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William Lee

Publications and source records attributed to William Lee.

18 recordsLinked to original sources
PubMed2006

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.

We sequenced approximately 400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV-primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs).

Animals↗
PubMed2006

Cathepsin A is the major hydrolase catalyzing the intracellular hydrolysis of the antiretroviral nucleotide phosphonoamidate prodrugs GS-7340 and GS-9131.

GS-7340 and GS-9131 {9-[(R)-2-[[(S)-[[(S)-1-(isopropoxycarbonyl)ethyl]amino]phenoxyphosphinyl]methoxy]-propyl]adenine and 9-(R)-4'-(R)-[[[(S)-1-[(ethoxycarbonyl)ethyl]amino]phenoxyphosphinyl]methoxy]-2'-fluoro-1'-furanyladenine, respectively} are novel alkylalaninyl phenyl ester prodrugs of tenofovir {9-R-[(2-phosphonomethoxy)propyl]adenine} (TFV) and a cyclic nucleotide analog, GS-9148 (phosphonomethoxy-2'-fluoro-2', 3'-dideoxydidehydroadenosine), respectively. Both prodrugs exhibit potent antiretroviral activity against both wild-type and drug-resistant human immunodeficiency virus type 1 strains and excellent in vivo pharmacokinetic properties. In this study, the main enzymatic activity responsible for the initial step in the intracellular activation of GS-7340 and GS-9131 was isolated from human peripheral blood mononuclear cells and identified as lysosomal carboxypeptidase A (cathepsin A [CatA]; EC 3.4.16.5). Biochemical properties of the purified hydrolase (native complex and catalytic subunit molecular masses of 100 and 29 kDa, respectively; isoelectric point [pI] of 5.5) matched those of CatA. Recombinant CatA and the isolated prodrug hydrolase displayed identical susceptibilities to inhibitors and identical substrate preferences towards a panel of tenofovir phosphonoamidate prodrugs. Incubation of both enzymes with 14C-labeled GS-7340 or [3H]difluorophosphonate resulted in the covalent labeling of identical 29-kDa catalytic subunits. Finally, following a 4-h incubation with GS-7340 and GS-9131, the intracellular concentrations of prodrug metabolites detected in CatA-negative fibroblasts were approximately 7.5- and 3-fold lower, respectively, than those detected in normal control fibroblasts. Collectively, these data demonstrate the key role of CatA in the intracellular activation of nucleotide phosphonoamidate prodrugs and open new possibilities for further improvement of this important class of antiviral prodrugs.

Adenine↗
PubMed2006

Effectiveness of a chronic kidney disease clinic in achieving K/DOQI guideline targets at initiation of dialysis--a single-centre experience.

BACKGROUND: Limited data exist about the effects of chronic kidney disease (CKD) clinics on quality-of-care indicators in patients before initiation of dialysis. METHODS: A single-centre retrospective chart review study was conducted on all patients who initiated dialysis at the Veterans Affairs Denver Healthcare System between 2000 and 2005. Patients initiating dialysis were evaluated at the start of dialysis and 12 months after dialysis initiation, as a function of care provided by nephrologists in training (renal-hypertension clinic) vs a trained renal nurse practitioner (CKD clinic). RESULTS: Data were available for 77 patients followed in the CKD clinic and 36 in the renal-hypertension clinic. There were no major demographic differences between the cohorts at the time of clinic referral. The length of follow-up before dialysis did not differ significantly between the cohorts (10.7+/-9.8 months for the patients in the CKD clinic cohort and 13.6+/-16.0 months for the patients in the renal-hypertension clinic cohort, P=0.3299). At the initiation of dialysis, patients followed in the CKD clinic had higher haemoglobin (11.6+/-1.5 vs 10.8+/-1.7 g/dl, P=0.0239) and serum albumin (3.4+/-0.5 vs 3.0+/-0.7 g/dl, P=0.0020) concentrations. More of the CKD clinic patients had a functioning permanent vascular access (P<0.0001). The number of all-cause hospitalizations in the 12 months after initiation of dialysis was significantly lower in the CKD clinic group (P=0.0024), but no significant differences were noted in all-cause mortality. CONCLUSIONS: Our data indicate that a single experienced renal nurse practitioner, working to a protocol, is more likely to adhere to guidelines than are multiple nephrology trainees rotating through a nephrology clinic.

Female↗
PubMed2006

Quantitative analysis of Variolin analog (PM01218) in mouse and rat plasma by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry.

PM01218 is a novel marine-derived alkaloid and has shown potent growth inhibitory activity against several human cancer cell lines. A rapid and sensitive high performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) method was developed and validated to quantify PM01218 in mouse and rat plasma. The lower limit of quantitation (LLOQ) was 0.05 ng/mL. The calibration curve was linear from 0.05 to 100 ng/mL (R(2)>0.999). The assay was specifically based on the multiple reaction monitoring (MRM) transitions at m/z 278.4-->184.2, no endogenous material interfaced with the analysis of PM01218 and its internal standard from blank mouse and rat plasma. The mean intra- and inter-day assay accuracy remained below 15 and 8%, respectively, for all calibration standards and QC samples. The intra- and inter-day assay precision was less than 12.8 and 8.5% for all QC levels, respectively. The utility of the assay was demonstrated by pharmacokinetics studies of i.v. (bolus) PM01218 on SD rats.

Animals↗
PubMed2006

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of PM02734, a novel antineoplastic agent, in dog plasma.

A rapid and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay was developed and validated to quantify a novel antineoplastic agent, PM02734, in dog plasma. The method was validated to demonstrate the specificity, limit of quantification (LOQ), accuracy, and precision of measurements. The calibration range for PM02734 was established using PM02734 standards from 0.05 to 100 ng/mL in blank plasma. The dominating ions were doubly charged molecular ions [M+2H]2+ at m/z 740.0 instead of singly charged ones at m/z 1478.4. The selected reaction monitoring (SRM), based on the m/z 740.0 --> 212.2 transition, was specific for PM02734, and that based on the m/z 743.8 --> 212.2 transition was specific for deuterated PM02734 (the internal standard, IS); no endogenous materials interfered with the analysis of PM02734 and IS from blank plasma. The assay was linear over the concentration range 0.05-100 ng/mL. In terms of sensitivity of assay 0.05 ng/mL is a very low LLOQ, especially considering PM02734 is a peptide. The correlation coefficients for the calibration curves ranged from 0.9990 to 0.9999. The mean intraday and interday accuracies for all calibration standards (n = 9) ranged from 93 to 111% (< or =11% bias) in dog plasma, and the mean interday precision for all calibration standards was less than 6.4%. The mean intra- and interday assay accuracy for all quality control replicates in dog plasma (n = 9), determined at each QC level throughout the validated runs, ranged from 85-111% (< or =15% bias) and from 99-109% (< or =9% bias), respectively. The mean intra- and interday assay precision was less than 12.1 and 13.3% for all QC levels, respectively. The assay has been used to support preclinical pharmacokinetic (PK) and toxicokinetic studies. The results showed that preclinical samples could be monitored for PM02734 up to 168 h after dosing, which allowed us to identify multiple elimination phases and accurately estimate PK information.

Animals↗
PubMed2005

Genome-wide requirements for resistance to functionally distinct DNA-damaging agents.

The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of approximately 4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.

Antifungal Agents↗
PubMed2005

Zinc inhibition of gamma-aminobutyric acid transporter 4 (GAT4) reveals a link between excitatory and inhibitory neurotransmission.

gamma-Aminobutyric acid (GABA) transporters (GATs) play an important role in inhibitory neurotransmission by clearing synaptically released GABA and by maintaining low resting levels of GABA in synaptic and extrasynaptic regions. In certain brain regions, vesicular zinc is colocalized and coreleased with glutamate and modulates the behavior of a number of channels, receptors, and transporters. We examined the effect of zinc on expressed GATs (GAT1, GAT2, GAT3, and GAT4) in Xenopus laevis oocytes by using tracer flux and electrophysiological methods. We show that zinc is a potent inhibitor of GAT4 (K(i) of 3 muM). Immunolocalization of GAT4 in the hippocampus revealed dense localization in the CA1 and CA3 regions of the hippocampus, regions which are known to be heavily populated by zinc-containing glutamatergic neurons. The results suggest a physiological role of synaptically released zinc in the hippocampus, because zinc released from hyperactive glutamatergic neurons may simultaneously bring about elevated GABAergic inhibition. Therefore, this mode of zinc function signifies a link between excitatory and inhibitory neurotransmission and may play a neuroprotective role against glutamate-induced excitotoxicity.

Animals↗
PubMed2005

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of PM00104, a novel antineoplastic agent, in mouse, rat, dog, and human plasma.

A rapid and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay was developed and validated to quantify a novel antineoplastic agent, PM00104, in mouse, rat, dog, and human plasma. The method was validated to demonstrate the specificity, limit of quantification (LOQ), accuracy, and precision of measurements. The calibration range for PM00104 was established using PM00104 standards from 0.01-5.0 ng/mL in blank plasma. The selected reaction monitoring (SRM), based on the m/z 692.2 --> 218.2 transition, was specific for PM00104, and that based on the m/z 697.2 --> 218.2 transition was specific for PM00104 ((13)C(2),(2)H(3)) (the internal standard, IS); no endogenous materials interfered with the analysis of PM00104 and IS from blank plasma. The assay was linear over the concentration range 0.01-5.0 ng/mL. The correlation coefficients for the calibration curves ranged from 0.9981-0.9999. The mean intra-day and inter-day accuracies for all calibration standards (n = 8) ranged from 97-105% (< or =5% bias) in human plasma, and the mean inter-day precision for all calibration standards was less than 8.5%. The mean intra- and inter-day assay accuracy for all quality control (QC) replicates in human plasma (n = 9), determined at each QC level throughout the validated runs, ranged from 96-112% (< or =12% bias) and from 102-105% (< or =5% bias), respectively. The mean intra- and inter-day assay precision was less than 15.0 and 11.8% for all QC levels, respectively. For the QC samples prepared in animal species plasma, the %CV values of the assays ranged from 1.8-8.8% in mouse plasma, from 3.7-13.8% in rat plasma, and from 3.0-7.2% in dog plasma. The assay accuracies ranged from 92-102% (< or =8% bias) for all QC levels prepared in mouse plasma; ranged from 93-106% (< or =7% bias) in rat plasma; and ranged from 95-114% (< or =14% bias) in dog plasma. The assay has been used to support preclinical pharmacokinetic and toxicokinetic studies and is currently used to measure PM00104 plasma concentrations to support clinical trials.

Animals↗
PubMed2005

Assessing the generality of global leaf trait relationships.

Global-scale quantification of relationships between plant traits gives insight into the evolution of the world's vegetation, and is crucial for parameterizing vegetation-climate models. A database was compiled, comprising data for hundreds to thousands of species for the core 'leaf economics' traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation-climate models could incorporate this knowledge. The core leaf traits were intercorrelated, both globally and within plant functional types, forming a 'leaf economics spectrum'. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.

Biological Evolution↗
PubMed2004

The worldwide leaf economics spectrum.

Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.

Biomass↗
PubMed2004

Codon usage between genomes is constrained by genome-wide mutational processes.

Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.

Animals↗
PubMed2004

Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy.

The N-terminal domain of HIV-1 glycoprotein 41,000 (gp41) participates in viral fusion processes. Here, we use physical and computational methodologies to examine the secondary structure of a peptide based on the N terminus (FP; residues 1-23) in aqueous and detergent environments. (12)C-Fourier transform infrared (FTIR) spectroscopy indicated greater alpha-helix for FP in lipid-detergent sodium dodecyl sulfate (SDS) and aqueous phosphate-buffered saline (PBS) than in only PBS. (12)C-FTIR spectra also showed disordered FP conformations in these two environments, along with substantial beta-structure for FP alone in PBS. In experiments that map conformations to specific residues, isotope-enhanced FTIR spectroscopy was performed using FP peptides labeled with (13)C-carbonyl. (13)C-FTIR results on FP in SDS at low peptide loading indicated alpha-helix (residues 5 to 16) and disordered conformations (residues 1-4). Because earlier (13)C-FTIR analysis of FP in lipid bilayers demonstrated alpha-helix for residues 1-16 at low peptide loading, the FP structure in SDS micelles only approximates that found for FP with membranes. Molecular dynamics simulations of FP in an explicit SDS micelle indicate that the fraying of the first three to four residues may be due to the FP helix moving to one end of the micelle. In PBS alone, however, electron microscopy of FP showed large fibrils, while (13)C-FTIR spectra demonstrated antiparallel beta-sheet for FP (residues 1-12), analogous to that reported for amyloid peptides. Because FP and amyloid peptides each exhibit plaque formation, alpha-helix to beta-sheet interconversion, and membrane fusion activity, amyloid and N-terminal gp41 peptides may belong to the same superfamily of proteins.

Amino Acid Sequence↗
PubMed2003

Validation of a sensitive assay for thiocoraline in mouse plasma using liquid chromatography-tandem mass spectrometry.

A sensitive high-performance liquid chromatography-tandem mass spectrometry assay for thiocoraline, an anti-tumor depsipeptide, in mouse plasma is described. Echinomycin, a quinoxaline peptide, was used as an internal standard. Thiocoraline was recovered from the mouse plasma using protein precipitation with acetonitrile and followed by solid-phase extraction of the supernatant. The mobile phase consisted of methanol (0.1% formic acid)-water (0.1% formic acid) (90:10, v/v). The analytical column was a YMC C(18). The standard curve was linear from 0.1 to 50 ng/ml (R(2)>0.99). The lower limit of quantitation was 0.1 ng/ml. The assay was specific based on the multiple reaction monitoring transitions at m/z 1157-->215 and m/z 1101-->243 for thiocoraline and the internal standard, echinomycin, respectively. The mean intra- and inter-day assay accuracies remained below 5 and 12%, respectively, for all calibration standards and quality control (QC) samples. The intra- and inter-day assay precisions were less than 11.4 and 9.5% for all QC levels, respectively. The utility of the assay was demonstrated by a pharmacokinetic study of i.v. (bolus) thiocoraline on CD-1 mice. Thiocoraline was stable in mouse plasma in an ice-water bath for 6 h and for three freeze-thaw cycles. The reconstituted thiocoraline after extraction and drying sample process was stable in the autosampler for over 24 h. The assay was able to quantify thiocoraline in plasma up to 48 h following dose. Pharmacokinetic analysis showed that thiocoraline has distinct pharmacokinetic profiling when dosed in different formulation solutions. The assay is currently used to measure thiocoraline plasma concentrations in support of a project to develop a suitable formulation with a desirable pharmacokinetic profile.

Animals↗
PubMed2003

Protein binding to polymer brush, based on ion-exchange, hydrophobic, and affinity interactions.

The major limitations associated with conventional packed bed chromatography for protein separation and purification can be overcome by using adsorptive microporous membranes as chromatographic media. Microporous membranes have advantages as support matrices in comparison to conventional bead supports because they are not compressible and they eliminate diffusion limitations. As a result, higher throughput and shorter processing times are possible using these membrane systems. In this paper, we review the current state of development in the area of attaching functionalized polymer brushes onto a microporous membrane to form a novel chromatographic medium for protein separation and purification. The functionalized polymer brushes were appended onto the pore surface of a microporous hollow-fiber membrane uniformly across the membrane thickness by radiation-induced graft polymerization and subsequent chemical modifications. We review various applications of this adsorptive membrane chromatography by focusing on polymer brushes bearing ion-exchange, hydrophobic and affinity groups. Proteins were captured in multilayers by the ion-exchange group-containing polymer brushes due to the formation of a three-dimensional space for protein binding via the electrostatic repulsion of the polymer brushes. In contrast, proteins were captured in a monolayer at most by the polymer brushes containing hydrophobic or affinity ligands. By permeating a protein solution through the pores rimmed by the polymer brushes, an ideal capturing rate of the proteins with a negligible diffusional mass-transfer resistance was achieved by the functionalized polymer brushes, based on ion-exchange, hydrophobic, and affinity interactions.

Chromatography, Affinity↗
PubMed2003

Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of Aplidin, a novel marine-derived antineoplastic agent, in human plasma.

A rapid and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay was developed and validated to quantify a novel marine-derived depsipeptide, Aplidin, in human plasma. The method was validated to demonstrate the specificity, recovery, limit of quantitation (LOQ), accuracy, and precision of measurements. The calibration range for Aplidin was established using Aplidin standards from 0.05-50 ng/mL in blank human plasma. The multiple reaction monitoring, based on the transition m/z 1110.7 --> 295.3, was specific for Aplidin, and that based on the transition m/z 1112.6 --> 297.3 was specific for didemnin B (the internal standard); no endogenous materials interfered with the analysis of Aplidin and didemnin B from blank human plasma. The assay was linear over the concentration range 0.05-50.0 ng/mL. The correlation coefficients for the calibration curves ranged from 0.9979 to 0.9999. The mean intra- and interday accuracies for all calibration standards (n = 12) ranged from 97 to 106% (</=6% bias), and the mean interday precision for all calibration standards was less than 8.3%. The mean intra- and interday assay accuracy for all quality control replicates (n = 12), determined at each QC level throughout the validated runs, remained below 12 and 7%, respectively. The mean intra- and interday assay precision was less than 13.1 and 10.7% for all QC levels, respectively. The assay is currently used to measure Aplidin plasma concentrations to support clinical trials.

Antineoplastic Agents↗
PubMed2002

Genome-tools: a flexible package for genome sequence analysis.

Genome-tools is a Perl module, a set of programs, and a user interface that facilitates access to genome sequence information. The package is flexible, extensible, and designed to be accessible and useful to both nonprogrammers and programmers. Any relatively well-annotated genome available with standard GenBank genome files may be used with genome-tools. A simple Web-based front end permits searching any available genome with an intuitive interface. Flexible design choices also make it simple to handle revised versions of genome annotation files as they change. In addition, programmers can develop cross-genomic tools and analyses with minimal additional overhead by combining genome-tools modules with newly written modules. Genome-tools runs on any computer platform for which Perl is available, including Unix, Microsoft Windows, and Mac OS. By simplifying the access to large amounts of genomic data, genome-tools may be especially useful for molecular biologists looking at newly sequenced genomes, for which few informatics tools are available. The genome-tools Web interface is accessible at http://genome-tools.sourceforge.net, and the source code is available at http://sourceforge.net/projects/genome-tools.

Base Sequence↗
PubMedDate not supplied

Highly multilayered urease decomposes highly concentrated urea.

Urease was immobilized at a density of 1.2 g of urease per gram of a matrix via ion-exchange binding of urease to an anion-exchange polymer chain grafted onto a pore surface of a porous hollow-fiber membrane and subsequent cross-linking of urease with transglutaminase. Urea was hydrolyzed during the permeation of a urea solution, the concentration of which ranged from 2 to 8 M, through the pores of the resultant membrane with a thickness of approximately 1 mm. Quantitative hydrolysis of 4 M urea was achieved at a permeation rate lower than 1 mL/h, i.e., a residence time longer than 5.1 min, at ambient temperature. This performance is ascribed to convective transport of urea through the pores rimmed by the urease-immobilized polymer chains at a high density. Urease was denatured in the presence of urea at concentrations higher than 6 M while hydrolyzing urea.

Adsorption↗