Positive Darwinian selection in human population: A review

This paper reviews a large number of genes under positive Darwinian selection in modern human populations, such as brain development genes, immunity genes, reproductive related genes, perception receptors. The research on the evolutionary property of thes

Positive selection drives population differentiation in the skeletal genes in modern humans

During the course of evolution, the human skeletal system has evolved rapidly leading to an incredible array of phenotypic diversity, including variations in height and bone mineral density. However, the genetic basis of this phenotypic diversity and the relatively rapid tempo of evolution have remained largely undocumented. Here, we discover that skeletal genes exhibit a significantly greater level of population differentiation among humans compared with other genes in the genome. The pattern is exceptionally evident at amino acid-altering sites within these genes. Divergence is greater between Africans and both Europeans and East Asians. In contrast, relatively weak differentiation is observed between Europeans and East Asians. SNPs with higher levels of differentiation have correspondingly higher derived allele frequencies in Europeans and East Asians. Thus, it appears that positive selection has operated on skeletal genes in the non-African populations and this may have been initiated with the human colonization of Eurasia. In conclusion, we provide genetic evidence supporting the rapid evolution of the human skeletal system and the associated diversity of phenotypes.

Evidence for Positive Selection on the Osteogenin (BMP3) Gene in Human Populations

Background: Human skeletal system has evolved rapidly since the dispersal of modern humans from Africa, potentially driven by selection and adaptation. Osteogenin (BMP3) plays an important role in skeletal development and bone osteogenesis as an antagonist of the osteogenic bone morphogenetic proteins, and negatively regulates bone mineral density. Methodology/Principal Findings: Here, we resequenced the BMP3 gene from individuals in four geographically separated modern human populations. Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality. The prevalent haplotypes of the first exon region in Europeans demonstrated features of long-range haplotype homogeneity. In contrast with findings in European, the derived allele SNP Arg192Gln shows higher extended haplotype homozygosity in East Asian. The worldwide allele frequency distribution of SNP shows not only a high-derived allele frequency in Asians, but also in Americans, which is suggestive of functional adaptation. Conclusions/Significance: In conclusion, we provide evidence for recent positive selection operating upon a crucial gene in skeletal development, which may provide new insight into the evolution of the skeletal system and bone development.

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Statistical analysis of sequence features of introns with positive transcriptional regulation in yeast genes

A great deal of experimental studies have shown that many introns of eukaryotic genes function as regulators of transcription. However, comprehensive studies of this problem have not yet been conducted. After checking the transcription frequencies of some Saccharomyces cerevisiae (yeast), genes and their introns, a remarkable phenomenon was discovered that generally the introns of the genes with higher transcription frequencies are longer, and the introns of the genes with lower transcription frequencies are shorter. This suggests that the longer introns of genes with higher transcription frequencies may contain some characteristic sequence structures, which could enhance the transcription of genes. Therefore, two sets of introns of yeast genes were chosen for further study. The transcription frequencies of the first set of genes are higher (>30), and those of the second set of genes are lower (less than or equal to10). Some oligonucleotides are detected by statistically comparative analyses of the occurrence frequencies of oligonucleotides (mainly tetranucleotides and pentanucleotides), whose occurrence frequencies in the first set of introns; are significantly higher than those in the second set of introns, and are also significantly higher than those in the exons flanking the introns of the first set. Some of these extracted oligonucleotides are the same as the regulatory elements of transcription revealed by experimental analyses. Besides, the distributions of these extracted oligonucleotides in the two sets of introns and the exons show that the sequence structures of the first set of introns are favorable for transcription of genes.

Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

A passive acoustic monitoring method applied to observation and group size estimation of finless porpoises

The present study aimed at determining the detection capabilities of an acoustic observation system to recognize porpoises under local riverine conditions and compare the results with sighting observations. Arrays of three to five acoustic data loggers were stationed across the main channel of the Tian-e-zhou Oxbow of China's Yangtze River at intervals of 100-150 m to record sonar. signals of free-ranging finless porpoises (Neophocaena phocaenoides). Acoustic observations, concurrent with visual observations, were conducted at two occasions on 20-22 October 2003 and 17-19 October 2004. During a total of 42 h of observation, 316 finless porpoises were sighted and 7041 sonar signals were recorded by loggers. The acoustic data loggers recorded ultrasonic signals of porpoises clearly, and detected the presence of porpoises with a correct detection level of 77.6% and a false alarm level of 5.8% within an effective distance of 150 m. Results indicated that the stationed passive acoustic observation method was effective in detecting the presence of porpoises and showed potential in estimating the group size. A positive linear correlation between the number of recorded signals and the group size of sighted porpoises was indicated, although it is faced with some uncertainty and requires further investigation. (C) 2005 Acoustical Society of America.

Positive effects of continuous low nitrate levels on growth and photosynthesis of Alexandrium tamarense (Gonyaulacales, Dinophyceae)

The growth and photosynthesis of Alexandrium tamarense (Lebour) Balech in different nutrient conditions were investigated. Low nitrate level (0.0882 mmol/L) resulted in the highest average growth rate from day 0 to day 10 (4.58 x 10(2) cells mL(-1) d(-1)), but the lowest cell yield (5420 cells mL(-1)) in three nitrate level cultures. High nitrate-grown cells showed lower levels of chlorophyll a-specific and cell-specific light-saturated photosynthetic rate (P-m(chl a) and P-m(cell)), dark respiration rate (R-d(chl a) and R-d(cell)) and chlorophyll a-specific apparent photosynthetic efficiency (alpha(chl a)) than was seen for low nitrate-grown cells; whereas the cells became light saturated at higher irradiance at low nitrate condition. When cultures at low nitrate were supplemented with nitrate at 0.7938 mmol/L in late exponential growth phase, or with nitrate at 0.7938 mmol/L and phosphate at 0.072 mmol/L in stationary growth phase, the cell yield was drastically enhanced, a 7-9 times increase compared with non-supplemented control culture, achieving 43 540 cells mL(-1) and 52 300 cells mL(-1), respectively; however, supplementation with nitrate in the stationary growth phase or with nitrate and phosphate in the late exponential growth phase increased the cell yield by no more than 2 times. The results suggested that continuous low level of nitrate with sufficient supply of phosphate may facilitate the growth of A. tamarense.

Positive selection on multiple antique allelic lineages of transferrin in the polyploid Carassius auratus

Transferrin polymorphism has been studied in the polyploid Carassius auratus by cloning and sequence analysis of cDNAs from its three subspecies C. auratus gibelio, C. auratus auratus, and C. auratus cuvieri. DNA polymorphism of extremely high extent was shown for the transferrin gene by the 248 segregation sites among coding region sequences of its alleles. The deduced amino acid sequences of the transferrin alleles showed variable theoretical physicochemical parameters, which might constitute molecular basis for their electrophoretic heterogeneity. Positive selection was inferred by the replacement/synonymous ratios larger than 1 in partial allelic lineages which was subsequently confirmed by likelihood simulation under neutral or selection models. Furthermore, the correspondent sites to these selected codons were collectively located at two planes in the crystallographic structure of rabbit transferrin, which suggested that the rapid evolution of C. auratus transferrin might correlate to its adaptation to variable environmental elements such as oxygen pressure. The minimal 26 recombination events were detected among coding sequences of C. auratus transferrin, with partial mosaic sequences and breakpoints identified by identity scanning and information site analyses. Phylogenetic analyses revealed multiple antique allelic lineages of transferrin, which was estimated to diverge fifteen to twenty MYA. All these features strongly suggested the role of balancing selection in long persistence of high transferrin polymorphism in C. auratus. Furthermore, owing to its particular evolutionary backgrounds, the silver crucian carp might possess a distinctive balancing selection mechanism.

Development of a positive-negative selection procedure for gene targeting in fish cells

The gene targeting technique is a powerful tool for analyzing functions of cloned genes and for generating transgenic animals with site-directed integration of foreign genes. In order to develop this technique in fish, positive-negative selection (PNS) and homologous recombination vectors were constructed, and their expression was examined in fish cells. A vector (pNK) for PNS consists of the neomycin resistance gene (neo) as a positive selectable marker gene and the herpes simplex virus (HSV) thymidine kinase (tk) gene as a negative selectable marker gene. Positive selection with geneticin (G418) of epithelioma papulosum of carp (EPC) cells transfected with linearized pNK vector yielded 350 colonies, while double selection of transfected EPC cells with G418 and gancyclovir (Gc) resulted in nearly complete cell death, demonstrating that the PNS procedure is effective in fish cells. Homologous recombination vectors consist of the Xiphophorus melanoma receptor kinase (X mrk(Y)) gene as homologous sequence in addition to the neo and tk genes. Conditions for homologous recombination vector transfection and drug selection were established. After verification of the feasibility of expression of homologous recombination vectors in EPC cells, the first gene targeting experiments were attempted in the Xiphophorus melanoma cell line, PSM. Positive-negative selection of the targeting vector-transfectants led to a low enrichment in this particular cell line. The reasons for the low enrichment in PSM cells were discussed. (C) 2002 Elsevier Science B.V. All rights reserved.

Positive magnetoresistance in In0.53Ga0.47As/In0.52Al0.48As quantum well

Magnetotransport measurements have been carried out on In0.53Ga0.17As/In0.52Al0.48 As quantum wells in a temperature range between 1.5 and 77 K. We have observed a large positive magnetoresistance in the low magnetic field range, but saturating in high magnetic fields. The magnetoresistance results from two occupied subbands in the two-dimensional electron gas. With the intersubband scattering considered, we obtained the subband mobility by analyzing the positive magnetoresistance. It is found that the second subband mobility is larger than that of the first due to the existence of the intersubband scattering.

Effect of implantation of nitrogen into SIMOX buried oxide on its fixed positive charge density

In order to obtain greater radiation hardness for SIMOX (separation by implanted oxygen) materials, nitrogen was implanted into SIMOX BOX (buried oxide). However, it has been found by the C-V technique employed in this work that there is an obvious increase of the fixed positive charge density in the nitrogen-implanted BOX with a 150 out thickness and 4 x 10(15) cm(-2) nitrogen implantation dose, compared with that unimplanted with nitrogen. On the other hand, for the BOX layers with a 375 nm thickness and implanted with 2 x 10(15) and 3 x 10(15) cm(-2) nitrogen doses respectively, the increase of the fixed positive charge density induced by implanted nitrogen has not been observed. The post-implantation annealing conditions are identical for all the nitrogen-implanted samples. The increase in fixed positive charge density in the nitrogen-implanted 150 nm BOX is ascribed to the accumulation of implanted nitrogen near the BOX/Si interface due to the post-implantation annealing process according to SIMS results. In addition, it has also been found that the fixed positive charge density in initial BOX is very small. This means SIMOX BOX has a much lower oxide charge density than thermal SiO2 which contains a lot of oxide charges in most cases.

Large positive and negative lateral displacements from total internal reflection configuration with a weakly absorbing dielectric film

It is theoretically shown that the simultaneously large positive and negative lateral displacements will appear when the resonant condition is satisfied for a TE-polarized light beam reflected from the total internal reflection configuration with a weakly absorbing dielectric film. Appearance of the enhanced negative lateral displacement is relative to the incidence angle, absorption of the thin Elm and its thickness. If we select an appropriate weakly absorbing dielectric film and its thickness, the simultaneously enhanced positive and negative lateral displacements will appear at different resonant angles. These phenomena may lead to convenient measurements and interesting applications in optical devices.

Controllable negative and positive group delay in transmission through a single quantum well at finite magnetic fields

We investigate the controllable negative and positive group delay in transmission through a single quantum well at the finite longitudinal magnetic fields. It is shown that the magneto-coupling effect between the longitudinal motion component and the transverse Landau orbits plays an important role in the group delay. The group delay depends not only on the width of potential well and the incident energy, but also on the magnetic-field strengthen and the Landau quantum number. The results show that the group delay can be changed from positive to negative by the modulation of the magnetic field. These interesting phenomena may lead to the tunable quantum mechanical delay line. (c) 2007 Elsevier B.V. All rights reserved.