Evidence for a coding pattern on the non-coding strand of the E. coli genome.

Analysis of codon usage frequency for the combined coding sequences of 52 E. coli genes, taken from the European Molecular Biology Laboratory Nucleotide Sequence Data Library, Release 2, shows that there is a significant positive correlation between the frequency with which a given codon appears on the coding strand and the frequency with which it appears, in phase, on the non-coding strand.     

Tooth components of mandibular deciduous molars of Homo sapiens sapiens and Homo sapiens neanderthalensis: a radiographic study.

Tooth components of deciduous molars were measured from standardized radiographs of Homo sapiens sapiens and Homo sapiens neanderthalensis. Enamel height and width were greater in deciduous teeth of Homo sapiens sapiens than in Homo sapiens neanderthalensis and the differences were statistically significant (p less than 0.01). Dentin height showed no significant differences between the two groups, but enamel to floor of pulp chamber and pulp height and width dimensions were significantly greater in Homo sapiens neanderthalensis. Discriminant analysis carried out between groups, using deciduous tooth components, showed an accuracy of 98-100% for identification of Homo sapiens sapiens and 83-92% for identification of Homo sapiens neanderthalensis. The results obtained in this study on dental dimensions support the hypothesis of a distinct evolutionary line for Neanderthals.     

Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Reduction of maxillary molars in Homo sapiens sapiens: a different perspective.

Crown and cusp areas, and buccolingual and mesiodistal diameters of maxillary molars of complete upper tooth rows (30 males, 30 females) were analysed in order to quantify changes in size and shape from the first to the third molar. Uni- and multivariate analyses revealed the mesial cusps, in particular the protocone (mesiolingual cusp), to be more stable than the other cusps. Although there is a gradient in size from the first to third molar, shape changes were found to be marked. Overall, the findings are in keeping with the field theory and the hypotheses of environmental constraints on later developing teeth. However, not all of the results could be entirely explained by these concepts. Functional aspects seem to account for the relative stability of the protocone and the buccolingual crown diameter. It appears that this functional complex is relatively stable despite the overall reduction of tooth size, which is probably secondary to processes occurring in the jaws and the cranium. This finding may have implications for studies on tooth reduction between populations of different time periods.     

利用生物信息学方法对人类(Homo sapiens)肌肉增强因子2(MEF2)的特性比较及进化分析

肌肉增强因子2(Myocyte enhancer factor 2,MEF2)是MADS(MCM1,agamous,deficiens和serum response factor)家族成员之一,在动物发育过程中起到重要的调节作用。为了进一步了解其调控的复杂性,本文根据NCBI中已有的人类MEF2相关数据,应用ExPASy在线序列分析工具、CBS在线分析服务器软件、Conserved Domain Database(CDD)数据库、SABLE在线分析软件等对人类MEF2蛋白的不同亚型序列进行比较分析,同时,根据相关序列的比对结果构建系统进化树进行分析。结果表明,MEF2在人体内以多种蛋白形式存在,其理化性质存在一定差别,可能的翻译后糖基化修饰多为O型糖基化且均存在较多磷酸化位点。人类各MEF2蛋白具明显MADS结构域,多数具有MEF2结构域和HJURP_C结构域。各MEF2蛋白二级结构均包括了螺旋、折叠和无规则卷曲等多种形式,其三级结构模式相似。系统进化树显示MEF2B蛋白与其他蛋白有着较大的序列差异及较远进化关系,可能较为原始。     

Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity.

The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham's group it has been apparent that genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes. Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend. Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurium closely resembles E. coli, while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans.     

Codon usage is associated with the evolutionary age of genes in metazoan genomes

Background  

Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes.     

Comparison of dinucleotide frequency and codon usage inToxoplasma andPlasmodium: Evolutionary implications

Summary The weight-averaged observed/expected dinucleotide frequencies for the sum total of the coding regions of fiveToxoplasma genes were compared with the same parameters previously determined for the coding regions of 21Plasmodium genes. In addition, codon usage in the fiveToxoplasma genes was compared with that in the 21Plasmodium genes, and the percent distribution of amino acids in theToxoplasma protein pool and thePlasmodium protein pool were compared with that in a general protein pool of 314 proteins. The results are consistent with the hypothesis that, contrary to currently held opinion, the generaToxoplasma andPlasmodium are not especially closely related.     

Allometry between length and cross-sectional dimensions of the femur and tibia in Homo sapiens sapiens

Allometric equations relating length and cross-sectional geometric properties of the femur and tibia are generated using skeletal remains from three recent human population samples. Approximate isometry, or geometric similarity, is found both within and between samples. Cross-sectional areas scale to approximately length2, while second moments of area scale to approximately length4. It is shown that this is consistent with the maintenance of equivalent mechanical stress in long bones of different length under dynamic loadings in vivo. Other evidence indicates that bending and torsional loadings are more critical than axial loadings in the determination of lower limb bone cross-sectional dimensions.     

Population structure and the evolution of Homo sapiens in Africa

It has been proposed that a multiregional model could describe how Homo sapiens evolved in Africa beginning 300,000 years ago. Multiregionalism would require enduring morphological or behavioral differences among African regions and morphological or behavioral continuity within each. African fossils, archeology, and genetics do not comply with either requirement and are unlikely to, because climatic change periodically disrupted continuity and reshuffled populations. As an alternative to multiregionalism, I suggest that reshuffling produced novel gene constellations, including one in which the additive or cumulative effect of newly associated genes enhanced cognitive or communicative potential. Eventual fixation of such a constellation in the lineage leading to modern H. sapiens would explain the abrupt appearance of the African Later Stone Age 50–45 thousand years ago, its nearly simultaneous expansion to Eurasia in the form of the Upper Paleolithic, and the ability of fully modern Upper Paleolithic people to swamp or replace non‐modern Eurasians.     

HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens

MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates.     

Foramen magnum position variation in Pan troglodytes, Plio-Pleistocene hominids, and recent Homo sapiens: implications for recognizing the earliest hominids

The anteroposterior position of the foramen magnum distinguishes living Homo sapiens from apes, and has been used as evidence for the hominid status of numerable fossils in the history of human paleontology. During the past decade, foramen magnum position has been cited as evidence of the hominid status of Ardipithecus and Sahelanthropus. Specifically, the basion of Ardpithecus is reported to be inline with the bicarotid chord, while the basion of Sahelanthropus is reported to both touch the biporion chord and intersect the bicarotid chord. In order to assess the effectiveness of anteroposterior foramen magnum position in distinguishing hominids from nonhominid apes, this study examined whether or not the positions of biporion and bicarotid relative to basion sufficiently distinguished Pan troglodytes from recent Homo sapiens and Plio-Pleistocene hominids. The distances from basion to the biporion chord (BSBIP) and from basion to the bicarotid chord (BSBIC) were measured on samples of chimpanzee (n = 69) and recent human (n = 42) crania and a sample of Plio-Pleistocene hominid fossils (n = 8). The data were used to test the hypothesis that BSBIP and BSBIC measurements do not sufficiently distinguish P. troglodytes from hominids. While basion to biporion (BSBIP) does not effectively distinguish P. troglodytes from Plio-Pleistocene hominids and humans when used univariately, basion to bicarotid (BSBIC), when used univariately or bivariately with BSBIP, can be used to test whether or not an unknown specimen is a hominid. These results are used to evaluate the hominid status of Ardipithecus and Sahelanthropus.     

西安地区现代人锁骨的人类学研究

关于国人四肢骨从各个方面研究的资料甚多,然而截止目前对锁骨的系统研究则较少。椎野(钅孝)太郎等在其《中国人骨骼人种学的研究》一文中首次涉及到锁骨。叶鹿鸣对锁骨作了观察。吴新智等观察了锁骨的年龄变化。赵振东对锁骨的滋养孔进行了观测。而较为系统地从人类学角度对锁骨进行测量统计者仅有石世庆和席焕久等,且这些资料皆限于我国的东北地区,而其他地区则尚未见有资料报道。临床实践表明,锁骨骨折较为常见, 且锁骨常作为其附近骨移植的取材。此外, 在人类学和法医学方面文可把从锁骨长估算身高的回归方程作为推算身高的5 种方法。
我国人口众多, 民族有数十个,地域辽阔,东西南北各地区自然条件差异甚大。因此, 人群体质的差异必然存在。故作者为了给临床骨科提供参考 数据, 同时又为国人体质资料增补内容, 对西安地区现代人成人锁骨100副(男50, 女50)进行了人类学测量统计,并将所侧得的结果与国内外学者报道的资料作了对照 。     

The effects of linear perspective on relative size discrimination in chimpanzees (Pan troglodytes) and humans (Homo sapiens)

In this study, we tested the corridor illusion in three chimpanzees and five humans, applying a relative size discrimination task to assess pictorial depth perception using linear perspective. The subjects were required to choose the physically larger cylinder of two on a background containing drawn linear perspective cues. We manipulated both background and cylinder size in each trial. Our findings suggest that chimpanzees, like humans, exhibit the corridor illusion.     

Anomalous dinucleotide frequencies in both coding and non-coding regions from the genome of the human malaria parasite Plasmodium falciparum

We have statistically analysed the distribution of nucleotides and dinucleotides in 21 genes of the 81% A + T-rich human malaria parasite Plasmodium falciparum. The mRNA-synonymous strands of this protozoan show in general a marked excess of purines over pyrimidines, correlated with abnormally high levels of Lys and Glu. We have used the large differences in base composition between coding and non-coding regions to estimate that the parasite possesses in the range of 2700-5400 genes. The dinucleotide preference patterns are compared with consensus patterns derived from other organisms [Nussinov, Nucl. Acids Res. 12 (1984) 1749-1763]. Patterns in the coding regions surprisingly resemble those of higher, rather than lower eukaryotes, particularly with respect to TG elevation and CG suppression. The latter is correlated with an abnormally low level of Arg in these parasites. In the non-coding regions, the four dinucleotides made up of C and/or G are found with significantly higher frequencies than expected (approx. 50-150%), specifically to the 5' side of the coding regions. The possible role of these dinucleotides in control sequences is discussed.     

The non-coding genome: a universe in expansion for fine-tuning the coding world

A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.We share 98% coding genome similarity with mouse and have about the same number of protein coding genes as worms, yet the differences in complexity are obvious. Where is this complexity encoded? A huge change in our understanding of genome evolution and regulation of gene expression arrived with the development of high-throughput sequencing technologies. It turns out that most of our genome is transcribed, but only a small percentage has coding information imbedded. The rest of the genome, the non-coding genome, mistakenly labeled as ‘junk DNA’, is where evolutionary complexity resides. In The Non-Coding Genome meeting, several research studies delved deeper into the importance of the non-coding genome, identifying novel classes of non-coding RNAs (ncRNAs) and novel regulatory functions, and expanding our knowledge about this new world, opening more exciting questions to study and answer.