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Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli.

The relationship between gene length and synonymous codon usage bias was investigated in Drosophila melanogaster, Escherichia coli and Saccharomyces cerevisiae. Simulation studies indicate that the correlations observed in the three organisms are unlikely to be due to sampling errors or any potential bias in the methods used to measure codon usage bias. The correlation was significantly positive in E.coli genes, whereas negative correlations were obtained for D. melanogaster and S.cerevisiae genes. When only ribosomal protein genes were used, whose expression levels are assumed to be similar, E.coli and S.cerevisiae showed significantly positive correlations. For the two eukaryotes, the distribution of effective number of codons was different in short genes (300-500 bp) compared with longer genes; this was not observed in E.coli. Both positive and negative correlations can be explained by translational selection. Energetically costly longer genes have higher codon usage bias to maximize translational efficiency. Selection may also be acting to reduce the size of highly expressed proteins, and the effect is particularly pronounced in eukaryotes. The different relationships between codon usage bias and gene length observed in prokaryotes and eukaryotes may be the consequence of these different types of selection.

Animals↗

Living donor kidney transplants: a biopsy study 1 year after transplantation, compared with baseline changes and correlation to kidney function at 1 and 3 years.

INTRODUCTION: Chronic changes in biopsies from long-term stable kidney allografts have been reported to correlate with graft prognosis. Morphological changes in baseline ('zero-hour') biopsies have been described as well, but their importance for long-term prognosis have been less clear. The aim of the present study was to evaluate biopsy changes from baseline to 1 year after transplantation in patients receiving kidneys from living donors, and to assess the possible prognostic implications of these findings. METHODS: Light microscopical changes in 18 gauge full-core biopsies were scored semi-quantitatively in 33 patients 1 year after transplantation, and compared to baseline changes previously reported [1]. All cases were also examined with transmission electron microscopy. The semi-quantitative data from baseline and at 1 year were correlated with kidney function 1 and 3 years after transplantation. The reproducibility of baseline findings regarding arteriosclerosis and arteriolar hyalinosis was tested by comparison with biopsies 1 week after transplantation (n = 43). RESULTS: We found a significant increase in mesangial glomerular sclerosis (P<0.001), interstitial fibrosis/tubular atrophy (if/ta) (P = 0.002), and mononuclear cell interstitial infiltration (P = 0.003) after 1 year, compared to baseline changes. There was an increase of arteriosclerosis (P = 0.028) and arteriolar hyalinosis (P = 0.006) when compared to biopsies taken 1 week after transplantation, but not when compared to the 'zero-hour' findings. Electron microscopy revealed one case of recurrent immune-complex glomerulonephritis and another case of recurrent light chain deposition kidney disease. Comparing 1-week vascular findings with baseline gave a low level of reproducibility, probably due to sampling error. Baseline biopsy findings could not predict long-term kidney function. In the 1-year biopsy, if/ta was significantly correlated with serum creatinine (P = 0.007) and glomerular filtration rate (GFR) (P<0.001) at 1 year, with serum creatinine at 3 years (P = 0.011), and with the first-year cumulative dose of methylprednisolone (P = 0.004). Serum creatinine at 1 year, however, was found to be the most accurate predictor of 3-year kidney function (P<0.001). Donor age was correlated to kidney function at 3 years (P = 0.013) but not at 1 year after transplantation. CONCLUSION: Morphological changes in baseline biopsies of living donor kidneys tend to become more pronounced in well-functioning allografts during the first year after transplantation. In the 1 year biopsy, if/ta seems to be the most reliable variate for grading of chronic changes. However, 1-year serum creatinine predicted long-term kidney function more precisely than did the biopsy scores. Based on the results of the present study, a protocol 1-year biopsy does not seem warranted in the management of the graft recipient with a stable kidney function.

Adult↗

Chronic non-ischaemic congestive heart disease and endomyocardial biopsies. Worth the extra?

The diagnostic yield of endomyocardial biopsies in patients with chronic congestive heart failure of non-ischaemic aetiology remains questionable and, therefore, the use of endomyocardial biopsies under such circumstances is at stake. The present report documents the correlation between the histologic interpretation of endomyocardial biopsies and the corresponding cardiac explants in 13 patients who underwent cardiac transplantation. The biopsy diagnoses in these patients varied from 'compatible with dilated cardiomyopathy' (n = 6) to 'non-conclusive' (n = 4), 'ischaemia' (n = 2) and 'borderline myocarditis' (n = 1). Correlation with the corresponding cardiac explants revealed hypertrophy of myocytes as the leading histologic feature in the majority of cases. Because of the non-specific histopathology of dilated cardiomyopathy, the discrepancy between biopsy diagnoses and the leading explant diagnosis is mostly a matter of semantics. Ischaemia was present at high incidence, but is considered a result of imparied myocardial perfusion rather than the prime mechanism of heart failure. In four cardiac explants myocarditis was encountered, while the corresponding biopsies showed no cellular inflammation. In two, the cellular infiltrates suggested an early state of repair. One heart contained an active and extensive lymphocytic myocarditis. The fourth case showed an eosinophilic myocarditis, most likely acquired after the biopsy was taken. These discrepancies almost certainly relate to the sampling error and the time interval between biopsy and onset of symptoms. The immediate diagnostic yield of the biopsy, in this particular subset of patients, was minimal, particularly with respect to the diagnosis 'myocarditis'. Nevertheless, biopsy diagnoses such as 'compatible with' and 'non-conclusive' do contribute to the final categorization and management of these patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

Allozyme variation and differentiation in African and Indian rhinoceroses.

We studied variation at 25 to 31 allozymic loci in African and Asian rhinoceroses. Four taxa in three genera were examined: African Ceratotherium simum simum (northern white rhinoceros), C. s. cottoni (southern white rhinoceros), Diceros bicornis (black rhinoceros), and Rhinoceros unicornis (Indian rhinoceros). Extremely small amounts of intraspecific variation were observed in sample sizes of 2 to 10 presumably unrelated individuals per taxon: P = .00-.10, H = 0.00-0.02. We examined demographic bottlenecks and sampling errors as possible reasons for the low levels of detectable variation. The very small intraspecific genetic distance (D = 0.005) between the two living white rhinoceros subspecies is far less than the distance that has been reported for other mammal subspecies. The mean D value of 0.32 +/- 0.11 between the two African genera was also less than expected given the divergence time of greater than 7 million years suggested by the fossil record. Rhinoceroses may be evolving more slowly at the structural gene loci than are some other mammal groups. The estimate of D = 1.05 +/- 0.24 for the African-Indian split supports this idea, as the lineage diverged at least 26 million years ago. Our results contribute to the currently available scientific information on which management decisions aimed toward saving endangered rhinoceroses should be based.

Animals↗

A stepwise algorithm for finding minimum evolution trees.

A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m-1)!/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.

Algorithms↗

Nuclear gene trees and the phylogenetic relationships of the mangabeys (Primates: Papionini).

Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys are polyphyletic within the Papionini; (2) Cercocebus is the sister taxon to the genus Mandrillus; and (3) Lophocebus belongs to a clade with Papio and Theropithecus, with Papio as its most likely sister taxon. Morphologically based phylogenies positing mangabey monophyly were evaluated by mapping the sequences for each locus on these trees. The data seem to fit these trees poorly in both maximum-parsimony and likelihood analyses. Incongruence among nuclear gene trees occurred in the interrelationships among Lophocebus, Papio, and Theropithecus. Several factors that may account for this incongruence are discussed, including sampling error, random lineage sorting, and introgression.

Animals↗

Analysis of higher-primate phylogeny from transversion differences in nuclear and mitochondrial DNA by Lake's methods of evolutionary parsimony and operator metrics.

In the companion paper (Holmquist et al. 1988), we concluded that there is no agreement on either the correct branching order or differential rates of evolution among the higher primates, and we examined in depth why this uncertainty in the evolutionary understanding of our closest living relatives persists. Recently, Lake developed two novel methods, based on group properties of transition and transversion operators, that (a) permit, in principle, objective resolution of problems of the above type and (b) attach a statistical significance level to the conclusions drawn. In the present paper, we develop formulas for using these two methods in tandem and apply them to study transversion differences in (1) nuclear DNA for a 7-kb segment of the psi eta-globin locus and a 3-kb intergenic region between the psi beta- and delta-globin loci and (2) mitochondrial DNA for the 896-bp fragment of Brown et al. Although each of these nucleotide sequence regions has its characteristic tempo and mode of evolution, the nuclear and mitochondrial data together, comprising a total of 10,939 base positions, support a Homo/Pan clade at the 97% confidence level. If we calibrate the divergence point for humans and chimpanzees at 5 Myr, consideration of the transversion branch lengths for the combined nuclear data indicates that the gorilla lineage branched off 600,000-900,000 years prior to that, although the 2 sigma sampling errors do not preclude either a temporal trifurcation for the three species or a considerably more ancient branch point for the gorilla. To resolve the length of this central branch to a relative accuracy of 25% and 30% will require a factor of 16 and nine times more data, respectively--i.e., in excess of 100,000 homologous nucleotides for each of the four primates. For the nuclear genes, heterogeneity in evolutionary rates between different parts of the genome is mostly restricted to the human lineage for these two segments. The lineage leading to chimpanzees has evolved 0.4 (3-kb fragment) to 3.5 (7-kb segment) times as rapidly as the lineage leading to humans, and that leading to the gorilla has evolved approximately one-fifth to one-half as rapidly as that leading to chimpanzees. Thus, even local molecular clocks can "tick" badly. As significant is the fact that virtually contiguous parts of the genome tick at markedly different rates.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

Genetic analysis of TAP2 in systemic lupus erythematosus patients from two ethnic groups.

The aim of this study was to determine whether the TAP2 (Transporter associated with Antigen Processing 2) locus is involved in susceptibility to systemic lupus erythematosus (SLE). We adopted the interethnic approach to overcome problems in the analysis resulting from linkage disequilibrium. The TAP2 gene polymorphisms of the codons corresponding to amino acid positions 379, 565 and 665 were investigated by amplification refractory mutation system polymerase chain reaction (ARMS-PCR) in 186 patients (151 white Europeans, 35 Afrocaribbeans) and 183 controls (79 white Europeans, 104 Afrocaribbeans). In the European SLE patients, the frequency of the TAP2 type V-A-TA was marginally lower compared with the control group (31% vs 42%), with negative linkage disequilibrium between this TAP2 type and DR3 probably accounting for the difference. For the European SLE patients, we confirmed a significant association of DR3 with disease status [odds ratio = 4.16, 95% confidence interval (CI), 2.08-8.39] and in the patients with DR3 there was a significantly high frequency of the TAP2 type V-A-T-. In the Afrocaribbean SLE patients, any associations of disease status with TAP2 phenotype were the inverse of those in the European patients. Thus, in these patients the frequency of V-A-TA was higher than in controls (46% vs 26%, OR = 2.4, 95% CI 1.01-5.74), while the frequency of V-A-T- was lower (26% vs 40%, not significant). Despite possible sampling error, the lack of a difference in TAP2 status between cases and controls within ethnic groups and, if anything, an inverse association across ethnic groups, makes it unlikely that the TAP2 polymorphism studied here is of primary relevance to SLE susceptibility.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Middle ear muscle activity (MEMA) in schizophrenia using a noninvasive technique.

Rapid eye movement (REM) sleep middle ear muscle activity (MEMA) was recorded in four diagnostic groups: schizophrenics (n = 18), schizoaffectives (n = 8), depressives (n = 11) and healthy, nonpsychiatric controls (n = 10). Previous work suggested that schizophrenics have higher than normal rates of REM sleep MEMA; this previous study employed the MEMA recording technique of impedance audiometry, which involves a 90-dB stimulus probe tone. The present study, which utilized a silent, pressure-sensitive transducer (i.e. no acoustic stimulus), was undertaken to determine if the stimulus tone might have elicited excess MEMA in the schizophrenics. In this present study, we observed no significant differences in REM sleep MEMA among the four diagnostic groups, suggesting that REM sleep MEMA cannot be used as a biological marker to differentiate clinical disorders. This failure to replicate our previous finding of high MEMA rates in schizophrenics is likely due to sampling error; alternatively, high REM sleep MEMA rates might be elicited in a subgroup of schizophrenics with an acoustic stimulus.

Acoustic Impedance Tests↗

Transpiration of a boreal pine forest measured by branch bag, sap flow and micrometeorological methods.

Three independent methods were used to evaluate transpiration of a boreal forest: the branch bag, sap flow and eddy covariance methods. The branch bag method encloses several thousand needles and gives a continuous record of branch transpiration. The sap flow method provides a continuous record of sap velocity and an estimate of tree transpiration. The eddy covariance method typically measures evaporation rates between a forest and the atmosphere. We deployed an extra eddy covariance system below the forest to estimate canopy transpiration by difference. The three systems detected small water vapor fluxes despite a plentiful supply of energy to drive evaporation. We also observed that transpiration rates were low even when the soil was well supplied with water. Low rates of transpiration were attributed to the canopy's low leaf area index and the marked reduction in stomatal conductance as vapor pressure deficits increased. Water vapor fluxes, derived from the sap flow method, lagged behind those derived by the branch bag method by 1 to 2 h. The sap flow method also suffered from sampling errors caused by the non-uniformity of flow across the sapwood and the spatial variability of sapwood cross section throughout the forest. Despite technical difficulties associated with hourly measurements, daily totals of transpiration agreed well with values derived from micrometeorological systems.

Journal Article↗

Problems in the necropsy diagnosis of alcoholic liver disease.

Problem areas in the necropsy diagnosis of alcoholic liver disease are reviewed, potential sources of confusion delineated, and diagnostic guidelines proposed. The entire spectrum of alcoholic liver disease, including alcoholic hepatitis, may be perfectly mimicked by severe obesity, diabetes, and perhexiline maleate toxicity. Focal fatty change in the liver introduces sampling errors in the assessment of steatosis. Nodular regenerative hyperplasia of the liver mimics a micronodular cirrhosis both clinically and macroscopically. Measurement of the liver iron concentration reliably differentiates between alcoholic liver disease with siderosis and idiopathic hemochromatosis. The evaluation of preexisting fibrosis or cirrhosis in cases of massive hepatic necrosis is aided by stains for elastic fibers. Alcohol abusers taking acetaminophen (paracetamol) in excessive, but not suicidal doses are at risk of developing fatal "late" acetaminophen hepatotoxicity. Fatal viral hepatitis may be overlooked in an alcoholic with preexisting liver disease.

Acetaminophen↗

Crohn's disease associated with pellagra and increased excretion of 5-hydroxyindolacetic acid.

A 47-year-old woman with seronegative polyarthritis, diarrhea, and photosensitivity dermatitis was found to have Crohn's disease and pellagra. The presence of high values of 5-hydroxyindolacetic acid in the urine began the exhaustive investigations and finally enterotomy. No mass lesion was found. Argyrophilic cells were not increased in areas of inflamed intestinal mucosa or the normal mucosa. The disagreement between biochemical and histologic findings was attributed to sampling error. Antiinflammatory treatment for Crohn's disease was given and the gastrointestinal and articular symptoms improved, excretion of 5-hydroxyindolacetic acid returned to normal and there was no relapse of pellagra. Pellagra as a complication of Crohn's disease has been described in 4 cases; malnutrition and intestinal malabsorption were the proposed mechanisms for the niacin deficiency and pellagra of those patients. In the current case, the pathogenesis of pellagra may be accounted to wastage of tryptophan by an increased pool of intestinal argyrophilic cells, suggested by increased urinary excretion of 5-hydroxyindolacetic acid.

Anti-Inflammatory Agents↗

Pelvic lymph node metastases in prostatic carcinoma. The value of touch imprint cytology.

Touch imprint cytology is a simple, rapid, reliable, and highly sensitive procedure when used for detecting lymph node metastases in men with clinically localized prostatic adenocarcinoma who are undergoing staging pelvic lymphadenectomy. Thirty-five men admitted for this procedure had frozen sections performed on the lymph nodes removed at surgery. Of these 35 patients, 19 had touch imprints made of their lymph nodes. In five patients classified as having Stage D disease, positive frozen section correlated with permanent section. In two of these cases, touch imprint cytology was performed and was positive for malignant cells. In seven patients classified as having Stage D disease, frozen sections were negative. Permanent sections were positive for metastatic tumor in five of these patients. In four of these cases, touch imprint cytology was performed. In two cases, cytology and permanent sections were positive and, in two cases, cytology alone was positive. Factors that contributed to the false negative rate for frozen section were: the presence of micrometastases, fatty lymph nodes that were difficult to process, and sampling errors on the part of the pathologist. Touch imprint cytology overcame the deficits of frozen section and proved useful in detecting metastatic disease in lymph nodes.

Adult↗

Endoscopic surveillance of columnar-lined esophagus: frequency of intestinal metaplasia detection and impact of antireflux surgery.

OBJECTIVE: To quantify the occurrence of intestinal metaplasia in columnar-lined esophagus (CLE) during endoscopic surveillance and to evaluate the impact of antireflux surgery on the development of intestinal metaplasia. SUMMARY BACKGROUND DATA: The malignant potential in segments of CLE is mainly restricted to those containing intestinal metaplasia. Patients with segments of CLE in which no intestinal metaplasia can be detected are rarely enrolled in a surveillance program but may still be at increased risk of developing esophageal adenocarcinoma because intestinal metaplasia may be missed or may develop with time. METHODS: The occurrence of intestinal metaplasia on biopsy samples was determined on repeated endoscopies in 177 patients enrolled in a surveillance program for CLE. The incidence of intestinal metaplasia in patients with no evidence of intestinal metaplasia on the two first endoscopies was evaluated on the subsequent endoscopies and compared in patients with medically and surgically treated gastroesophageal reflux disease. RESULTS: Intestinal metaplasia was found in 53% of the patients (94/177) on their first surveillance endoscopy and was more prevalent in long segments of CLE. The prevalence of intestinal metaplasia increased markedly with increasing number of surveillance endoscopies. Intestinal metaplasia tended to be detected early in patients with long segments of CLE; in patients with shorter segments, intestinal metaplasia was also detected late in the course of endoscopic surveillance. Patients with surgically treated reflux disease were 10.3 times less likely to develop intestinal metaplasia compared with a group receiving standard medical therapy. CONCLUSION: Biopsy samples from a single endoscopy, despite an adequate biopsy protocol, are insufficient to rule out the presence of intestinal metaplasia. Patients in whom biopsy specimens from a segment of CLE show no intestinal metaplasia have a significant risk of having undetected intestinal metaplasia or of developing intestinal metaplasia with time. Sampling error is probably the reason for the absence of intestinal metaplasia in segments of CLE longer than 4 cm, whereas development of intestinal metaplasia is common in patients with shorter segments of CLE. Antireflux surgery protects against the development of intestinal metaplasia, possibly by better control of reflux of gastric contents.

Aged↗

Effects of using two or more standardized patients to simulate the same case on case means and case failure rates.

The effects of using two or more standardized patients (multiple SPs) to simulate the same case in a performance-based examination were studied at the case level by comparing case means and case failure rates for multiple SPs simulating the same case, using data from the classes of 1988, 1989, and 1990 at the Southern Illinois University School of Medicine. For total scores and scores on the students' written answers, the effects on means and failure rates were negligible and could be explained as due to sampling error. For scores on the checklists completed by the SPs, there were more significant differences than would be expected by chance alone, even though the number of significant differences was relatively small. The results demonstrate a need for caution in the interpretation of scores obtained from a case checklist completed by multiple SPs, particularly in regard to making pass-fail decisions.

Achievement↗

An international intercomparison of soil gas radon and radon exhalation measurements.

The Environmental Measurements Laboratory hosted the Sixth International Radon Metrology Programme Intercomparison Test and Workshop (IRMP6) from 12-15 June 1995. Thirty participants representing 24 different institutions from 11 countries attended. Laboratory exercises consisted of 220Rn and 222Rn concentration measurements from a source container, and exhalation measurements from a 226Ra-spiked concrete slab and a "normal" concrete slab. Field exercises included soil gas radon measurements and radon exhalation measurements. In this report, we pooled the participants' data and used the ratio of the standard deviation (SD) to the arithmetic mean, expressed as a percentage, to assess participant agreement for each exercise. For the exhalation measurements from the 226Ra-spiked slab, this value is 37%; for soil gas 222Rn, this value is 120%, 36% and 27% for each depth range, 0.4-0.5, 0.6-0.75 and 0.9-1.0 m, respectively; for the surface exhalation measurements, this value is 34%. For the drum 222Rn measurements, the percent SD after removing a linear trend was 13%. These results indicate that sampling errors are greater than instrument errors.

Air Pollutants, Radioactive↗

MR-based correction of brain PET measurements for heterogeneous gray matter radioactivity distribution.

Partial volume and mixed tissue sampling errors can cause significant inaccuracy in quantitative positron emission tomographic (PET) measurements. We previously described a method of correcting PET data for the effects of partial volume averaging on gray matter (GM) quantitation; however, this method may incompletely correct GM structures when local tissue concentrations are highly heterogeneous. We have extended this three-compartment algorithm to include a fourth compartment: a GM volume of interest (VOI) that can be delineated on magnetic resonance (MR) imaging. Computer simulations of PET images created from human MR data demonstrated errors of up to 120% in assigned activity values in small brain structures in uncorrected data. Four-compartment correction achieved full recovery of a wide range of coded activity in GM VOIs such as the amygdala, caudate, and thalamus. Further validation was performed in an agarose brain phantom in actual PET acquisitions. Implementation of this partial volume correction approach in [18F]fluorodeoxyglucose and [11C]-carfentanil PET data acquired in a healthy elderly human subject was also performed. This newly developed MR-based partial volume correction algorithm permits the accurate determination of the true radioactivity concentration in specific structures that can be defined by MR by accounting for the influence of heterogeneity of GM radioactivity.

Aged↗

Regional heterogeneity in the proliferative activity of human gliomas as measured by the Ki-67 labeling index.

The effects of regional heterogeneity on the accuracy of histological grading of gliomas are well known, but little has been reported about its implications for other diagnostic modalities. This study investigated the relationships of regional heterogeneity in tumor proliferative activity, measured by Ki-67 labeling indices (LI), and histological grades for 16 regionally sampled glioma resections. There was a strong correlation between histological grades and Ki-67 LI in individual regions (p < 0.001), and both methods demonstrated comparable heterogeneity. Heterogeneity increased with tumor grade, probably as an expression of the increased genetic instability that accompanies tumor progression. Similarly, regions with comparable proliferative activity tended to cluster, paralleling clonal expansion. Thus, both histological grading and Ki-67 LI are subject to heterogeneity-induced sampling errors that limit their diagnostic accuracy, particularly in small biopsies. However, fewer grading errors occurred when using both methods together than when using either method alone, suggesting that the use of multiple techniques may reduce the adverse effects of regional heterogeneity on diagnostic accuracy. Regional heterogeneity appears to be a ubiquitous feature of gliomas: it also has been reported in karyotype, p53 oncogene mutations, and PDGF and EGFR expression. The effects of regional heterogeneity on new methods for studying gliomas need to be considered.

Brain Neoplasms↗