Structure and evolution of mammalian ribosomal proteins

Mammalian (rat) ribosomes have 80 proteins; the sequence of amino acids in 75 have been determined. What has been learned of the structure of the rat ribosomal proteins is reviewed with particular attention to their evolution and to amino acid sequence motifs. The latter include: clusters of basic or acidic residues; sequence repeats or shared sequences; zinc finger domains; bZIP elements; and nuclear localization signals. The occurrence and the possible significance of phosphorylated residues and of ubiquitin extensions is noted. The characteristics of the mRNAs that encode the proteins are summarized. The relationship of the rat ribosomal proteins to the proteins in ribosomes from humans, yeast, archaebacteria, and Escherichia coli is collated.     

Rapid sequence evolution of the mammalian sex-determining gene SRY

In mammals, induction of male sex determination requires the Y-chromosome gene SRY. SRY encodes a protein with a central 'high mobility group' domain (HMG box) of about 78 amino acids. HMG boxes are found in a wide variety of proteins that bind to DNA with high affinity but differing degrees of sequence specificity. The human SRY protein binds to linear DNA with sequence specificity and to cruciform DNA structures without sequence specificity. The DNA-binding activity of the SRY protein resides in the HMG box and mutations in this region are associated with sex reversal in XY females. No function has been ascribed to the portions of the SRY protein outside the HMG box. SRY belongs to a family of genes that are related by sequence homology within the DNA-binding domain: the genes most similar to SRY (> 60%) have been named SOX genes (SRY box genes). None of the known SOX genes is homologous to SRY outside the HMG-box region. Although SRY is an important developmental regulator, its sequence is poorly conserved between species apart from the HMG-box domain. Here we investigate the coding sequence of SRY in primates and find that evolution has been rapid in the regions flanking the conserved domain. The high degree of sequence divergence and the frequency of non-synonymous mutations suggest either that the majority of the coding sequence has no functional significance or that directional selection has occurred.     

A new symmetrodont mammal from China and its implications for mammalian evolution

A new symmetrodont mammal has been discovered in the Mesozoic era (Late Jurassic or Early Cretaceous period) of Liaoning Province, China. Archaic therian mammals, including symmetrodonts, are extinct relatives of the living marsupial and placental therians. However, these archaic therians have been mostly documented by fragmentary fossils. This newfossil taxon, represented by a nearly complete postcranial skeleton and a partial skull with dentition, is the best-preserved symmetrodont mammal yet discovered. It provides a new insight into the relationships of the major lineages of mammals and the evolution of the mammalian skeleton. Our analysis suggests that this new taxon represents a part of the early therian radiation before the divergence of living marsupials and placentals; that therians and multituberculates are more closely related to each other than either group is to other mammalian lineages; that archaic therians lacked the more parasagittal posture of the forelimb of most living therian mammals; and that archaic therians, such as symmetrodonts, retained the primitive feature of a finger-like promontorium (possibly with a straight cochlea) of the non-therian mammals. The fully coiled cochlea evolved later in more derived therian mammals, and is therefore convergent to the partially coiled cochlea of monotremes.     

Otx1 and Otx2 in the development and evolution of the mammalian brain

In the last decade, a number of genes related to the induction, specification and regionalization of the brain were isolated and their functional properties currently are being dissected. Among these, Otx1 and Otx2 play a pivotal role in several processes of brain morphogenesis. Findings from several groups now confirm the importance of Otx2 in the early specification of neuroectoderm destined to become fore-midbrain, the existence of an Otx gene dosage-dependent mechanism in patterning the developing brain, and the involvement of Otx1 in corticogenesis. Some of these properties appear particularly fascinating when considered in evolutionary terms and highlight the central role of Otx genes in the establishment of the genetic program defining the complexity of a vertebrate brain. This review deals with the major aspects related to the roles played by Otx1 and Otx2 in the development and evolution of the mammalian brain.     

The role of the striatum in the evolution of the mammalian forebrain

AIM: To test if anesthetic procedures change the hemodynamic pattern in animals with experimental septic shock. METHODS: The effect of two anesthetics on systemic hemodynamic and skeletal muscle microcirculatory responses in high cardiac output live E. coli bacteremia was studied in rats and compared to the effect of two other anesthetic procedures in previously published studies. RESULTS: Baseline blood pressures and cardiac outputs were similar in rats with decerebrate, ketamine/xylazine, pentobarbital or urethane/chloralose anesthesia. There was a relative baseline tachycardia in decerebrate rats. Ketamine/xylazine anesthetized rats had reduced blood pressure, cardiac output, and heart rate. In decerebrate, pentobarbital, and urethane/chloralose anesthesia, cardiac output increased initially during bacteremia but did not remain elevated in pentobarbital anesthesia. Blood pressure and heart rate remained constant in pentobarbital, decerebrate, and urethane/chloralose anesth esia. During bacteremia, cardiac output, blood pressure, and vascular resistance did not change with ketamine/xylazine, but the heart rate increased. Baseline diameters of cremaster muscle large (A1) arterioles were higher in decerebrate anesthesia. A1 arterioles constricted during high cardiac output bacteremia in decerebrate rats, and pentobarbital or urethane/chloralose-anesthetized rats. A4 arterioles in bacteremia dilated in decerebrate and pentobarbital anesthesia, but did not change under urethane/chloralose and ketamine/xylazine anesthesia. CONCLUSION: Anesthetics influence baseline systemic variables and the response of systemic hemodynamics of rats to E. coli bacteremia. During bacteremia, anesthetics primarily affect the reactivity of skeletal muscle small arterioles. Ketamine/xylazine anesthesia has the most pronounced effect on systemic and microcirculatory variables and seems to be an inappropriate choice in sepsis experiments in rats.     

Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor

The repeatability of patterns of variation in Ka/Ks and Ks is expected if such patterns are the result of deterministic forces. We have contrasted the molecular evolution of the mammalian insulin-like growth factor type II receptor (Igf2r) in the mouse-rat comparison with that in the human-cow comparison. In so doing, we investigate explanations for both the evolution of genomic imprinting and for Ks variation (and hence putatively for mutation rate evolution). Previous analysis of Igf2r, in the mouse-rat comparison, found Ka/Ks patterns that were suggested to be contrary to those expected under the conflict theory of imprinting. We find that Ka/Ks variation is repeatable and hence confirm these patterns. However, we also find that the molecular evolution of Igf2r signal sequences suggests that positive selection, and hence conflict, may be affecting this region. The variation in Ks across Igf2r is also repeatable. To the best of our knowledge this is the first demonstration of such repeatability. We consider three explanations for the variation in Ks across the gene: (1) that it is the result of mutational biases, (2) that it is the result of selection on the mutation rate, and (3) that it is the product of selection on codon usage. Explanations 2 and 3 predict a Ka-Ks correlation, which is not found. Explanation 3 also predicts a negative correlation between codon bias and Ks, which is also not found. However, in support of explanation 1 we do find that in rodents the rate of silent C --> T mutations at CpG sites does covary with Ks, suggesting that methylation-induced mutational patterns can explain some of the variation in Ks. We find evidence to suggest that this CpG effect is due to both variation in CpG density, and to variation in the frequency with which CpGs mutate. Interestingly, however, a GC4 analysis shows no covariance with Ks, suggesting that to eliminate methyl-associated effects CpG rates themselves must be analyzed. These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations.     

Molecular evolution modeled as a fractal Poisson process in agreement with mammalian sequence comparisons

The fractal doubly stochastic Poisson process (FDSPP) model of molecular evolution, like other doubly stochastic Poisson models, agrees with the high estimates for the index of dispersion found from sequence comparisons. Unlike certain previous models, the FDSPP also predicts a positive geometric correlation between the index of dispersion and the mean number of substitutions. Such a relationship is statistically proven herein using comparisons between 49 mammalian genes. There is no characteristic rate associated with molecular evolution according to this model, but there is a scaling relationship in rates according to a fractal dimension of evolution. The FDSPP is a suitable replacement for the homogeneous Poisson process in tests of the lineage dependence of rates and in estimating confidence intervals for divergence times. As opposed to other fractal models, this model can be interpreted in terms of Darwinian selection and drift.     

川西拗陷须家河组致密砂岩成岩作用特征及其对储层的影响

通过对川西拗陷须家河组储层的岩石学、矿物学、物性等特征研究,明确了砂岩成岩作用特征及其对储层质量演化的影响.受沉积相和成岩作用的影响,川西拗陷须家河组砂岩储层致密-超致密并具极强非均质性.影响储层质量的成岩事件包括机械压实作用、石英颗粒压溶作用、自生矿物胶结作用、溶蚀作用以及绿泥石衬边的形成.压实作用是造成砂岩孔隙度降低的最主要因素.晚期碳酸盐胶结作用在须四段钙屑砂岩和须二段细粒砂岩中较为普遍,较高含量碳酸盐胶结物对储层具有明显的破坏作用.自生石英主要来自碎屑石英的压溶,在须二段砂岩中含量较高.具一定厚度、连续性较好的绿泥石衬边可以抑制石英胶结物的形成以及压溶作用进行,对须家河组,特别是须二段砂岩储层孔隙保存具有双倍积极作用.须家河组相对优质砂岩储层主要孔隙类型为剩余粒间孔和粒间溶蚀扩大孔,原生孔隙的保存对次生 孔隙形成以及储层质量至关重要.破裂作用可以提高砂岩的储渗能力,同时也有利于砂岩中溶蚀孔隙的形成.     

CD1d-mediated recognition of an alpha-galactosylceramide by natural killer T cells is highly conserved through mammalian evolution

BACKGROUND: Although increasing rates of breast carcinoma incidence have been observed in Asian countries, appropriate strategies for detecting early stage breast carcinoma in such communities have been difficult to formulate, particularly because no large population screening trial specifically involving Asian women has been reported. The objective of this study was to evaluate the effectiveness and quality of mammography as a screening technique for Singaporean women, who are predominantly Chinese. METHODS: In this prospective study, 166,600 women in Singapore ages 50-64 years were randomized to either 2-view mammography without physical examination (67,656) or observation (97,294, controls) over 2 years. RESULTS: Of these women, 28,231 (41.7%) responded and were screened; they were more likely to be married, have more formal education, be working, be Chinese, and be in a higher socioeconomic group (P < 0.001 for all variables). To assess for response bias that could affect outcome, results were also evaluated for nonrespondents (n = 39,425). The incidence rate of cancers among nonrespondents (1 per 1000 woman-years) was less than the 1.3 in women not invited to have screening (P = 0.03, relative risk [RR], 1.3; 95% confidence interval [CI], 1.0-1.7). However, cancers arising from nonrespondents did not differ significantly in stage distribution when compared with cancers within the control group. For every 1000 women screened, 4.8 cancers were detected. The prevalence ratio (the number of cancers detected per 1000 women at first screening divided by the corresponding incidence rate in controls per year) was 3.6 for screened women and 2.4 for women invited to have screening. The majority of cancers detected through screening were early stage, with 64% as either ductal carcinoma in situ (26%) or Stage I disease (38%) and was significantly more than the corresponding 26% in women not invited to have screening (P < 0.001). When only invasive cancers were considered, screened women still had more early cancers, with 65% having no lymph node involvement, compared with 47% in the group not invited to have screening (P = 0.001; RR, 1.4; 95% CI, 1.2-1.7). Women who were screened had half the risk of having Stage II or later cancers (P < 0.0001; RR, 0.5; 95% CI, 0.4-0.7) when compared with women not invited to have screening. This higher detection rate of early cancers through screening was accomplished with acceptable recall rates of 8% for further mammographic films or physical examination and a biopsy rate of 1.0% (10 per 1000 women screened). The interval cancer rate was 2.1 per 10,000 women screened in the first year of follow-up. CONCLUSIONS: These positive results of intermediate measures suggest that, in Asian communities, screening mammography could be an important modality for detecting early stage breast carcinoma. However, the low compliance rates suggest that health education efforts must focus on issues related to acceptability if such programs are to succeed.     

Ageing and mammalian mitochondrial genetics

Pig mange was investigated serologically with ELISA using Chekit Sarcoptest. The test consists of a homogenized antigen of Sarcoptes scabiei var. vulpes. A total of 356 sows sera samples were collected from 16 mange free breeding units and 19 units with clinical manifestation of mange infestation. The specificity of the test was 99.34% and the mean sensitivity value was 62%. This test will allow in the future not only the rapid and certain diagnosis of pig mange but also the screening of the pig breeding units after eradication of the disease.     

Genomic imprinting and mammalian development

Composites of chitin with calcium phosphate were obtained by in situ precipitation of the mineral from a supersaturated solution onto chitin scaffolds. The chitin scaffolds were obtained by freeze drying to give a highly porous structure possessing a polar surface favorable for apatite nucleation and growth. THe extent and arrangement of calcium phosphate deposits on the chitin and substituted chitin scaffolds were explored. Up to 55% by mass of calcium phosphate could be incorporated into chitin scaffolds. Deposits on the chitin surface were a continuous apatite carpet nature while deposits on carboxymethylated chitin surfaces displayed a spherical morphology. Carboxymethylation of chitin exerts an overall inhibitory effect towards calcium phosphate deposition, but it provides for site-specific nucleation of the mineral phase. In situ precipitation can be an important route in the future production of various polymer-calcium phosphate composites.     

Engineering mammalian chromosomes

Construction of a mammalian artificial chromosome (MAC) will develop our understanding of the requirements for normal chromosome maintenance, replication and segregation while offering the capacity for introducing genes into cells. Construction of MACs with telomere, centromere and replication function has been approached by two methods. The 'top down' strategy uses artificially induced chromosome truncations as a means to define a minimal chromosome that retains the mitotic properties of a normal chromosome. The 'build up' approach has focused on attempts to assemble MAC vectors containing functionally defined telomere repeats together with candidate centromere and replication origin sequences. Here we report on significant advances in both areas, with particular emphasis on two reports showing that stable, low copy number MACs containing a functional centromere can be produced following transfection of naked DNA into the human HT1080 cell line. One approach used a transfection mixture of cloned synthetic alpha-satellite arrays up to 1 Mb in length and unlinked telomeric DNA, in either the presence or absence of random human genomic DNA fragments. In the second approach, MACs were formed from a defined yeast artificial chromosome (YAC) DNA molecule containing 100 kb of highly homo- geneous alphoid DNA retrofitted with human telomere repeats. These results demonstrate for the first time that alpha-satellite DNA can seed de novo centromeres in human cells, indicating that this repetitive sequence family plays an important role in centromere function. The stability of these MACs suggests that they have potential to be developed as gene delivery vectors.     

Evidence for an early appearance of modern post-switch isotypes in mammalian evolution; cloning of IgE, IgG and IgA from the marsupial Monodelphis domestica

In birds, reptiles and amphibians the IgY isotype exhibits the functional characteristics of both of IgG and IgE. Hence, the gene for IgY most likely duplicated some time during early mammalian evolution and formed the ancestor of present day IgG and IgE. To address the question of when IgY duplicated and formed two functionally distinct isotypes, and to study when IgG and IgA lost their second constant domains, we have examined the Ig expression in a non-placental mammal, the marsupial Monodelphis domestica (grey short-tailed opossum). Screening of an opossum spleen cDNA library revealed the presence of all three isotypes in marsupials. cDNA clones encoding the entire constant regions of opossum IgE (epsilon chain), IgG (gamma chain) and IgA (alpha chain) were isolated, and their nucleotide sequences were determined. A comparative analysis of the amino acid sequences for IgY, IgA, IgE and IgG from various animal species showed that opossum IgE, IgG and IgA on the phylogenetic tree form branches clearly separated from their eutherian counterparts. However, they still conform to the general structure found in eutherian IgE, IgG and IgA. Our findings indicate that all the major evolutionary changes in the Ig isotype repertoire, and in basic Ig structure that have occurred since the evolutionary separation of mammals from the early reptile lineages, occurred prior to the evolutionary separation of marsupials and placental mammals.     

Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution

In order to generate anchor points connecting the rat cytogenetic and genetic maps, the cytogenetic position of 62 rat markers (including 55 genes) already localized genetically was determined by fluorescence in situ hybridization. Whenever possible, markers located near one end of the linkage groups were included. These new localizations allowed us to unambiguously orient the 20 autosomal and the X chromosome linkage groups. The position of the centromere in the linkage map could also be determined in the case of several metacentric chromosomes. In addition, the regional localization of 15 other rat genes was determined. These new data bring useful information with respect to comparative mapping with the mouse and the human and to mammalian evolution. They illustrate, for instance, that groups of genes can remain syntenic during mammalian evolution while being subjected to intrachromosomal rearrangements in some lineages (synteny is conserved while gene order is not). This analysis also disclosed cases of synteny conservation in one the two rodent species and the human, while the synteny is split in the other rodent species: such configurations are likely examples of lineage-specific interchromosomal rearrangements associated with speciation.     

长寿-涪陵地区下三叠统早期地层特征及沉积环境研究

长寿-涪陵地区下三叠统早期地层层位齐全,界线清楚,出露良好,总体岩性以海相碳酸盐岩为主,总厚度达600余米,自西向东碎屑岩逐渐减少,碳酸盐岩逐渐增加。根据地层划分与对比,自下至上、自西而东划分为飞仙关组和大冶组。研究表明,早三叠世早期海平面有弱的振荡升降,为碳酸盐台地-陆棚-海槽沉积环境;至早三叠中晚期,海侵发展到最高峰,沉积一套潮间-潮上的以薄层状灰岩为主的地层,为开阔台地沉积环境。     

Bone structures in avian and mammalian lungs

Ectopic bone was found in the interstitium of lungs of birds, guinea pigs and minks. There was no evidence of a relation between the ectopic bone and the occurrence of disease.