Evolutionary analyses of the human genome

The completion of the human genome will greatly accelerate the development of a new branch of science--evolutionary genomics. We can now directly address important questions about the evolutionary history of human genes and their regulatory sequences. Computational analyses of the human genome will reveal the number of genes and repetitive elements, the extent of gene duplication and compositional heterogeneity in the human genome, and the extent of domain shuffling and domain sharing among proteins. Here we present some first glimpses of these features.

Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1

Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 61 humans (20 Africans, 20 Asians, and 21 Europeans) and for 1 chimpanzee, 1 gorilla, and 1 orangutan. We found 52 polymorphic sites among the 122 human sequences and 382 variant sites among the human, chimpanzee, gorilla, and orangutan sequences. For the introns sequenced (8,991 bp), the nucleotide diversity (pi) was 0.058% among all sequences, 0.076% among the African sequences, 0.047% among the Asian sequences, and 0.045% among the European sequences. A compilation of data revealed that autosomal regions have, on average, the highest pi value (0.091%), X-linked regions have a somewhat lower pi value (0.079%), and Y-linked regions have a very low pi value (0.008%). The lower polymorphism in the present region may be due to a lower mutation rate and/or selection in the gene containing these introns or in genes linked to this region. The present region and two other 10-kb noncoding regions all show a strong excess of low-frequency variants, indicating a relatively recent population expansion. This region has a low mutation rate, which was estimated to be 0.74 x 10 per nucleotide per year. An average estimate of approximately 12,600 for the long-term effective population size was obtained using various methods; the estimate was not far from the commonly used value of 10,000. Fu and Li's tests rejected the assumption of an equilibrium neutral Wright-Fisher population, largely owing to the high proportion of low-frequency variants. The age of the most recent common ancestor of the sequences in our sample was estimated to be more than 1 Myr. Allowing for some unrealistic assumptions in the model, this estimate would still suggest an age of more than 500,000 years, providing further evidence for a genetic history of humans much more ancient than the emergence of modern humans. The fact that many unique variants exist in Europe and Asia also suggests a fairly long genetic history outside of Africa and argues against a complete replacement of all indigenous populations in Europe and Asia by a small Africa stock. Moreover, the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck. We suggest that both the "Out of Africa" and the multiregional models are too simple to explain the evolution of modern humans.

Bushbaby growth hormone is much more similar to nonprimate growth hormones than to rhesus monkey and human growth hormones

Unlike other mammals, Old World primates have five growth hormone-like genes that are highly divergent at the amino acid level from the single growth hormone genes found in nonprimates. Additionally, there is a change in the interaction of growth hormone with its receptor in humans such that human growth hormone functions in nonprimates, whereas nonprimate growth hormone is ineffective in humans. A Southern blotting analysis of the genome of a prosimian, Galago senegalensis, revealed a single growth hormone locus. This single gene was PCR-amplified from genomic DNA and sequenced. It has a rate of nonsynonymous nucleotide substitution less than one fourth that of the human growth hormone gene, while the rates of synonymous substitution in the two species are less different. Human and rhesus monkey growth hormones exhibit variation at a number of amino acid residues that can affect receptor binding. The galago growth hormone is conservative at each of these sites, indicating that this growth hormone is functionally like nonprimate growth hormones. These observations indicate that the amplification and rapid divergence of primate growth hormones occurred after the separation of the higher primate lineage from the galago lineage.

Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence

The densities of repetitive elements in the human genome were calculated in each GC content class using non-overlapping windows of 50kb. The density of Alu is two to three times higher in GC-rich regions than in AT-rich regions, while the opposite is true for LINE1. In contrast, LINE2 and other elements, such as DNA transposons, are more uniformly distributed in the genome. The number of Alus in the human genome was estimated to be 1.4 million, higher than previous estimates. About 40% of the autosomes and approximately 51% of the X and Y chromosomes are occupied by repetitive elements. In total, the human genome is estimated to contain more than 4 million repetitive elements. The GC contents (%) of repetitive elements and their flanking regions were also calculated. The GC contents of almost all kinds of repeats are positively correlated with the window GC contents, suggesting that a repetitive sequence is subject to the same mutation pressure as its surrounding regions, so it tends to have the same GC content as its surrounding regions. This observation supports the regional mutation hypothesis. The only two exceptions are AluYa and AluYb8, the two youngest Alu subfamilies. The GC content of AluYb8 is negatively correlated with that of its surrounding regions, while AluYa shows no correlation, suggesting different insertion patterns for these two young Alu subfamilies. This suggestion was supported by the fact that the average genetic distance between members of AluYb8 in each GC window class is positively correlated with the GC content of the window, but no correlation was found for AluYa. AluYa is more frequent in Y chromosome than in other chromosomes; the same is true for LTR retroviruses. This pattern might be correlated with the evolutionary history of Y chromosome.

Assessment of compositional heterogeneity within and between eukaryotic genomes

Using large amounts of long genomic sequences, we studied the compositional patterns of eukaryotic genomes. We developed a simple measure, the compositional heterogeneity (or variability) index, to compare the differences in compositional heterogeneity between long genomic sequences. The index measures the average difference in GC content between two adjacent windows normalized by the standard error expected under the assumption of random distribution of nucleotides in a window. We report the following findings: (1) The extent of the compositional heterogeneity in a genomic sequence strongly correlates with its GC content in all multicellular eukaryotes studied regardless of genome size. (2) The human genome appears to be highly compositionally heterogeneous both within and between individual chromosomes; the heterogeneity goes much beyond the predictions of the isochore model. (3) All genomes of multicellular eukaryotes examined in this study are compositionally heterogeneous, although they also contain compositionally uniform segments, or isochores. (4) The true uniqueness of the human (or mammalian) genome is the presence of very high GC regions, which exhibit unusually high compositional heterogeneity and contain few long homogeneous segments (isochores). In general, GC-poor isochores tend to be longer than GC-rich ones. These findings indicate that the genomes of multicellular organisms are much more heterogeneous in nucleotide composition than depicted by the isochore model and so lead to a looser definition of isochores.

Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22

Human DNA sequence variation data are useful for studying the origin, evolution, and demographic history of modern humans and the mechanisms of maintenance of genetic variability in human populations, and for detecting linkage association of disease. Here, we report worldwide variation data from a approximately 10-kilobase noncoding autosomal region. We identified 75 variant sites in 64 humans (128 sequences) and 463 variant sites among the human, chimpanzee, and orangutan sequences. Statistical tests suggested that the region is selectively neutral. The average nucleotide diversity (pi) across the region was 0.088% among all of the human sequences obtained, 0.085% among African sequences, and 0.082% among non-African sequences, supporting the view of a low nucleotide diversity ( approximately 0.1%) in humans. The comparable pi value in non-Africans to that in Africans indicates no severe bottleneck during the evolution of modern non-Africans; however, the possibility of a mild bottleneck cannot be excluded because non-Africans showed considerably fewer variants than Africans. The present and two previous large data sets all show a strong excess of low frequency variants in comparison to that expected from an equilibrium population, indicating a relatively recent population expansion. The mutation rate was estimated to be 1.15 x 10(-9) per nucleotide per year. Estimates of the long-term effective population size N(e) by various statistical methods were similar to those in other studies. The age of the most recent common ancestor was estimated to be approximately 1.29 million years ago among all of the sequences obtained and approximately 634,000 years ago among the non-African sequences, providing the first evidence from a noncoding autosomal region for ancient human histories, even among non-Africans.

NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods

In the reconstruction of a large phylogenetic tree, the most difficult part is usually the problem of how to explore the topology space to find the optimal topology. We have developed a "divide-and-conquer" heuristic algorithm in which an initial neighbor-joining (NJ) tree is divided into subtrees at internal branches having bootstrap values higher than a threshold. The topology search is then conducted by using the maximum-likelihood method to reevaluate all branches with a bootstrap value lower than the threshold while keeping the other branches intact. Extensive simulation showed that our simple method, the neighbor-joining maximum-likelihood (NJML) method, is highly efficient in improving NJ trees. Furthermore, the performance of the NJML method is nearly equal to or better than existing time-consuming heuristic maximum-likelihood methods. Our method is suitable for reconstructing relatively large molecular phylogenetic trees (number of taxa >/= 16).

Gene admixture in the silk road region of China: evidence from mtDNA and melanocortin 1 receptor polymorphism

Mitochondrial DNA control region segment I sequences and melanocortin 1 receptor (MC1R) gene polymorphism were examined in ethnic populations in the silk road region of China. Both the frequencies of the MC1R variants and the results of mtDNA data in this region presented intermediate values between those of Europe and East and Southeast Asia, which suggested extensive gene admixture in this area and was in general agreement with previous studies. Phylogenetic analysis of the ethnic populations in the Silk Road region that based on mtDNA data didn't show expected cluster pattern according to their ethnogenesis. We suspect that a high migration rate in female among these closely related populations and other three demographic events might account for it.

FTIR fiber optics and FT-Raman spectroscopic studies for the diagnosis of cancer

The authors' preliminary investigation has shown that FTIR spectroscopy in conjunction with fiber optics can reflect differences between normal and malignant tissues. Further studies are being conducted to determine the applicability of the technique to cancer diagnosis.

A rapid heuristic algorithm for finding minimum evolution trees

The minimum sum of branch lengths (S), or the minimum evolution (ME) principle, has been shown to be a good optimization criterion in phylogenetic inference. Unfortunately, the number of topologies to be analyzed is computationally prohibitive when a large number of taxa are involved. Therefore, simplified, heuristic methods, such as the neighbor-joining (NJ) method, are usually employed instead. The NJ method analyzes only a small number of trees (compared with the size of the entire search space); so, the tree obtained may not be the ME tree (for which the S value is minimum over the entire search space). Different compromises between very restrictive and exhaustive search spaces have been proposed recently. In particular, the "stepwise algorithm" (SA) utilizes what is known in computer science as the "beam search," whereas the NJ method employs a "greedy search." SA is virtually guaranteed to find the ME trees while being much faster than exhaustive search algorithms. In this study we propose an even faster method for finding the ME tree. The new algorithm adjusts its search exhaustiveness (from greedy to complete) according to the statistical reliability of the tree node being reconstructed. It is also virtually guaranteed to find the ME tree. The performances and computational efficiencies of ME, SA, NJ, and our new method were compared in extensive simulation studies. The new algorithm was found to perform practically as well as the SA (and, therefore, ME) methods and slightly better than the NJ method. For searching for the globally optimal ME tree, the new algorithm is significantly faster than existing ones, thus making it relatively practical for obtaining all trees with an S value equal to or smaller than that of the NJ tree, even when a large number of taxa is involved.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e. , represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau. On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister taxa of one steppe dweller and one shrub dweller is very low. These findings support the hypothesis that pikas have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution.

Size-induced transition from magnetic ordering to kondo behavior in (Ce,Al) compounds

Magnetic ordering and Kondo behavior coexist in three (Ce,Al)-based compounds: CeAl2, Ce3Al, and Ce3Al11. A common feature apparently independent of crystal structures also prevails in terms of the size-induced transition between these two magnetic phenomena. As the particle size is reduced to nanoscale, the specific heat anomaly associated with the magnetic ordering diminishes. Although the Kondo temperature also decreases, the entropy associated with Kondo anomaly exhibits a large increase. This results in an enhancement of the Kondo behavior and an increased coefficient gamma of the linear term in specific heat. For example, in 80 A CeAl2 the extrapolated r(0) reaches 9000 mJ mol Ce-1 K-2.

Cellular regulation of cytosolic group IV phospholipase A2 by phosphatidylinositol bisphosphate levels

Cytosolic group IV phospholipase A2 (cPLA2) is a ubiquitously expressed enzyme with key roles in intracellular signaling. The current paradigm for activation of cPLA2 by stimuli proposes that both an increase in intracellular calcium and mitogen-activated protein kinase-mediated phosphorylation occur together to fully activate the enzyme. Calcium is currently thought to be needed for translocation of the cPLA2 to the membrane via a C2 domain, whereas the role of cPLA2 phosphorylation is less clearly defined. Herein, we report that brief exposure of P388D1 macrophages to UV radiation results in a rapid, cPLA2-mediated arachidonic acid mobilization, without increases in intracellular calcium. Thus, increased Ca2+ availability is a dispensable signal for cPLA2 activation, which suggests the existence of alternative mechanisms for the enzyme to efficiently interact with membranes. Our previous in vitro data suggested the importance of phosphatidylinositol 4,5-bisphosphate (PtdInsP2) in the association of cPLA2 to model membranes and hence in the regulation of cPLA2 activity. Experiments described herein show that PtdInsP2 also serves a similar role in vivo. Moreover, inhibition of PtdInsP2 formation during activation conditions leads to inhibition of the cPLA2-mediated arachidonic acid mobilization. These results suggest that cellular PtdInsP2 levels are involved in the regulation of group IV cPLA2 activation.

Molecular evolution of growth hormone and receptor in the guinea-pig, a mammal unresponsive to growth hormone

Growth in the guinea-pig is completely unresponsive to endogenous or exogenous growth hormone, despite the fact that the guinea-pig produces normal to high levels of growth hormone and receptor. In primates and artiodactyls, growth hormone exhibits accelerated rates of evolution that appear to be correlated with changes in function. Surprisingly, both guinea-pig growth hormone and receptor exhibit slow rates of evolution similar to those seen in other mammals, implying that both proteins are as functionally conserved in the guinea-pig as in other mammals or that any loss or relaxation of functional constraint was very recent. However, the guinea-pig growth hormone and receptor both exhibit a single amino acid replacement at a site known to have functional significance. Nevertheless, it is unclear whether the aberrant nature of the guinea-pig growth hormone-growth hormone receptor axis is due to these replacements or whether it is due to a defect in post-receptor signalling.

Selective constraints, amino acid composition, and the rate of protein evolution

What are the major forces governing protein evolution? A common view is that proteins with strong structural and functional requirements evolve more slowly than proteins with weak constraints, because a stringent negative selection pressure limits the number of substitutions. In contrast, Graur claimed that the substitution rate of a protein is mainly determined by its amino acid composition and the changeabilities of amino acids. In this paper, however, we found that the relative changeabilities of amino acids in mammalian proteins are different for transmembranal and nontransmembranal segments, which have very distinct structural requirements. This indicates that the changeability of a given residue is influenced by the structural and functional context. We also reexamined the relationship between substitution rate and amino acid composition. Indeed, the two kinds of segments exhibit contrasting amino acid compositions: transmembranal regions are made up mainly of hydrophobic residues (a total frequency of approximately 60%) and are very poor in polar amino acids (<5%), whereas nontransmembranal segments have frequencies of 30% and 22%, respectively. Interestingly, we found that within a given integral membrane protein, nontransmembranal segments accumulate, on average, twice as many substitutions as transmembranal regions. However, regression analyses showed that the variability in amino acid frequencies among proteins cannot explain more than 30% of the variability in substitution rate for the transmembranal and nontransmembranal data sets. Furthermore, transmembranal and nontransmembranal segments evolving at the same rate in different proteins have different compositions, and the compositions of slowly evolving and rapidly evolving segments of the same type are similar. From these observations, we conclude that the rate of protein evolution is only weakly affected by amino acid composition but is mostly determined by the strength of functional requirements or selective constraints.

Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S-25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis, Cardaminopsis, Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.

Superchirped moiré grating based on an acousto-optic superlattice with a chirped fiber Bragg grating

A superchirped moiré grating has multiple superimposed chirped Bragg gratings. We show that a superchirped moiré grating can be formed in an acousto-optic superlattice with a chirped fiber Bragg grating. There are multiple transmission peaks related to Fabry-Perot resonance in the transmission spectrum. The peak spacing is varied by the acoustic frequency. The proposed devices can be used as tunable multiple-passband transmission filters and switches.

Effects of berbamine on intracellular calcium concentration in cultured HeLa cells

AIM

To study the involvement of Ca2+ signaling and the effects of berbamine (Ber) on intracellular calcium concentration ([Ca2+]i) elevated in cultured HeLa cells.

METHODS

[Ca2+]i was measured by confocal microscopy in single HeLa cell loaded with Fluo 3-AM. The change of [Ca2+]i was represented by fluorescent intensity (FI).

RESULTS

(1) In the presence of extracellular Ca2+ 1.3 mmol.L-1, the resting level of FI was 186 +/- 44, n = 49 cells from all control experiments, and KCl, NE, caffeine, and calcimycin (Cal) all induced [Ca2+]i elevations in cultured HeLa cells. (2) The resting level of FI was not affected by pretreatment with Ber. The FI increased by KCl 60 mmol.L-1, NE 100 micromol.L-1, and Cal 30 micromol.L-1 were attenuated (P < 0.05 or P < 0.01), the slope and the time to peak of FI increase were decreased and prolonged. (3) In the absence of extracellular Ca2+, caffeine 80 mmol.L-1-induced [Ca2+]i mobilization was not inhibited by Ber 100 micromol.L-1 pretreatment. (4) These effects of Ber were similar to those of verapamil (Ver) 10 mumol.L-1.

CONCLUSION

Although it was derived from cervical cancer, the HeLa cells which were belong to the nonexcitable cell possessed the similar biological properties with excitable cells, and Ca2+ also played a crucial role in signal transduction processes.

High prevalence of human papillomavirus type 58 in Chinese women with cervical cancer and precancerous lesions

The prevalence of human papillomavirus (HPV) among 332 Hong Kong Chinese women with abnormal Papanicolaou smears were determined by polymerase chain reaction and restriction fragment length polymorphism analysis. The overall HPV positive rate was 44.3% with 18.6% (16/86) for normal/inflamed cervices, 36.4% (32/88) for condyloma, 64.7% (33/51) for cervical intraepithelial neoplasia grade 1 (CIN 1), 37.9% (11/29) for CIN 2, 68.3 (41/60) for CIN 3, and 77.8% (14/18) for carcinoma. Double HPV infection was detected in 17 of the 147 positive samples, with a significantly higher proportion in patients with normal or inflamed cervices than those with CIN or carcinoma (31.3% vs 10.5%, P =.029). The six most commonly identified genotypes were HPV 16 (33.3%), HPV 58 (23.8%), HPV 11, 18, 31 (8.8% each), and HPV 33 (6.8%). The worldwide uncommon genotype HPV 58 was found to be the second most common genotype detected in patients with cervical carcinoma (6 of 18 patients). HPV 58 infection showed a significant association with CIN/carcinoma (odds ratio [OR] = 3.98; 95% confidence interval [CI] = 1.22-14.35) and a significant trend of increase in prevalence with increasing severity of cervical lesion (chi(2) = 5.84; P =.016). Among Hong Kong Chinese women with abnormal cervical cytology, the detection of HPV 58 carried a positive predictive value of 68.6% for a cervical lesion of CIN 1 or higher severity. The high prevalence of HPV 58 among Chinese women, particularly in patients with carcinoma, has an implication on the design of HPV detection methods and the development of vaccines.

Coalescing into the 21st century: An overview and prospects of coalescent theory

Coalescent theory represents the most significant progress in theoretical population genetics in the past two decades of this century. It is now widely recognized as a cornerstone for rigorous statistical analyses of molecular data from populations. In the future, challenges from the rapidly expanding body of molecular data will continue to inject fresh blood into the development of coalescent theory. As the 21st century looms, we review recent progress in coalescent theory and discuss some prospects for future developments, particularly with regard to human population genetics.

Effects of berbamine on ATP-induced [Ca2+]i mobilization in cultured vascular smooth muscle cells and cardiomyocytes

AIM

To study the effects of berbamine (Ber) on [Ca2+]i homeostasis induced by adenosine triphosphate (ATP) in vascular smooth muscle cells (VSMC) of rabbits and cardiomyocytes of rats.

METHODS

Both cell types were cultured and loaded with Fura 3-AM. [Ca2+]i was measured by fluorescent intensity (FI) in each cell with confocal microscopy.

RESULTS

(1) ATP 30 mumol.L-1 elevated [Ca2+]i in VSMC and cardiomyocytes, FI values reached 660 +/- 258 and 1058 +/- 252 from 250 +/- 84 and 218 +/- 76 at 19 s +/- 5 s and 11.8 s +/- 2.4 s, but FI in nucleus was not changed in VSMC. (2) Ber 30 mumol.L-1 did not affect the resting FI in both cell types, but prolonged the time to peak (P < 0.01) and reduced the FI elevated by ATP (P < 0.01), but not completely inhibited even at 100 mumol.L-1. (3) In D-Hanks' solution or in the presence of egtazic acid (EGTA) 3 mmol.L-1, the inhibitory effect of Ber was not seen (P > 0.05). (4) All effects of Ber on ATP-induced [Ca2+]i mobilization were similar to those of Ver 10 mumol.L-1.

CONCLUSION

In VSMC and cardiomyocytes, ATP-induced CA2+ influx was inhibited by Ber and Ver, while the Ca2+ release was not.

Performance of the relative-rate test under nonstationary models of nucleotide substitution

Relative-rate tests have previously been developed to compare the substitution rates of two sequences or two groups of sequences. These tests usually assume that the process of nucleotide substitution is stationary and the same for all lineages, i.e., uniform. In this study, we conducted simulations to assess the performance of the relative-rate tests when the molecular-clock (MC) hypothesis is true (i.e., there is no rate difference between lineages), but the stationarity and uniformity assumptions are violated. Kimura's and bias-corrected LogDet distances were used. We found that the computation of the variances and covariances of LogDet distances had to be modified, because the constraint that the sum of the frequencies of the 16 nucleotide pair types is equal to 1 must be imposed. Comparison of the rates of two single sequences (Wu and Li's test) or two groups of sequences (Li and Bousquet's test) gave similar results. When the sequences are long (> or = 500 nt), the test based on LogDet distances and their appropriate variances and covariances is appropriate even when the substitution process is not stationary and/or not uniform. That is, at the 5% significance level, the test rejects the MC hypothesis in about 5% of the simulation replicates. In contrast, if the sequences are short (< or = 200 bases) and highly divergent, the LogDet test is very conservative due to overestimation of the variances of the distances. When the uniformity assumption is violated, the relative-rate test based on Kimura's distances can be severely misleading because of differences in base composition between sequences. However, if the uniformity assumption held and so the base frequencies remained similar among sequences, the rate of rejection turned out to be close to 5%, especially with short sequences. Under such conditions, the test using Kimura's distances performs better than the LogDet test. The reason seems to be that these distances are less affected by a reduction in the number of sites than the LogDet distances because they depend on only two parameters.

Effects of MK-447 on platelet shape change, aggregation, and ATP release by collagen, ADP, and stable analogue of thromboxane A2 in rabbit platelets

AIM

To investigate the effects of MK-447 on platelet shape change, aggregation, and ATP release by collagen (Col), ADP, and stable analogue of thromboxane A2 (STA2) in rabbits.

METHODS

Platelet shape change and aggregation were quantified in light transmission by turbidimetric method and release reaction was assessed by the amount of ATP in platelet-rich plasma (PRP).

RESULTS

(1) MK-447 100-700 mumol.L-1 caused only the shape change, which was not inhibited by indometacin 3 mumol.L-1. Platelet shape changes by Col, ADP, and STA2 were reduced (P < 0.01) after the addition of MK-447. The lag phase was prolonged (P < 0.01) in Col and shortened (P < 0.01) in ADP. (2) MK-447 reduced the aggregation by Col 5 mg.L-1 (P < 0.01), and enhanced that by ADP 0.3-10 mumol.L-1 and STA2 0.1-3 mumol.L-1 (P < 0.01). (3) The release reaction by STA2 1-3 mumol.L-1 was also increased (P < 0.01). The effects of MK-447 on STA2 were not inhibited by S-145.

CONCLUSION

MK-447 induced the platelet shape change, and showed the dual effects, inhibition or enhancement, on the actions by different aggregating agents.