Recent discoveries of Dryopithecus shed new light on evolution of great apes

The origin and early evolution of the great ape/human clade (Hominidae) is currently a subject of debate. The controversy is fuelled by the fragmentary nature of the fossils which renders it difficult to determine clearly derived features that permit the recognition of fossil members of this clade. We report here the recent discovery of a facial skeleton and a temporal fragment with the petrosal bone of Dryopithecus laietanus, which provides a way out of an impasse. The lack of the fossa subarcuata is a great ape and human clade synapomorphy, and proves unequivocally that Dryopithecus belongs to this clade. The zygomatic possesses derived characters which reveal that Dryopithecus is related to the Ponginae and not to the African apes/humans, as recently suggested. The remaining morphological features are plesiomorphic and thus provide a good model of a common ancestor of all Hominidae.     

Association of myopathy with large-scale mitochondrial DNA duplications and deletions: which is pathogenic?

We identified large-scale heteroplasmic mitochondrial DNA (mtDNA) rearrangements in a 50-year-old woman with an adult-onset progressive myopathy. The predominant mtDNA abnormality was a 21.2-kb duplicated molecule. In addition, a small population of the corresponding partially deleted 4.6-kb molecule was detected. Skeletal muscle histology revealed fibers that were negative for cytochrome c oxidase (COX) activity and had reduced mtDNA-encoded COX subunits. By single-fiber polymerase chain reaction analysis, COX-negative fibers contained a low number of wild-type or duplicated mtDNA molecules (ie, nondeleted). In situ hybridization demonstrated that the abnormal fibers contained increased amounts of mtDNA compared with normal fibers and that most of the genomes were deleted. We concluded that deleted mtDNA molecules were primarily responsible for the phenotype in this patient.     

Genetic transmission of major affective disorders: Quantitative models and linkage analyses.

We comprehensively reviewed 2 types of studies aimed at specifying the mode of inheritance of major affective disorders: quantitative models and linkage analyses. Quantitative models attempt to represent the genetic mechanism responsible for the familial distribution of a disorder. Despite efforts to refine models by incorporating the bipolar–unipolar distinction or the sex effect, consistent support for a specific mode of transmission has not been found. Some mixed genetic models support single major locus inheritance, but transmission probabilities do not conform to Mendelian expectations. Linkage analysis is a more powerful technique used for testing the single gene hypothesis. Linkage results have also been inconsistent, showing moderate support for an X-linked variant of bipolar-related disorder and equivocal support for linkages to Chromosomes 6 and 11. However, relatively few genetic loci have been examined. Methodological factors, genetic heterogeneity, and phenotypic heterogeneity are discussed as potential explanations for inconsistent findings. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Genetic susceptibility factors in type 1 diabetes: linkage, disequilibrium and functional analyses

Rehabilitation after soft-tissue autograft reconstructions is controversial because there is indirect evidence that some grafts fail by creeping over time. The vulnerability of soft-tissue grafts to creep over healing time and the effects of the load environment during healing on this vulnerability have never been studied specifically. We hypothesized that immobilization would decrease the magnitude of the vulnerability of ligament grafts to creep. Thirty-nine skeletally mature New Zealand White rabbits underwent a standardized medial collateral ligament autograft procedure to the right hindlimb, and 19 of the rabbits also had the limb rigidly pinned into flexion. Subgroups were killed at 3 or 8 weeks, and all isolated tibia/medial collateral ligament/femur complexes were tested for creep at 4.1 MPa under a standardized protocol. Eight normal medial collateral ligament controls were tested similarly. Results showed that all grafts were quantitatively more susceptible to cyclic and static creep than were normal medial collateral ligament controls (p < 0.05). By 3 weeks of healing, immobilization significantly increased the magnitude of the vulnerability of the grafts to cyclic, static, and total creep (all: p < 0.05). Furthermore, the grafts had more unrecovered creep strain than did the controls following a 20-minute recovery period. Contrary to our hypothesis, immobilization resulted in increased vulnerability of these ligament autografts to creep even with this relatively nonprovocative test of short duration and low stress. We postulate that following immobilization, this increase in the magnitude of susceptibility of the grafts to creep will result in functionally significant elongation of the graft if it is exposed to higher loads and over longer periods of time in vivo.     

The genome of Treponema pallidum: new light on the agent of syphilis

Covert brain activity related to task-free, spontaneous (i.e. unrequested), emotional evaluation of human face images was analysed in 27-channel averaged event-related potential (ERP) map series recorded from 18 healthy subjects while observing random sequences of face images without further instructions. After recording, subjects self-rated each face image on a scale from "liked" to "disliked". These ratings were used to dichotomize the face images into the affective evaluation categories of "liked" and "disliked" for each subject and the subjects into the affective attitudes of "philanthropists" and "misanthropists" (depending on their mean rating across images). Event-related map series were averaged for "liked" and "disliked" face images and for "philanthropists" and "misanthropists". The spatial configuration (landscape) of the electric field maps was assessed numerically by the electric gravity center, a conservative estimate of the mean location of all intracerebral, active, electric sources. Differences in electric gravity center location indicate activity of different neuronal populations. The electric gravity center locations of all event-related maps were averaged over the entire stimulus-on time (450 ms). The mean electric gravity center for disliked faces was located (significant across subjects) more to the right and somewhat more posterior than for liked faces. Similar differences were found between the mean electric gravity centers of misanthropists (more right and posterior) and philanthropists. Our neurophysiological findings are in line with neuropsychological findings, revealing visual emotional processing to depend on affective evaluation category and affective attitude, and extending the conclusions to a paradigm without directed task.     

The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression

The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.     

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.     

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis

A nonhomogeneous, nonstationary stochastic model of DNA sequence evolution allowing varying equilibrium G + C contents among lineages is devised in order to deal with sequences of unequal base compositions. A maximum-likelihood implementation of this model for phylogenetic analyses allows handling of a reasonable number of sequences. The relevance of the model and the accuracy of parameter estimates are theoretically and empirically assessed, using real or simulated data sets. Overall, a significant amount of information about past evolutionary modes can be extracted from DNA sequences, suggesting that process (rates of distinct kinds of nucleotide substitutions) and pattern (the evolutionary tree) can be simultaneously inferred. G + C contents at ancestral nodes are quite accurately estimated. The new method appears to be useful for phylogenetic reconstruction when base composition varies among compared sequences. It may also be suitable for molecular evolution studies.     

Molecular evolution and host adaptation of Bordetella spp.: phylogenetic analysis using multilocus enzyme electrophoresis and typing with three insertion sequences

A total of 188 Bordetella strains were characterized by the electrophoretic mobilities of 15 metabolic enzymes and the distribution and variation in positions and copy numbers of three insertion sequences (IS). The presence or absence of IS elements within certain lineages was congruent with estimates of overall genetic relationships as revealed by multilocus enzyme electrophoresis. Bordetella pertussis and ovine B. parapertussis each formed separate clusters, while human B. parapertussis was most closely related to IS1001-containing B. bronchiseptica isolates. The results of the analysis provide support for the hypothesis that the population structure of Bordetella is predominantly clonal, with relatively little effective horizontal gene flow. Only a few examples of putative recombinational exchange of an IS element were detected. Based on the results of this study, we tried to reconstruct the evolutionary history of different host-adapted lineages.     

The organization of human leucocyte antigen class I epitopes in HIV genome products: implications for HIV evolution and vaccine design

Knowledge of human leucocyte antigen (HLA) peptide binding motifs permits rapid selection of candidate viral protein fragments for induction of T cell-mediated immunity. A search for HLA class I peptide binding motifs in structural proteins of human immunodeficiency virus (HIV) of different genetic lineages provides a map of the genetic organization of potential T cell antigenic sites, and at the same time identifies all motifs in highly conserved regions of HIV-1 env, gag and pol. The density of motifs is anomalous at both the high and low end of the spectrum: local organization is characterized by clustering in relatively short regions, while large scale organization is characterized by anomalously long runs between motifs. The former is expected simply due to the fact that motifs often have overlapping anchor residue sets. A detailed statistical analysis of the latter, however, shows that the length of the runs cannot be accounted for by chance alone. Although motif clusters show no preference to be in either conserved or variable regions, low motif density stretches occur preferentially in variable portions of the protein sequence, which suggests that the virus may be mutating to evade the cellular arm of the immune system.     

Bladder PDT with intravesical clear and light scattering media: effect of an eccentric isotropic light source on the light distribution

To optimize the performance of off-road bicycle suspension systems, a dynamic model of the bicycle/rider system would be useful. This paper takes a major step toward this goal by developing a dynamic system model of the cyclist. To develop the cyclist model, a series of four vibrational tests utilizing random inputs was conducted on seven experienced off-road cyclists. This allowed the transfer functions for the arms and legs to be determined. To reproduce the essential features (i.e., resonance peaks) of the experimental transfer functions, the system model included elements representing the visceral mass along with the arms and legs. Through simulations, the frequency responses of the system model of the rider in each of the four tests were computed. Optimal stiffness and damping parameter values for each subject were determined by minimizing the difference between the experimental and simulation results. Good agreement between experimental and simulation results indicates that modeling the rider as a lumped parameter system with linear springs and dampers is possible.     

出土文字资料与东亚古代史研究——以中日韩三国古代木简为例

公元前108年以后,汉王朝先后在朝鲜半岛北部设四郡,即乐浪、真蕃、玄菟、临屯,中国的文物制度更多地传入朝鲜半岛,并经由半岛传入日本.中国的汉字文化是通过不同的载体传播的,除写在铜镜、铁制刀剑上的铭文外,还可以推测到通过简牍的汉字传播.朝鲜半岛和日本之所以能够积极地引进中国的汉字文化,是因为秦汉以后中国的汉字文化已经发展得相当成熟.汉字文化实际上包括成熟的汉字、成熟的书写工具和书写材料,以及成熟的书体.所谓汉字的东传也可以理解成是与汉字有关的成套技术的东传.本文介绍和分析中、日、朝鲜半岛古代木简的发掘及其各自的特点.     

Emotion recognition across cultures: The influence of ethnicity on empathic accuracy and physiological linkage.

The present study tested whether empathic accuracy and physiological linkage during an emotion recognition task are facilitated by a cultural match between rater and target (cultural advantage model) or unaffected (cultural equivalence model). Participants were 161 college students of African American, Chinese American, European American, or Mexican American ethnicity. To assess empathic accuracy—knowing what another person is feeling—participant’s (raters) used a rating dial to provide continuous, real-time ratings of the valence and intensity of emotions being experienced by 4 strangers (targets). Targets were African American, Chinese American, European American, or Mexican American women who had been videotaped having a conversation with their dating partner in a previous study and had rated their own feelings during the interaction. Empathic accuracy was defined as the similarity between ratings of the videotaped interactions obtained from raters and targets. To assess emotional empathy—feeling what another person is feeling—we examined physiological linkage (similarity between raters’ and targets’ physiology). Our findings for empathic accuracy supported the cultural equivalence model, while those for physiological linkage provided some support for the cultural advantage model. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features

The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We analyzed its sequence features and found that this region contained at least 894 potential open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any other genes. A homology search of the ORFs also identified several new gene clusters. Those include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a cluster of five genes coding for the homologues of degradation enzymes for aromatic hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.     

Abundant (A)n.(T)n mononucleotide repeats in the pig genome: linkage mapping of the porcine APOB, FSA, ALOX12, PEPN and RLN loci

A computer analysis revealed that the mononucleotide repeat (A)n.(T)n is about five times as common as (CA)n.(GT)n repeats in the porcine genome, with frequency estimates of one every 7kb and 30kb, respectively. Seven mononucleotide repeats with n = 12-25 located close to coding sequences were analysed for polymorphism using polymerase chain reaction (PCR) amplification and polyacrylamide gel electrophoresis. All loci were variable with 3-6 alleles and heterozygosities of 0.26-0.69 based on investigation of 10 unrelated pigs (two wild boars and eight domestic sows). Repeat length correlated with degree of polymorphism. A comparison with (CA)n.(GT)n polymorphisms suggested that the number of repeat units rather than the total length of the repeat region is the common denominator that governs polymorphism at both mono- and dinucleotide repeat loci. (A)n.(T)n polymorphisms allowed linkage mapping of relaxin to chromosome 1, apolipoprotein B to chromosome 3, aminopeptidase N to chromosome 7, arachidonate 12-lipoxygenase to chromosome 12, and follistatin to chromosome 16. The rich abundance of potentially informative (A)n.(T)n repeats will increase the chances of finding a PCR-based marker near any DNA sequence of interest.