Biomedical subjects

David Lee

Publications and source records attributed to David Lee.

At least 19 recordsLinked to original sources

PubMed2026

Genomic and Phenotypic Characterization of Two Novel Enterobacter Phages With EDTA-Enhanced Antibiofilm Activity.

Multidrug-resistant members of the Enterobacter cloacae complex (ECC) are increasingly linked to difficult-to-treat infections and biofilm-mediated antimicrobial tolerance. Here, two lytic phages, vB_EhoIP_HHH and vB_EluM_RZH, displaying podovirus-like and myovirus-like morphology, respectively, were isolated from the River Chelt. HHH has a 39,582 bp genome (51.2% GC, 63 ORFs), while RZH has a 174,197 bp genome (39.4% GC, 314 ORFs), with neither genome carrying antimicrobial resistance, virulence or lysogeny-associated genes. VIRIDIC and VICTOR analyses placed HHH within Kayfunavirus and RZH within Karamvirus, supporting their classification as distinct species. Both phages demonstrated rapid adsorption, short latent periods and stability across physiological pH and temperature ranges. A phage cocktail targeting MDR ECC strain was evaluated with EDTA against established biofilms. Crystal violet assays showed the greatest biomass reduction at MOI 10 with 0.5-0.75 mM EDTA. Bliss independence analysis revealed localized synergy within this window but significant overall antagonism at higher EDTA concentrations. CFU enumeration confirmed greater activity against 24 h than 48 h biofilms. The optimized combination also reduced recoverable bacteria in a fibroblast infection model while maintaining low LDH release. These findings identify two novel lytic Enterobacter phages and support a narrow EDTA concentration window for enhanced phage-mediated antibiofilm activity.

Biofilms↗

PubMed2006

Non-concordance between genetic profiles of olive oil and fruit: a cautionary note to the use of DNA markers for provenance testing.

To investigate the contribution of paternal alleles to the DNA content of olive oil, genetic analyses of olive DNA samples from fruits, leaves, and oil derived from the same tree (cv. Leccino) were carried out. DNA extracted from maternal tissues--leaves and flesh--from different fruits showed identical genetic profiles using a set of DNA markers. Additional simple sequence repeat (SSR) alleles, not found in the maternal samples, were amplified in the embryos (stone), and they were also detected in DNA extracted from the paste obtained by crushing whole fruits and from the oil pressed from this material. These results demonstrate that the DNA profile obtained from olive oil is likely to represent a composite profile of the maternal alleles juxtaposed with alleles contributed by various pollen donors. Therefore, care needs to be taken in the interpretation of DNA profiles obtained from DNA extracted from oil for resolving provenance and authenticity issues.

Alleles↗

PubMed2006

A phase-I trial using a universal GM-CSF-producing and CD40L-expressing bystander cell line (GM.CD40L) in the formulation of autologous tumor cell-based vaccines for cancer patients with stage IV disease.

BACKGROUND: Significant antitumor T-cell responses are generated in vitro when human lymphocytes are stimulated with autologous tumor cells in the presence of bystander cells transfected with CD40L and GM-CSF. Our goal was to test this bystander-based vaccine strategy in vivo in cancer patients with stage IV disease. METHODS: Patients received three intradermal vaccine injections (irradiated autologous tumor cells plus GM.CD40L bystander cells) at 28-day intervals. Patients with no disease progression received three additional vaccines at 4, 12, and 24 months. Patients were monitored for toxicity, tumor response, and tumor-specific immune responses. RESULTS: Twenty-one patients received at least three vaccine injections, with no toxicity attributable to the vaccine. Immunohistochemistry of vaccine injection site biopsies with CD1a and CD86 antibodies confirmed recruitment and activation of dendritic cells. There was no tumor regression after vaccination, but many patients had stable disease, including six of ten melanoma patients. Four patients developed tumor-specific T-cell responses on ELISPOT testing. One patient, who had stable disease for 24 months, demonstrated an increase in MART-1-specific T-cells by tetramer analysis after re-immunization; biopsy of the tumor that progressed 2 years after the onset of vaccination revealed a massive peritumoral and intratumoral T-cell infiltrate. CONCLUSIONS: Vaccination of cancer patients with autologous tumor cells and GM.CD40L bystander cells (engineered to express GM-CSF and CD40L) is safe, can recruit and activate dendritic cells, and can elicit tumor-specific T-cell responses. Phase-II trials are underway to evaluate the impact of bystander-based vaccines on melanoma and mantle cell lymphoma.

Adjuvants, Immunologic↗

PubMed2006

Effect of neonatal administration of a retroviral vector expressing alpha-L-iduronidase upon lysosomal storage in brain and other organs in mucopolysaccharidosis I mice.

Mucopolysaccharidosis I (MPS I) due to deficient alpha-L-iduronidase (IDUA) activity results in accumulation of glycosaminoglycans in many cells. Gene therapy could program cells to secrete IDUA modified with mannose 6-phosphate (M6P), and enzyme could be taken up by other cells via the M6P receptor. We previously reported that newborn MPS I mice that were injected intravenously with 10(9) (high-dose) or 10(8) (low-dose) transducing units/kg of a retroviral vector (RV) expressing canine IDUA achieved stable levels of IDUA activity in serum and had reduced disease in heart, eye, ear, and bone in a dose-dependent fashion. However, the dose required for improvement in manifestations of disease in other organs was not reported. High-dose and low-dose RV mice with an average serum IDUA activity of 1037+/-90 U/ml (471-fold normal) and 43+/-12 U/ml (20-fold normal), respectively, had complete correction of biochemical and pathological evidence of disease in the liver, spleen, kidney, and small intestines. Although mice that received high-dose RV had complete correction of lysosomal storage in thymus, ovary, lung, and testis, correction in these organs was only partial for those that received low-dose RV. Storage in brain was almost completely corrected with high-dose RV, but was not improved with low-dose RV. The correction of disease in brain may be due to diffusion of enzyme from blood. We conclude that high-dose RV prevents biochemical and pathological manifestations of disease in all organs in MPS I mice including brain.

Animals↗

PubMed2006

Electron paramagnetic resonance oxygen images correlate spatially and quantitatively with Oxylite oxygen measurements.

Tumor oxygenation predicts cancer therapy response and malignant phenotype. This has spawned a number of oxymetries. Comparison of different oxymetries is crucial for the validation and understanding of these techniques. Electron paramagnetic resonance (EPR) imaging is a novel technique for providing quantitative high-resolution images of tumor and tissue oxygenation. This work compares sequences of tumor pO2 values from EPR oxygen images with sequences of oxygen measurements made along a track with an Oxylite oxygen probe. Four-dimensional (three spatial and one spectral) EPR oxygen images used spectroscopic imaging techniques to measure the width of a spectral line in each image voxel from a trityl spin probe (OX063, Amersham Health R&D) in the tissues and tumor of mice after spin probe injection. A simple calibration allows direct, quantitative translation of each line width to an oxygen concentration. These four-dimensional EPR images, obtained in 45 minutes from FSa fibrosarcomas grown in the legs of C3H mice, have a spatial resolution of approximately 1 mm and oxygen resolution of approximately 3 Torr. The position of the Oxylite track was measured within a 2-mm accuracy using a custom stereotactic positioning device. A total of nine images that involve 17 tracks were obtained. Of these, most showed good correlation between the Oxylite measured pO2 and a track located in the tumor within the uncertainties of the Oxylite localizability. The correlation was good both in terms of spatial distribution pattern and pO2 magnitude. The strong correlation of the two modalities corroborates EPR imaging as a useful tool for the study of tumor oxygenation.

Animals↗

PubMed2006

Targeted inhibition of farnesyltransferase in locally advanced breast cancer: a phase I and II trial of tipifarnib plus dose-dense doxorubicin and cyclophosphamide.

PURPOSE: To determine the recommended phase II dose (RPTD) of the farnesyltransferase (FTase) inhibitor tipifarnib when combined with doxorubicin and cyclophosphamide (AC) in patients with advanced breast cancer, the pathologic complete response (pCR) rate after preoperative treatment with four cycles of the combination in locally advanced breast cancer (LABC), and the effect of tipifarnib on primary tumor FTase enzyme activity in vivo. PATIENTS AND METHODS: Thirty-two patients with metastatic breast cancer (n = 11) or LABC (n = 21) received AC (doxorubicin 60 mg/m2 and cyclophosphamide 600 mg/m2) administered intravenously on day 1 plus tipifarnib (100, 200, or 300 mg bid for 6 to 14 days) without (n = 2) or with (n = 30) granulocyte colony-stimulating factor (G-CSF) for up to four cycles. Patients with LABC underwent surgery after up to four cycles of the combination. RESULTS: When combined with AC every 2 weeks plus G-CSF, the RPTD of tipifarnib was 200 mg bid administered on days 2 to 7. Seven (33%) of 21 patients (95% CI, 15% to 55%) with LABC treated with up to four cycles of the combination at the RPTD had a pCR in the breast at surgery. The five patients had serial biopsies that demonstrated at least 50% FTase enzyme inhibition in the primary tumor (median, 100%; range, 55% to 100%) after tipifarnib. CONCLUSION: Tipifarnib may be safely combined with dose-dense AC using a dose and schedule that significantly inhibits FTase enzyme activity in human breast cancer in vivo and may enhance the pCR rate after four cycles of preoperative dose-dense AC.

Adult↗

PubMed2006

Endovascular versus open mesenteric revascularization: immediate benefits do not equate with short-term functional outcomes.

BACKGROUND: Percutaneous therapy for symptomatic visceral occlusive disease is rapidly gaining popularity in many centers. This study evaluates the anatomic and functional outcomes of open and endovascular therapy for chronic mesenteric ischemia at an academic medical center. STUDY DESIGN: We performed a retrospective review of patients who underwent endovascular or open mesenteric arterial revascularization for chronic mesenteric ischemia between January 1989 and September 2003. Indications for revascularization included postprandial abdominal pain (92%) or weight loss (54%). All had atherosclerotic visceral occlusive disease with a median of 2 vessels with more than 50% stenosis or occlusion on angiography. Sixty patients (44 women, mean age 66 years) underwent 67 interventions (43 vessels bypassed, 23 vessel endarterectomies, 22 vessel angioplasty and stents). The median numbers of vessels revascularized were two in the open group and one in the endovascular group. RESULTS: Thirty-day mortality and cumulative survival at 3 years were similar (open, 15% and 62% +/- 9%; endovascular, 21% and 63%+/-14%, respectively; p=NS). Cumulative patencies at 6 months were 83%+/-7% and 68%+/-14% in the open and endovascular groups, respectively (p=NS). Major morbidity, median postoperative length of stay, and cumulative freedom from recurrent symptoms at 6 months were significantly greater in the open group (open, 46%, 23 days, and 71%+/-7%, respectively; endovascular, 19%, 1 day, and 34%+/-10%, respectively; p < 0.01). CONCLUSIONS: Endovascular revascularization is attractive because it carries equivalent patency to open revascularization. Symptomatic benefit of endovascular revascularization is not achieved, probably as a result of incomplete revascularization. Despite incomplete revascularization, endovascular therapy has equivalent survival and lower morbidity compared with open revascularization. Complete endovascular revascularization needs further evaluation to determine if it is superior to open revascularization. In the interim, endovascular therapy should be reserved for the patient unable to undergo open revascularization.

Adult↗

PubMed2006

Evaluating the optimal activated clotting time during carotid artery stenting.

Carotid artery stenting is an alternative to carotid endarterectomy for patients at high risk for surgery for carotid artery stenosis. Although unfractionated heparin is routinely used, there are no published data evaluating the optimal activated clotting time during carotid stenting. In a retrospective analysis of 605 patients who underwent carotid stenting using unfractionated heparin at the Cleveland Clinic Foundation, the optimal peak procedural activated clotting time associated with the lowest combined incidence of death, stroke, or myocardial infarction was 250 to 299 seconds.

Aged↗

PubMed2006

Exploiting protein structure data to explore the evolution of protein function and biological complexity.

New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms. We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms. When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.

Algorithms↗

PubMed2006

Calbindin-D28k decreases L-type calcium channel activity and modulates intracellular calcium homeostasis in response to K+ depolarization in a rat beta cell line RINr1046-38.

Calbindin-D(28k), acts as a modulator of depolarization induced calcium transients in the pancreatic beta cell. However, specific mechanisms have not been defined. Here we show for the first time that the calcium binding protein calbindin-D(28k) acts by affecting calcium influx through voltage-dependent calcium channels in RIN pancreatic beta cells. Whole-cell patch-clamp recordings revealed that Ca(2+) current amplitudes of calbindin-D(28k) expressing RINr1046-38 beta cells were smaller than the Ca(2+) current amplitudes in control cells in response to depolarizing pulses. The peak current was observed at +20mV and the average amplitude was approximately 50pA in the calbindin expressing cells compared to approximately 250pA in control cells. In calbindin-D(28k) expressing cells, the channels had enhanced sensitivity to Ca(2+) dependent inactivation and currents decayed much more rapidly than in control cells. The Ca(2+) channels affected by calbindin were found to have biophysical properties consistent with dihydropyridine-sensitive L-type calcium channels. In response to depolarizing concentrations of K(+), calbindin expression caused a five-fold decrease in the rate of rise of [Ca(2+)](i) and decay was slower in the calbindin expressing cells. Application of verapamil resulted in a drop in the [Ca(2+)](i) signal to pre-stimulation levels indicating that the Ca(2+) channel responsible for the depolarization evoked Ca(2+) entry, modulated by calbindin, is the L-type. Co-immunoprecipitation and GST pull-down assays indicate that calbindin-D(28k) can interact with the alpha(1) subunit of Ca(v)1.2. We thus conclude that calbindin-D(28k) can regulate calcium influx via L-type calcium channels. Our findings suggest a role for calbindin-D(28k) in the beta cell in modulating Ca(2+) influx via L-type voltage-dependent calcium channels.

Animals↗

PubMed2006

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 well-characterized domain families with the remaining domain-like regions belonging to a much larger number of small uncharacterized families that are largely species specific. Our comprehensive domain annotation of 203 genomes enables us to provide more accurate estimates of the number of multi-domain proteins found in the three kingdoms of life than previous calculations. We find that 67% of eukaryotic sequences are multi-domain compared with 56% of sequences in prokaryotes. By measuring the domain coverage of genome sequences, we show that the structural genomics initiatives should aim to provide structures for less than a thousand structurally uncharacterized Pfam families to achieve reasonable structural annotation of the genomes. However, in large families, additional structures should be determined as these would reveal more about the evolution of the family and enable a greater understanding of how function evolves.

Algorithms↗

PubMed2006

Evaluating genetic containment strategies for transgenic plants.

One of the primary concerns about genetically engineered crop plants is that they will hybridize with wild relatives, permitting the transgene to escape into the environment. The likelihood that a transgene will spread in the environment depends on its potential fitness impact. The fitness conferred by various transgenes to crop and/or wild-type hybrids has been evaluated in several species. Different strategies have been developed for reducing the probability and impact of gene flow, including physical separation from wild relatives and genetic engineering. Mathematical models and empirical experimental evidence suggest that genetic approaches have the potential to effectively prevent transgenes from incorporating into wild relatives and becoming established in wild populations that are not reproductively isolated from genetically engineered crops.

Chimera↗

PubMed2006

Gene3D: modelling protein structure, function and evolution.

The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

Databases, Protein↗

PubMed2006

Correlates and outcomes of retroperitoneal hemorrhage complicating percutaneous coronary intervention.

BACKGROUND: Retroperitoneal hemorrhage (RPH) is an infrequent but occasionally fatal complication of percutaneous coronary intervention (PCI). Therefore, it has been studied in relatively small numbers of patients. METHODS: Prospectively collected data on 28,378 consecutive patients treated between 1992 and 2003 were examined, supplemented by a date-based case control cohort study (76 RPH and 76 non-RPH patients) to examine elements not routinely recorded prospectively. Independent correlates of RPH were determined using logistical regression analysis. RESULTS: One hundred sixty-three patients (0.57%) developed RPH; of these 73.5% required blood transfusions and 10.4% expired during hospitalization (P < 0.001 for both compared with patients without RPH). RPH was independently associated with femoral artery sheath placement superior to the inferior epigastric artery (P < 0.001), female sex (P < 0.001), use of Angioseal Device (P < 0.001), glycoprotein IIb/IIIa inhibitor use (P = 0.001), and patient presentation with the acute myocardial infarction (P = 0.035), and was inversely related to patient weight (P = 0.014). Of the 17 patient deaths, 6 were directly related to RPH, 2 of which occurred in association with delays in resuscitation efforts consequent to attempts to obtain diagnostic confirmation with CT imaging. CONCLUSIONS: RPH remains an infrequent but serious complication of PCI. Appropriate management of the femoral access site and the patient once this complication is suspected may minimize adverse outcomes.

Aged↗

PubMed2006

Perception of blood transfusion risk.

Perceptions of risk ultimately drive the responses of individuals and society to risk issues, and transfusion risk is no exception. Surveys of lay people over the past decade indicate that public concern about transfusion safety has remained prevalent, dominated by the ongoing fear of contracting HIV infection. Such perceptions persist despite the acknowledgment that blood transfusion is safer now than in years past. Judgements by the lay public that may, at first glance, seem irrational can often be understood when the heuristics, biases, and models of human judgements of risk are considered. Risk perception research suggests that how lay people perceive risk has less to do with the unidimensional view of risk as a probabilistic expression and more to do with a complex multidimensional construct in which affect, reason, worldviews, trust, and other factors are intertwined. This review summarizes some of the principles of risk perception as applicable to transfusion medicine.

Blood Transfusion↗

PubMed2006

Comparison of basic elements of human performance scores between urologists with various extents of experience.

BACKGROUND AND PURPOSE: An objective evaluation of innate ability and its ability to predict potential success as a surgical trainee is an appealing concept for the selection process of residency applications. The objective of this study was to evaluate whether basic elements of performance (BEP) could discriminate among resident applicants and urologists with various extents of surgical experience. SUBJECTS AND METHODS: One hundred forty-five participants were divided into four study groups: group A, 57 urology residency applicants to the 2002 and 2003 interview process; group B, 8 post-internship urology residents; group C, 19 urologists tested with BEP within 10 years of graduation from their residency training program; and group D, 61 urologists who had graduated from their residency training program more than 10 years prior to testing. The BEP measures consisted of 13 basic performance resources (BPR) including visual-information processing speed, visual-spatial immediate-recall capacity, and neuromotor channel capacity. RESULTS: The four study groups differed significantly in their mean age: group A=27.6 years, group B=29.1 years, group C=37.1 years, and group D=48.9 years (P<0.0005). There was essentially no significant difference between the groups with regard to immediate-recall memory, reaction time simple, or reaction time complicated. The younger participants (groups A and B) were faster than the older surgeons (groups C and D) (P<0.02). However, the older surgeons (groups C and D) were significantly more accurate than the younger groups (A and B) (P<0.0005). The only sex differences noted were in hand-grip strength and shoulder-strength scores, which were all higher in the men. CONCLUSIONS: There generally appears to be a lack of direct correlation between innate abilities and surgical experience. Urology resident applicants with no surgical experience and urology residents with limited surgical experience are faster but less accurate in innate skills testing than experienced practicing urologists.

Adult↗

PubMed2006

Protracted hiccups due to severe erosive esophagitis: a case series.

BACKGROUND: Hiccups although a common annoyance of life, have been linked with significant morbidity and even death. There are numerous causes of prolonged hiccups, including diseases of the gastrointestinal tract. Hiccups are reported to represent an atypical manifestation of gastroesophageal reflux disease. CASES: We report 4 cases of prolonged hiccups in patients who failed to respond to initial treatment with abortive neurologic medications and who subsequently improved on proton-pump inhibitors. Endoscopic examination revealed severe reflux esophagitis. CONCLUSION: Hiccups are an atypical manifestation and may represent a more severe course of gastroesophageal reflux disease.

Adult↗

PubMed2006

Independent quantitative trait loci influence ventral and dorsal hippocampal volume in recombinant inbred strains of mice.

Anatomical and functional studies support segregation of the hippocampus into ventral and dorsal components along its septotemporal axis. However, it is unknown whether the development of these two components of the hippocampus is influenced by common or separate genetic factors. In this study, we used recombinant inbred strains of mice to determine whether the same or different quantitative trait loci (QTL) influence ventral and dorsal hippocampal volume. Using two sets of strains of recombinant inbred mice (BXD and AXB/BXA), we identified separate QTLs for ventral and dorsal hippocampal volume. In BXD mice, suggestive QTLs for ventral hippocampus were identified on chromosomes 2, 8 and 13, and a significant QTL for dorsal hippocampal volume was identified on chromosome 15. There was also a suggestive QTL for dorsal hippocampal volume on chromosome 13. In AXB/BXA mice, there were no significant or suggestive QTLs for ventral hippocampal volume, but a significant QTL for dorsal hippocampus was identified on chromosome 5. These findings suggest that the development of the ventral and dorsal components of the hippocampus is influenced by separate genetic loci.

Age Factors↗