Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi

Hyphae, 2 to 8 days postinoculation (dpi), and haustoria, 5 dpi, were isolated from Uromyces appendiculatus infected bean leaves (Phaseolus vulgaris cv. Pinto 111) and a separate cDNA library prepared for each fungal preparation. Approximately 10,000 hyphae and 2,700 haustoria clones were sequenced from both the 5' and 3' ends. Assembly of all of the fungal sequences yielded 3,359 contigs and 927 singletons. The U. appendiculatus sequences were compared with sequence data for other rust fungi, Phakopsora pachyrhizi, Uromyces fabae, and Puccinia graminis. The U. appendiculatus haustoria library included a large number of genes with unknown cellular function; however, summation of sequences of known cellular function suggested that haustoria at 5 dpi had fewer transcripts linked to protein synthesis in favor of energy metabolism and nutrient uptake. In addition, open reading frames in the U. appendiculatus data set with an N-terminal signal peptide were identified and compared with other proteins putatively secreted from rust fungi. In this regard, a small family of putatively secreted RTP1-like proteins was identified in U. appendiculatus and P. graminis.

Characterization of human cytomegalovirus strains by analysis of short tandem repeat polymorphisms

Human cytomegalovirus (HCMV) strains display genetic polymorphisms, and these polymorphisms can be analyzed to study viral transmission and pathogenesis. Recently, short tandem repeat (STR) length polymorphisms have been identified in the HCMV genome. We assessed the utility of STRs in characterizing HCMV strains and found that a multiplexed PCR assay using primers based upon these STRs accurately maps HCMV strains. Using primers for 10 microsatellite regions, the STR profiles of 44 wild-type and 2 laboratory strains of HCMV were characterized. The results of STR analysis were compared with those for strain characterization using nucleotide sequencing and restriction fragment length polymorphism analysis. In each instance, STR analysis accurately and specifically identified strains that were indistinguishable or distinct by conventional molecular analysis. Analysis of short tandem repeats also detected polymorphisms that supported simultaneous excretion of two HCMV strains. These results indicate that STR analysis allows rapid, precise molecular characterization of HCMV strains.

A molecular variant of the APC gene at codon 1822: its association with diet, lifestyle, and risk of colon cancer

The adenomatous polyposis coli (APC) gene is important in the etiology of colon cancer. Although germ-line mutations of this gene rarely occur in the population, less penetrant variants of the gene have been reported. One variant, producing an aspartate to valine change at codon 1822 (D1822V) [corrected] has been previously reported as having an allele frequency of 10%. The purpose of this study was to determine whether this D1822V [corrected] variant of the APC gene is associated with colon cancer and whether its association is influenced by other genetic or environmental factors. We used data collected as part of a multicenter study of 1,585 incident cases of colon cancer and 1,945 age- and sex-matched population-based controls to evaluate genetic, dietary, and environmental associations with the D1822V [corrected] variant of the APC gene. The frequency of the valine/valine allele at codon 1,822 was 22.8% in this population. In the control population, 61.5% were homozygote wild type, 33.3% were heterozygotes, and 5.2% were homozygote variant. Cases were slightly less likely to have the homozygous variant APC genotype than were controls [odds ratio (OR), 0.8; 95% confidence interval (CI), 0.6-1.1]; for those diagnosed after age 65, the homozygous APC variant was associated with reduced risk of colon cancer (OR, 0.6; 95% CI, 0.4-1.0). Assessment of the homozygous APC variant with dietary, genetic, and environmental factors showed that individuals with this genotype were at lower risk if they consumed a low-fat diet (OR, 0.2; 95% CI, 0.1-0.5) relative to those who were homozygous wild type and ate a high-fat diet. This finding was specific to a low-fat diet and was unrelated to other dietary variables. These results suggest that the codon 1,822 variant of the APC gene may have functional significance. Individuals who have the valine/valine variant of this gene may be at reduced risk of colon cancer if they eat a low-fat diet.

Associations between cigarette smoking, lifestyle factors, and microsatellite instability in colon tumors

BACKGROUND

Microsatellite instability (MSI) has been reported to occur in approximately 10%-15% of colon tumors. MSI is characterized by the presence of mutations in tandemly repeated DNA sequences known as microsatellites. Some individuals with unstable tumors have inherited mutations in mismatch repair genes, but MSI is also observed in sporadic colon cancer. It is unknown whether lifestyle factors associated with colon cancer, such as physical activity, body size, cigarette smoking, or use of aspirin and/or nonsteroidal anti-inflammatory drugs, contribute to MSI in sporadic tumors.

METHODS

Data from a population-based, case-control study of colon cancer were used. Case subjects were between 30 and 79 years of age at the time of diagnosis and included both men and women. Questionnaire data were used to obtain information on lifestyle factors. Tumor MSI was determined with the use of a panel of 10 tetranucleotide repeats and two mononucleotide repeats. A total of 1510 case subjects had valid questionnaire data and tumor DNA from which we were able to obtain MSI status. Questionnaire data were compared with lifestyle factors reported by 2410 population-based control subjects. All statistical tests were two-sided.

RESULTS

MSI-positive (MSI(+)) tumors were most common in older people and women and in the proximal colon. Patients with MSI(+) tumors were more likely to smoke 20 or more cigarettes a day than case subjects with MSI-negative (MSI(-)) tumors (odds ratio for being a smoker = 1.6 [95% confidence interval = 1.0-2.5] for men and 2.2 [95% confidence interval = 1.4-3.5] for women). The association between MSI(+) tumors and cigarette smoking was strongest among case subjects who started to smoke at a young age, smoked for 35 or more years, and were either current smokers or had stopped fewer than 15 years before diagnosis. A statistically significant linear trend of increased risk of MSI(+) tumors was observed with increasing amount smoked (P<.01).

CONCLUSIONS

This study suggests that smoking cigarettes statistically significantly contributes to MSI in colon tumors. We estimate that approximately 21% of MSI in colon tumors may be attributable to cigarette smoking.

Inpatients with menometrorrhagia: etiologies, treatments, and outcomes

BACKGROUND

Abnormal uterine bleeding is commonly seen in emergency departments and gynecologic clinics. In a southern, inner-city hospital, a seemingly large number of women are admitted with life-threatening anemia of benign gynecologic origin. We examine its causes, review treatments and outcomes, and discuss optimization of therapy.

METHODS

A chart review of patients requiring emergency admission for anemia of gynecologic origin yielded 48 patients from July 1, 1994, through April 30, 1998. Patients with known or obvious gynecologic malignancies were excluded.

RESULTS

Of 48 patients, 69% were black. Mean age was 41 years. Sixty-three percent had had no previous treatment. Almost one fourth had a history of mental illness and/or substance abuse. Two thirds had uterine leiomyomata. Most (81%) required transfusion; 25% had surgery during initial hospitalization. Of those who did not receive definitive therapy (hysterectomy), 13% were subsequently readmitted for active bleeding and/or symptomatic anemia.

CONCLUSIONS

Our study patients were admitted with potentially life-threatening anemia. All were adequately resuscitated using a variety of measures, including high-dose estrogen therapy and transfusion. Optimal therapy for those requiring emergency treatment should include hormonal therapy and transfusion if necessary, early surgical intervention unless otherwise contraindicated, and close follow-up until definitive therapy is achieved.

Effects of high pressure and temperature on the wild-type and F29W mutant forms of the N-domain of avian troponin C

The N-domain of troponin C (residues 1-90) regulates muscle contraction through conformational changes induced by Ca2+ binding. A mutant form of the isolated domain of avian troponin C (F29W) has been used in previous studies to observe conformational changes that occur upon Ca2+ binding, and pressure and temperature changes. Here we set out to determine whether the point mutation itself has any effects on the protein structure and its stability to pressure and temperature in the absence of Ca2+. Molecular dynamics simulations of the wild-type and mutant protein structures suggested that both structures are identical except in the main chain and the loop I region near the mutation site. Also, the simulations proposed that an additional cavity had been created in the core of the mutant protein. To determine whether such a cavity would affect the behavior of the protein when subjected to high pressures and temperatures, we performed 1H-NMR experiments at 300, 400, and 500 MHz on the wild-type and F29W mutant forms of the chicken N-domain troponin C in the absence of Ca2+. We found that the mutant protein at 5 kbar pressures had a destabilized beta-sheet between the Ca2+-binding loops, an altered environment near Phe-26, and reduced local motions of Phe-26 and Phe-75 in the core of the protein, probably due to a higher compressibility of the mutant. Under the same pressure conditions, the wild-type domain exhibited little change. Furthermore, the hydrophobic core of the mutant protein denatured at temperatures above 47 degrees C, while the wild-type was resistant to denaturation up to 56 degrees C. This suggests that the partially exposed surface mutation (F29W) significantly destabilizes the N-domain of troponin C by altering the packing and dynamics of the hydrophobic core.

High-resolution, high-pressure NMR studies of proteins

Advanced high-resolution NMR spectroscopy, including two-dimensional NMR techniques, combined with high pressure capability, represents a powerful new tool in the study of proteins. This contribution is organized in the following way. First, the specialized instrumentation needed for high-pressure NMR experiments is discussed, with specific emphasis on the design features and performance characteristics of a high-sensitivity, high-resolution, variable-temperature NMR probe operating at 500 MHz and at pressures of up to 500 MPa. An overview of several recent studies using 1D and 2D high-resolution, high-pressure NMR spectroscopy to investigate the pressure-induced reversible unfolding and pressure-assisted cold denaturation of lysozyme, ribonuclease A, and ubiquitin is presented. Specifically, the relationship between the residual secondary structure of pressure-assisted, cold-denatured states and the structure of early folding intermediates is discussed.

A high-pressure, high-resolution NMR probe for experiments at 500 MHz

A novel high-pressure, high-resolution NMR probe is described which operates at a frequency of 500 MHz. The design features an alternative RF coil (8 mm sample tube) for high frequency, sensitivity, probe power, and resolution (< 3.0 x 10(-9)). The probe is capable of pressures to at least 5 kbar over a temperature range of -30 to 80 degreesC, and has a double-tuned 1H/2H circuit which can tune at 1H frequencies of either 300 or 500 MHz. The sensitivity of the 300-MHz circuit is over twice that of previous 10-mm high-pressure NMR probe designs, while at 500 MHz the sensitivity is nearly five times that of previous 300-MHz pressure probes. Potential biochemical applications are demonstrated by 2D NOESY spectra of a Troponin C mutant.

The chromosome location of the human homolog of the mouse mammary tumor-associated gene INT6 and its status in human breast carcinomas

The INT6 gene is a common integration site for the mouse mammary tumor virus in mouse mammary tumors. We have determined that the human homolog of INT6 is located on chromosome region 8q22-q23. A processed INT6 pseudogene is located on chromosome 6q. INT6 is composed of 13 exons that span 45 kb of genomic DNA. The deduced amino acid sequence of the gene product is identical to the mouse protein and contains three potential translation start signals. We have examined 100 primary breast carcinoma DNAs for evidence of genetic alteration affecting INT6. Loss of heterozyosity (LOH) was detected in 11 of 39 (28%) of the tumor samples informative for a polymorphic sequence in intron 7 of INT6. Since single-strand conformation and hybrid mismatch analysis of the remaining allele in these tumor DNAs failed to detect any mutations, we conclude that the target gene for LOH must be closely linked to INT6.

High-Resolution NMR Probe for Experiments at High Pressures

A 300 MHz high-resolution, high-pressure NMR probe which operates in the pressure range of 1 bar to 9 kbar at temperatures of -30 to 100&deg;C is described. Specialized novel design features of the probe are discussed and test spectra showing resolution better than 1 Hz (<3.0 x 10(-9)) for 8 mm samples are presented. Potential biochemical applications of this probe are illustrated by experiments dealing with the pressure-induced unfolding of hen egg white lysozyme.

A strategy for constructing high-resolution genetic maps of the human genome: a genetic map of chromosome 17p, ordered with meiotic breakpoint-mapping panels

Genetic linkage analyses with genotypic data obtained from four CEPH reference families initially assigned 24 new PCR-based markers to chromosome 17 and located the markers at specific intervals of an existing genetic map of chromosome 17p. Each marker was additionally genotyped with an ordered set of obligate, phase-known recombinant chromosomes. The breakpoint-mapping panels for each family consisted of two parents, one sib with a nonrecombinant chromosome, and one or more sibs with obligate recombinant chromosomes. The relative order of markers was determined by sorting segregation patterns of new markers and ordered anchor markers and by minimizing double-recombination events. Consistency of segregation patterns with multiple flanking loci constituted support for order. A genetic map of chromosome 17p was completed with 39 markers in 23 clusters, with an average space of 3 cM between clusters. The collection of informative genotypes was highly efficient, requiring fivefold fewer genotypes than would be collected with all the CEPH families. Given the availability of large numbers of highly informative PCR-based markers, meiotic breakpoint mapping should facilitate construction of a human genomic map with 1-cM resolution.

A PCR-based genetic map for human chromosome 3

Oligonucleotide primers for 125 simple sequence repeat microsatellite-based genetic markers have been assayed by polymerase chain reaction (PCR) in the CEPH reference family panel. These microsatellites include 101 dinucleotide repeats as well as 24 new tetranucleotide repeats. The average heterozygosity of this marker set was 72.4%. Genetic data were analyzed with the genetic mapping package LINKAGE. A subset of these microsatellite markers define a set of 56 uniquely ordered loci (> 1000:1 against local inversion) that span 271 cM. Sixty-seven additional loci were tightly linked to markers on the uniquely ordered map, but could not be ordered with such high precision. These markers were positioned by CMAP into confidence intervals. One hundred thirteen of the microsatellite markers were also tested on a chromosome 3 framework somatic cell hybrid panel that divides this chromosome into 23 cytogenetically defined regions, integrating the genetic and physical maps of this chromosome. The high density, high heterozygosity, and PCR format of this genetically and physically mapped set of markers will accelerate the mapping and positional cloning of new chromosome 3 genes.

Genetic mapping of the BRCA1 region on chromosome 17q21

Chromosome 17q21 harbors a gene (BRCA1) associated with a hereditary form of breast cancer. As a step toward identification of this gene itself we developed a number of simple-sequence-repeat (SSR) markers for chromosome 17 and constructed a high-resolution genetic map of a 40-cM region around 17q21. As part of this effort we captured genotypes from five of the markers by using an ABI sequencing instrument and stored them in a locally developed database, as a step toward automated genotyping. In addition, YACs that physically link some of the SSR markers were identified. The results provided by this study should facilitate physical mapping of the BRCA1 region and isolation of the BRCA1 gene.

A radiation hybrid map of the BRCA1 region

A locus on chromosome 17q, designated "BRCA1," has been identified as a predisposition gene for breast cancer. A panel of chromosome 17-specific radiation-reduced somatic cell hybrid clones has been assembled for high-resolution mapping of chromosome 17. A series of 35 markers, known to span the BRCA1 locus, were tested against this hybrid panel by PCR assays. Statistical analysis of these data yields a BRCA1 radiation hybrid map at a density sufficient to initiate YAC cloning and pulsed-field gel electrophoretic mapping of the candidate region. In addition, many of the markers reveal genetic polymorphisms and may be tested in breast cancer families and in loss-of-heterozygosity studies of sporadic breast cancers to better define the BRCA1 gene candidate region.

A genetic linkage map with 29 loci spanning human chromosome 13q

A genetic linkage map for the long arm of human chromosome 13 contains 29 loci derived from 38 probe and enzyme combinations and two protein polymorphisms. Thirteen loci form a continuous linkage map of 106 cM in males and 230 cM in females; each was placed on the map with support of at least 1000:1 against alternative orders. On a sex-combined basis, the mean distance between markers is less than 13 cM. The order of loci on the genetic map agrees with physical localization data that show that together these 13 loci cover 13q13 to 13q34. This map was used to regionally localize the 16 remaining loci. The linkage maps reported here should prove to be useful to investigators mapping disease genes and other genetic markers on human chromosome 13.

Peripheral myelin protein-22 gene maps in the duplication in chromosome 17p11.2 associated with Charcot-Marie-Tooth 1A

Charcot-Marie-Tooth disease 1A (CMT1A) is a hereditary demyelinating peripheral neuropathy, associated with a DNA duplication on chromosome 17p11.2. A related disorder in the mouse, trembler (Tr), maps to mouse chromosome 11 which has syntenic homology to human chromosome 17p. Recently, the peripheral myelin protein-22 (pmp-22) gene was identified as the likely Tr locus. We have constructed a partial yeast artificial chromosome contig spanning the CMT1A gene region and mapped the PMP-22 gene to the duplicated region. These observations further implicate PMP-22 as a candidate gene for CMT1A, and suggest that over-expression of this gene may be one mechanism that produces the CMT1A phenotype.

Three-year follow-up of older schizophrenics: extrapyramidal syndromes, psychiatric symptoms, and ventricular brain ratio

Longitudinal evaluation of psychiatric patients often yields information that cross-sectional study does not. We previously examined 31 older (age greater than 55) chronic schizophrenics for prevalence of extrapyramidal side effects, severity of psychiatric symptoms, and ventricular brain ratio (VBR). We reexamined 22 of these patients after 2-4 years. Tardive dyskinesia (TD) and drug-induced parkinsonism (DIP) were common (mean prevalences were 52% and 62%, respectively) and often occurred together (38%). The overall prevalences of the disorders did not change significantly with time, although there was some individual fluctuation in diagnosis. Severity of TD was constant, but severity of DIP decreased, probably because neuroleptic doses were significantly decreased. Magnitude of DIP was positively correlated with VBR and severity of negative symptoms of schizophrenia. The correlation of DIP and negative symptoms occurred primarily because of the similarity between masked facies and blunted affect. VBR did not change over the follow-up period. Negative symptoms of schizophrenia were prevalent, moderately severe, and quite stable over time in this cohort. Positive symptoms were less severe but highly variable between examinations.

Electrical stimulation versus electromyographic biofeedback in the recovery of quadriceps femoris muscle function following anterior cruciate ligament surgery

Both electrical stimulation and electromyographic biofeedback have been shown to be more effective than voluntary isometric exercise alone in the recovery of quadriceps femoris muscle force following anterior cruciate ligament (ACL) reconstruction. In a comparison of these two modalities, 30 patients with ACL reconstruction were randomly assigned to either a group receiving electrical stimulation in conjunction with voluntary isometric exercise or a group receiving biofeedback in conjunction with voluntary isometric exercise. Following 6 weeks of a rehabilitative exercise protocol, the quadriceps femoris muscle isometric peak torque in the operative limb was compared with that in the nonoperative limb. A t test of independent samples indicated that the biofeedback group recovered a significantly greater percentage of their nonoperative limb's peak torque than did the electrical stimulation group. Measurements of active knee extension were taken at weeks 1, 2, 4, and 6 of the exercise program. A two-way analysis of variance (groups x weeks) indicated no significant difference between the rate at which each group recovered full active extension. The authors concluded that biofeedback is more effective than electrical stimulation in facilitating the recovery of peak torque and that biofeedback is comparable to electrical stimulation in the recovery of active knee extension.

Characterization of eight VNTR loci by agarose gel electrophoresis

Allelic frequencies and their confidence intervals were obtained for eight independent VNTR loci from a sample of more than 75 Utah Caucasians. Using high-resolution agarose gel electrophoresis, we were able to resolve alleles at the D17S5 locus that differed by only one repeating unit; it was therefore possible to name the alleles according to the number of repeating units each contained. Two a priori probabilities were calculated for each VNTR locus separately and for all eight loci jointly: (i) the "power of exclusion" for an alleged father/mother/child trio and for an alleged parent/child duo, and (ii) the "probability of matching" when two unrelated individuals or two siblings are genotyped.

Membrane cofactor protein of complement is present on human fibroblast, epithelial, and endothelial cells

Membrane cofactor protein (MCP) of the complement system is a iC3/C3b binding molecule with cofactor activity that has been identified on all human peripheral blood cells except erythrocytes. Human mononuclear and platelet MCP is dimeric with molecular weights of 68,000 and 63,000 and is expressed in three phenotypic patterns. To further determine its tissue distribution, surface-labeled human fibroblast, epithelial, and endothelial cells and cell lines were assessed for the presence of MCP by iC3 affinity chromatography and by immunoprecipitation with a monospecific anti-MCP rabbit polyclonal antibody. All sources of adult and fetal fibroblast and epithelial cells and cell lines examined and umbilical vein endothelial cells expressed MCP. The molecular weight and phenotypic patterns of MCP were similar to those of peripheral blood cells. MCP was synthesized by fibroblast and epithelial cell lines. Solubilized extracts of these cell lines expressed factor I-dependent cofactor activity for the first cleavage of iC3/C3b which was abrogated by removal of MCP. Expression of MCP was modulated by SV40 transformation of two fetal fibroblast lines. There was a 5- to 10-fold increase in expression of MCP and a preferential expression of the lower species such that the phenotypic designation was changed. The wide tissue distribution and activity profile of MCP suggest that it is likely to play an important role in the regulation of the complement cascade.