Conformational restriction of flexible ligands guided by the transferred noe experiment: potent macrocyclic inhibitors of farnesyltransferase.
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Alkyl and Aryl Transferases↗
Biomedical subjects
T M Williams
Publications and source records attributed to T M Williams.
High-performance liquid chromatography/mass spectrometry characterization of Ki4B-Ras in PSN-1 cells treated with the prenyltransferase inhibitor L-778,123.
Cellular transformation by Ras oncoproteins requires the posttranslation modification of farnesylation in a reaction catalyzed by farnesyl protein transferase (FPTase). Thus, inhibitors of FPTase have been developed as potential anticancer agents. However, recent studies with selective inhibitors of FPTase have shown that Ki4B-Ras retains its ability to transform cells by undergoing alternative prenylation by the related geranylgeranyl protein transferase I (GGPTase-I) in human tumor cells. We have developed a high-performance liquid chromatography/mass spectrometry assay for the detection and quantitation of the different processing states of Ki4B-Ras isolated from PSN-1 cells (a human pancreatic cell line with an activating Gly12 to Arg mutation) treated with the prenyltransferase inhibitor, L-778,123. Recently tested in the clinic, L-778,123 is a potent inhibitor of FPTase (in vitro IC50 = 2 nM) with some activity against GGPTase-I (in vitro IC50 = 98 nM). We find primarily farnesylated-Ki4B-Ras in vehicle-treated PSN-1 cells, a mixture of farnesylated- and geranylgeranylated-Ki4B-Ras in cells treated with nanomolar concentrations of L-778,123, and a mixture of unprocessed, farnesylated, and geranylgeranylated-Ki4B-Ras in cells treated with micromolar concentrations of compound. Of importance, this technique does not require metabolic labeling and may be used as a pharmacodynamic assay for Ki4B-Ras processing in mouse models.
Alkyl and Aryl Transferases↗
Oxo-piperazine derivatives of N-arylpiperazinones as inhibitors of farnesyltransferase.
The evaluation of SAR associated with the insertion of carbonyl groups at various positions of N-arylpiperazinone farnesyltransferase inhibitors is described herein. 1-Aryl-2,3-diketopiperazine derivatives exhibited the best balance of potency and pharmacokinetic profile relative to the parent 1-aryl-2-piperazinones.
Alkyl and Aryl Transferases↗
Translational control of the proteome: relevance to cancer.
Translational control is an important but relatively unappreciated mechanism that regulates levels of protein products. In addition to a global translational control that regulates the cell's response to external stimuli such as growth factors, cytokines, stress and viral infections, selective translational control has recently been demonstrated to affect many genes related to growth and apoptotic processes. Modifications in the 5'untranslated region of these specific mRNAs may lead to an up-regulation of the protein product by as much as 100-fold. Translational infidelity has been reported in some human cancers for oncogenes such as c-myc and mdm2. Furthermore, modulation of selective translational control has also been demonstrated in cells over-expressing the translation initiation factor elF4E. Elevated levels of elF4E were found in a broad spectrum of solid tumors (breast, head and neck, colon and bladder carcinomas as well as in non-Hodgkin's lymphomas). Other translation initiation factors and translation components such as elongation factors and ribosomal proteins have also been reported to be overexpressed in some human tumors. This review discusses the relevance of these observations to a cell's proteome and for tumorigenesis and how the genomics and proteomics can be used to advance our understanding of the role of translational control in cancer.
Eukaryotic Initiation Factor-4E↗
Analysis of gene expression using high-density and IFN-gamma-specific low-density cDNA arrays.
The combination of high and low density cDNA filter array technology potentially permits both the identification of subsets of induced genes and convenient and rapid multisample expression profiling of such subsets under a variety of conditions. The JAK/STAT1 pathway for IFN-gamma signaling in human cells has been well characterized, but the extent and importance of additional pathways remain to be established. Here, using high-density filter arrays of the RZPD UniGene set, we identified 18 novel IFN-gamma-inducible genes. Expression profiling was carried out using low-density arrays representing both novel and known IFN-gamma-inducible genes. Initial experiments failed to detect evidence for any novel non-JAK-dependent pathways in cells expressing a kinase-dead JAK2. The data, however, validated the potential of the combined methods in establishing rapid and convenient expression profiling of several hundred genes in response to any ligand of choice.
Gene Expression Profiling↗
The development of diving in marine endotherms: preparing the skeletal muscles of dolphins, penguins, and seals for activity during submergence.
Myoglobin is an important oxygen store for supporting aerobic diving in endotherms, yet little is known about its role during postnatal development. Therefore, we compared the postnatal development of myoglobin in marine endotherms that develop at sea (cetaceans) to those that develop on land (penguins and pinnipeds). We measured myoglobin concentrations in the major locomotor muscles of mature and immature bottlenose dolphins (Tursiops truncatus) and king penguins (Aptenodytes patagonicus) and compared the data to previously reported values for northern elephant seals (Mirounga angustirostris). Neonatal dolphins, penguins, and seals lack the myoglobin concentrations required for prolonged dive durations, having 10%, 9%, and 31% of adult values, respectively. Myoglobin contents increased significantly during subsequent development. The increases in myoglobin content with age may correspond to increases in activity levels, thermal demands, and time spent in apnea during swimming and diving. Across these phylogenetically diverse taxa (cetaceans, penguins, and pinnipeds), the final stage of postnatal development of myoglobin occurs during the initiation of independent foraging, regardless of whether development takes place at sea or on land.
Age Factors↗
Biopsy features are associated with primary symptoms in interstitial cystitis: results from the interstitial cystitis database study.
The purpose of this study was to investigate associations between bladder biopsy features and urinary symptoms for patients enrolled in the Interstitial Cystitis Database (ICDB) Study. Bladder biopsies were obtained during baseline screening in the ICDB Study and were evaluated for histopathologic features. Multivariable models for nighttime voiding frequency, urinary urgency, and pain were developed, incorporating biopsy features from the most diseased area of the bladder as predictors, adjusting for significant clinical factors, and clinical center variation. Among 204 interstitial cystitis (IC) patients providing biopsy specimens, cystoscopic pathology findings were not statistically associated (P >0.1) with primary IC symptoms, although the presence of Hunner's ulcer (n = 12) was suggestive of increased urinary frequency. Within a multivariable predictive model for nighttime voiding frequency, adjusting for age and minimum volume per void, 4 pathology features were noted: (1) mast cell count in lamina propria on tryptase stain; (2) complete loss of urothelium; (3) granulation tissue in lamina propria; and (4) vascular density in lamina propria on factor VIII (F8) stain were statistically significant (P <0.01). Similarly, in a multivariable model for urinary urgency, minimum volume, and percentage of submucosal granulation tissue remained statistically significant (P <0.01). Finally, the percentage of mucosa denuded of urothelium and the percentage of submucosal hemorrhage remained highly associated (P <0.01) with pain in a multivariable predictive model. The fact that the presence or severity of glomerulations was not selected for any of these predictive models suggests that cystoscopic findings of glomerulations are not predictive of IC symptoms. Furthermore, these results suggest an important role for certain pathologic features in the predictive modeling of IC symptoms.
Analysis of Variance↗
Three-dimensional movements and swimming activity of a northern elephant seal.
We attached a video system and data recorder to a northern elephant seal to track its three-dimensional movements and observe propulsive strokes of the hind flippers. During 6 h of recording, the seal made 20 dives and spent 90% of the time submerged. Average dive duration, maximum depth and swimming speed were 14.9 min+/-6.1 S.D., 289 m+/-117 S.D. and 1.1 m s(-1)+/-0.12 S.D., respectively. The distance swum during a dive averaged 925 m+/-339 S.D., and the average descent and ascent angles were 41 degrees +/-18 S.D. and 50 degrees +/-21 S.D., respectively. Dive paths were remarkably straight suggesting that the seal was navigating while submerged. We identified three modes of swimming based on the interval between propulsive strokes: continuous stroking; stroke-and-glide swimming; and prolonged gliding. The seal used continuous stroking from the surface to a mean depth of 20 m followed by stroke-and-glide swimming. Prolonged gliding started at a mean depth of 60 m and continued to the bottom of dives. For dives to depths of 300 m or more, 75% of the descent time was spent in prolonged gliding and 10% in stroke-and-glide swimming, amounting to 5.9-9.6 min of passive descent per dive. Average swimming speed varied little with swimming mode and was not a good indicator of propulsive effort. It appears that the seal can use prolonged gliding to reduce the cost of transport and increase dive duration. Energetically efficient locomotion may help explain the long and deep dives that routinely exceed the theoretical aerobic dive limit in this species.
Animals↗
A killer appetite: metabolic consequences of carnivory in marine mammals.
Among terrestrial mammals, the morphology of the gastrointestinal tract reflects the metabolic demands of the animal and individual requirements for processing, distributing, and absorbing nutrients. To determine if gastrointestinal tract morphology is similarly correlated with metabolic requirements in marine mammals, we examined the relationship between basal metabolic rate (BMR) and small intestinal length in pinnipeds and cetaceans. Oxygen consumption was measured for resting bottlenose dolphins and Weddell seals, and the results combined with data for four additional species of carnivorous marine mammal. Data for small intestinal length were obtained from previously published reports. Similar analyses were conducted for five species of carnivorous terrestrial mammal, for which BMR and intestinal length were known. The results indicate that the BMRs of Weddell seals and dolphins resting on the water surface are 1.6 and 2.3 times the predicted levels for similarly sized domestic terrestrial mammals, respectively. Small intestinal lengths for carnivorous marine mammals depend on body size and are comparatively longer than those of terrestrial carnivores. The relationship between basal metabolic rate (kcal day(-1)) and small intestinal length (m) for both marine and terrestrial carnivores was, BMR=142.5 intestinal length(1.20) (r(2)=0.83). We suggest that elevated metabolic rates among marine mammal carnivores are associated with comparatively large alimentary tracts that are presumably required for supporting the energetic demands of an aquatic lifestyle and for feeding on vertebrate and invertebrate prey.
Animals↗
Human leukocyte antigen gene polymorphism and the histocompatibility laboratory.
The human leukocyte antigens (HLA) encoded by genes within the major histocompatibility complex display an impressive degree of polymorphism. This variability is apparently maintained in human populations through the need to successfully display a wide range of processed foreign peptides to the T cell antigen receptor. The large number of alleles at the Class I and Class II loci pose a significant problem for molecular diagnosis. Knowledge of allele groups and specific alleles present in individuals has important implications in organ and stem cell transplantation and in disease association studies. Histocompatibility laboratories have transformed themselves during the past decade as they have adapted the techniques of molecular diagnostics to the challenge of identifying HLA alleles.
Alleles↗
Novel HLA-B alleles identified in potential marrow donors: B*3917, B*1405 and B*3528.
Sequence-specific oligonucleotide probe hybridization and sequence-specific primer polymerase chain reaction (PCR) typing of volunteer bone marrow donors suggested the presence of variants of known HLA-B alleles in five individuals. PCR products encompassing HLA-B locus exons 1 through 3 were prepared and subcloned. Three African-American individuals had a novel HLA-B*39 allele (B*3917), and another African-American was found to have a novel HLA-B*14 allele (B*1405). In a third individual of Hispanic origin, a novel HLA-B*35 allele (B*3528) was identified. These findings further illustrate the substantial genetic variation present at the HLA-B locus within human populations.
Alleles↗
Three new DP alleles identified in a study of 800 unrelated bone marrow donor-recipient pairs.
HLA-DP genotyping of 800 unrelated donor-recipient pairs in phase 5 of a retrospective analysis of unrelated bone marrow transplantation, sponsored by the National Marrow Donor Program (NMDP), has identified two new DPB1 alleles (DPB1*8701 and DBP1*8801) and one new DPA1 (DPA1*0108) allele. Sequencing confirmed that all three of these new alleles represent novel combinations of previously described sequence motifs, reinforcing the notion that "gene conversion-like" events play an important role in generating HLA allelic diversity. The identification of these new alleles brings the total number of DPA1 alleles to 20 and the total number of DPB1 alleles to 94.
Alleles↗
Characterization of tert-butyl alcohol binding to alpha2u-globulin in F-344 rats.
tert-Butyl alcohol (TBA) is widely used in the manufacturing of certain perfumes, cosmetics, drugs, paint removers, methyl tert-butyl ether (MTBE), and industrial solvents. In both rodents and humans, TBA is a major metabolite of MTBE, an oxygenated fuel additive. Chronic TBA exposure causes protein droplet nephropathy, alpha2u-globulin (alpha2u) accumulation, renal cell proliferation, and with chronic exposure, renal tumors in male, but not female, rats. These effects suggest an alpha2u-mediated mechanism for renal tumors. The objective of the present study was to determine whether TBA or its metabolites bind to alpha2u. Mature male and female F-344 rats were administered a single gavage dose of 500 mg/kg TBA, 500 mg/kg (14)C-TBA, or corn oil. TBA equivalents/gram or ml of tissue in the male rat kidney, liver, and blood were higher than the levels measured in female rat tissue 12 h after (14)C-TBA administration. Gel filtration and anion-exchange chromatography demonstrated that (14)C-TBA-derived radioactivity co-eluted with alpha2u from male kidney cytosol. Protein dialysis studies demonstrated that the interaction between (14)C-TBA-derived radioactivity and alpha2u was reversible. Incubations of the low-molecular-weight protein fraction (LMWPF) isolated from (14)C-TBA-treated male rat kidneys with d-limonene oxide (a chemical with a high affinity to alpha2u) demonstrated that (14)C-TBA-derived radioactivity was displaced. Gas chromatography-mass spectrometry analysis confirmed that TBA was present in this LMWPF fraction. These results demonstrate that TBA interacts with alpha2u, which explains the accumulation of alpha2u in the male rat kidney following TBA exposure.
Alpha-Globulins↗
The historical and geomedical immunogenetics of pemphigus among the descendants of Sephardic Jews in New Mexico.
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HLA-DQ Antigens↗
Sink or swim: strategies for cost-efficient diving by marine mammals.
Locomotor activity by diving marine mammals is accomplished while breath-holding and often exceeds predicted aerobic capacities. Video sequences of freely diving seals and whales wearing submersible cameras reveal a behavioral strategy that improves energetic efficiency in these animals. Prolonged gliding (greater than 78% descent duration) occurred during dives exceeding 80 meters in depth. Gliding was attributed to buoyancy changes with lung compression at depth. By modifying locomotor patterns to take advantage of these physical changes, Weddell seals realized a 9.2 to 59.6% reduction in diving energetic costs. This energy-conserving strategy allows marine mammals to increase aerobic dive duration and achieve remarkable depths despite limited oxygen availability when submerged.
Animals↗
Detection of leukemia-associated MLL-GAS7 translocation early during chemotherapy with DNA topoisomerase II inhibitors.
Leukemias with MLL gene translocations are a complication of primary cancer treatment with DNA topoisomerase II inhibitors. How early translocations appear during primary cancer treatment has not been investigated. We tracked the leukemic clone with an MLL gene translocation during neuroblastoma therapy in a child who developed acute myeloid leukemia. The karyotype of the leukemic clone showed del(11)(q23). We used panhandle PCR-based methods to isolate the breakpoint junction involving MLL and an unknown partner gene. Marrow DNA from neuroblastoma diagnosis and DNA and RNA from serial preleukemic marrows were examined for the translocation. The karyotypic del(11)(q23) was a cryptic t(11;17). GAS7, a growth arrest-specific gene at chromosome band 17p13, was the partner gene of MLL. Two different MLL-GAS7 fusion transcripts were expressed. The translocation was already detectable by 1.5 months after the start of neuroblastoma treatment. The translocation was not detectable in the marrow at neuroblastoma diagnosis or in peripheral blood lymphocyte DNAs of six normal subjects. GAS7 is a new partner gene of MLL in treatment-related acute myeloid leukemia. MLL gene translocations can be present early during anticancer treatment at low cumulative doses of DNA topoisomerase II inhibitors. Although MLL has many partner genes and most have not been characterized, panhandle PCR strategies afford new means for detecting MLL gene translocations early during therapy when the partner gene is unknown.
Adolescent↗
Evolutionary history of B1 retroposons in the genus Mus.
Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from the GenBank nucleotide database using various B1 subfamily consensus query sequences to determine their integration times into the mouse genome. A comparison of orthologous loci in various species of the genus Mus demonstrated that four subfamilies of B1 elements have been amplifying within the last 1-3 million years. Therefore, B1 sequences are generated by coexisting source genes. Additionally, three B1 subfamilies have been concurrently propagated during subspecies divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patterns of intra- and interspecies variations of orthologous loci demonstrate the usefulness of B1 integrations as a phylogenetic tool. A single inconsistency in the phylogenetic trends was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved B1 element that integrated at least 4-6 million years ago suggests the possibility of occasional function for B1 integrations.
Animals↗
Body size and skeletal muscle myoglobin of cetaceans: adaptations for maximizing dive duration.
Cetaceans exhibit an exceptionally wide range of body mass that influence both the capacities for oxygen storage and utilization; the balance of these factors is important for defining dive limits. Furthermore, myoglobin content is a key oxygen store in the muscle as it is many times higher in marine mammals than terrestrial mammals. Yet little consideration has been given to the effects of myoglobin content or body mass on cetacean dive capacity. To determine the importance of myoglobin content and body mass on cetacean diving performance, we measured myoglobin content of the longissimus dorsi for ten odontocete (toothed whales) and one mysticete (baleen whales) species ranging in body mass from 70 to 80000 kg. The results showed that myoglobin content in cetaceans ranged from 1.81 to 5.78 g (100 g wet muscle)(-1). Myoglobin content and body mass were both positively and significantly correlated to maximum dive duration in odontocetes; this differed from the relationship for mysticetes. Overall, the combined effects of body mass and myoglobin content accounts for 50% of the variation in cetacean diving performance. While independent analysis of the odontocetes showed that body mass and myoglobin content accounts for 83% of the variation in odontocete dive capacity.
Adaptation, Physiological↗