CFP/Yit: An Inbred Mouse Strain with Slow Gastrointestinal Transit

BACKGROUND

Gastrointestinal transit (GIT) is influenced by factors including diet, medications, genetics, and gut microbiota, with slow GIT potentially indicating a functional disorder linked to conditions, such as constipation. Although GIT studies have utilized various animal models, few effectively model spontaneous slow GIT.

AIMS

We aimed to characterize the GIT phenotype of CFP/Yit (CFP), an inbred mouse strain with suggested slow GIT.

METHODS

Female and male CFP mice were compared to Crl:CD1 (ICR) mice in GIT and assessed based on oral gavage of fluorescent-labeled 70-kDa dextran, feed intake, fecal amount, and fecal water content. Histopathological analysis of the colon and analysis of gut microbiota were conducted.

RESULTS

CFP mice exhibited a shorter small intestine and a 1.4-fold longer colon compared to ICR mice. The median whole-GIT time was 6.0-fold longer in CFP mice than in ICR mice. CFP mice demonstrated slower gastric and cecal transits than ICR mice, with a median colonic transit time of 4.1 h (2.9-fold longer). CFP mice exhibited lower daily feed intakes and fecal amounts. Fecal water content was lower in CFP mice, apparently attributed to the longer colon. Histopathological analysis showed no changes in CFP mice, including tumors or inflammation. Moreover, CFP mice had a higher Firmicutes/Bacteroidota ratio and a relative abundance of Erysipelotrichaceae in cecal and fecal contents.

CONCLUSIONS

This study indicates that CFP mice exhibit slow transit in the stomach, cecum, and colon. As a novel mouse model, CFP mice can contribute to the study of gastrointestinal physiology and disease.

Evolutionary game theory of continuous traits from a causal perspective

Modern evolutionary game theory typically deals with the evolution of continuous, quantitative traits under weak selection, allowing the incorporation of rich biological detail and complicated nonlinear interactions. While these models are commonly used to find candidates for evolutionary endpoints and to approximate evolutionary trajectories, a less appreciated property is their potential to expose and clarify the causal structure of evolutionary processes. The mathematical step of differentiation breaks a nonlinear model into additive components which are more intuitive to interpret, and when combined with a proper causal hypothesis, partial derivatives in such models have a causal meaning. Such an approach has been used in the causal analysis of game-theoretical models in an informal manner. Here we formalize this approach by linking evolutionary game theory to concepts developed in causal modelling over the past century, from path coefficients to the recently proposed causal derivative. There is a direct correspondence between the causal derivative and the derivative used in evolutionary game theory. Some game theoretical models (e.g. kin selection) consist of multiple causal derivatives. Components of these derivatives correspond to components of the causal derivative, to path coefficients, and to edges on a causal graph, formally linking evolutionary game theory to causal modelling. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.

Human gut microbiota influences drug-metabolizing enzyme hepatic Cyp3a: A human flora-associated mice study

Several studies revealed that gut microbiota affects the hepatic drug-metabolizing enzyme cytochrome P450 (Cyp). We hypothesized that individual gut microbiota variations could contribute to CYP activity. Human flora-associated (HFA) mice are established from germ-free mice using human feces and are often used to determine the effect of the human gut microbiota on the host. This study generated two groups of HFA mice using feces from two healthy individuals. Then, the composition of gut microbiota and hepatic Cyp activity was compared to analyze the effects of gut microbiota in healthy individuals on hepatic Cyp activity. A principal coordinate analysis based on the UniFrac distance for the composition of the cecal and fecal microbiota revealed apparent differences between the recipient groups. Hepatic Cyp, which is a marked difference in Cyp3a activity and Cyp3a11 gene expression, was observed between the recipient groups. Cyp2c and Cyp1a activities did not differ between recipient groups, with significantly lower enzymatic activities in recipients than in germ-free mice. These results indicate that the human gut microbiota affects hepatic Cyp activity. Especially, human gut microbiota composition differences have a pronounced effect on Cyp3a activity via Cyp3a11 gene expression regulation. Therefore, human gut microbiota variations among individuals may affect numerous drug metabolism, leading to drug efficacy and toxicity.

One step fabrication of aligned carbon nanotubes using gas rectifier

We report the one-step fabrication of aligned and high-quality carbon nanotubes (CNTs) using floating-catalyst chemical vapor deposition (FCCVD) with controlled fluidic properties assisted by a gas rectifier. The gas rectifier consists of one-dimensional straight channels for regulating the Reynolds number of the reaction gas. Our computational fluid dynamics simulation reveals that the narrow channels of the gas rectifier provide steady and accelerated laminar flow of the reaction gas. In addition, strong shear stress is induced near the side wall of the channels, resulting in the spontaneous formation of macroscopic CNT bundles aligned along the direction of the gas flow. After a wet-process using chlorosulfonic acid, the inter-tube voids inherently observed in as-grown CNT bundles are reduced from 16 to 0.3%. The resulting CNT fiber exhibits a tensile strength of 2.1 ± 0.1 N tex⁻¹ with a Young’s modulus of 39 ± 4 N tex⁻¹ and an elongation of 6.3 ± 0.6%. FCCVD coupled with the strong shear stress of the reaction gas is an important pre-processing route for the fabrication of high-performance CNT fibers.

Normal variation of the gut microbiota affects hepatic cytochrome P450 activity in mice

Several studies revealed that substantial artificial changes in the gut microbiota resulted in modification of hepatic cytochrome P450 3a (Cyp3a) in mice. Consequently, we hypothesized that "normal" variation of the gut microbiota might also alter hepatic Cyp activity and lead to individual differences in drug metabolism. Therefore, this study investigated the effects of normal gut microbiota variation on hepatic Cyp activity under the same genetic and environmental conditions using ex-germ-free mice. Using the feces of three breeder BALB/c mice (Jcl, Slc, and Crj), germ-free BALB/cYit mice were conventionalized (Yit-Jcl, Yit-Slc, and Yit-Crj). The gut microbiota composition and hepatic Cyp activity of these donors and recipients were evaluated. 16S rRNA sequencing revealed clear differences of the gut microbiota among donors and among recipients. Cyp3a activity was significantly higher in Slc mice than in Jcl and Crj mice. Notably, among recipients, Cyp3a activity was significantly higher in Yit-Slc and Yit-Crj mice than in Yit-Jcl mice. Cyp2b activity was significantly higher in Slc mice than in Jcl and Crj mice. Cyp2b activity was significantly higher in Yit-Slc mice than in Yit-Jcl mice. Additionally, in correlation analysis, some genera displayed significant positive or negative correlations with Cyp activity, particular the strong positive correlation between Clostridium sensu stricto 1 with Cyp3a activity. In conclusion, this study demonstrated that normal variation of the gut microbiota affected hepatic Cyp3a and Cyp2b activity, which might result in individual differences of drug metabolism.

Development of incident severity classification for laboratory animals

An incident reporting system (IRS) prevents possible adverse events by collecting and analyzing incidents that occur. However, few studies are available regarding IRSs in the laboratory animal field. This study aimed to develop an incident severity classification for laboratory animals (ISCLA) to evaluate the usefulness of the IRS in laboratory animal facilities. Twenty-three incidents reported from March 2019 to February 2020 on our IRS were retrospectively reviewed. Three of the 23 incidents failed to obtain some experimental data. Two of these incidents were harmless to animals, but the other caused the animals moderate distress. In addition, two of the three incidents made animals unsuitable for experiments. Since the inconsistent impact of incidents on animals and experiments prevented the comparison of the severity of individual incidents, we developed the ISCLA. According to the ISCLA, the above three incidents were classified into Category 3b and 4a. The others were classified into Category 0 (n=5), 1 (n=6), 2 (n=3), and 3a (n=6) in ascending order of severity. No incident was classified into Category 4b and 5. Furthermore, incidents occurring in the animal housing area were more severe than those occurring in the supporting area (P=0.002). This study showed that incident occurrences had characteristics that were not visible from individual incidents alone. Moreover, the ISCLA was considered useful when conducting the IRS and taking improvement measures in laboratory animal facilities.

Effects of gut microbiota on in vivo metabolism and tissue accumulation of cytochrome P450 3A metabolized drug: Midazolam

The link between drug‐metabolizing enzymes and gut microbiota is well established. In particular, hepatic cytochrome P450 (CYP) 3A activities are presumed to be affected by gut microbiota. However, there is no direct evidence that the gut microbiota affects CYP3A metabolism or the clearance of clinically relevant drugs in vivo. Our purpose was to evaluate the effects of gut microbiota on in vitro and in vivo drug metabolism and on the clearance of midazolam, which is a standard CYP3A metabolized drug. Hepatic Cyp3a activity and in vitro midazolam hydroxylase activity were compared using specific pathogen‐free (SPF) and germ‐free (GF) mice. In a pharmacokinetics (PK) study, SPF and GF mice were intraperitoneally injected with 60 mg/kg of midazolam, and plasma and tissue concentrations were measured. Hepatic Cyp3a activity and midazolam hydroxylase activity were significantly lower in GF mice than in SPF mice. Notably, in the PK study, the area under the plasma concentration–time curve from time zero to infinity and the elimination half‐life were approximately four‐fold higher in GF mice compared with SPF mice. Furthermore, the concentration of midazolam in the brain 180 min after administration was about 14‐fold higher in GF mice compared with SPF mice. Together, our results demonstrated that the gut microbiota altered the metabolic ability of Cyp3a and the tissue accumulation of midazolam.

The Price equation and the causal analysis of evolutionary change

Though the Price equation in itself is simply a statistical identity, biologists have often adopted a 'causal interpretation' of the equation, in the sense that its component terms have been supposed to correspond to distinct causal processes in evolution, such as natural selection and transmission bias. In this paper, we bring the issue of causal interpretation to the fore, by studying the conditions under which it is legitimate to read causal meaning into the Price equation. We argue that only if substantive assumptions about causal structure are made, which can be represented in the form of a causal model, can the component terms of the Price equation be interpreted as causally meaningful. We conclude with a reflection on the epistemic uses of the Price equation, emphasizing the difference between the description, explanation and prediction of evolutionary change. This article is part of the theme issue 'Fifty years of the Price equation'.

Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library

We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology. We show how a combination of classification systems and mixed-membership models trained over large digital libraries can inform resource discovery in this domain. Through a novel approach of "drill-down" topic modeling-simultaneously reducing both the size of the corpus and the unit of analysis-we are able to reduce a large collection of fulltext volumes to a much smaller set of pages within six focal volumes containing arguments of interest to historians and philosophers of comparative psychology. The volumes identified in this way did not appear among the first ten results of the keyword search in the HathiTrust digital library and the pages bear the kind of "close reading" needed to generate original interpretations that is the heart of scholarly work in the humanities. Zooming back out, we provide a way to place the books onto a map of science originally constructed from very different data and for different purposes. The multilevel approach advances understanding of the intellectual and societal contexts in which writings are interpreted.

Discovering phenotypic causal structure from nonexperimental data

The evolutionary potential of organisms depends on how their parts are structured into a cohesive whole. A major obstacle for empirical studies of phenotypic organization is that observed associations among characters usually confound different causal pathways such as pleiotropic modules, interphenotypic causal relationships and environmental effects. The present article proposes causal search algorithms as a new tool to distinguish these different modes of phenotypic integration. Without assuming an a priori structure, the algorithms seek a class of causal hypotheses consistent with independence relationships holding in observational data. The technique can be applied to discover causal relationships among a set of measured traits and to distinguish genuine selection from spurious correlations. The former application is illustrated with a biological data set of rat morphological measurements previously analysed by Cheverud et al. (Evolution 1983, 37, 895).

A dose-escalation study of rituximab for treatment of systemic lupus erythematosus and Evans' syndrome: immunological analysis of B cells, T cells and cytokines

OBJECTIVE

Accumulating evidence suggests that B-cell depletion therapy by rituximab may be effective for autoimmune disorders. However, an optimal dose of rituximab and a mechanism of its action remain to be established. We performed a dose-escalation study for treatment of Japanese patients with autoimmune diseases including eight with SLE and one with Evans' syndrome.

METHODS

Rituximab was infused intravenously, weekly 4 times in a dose-escalating fashion at three different doses of 100, 250 or 375 mg/m(2) to three patients each. Immunological parameters were monitored at certain points until 12 months after the treatment.

RESULTS

Rituximab was well tolerated and safe in these patients. Seven out of eight SLE patients and one with Evans' syndrome clinically responded completely or partially to the treatment. Four patients achieved long-term remission (18-30 months) without any additional treatment. In these patients, a significant decrease in circulating B cells continued for 6 months after the treatment. The mean fluorescence intensities of CD19, CD21, CD40 and BR3 on the residual B cells as well as the percentage of CD69+ CD4+ T cells decreased significantly. Serum TNF-alpha levels decreased significantly on day 2. The Th1/Th2 balance of CD4+ T cells gradually shifted towards a Th1 type by 6 months.

CONCLUSION

In addition to B-cell depletion, modification of B-cell and T-cell phenotypes as well as cytokine profiles may be involved in the action of rituximab.

Malignant transformation of endometriosis and genetic alterations of K-ras and microsatellite instability

OBJECTIVES

To clarify the role of specific genetic alterations in the multi-step process of malignant transformation of endometriosis.

METHODS

In cases of ovarian endometrioid carcinoma, we separated regions of normal endometriosis, atypical endometriosis and ovarian endometrioid carcinoma by laser microdissection, and examined K-ras mutation and microsatellite instability in each separated tissue sample.

RESULTS

We detected K-ras mutation and microsatellite instability in endometrioid carcinoma tissue, but not in normal or atypical endometriosis bordering the cancerous region.

CONCLUSIONS

The present findings suggest that K-ras mutation and microsatellite instability are associated with malignant transformation from atypical endometriosis to ovarian endometrioid carcinoma.

Association of MBL gene polymorphisms with major bacterial infection in patients treated with high-dose chemotherapy and autologous PBSCT

A growing body of evidence indicates that genetic factors are involved in an increased risk of infection. We investigated whether mannose-binding lectin (MBL) gene polymorphisms that cause low levels of MBL are associated with the occurrence of major infections in patients, mainly bearing hematological malignancies, after high-dose chemotherapy (HDT) rescued by autologous peripheral blood stem cell transplantation (auto-PBSCT). A retrospective evaluation of 113 patients treated with HDT and auto-PBSCT revealed that the low-producing genotypes, B/B and B/LXA, were associated with major bacterial infection (P=0.0016, OR 7.9). We next performed a nation-wide large-scale study to assess the allele frequency of the MBL coding mutation in a total of 2623 healthy individuals in Japan. The frequency of allele B was estimated to be approximately 0.2, almost the same in seven different areas of Japan. This common occurrence suggests that MBL deficiency may play an important role in the clinical settings of immunosuppression.

117 CYTOPLASMIC FACTORS INFLUENCE DEVELOPMENTAL POTENTIAL OF SAMP1/Yit MOUSE EMBRYOS

Nuclear transplantation is an efficient means to investigate nucleo-cytoplasmic interactions of mammalian embryos during early development. A recent study has shown that the developmental potential of embryos is affected by the type of cytoplasm. The SAMP1/Yit mouse, an inbred strain that develops spontaneous chronic ileitis resembling Crohn's disease (Matsumoto S 1999 Bioscience Microflora 18, 1–9), has poor reproductive performance, and the developmental ability of embryos is low (unpublished data). Therefore we need to enhance productivity of the SAMP1/Yit mouse. Recently it was reported that cytoplasm of F1 mouse egg supported the development of embryos which have low developmental ability (Muggleton-Harris A et al. 1982 Nature 299, 460–462). In the present study, we examined the influences of the nucleus and cytoplasm on the development of reconstructed embryos in vitro and in vivo, using reciprocal nuclear transplantation between SAMP1/Yit and B6P1F1 (C57BL/6J × SAMP1/Yit) mouse embryos. We evaluated the developmental ability of reconstructed embryos by the development rate into blastocysts in vitro and by the rate of offspring after transfer of blastocysts to recipient mice. Pronuclear transplantation was carried out as reported previously (McGrath J and Solter D 1983 Science 220, 1300–1302). Briefly, karyoplasts from one-cell SAMP1/Yit embryos were introduced into enucleated B6P1F1 zygotes (SAMP1/B6P1F1) and fused by addition of inactivated HVJ (2700 U L−1). The other group of reconstructed embryos (B6P1F1/SAMP1) was manipulated similarly. After fusion, reconstructed embryos were cultured in drops of KSOM medium for 120 h at 37°C in 5% CO2 in humidified air. Some reconstructed and control (unmanipulated) embryos that developed to the blastocyst stage were transferred to the uteri of recipient mice. Data were compared using chi-square test; differences were considered significant at P < 0.01. The development rate of [SAMP1/B6P1F1] embryos to the blastocyst stage was significantly (P < 0.01) higher (75.0%) than that of SAMP1/Yit controls (39.1%). The rate of offspring in [SAMP1/B6P1F1] was also significantly (P < 0.01) higher (47.5%) than that of SAMP1/Yit controls (22.1%). On the other hand, [B6P1F1/SAMP1] embryos showed low developmental potential compared to B6P1F1 control embryos. These results indicate that the source of the cytoplasm strongly influences the development of reconstructed embryos containing SAMP1/Yit karyoplasts. Table 1.

Raised serum APRIL levels in patients with systemic lupus erythematosus

OBJECTIVE

To determine whether serum levels of a proliferation-inducing ligand (APRIL) are raised in patients with systemic lupus erythematosus (SLE) and correlate with autoantibody titres or disease activity, or both.

METHODS

Serum samples from 48 patients with SLE, 41 normal healthy subjects, and 21 patients with rheumatoid arthritis (RA) were assayed for APRIL by enzyme linked immunosorbent assay. Medical charts were retrospectively reviewed for autoantibody titres and immunoglobulin levels. Disease activity was assessed using the British Isles Lupus Assessment Group (BILAG) index.

RESULTS

The APRIL levels in the serum samples from patients with SLE were significantly higher than in those from healthy controls and those from patients with RA. Serum APRIL levels did not correlate with serum IgG and IgM levels, but had a tendency to correlate with anti-double stranded DNA antibody titres. Moreover, serum APRIL levels correlated significantly with musculoskeletal manifestations among patients with SLE when assessed by the BILAG index.

CONCLUSION

APRIL may be an important factor in raised autoantibody titres and musculoskeletal disease in patients with SLE. Patients with raised serum APRIL levels may be ideal candidates for therapeutic targeting of APRIL.

Detection of p53 mutations in the plasma DNA of patients with ovarian cancer

Mutation of p53 is one of the most common genetic abnormalities detected in up to 81% of cases of ovarian cancer. To evaluate the use of plasma DNA analysis as a method for somatic mutation screening, we measured the presence of p53 mutations in DNA isolated from plasma and cancer tissue from patients with ovarian cancer. We analyzed the plasma DNA for the presence of p53 mutations (exons 5-8). Of 27 cases of ovarian cancer, 12 cases (44%) had mutations of p53 in cancer tissue. In two of the 12 cases (16.7%), identical mutations were detected in DNA of their preoperative plasma. In our follow-up of the two patients with p53 mutations in their plasma, mutant DNA was undetectable in their plasma after surgery. In one case, the p53 mutation re-surfaced in their plasma 16 months after surgery, and the patient died 2 months later. We have shown that tumor-derived DNA can be detected in the plasma of some patients with ovarian cancer, particularly in those with more advanced stage.

Aberrant HS1 molecule in a patient with systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the activation of autoreactive B lymphocytes, which are supposed to carry aberrant signal transduction after the stimulation of B-cell receptor (BCR). To investigate abnormalities in BCR-mediated signaling pathway in lupus B lymphocytes, we analyzed HS1, a molecule downstream of BCR, in 80 Japanese SLE patients. We identified 37 amino acid deletion of HS1 in a 25-year-old female patient, and the aberrant HS1 lacked a part of a functional motif. Analysis of genomic DNA revealed that the aberrant HS1 was caused by exon skipping. Family study showed that the patient as well as her father and sister are heterozygous for the abnormality. WEHI-231 cell, a mouse B cell line, transfected with the aberrant HS1 displayed a significantly increased cell death upon cross-linking of BCR. Additionally, peripheral B lymphocytes from the patient exerted increased apoptosis after BCR stimulation compared to those from control SLE patients. These data suggest that the aberrant HS1 molecule may transmit an accelerated signal after BCR stimulation and may play a role in the activation of autoreactive B lymphocytes.

Optimal equilibration conditions for practical vitrification of two-cell mouse embryos

The objective of the study reported here was to elucidate the optimal equilibration conditions for carrying out vitrification of two-cell mouse embryos, using a solution containing 2M dimethyl sulfoxide, 1M acetamide, and 3M propylene glycol (DAP213) as a cryoprotectant. Embryos were subjected to an equilibration process under 20 conditions of a combination of different temperatures (10 to 37 degrees C) and times (5 to 90 sec), and viability of the embryos was assessed by the rate of development into blastocysts and into live fetuses. As a result, these rates of development into blastocysts did not differ from those for unfrozen embryos. The rate of development of frozen-thawed embryos into live fetuses under conditions of 30 sec. at 20 degrees C, which was selected as having by highest operability, was 55.2%, comparable to the value (65.0%) for unfrozen embryos. Thus, the optimal equilibration condition for vitrification of two-cell mouse embryos, using DAP213 solution, was 30 sec at 20 degrees C, under which embryo viability was maximized, and this equilibration process was considered useful as a practical two-cell embryo freezing process in the vitrification method.

The influence of selection on the evolutionary distance estimated from the base changes observed between homologous nucleotide sequences

In most studies of molecular evolution, the nucleotide base at a site is assumed to change with the apparent rate under functional constraint, and the comparison of base changes between homologous genes is thought to yield the evolutionary distance corresponding to the site-average change rate multiplied by the divergence time. However, this view is not sufficiently successful in estimating the divergence time of species, but mostly results in the construction of tree topology without a time-scale. In the present paper, this problem is investigated theoretically by considering that observed base changes are the results of comparing the survivals through selection of mutated bases. In the case of weak selection, the time course of base changes due to mutation and selection can be obtained analytically, leading to a theoretical equation showing how the selection has influence on the evolutionary distance estimated from the enumeration of base changes. This result provides a new method for estimating the divergence time more accurately from the observed base changes by evaluating both the strength of selection and the mutation rate. The validity of this method is verified by analysing the base changes observed at the third codon positions of amino acid residues with four-fold codon degeneracy in the protein genes of mammalian mitochondria; i.e. the ratios of estimated divergence times are fairly well consistent with a series of fossil records of mammals. Throughout this analysis, it is also suggested that the mutation rates in mitochondrial genomes are almost the same in different lineages of mammals and that the lineage-specific base-change rates indicated previously are due to the selection probably arising from the preference of transfer RNAs to codons.

Development of colonic necrosis following severe acute pancreatitis

We herein describe a 70-year-old male patient who developed colonic necrosis following severe acute pancreatitis. He was referred to our hospital with a diagnosis of acute pancreatitis. In the course of the disease, he developed sudden and massive hematochezia and died. The autopsy findings revealed large bowel ischemia with transmural infarction. The possible pathogenic mechanisms of colonic ischemia are also discussed.

Similarity relations of DNA and RNA polymerases investigated by the principal component analysis of amino acid sequences

The principal component analysis based on the physicochemical properties of amino acid residues is applied to DNA and RNA polymerases to assign the sequence motifs for the polymerization activities of these proteins. After the reconfirmation of the sequence motifs of families A and B of DNA polymerases indicated previously, it elucidates the sequence motifs for the polymerization activity of DNA polymerase III (family C) by the similarity to the polymerization center of multimeric DNA dependent RNA polymerases. This identification proceeds to clarify the sequence motifs for polymerization activities of primases; eukaryotic and archaebacterial primases carry motifs similar to those of family C, while the motifs of eubacterial primase fall into the category of the motifs in family B DNA polymerases such as alpha, delta, epsilon and II. This finding means that DNA dependent RNA polymerases are also divided into groups corresponding to three families, A, B and C, because the monomeric DNA dependent RNA polymerases in phages are reconfirmed to carry sequence motifs similar to those of family A DNA polymerases. Furthermore, the three families of polymerization motifs are found to fall within the variation range of polymerization motifs displayed by many RNA dependent RNA polymerases, suggesting a close evolutionary relation between them. The sequence motifs for polymerization activities of reverse transcriptase and telomerase seem to be the intermediate between family A DNA polymerase and some RNA dependent RNA polymerases, e.g., from Leviviridae. On the contrary, the sequence fragments similar to the nucleotidyltransferase superfamily including DNA polymerase beta are not found in any RNA dependent RNA polymerase, suggesting their other lineage of polymerization motifs.

Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs

In order to obtain the evolutionary distance data that are as purely additive as possible, we have developed a novel method for evaluating the evolutionary distances from the base-pair changes in stem regions of ribosomal RNAs (rRNAs). The application of this method to small-subunit (SSU) and large-subunit (LSU) rRNAs provides the distance data, with which both the unweighted pair group method of analysis and the neighbor-joining method give almost the same tree topology of most organisms except for some Protoctista, thermophilic bacteria, parasitic organisms, and endosymbionts. Although the evolutionary distances calculated with LSU rRNAs are somewhat longer than those with SSU rRNAs, the difference, probably due to a slight difference in functional constraint, is substantially decreased when the distances are converted into the divergence times of organisms by the measure of the time scale estimated in each type of rRNAs. The divergence times of main branches agree fairly well with the geological record of organisms, at least after the appearance of oxygen-releasing photosynthesis, although the divergence times of Eukaryota, Archaebacteria, and Eubacteria are somewhat overestimated in comparison with the geological record of Earth formation. This result is explained by considering that the mutation rate is determined by the accumulation of misrepairs for DNA damage caused by radiation and that the effect of radiation had been stronger before the oxygen molecules became abundant in the atmosphere of the Earth.

A method for comparing circular genomes from gene locations: application to mitochondrial genomes

MOTIVATION

Data on the entire structures of organelle and bacterial genomes, most of which are known to be circular, have accumulated at a rapid pace. This information enables us to utilize the locations of homologous gene pairs for measuring the dissimilarity between complete genomic structures.

RESULTS

A macroscopic distance is presented for comparing circular genomes from their overall structures, on the basis of the locations of two pairs of homologous genes on the compared genomes. The novel aspect of our method is that the comparison between the genomes automatically reveals a relationship based on the information on all gene locations, by incorporating the mobility of each gene, which includes not only the gene order, but also the relative location between gene pairs. The plausibility of the newly defined distances is evaluated by means of 44 mitochondrial genomes. The genome distance shows high performance for quantitatively describing the differences between the gene organizations of the genomes.

AVAILABILITY

Since the programs implementing these calculations require well-arranged gene organization data, they have not been released yet. However, one of the authors will analyze circular genomes upon request. Data on the gene organizations may be submitted electronically to the address below.

Self-reproducing system can behave as Maxwell's demon: theoretical illustration under prebiotic conditions

The recent discovery of polymerase activity in a ribosomal RNA intervening sequence as well as other studies of RNA-replicating systems suggest that the first living molecules were RNAs called replicases. According to this suggestion from biochemical studies, the replicase system is chosen as the simplest case of self-reproducing systems, and the fundamental problem of "what is life" is theoretically investigated by analysing the behavior of a replicase system with a supply of organic materials under prebiotic conditions. In this analysis, it is essential to consider (i) self-reproduction on the basis of its own information, (ii) maintenance and improvement of the information by selection and (iii) environmental event of non-biologically generating organic materials from inorganic matter by photochemical reactions, probably occurring in prebiotic conditions on the Earth. The replicases can retain and further elevate their self-reproducibility through competition among their descendant mutants for acquiring a limited quantity of materials, if the initial ability of self-reproduction and the concentration of replicases are above some critical values. By this selection, the replicase molecules retain a narrowed range of nucleotide sequences, or a state of lower entropy, against the natural tendency of sequence divergence, but this entropy reduction is sufficiently compensated by the entropy production in the environmental event of energy conversion from photons to heat. Once the stability of a self-reproducing system is established in the above sense, the self-reproducing system can operate as Maxwell's demon to regulate the outside flow of matter by its catalytic function without any contradiction to the second law of thermodynamics.

A theoretical method for evaluating the relative importance of positive selection and neutral drift from observed base changes

To evaluate the relative importance of positive selection and neutral drift from the nucleotide base changes observed in the homologous alignment of genes, a theoretical equation of base changes is formulated by including both the influence of selection and the base substitutions due to mutations. Under the assumption that the average rate of base substitutions estimated from synonymous changes is the "true" mutation rate applicable at all positions, this method is applied to the vertebrate globin gene family, and evaluates the departures of base change rates from the "true" mutation rate at the first and second codon positions as a consequence of preferential selection for the conservation of important function. In addition to the strong effect of selection on the amino acid residues in the internal region mostly common to myoglobin and hemoglobin chains, the distinctive directions of selective parameter values are seen at sites on the globin surface, distinguishing the subunit contact residues of hemoglobins from the polar residues on the surface of myoglobins. Moreover, this effect of selection distinguishing between the myoglobin and hemoglobin chain genes becomes weaker in cold-blooded vertebrates, especially in fish, strongly suggesting the possibility that the clear distinction between these globins is a result of selection out of the changes regarded as neutral ones in an ancestor of vertebrates. Thus, the present method may also serve to investigate the homology of many other proteins from the aspect of molecular evolution, mainly focusing on the evolution of their biological functions.

A theoretical study on the nucleotide changes under a definite functional constraint of forming stable base-pairs in the stem regions of ribosomal RNAs; its application to the phylogeny of eukaryotes

Homologous alignment of 5 S rRNAs shows the characteristic features that (i) nucleotide changes are more remarkably seen in the stem region than in the loop region and (ii) most of the changes in the former region occur under a definite functional constraint of maintaining the stable base pairs G:C, C:G, A:U and U:A. In order to obtain a better evolutionary measure, we derived a theoretical equation for expressing the changes between the stable base-pairs in the stem region from an elementary process, in which the nucleotides in a pair mutate individually and the mis-matched pairs thus generated are eliminated by selection or return to the stable pairs by successive mutations. This equation leads us to a simple method of estimating the base-pair change rate by formally enumerating the base-pair changes observed in the pairwise comparison of homologous sequences from different species, just like the estimation of the change rate of individual nucleotides. The application of this method to 5 S rRNAs of eukaryotes reveals a new feature, in which the evolutionary distance of yeasts (Saccharomyces, Pichia and Hansenula) from higher plants and animals is much more expanded than that obtained previously by the enumeration of individual nucleotide changes observed in a whole region of 5 S rRNA and many other fungi, protozoans and algae are allocated to the middle positions between the yeasts and higher plants. The base-pair change rate is estimated to be about 2 x 10(-10) year-1, which is less than the mutation rate by one order of magnitude, and is suitable for resolving the phylogeny of species which diverged a few billion years ago. The selective term for eliminating the mis-matched pairs is also evaluated to be stronger than the mutation rate by about one order of magnitude even for the outstanding mis-matched pair of G:U and U:G.

Evolution of the self-reproducing system to the biosynthesis of the membrane: an approach from the amino acid sequence similarity in proteins

In order to study the problem of how the biomembrane synthesis started in the evolutionary process of the self-reproducing system, we carry out an extensive similarity search of the sequence data stored in databases, using the acetyl-CoA carboxylase, fatty acid synthase and the enzyme proteins leading to the combination of sn-glycerol 3-phosphate and fatty acid as the query sequences. With the use of the FASTA program (Pearson & Lipman, 1988), the proteins that carry an amino acid sequence showing similarity to any of the query sequences are picked up under the criterion of statistical significance of more than 6.0 for the homology, then classified according to the functional blocks where they operate. Finally they are filtered to the enzyme proteins in the metabolic pathways and to the DNA- or RNA-interacting proteins in the translation, transcription and replication apparatuses by eliminating proteins such as membrane proteins, lipase etc. which seem to have been generated after the appearance of the biomembrane. The distribution of the proteins thus selected shows a clear pattern that the amino acid sequences showing considerable similarity to the biomembrane synthetic proteins are concentrically found in the enzyme proteins in and around the section of glycolytic pathway from glyceraldehyde 3-phosphate to pyruvate while the DNA- or RNA-interacting proteins similar to the query sequences are distributed sparsely over the translation, transcription and replication systems. The assignment of similarity regions ascertains that considerable regions of most biomembrane synthetic proteins are covered by the enzyme proteins in and around the glycolytic pathway. Although acetyl-CoA carboxylase and fatty acid synthase are full of variety in the constitution of active domains depending on species, the above-mentioned pattern is also obtained by using either the monofunctional or the multifunctional type of proteins as the query sequences. Thus, the evolution towards biomembrane synthesis may be positioned as an event following the establishment of a section of glycolytic pathway from glyceraldehyde 3-phosphate to pyruvate. The causality of this evolution from the glycolytic pathway to the biomembrane synthesis is also discussed in connection with the absorption of protons released in the glycolytic process.

Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli

As an advanced molecular study of the problems of the evolution of organisms, the transcriptional regulation system is studied by investigating the amino acid sequence similarities between the proteins in the regulation system of Escherichia coli in which the data of sequenced proteins as well as of regulator-regulon relationships are accumulated. The similarities between the proteins are calculated by the FASTA algorithm and their homology is also evaluated in terms of statistical significance with the use of the RDF2 program. This investigation reveals that the similarity between the regulatory protein and the regulated protein is hardly found, but many similarities are found between regulatory proteins and between regulated proteins. These similarity relations are compared with the regulator-regulon relationships ascertained experimentally. From this comparison, it is found that similar regulatory proteins rarely regulate the transcription of similar protein genes. As most of the highly similar proteins are considered to have diverged from a common ancestral protein, this finding strongly suggests the possibility that descendant regulatory proteins have been promiscuously coupled with descendant operons, independently of their ancestral regulator-regulon relationship, and that some of the couplings have been fixed by selection to form the present system of transcriptional regulation. The compatibility of such promiscuous coupling with regulatory organization is illustrated in the carbohydrate transport systems and the succeeding metabolic pathways, whose organization is comprehensive in sending nutritious substances to the central path of glycolysis under different environmental conditions. The benefit of flexibility in regulator-regulon relationships in evolutionary processes is also discussed in connection with the punctuational divergence of species in macroevolution and the cell differentiation in multicellular organisms.

A comprehensive representation of extensive similarity linkage between large numbers of proteins

A method is described for the representation of a bird's-eye view of similarity relationships between large numbers of proteins. With the aid of single-linkage clustering, proteins are clustered into groups on the basis of various types of similarity such as sequence similarity estimated between all the protein pairs. Proteins in a group are directly or indirectly connected to all proteins in the same group by similarities higher than a given threshold and show no similarity higher than the threshold to any proteins outside the group. Thus, all the proteins directly or indirectly related to a protein can be selected out of a large number of proteins by the clustering. Recursion of this clustering of proteins in each group leads to further classification of the proteins. The similarity relationships in each group are visually represented by a similarity matrix. This representation has the advantage of easy detection of the existence of multidomain proteins and diverged families as well as closely related proteins. Such as exhaustive approach to similarity relationships of proteins will be useful for revealing functional/structural/evolutionary units in proteins.

A simple procedure for assigning a sequence motif with an obscure pattern: application to the basic/helix-loop-helix motif

We have developed a simple method to assign a sequence motif with an obscure pattern. Given a multiple sequence alignment for a region of protein that is known or strongly believed to have the same secondary and tertiary structures, the quantification method by principal component analysis is designed to find the regions most likely to have the same structure in a protein outside of the original set. The potential of this newly developed method was evaluated with reference to the known basic/helix-loop-helix (bHLH) motifs, and its characteristics were discussed with four obscure but well-defined motifs and compared with the other methods for searching sequence motifs. The method was also applied to assign the bHLH motif in Epstein-Barr virus nuclear antigen 1 (EBNA-1). This application revealed one candidate for the basic/helix 1 region and two candidates for the helix 2 region in the bHLH motif, within the region from amino acid residues 460 to 600, which is in good agreement with our previous experimental studies on the DNA binding region of EBNA-1. The basic/helix-loop-helix-loop-helix structure thus assigned suggests a function of EBNA-1 which is associated with both replication and transcription.

Evolution of genetic information flow from the viewpoint of protein sequence similarity

As a course of inquiry into the evolution of genetic information flow, similarity relations of amino acid sequences between the proteins involved in translation, transcription and replication are investigated. The sequence data of these proteins are mostly accumulated from Escherichia coli, and the present investigation is carried out mainly on this organism by the FASTP program. This result reveals an interesting similarity linkage extending from ribosomal proteins to the proteins participating in translational elongation process and to the proteins in transcription and replication. Although the ribosomal proteins are of relatively short polypeptide chains, our systematic comparison between these proteins finds many similarity relations, being more than 100 in terms of "overlap", reducing them to about 14 elementary ribosomal proteins from which other ribosomal proteins would have diverged. Moreover, the proteins involved in translation, transcription and replication contain the regions similar to the elementary ribosomal proteins. In particular, some initiation and elongation factors in translation process are assigned to be similar to the elementary ribosomal proteins almost over the whole regions. To such an elongation factor Tu, the alpha and sigma 70 subunits of RNA polymerase and primase also show similarity in the wider regions than the individual ribosomal proteins, and they are shown to be fundamental for the similarity linkage extending to the other polypeptide chains involved in transcription and replication processes, although the latter polypeptide chains contain regions not similar to any ribosomal protein. This divergence pattern of similarity relations strongly suggests that the proteins involved in the contemporary genetic information flow DNA-->RNA-->protein have evolved from some elementary ribosomal proteins, first by gene fusion, in a primitive organism of the RNA-protein world, and then by the addition of the mechanism of domain shuffling from other genes in the DNA-RNA-protein world.

Permeability of mammary gland capillaries to ferritin in mice

The permeability of mammary gland capillaries to ferritin was investigated by transmission electron microscopy. In virgin mice, the concentration of tracers in perivascular spaces increased with the advance of time after injection. The ferritin never passed through the intercellular junction of the endothelial cells. In the early to middle stages of lactation, numerous ferritin particles were observed in the basal cytoplasm of alveolar epithelial cells after only 1 min of circulation. These findings indicate that a large amount of materials quickly pass through the capillary walls during these periods for milk production. The number of vesicles labelled with ferritin per micron2 of endothelial cytoplasm decreased remarkably in the late stage of lactation. This result suggests that the permeability of vesicles declines along with the degeneration of alveolar cells.

Divergence pattern and selective mode in protein evolution: the example of vertebrate myoglobins and hemoglobin chains

The evolutionary relation of vertebrate myoglobin and the hemoglobin chains including the agnathan hemoglobin chain is investigated on the basis of a new view of amino acid changes that is developed by canonical discriminant analysis of amino acid residues at individual sites. In contrast to the clear discrimination of amino acid residues between myoglobin, hemoglobin alpha chain, and hemoglobin beta chain in warm-blood vertebrates, the three types of globins in the lower class of vertebrates show so much variation that they are not well discriminated. This is seen particularly at the sites that are ascertained in mammals to carry the amino acid residues participating in stabilizing the monomeric structure in myoglobin and the residues forming the subunit contacts in hemoglobin. At these sites, agnathan hemoglobin chains are evaluated to be intermediate between the myoglobin and hemoglobin chains of gnathostomes. The variation in the phylogenetically lower class of globins is also seen in the internal region; there the amino acid residues of myoglobin and hemoglobin chains in the phylogenetically higher class exhibit an example of parallel evolution at the molecular level. New quantities, the distance of sequence property between discriminated groups and the variation within each group, are derived from the values of discriminant functions along the peptide chain, and this set of quantities simply describes an overall feature of globins such that the distinction between the three types of globins has been clearer as the vertebrates have evolved to become jawed, landed, and warm-blooded. This result strongly suggests that the functional constraint on the amino acid sequence of a protein is changed by living conditions and that severe conditions constitute a driving force that creates a distinctive protein from a less-constrained protein.

Effects of estrogen and progesterone on the development of the mammary gland and the associated blood vessels in ovariectomized mice

Effects of estrogen and progesterone on the first abdomino-inguinal mammary gland and the associated blood vessels in ovariectomized mice were investigated morphometrically, and light and electron microscopically. Although there were no significant differences in the area of the fat pad of the mammary gland among the experimental groups, the area of the mammary parenchyma and diameters of the blood vessels supplying the mammary gland, i.e., A. et V. circumflexa ilium profunda and A. et V. epigastrica caudalis superficialis, reached the maximal value in ovariectomized mice treated with estradiol (E) + progesterone (P). Similarly, the blood capillaries around buds and ducts of the mammary gland were most densely distributed in E + P treated mice. In the adipose tissues of the mammary stroma in intact mice, fat cells were of multilocular type in the peripheral regions around the main vessel, and of unilocular type in the other part. In E and E + P treated mice, however, fat cells were mostly of unilocular type. These findings suggest that the formation of mammary fat tissues may occur in advance of that of the mammary parenchyma. By TEM, epithelial cells of the mammary parenchyma contained a large number of mitochondria and ribosomes, well-developed Golgi apparatus and rER, and large lipid droplets. Endothelial cells of blood capillaries displayed numerous pinocytotic vesicles, longer marginal folds and microvillous processes. Each organelle in these two cell types increased in number or developed to a greater degree in E + P treated mice than the other experimental groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes

In order to get an insight into the evolutionary aspect of metabolic pathways, especially of the ubiquitous glycolytic pathway, we have carried out an extensive search of sense-sense and sense-antisense similarities for enzyme proteins in the glycolytic pathway, the pentose phosphate cycle, alcohol and lactate fermentation pathways and the TCA cycle. This investigation of amino acid sequences reveals a curious pattern of similarity relations; no similarity can be found between the enzyme proteins in a section of the glycolytic pathway where the glyceraldehyde-3-phosphate or even glycerol-3-phosphate is converted into the pyruvate while many examples of sense-sense and sense-antisense similarities are found even between enzyme proteins in distant blocks, e.g. between the proteins in the TCA cycle and those in the pentose phosphate cycle, as well as between the functionally associated proteins in each of these blocks. Complementary to this characteristic pattern of amino acid sequence similarity, the search for similarities of nucleotide sequences also finds that the similarities of glycolytic enzyme genes, some sense-sense and others sense-antisense similarities, are concentrated on the nucleotide sequences of prokaryotic 16S or eukaryotic 18S ribosomal RNA gene with its flanks, although some of the copy sequences are also found in transfer RNA genes as well as in 23S or 26S ribosomal RNA gene. These results strongly suggest that the metabolic pathways have been developed by the chance assembly of enzyme proteins generated from the sense and antisense strands of pre-existing genes, e.g. the fermentation pathways and pentose phosphate cycle by the proteins from the genes of enzymes in the glycolytic pathway and the TCA cycle from all these successively increased genes, ascribing the origin of metabolic enzyme genes to the close relation between the glycolytic enzyme protein genes and the RNA gene cluster.

Fine structure of the parotid gland in the crest-tailed marsupial-rat (Dasyuroides byrnei)

The parotid gland of Dasyuroides byrnei was examined by light microscopy, and transmission and scanning electron microscopy. The acini were composed predominantly of seromucous cells with a few mucous cells. The seromucous cells were light or dark cells containing acidophilic spherical granules of moderate to high electron density and had well-developed cytoplasmic organelles-ordinary mitochondria and large mitochondria with tubular cristae, RER with vesicular or tubular elements, and Golgi apparatus with lamellae, vesicles and vacuoles. The mucous cells had basophilic amorphous granules of low electron density, like those of ordinary mucous cells. The intercalated ducts were composed of simple cuboidal light cells having a few electron-dense granules. The striated ducts consisted of tall columnar light cells containing numerous vesicles and mitochondria with tubular cristae, the same as found in acinar seromucous cells.

Pregnancy and lactation affect the microvasculature of the mammary gland in mice

Microvascular changes in the mammary gland in mice during pregnancy and lactation were investigated by scanning electron microscopy (SEM) with a corrosion cast method, transmission electron microscopy (TEM) and morphometry. By SEM, duct-associated capillary plexuses were sparsely distributed to branch into adipocytes during virgin period. With advance in pregnancy, both branches from the capillary plexuses and branches from the vessels surrounding adipocytes extended further to form capillary networks. The basket-like architecture was completed by day 18 of pregnancy. These findings may indicate that angiogenesis occurs frequently during this period. During lactation, the basket-like architecture still remained and the capillaries surrounding alveoli meandered. After weaning, the regression of microvasculature followed the degeneration of alveoli. By TEM and morphometry, the density of pinocytotic vesicles (PVs) (number of PVs per microns 2 of endothelium cytoplasm) increased twofold from day 18 of pregnancy to day 5 of lactation, furthermore increased threefold from days 10 to 20 of lactation, and subsequently decreased after weaning. Marginal folds and microvillous processes gradually increased in length with advance in pregnancy, reached the maximum from days 5 to 15 of lactation, and thereafter decreased. In addition, the capillaries with thinner walls were in close contact with alveoli during the late stage of pregnancy and during lactation. Furthermore, the alveolar epithelial cells had well-developed basal infoldings during lactation. These findings suggest that the capillaries play an important role in transporting materials necessary for milk production.

Structure model of core proteins in photosystem I inferred from the comparison with those in photosystem II and bacteria; an application of principal component analysis to detect the similar regions between distantly related families of proteins

A principal component analysis based on the physico-chemical properties of amino acid residues is developed to assign similar regions between distantly related families of proteins, taking account of the species diversities in respective families. The most important advantage of this analysis should be that it reflects different physico-chemical properties and thus can predict more detailed structural properties, including the transmembrane helices, than the hydropathy analysis. Its first application reconfirms the similarity between the core proteins of photosynthetic reaction center in purple bacteria and those of photosystem II, indicating that the low percentage of identical amino acid residues estimated previously between them is due to much allowance for amino acid substitutions in purple bacteria. The application of this analysis to the core proteins of photosystem I reveals that any of these proteins includes two domains, each showing high similarity to the amino acid sequences of core proteins in photosystem II and purple bacteria. A core structure model of A1 and A2 proteins folded into four layers of sheets of transmembrane helices is proposed to provide a molecular basis for the electron pathway suggested by spectroscopic experiments as well as for the interaction sites with plastocyanin, 9 kDa protein and LHC proteins.

A protein secondary structure database (PSS)

A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.

Principal component analysis to detect the similarity of distantly related proteins; its application to cytochromes c, c1 and f

A new method has been developed for detecting the similarity between distantly related families of proteins. The amino acid sequences of each family of proteins are vertically aligned by a homologous alignment method and the physico-chemical properties of the amino acid residues at the corresponding site are evaluated simultaneously, by method of the principal component analysis. Taking into account the species diversity of each family of proteins, we assign the similar regions between the different families of proteins by the overlapping degree of the standard deviations around the mean values of the first principal component. To investigate the homologous relationship between the electron transport proteins in photosynthetic and O2 respiratory systems, this method has been applied to 70 species of mitochondrial cytochrome c, 4 species of cytochrome c1 and 7 species of cytochrome f. This analysis reveals that both cytochrome f and cytochrome c1 have large regions which are similar to those of cytochrome c. Assuming that these similar regions have the same stereochemical structures as those in cytochrome c, we can predict the outlines of the tertiary structures of cytochrome c1 and cytochrome f, respectively, each able to interact with its electron acceptor, cytochrome c and plastocyanin.

Discrimination between adaptive and neutral amino acid substitutions in vertebrate hemoglobins

A discriminant analysis on the basis of the physicochemical properties of amino acid residues is developed to investigate the accumulation pattern of amino acid substitutions in a family of proteins. The application of this analysis to vertebrate hemoglobins reveals the following new results. (1) The major components of teleost fish and amphibian hemoglobins showing the Root effect are sharply discriminated from mammalian hemoglobins in several regions of the alpha and beta chains, whereas shark, minor components of teleost fish and amphibian, reptile, and bird hemoglobins showing no Root effect exhibit a gradual change to mammalian hemoglobin in a straightforward way. This result suggests at least two lines of molecular evolution in vertebrate hemoglobins. (2) The nonadult hemoglobin chains are allocated to the latter line, i.e., tadpole, zeta, and pi chains are similar to shark and trout I chains, and epsilon and gamma chains are similar to some of the reptile chains. (3) In any case, most of the amino acid residues causing the discrimination are located near the sites that carry the amino acid residues conserved well throughout all classes of vertebrates, suggesting that modifications adapting to the respective living conditions or respiratory organs have taken place effectively near the amino acid residues essential for the manifestation of cooperative oxygen binding. (4) The amino acid residues at other sites are changed from one to another species even within the same class, showing a constant substitution rate as a whole. These amino acid substitutions may be nearly neutral, being under a weak functional constraint. The number of sites allowing such neutral substitutions is rather small, less than one-half of all the sites in the adult hemoglobins of bird and mammal, whereas it amounts to two-thirds in teleost fish hemoglobins.

Escherichia coli K12 genomic database

We have compiled the genomic nucleic acid sequence data of Escherichia coli K12 available from the existing major data collections and from the literature. The collected data are structured as a database for easy access and analysis. The sequence segments in the database are ordered by genetic map position. Sequence redundancy has been completely removed by combining overlapping sequences; therefore, our sequence data are amenable to statistical analysis. We have specified with a plus or minus (+ or -) on which of the two DNA strands the segment exists. The database currently contains a total of 954,392 bp, which corresponds to about 20% of the entire genome size. The sequence data are available on request.

Fine structure of the mandibular gland in crest-tailed marsupial-rat (Dasyuroides byrnei)

The mandibular glands of Dasyuroides byrnei were examined by light microscopy, and transmission and scanning electron microscopy. The secretory units consisted of numerous seromucous acini and a few seromucous demilunes. The seromucous acini were almost always capped by demilunes. The acinar seromucous cells contained faintly basophilic, light, coarse, bipatite secretory granules with matrix of low and moderate densities. The demilunar cells were dark compared with acinar seromucous cells and contained acidophilic secretory granules with a fibrillogranular matrix of moderate density. Preacinar cells with a seromucous nature were occasionally present at the junction between the acinus and intercalated duct. These cells had numerous basophilic granules, which were similar to those of acinar seromucous cells. The intercalated ducts consisted of simple cuboidal light cells that had a few small electron-dense granules. The striated ducts were composed of tall columnar light cells containing numerous vesicles, but no secretory granules. The mandibular acini of D. byrnei were composed of two cell types having a seromucous nature, unlike those of the opossum and many other mammals.

Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA

An extensive set of 216 eukaryotic 5S rRNA sequences are compared and the previous observations, that (i) invariable base positions are located primarily in loop regions and (ii) stem regions are more variable but the number of mispairings is kept small, are confirmed. On the basis of a comparison of the contemporary sequences, evolutionary processes of base substitutions in stem regions are discussed. It is found that there is no evident selective pressure to keep a particular kind of base pair in stem regions and individual bases may change freely as long as mispairings are kept few. It is also found that the secondary structure of 5S rRNA has been maintained stable by an equilibrium between base pair formation- and destruction-substitutions and that the low occurrence of mispairings in stem regions is attributable to a high value (ca. 90) of the equilibrium constant. The present analyses suggest a structure-function relationship of the eukaryotic 5S rRNA; stem regions structurally help loop regions to interact well with other ribosomal components and therefore, there is a marked selection pressure to maintain the secondary structure under the evolutionary noise of mutation.

Fine structure of the mandibular gland in volcano rabbit

The mandibular glands of 6 male and 6 female volcano rabbits were examined by means of light and transmission electron microscopy. The acinar cells of the glands were seromucous in nature, and contained faintly basophilic granules. The cells were classified into the light cells containing granules of low or moderate densities and the clear cells having polygonal granules of low density. The preacinar cells were occasionally observed at the site between acinus and intercalated duct. These cells had many weakly basophilic granules which contained fine granular materials of moderate density. The intercalated ducts were composed of light cells containing cored granules. The striated duct cells consisted of light cells and dark cells. Both of them contained a few vacuoles and vesicles, but no secretory granules. No sex-and age-related differences were observed in the mandibular gland of the volcano rabbit. The mandibular gland of the volcano rabbit was similar to the rabbit mandibular gland rather than the pika mandibular gland morphologically.

A study on the quaternary structure change of hemoglobin in the ligation process

In order to inquire into the molecular mechanism underlying the cooperative ligand binding to hemoglobin (Hb), conformational interaction at the interfaces between subunits are investigated on the basis of the atomic coordinates of human deoxy and human carbonmonoxy Hbs. Hypothetical intermediate structures are used, each of which is obtained from the procedure where one or more subunits in deoxy Hb are replaced by the corresponding CO-liganded subunits in carbonmonoxy Hb using the method of superimposition of two sets of atomic coordinates. When either alpha or beta subunit is substituted with the corresponding subunit in carbonmonoxy Hb, serious steric hindrances are produced between alpha 1FG4(92)Arg and beta 2C3(37)Trp or between alpha 1C6(41)Thr and beta 2FG4(97)His, all of which belong to the allosteric core affected directly by ligand binding. These steric hindrances become more serious when both alpha 1(alpha 2) and beta 2(beta 1) subunits are substituted. Therefore the change in the relative distance between iron atom and porphyrin by ligation results in strain in the C-terminal residues as an effect of the steric hindrance between the FG and C segments. However, no steric hindrance can be seen between subunits when the subunits in carbonmonoxy Hb are substituted with the corresponding subunits in deoxy Hb. The nature of the quaternary structural change from liganded to deoxy Hb seems to be different from that from deoxy to liganded Hb.

Accumulation pattern of amino acid substitutions in protein evolution

A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This "two clock" interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.