Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube 1 genes and pseudogenes

Using sequence data from the last introns of ZFX and ZFY genes, we previously estimated the male-to-female ratio (alpha) of mutation rate to be close to 6 in higher primates and 1.8 in rodents. As the mutation rate may vary among different regions of the mammalian genome, it is interesting to see whether sequence data from other regions will give similar estimates. In this study, we have determined the partial genomic sequences of the ubiquitin-activating enzyme E1 genes (Ube 1x and Ube 1y for the X-linked and Y-linked homologues, respectively) of mice and rats and two mouse Ube 1y pseudogenes. From the intron sequences of the Ube 1 genes, we calculated the divergence of the Y-linked genes (Y = 0.161) and that of the X-linked genes (X = 0.107) between mouse and rat, and found the Y/X ratio to be 1.50. This ratio led to an estimate of alpha = 2.0 with a 95% confidence interval of (1.0, 3.9). Similar estimates of alpha were obtained if mouse Ube 1y pseudogenes were used instead of the mouse Ube 1y functional gene. These estimates are consistent with our previous estimate for rodents and suggest that the sex ratio of mutation rate in rodents is approximately only one-third of that in higher primates. Our estimate of the divergence time between Ube 1x and Ube 1y supports the view that the two genes separated before the eutherian radiation.

Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes

We have sequenced the entire exon (approximately 1.180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 bp were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans in considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes.

Evolution of base composition in the insulin and insulin-like growth factor genes

The genomes of homeothermic (warm-blooded) vertebrates are mosaic interspersions of homogeneously GC-rich and GC-poor regions (isochores). Evolution of genome compartmentalization and GC-rich isochores is hypothesized to reflect either selective advantages of an elevated GC content or chromosome location and mutational pressure associated with the timing of DNA replication in germ cells. To address the present controversy regarding the origins and maintenance of isochores in homeothermic vertebrates, newly obtained as well as published nucleotide sequences of the insulin and insulin-like growth factor (IGF) genes, members of a well-characterized gene family believed to have evolved by repeated duplication and divergence, were utilized to examine the evolution of base composition in nonconstrained (flanking) and weakly constrained (introns and fourfold degenerate sites) regions. A phylogeny derived from amino acid sequences supports a common evolutionary history for the insulin/IGF family genes. In cold-blooded vertebrates, insulin and the IGFs were similar in base composition. In contrast, insulin and IGF-II demonstrate dramatic increases in GC richness in mammals, but no such trend occurred in IGF-I. Base composition of the coding portions of the insulin and IGF genes across vertebrates correlated (r = 0.90) with that of the introns and flanking regions. The GC content of homologous introns differed dramatically between insulin/IGF-II and IGF-I genes in mammals but was similar to the GC level of noncoding regions in neighboring genes. Our findings suggest that the base composition of introns and flanking regions is determined by chromosomal location and the mutational pressure of the isochore in which the sequences are embedded. An elevated GC content at codon third positions in the insulin and the IGF genes may reflect selective constraints on the usage of synonymous codons.

Mouse very-low-density-lipoprotein receptor (VLDLR) cDNA cloning, tissue-specific expression and evolutionary relationship with the low-density-lipoprotein receptor

The very-low-density-lipoprotein receptor (VLDLR) is a recently described lipoprotein receptor that shows considerable similarity to the low-density-lipoprotein receptor (LDLR). This receptor has been suggested to be important for the metabolism of apoprotein-E-containing triacylglycerol-rich lipoproteins, such as very-low-density-lipoprotein (VLDL), beta-migrating VLDL and intermediate-density lipoprotein. cDNA clones that code for the VLDLR were isolated from a mouse heart cDNA library. The deduced amino acid sequence predicts a mature protein of 846 amino acids preceded by a 27-residue signal peptide. Three mRNA species for the VLDLR with sizes of 3.9, 4.5 and 7.9 kilobases were present in high concentration in heart and muscle, which utilize triacylglycerols as an energy source. VLDLR mRNA is also detected in decreasing amounts in kidney, brain, ovary, testis, lung and adipose tissue. It is essentially absent in liver and small intestine. The amino acid sequence of the VLDLR is highly conserved among rabbit, human and mouse. VLDLR contains five structural domains very similar to those in LDLR, except that the ligand-binding domain in VLDLR has an eightfold repeat instead of a sevenfold repeat in LDLR. Sequence conservation among animal species is much higher for the VLDLR than the LDLR. Sequences of the VLDLR from three vertebrate species and the LDLR from five vertebrate species were aligned and a phylogenetic tree was reconstructed. Although both receptors contain five domains and share amino acid sequence similarity, our computations showed that they diverged before the divergence between mammals and amphibians. In addition, sequence comparison of both receptor sequences suggests that the rabbit is evolutionarily closer to man than to the mouse. These results are consistent with the hypothesis that the VLDLR and the LDLR have evolved from a common ancestral gene to play distinct roles in lipoprotein metabolism and that the metabolic handling of triacylglycerol by the body via the VLDLR is a highly conserved mechanism.

[Effects of sodium diethyldithiocarbamate on ischemia-reperfusion-induced brain injury in Mongolian gerbil]

Brain injury in Mongolian gerbil (Merisones unguiculatus) was induced by occluding bilateral common carotid arteries for 60 min followed by reperfusion for 5 or 30 min. Oxygen free radicals in brain tissue were measured by electron spin resonance (ESR) technique, malondialdehyde (MDA) was measured by fluorescence spectrometry, and superoxide dismutase (SOD) was measured by nitrite kit. Oxygen free radicals and MDA were not significantly increased, but activities of T-SOD and Mn-SOD were decreased after 60 min of cerebral ischemia. The free radicals were increased at 5-min reperfusion, and then reduced to the level of ischemia group after 30-min reperfusion. MDA was increased remarkably after reperfusion of 30 min, whereas the activity of SOD continued to decrease. Sodium diethyldithiocarbamate (DTC), i.v. 5-100 mg.kg-1 15 min before occlusion, decreased the production of MDA and increased the activities of T-SOD and Mn-SOD. The formation of oxygen free radicals was depressed by i.v. DTC 50 mg.kg-1. The result suggested that the protective effects of DTC on ischemia-reperfusion-induced brain injury might be induced by scavenging the oxygen free radicals, increasing the Mn-SOD activity and decreasing the production of MDA.

Intronic gene conversion in the evolution of human X-linked color vision genes

Human red and green visual pigment genes are X-linked duplicate genes. To study their evolutionary history, introns 2 and 4 (1,987 and 1,552 bp, respectively) of human red and green pigment genes were sequenced. Surprisingly, we found that intron 4 sequences of these two genes are identical and that the intron 2 sequences differ by only 0.3%. The low divergences are unexpected because the duplication event producing the two genes is believed to have occurred before the separation of the human and Old World monkey (OWM) lineages. Indeed, the divergences in the two introns are significantly lower than both the synonymous divergence (3.2% +/- 1.1%) and the nonsynonymous divergence (2.0% +/- 0.5%) in the coding sequences (exons 1-6). A comparison of partial sequences of exons 4 and 5 of human and OWM red and green pigment genes supports the hypothesis that the gene duplication occurred before the human-OWM split. In conclusion, the high similarities in the two intron sequences might be due to very recent gene conversion, probably during evolution of the human lineage.

A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores

Based on the biochemical kinetics of DNA replication and mutagenesis, including misincorporation and correction, a model has been developed for studying the relationships among the mutation rate (u), the G+C content of the sequence (f), and the G+C proportion in the nucleotide precursor pool (N). Also a measure for the next-nucleotide effect, called the maximum capacity of the next-nucleotide effect (MC), has been proposed. Under the normal physiological conditions of mammalian germ cells, our results indicate: (1) the equilibrium G+C content in a sequence is approximately equal to the G+C proportion in the nucleotide precursor pool, i.e., f approximately N, which is independent of the next-nucleotide effect; (2) an inverted-V-shaped distribution of mutation rates with respect to G+C contents is predicted, when the next-nucleotide effect is week, i.e., MC approximately 1; (3) the distribution becomes flatter (i.e., inverted-U-shaped) as MC increases, but the peak at 50% GC is still observed when MC < 2; and (4) the peak disappears when MC > 2.8, that is, when the next-nucleotide effect becomes strong. Our results suggest that changes in the relative concentrations of nucleotide precursors can cause variations among genes both in mutation rate and in G+C content and that compositional isochores (DNA segments with a homogeneous G+C content) can arise in a genome due to differences in replication times of DNA segments.

[A benign neuroendocrine tumor of the lung: study on the origin of the so-called sclerosing hemangioma of the lung]

31 cases of the so-called sclerosing hemangiomas of the lung were studied by light microscope, immunohistochemical and electron microscopy. This tumor is benign and has 3 histologic patterns: papillary, hemangioma-like and solid type. Characteristic morphology being uniform round tumor cells, lying within the stroma in different patterns and regarded as the major component of sclerosing hemangioma, expressing neuroendocrine markers which include chromagranin A, neuron-specific enolase, ACTH, growth hormone, calcitonin and gastrin. Only a few tumor cells were positive for epithelial membrane antigen (EMA) and carcinoembryonic antigen (CEA), all the tumor cells were negative for keratin (Polyclonal, Z622) stain. However, in contrast to the round tumor cells, the cells lining papillary projections or cystic spaces, which presented as normal or hyperplastic alveolar cells, stained positive for keratin, EMA and CEA but negative for neuroendocrine markers. Both the surface cells and tumor cells were negative for Factor VIII-related antigen and alpha 1-AT. Therefore, pulmonary sclerosing hemangioma was regarded to be a benign tumor originating from the neuroendocrine cells of the lung and we suggest that it be renamed as benign neuroendocrine tumor of the lung (LBNET). This viewpoint has not been previously reported in the literature.

Weak male-driven molecular evolution in rodents

In humans and rodents the male-to-female ratio of mutation rate (alpha m) has been suggested to be extremely large, so that the process of nucleotide substitution is almost completely male-driven. However, our sequence data from the last intron of the X chromosome-linked (Zfx) and Y chromosome-linked (Zfy) zinc finger protein genes suggest that alpha m is only approximately 2 in rodents with a 95% confidence interval from 1 to 3. Moreover, from published data on oogenesis and spermatogenesis we estimate the male-to-female ratio of the number of germ cell divisions per generation to be approximately 2 in rodents, confirming our estimate of alpha m and suggesting that errors in DNA replication are the primary source of mutation. As the estimated alpha m for rodents is only one-third of our previous estimate of approximately 6 for higher primates, there appear to be generation-time effects--i.e., alpha m decreases with decreasing generation time.

Insulin-like growth factor II intron sequences support the hominoid rate-slowdown hypothesis

Nucleotide sequences were obtained from the approximately 1.7 kb intron 7 of the insulin-like growth factor II gene in human and representatives of both Old World and New World monkeys and analyzed with additional published noncoding regions (both introns and flanking regions) that differ substantially in base composition (GC content). Relative rate tests, utilized to examine differential rates of molecular evolution between humans and Old World monkeys, support the hypothesis that the rate of nucleotide substitution is slower in humans than in Old World monkeys. Comparisons of approximately 4,300 nucleotide positions revealed a significantly higher evolutionary rate in the Old World monkey lineage than in the human lineage for both intron sequences and flanking regions. The data indicate that the molecular clock hypothesis is not applicable to the human and Old World monkey lineages and that the hominoid rate slowdown is a general phenomenon--it is not unique to a particular gene region and is not influenced by regional differences in base composition.

So, what about the molecular clock hypothesis?

Recent studies have provided strong evidence for significant variation in rates of nucleotide substitution among evolutionary lineages. They have also provided evidence for germ-cell division as a major source of mutation (i.e. the generation-time effect hypothesis). Moreover, they have suggested the importance of differences in metabolic rate as a cause of rate variation.

The phylogenetic position of Taxaceae based on 18S rRNA sequences

The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a.cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones.

Primary structure of Beijing duck apolipoprotein A-1

The primary structure of Beijing duck apolipoprotein A-1 was determined by sequencing peptide fragments derived from tryptic and endoproteinase Asp-N digestion of the protein, and alignment with homologous chicken apo A-1. All of the peptide fragments were isolated by high-pressure liquid chromatography (HPLC) with a Vydac C18 column using a trifluoroacetic acid (TFA) buffer system. The N-terminus of the protein was determined to be aspartic acid by directly sequencing 52 residues of the intact protein. The C-terminus was alanine. The protein contains 240 amino acid residues. By analysis of the whole protein and its tryptic peptides, a six amino acid (Arg-Tyr-Phe-Trp-Gln-His) prosegment was determined. No cross-reactivity between duck and human apo A-1 with a goat antiserum against human apo A-1 was found. Sequence analysis of apo A-1 of other species indicates that amino acid substitutions in rat are more extensive than in other mammals. Isoleucine residues in apo A-1 are inversely correlated to the homology of human to other species, except dog.

[Carcinoma of the hilar bile duct: a clinical and pathological study]

From 1986 through 1990, 50 patients suffering from hilar bile duct carcinoma underwent exploration with the resection of the tumor in 31 (62%), and hepatic lobectomy in 16 (51.6%). There was no operative mortality. Resection of the recurrent tumor was successfully performed in 5 cases, among them 4 were still alive upon 1-4 year follow-up. The median survival period was 15 months for the resection group and late deaths were frequently caused by local recurrence. Pathological study based on 27 surgically resected specimens and 5 autopsies classified the tumors into 4 types: (1)papillary adenocarcinoma (6 cases), (2)well differentiated adenocarcinoma (21 cases), (3) poorly differentiated carcinoma (3 cases), and (4) carcinoma simplex (2 cases). The authors discussed the biological behaviour of such tumors, and stressed the need of early diagnosis of hilar bile duct carcinoma at its subclinical stage.

[Morphological and immunohistochemical observations on 30 cases of neuroendocrine carcinoma of the lung]

30 cases of resected pulmonary neuroendocrine carcinoma (NEC) collected from September 1983 to February 1992 were confirmed by microscopy, electron microscopy and immunohistochemical observations. Of the 30 cases, 8 were typical carcinoid (TC), 15 atypical carcinoid (AC), 5 small cell lung carcinoma (SCLC) and 2 cases of giant cell neuroendocrine carcinoma (LCNEC), which have never been reported in the literature. This series of pulmonary NEC exhibited their specific morphology under light microscope. Electron microscopic examination found the common feature of neuroendocrine granules in the cytoplasm of carcinoma cells. Immunohistochemical studies with neuroendocrine cell markers for NEC gave positive results. The morphological features and differential diagnosis of the various NEC under light microscope and electron microscope were compared and are discussed. Complimental devise to the classification of NECs of the lung is suggested.

Maximum likelihood estimation of population parameters

One of the most important parameters in population genetics is theta = 4Ne mu where Ne is the effective population size and mu is the rate of mutation per gene per generation. We study two related problems, using the maximum likelihood method and the theory of coalescence. One problem is the potential improvement of accuracy in estimating the parameter theta over existing methods and the other is the estimation of parameter lambda which is the ratio of two theta's. The minimum variances of estimates of the parameter theta are derived under two idealized situations. These minimum variances serve as the lower bounds of the variances of all possible estimates of theta in practice. We then show that Watterson's estimate of theta based on the number of segregating sites is asymptotically an optimal estimate of theta. However, for a finite sample of sequences, substantial improvement over Watterson's estimate is possible when theta is large. The maximum likelihood estimate of lambda = theta 1/theta 2 is obtained and the properties of the estimate are discussed.

[The clinical cardiac electrophysiologic effects of tetrandrine]

Acute electrophysiologic effects of intravenous tetrandrine were evaluated with programmed electrical stimulation in 20 patients. The results showed that: (1) tetrandrine significantly lengthened SCL and A-H interval (P < 0.001), AVNERP, AVNWCL and SPERP (P < 0.05). It did not affect the SACT, SNRT, P-A, H-V, Q-T intervals and the ERP of atrium, ventricle and accessory pathway significantly. Its electrophysiologic property is similar to verapamil. (2) It prevented induction of SVT in 4 cases, 4 cases of sustained SVT were no longer sustained, the effective rate is 85.7%. The curative effect on AVNRT (100%) is better than that on AVRT (71.4%). (3) No severe side effect was observed. Therefore, tetrandrine is an effective drug for the treatment of SVT.

Potential problems in estimating the male-to-female mutation rate ratio from DNA sequence data

It is commonly believed that the rate of mutation is much higher in males than in females because the number of germ-cell divisions per generation is much larger in males than in females. However, the precise magnitude of the male-to-female mutation rate ratio (alpha m) remains unknown. Recently there have been efforts to estimate alpha m by using DNA sequence data from different species. We have studied the potential problems in such an approach. We found that the rate of synonymous substitution varies about fivefold among X-linked genes, as large as the variation among autosomal genes. This large variation makes the assumption of selective neutrality of synonymous changes dubious, so one should be cautious in using the synonymous rates in X-linked and autosomal genes to estimate alpha m. A similar difficulty was also observed in using nonhomologous intron sequences to estimate alpha m. Contrary to the expectation that X-linked sequences should evolve more slowly than autosomal sequences, the Alu repeat in the last intron of the X-linked zinc finger gene has evolved faster than the four autosomal Alu repeats used in this study. It appears that the best way to estimate alpha m is to use homologous sequences. However, such sequences may be involved in gene conversion events. In fact, we found evidence that the Y-linked and X-linked zinc finger genes have been involved in multiple conversion events during primate evolution. Thus, the possibility of gene conversion should be considered when using homologous sequences to estimate alpha m.

The Cape Mendocino, California, Earthquakes of April 1992: Subduction at the Triple Junction

The 25 April 1992 magnitude 7.1 Cape Mendocino thrust earthquake demonstrated that the North America-Gorda plate boundary is seismogenic and illustrated hazards that could result from much larger earthquakes forecast for the Cascadia region. The shock occurred just north of the Mendocino Triple Junction and caused strong ground motion and moderate damage in the immediate area. Rupture initiated onshore at a depth of 10.5 kilometers and propagated up-dip and seaward. Slip on steep faults in the Gorda plate generated two magnitude 6.6 aftershocks on 26 April. The main shock did not produce surface rupture on land but caused coastal uplift and a tsunami. The emerging picture of seismicity and faulting at the triple junction suggests that the region is likely to continue experiencing significant seismicity.

Male-driven evolution of DNA sequences

It is commonly believed that the mutation rate is much higher in the human male germ line than in the female germ line because the number of germ-cell divisions per generation is much larger in males than in females. But direct estimation of mutation rates is difficult, relying mainly on sex-linked genetic diseases, so the ratio (alpha m) of male to female mutation rates is not clear. It has been noted that if alpha m is very large, then the rate of synonymous substitution in X-linked genes should be only 2/3 of that in autosomal genes, and comparison of human and rodent genes supported this prediction. As the number of X-linked genes used in the study was small and the X-linked and autosomal sequences were non-homologous, and given that the synonymous rate varies among genes, we sequenced the last intron (approximately 1 kb) of the Y-linked and X-linked zinc-finger-protein genes (ZFY and ZFX) in humans, orang-utans, baboons and squirrel monkeys. The ratio Y/X of the substitution rate in the Y-linked intron to that in the X-linked intron is approximately 2.3, which is close to that estimated from synonymous rates in the ZFY and ZFX genes and implies alpha m approximately 6. This estimate of alpha m supports the view that the evolution of DNA sequences in higher primates is male-driven. It is, however, much lower than the previous estimate and therefore raises a number of issues.

Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes

We have sequenced the mitochondrial cytochrome b gene from the guinea pig, the African porcupine, and a South American opossum. A phylogenetic analysis, which includes 22 eutherian and four other vertebrate cytochrome b sequences, indicates that the guinea pig and the porcupine constitute a natural clade (Hystricomorpha) that is not a sister group to the clade of mice and rats (Myomorpha). Therefore, the hypothesis that the Rodentia is paraphyletic receives additional support. The artiodactyls, the perissodactyls, and the cetaceans form a group that is separated from the primates and the rodents. The 26 sequences are used to study the structure/function relationships in cytochrome b, whose function is electron transport. Most of the amino acid residues involved in the two reaction centers are well conserved in evolution. The four histidines that are believed to ligate the two hemes are invariant among the 26 sequences, but their nearby residues are not well conserved in evolution. The eight transmembrane domains represent some of the most divergent regions in the cytochrome b sequence. The rate of nonsynonymous substitution is considerably faster in the human and elephant lineages than in other eutherian lineages; the faster rate might be due to coevolution between cytochrome b and cytochrome c.

Statistical tests of neutrality of mutations

Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occurred in the external branches and internal mutations are mutations that occurred in the internal branches of the genealogy. Under the assumption of selective neutrality, the expected number of external mutations is equal to theta = 4Ne mu, where Ne is the effective population size and mu is the rate of mutation per gene per generation. Interestingly, this expectation is independent of the sample size. The number of external mutations is likely to deviate from its neutral expectation when there is selection while the number of internal mutations is less affected by the presence of selection. Statistical properties of the numbers of external mutations and of internal mutations are studied and their relationships to two commonly used estimates of theta are derived. From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.

Unbiased estimation of the rates of synonymous and nonsynonymous substitution

The current convention in estimating the number of substitutions per synonymous site (KS) and per nonsynonymous site (KA) between two protein-coding genes is to count each twofold degenerate site as one-third synonymous and two-thirds nonsynonymous because one of the three possible changes at such a site is synonymous and the other two are nonsynonymous. This counting rule can considerably overestimate the KS value because transitional mutations tend to occur more often than transversional mutations and because most transitional mutations at twofold degenerate sites are synonymous. A new method that gives unbiased estimates is proposed. An application of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives a KS value very close to the number of substitutions per four-fold degenerate site whereas the old method gives a value 30% higher. Both methods give a KA value close to the number of substitutions per nondegenerate site.

The molecular clock ticks regularly in muroid rodents and hamsters

Extensive DNA sequence data are used to compare the rates of nucleotide substitution in the mouse, rat, and hamster lineages. A relative rate test using hamster sequences as references shows that the rates of synonymous and nonsynonymous substitution in the mouse and rat lineages are nearly equal and a test using human sequences as references shows that the rates in the mouse, rat, and hamster lineages are also nearly equal. Under the assumptions that the guinea pig lineage and the myomorph (mouse, rat, and hamster) lineage diverged 70-100 million years (Myr) ago and that the rate of nucleotide substitution has been constant in all these lineages since their divergence, the date of the mouse-rat split is estimated to be between 20 and 29 Myr ago, which is considerably older than the date (approximately 12 Myr) suggested by available rodent fossils and considerably younger than the date (approximately 35 Myr) suggested by Wilson and colleagues. The murid-hamster split is estimated to be 1.6 times older than the mouse-rat split.

Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock

The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences are studied by using model trees of three taxa with an outgroup and by assuming a constant rate of nucleotide substitution. The maximum-parsimony method of tree reconstruction is used. An analytic formula is derived for estimating the sequence length that is required if P, the probability of obtaining the true tree from the sampled sequences, is to be equal to or higher than a given value. Bootstrap estimation is formulated as a two-step sampling procedure: (1) sampling of sequences from the evolutionary process and (2) resampling of the original sequence sample. The probability that a bootstrap resampling of an original sequence sample will support the true tree is found to depend on the model tree, the sequence length, and the probability that a randomly chosen nucleotide site is an informative site. When a trifurcating tree is used as the model tree, the probability that one of the three bifurcating trees will appear in > or = 95% of the bootstrap replicates is < 5%, even if the number of bootstrap replicates is only 50; therefore, the probability of accepting an erroneous tree as the true tree is < 5% if that tree appears in > or = 95% of the bootstrap replicates and if more than 50 bootstrap replications are conducted. However, if a particular bifurcating tree is observed in, say, < 75% of the bootstrap replicates, then it cannot be claimed to be better than the trifurcating tree even if > or = 1,000 bootstrap replications are conducted. When a bifurcating tree is used as the model tree, the bootstrap approach tends to overestimate P when the sequences are very short, but it tends to underestimate that probability when the sequences are long. Moreover, simulation results show that, if a tree is accepted as the true tree only if it has appeared in > or = 95% of the bootstrap replicates, then the probability of failing to accept any bifurcating tree can be as large as 58% even when P = 95%, i.e., even when 95% of the samples from the evolutionary process will support the true tree. Thus, if the rate-constancy assumption holds, bootstrapping is a conservative approach for estimating the reliability of an inferred phylogeny for four taxa.

Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock

The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences were studied by considering model trees of three taxa with an outgroup. The cases of constant and varying rates of nucleotide substitution were compared. From sequences obtained by simulation, phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The effectiveness and consistency of the MP method were studied in terms of proportions of informative sites. The results of simulation showed that bootstrap estimation of the confidence level for an inferred phylogeny can be used even under unequal rates of evolution if the rate differences are not large so that the MP method is not misleading. The condition under which the MP method becomes misleading (inconsistent) is more stringent for slowly evolving sequences than for rapidly evolving ones, and it also depends on the length of the internal branch. If the rate differences are large so that the MP method becomes consistently misleading, then bootstrap estimation will reinforce an erroneous conclusion on topology. Similar conclusions apply to the NJ method with uncorrected distances. The NJ method with corrected distances performs poorly when the sequence length is short but can avoid the inconsistency problem if the sequence length is long and if the distances can be estimated accurately.

[An ultrastructural classification of carcinomas of the lung]

For the purpose of providing more accurate histological typing of lung carcinoma, it is necessary to classify carcinomas of the lung by electron microscopy. One hundred and fifty cases of resected lung carcinoma were examined under electron microscope. The results of ultrastructural typing of lung carcinoma were as follows: 1. carcinomas showed differentiated features of glandular and squamous epithelium, including squamous cell carcinoma (28 cases), adenocarcinoma (35 cases), and adenosquamous carcinoma (29 cases). Among them, some cases were associated with neuroendocrine differentiation. In addition, solid mucinous cell carcinoma (4 cases) and adenoid cystic carcinoma (2 cases) were seen. 2. Carcinomas showed differentiated features of bronchioloalveolar epithelium, subdividing into clara cell (9 cases), type II pneumocyte (3 cases), mucinous cell (5 cases) and mixed type (4 cases). 3. Carcinomas showed differentiated features of neuroendocrine cell (Kulchitsky cell), including well differentiated (carcinoid, 13 cases), intermediately differentiated (atypical carcinoid, 12 cases), and poorly differentiated (small cell carcinoma, 6 cases). Among them, some cases were associated with squamous differentiation. The ultrastructural classification was compared with histological classification of lung carcinomas and the differences between them are discussed.

Higher rates of amino acid substitution in rodents than in humans

An analysis of 54 protein sequences from humans and rodents (mice or rats), with the chicken as an outgroup, indicates that, from the common ancestor of primates and rodents, 35 of the proteins have evolved faster in the lineage to mouse or rat (rodent lineage) whereas only 12 proteins have evolved faster in the lineage to humans (human lineage). The average rate of amino acid substitution is significantly faster in the rodent lineage than in the human lineage. In addition, the average rate of insertion/deletion is also faster in rodents than in humans and there is a positive correlation between the rate of amino acid substitution and the rate of insertion/deletion in a protein sequence.

Effects of berbamine on contraction and Ca2+ influx of pig basilar artery

Effects of berbamine (Ber) on KCl- and 5-HT-induced contraction of basilar artery (BA) of pigs were studied in vitro. Ber relaxed markedly KCl-induced contraction of BA (IC50 = 4.63 mumol.L-1) and its effect was antagonized by increasing the concentration of extracellular Ca2+; Ber inhibited 5-HT-induced contraction of BA, showing significant inhibition of sustained tonic contraction (STC) (IC50 = 0.64 mumol.L-1) whereas the initial fast phasic contraction (FPC) was relatively unaffected (IC50 = 19.8 mumol.L-1); the 5-HT-induced contraction of BA was dependent on the concentration of extracellular Ca2+, especially STC. The results of Ca2+ withdrawal and replacement indicated that STC was due to 5-HT-stimulated Ca2+ influx, while 5-HT-induced release of intracellular Ca2+ resulted in FPC. Ber 0.8 mumol.L-1 produced markedly inhibitory effect on Ca2+ influx induced by 5-HT (P < 0.01). The effects of Ber were similar to those of nimodipine (Nim). The present results suggested that Ber has antagonistic effect on the potential sensitive channels (PSC) and the receptor operated channels (ROC).

Surgical treatment of hilar bile duct carcinoma. Clinical and pathological studies

Resection of the extrahepatic bile tract for hilar bile duct carcinoma was performed at the PLA General Hospital, with a resectability rate of 62% (31/50) and no operative mortality. Hepatic lobectomy was performed at the same time in 16 cases (51.6%). Reoperative resections were successfully done in 5 cases; 4 cases are still living 1-4 years after the second operation. The cause of late death was mainly biliary infection due to local recurrence and bile duct obstruction. The median survival period was 15 months. 32 cases were studied pathologically, of which 27 were resected surgical specimens and 5 autopsies. The tumors were histologically classified into 4 types: papillary adenocarcinoma (6 cases); well differentiated adenocarcinoma (21); poorly differentiated adenocarcinoma (3); and simple carcinoma (2). The importance of early diagnosis of hilar bile duct carcinoma at its subclinical stage before appearance of clinical jaundice is stressed.

The molecular taxonomy and evolution of the guinea pig

On the basis of 18 protein sequences totaling 2,413 aligned amino acid sites, it is suggested that the guinea pigs and the myomorphs (rat-like rodents) are not monophyletic. Rather, the evolutionary lineage leading to the guinea pig seems to have branched off prior to the divergence among myomorphs, lagomorphs, primates, chiropterans, artiodactyls, and carnivores. It is suggested therefore that the Caviomorpha (guinea pig-like rodents) and possibly the Hystricomorpha (porcupine-like rodents) should be elevated in taxonomic rank and conferred an ordinal status distinct from the Rodentia. This suggestion calls for a reevaluation of the morphological evolution of guinea pigs and further molecular studies on the possibility of paraphyly of the order Rodentia. If the monophyly of rodents holds, it must be concluded that the pattern of molecular evolution in many guinea pig genes has been extremely unusual and that the causes for this pattern should be sought. It is also suggested that claims of large differences in the rate of molecular evolution between guinea pigs and myomorphs may have been exaggerated in many cases as a result of an erroneous phylogenetic position for the guinea pig. The average rate of amino acid replacement in the guinea pig seems to be comparable to that in the rat and the mouse. However, the data indicate that myomorph and caviomorph genes evolve, on average, about two times faster than their human counterparts. Finally, our analysis provides evidence against the hypothesis that the gundi (an African rodent) represents the most ancient rodent lineage.

Construction of linear invariants in phylogenetic inference

An analytical method is presented for constructing linear invariants. All linear invariants of a k-species tree can be derived from those of (k-1)-species trees using this method. The new method is simpler than that of Cavender, which relies on numerical computations. Moreover, the new method provides a convenient tool to study the relationships between linear invariants of the same tree or of different trees. All linear invariants of trees of up to five species are derived in this study. For four species, there are 16 independent linear invariants for each of the three possible unrooted trees, 14 of which are shared by two unrooted trees and 12 of these are shared by all three unrooted trees; the last types of linear invariants can be used to construct tests on the assumptions about nucleotide substitutions. The number of linear invariants for a tree is found to increase rapidly with the number of species.

The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order rodentia

1. Molecular data indicate that caviomorphs (guinea-pig-like rodents) and myomorphs (rat-like rodents) are not monophyletic. 2. Rather, the evolutionary lineage leading to the guinea-pig may have branched off prior to the divergence among myomorphs, lagomorphs, primates, chiropterans, artiodactyls, and carnivores. 3. Thus, the guinea-pig lineage probably represents an ancient eutherian lineage, and should be conferred an independent ordinal status. 4. The gundis (Ctenodactylidae) also seem to have branched off before the divergence among myomorphs, primates, and artiodactyls, but after the divergence of the guinea-pig. 5. Therefore, the order Rodentia as defined at the present time is in all probability a paraphyletic group devoid of taxonomic validity. 6. Previous claims pertaining to large differences in the rate of molecular evolution between guinea-pigs and myomorphs may have been exaggerated in many cases as a result of the erroneous phylogenetic position attributed to the guinea-pig. 7. The average rate of amino acid replacement in the guinea-pig is comparable to that in the rat and the mouse. 8. Protein-coding genes of myomorphs and caviomorphs evole, on average, about two times faster than their counterparts in gundis and humans.

[Pathological study on 10 cases of inflammatory pseudotumour of the liver]

Histopathological changes of 10 cases of resected inflammatory pseudotumour of liver were observed. These cases were considered to be the primary liver carcinomas or malignant tumours clinically. Morphologically, the inflammatory pseudotumour of liver exhibited varied histological features, including plasma cell granuloma, xanthogranuloma, fibrous proliferation, endophlebitis, necrosis etc. All these cases showed the characteristics of an inflammatory proliferative mass. The causes and the diagnosis criteria of inflammatory pseudotumours of liver were briefly discussed.

Sequences of primate insulin genes support the hypothesis of a slower rate of molecular evolution in humans and apes than in monkeys

The chimpanzee and African green monkey insulin genes have been cloned and sequenced. These two sequences together with the previously reported sequences for the human and owl monkey insulin genes provide additional support for the hominoid-rate-slowdown hypothesis, i.e., a slower rate of nucleotide substitution in humans and apes than in monkeys. When these sequences and other primate sequences available for the relative-rate test were considered together, the substitution rate in the Old World monkey lineage was shown to be significantly higher than the rates in the human and chimpanzee lineages. This was true regardless of whether the eta-globin pseudogene was included in the analysis. Therefore, in contrast to the claim by Easteal, the hominoid-rate-slowdown is not unique to the eta-globin pseudogene but appears to be a rather general phenomenon. On average, the substitution rate at silent sites is about 1.5 times higher in the Old World monkey lineage than in the human and chimpanzee lineages.

Necessary and sufficient conditions for the existence of linear invariants in phylogenetic inference

The necessary and sufficient conditions for the existence of linear invariants under semigroups of probability transition matrices are derived. It is found that a biologically meaningful nucleotide substitution model has linear invariants if and only if it is a submodel of one of the three most general models, which include the so-called balanced and unbalanced transversion models. Each of these three general models is a nucleotide substitution model with six parameters.

Structure and evolution of the lipase superfamily

The lipase superfamily includes three vertebrate and three invertebrate (dipteran) proteins that show significant amino acid sequence similarity to one another. The vertebrate proteins are lipoprotein lipase (LPL), hepatic lipase (HL), and pancreatic lipase (PL). The dipteran proteins are Drosophila yolk proteins 1, 2, and 3. We review the relationships among these proteins that have been established according to gene structural relatedness and introduce our findings on the phylogenetic relationships, distance relationships, and evolutionary history of the lipase gene superfamily. Drosophila yolk proteins contain a 104 amino acid residue segment that is conserved with respect to the lipases. We have used the yolk proteins as an outgroup to root a phylogeny of the lipase family. Our phylogenetic reconstruction suggests that ancestral PL diverged earlier than HL and LPL, which share a more recent root. Human and bovine LPL are shown to be more closely related to murine LPL than to guinea pig LPL. A comparison of the distance (a measure of the number of substitutions between sequences) between mammalian and avian LPL reveals that guinea pig LPL has the largest distance from the other mammals. Human, rodent, and rabbit HL show marked divergence from one another, although they have similar relative rates of amino acid substitution when compared to human LPL as an outgroup. Human and porcine PL are not as divergent as human and rat HL, suggesting that PL is more conserved than HL. However, canine PL demonstrates an unusually rapid rate of substitution with respect to the other pancreatic lipases. The lipases share several structurally conserved features. One highly conserved sequence (Gly-Xaa-Ser-Xaa-Gly) contains the active site serine. This feature, which agrees with that found in serine esterases and proteases, is found within the entire spectrum of lipases, including the evolutionarily unrelated prokaryotic lipases. We review the location and possible activity of putative lipid binding domains. We have constructed a conservation index (CI) to display conserved structural features within the lipase gene family, a CI of 1.0 signifying perfect conservation. We have found a correlation between a high CI and the position of conserved functional structures. The putative lipid-binding domains of LPL and HL, the disulfide-bridging cysteine residues, catalytic residues, and N-linked glycosylation sites of LPL, HL, and PL all lie within regions having a CI of 0.8 or higher. A number of amino acid substitutions have been identified in familial hyperchylomicronemia which result in loss of LPL function.(ABSTRACT TRUNCATED AT 400 WORDS)

Low nucleotide diversity in man

The nucleotide diversity (pi) in humans is studied by using published cDNA and genomic sequences that have been carefully checked for sequencing accuracy. This measure of genetic variability is defined as the number of nucleotide differences per site between two randomly chosen sequences from a population. A total of more than 75,000 base pairs from 49 loci are compared. The DNA regions studied are the 5' and 3' untranslated regions and the amino acid coding regions. The coding regions are divided into nondegenerate sites (i.e., sites at which all possible changes are nonsynonymous), twofold degenerate sites (i.e., sites at each of which one of the three possible changes is synonymous) and fourfold degenerate sites (i.e., sites at which all three possible changes are synonymous). The pi values estimated are, respectively, 0.03 and 0.04% for the 5' and 3' UT regions, and 0.03, 0.06 and 0.11% for nondegenerate, twofold degenerate and fourfold degenerate sites. Since the highest pi value is only 0.11%, which is about one order of magnitude lower than those in Drosophila populations, the nucleotide diversity in humans is very low. The low diversity is probably due to a relatively small long-term effective population size rather than any severe bottleneck during human evolution.

[Orthotopic xenotransplantation of human lung giant cell carcinoma and study on its invasion and metastasis]

Human lung giant cell carcinoma cell strains were implanted into the lungs of nude mice via an intrabronchial procedure. Tumorigenicity, invasion and metastasis of the xenografts, and their morphological features, including the findings by light and electronic microscopy and immunohistochemistry were investigated. Dissemination of xenografts within the airway (2/8), invasion to diaphragm (5/8), and development of bloody hydrothorax (5/8), were discovered. Metastasis via lymphatic and blood vessel routes as well as seeding metastasis occurred in all the tumor-bearing animals. The morphological features of xenografts were consistent with those of the parental giant cell carcinoma. These results indicate that lung cancer cell strains grow autonomously and the behavior of invasion and metastasis of the xenografts imitates more closely the clinical manifestation of lung cancer than their subcutaneous counterparts. Since microenvironment influences the biological behavior of the transplants, this model seemed to be more ideal for further investigation experimentally.

Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree

Invariants are functions of the probabilities of state configurations among lineages, with expected values equal to zero under certain phylogenies. For two-state sequences, the existence of certain quadratic invariants requires a symmetric substitution model. For sequences with more than two states, the necessary condition for the existence of certain quadratic invariants in terms of independent events is much stronger than symmetry. For DNA sequences, only three parameters are allowed in the substitution model, which includes Kimura's two-parameter model as a special case.

Is the guinea-pig a rodent?

The guinea-pig (Cavia porcellus), traditionally classified as a New World hystricomorph rodent, often shows anomalous morphological and molecular features in comparison with other eutherian mammals. For example, its insulin differs from that of other mammals in anabolic and growth-promoting activities and in its capability to form hexamers. Indeed, the literature about the molecular evolution of guinea-pigs abounds in references to 'convergent evolution', 'extremely rapid rates of substitution', and 'unique evolutionary mechanisms'. These claims are based on the assumption that the guinea-pig is a rodent. Our phylogenetic analyses of amino-acid sequence data, however, imply that the guinea-pig diverged before the separation of the primates and the artiodactyls from the myomorph rodents (rats and mice). If true, then the myomorphs and the caviomorphs do not constitute a natural clade, and the Caviomorpha (or the Histricomorpha) should be elevated in taxonomical rank and regarded as a separate mammalian order distinct from the Rodentia. If, as suggested by recent data, the myomorphs branched off before the divergence among the carnivores, lagomorphs, artiodactyls and primates, then the new order would represent an early divergence in eutherian radiation.

[An ultrastructural and immunohistochemical observation of squamous cell carcinoma of the lung with neuroendocrine differentiation]

Thirteen cases (10.5%) of squamous cell carcinoma of the lung with neuroendocrine differentiation were identified ultrastructurally in 124 cases of resected pulmonary carcinoma. In addition to the features of epidermoid differentiation, i.e. presence of tonofilaments and desmosones, a small amount of cancer cells containing neurosecretory granules were found in all the 13 cases. Ultrastructures indicated that both epidermoid and neuroendocrine differentiations were present simultaneously in individual cancer cell. Immunohistochemical staining for NSE was performed in 12 cases. Positive reaction was obtained in all but one (91.7%). NSE positive cancer cells distributed focally or in single cell scattered in the cancer cell nests. The results suggest that biphasic differentiation of pulmonary squamous cell carcinoma diagnosed by light microscopy may not originate from different cells of different derms, but may be derived from a common stem cell of the bronchial epithelium which possesses the ability of multipotential differentiation.

Cloning and sequencing of bovine apolipoprotein E complementary DNA and molecular evolution of apolipoproteins E, C-I, and C-II

Apolipoprotein (apo) E, a major protein component of plasma lipoproteins, is a physiological ligand for the low density lipoprotein (LDL) receptor as well as for a specific apoE receptor; it is therefore an important modulator of lipoprotein metabolism. In this study we cloned and sequenced bovine apoE complementary DNA. Comparison of nucleotide substitution rates shows that apoE is less conservative than apoA-I and evolves about 30% faster than an average mammalian protein. Although apoE is not a conservative protein, several regions have been well conserved among all eight mammalian sequences now available. These include a 33-amino-acid block immediately upsteam from the third intron/exon junction and the LDL receptor binding region. We have also compared published apoC-I and apoC-II sequences. Both proteins are less conservative than apoE. In particular, apoC-I shows no well-conserved region except for a small region in the common 33-amino-acid block, suggesting that the function of apoC-I does not have stringent structural requirements. On the other hand, in apoC-II the region encoded by exon 4, which consists of the last 29 amino acids of the polypeptide, has been rather well conserved, probably because this region is important for the activation of lipoprotein lipase and chylomicron and very low density lipoprotein metabolism.