Two types of cis-trans compensation in the evolution of transcriptional regulation.

Because distant species often share similar macromolecules, regulatory mutations are often considered responsible for much of their biological differences. Recently, a large portion of regulatory changes has been attributed to cis-regulatory mutations. Here, we examined an alternative possibility that the putative contribution of cis-regulatory changes was, in fact, caused by compensatory action of cis- and trans-regulatory elements. First, we show by stochastic simulations that compensatory cis-trans evolution maintains the binding affinity of a transcription factor at a constant level, thereby spuriously exaggerating the contribution of cis-regulatory mutations to gene expression divergence. This exaggeration was not observed when changes in the binding affinity were compensated by variable transcription factor concentration. Second, using reciprocal introgressions of Drosophila, we show that relative expression of heterozygous alleles from two distinct species often varied significantly between different species backgrounds, indicating the possible action of cis-trans compensation. Taken together, we propose that cis-trans hybrid incompatibilities are accumulating much faster than generally considered.

The direction of linkage disequilibrium: a new measure based on the ancestral-derived status of segregating alleles.

A new measure of directional linkage disequilibrium is developed for detecting epistatic selection on interacting genes. Simulations show that by orienting the direction of linkage disequilibrium on the basis of the ancestral-derived status of alleles, the new measure indeed improves the power to detect a positive fitness interaction between two new mutations.

Coalescent under the evolution of coadaptation.

Adaptation to novel environments arises either from new beneficial mutations or by utilizing pre-existing genetic variation. When standing variation is used as the source of new adaptation, fitness effects of alleles may be altered through an environmental change. Alternatively, changes in epistatic genetic backgrounds may convert formerly neutral mutations into beneficial alleles in the new genetic background. By extending the coalescent theory to describe the genealogical histories of two interacting loci, I here investigated the hitchhiking effect of epistatic selection on the amount and pattern of sequence diversity at the linked neutral regions. Assuming a specific form of epistasis between two new mutations that are independently neutral, but together form a coadapted haplotype, I demonstrate that the footprints of epistatic selection differ markedly between the interacting loci depending on the order and relative timing of the two mutational events, even though both mutations are equally essential for the formation of an adaptive gene combination. Our results imply that even when neutrality tests could detect just a single instance of adaptive substitution, there may, in fact, be numerous other hidden mutations that are left undetected, but still play indispensable roles in the evolution of a new adaptation. We expect that the integration of the coalescent framework into the general theory of polygenic inheritance would clarify the connection between factors driving phenotypic evolution and their consequences on underlying DNA sequence changes, which should further illuminate the evolutionary foundation of coadapted systems.

Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations.

Segmental duplications are enriched within many eukaryote genomes, and their potential consequence is gene duplication. While previous theoretical studies of gene duplication have mainly focused on the gene silencing process after fixation, the process leading to fixation is even more important for segmental duplications, because the majority of duplications would be lost before reaching a significant frequency in a population. Here, by a series of computer simulations, we show that purifying selection against loss-of-function mutations increases the fixation probability of a new duplicate gene, especially when the gene is haplo-insufficient. Theoretically, the probability of simultaneous preservation of both duplicate genes becomes twice the loss-of-function mutation rate (u(c)) when the population size (N), the degree of dominance of mutations (h) and the recombination rate between the duplicate genes (c) are all sufficiently large (Nu(c)>1, h>0.1 and c>u(c)). The preservation probability declines rapidly with h and becomes 0 when h=0 (haplo-sufficiency). We infer that masking deleterious loss-of-function mutations give duplicate genes an immediate selective advantage and, together with effects of increased gene dosage, would predominantly determine the fates of the duplicate genes in the early phase of their evolution.

Association between duplicated maltase genes and the transcriptional regulation for the carbohydrate changes in Drosophila melanogaster.

Gene duplication could promote phenotypic and genetic adaptation to various environments. To understand the effects of gene duplication on transcriptional regulation associated with environmental changes, we focused on the starch hydrolysis pathway, in which amylase enzymes together with maltase enzymes hydrolyze starch into glucose. Drosophila genomes involve ten duplicated Maltase genes. We examined the levels of transcription of the nine of these genes in 36 lines of Drosophila melanogaster collected from a natural population. In the investigated population, the levels of transcription were different between the two dietary carbohydrate sources, glucose and starch. At the transcriptional level, a single Maltase gene, which transcribes the specific Maltase transcripts, worked together with an Amylase gene in the pathway. The three of nine genes responded to carbohydrate changes, and the degree of the response was similar to Amylase gene. Our results suggest that gene duplication could increase capacity of the transcriptional regulation associated with environmental changes.

Evolution of coadaptation in a subdivided population.

The interplay between population subdivision and epistasis is investigated by studying the fixation probability of a coadapted haplotype in a subdivided population. Analytical and simulation models are developed to study the evolutionary fate of two conditionally neutral mutations that interact epistatically to enhance fitness. We find that the fixation probability of a coadapted haplotype shows a marked increase when the population is genetically subdivided and subpopulations are loosely connected by migration. Moderate migration and isolation allow the propagation of the mutant alleles across subpopulations, while at the same time preserving the favorable allelic combination established within each subpopulation. Together they create the condition most favorable for the ultimate fixation of the coadapted haplotype. On the basis of the analytical and simulation results, we discuss the fundamental role of population subdivision and restricted gene flow in promoting the evolution of functionally integrated systems, with some implications for the shifting-balance theory of evolution.

Mutational pattern and frequency of induced nucleotide changes in mouse ENU mutagenesis.

BACKGROUND: With the advent of sequence-based approaches in the mutagenesis studies, it is now possible to directly evaluate the genome-wide pattern of experimentally induced DNA sequence changes for a diverse array of organisms. To gain a more comprehensive understanding of the mutational bias inherent in mouse ENU mutagenesis, this study describes a detailed evaluation of the induced mutational pattern obtained from a sequence-based screen of ENU-mutagenized mice. RESULTS: Based on a large-scale screening data, we derive the sequence-based estimates of the nucleotide-specific pattern and frequency of ENU-induced base replacement mutation in the mouse germline, which are then combined with the pattern of codon usage in the mouse coding sequences to infer the spectrum of amino acid changes obtained by ENU mutagenesis. We detect a statistically significant difference between the mutational patterns in phenotype- versus sequence-based screens, which presumably reflects differential phenotypic effects caused by different amino acid replacements. We also demonstrate that the mutations exhibit strong strand asymmetry, and that this imbalance is generated by transcription, most likely as a by-product of transcription-coupled DNA repair in the germline. CONCLUSION: The results clearly illustrate the biased nature of ENU-induced mutations. We expect that a precise understanding of the mutational pattern and frequency of induced nucleotide changes would be of practical importance when designing sequence-based screening strategies to generate mutant mouse strains harboring amino acid variants at specific loci. More generally, by enhancing the collection of experimentally induced mutations in unambiguously defined genomic regions, sequence-based mutagenesis studies will further illuminate the molecular basis of mutagenic and repair mechanisms that preferentially produce a certain class of mutational changes over others.

Evolution of coadaptation in a two-locus epistatic system.

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.

Behavioural characterization of substance P-induced nociceptive response in mice.

Intrathecal injection of substance P produced a behavioural syndrome, consisting of reciproacal hindlimb scratching and biting or fore- and hind-licking. Pretreatment with either an analogue of substance P, (D-Pro2, D-Trp7,9)-substance P (DPDT-SP) or (D-Arg1, D-Pro2,4, D-Trp7,9, Leu11)-substance P, given intrathecally, reduced the response to substance P in a dose-dependent manner. The behaviour induced by substance P was also inhibited by intrathecal, intracerebroventricular (i.c.v.) or intraperitoneal (i.p.) injection of morphine. Intrathecal or subcutaneous injection of naloxone showed a biphasic effect on substance P response; the substance P-induced nociceptive response was increased by a small dose of naloxone, while it was inversely decreased by a large dose of naloxone. The results with analogues of substance P support the hypothesis that substance P, injected intrathecally, acts directly on substance P receptors in the spinal cord. The nociceptive response induced by substance P appears to be controlled by endogenous opioids in the spinal cord.

Models of selective mating and the initiation of the Fisherian process.

The effects of various rules of selective mating on the initial stages of Fisherian sexual selection are investigated. A comparison of three models of selective mating, fixed relative preference, best of N males and absolute preference is provided, with a special emphasis on their mathematical properties. Using a two-locus haploid model of sexual selection in a polygamous population, I show that the absolute preference rule of selective mating may lower the threshold frequency of the preference trait, required for the initiation of the Fisherian process, as low as zero. This was not observed in the previous analyses with fixed relative preference or best of N male rules. It is then argued that absolute preference may cause the initiations of the Fisherian process more easily without introducing additional assumptions such as pleiotropy or random genetic drift. Some problems associated with the mating rule are also discussed.

Complement receptor expression of primates and non-primates detected by the rosette formation technique.

The expression of complement receptors were studied on erythrocytes and platelets from 14 non-human primates and 3 non-primate species by rosette formation. It was found that the reactivity of erythrocytes with the cell bound complement is deeply dependent on which species are used as the complement source. The erythrocytes from Prosimian do not react with any kind of complement, while their platelets react with many kinds of complement. New World monkey erythrocytes do not react with indicator cells binding complements from guinea pig or man, while some of them react with indicators binding complements from non-human primate species. Contrarily Old World monkey erythrocytes react with complements from guinea pig, man and non-human primate. Hominoidea erythrocytes reacted with all the complements tested. Rabbit expresses C3 receptors on their erythrocytes for rabbit C3 and on their platelets for rabbit, guinea pig or mouse C3. Guinea pig expresses receptors on their erythrocytes for guinea pig and mouse C3, and on their platelets for guinea pig, mouse, rabbit and human C3. It becomes clear that not all of erythrocytes from primate and platelets from non-primate always express complement receptors as has been stated in the text books.

Muscle nerve sympathetic activity during sleep and its change with arousal response.

Muscle nerve sympathetic activity (MSA) was recorded from the peroneal nerve during wakefulness and in different sleep states in healthy young adults. The burst rate (BR) of MSA significantly decreased in NREM, but not in REM sleep, compared with that during wakefulness. Transient increases of MSA frequently appeared in association with rapid eye movements during REM sleep. K-complexes in Stage 2 were almost always accompanied by a burst of MSA, and were followed by a transient elevation of arterial blood pressure. Auditory stimuli applied in sleep induced a burst of MSA followed by a transient increase of arterial blood pressure, only when they elicited an arousal response in the EEG, such as a K-complex, transient EEG desynchronization, or a short train of alpha waves. The same stimuli applied during wakefulness did not induce such changes in MSA and in arterial blood pressure.

Prostacyclin-independence in beta-adrenoceptor mediated renin release from dog renal cortical slices.

There is some controversy regarding whether stimulation of renin release by the beta-adrenergic system is dependent on prostaglandin (PG) production. We have examined this problem in renal cortical slices of the dog and have obtained the following results: (1) Isoproterenol (4 X 10(-6) M) stimulated renin release, but had no effect on the formation of 6-keto PGF1 alpha, a stable metabolite of PGI2; (2) Indomethacin (2 X 10(-5) M) had no effect on isoproterenol stimulated renin release, but inhibited 6-keto PGF1 alpha formation; (3) Dibutyryl cyclic AMP (10(-3) M) stimulated both renin release, and 6-keto PGF1 alpha release. Indomethacin (2 X 10(-5) M) did not inhibit dibutyryl cyclic AMP-stimulated renin release, but did inhibit the production of 6 keto PGF1 alpha. These results indicate that the beta-adrenoceptor mediated renin release does not depend on the formation of PGI2, but renin release is dependent on cyclic AMP formation.

Intraocular lens implantation in a child with monocular cataract and anterior persistent hyperplastic primary vitreous.

A 3-year-old girl had phacoemulsification during which the presence of anterior persistent hyperplastic primary vitreous (PHPV) was discovered. Visual rehabilitation comprised contact lens use for 1 year. However, visual acuity deteriorated gradually because of secondary cataract formation. In a second surgery 1 year after the first, the posterior capsule was incised, followed by an anterior vitrectomy and intraocular lens implantation. At the last follow-up 6 months after the second surgery, there was no evidence of ocular complications and best corrected visual acuity was 0.6.

Tuberculous pseudoaneurysm of the celiac artery. A case report.

We report a case of tuberculous pseudoaneurysm in the neck of the celiac artery involving the aorta. Recurrence of the aneurysm occurred after attempted direct repair. Therefore redo-surgery was performed, which involved resection of aneurysm and removal of the infected tissue with bilateral axillofemoral bypass.

[Therapeutic effect of ofloxacin on intractable pulmonary tuberculosis and ofloxacin resistance of tubercle bacilli isolated from the patients. Chest DIsease Cooperative Study Unit of National Sanatoriums in Kinki District].

Ofloxacin, a synthetic antibacterial pyridone-carboxylic acid derivative, was used in the treatment of intractable pulmonary tuberculosis. In this study, the therapeutic effect of Ofloxacin on pulmonary tuberculosis and Ofloxacin resistance were analyzed. All patients had been hospitalized in eight national sanatoria in Kinki district, and were excreting tubercle bacilli resistant to various anti-tuberculosis drugs agents. Ofloxacin was given to 118 patients orally at a daily dose of 300 mg to 600 mg for more than 3 months. A few anti-tuberculosis drugs, which had failed in the negative conversion of bacilli previously, were used in combination. By Ofloxacin, 23 patients (19.5%) showed negative conversion of tubercle bacilli in sputum culture within 5 months, and they remained culture-negative for at least 6 months after conversion. Side-effects were observed in 2 patients. One complained of arthralgia and the other felt abdominal fullness. But both were not serious. From these results, it was concluded that Ofloxacin was effective for intractable pulmonary tuberculosis. The resistance of tubercle bacilli to Ofloxacin increased significantly after it was used.

Mutation accumulation in a selfing population: consequences of different mutation rates between selfers and outcrossers.

Currently existing theories predict that because deleterious mutations accumulate at a higher rate, selfing populations suffer from more intense genetic degradation relative to outcrossing populations. This prediction may not always be true when we consider a potential difference in deleterious mutation rate between selfers and outcrossers. By analyzing the evolutionary stability of selfing and outcrossing in an infinite population, we found that the genome-wide deleterious mutation rate would be lower in selfing than in outcrossing organisms. When this difference in mutation rate was included in simulations, we found that in a small population, mutations accumulated more slowly under selfing rather than outcrossing. This result suggests that under frequent and intense bottlenecks, a selfing population may have a lower risk of genetic extinction than an outcrossing population.