due to both basic research and new technologies recently developed in this field. This review will illustrate the impact of some new immunological technologies and how the latter resulted in the exploration of new territories in cancer immunology and the emergence of new concepts that allowed to revisit the immunosurveillance concept and permitted to improve the patient monitoring.

Antigens, Neoplasm↗

PubMed2001

Clinical manifestation of tuberculous and pyogenic spine infection.

The authors compared clinical and baseline parameters between patients with tuberculous spondylitis (67 patients) and pyogenic vertebral osteomyelitis (34 patients). The average age was 50.8 (range, 1 to 82 years). Males were slightly more predominant in both pyogenic and tuberculous infections. Seventy per cent of patients with pyogenic infection had had symptoms for less than 3 months, while this was the case for only 44 per cent of the tuberculous patients. Lumbar spine was the most common site of involvement. Associated infections were more commonly found in tuberculous infection. Thirty per cent of tuberculous spondylitic patients were initially misdiagnosed, while 44 per cent of patients with pyogenic vertebral osteomyelitis had delayed diagnosis. Only 20 per cent and 30 per cent of tuberculous and pyogenic patients had fever, respectively. Neurological deficit occurred more frequently in pyogenic than in tuberculous infection (79% vs 59%), while bowel bladder involvement was more commonly found in tuberculous spondylitis. Kyphosis was significantly more common in tuberculosis than in pyogenic infection (50.8% vs 26.5%, respectively). Sinus tract formation, subcutaneous abscess formation and positive for SLRT (straight-leg-raising test) were found in only a small percentage of the patients. Duration of symptoms, site, associated infection, kyphosis and neurological deficit could be used for differentiation of spinal infection.

Adolescent↗

PubMed2001

Misdiagnosis in vertebral osteomyelitis: problems and factors.

One hundred and one cases diagnosed with vertebral osteomyelitis were evaluated for misdiagnosis and both factors and outcomes of misdiagnosis were assessed. There were 67 patients with tuberculous spondylitis and 34 patients with pyogenic vertebral osteomyelitis. Misdiagnosis occurred in 33.7 per cent of the cases. The average delayed diagnosis time was 2.6 months (range, 0.2 to 12). Age between 60 to 70 years was the most frequent group for misdiagnosis, while the most frequent area of misdiagnosis was the lumbar spine. Metastatic carcinoma, spinal stenosis, herniated nucleus palposus and back strain were common initial misdiagnoses. The factors, age group, absence of fever and positive straight leg raising test (SLRT) were associated with misdiagnosis in univariate analysis and multivariate analysis (odds ratio 3.40 (95%CI:1.07-11.94), 3.47 (95%CI:1.20-10.05), and 24.47 (95%CI:2.18-274.28), respectively) Misdiagnosis was statistically significantly associated with the result of treatment. This paper emphasizes that the elderly age group, absence of fever and positive SLRT are the independent factors which increase the risk of misdiagnosis of vertebral osteomyelitis.

Adolescent↗

PubMed2000

Frequent contribution of T cell clonotypes with public TCR features to the chronic response against a dominant EBV-derived epitope: application to direct detection of their molecular imprint on the human peripheral T cell repertoire.

In an attempt to provide a global picture of the TCR repertoire diversity of a chronic T cell response against a common Ag, we performed an extensive TCR analysis of cells reactive against a dominant HLA-A2-restricted EBV epitope (hereafter referred to as GLC/A2), obtained after sorting PBL or synovial fluid lymphocytes from EBV-seropositive individuals using MHC/peptide multimers. Although TCR beta-chain diversity of GLC/A2+ T cells was extensive and varied greatly from one donor to another, we identified in most cell lines several recurrent Vbeta subsets (Vbeta2, Vbeta4, and Vbeta16 positive) with highly conserved TCRbeta complementarity-determining region 3 (CDR3) length and junctional motifs, which represented from 11 to 98% (mean, 50%) of GLC/A2-reactive cells. While TCR beta-chains expressed by these subsets showed limited CDR1, CDR2, and CDR3 homology among themselves, their TCR alpha-chains comprised the same TCRAV region, thus suggesting hierarchical contribution of TCR alpha-chain vs TCR beta-chain CDR to recognition of this particular MHC/peptide complex. The common occurrence of T cell clonotypes with public TCR features within GLC/A2-specific T cells allowed their direct detection within unsorted PBL using ad hoc clonotypic primers. These results, which suggest an unexpectedly high contribution of public clonotypes to the TCR repertoire against a dominant epitope, have several implications for the follow-up and modulation of T cell-mediated immunity.

Amino Acid Motifs↗

PubMed2000

Retrovirus-mediated gene transfer in primary T lymphocytes: influence of the transduction/selection process and of ex vivo expansion on the T cell receptor beta chain hypervariable region repertoire.

We have initiated a phase I/II clinical trial, involving the use of herpes simplex thymidine kinase gene (HS-tk)-expressing donor primary T cells, in order to modulate the graft-versus-host disease (GvHD) occurring after allogeneic hematopoietic stem cell transplantation. The preparation of gene-modified T cells (TkTCs) required a 12-day ex vivo culture comprising an initial OKT3 and IL-2 stimulation, a retrovirus-mediated transduction, and a 7-day selection step in the presence of G418 and IL-2. The low transduction efficiency as well as the culture conditions may significantly alter the diversity of the T cell repertoire. We therefore examined the T cell repertoire of HS-tk-expressing T cell samples from 11 different donors by the Immunoscope method. This method analyzes the hypervariable region of the T cell receptor beta chain (TCRBV) by amplifying the complementarity-determining region 3 (CDR3) and determining size diversity. In all examined samples (four of which were infused into patients), all TCRBV subfamilies were represented with, however, a significant skewing within a minority of subfamilies. Kinetic studies demonstrated that this skewing appeared between day 7 and day 12, with dates of appearance variable from one subfamily to another. In addition, the repertoire analysis of two different culture products, harvested and produced at different times from the same donors, suggested that some repertoire abnormalities could be donor specific. Quantitative analysis revealed no major modifications in gene usage, even in skewed TCRBV subfamilies, with a few clonal expansions concerning a limited number of TCRBV subfamilies. Importantly, identical abnormalities were found in control cells grown in parallel under similar conditions but not transduced or selected, thus demonstrating that these abnormalities were not related to the transduction or the selection process, but rather to the ex vivo culture. The initial stimulus used for T cell activation is a major source of TCRBV perturbation, since replacing the OKT3 + IL-2 stimulus by CD3 + CD28 monoclonal antibody-coated beads prevented the occurrence of alterations. Overall, the HS-tk-expressing T cells used in our clinical trial exhibit limited TCR repertoire skewing that is not due to the transduction/selection procedure. However, future T cell gene transfer protocols for clinical trials should be designed to take into account or possibly prevent such T cell repertoire alterations.

CD28 Antigens↗

PubMed2000

Drug target validation: lethal infection blocked by inducible peptide.

Genome projects are generating large numbers of potential new targets for drug discovery. One challenge is target validation, proving the usefulness of a specific target in an animal model. In this paper, we demonstrate a new approach to validation and assay development. We selected in vitro specific peptide binders to a potential pathogen target. By inducing the expression of a selected peptide in pathogen cells causing a lethal infection in mice, the animals were rescued. Thus, by combining in vitro selection methods for peptide binders with inducible expression in animals, the target's validity was rigorously tested and demonstrated. This approach to validation can be generalized and has the potential to become a valuable tool in the drug discovery process.

Amino Acid Sequence↗

PubMed2000

Betabellins 15D and 16D, de Novo designed beta-sandwich proteins that have amyloidogenic properties.

The betabellin structure is a de novo designed beta-sandwich protein consisting of two 32-residue beta-sheets packed against one another by hydrophobic interactions. d-Amino acid residues are used to energetically favor formation of type-I' beta turns. Air oxidation of betabellin 15S (B15S) (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, where p denotes d-Pro, h denotes d-His, and k denotes d-Lys) yields betabellin 15D (B15D), a 64-residue disulfide-bridged protein. The amino acid sequence of B15D contains a conformationally constrained d-Pro residue at the i + 1 position of each type-I' beta turn. To test whether d-Pro residues are necessary for folding at these positions, the six d-Pro residues of B15D are replaced by d-Ala residues in betabellin 16D (B16D). Previously, transmission electron microscopy showed that B15D forms unbranched, 35-A wide fibrils that associate into bundles in 5.0 mM 3-(N-morpholino)propanesulfonate and 250 mM NaCl at pH 7; under these conditions, B16D forms ribbon-like assemblies. The B15D fibrils resemble the protofilaments that constitute amyloid fibrils. The present studies show that both B15D and B16D have characteristics of amyloidogenic proteins: the unbranched fibrils and ribbons stained with Congo red and displayed a green birefringence, exhibited a cross-beta structure, and bound 1-anilino-8-naphthalenesulfonate. Thus, these de novo designed beta-sandwich proteins should provide useful models for studying the mechanism of amyloid protofilament formation and assembly into amyloid fibrils and for designing potential inhibitors of amyloidogenesis.

Amino Acid Sequence↗

PubMed2000

Detection of small-molecule enzyme inhibitors with peptides isolated from phage-displayed combinatorial peptide libraries.

BACKGROUND: The rapidly expanding list of pharmacologically important targets has highlighted the need for ways to discover new inhibitors that are independent of functional assays. We have utilized peptides to detect inhibitors of protein function. We hypothesized that most peptide ligands identified by phage display would bind to regions of biological interaction in target proteins and that these peptides could be used as sensitive probes for detecting low molecular weight inhibitors that bind to these sites. RESULTS: We selected a broad range of enzymes as targets for phage display and isolated a series of peptides that bound specifically to each target. Peptide ligands for each target contained similar amino acid sequences and competition analysis indicated that they bound one or two sites per target. Of 17 peptides tested, 13 were found to be specific inhibitors of enzyme function. Finally, we used two peptides specific for Haemophilus influenzae tyrosyl-tRNA synthetase to show that a simple binding assay can be used to detect small-molecule inhibitors with potencies in the micromolar to nanomolar range. CONCLUSIONS: Peptidic surrogate ligands identified using phage display are preferentially targeted to a limited number of sites that inhibit enzyme function. These peptides can be utilized in a binding assay as a rapid and sensitive method to detect small-molecule inhibitors of target protein function. The binding assay can be used with a variety of detection systems and is readily adaptable to automation, making this platform ideal for high-throughput screening of compound libraries for drug discovery.

Alcohol Dehydrogenase↗