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PubMed2000

Ribosomal DNA and resolution of branching order among the ascomycota: how many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade.

Ascomycota↗
PubMed2001

The Gd(3+) complex of a fatty acid analogue of DOTP binds to multiple albumin sites with variable water relaxivities.

The 20 MHz water relaxivity (r(1)) of gadolinium(III) complexes formed with two fatty acid analogues of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylene phosphonate) were shown to increase substantially in the presence of albumin. The r(1) values of Gd(C(8)-DOTP)(5-) and Gd(C(11)-DOTP)(5-) in water were similar to that of the parent GdDOTP(5-), a q = 0 complex known to relax water very efficiently via an outer-sphere mechanism. Neither fatty acid analogue formed apparent aggregates or micelles in water up to 20 mM, but both showed dramatic increases in r(1) upon addition of albumin. Further ultrafiltration studies of Gd(C(11)-DOTP)(5-) in the presence of non-defatted HSA showed that the complex binds at a minimum of five high-affinity fatty acid sites with stepwise binding constants ranging from 1.27 x 10(5) to 2.7 x 10(3) M(-1). The 20 MHz relaxivity of Gd(C(11)-DOTP)(5-) in the presence of excess HSA was 23 mM(-1) s(-1) at 25 degrees C. The NMRD curve showed a broad maximum 20-30 MHz which fitted well to standard theory for a q = 0 complex with rapid outer-sphere water exchange. The r(1b) of Gd(C(11)-DOTP)(5-) bound at the tightest site on HSA was approximately 40 mM(-1) s(-1) at 5 degrees C, an extraordinarily high value for an outer-sphere complex. However, the r(1b) of Gd(C(11)-DOTP)(5-) bound at the weaker sites on HSA was considerably lower, approaching the relaxivity of the free complex in water. This suggests that the complex bound in the highest affinity fatty acid site is less mobile than the same complex bound at the weaker affinity fatty acid sites. This combined ultrafiltration and relaxivity study demonstrates that the common assumption of a single r(1b) value for a Gd(3+) complex bound at several protein sites is not a valid approximation.

Algorithms↗
PubMed1995

Evolution of the rDNA spacer, ITS 2, in the ticks Ixodes scapularis and I. pacificus (Acari: Ixodidae).

Evolution of the rDNA spacer, ITS 2, is examined by comparing 17 DNA sequences of the ticks, Ixodes scapularis and I. pacificus. The distribution of fixed interspecific differences and the relative frequency of base changes vs. insertions/deletions (indels) matches the distribution and relative frequency for intraspecifically variable sites. This suggests that most intraspecific variation is not effectively selected against. The base composition of the ITS 2 transcript is G- and U-biased. But, 5-base regions enriched (> 80 per cent) for A or U occur more frequently than expected while G- and C-enriched regions occur less frequently than expected. Enriched sequences may be prone to replication slippage, accounting for the A/T bias in insertions. Slippage-mediated gains and losses of A/T-rich tandem repeats apparently account for most indels. Minimum-energy conformations of the two species' folded transcripts share major structural features. Structural inertia arises from intramolecular base pairing within stems that allows most mutations to be absorbed as new bulges off stems. Yet, there is evidence of selection to maintain the conformation. First, intraspecifically variable sites are concentrated at the ends of stems in loops and intersections, structures that do not contribute to intramolecular base pairing. Moreover, some indels that have become fixed in one species compensate for the presence of conformation-destabilizing indels. However, high rates of sequence evolution within stems and absence of compensatory base evolution contraindicates selective constraint. Degenerate dispersed and tandem copies of two subrepeats, each approximately 20 bases long, may account for much of the ITS 2 sequence. These are approximately inverses of each other and are, consequently, capable of significant intramolecular hydrogen bonding to produce folded transcripts of low energy. Evolution of the ITS 2 sequence may largely entail replication slippage-mediated gains and losses of these repeats or their composite subrepeats.

Animals↗
PubMed1994

Peptide synthesis catalyzed by an antibody containing a binding site for variable amino acids.

Monoclonal antibodies, induced with a phosphonate diester hapten, catalyzed the coupling of p-nitrophenyl esters of N-acetyl valine, leucine, and phenylalanine with tryptophan amide to form the corresponding dipeptides. All possible stereoisomeric combinations of the ester and amide substrates were coupled at comparable rates. The antibodies did not catalyze the hydrolysis of the dipeptide product nor hydrolysis or racemization of the activated esters. The yields of the dipeptides ranged from 44 to 94 percent. The antibodies were capable of multiple turnovers at rates that exceeded the rate of spontaneous ester hydrolysis. This achievement suggests routes toward creating a small number of antibody catalysts for polypeptide syntheses.

Antibodies, Catalytic↗
PubMed2005

Impact of inadequate initial antimicrobial therapy on mortality in infections due to extended-spectrum beta-lactamase-producing enterobacteriaceae: variability by site of infection.

BACKGROUND: Infections due to extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species (ESBL-EK) have increased markedly in recent years. Risk factors for mortality among ESBL-EK infections have not been studied. METHODS: This retrospective cohort study was conducted in a 625-bed tertiary care medical center and a 344-bed urban community hospital to determine whether inadequate initial antimicrobial therapy (IIAT) (>48 hours between the time a culture was obtained and initiation of an agent to which the infecting organism was susceptible) is associated with mortality in ESBL-EK infections. All hospitalized patients with an ESBL-EK infection between June 1, 1997, and December 31, 2002, were eligible for inclusion. Subsequently, we conducted a nested case-control study to identify risk factors for IIAT. RESULTS: Of 187 subjects, 32 (17.1%) died while in the hospital. Clinical site of infection was a significant effect modifier in the association between IIAT and mortality. The presence of IIAT was an independent risk factor for mortality, but only for nonurinary ESBL-EK infections (adjusted odds ratio [95% confidence interval], 10.04 [1.90-52.96]). Independent risk factors for IIAT were (1) infection with a multidrug-resistant ESBL-EK (ie, resistant to sulfamethoxazole-trimethoprim, aminoglycosides, and quinolones) (14.58 [1.91-111.36]) and (2) health care-acquired ESBL-EK infection (4.32 [1.49-12.54]). CONCLUSIONS: Inadequate initial antimicrobial therapy is an independent risk factor for mortality in ESBL-EK infections, but only among nonurinary infections. Multidrug resistance was a strong risk factor for IIAT.

Aged↗
PubMed2000

Aspiration subsequent to a pure medullary infarction: lesion sites, clinical variables, and outcome.

BACKGROUND: Aspiration as a symptom of dysphagia and its apparent sequela, aspiration pneumonia, are common consequences of a stroke in the medulla. Previous reports that focused on dysphagia due to a medullary lesion were studies of single cases or a relatively small number of patients with multiple lesion loci. Moreover, the interval between the onset of stroke and the evaluation time of swallowing was not controlled and varied largely among patients. Thus, prediction of the swallowing status of patients with a medullary lesion has not been tenable. OBJECTIVES: To investigate the relation between the loci of pure medullary lesions and aspiration, to examine swallowing function over time, and to explore clinical variables that can predict aspiration. METHODS: We investigated 23 patients with pure medullary infarctions using the videofluoroscopic swallowing study and compared the airway status findings with the lesion location as determined with magnetic resonance imaging. The patients were classified by 6 medullary lesion-level categories (lower, lower-middle, middle, lower-middle-upper, middle-upper, and upper) and by 5 intralevel lesion loci (inferior-dorsal, large inferior-dorsolateral, para-median, midlateral, and dorsolateral). From the results of the videofluoroscopic swallowing studies, 2 patient groups were formed: one with aspiration and the other without aspiration. The clinical variables related to aspiration and outcome measures were also explored. RESULTS: Ten (44%) of the 23 patients manifested aspiration on swallowing: 9 (69%) of 13 with only middle-level lesions or lesions in multilevels, including the middle level; 1 (33%) of 3 with only upper-level lesions; and 0 (0%) of 7 with only lower-level medullary lesions. A lesion running the length of the middle and the lower medullary levels always resulted in aspiration. When an upper-level lesion was additionally involved, the incidence of aspiration depended on the horizontal extension of the lesion. We were able to discriminate the 2 patient groups with 95.7% accuracy using such variables as dysphonia, soft palate dysfunction, and facial hypesthesia. Most of the patients with aspiration symptoms due to a pure medullary infarction recovered rather quickly. CONCLUSIONS: Medullary infarctions often cause aspiration, but the occurrence may depend on the levels along the neuraxis and intralevel lesion loci. When different lesion levels and loci and their related clinical findings are considered as possible variables, aspiration becomes predictable. The outcome data prove that systematic control of evaluation time of swallowing was critical as we engaged in this study, since many aspirators with pure medullary infarctions resolve their swallowing difficulties rather quickly.

Adult↗
PubMed1987

Conservation and variation in orf virus genomes.

The genomes of several orf virus strains were analyzed with the restriction endonucleases EcoRI, HindIII, BamHI, and KpnI, and cleavage site maps were deduced. In general, the right half of the genome showed conservation of restriction sites compared with the left half. Variations in size of up to 0.5 kbp were found within an inverted terminal repetition, and a 1-kbp deletion was detected in some strains in a subterminal fragment at the left end. A region of approximately 20 kbp, some 12 kbp in from the left end, showed the greatest cleavage site variability although there was no evidence of large deletions in this region. A 1.55-kbp cloned DNA fragment from the internal variable region of NZ2 failed to hybridize to the DNA from three other strains. A fragment in the variable region of strain NZ7 was cloned and compared by hybridization and restriction endonuclease analysis with cloned NZ2 fragments from the same region. The region of nonhomology extended for at least 2.75 kbp. It is suggested that this internal variable region may provide sites for the insertion of foreign genes.

Animals↗
PubMed2001

Structural analyses of a malate dehydrogenase with a variable active site.

Malate dehydrogenase specifically oxidizes malate to oxaloacetate. The specificity arises from three arginines in the active site pocket that coordinate the carboxyl groups of the substrate and stabilize the newly forming hydroxyl/keto group during catalysis. Here, the role of Arg-153 in distinguishing substrate specificity is examined by the mutant R153C. The x-ray structure of the NAD binary complex at 2.1 A reveals two sulfate ions bound in the closed form of the active site. The sulfate that occupies the substrate binding site has been translated approximately 2 A toward the opening of the active site cavity. Its new location suggests that the low catalytic turnover observed in the R153C mutant may be due to misalignment of the hydroxyl or ketone group of the substrate with the appropriate catalytic residues. In the NAD.pyruvate ternary complex, the monocarboxylic inhibitor is bound in the open conformation of the active site. The pyruvate is coordinated not by the active site arginines, but through weak hydrogen bonds to the amide backbone. Energy minimized molecular models of unnatural analogues of R153C (Wright, S. K., and Viola, R. E. (2001) J. Biol. Chem. 276, 31151-31155) reveal that the regenerated amino and amido side chains can form favorable hydrogen-bonding interactions with the substrate, although a return to native enzymatic activity is not observed. The low activity of the modified R153C enzymes suggests that precise positioning of the guanidino side chain is essential for optimal orientation of the substrate.

Binding Sites↗
PubMed2005

Characteristics predicting nursing home admission in the program of all-inclusive care for elderly people.

PURPOSE: This study determined overall risk and predictors of long-term nursing home admission within the Program of All-Inclusive Care for the Elderly (PACE). DESIGN AND METHODS: DataPACE records for 4,646 participants aged 55 years or older who were enrolled in 12 Medicare- and Medicaid-capitated PACE programs during the period from June 1, 1990, to June 30, 1998, were obtained. Participants were enrolled for at least 30 days and had baseline evaluations within 30 days of enrollment. Cox proportional hazard models predicting an outcome of nursing home admission of 30 days or longer were estimated. RESULTS: The cumulative risk of admission to nursing homes for 30 days or longer was 14.9% within 3 years. Individuals enrolled from a nursing home were at very high risk for future admission, with a relative risk of 5.20 when compared with those living alone. Among individuals enrolled in PACE from the community, age, instrumental activity of daily living dependence, and bowel incontinence were predictive of subsequent nursing home admission. Asians and Blacks had a lower risk of institutionalization than Whites. However, other characteristics were not independently predictive of institutionalization, namely poor cognitive status, number of chronic conditions, activity of daily living deficits, urinary incontinence, several behavioral disturbances, and duration of program operation. Before adjusting for other variables, there was substantial site variability in risk of nursing home admission; this decreased considerably after other characteristics were adjusted for. IMPLICATIONS: Despite the fact that 100% of the PACE participants were nursing home certifiable, the risk of being admitted to a nursing home long term following enrollment from the community is low. The presence of some reversible risk factors may have implications for early intervention to reduce risk further, although the effect of these interventions is likely to be modest. Individuals who received long-term care in a nursing home prior to enrollment in PACE remain at high risk of readmission, despite the availability of comprehensive services.

Aged↗
PubMed1985

Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion.

Simple but exact statistical tests for detecting a cluster of associated nucleotide changes in DNA are presented. The tests are based on the linear distribution of a set of s sites among a total of n sites, where the s sites may be the variable sites, sites of insertion/deletion, or categorized in some other way. These tests are especially useful for detecting gene conversion and intragenic recombination in a sample of DNA sequences. In this case, the sites of interest are those that correspond to particular ways of splitting the sequences into two groups (e.g., sequences A and D vs. sequences B, C, and E-J). Each such split is termed a phylogenetic partition. Application of these methods to a well-documented case of gene conversion in human gamma-globin genes shows that sites corresponding to two of the three observed partitions are significantly clustered, whereas application to hominoid mitochondrial DNA sequences--among which no recombination is expected to occur--shows no evidence of such clustering. This indicates that clustering of partition-specific sites is largely due to intragenic recombination or gene conversion. Alternative hypotheses explaining the observed clustering of sites, such as biased selection or mutation, are discussed.

Animals↗
PubMed2000

Large amounts of genetic divergence among Italian species of the genus Orchesella (Insecta, collembola) and the relationships of two new species.

The phylogenetic position of two putative new species of the collembolan genus Orchesella was investigated by comparison with four other Italian species of the genus using a fragment of the mitochondrial gene encoding for subunit I of cytochrome c oxidase (COI). The gene showed the well-known A + T bias, typical of insect mitochondrial DNA, although A + T content was not as high as that observed in species belonging to more derived insect orders. The large number of variable sites in 3rd codon positions (85.2% variable) suggested that these sites contain significant homoplasy due to multiple hits. Despite the lack of morphological differentiation, the COI portion examined shows remarkable levels of genetic divergence between the putative species and their closest relatives. Phylogenetic analysis suggests that one of the putative new species is related to O. villosa, whereas the other is included in a clade with O. cincta and O. ranzii. The species O. chiantica appears to be related to O. villosa, agreeing with previous allozyme data.

Animals↗
PubMed2000

Relationships of Nematodirus species and Nematodirus battus isolates (Nematoda: Trichostrongyloidea) based on nuclear ribosomal DNA sequences.

Nuclear ribosomal sequence data from the internal transcribed spacers (ITS-1 and ITS-2), 5.8S subunit, and regions of the 18S and 28S genes were used to investigate sequence diversity among geographic samples of Nematodirus battus, and to infer phylogenetic relationships among Nematodirus species. Phylogenetic analysis of these data yielded strong support for relationships among species, depicting Nematodirus helvetianus and Nematodirus spathiger as sister-taxa and a clade of these 2 species and Nematodirus filicollis. This tree is consistent with caprine bovids as ancestral hosts, with a subsequent host shift to Bovinae in N. helvetianus. Eleven of 14 N. battus sequences were unique, with 19 variable sites among sequences representing 5 geographic samples. The lowest number of variable nucleotide sites was observed in samples representing apparently recent introductions to the United States and Canada, which is consistent with a population bottleneck concomitant with translocation. Comparison of directly sequenced polymerase chain reaction products and clones revealed evidence for intraindividual variation at some of the sequence sites, and this pattern of variation and that within geographic samples indicates incomplete rDNA repeat homogenization within species. This pattern of variation is not conducive for inferring phylogenetic relationships among sequences representing N. battus or addressing the putative history of introduction.

Animals↗
PubMed2002

The pattern of amino acid replacements in alpha/beta-barrels.

The determinants of site-to-site variability in the rate of amino acid replacement in alpha/beta-barrel enzyme structures are investigated. Of 125 available alpha/beta-barrel structures, only 25 meet a variety of phylogenetic and statistical criteria necessary to ensure sufficient data for reliable analysis. These 25 enzyme structures (from a wide variety of taxa with diverse lifestyles in diverse habitats) differ greatly in size, number, and topology of domains in addition to the alpha/beta-barrel, quaternary structure, metabolic role, reaction catalyzed, presence of prosthetic groups, regulatory mechanisms, use of cofactors, and catalytic mechanisms. Yet, with the exception of ribulose-1,5-bisphosphate carboxylase, all structures have similar frequency distributions of amino acid replacement rates. Hence, site-specific variability in rates of evolution is largely independent of differences in biology, biochemistry, and molecular structure. A correlation between site-specific rate variation and (1) distance from the active site, (2) solvent accessibility, and (3) treating glycines in unusual main-chain conformations as a separate class, explains approximately half the causal variation. Secondary structure exerts little influence on the pattern and distribution of replacements. Additional domains and subunits, side-chain hydrogen bonds, unusual side-chain rotamers, nonplanar peptide bonds, strained main-chain conformations, and buried hydrophilic-charged residues contribute little to variability among sites because they are rare. Nonlinear models do not improve the fits. In several enzymes, deviations from the typical pattern of replacements suggest the possible action of natural selection. A statistical analysis shows that, in all cases, much of the remaining unexplained variation is not attributable to chance and that other, as yet unidentified, causal relations must exist.

Amino Acid Sequence↗
PubMed2004

Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set.

The Scientific Working Group on DNA Analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, the East Asian haplogroup patterns in the SWGDAM data sets were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Asians (n = 753; with a breakdown of individuals from China n = 356, Korea n = 182, Japan n = 163, and Thailand n = 52). We focus on the patterns observed in the SWGDAM Chinese data set and refer to interesting differences in the smaller subgroup data sets for the other East Asian populations (Japanese, Korean, and Thai). A total of 218 SNPs were observed in the data set, including 37 observed positions not previously reported. In the largest of the East Asian SWGDAM data sets (Chinese), these SNPs ranged from having 1 to 29 changes in the phylogenetic tree, with site 16519 being the most variable. On average there were 4.5 changes for a character on the tree. The most variable sites (with 14 or more changes each listed from fastest to slowest) observed were 16519 (L = 29), 16311 (L = 27), 152 (L = 24), 146 (L = 21), 16172 (L = 17), 16189 (L = 17), 195 (L = 16), 16362 (L = 15), 16093 (L = 14), 16129 (L = 14) and 150 (L = 14). These rapidly changing sites are consistent with other published analyses. Only 28 SNPs are needed to identify all clusters containing 1% (n = 7) or more individuals in the East Asian data set. All 36 haplogroups previously observed in East Asian populations were also seen in the SWGDAM data sets and include: A, B, B4, B4a, B4b, B5a, B5b, C, D, D4, D4a, D4b, D5, D5a, F, F1, F1a, F1b, F1c, F2a, G2, G2a, M, M7a1, M7b, M7b1, M7b2, M7c, M8a, M9, M10, N9a, R, R9a, Y, and Z. Haplogroups A, B4a, D4, and F1a were the most commonly observed clusters in the Chinese data set (the largest of the data sets) with each of these occurring in more than 6% of the samples in the data set. The next most common haplogroups in the Chinese data set include the clusters C, M7b1, and N9a with each observed at frequencies greater than or equal to 4%. European Caucasian, and African haplogroups were rarely observed within the East Asian data sets. The various analyses revealed that the data set was similar to published East Asian data sets such as those from Han Chinese.

Asian People↗
PubMed2004

Fluorescence of leachates from three contrasting landfills.

Landfill leachates are composed of a complex mixture of degradation products including dissolved organic matter, which includes a wide range of potentially fluorescent organic molecules and compounds. Here we investigate the excitation-emission matrix fluorescence of landfill leachates from three contrasting landfill sites. Landfill fluorescence properties are all characterized by intense fluorescence at lambda(ex) =220-230nm, and lambda(em) =340-370nm which we suggest derives from fluorescent components of the Xenobiotic Organic Matter fraction such as naphthalene, as well as at lambda(ex) =320-360nm, and lambda(em) =400-470nm from a higher molecular weight fulvic-like fraction. Landfill leachates are characterized by intense fluorescence, with approximately 10(2) intensity units of fluorescence at lambda(ex)=220-230nm, and lambda(em)=340-370nmmg(-1) of total organic carbon, demonstrating leachate detection limits of <0.1mgl(-1) total organic carbon. We demonstrate that for all landfill sites, leachate fluorescence intensity has a strong correlation with ground water quality determinants ammonia, total organic carbon and biochemical oxygen demand. We investigate both within-site and between-site leachate fluorescence properties, and demonstrate that although there is significant within-site variability, leachates from all 3 sites can be statistically discriminated using just fluorescence properties (65% success rate) or with a combination of fluorescence and basic geochemical parameters (85%). Our findings suggest that fluorescence can be used as a rapid and sensitive tracer of leachate contamination of ground water, as well as help discriminate, together with geochemical determinants, leachates from different landfill sources.

Ammonia↗
PubMed1998

Asymmetrical directional mutation pressure in the mitochondrial genome of mammals.

The base composition of 25 complete mammalian mitochondrial (mt) genomes has been analyzed taking into account all three codon positions (P1230 and fourfold degenerate sites (P4FD) of H-strand genes. In the nontranscribed L strand, G is the less represented base and A is the most represented one in all cases, while C and T differ among species. H-strand protein-coding genes show an asymmetric distribution of the four bases between the two strands. The asymmetry indexes AT and GC skews on P4FD are much higher than those on P123, suggesting the existence of asymmetrical directional mutation pressure. Relationships between the compositional features and transcription of replication processes have been investigated in order to find a possible mechanism that could explain the origin of this asymmetry. AT and GC skews, the base composition in fourfold degenerate sites, and the number of variable sites for each gene are significantly correlated with the duration of single-stranded state of the H-stranded genes during replication. We tested different replication-related hypotheses, such as the existence of biased dNTP pools, gamma DNA polymerase mispairing, and the asymmetric replication itself. Most of them failed to explain the observed results, hydrolytic deaminations being the only one in agreement with our data. Thus, we hypothesize that one of the crucial processes for the origin of asymmetric and biased base composition of mammalian mitochondrial genomes is the spontaneous deamination of C and A in the H strand during replication.

Animals↗
PubMed1998

The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequence.

MOTIVATION: A modified Sherman statistic can be used to test whether the differences between two aligned sequences are distributed at random along the sequences, or whether they are clustered, which suggests anomalies of evolution such as partial gene recombination or functional constraints. The presence of evenly spaced constant sites (such as constancy at the second codon position in genes coding for proteins) lowers the statistic and makes the significance less than it should be. RESULTS: The magnitude of the constant-site effect is shown by simulation to depend mainly on the proportion of differences between two sequences and on the number of constant sites that are added after each variable site. This latter number can be estimated from the variance of sites in a sequence matrix at the first, second and third codon positions, to obtain a ratio that corrects the statistic. When expressed as standard errors, the uncorrected results are too low (typically half to one unit when almost all the variation is at the third codon position). Correction raises the standard errors to levels close to expectation. If the data show no marked ternary periodicity, the correction is very small. The method is illustrated with biological data that show close to random behaviour, and with data that exhibit strong clustering. AVAILABILITY: The software is available from the author and has also been placed on the EMBL file server (Software@embl-ebi.ac.uk). CONTACT: phas1@le.ac.uk

Algorithms↗
PubMed1995

Localisation and characteristics of natriuretic peptide receptors in the gills of the Atlantic hagfish Myxine glutinosa (Agnatha).

Specific binding of iodinated natriuretic peptides 125I-ANP and 125I-CNP was examined in the gill of the Atlantic hagfish Myxine glutinosa by tissue section autoradiography, saturation and competition analysis of binding to membrane preparations, affinity cross-linking, followed by SDS-PAGE and guanylate cyclase assays. Autoradiographs showed specific, saturable binding on the respiratory lamellar epithelium. In vitro analysis of the binding sites demonstrated that 125I-ANP bound to two receptor sites with the same affinity (Kd = 15.4 +/- 1.6 pmol l-1; Bmax = 45.9 +/- 3.0 fmol mg-1 protein). 125I-CNP bound to high- and low-affinity receptor sites; variables for the high-affinity site (Kd = 12.9 +/- 4.7 pmol l-1; Bmax = 23.4 +/- 6.5 fmol mg-1 protein) did not differ from those for the 125I-ANP sites. The low-affinity site had an apparent Kd and Bmax of 380 +/- 80 pmol l-1 and 120 +/- 21 fmol mg-1 protein, respectively. All receptors had an apparent molecular mass of approximately 150 kDa, with no indication of a mammalian type NPR-C at a lower apparent molecular mass. 1 nmol l-1 unlabelled rANP and 20 and 30 nmol l-1 unlabelled pCNP and C-ANF, respectively, competed for 50% of 125I-ANP sites. 0.1 nmol l-1 rANP and pCNP and 8 nmol l-1 C-ANF competitively inhibited 50% of 125I-CNP binding. Both rANP and pCNP stimulated cyclic GMP production, although rANP was a more potent stimulator than was pCNP. C-ANF did not stimulate cyclic GMP production. These data suggest the existence of an ANP guanylate-cyclase-linked receptor similar to the mammalian NPR-A and an ANP/CNP receptor that may be similar to, although not structurally homologous with, the mammalian NPR-C clearance receptor.

Animals↗