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Showing papers in "Journal of Genetics in 2005"


Journal ArticleDOI
TL;DR: It is suggested that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome, as pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.
Abstract: A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.

108 citations


Journal ArticleDOI
TL;DR: The prestigious journal Nature Genetics devoted a large supplement to the question of whether human races exist and, if so, what they mean, and some geneticists offered their views.
Abstract: Shortly after last year’s tsunami devastated the lands on the Indian Ocean, The Times of India ran an article with this headline: ‘Tsunami may have rendered threatened tribes extinct’. The tribes in question were the Onge, Jarawa, Great Andamanese and Sentinelese – all living on the Andaman Islands and they numbered some 400 people in all. The article, noting that several of the archipelago’s islands were low-lying, in the direct path of the wave, and that casualties were expected to be high, said, ‘Some beads may have just gone missing from the Emerald Necklace of India’. The metaphor is as colorful as it is well intentioned. But what exactly does it mean? After all, in a catastrophe that cost more than 150,000 lives, why should the survival of a few hundred tribal people have any special claim on our attention? There are several possible answers to this question. The people of the Andamans have a unique way of life. True, their material culture does not extend beyond a few simple tools, and their visual art is confined to a few geometrical motifs, but they are hunter-gatherers and so a rarity in the modern world. Linguists, too, find them interesting since they collectively speak three languages seemingly unrelated to any others. But The Times of India took a slightly different tack. These tribes are special, it said, because they are of ‘Negrito racial stocks’ that are ‘remnants of the oldest human populations of Asia and Australia’. It’s an old-fashioned, even Victorian, sentiment. Who speaks of ‘racial stocks’ anymore? After all, to do so would be to speak of something that many scientists and scholars say does not exist. If modern anthropologists mention the concept of race, it is invariably only to warn against and dismiss it. Likewise many geneticists. ‘Race is a social concept, not a scientific one’, according to Dr Craig Venter – and he should know, since he was first to sequence the human genome. The idea that human races are only social constructs has been the consensus for at least 30 years. But now, perhaps, that is about to change. Last fall, the prestigious journal Nature Genetics devoted a large supplement to the question of whether human races exist and, if so, what they mean. The journal did this in part because various American health agencies are making race an important part of their policies to best protect the public – often over the protests of scientists. In the supplement, some two dozen geneticists offered their views. Beneath the jargon, cautious phrases and academic courtesies, one thing was clear: the consensus about social constructs was unraveling. Some even argued that, looked at the right way, genetic data show that races clearly do exist. The notion that human races do not exist can be dated to 1972. This is when Richard Lewontin, a Harvard geneticist, wrote an influential review showing that most human genetic variation can be found within any given ‘race’ (Lewontin 1972). If one looked at genes rather than faces, he claimed, the difference between an African and a European would be scarcely greater than the difference between any two Europeans. A few years later he wrote that the continued popularity of race as an idea was an ‘indication of the power of socioeconomically based ideology over the supposed objectivity of knowledge’ (Lewontin 1974). Most scientists are thoughtful, liberal-minded and socially aware people. It was just what they wanted to hear. Three decades later, it seems that Dr Lewontin’s facts were correct, and have been abundantly confirmed by ever better techniques of detecting genetic variety (e.g. Barbujani et al. 1997). His reasoning, however, was wrong. His error was an elementary one, but such was the appeal of his argument that it was only a couple of years ago that a Cambridge University statistician, A. W. F. Edwards, put his finger on it (Edwards 2003). The error is easily illustrated. If one were asked to judge the ancestry of 100 New Yorkers, one could look at the colour of their skin. That would do much to single out the Europeans, but little to distinguish the Senegalese from the Solomon Islanders. The same is true for any other feature of our bodies. The shapes of our eyes, noses and skulls; the colour of our eyes and our hair; the heaviness, height and hairiness of our bodies are all, individually, poor guides to ancestry. But this is not true when the features are taken together. Certain skin colours tend to go with certain kinds of eyes, noses, skulls and bodies. When we glance at a stranger’s face we use those associations to infer what continent, or even what country, he or his ancestors came from – and we usually get it right. To put it more abstractly, human physical variation is correlated; and correlations contain information. INVITED EDITORIAL

81 citations


Journal ArticleDOI
Mehmet Karaca1, Mehmet Bilgen1, A. Naci Onus1, Ayse Gul Ince1, S Elmasulu1 
TL;DR: The results revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.
Abstract: Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as ‘organs’, ‘tissues’, ‘cell lines’ and ‘development stages’ for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.

45 citations


Journal ArticleDOI
TL;DR: Chiasma frequency and distribution, as well as chromosomal association and segregation, in ten Iranian populations of six Bromus species from the section Genea are studied, uncovered several hitherto undescribed inter-population variations in cytological characteristics.
Abstract: The genus Bromus L. (tribe Bromeae, family Poaceae) comprises about 160 annual and perennial species (Acedo and Liamas 2001), distributed all over the world. Bromus species are among important range grasses of Iran and are placed in six sections, of which section Genea Dum. contains six perennial species found in Iran (Bor 1970). The available literature dealing with cytogenetics of Bromus (e.g. Devesa et al. 1990; Lövkvist and Hultgård 1999), indicates the importance of such cytological studies for understanding the evolution of the genus Bromus. Therefore, we studied chiasma frequency and distribution, as well as chromosomal association and segregation, in ten Iranian populations of six Bromus species from the section Genea. The results uncovered several hitherto undescribed inter-population variations in cytological characteristics.

39 citations


Journal ArticleDOI
TL;DR: The absence of early meiotic stages in the Hsp60C1 homozygous testes contrasts with the effect of testis-specificHsp60B (21D) gene, whose mutation affects individualization of sperm bundles later in spermiogenesis, and it is likely that, besides its functions as a chaperone, HSp60C may have signalling functions and may also be involved in cation transport across the developing tracheal epithelial cells.
Abstract: Earlier studies have shown that of the four genes (Hsp60A, Hsp60B, Hsp60C, Hsp60D genes) predicted to encode the conserved Hsp60 family chaperones inDrosophila melanogaster, theHsp60A gene (at the 10A polytene region) is expressed in all cell types of the organism and is essential from early embryonic stages, while theHsp60B gene (at 21D region) is expressed only in testis, being essential for sperm individualization. In the present study, we characterized theHsp60C gene (at 25F region), which shows high sequence homology with the other threeHsp60 genes ofD. melanogaster. In situ hybridization of Hsp60C-specific riboprobe shows that expression of this gene begins in late embryonic stages (stage 14 onwards), particularly in the developing tracheal system and salivary glands; during larval and adult stages, it is widely expressed in many cell types but much more strongly in tracheae and in developing and differentiating germ cells. A P-insertion mutant (Hsp60C 1 ) allele with the P transposon inserted at -251 position of theHsp60C gene promoter was generated. This early larval recessive lethal mutation significantly reduces levels ofHsp60C transcripts in developing tracheae and this is associated with a variety of defects in the tracheal system, including lack of liquid clearance. About 10% of the homozygotes survive as weak, shortlived and completely sterile adults. Testes of the surviving mutant males are significantly smaller, with fewer spermatocytes, most of which do not develop beyond the round spermatid stage.In situ and Northern hybridizations show significantly reduced levels of theHsp60C transcripts inHsp60C 1 homozygous adult males. The absence of early meiotic stages in theHsp60C 1 homozygous testes contrasts with the effect of testis-specificHsp60B (21D) gene, whose mutation affects individualization of sperm bundles later in spermiogenesis. In view of the specific effects in tracheal development and in early stages of spermatogenesis, it is likely that, besides its functions as a chaperone, Hsp60C may have signalling functions and may also be involved in cation transport across the developing tracheal epithelial cells.

33 citations


Journal ArticleDOI
TL;DR: Cultivated varieties from Russia and Mongolia show many promising agronomic traits, but show weak adaptability and are slow-growing, while sea buckthorn breeding in China also faces serious problems, such as unstable adaptability, unsteady yield and quality of introduced varieties, and difficulty of harvesting native varieties with thorns.
Abstract: The genus Hippophae includes 7 species and 8 subspecies in the world (Swenson and Bartish 2002; Bartish et al. 2002; Sun et al. 2002), these species are all diploid of 2n = 24 and are restricted to Qinghai-Xizang plateau and adjacent areas except Hippophae rhamnoides L. which is naturally distributed from Asia to Europe and was introduced to South and North America (Rousi 1971; Lu 1997; Heinz and Barbaza 1998; Lian et al. 2000; Bartish et al. 2000a, 2002; Roy et al. 2003). Sea buckthorn (H. rhamnoides) has shown enormous agricultural, ecological, nutritional, medical and ornamental values (Vikberg and Itamies 1999; Zadernowski et al. 2002; Cheng et al. 2003; Tsydendambael and Vereshchagin 2003). Commercially, sea buckthorn has been suggested as a hardy, multi-purpose plant with orange, red or yellow berries, and being widely introduced and extended in the world, especially in China. H. rhamnoides ssp. sinensis and H. rhamnoides ssp. mongolica of six subspecies of H. rhamnoides are mainly and widely distributed in China, Mongolia, Russia and other countries of Asia and eastern Europe. Breeding programmes for improving adaptability, tolerance and yield have been carried out since 1960. Some fine cultivated varieties have been successfully selected or bred by scientists of these countries, especially in China, Russia and Mongolia. However, the different cultivated varieties have advantages and disadvantages. Cultivated varieties from China have strong adaptability and are fast-growing, but bear small fruits, more thorns, short fruit stalk, and have lower content of bioactive substances, and are more prone to dried-shrink disease. Cultivated varieties from Russia and Mongolia show many promising agronomic traits, such as big fruits, few or no thorns, long fruit stalk and high content of bioactive substances, and resistance to dried-shrink disease (some varieties), but show weak adaptability and are slow-growing. Many cultivated varieties from Russia and Mongolia have been introduced into China since 1991 to supply and improve sea buckthorn germplasm of China and to gain commercial benefit. Some of them adapt very well to the new habitat and yield high economic benefit. Some of the fine cultivated varieties from Russia and Mongolia selected and bred by Chinese breeders are being planted on a large scale in China. However, sea buckthorn breeding in China also faces serious problems, such as unstable adaptability, unsteady yield and quality of introduced varieties, and difficulty of harvesting native varieties with thorns. An available approach for breeding fine varieties is crossing between H. rhamnoides ssp. sinensis and H. rhamnoides ssp. mongolica, and crosses between them once bred two fine hybrids (Liaohuyihao and Liaohuerhao) in China, but selecting parents is still a major problem. Knowledge of genetic relationships in parental varieties could improve the effectiveness of breeding programmes (Le Thierry d’ Ennequin et al. 2000). Moreover, some of the commercially desirable sea buckthorn cultivated varieties could be reproduced by micropropagation; thus, unauthorized commercialization of patented varieties leads to lawsuits requiring careful technical investigation. However, investigators often look only at morphological characters, which do not always yield clear

32 citations


Journal ArticleDOI
TL;DR: This study aims at establishing the activation behaviour of two types of regulatory motifs, called ACGT and GT elements, when placed upstream of a minimal promoter in one or two copies, at different positions from the TATA -box.
Abstract: A variety of cis-acting DNA sequences regulate gene expression from basal promoter. In this study, two types of regulatory motifs, called ACGT and GT elements were placed at different distances from TATA -box to examine their affect on reporter gene expression in transient tran s-formation of tobacco leaf. The ACGT core motif is re-cognized by transcription factors of the bZIP family. The core ACGT element occurs at different relative positions in one or more copies upstream of the minimal promoter region. Protein-DNA interaction studies have shown that sequences flanking the ACGT core affect bZIP protein binding specificity. The bZIP transcription factors regu-late a variety of processes like pathogen defence (Zhou et al. 2000), light (Weisshaar et al. 1991) and flower deve -lopment (Chuang et al. 1999). The GT elements have a core sequence with T and A, preceeded by one to two G nucleotides on the 5 ′ side (Zhou 1999). Though hig h de-generacy makes it difficult to identify them by sequence search, a variety of such sequences are present in the genes encoding diverse functions like light regulation (Dehesh et al. 1990), tissue specificity (Villain et al. 1994) and pathogen defence ( Buchel et al. 1996). These are recognized by a family of transcription regulatory proteins called GT-factors (Buchel et al. 1999). The dif-ferences in binding affinity and the nature of transcrip-tional complex formed on promoters have been related to differ ences in regulatory functions of the GT sequence motifs (Puente et al. 1996). The GT elements are usually present in tandem repeats within a relatively long pro-moter region. An increase in spacing between two ele-ments by as little as 2 bp can dramatically reduce the transcript level (Gilmartin and Chua 1990) as in the case of rbcS -3A , suggesting critical sequence requirements for the activation of gene expression. This study aims at establishing the activation behaviour of these two ele-ments, when placed upstream of a minimal promoter in one or two copies, at different positions from the TATA -box.

32 citations


Journal ArticleDOI
TL;DR: The sequences of the 16 silkworm strains were analysed with DNASTAR software and a phylogenic tree was constructed using PHYLIP software and it was inferred that the strains Yanhe-1 and Chuxiong originated independently from southwest China.
Abstract: Pupae from the Chinese wild mulberry silkworm,Bombyx mandarina, and 11 representative strains of the domesticated silkworm,Bombyx mori were selected for preparation of mitochondrial DNA. The 5′-end fragments ofcytochrome b genes (Cytb) were generated by polymerase chain reaction products and sequenced directly. The homologous sequences of the JapaneseB. mandarina and three strains ofB. mori were from the GenBank database. The sequences of the 16 silkworm strains were analysed with DNASTAR software and a phylogenic tree was constructed using PHYLIP software. The result showed that: (i) The sequence divergence between the strains ofB. mori and the JapaneseB. mandarina was larger (5.4% ≈ 5.8%) compared with that between strains ofB. mori and the ChineseB. mandarina (0.8% ≈ 1.9%). Analysis of clustering also showed that the sequences ofB. mori strains and ChineseB. mandarina clustered into group (B group), while that of JapaneseB. mandarina (A group) was outside this cluster. This may be evidence for the hypothesis thatB. mori originated from ChineseB. mandarina. (ii) Among 14 strains ofB. mori, sequence divergence was small and the most divergence was seen between strains Yanhe-1 and Chuxiong, whose sequences branched off from those of the otherB. mori strains on the phylogenetic tree. From this and from historical records, we infer that the strains Yanhe-1 and Chuxiong originated independently from southwest China.

30 citations


Journal ArticleDOI
Guo Li Zhou1, Hai Guo Jin, Qi Zhu1, Shan Li Guo1, Yu Hou Wu1 
TL;DR: The purpose of the present study was to examine genetic diversity among five native Chinese cattle breeds through examining microsatellite DNA polymorphisms and estimated the genetic differentiation and the genetic relationship within and between the five nativeChinese cattle breeds.
Abstract: Microsatellites have proved to be useful polymorphic markers for the analysis of genetic diversity. Microsatellite based studies in livestock have mainly concentrated on pig, cattle and sheep, and there are now more than a thousand cattle microsatellite markers to choose from (Barendse et al. 1994; Kappes et al. 1997). Genotyping of cattle can be done on most tissues and cell types, and international comparison tests under the auspices of the International Society for Animal Genetics (ISAG) to establish international standards exist. Awareness of the value of genetic resources in livestock has stimulated the study of the genetic diversity of native breeds. However most of such studies have been done on European cattle breeds and very little information is available concerning the genetic diversity of cattle breeds native to China. The purpose of the present study was to examine genetic diversity among five native Chinese cattle breeds through examining microsatellite DNA polymorphisms. We also estimated the genetic differentiation and the genetic relationship within and between the five native Chinese cattle breeds.

27 citations


Journal ArticleDOI
TL;DR: A normal ‘L’ shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders.
Abstract: Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (±s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, FIS (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significantM ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

17 citations


Journal ArticleDOI
TL;DR: RFLP analysis of cytochrome b gene is used to show that the differences between the two are not large enough to justify C. ectenes taihuensis being classified as a subspecies of C.ectenes.
Abstract: The current taxonomic status of Coilia ectenes taihuensis is unclear. One study claims that it has differentiated from Coilia ectenes to the level of subspecies, while two other studies refute this claim. In this study, we used RFLP analysis of cytochrome b gene to show that the differences between the two are not large enough to justify C. ectenes taihuensis being classified as a subspecies of C. ectenes. Coilia fishes are small to moderate in size and China has four species of them (Zhang 2001). C. ectenes (Jordan and Seale 1905) is an anadromous fish which migrates from near ocean waters to fresh waters areas every year during the spawning season. Mature C. ectenes migrate upriver, and spawn in the lower and middle reaches of the Yangtze river. Some C. ectenes also some spawn in the lakes adjacent to the Yangtze river. C. ectenes taihuensis is an autochthonous group of C. ectenes. It has no migration habit and lives throughout its life in Taihu lake, which is the third largest freshwater lake in China (East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences and Shanghai Fisheries Research Institute 1990). The taxonomic relationship between C. ectenes and C. ectenes taihuensis is still controversial. Yuan et al. (1976) considered C. ectenes taihuensis to be a subspecies of C. ectenes according to traditional meristic characters, and ecological and physiological differences. But isozyme and anatomical data of Liu (1995) and morphometric data of Cheng and Han (2004) suggest that the differences between the two have not risen to subspecies level. Mitochondrial DNA (mtDNA) is extranuclear DNA that has proven to be a useful molecular marker for evolutionary studies in animal populations because of its predominantly maternal inheritance, relatively rapid base substitution rate, and lack of recombination (Avise et al. 1987). cytochrome b – a protein coding mitochondrial gene – is widely used in fish population and evolutionary genetic studies (Johns and Avise 1998; Xiao et al. 2001). Restriction fragment length polymorphism (RFLP) analysis of mtDNA has proved to be effective in distinguishing among three different species of catfish in the Arabian Gulf, two of which could hardly be differentiated based on morphological traits alone (Simsek et al. 1990). In the present study, RFLP analysis of the cytochrome b gene was employed to assess the levels of genetic diversity within, and genetic differentiation between C. ectenes and C. ectenes taihuensis. Seven restriction enzymes were found to have at least one recognition site at this gene. Six different haplotypes were detected between the populations studied. About one to two restriction patterns of each enzyme were revealed. We found very low levels of genetic partitioning, with less than 0.1% of the total variation attributed to between population differences, and lack of genetic structure, thus supporting the view that the differences between C. ectenes taihuensis and C. ectenes have not risen to subspecies level.

Journal ArticleDOI
TL;DR: The analysis of genetic behaviour within and between species provides important clues about the forces shaping the evolution of behavioural genes, as well as clues to the origins of genetic flexibility and plasticity in an organism’s response.
Abstract: The analysis of genetic behaviour within and between species provides important clues about the forces shaping the evolution of behavioural genes. Genes can affect natural behavioural variation in different ways. Allelic variation causes alternative behavioural phenotypes, whereas changes in gene expression can influence the initiation of behaviour at different ages. Identifying the genes involved in polygenic traits has been difficult. Chromosomal analysis has been widely used as a first step in elucidating the genetic architecture of several behaviours ofDrosophila. Behavioural genetic and molecular studies helped to reveal the genetic basis of circadian time keeping and rhythmic behaviours. InDrosophila, a number of key processes such as emergence from the pupal case, locomotor activity, feeding, olfaction and aspects of mating behaviour are under circadian regulation. Evolutionary biology considers migration behaviour as central in genetic structure of populations and speciation. Genetic loci that influence behaviour are often difficult to identify and localise in part due to the quantitative nature of behavioural phenotypes. Diapause is a hormonally mediated delayed response to future adverse conditions and can occur at any stage of development in an insect. Diapauseassociated gene expression was studied inDrosophila using subtractive hybridisation. Several approaches have been made to unravel the genetic complexity of the behaviour, which have provided information that may be useful in different ways. There is evidence that species do differ in genetic architecture of photoresponse and this may be related to their natural environment. The classical experiments by Jerry Hirsh and Th. Dobzhansky to know the nature of genetic basis for extreme selected geotactic behaviour in fruit flies constituted the first attempt at the genetic dissection of a complex, polygenic behaviour. Understanding the genetic differences between these selected lines would provide an important point of entry into the study of genetic mechanisms of sensing and responding to gravity, as well as clues to the origins of genetic flexibility and plasticity in an organism’s response.


Journal ArticleDOI
TL;DR: The analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans.
Abstract: In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans.

Journal ArticleDOI
TL;DR: This commentary will discuss the context of this work examining the genetic architecture of the crossveinless phenocopy both within the light of current studies of evolutionary genetics, and modern evolutionary-developmental biology.
Abstract: Clearly spurred on by Waddington, Bateman (1959) continued the work on the crossveinless phenocopy in Drosophila melanogaster and helped to establish it as a model system in quantitative genetics for threshold traits. In this commentary, I will discuss the context of this work examining the genetic architecture of the crossveinless phenocopy both within the light of current studies of evolutionary genetics, and modern evolutionary-developmental biology. Far from being a historical curiosity, it appears that this phenotype may be a relevant and powerful model system for current studies of cryptic genetic variation and possibly for examining allelic architecture of complex diseases. I will discuss what future research directions will allow for this possibility.

Journal ArticleDOI
TL;DR: Methodological details are presented and exemplified by a newly detected SNP in codon 155 of the catechol-O-methyltransferase (COMT) gene in a patient with severe alcoholism.
Abstract: Real time polymerase chain reaction (RT-PCR) is a new technique in molecular genetics which allows quantification of polymorphic DNA regions and genotyping of single nucleotide polymorphisms (SNPs) in one run. A byproduct of real time PCR is the opportunity to identify new SNPs in the proximity of gene loci of interest. In this paper methodological details are presented and exemplified by a newly detected SNP in codon 155 of the catechol-O-methyltransferase (COMT) gene in a patient with severe alcoholism. Some years ago genotyping of single nucleotide polymorphisms was conducted in two steps. First a DNA region of approximately 200 basepairs around the SNP was amplified millions to billions of times by means of a PCR before the PCR product had to be sequenced or digested by an enzyme with ensuing gel electrophoresis in order to genotype the polymorphic regions. The invention of RTPCR extremely facilitates the analysis, because quantification of target DNA sequences and genotyping can be done in one single PCR run. Besides the higher speed of RT-PCR machines – notably less than one hour for one PCR run – the risk for contamination is minimised because the PCR product remains in the machine for genotyping. Moreover, the amplification process can be monitored online so that unsuccessful PCR runs can be terminated betimes. Online monitoring of the amplification process as well as genotyping by melting curve analysis is possible by the use of hybridisation probes. These hybridisation probes are sequence-specific oligonucleotide probes, labelled by fluorescence dyes. For the detection of a SNP two hybridisation probes are required, one that binds to the DNA strand in a way that the polymorphic region is covered (sensor hybridisation probe) and a second probe (anchor probe) that binds to a site in close proximity (only 1–5 bases between the probes) to the sensor probe. The sensor probe is labelled by fluorescein and the anchor probe by LC Red 640. During amplification the hybridisation probes anneal to the amplified DNA segment. By means of an LED the RT-PCR machine excites the fluorescein of the sensor probe which then emits green light. The energy of the green light in turn excites the LC Red 640 dye which then emits red fluorescent light. The energy transfer is referred to as fluorescence resonance energy transfer (FRET). The optical unit of the RT-PCR machine is able to measure the intensity of the red light at 640 nm. The more new target DNA sequences are built the stronger is the FRET signal, because more probes can hybridise to the DNA. Therefore, the FRET signal is a direct measure of DNA copies in a PCR run. In the elongation phase of the PCR run the temperature is raised causing the displacement of the hybridisation probes from the DNA. After amplification, point mutations can be detected by a melting-curve analysis. Hereby the temperature is slowly raised from 40° to 75°C and the critical temperature, Tm, at which the hybridisation probes are melted off the DNA strand, is an indicator for the presence or absence of a mutation. If the sensor probe is designed in a way that it perfectly fits the DNA strand, then it melts off at a higher temperature than in case there is a mismatch of one base (the single nucleotide mutation) causing the probe to melt off earlier at a lower temperature. The result of the melting curve analysis can yield three characteristic curves: a curve with a single early peak (homozygous wildtype), a curve with a single late peak (homozygous mutant) and a curve with two peaks (heterozygous genotype). It has to be mentioned that the *For correspondence. E-mail: martin.reuter@psychol.uni-giessen.de. RESEARCH NOTE

Journal ArticleDOI
TL;DR: The evaluation of F1, F2 and F3 generations and F6 SSD families from the cross of CSP44 with susceptible wheat cultivar WL711 for stripe rust severity indicated that the resistance in CSP43 is based on two genes showing additive effect, one of which isYr18 and the second gene is not yet described.
Abstract: Wheat line CSP44, a selection from an Australian bread wheat cultivar Condor, has shown resistance to stripe rust in India since the last twenty years. Seedlings and adult plants of CSP44 showed susceptible infection types against stripe rust race 46S119 but displayed average terminal disease severity of 2.67 on adult plants against this race as compared to 70.33 of susceptible Indian cultivar, WL711. This suggests the presence of nonhypersensitive adult plant stripe rust resistance in the line CSP44. The evaluation of F1, F2 and F3 generations and F6 SSD families from the cross of CSP44 with susceptible wheat cultivar WL711 for stripe rust severity indicated that the resistance in CSP44 is based on two genes showing additive effect. One of these two genes isYr18 and the second gene is not yet described.

Journal ArticleDOI
TL;DR: The demonstration of structural changes in mRNA transcripts as a result of splice-site polymorphisms implies that they may be of biological significance in certain pathological conditions.
Abstract: Genetic polymorphisms associated with structural changes of their gene product are important in terms of their pote ntial relation with diseases. Therefore, in this study, splice -site variants of the transmembrane serine protease gene TMPRSS4, nephronophthis is gene NPHP4, and organic-cation transporter gene ORCTL4, were selected from the dbSNP single nucleotide polymorphism database as candidates to identify genetic pol ymorphisms associated with a structural change in their mRNA transcripts. The allele frequencies of the TMPRSS4 c.4-7A>G, NPHP4 c.2818-2A>T, and ORCTL4 c.517-2A>C polymorphisms in a Japanese population were determined to be 0.42, 0.10, and 0.27, r espectively, by PCR -SSCP analysis. Next, the effect of these polymorphisms on the mode of pre -mRNA splicing was investigated by RT -PCR analysis followed by sequencing analysis. The TMPRSS4, NPHP4, and ORCTL4 polymorphisms were associated with the production of the r.4-6_4-1ins transcript, the r.2818_2823del and r.2818_2859del transcripts, and the r.517-94_517-1ins; r.517-2a>c and r.517_620del transcripts, respectively . Since the proteins encoded by all these transcripts are associated with relatively significant structural changes in the form amino acid inse rtion/deletion and premature termination, their functional ability may be greatly reduced. Our demonstration of structural changes in mRNA transcripts as a result of splice -site polymorphisms implies that they may be of biological significance in certain pathological co nditions.

Journal ArticleDOI
TL;DR: This research presents a novel and scalable approach to personalized medicine that aims to provide real-time information about the immune system’s response to chemotherapy and its applications in medicine and pediatrics.
Abstract: S A N T H O S H G I R I R A J A N 1 a n d S A R A H H . E L S E A 2 * Department of Human Genetics, P.O. Box # 980441, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, 23298, United States of America Department of Pediatrics and Human Genetics, 12-018 Sanger Hall, 1101 E Marshall streeet, P.O. Box # 980441, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, 23298, United States of America

Journal ArticleDOI
TL;DR: A population genetic study of chromosome inversion polymorphisms in hitherto unanalysed population samples from Southeast (SE) Asia found a high frequency of each of the four common cosmopolitan inversions in comparison to populations from Africa, Asia, and Australia, however, it could not detect differences in inversion frequencies among populations.
Abstract: East AsianDrosophila melanogaster are known for great variation in morphological and physiological characters among populations, variation that is believed to be maintained by genetic drift. To understand the genetic properties of AsianD. melanogaster populations, we initiated a population genetic study of chromosome inversion polymorphisms in hitherto unanalysed population samples from Southeast (SE) Asia. We generally found a high frequency of each of the four common cosmopolitan inversions in comparison to populations from Africa, Asia, and Australia. In contrast to the great phenotypic variation among Asian populations, however, we could not detect differences in inversion frequencies among populations. Furthermore, we observed neither correlations of inversion frequencies with population latitude and longitude, nor evidence for linkage disequilibrium between different inversion loci. We propose two explanations for the observed genetic homogeneity among these SE AsianD. melanogaster populations: (i) the observed pattern simply reflects the retention of ancestral polymorphisms originating from a panmictic population that was once present on a large single landmass (Sundaland), and/or is a consequence of high recent gene flow between populations; and (ii) it is caused by selective forces (e.g. balancing selection).

Journal ArticleDOI
TL;DR: On the occasion of his 100th birthday, Ernst Mayr as mentioned in this paper has written a special essay reminiscing about the history of evolutionary biology over the last 80 years and his many contributions to this lively field.
Abstract: On the occasion of his 100th birthday, we have invited Ernst Mayr to write a special essay reminiscing about the history of evolutionary biology over the last 80 years and his many contributions to this lively field.

Journal ArticleDOI
TL;DR: Three inactivating mutations were identified in the group of 30 Czech ovarian cancer patients: the 5382insC mutation in two unrelated patients and a deletion of exons 21 and 22 in another patient.
Abstract: Ovarian cancer is one of the most severe of oncological diseases. Inherited mutations in cancer susceptibility genes play a causal role in 5–10% of newly diagnosed tumours.BRCA1 andBRCA2 gene alterations are found in the majority of these cases. The aim of this study was to analyse theBRCA1 gene in the ovarian cancer risk group to characterize the spectrum of its mutations in the Czech Republic. Five overlapping fragments amplified on both genomic DNA and cDNA were used to screen for the whole proteincoding sequence of theBRCA1 gene. These fragments were analysed by the protein truncation test (PTT) and direct sequencing. Three inactivating mutations were identified in the group of 30 Czech ovarian cancer patients: the 5382insC mutation in two unrelated patients and a deletion of exons 21 and 22 in another patient. In addition, we have found an alternatively spliced product lacking exon 5 in two other unrelated patients. The 5382insC is the most frequent alteration of theBRCA1 gene in Central and Eastern Europe. The deletion of exons 21 and 22 affects the BRCT functional domain of the BRCA1 protein. Although large genomic rearragements are known to be relatively frequent in Western European populations, no analyses have been performed in our region yet.


Journal ArticleDOI
TL;DR: The findings and implications suggest that the orchid flowers might have evolved through the quantum evolution of CYC-L gene from their lily-like ancestors.
Abstract: A framework on orchid flower evolution has been proposed based on three different findings and their resultant implications. (i) The general occurrence of semipeloric natural orchid mutants suggest a common underlying genetic mechanism. (ii) The phenotypic expressions of both wild-type orchids and the semipeloric mutants can be explained by the ABC model of flower development and the polar coordinate model for zygomorphy which explains the phenotypic expression of flower symmetry in wild type and semipeloric flowers of Antirrhinum by the CYCLOIDEA, CYC gene. Similarly, the presence of such a similar gene in orchids CYCLOIDEA like, CYC-L gene has already been proposed (iii) The origin of three evolutionarily distant column types (e.g. triandrous, diandrous and monandrous) of orchids representing different sub-families too can be explained with these models suggesting the presence of three different homologues of CYC-L gene within the Orchidaceae. These findings and implications suggest that the orchid flowers might have evolved through the quantum evolution of CYC-L gene from their lily-like ancestors. Further experiments for verification of the phenomenon have been suggested.

Journal ArticleDOI
Xue-Chang Wu1
TL;DR: Compared genetic diversity of historical collections of Chinese paddlefishes with recent collections is compared, to see whether there has been a loss of genetic diversity in this species as its range and population size have changed.
Abstract: Examining patterns of genetic diversity has become an integral component of many management plans concerning endangered species. Chinese paddlefish (Psephurus gladius Martens), a large-sized freshwater fish, is the only member of the family Polyodontidae present in Asia and in the main stream of the Yangtze river. Since the Gezhouba Dam, which was built in 1981, blocked the channel and prevented sturgeon from swimming into the lower-middle section of the Yangtze river, currently the Chinese paddlefish is found only in the upper main stem of the Yangtze river. Furthermore, in the last two decades, the over-catching, habitat destruction and pollution have caused a rapid reduction of the wild population of Chinese paddlefishes, such that the species is now listed as endangered (Category I of the State Key Protected Wildlife List, in the CR Category of the IUCN and on Appendix II of the CITES; Yue et al. 1998). Multiple factors are implicated in species extinction, including habitat loss, and fragmentation, demographic instability, inbreeding and other genetic factors (Lande 1988). If one of these factors, namely recent changes in genetic diversity, can be tested and perhaps rejected, then research and management can focus on the other extinction mechanisms. Moreover, species endangerment often derives from the erosion of genetic diversity (Chen 1993). The loss of genetic diversity predicts lower individual fitness and lower population adaptability (Lande 1998). Consequently, information on genetic diversity may contribute to a better understanding of the causes of species endangerment and thereby help in the development of management strategies for species conservation. Genetic diversity surveys in endangered populations typically determine the variation currently maintained in the population rather than the magnitude or rate of loss of genetic diversity over time (Matocq et al. 2001). Finding evidence of temporal changes in genetic diversity is challenging. Difficulties include finding appropriate molecular markers, methods of analysis (Luikart et al. 1998) and establishing a baseline or reference point from previous specimens against which to measure change (Taylor et al. 1994). DNA fingerprinting is a good marker system for small populations (Wan et al. 2004) and has revealed the loss of genetic diversity (Wan and Fang 2002, 2003; Wan et al. 2003a), genetic variation between subpopulations (Fang et al. 2002a, 2003), and genetic differentiation of populations (Wan et al. 2003b) of endangered animals. Besides a reliable genetic marker, detecting the loss of genetic diversity also requires archival specimens from which DNA can be obtained. A considerable number of historic samples were preserved by formalin-fixation. The formalin-induced cross-linking between DNA and proteins resulted in the extraction of only fragmented DNA from fixed samples, limiting the use of these archival specimens in conservation genetics (Wan et al. 2004). However, a recent study reported the isolation of high molecular weight DNA from formalin-fixed samples and the successful use of such DNA for fingerprinting studies (Fang et al. 2002b). In this study, we compared genetic diversity of historical collections of Chinese paddlefishes with recent collections, to see whether there has been a loss of genetic diversity in this species as its range and population size

Journal ArticleDOI
TL;DR: Ernst Mayr was one of the principal architects of 20th century evolutionary biology and his principal contribution was the elaboration of the idea of allopatric speciation, the idea that geographic isolation leads to reproductive isolation leading ultimately to new species.
Abstract: The story goes that, with the intention of celebrating Ernst Mayr’s 100th birthday by commissioning an essay on his life and work, Science asked him who would be the best person to write such an essay. Ernst Mayr is supposed to have replied, “Ernst Mayr of course”! The resulting essay entitled “80 Years of Watching the Evolutionary Scenery” (Mayr 2004) – as sharp and precise as it is rich in historical detail – is a special gift to be savoured as it gives us a unique glimpse of the evolution of evolutionary thought in the 20th century. Even more important, it gives us a glimpse of the evolution of Ernst Mayr’s thoughts. And there is very good reason to be interested in the evolution of Ernst Mayr’s thoughts, not only because it spanned a record 80 years, but also because he was one of the principal architects of 20th century evolutionary biology. Ernst Mayr remains best known for his early work in the 1930’s and 1940’s, culminating in his Systematics and the Origin of Species (1942). This, along with Theodosius Dobzhansky’s Genetics and the Origin of Species (1937) and George Gaylord Simpson’s Tempo and Mode in Evolution (1944), constituted the “Modern Synthesis” of evolution. The modern synthesis brought together genetics, systematics and paleontology to explain the mechanism of the origin of species with a degree of success that, notwithstanding the title of his book, was impossible for Darwin. Mayr’s principal contribution was the elaboration of the idea of allopatric speciation, the idea that geographic isolation leads to reproductive isolation leading ultimately to new species. This stemmed from his biological species concept which led him to famously define species as “a group of actually or potentially interbreeding natural populations reproductively isolated from other such populations”. Mayr’s early ideas evolved in the backdrop of his field work on the birds of New Guinea and the tropical southwest Pacific islands. Less well known to non specialists are Mayr’s mammoth contributions as an ornithologist – he is said to have “described more species and subspecies of living birds than anyone else of his or subsequent generations” (Diamond 2005). All this came about by a curious set of circumstances. Born in Kempton, Germany, on 5 July 1904, Mayr was all set to faithfully follow the family tradition of a career in medicine when he sighted and carefully observed a pair of rare ducks called red-crested pochards, a species that had not been sighted in Germany for 77 years. This of course was only possible because his father had inculcated in him an abiding interest in nature by taking him out on Sunday natural history expeditions. That’s something to think about and emulate for those of us in India who keep complaining about our young people being blindly driven to medical and engineering colleges! The citing of the pochards brought Mayr in contact with Erwin Stresemann, a famous German ornithologist of the time. Interestingly, it is the same Erwin Stresemann that India’s foremost ornithologist Salim Ali went to train with and about whom he wrote “I considered him my guru to the OBITUARY

Journal ArticleDOI
TL;DR: The paper discusses modern problems in understanding games at the genetic level using the examples of conflict between endosymbionts and their hosts, and the molecular interactions between parasites and the mammalian immune system.
Abstract: This paper is written in memory of John Maynard Smith. In a brief survey it discusses essential aspects of how game theory in biology relates to its counterpart in economics, the major transition in game theory initiated by Maynard Smith, the discrepancies between genetic and phenotypic models in evolutionary biology, and a balanced way of reconciling these models. In addition, the paper discusses modern problems in understanding games at the genetic level using the examples of conflict between endosymbionts and their hosts, and the molecular interactions between parasites and the mammalian immune system.


Journal ArticleDOI
TL;DR: This research identified and localised re-peat sequences in Korean cattle (Hanwoo) which may be a basis for future genetic studies and sequenced 2,794 clones successfully at both 5′ and 3′ terminals.
Abstract: The aim of this research was to identify and localise re-peat sequences in Korean cattle (Hanwoo), which may be a basis for future genetic studies To achieve this, a Ha n-woo BAC library containing a total of 150,000 clones with an average size of 130–140 kb was constructed us-ing two different restriction enzymes Eco RI and Hind III A total of 2,794 clones were sequenced successfully at both 5′ and 3′ terminals using RP2 and T7 primers, ge n-erating 5,588 mate-pairs end sequences amounting to a total of 33 × 10

Journal ArticleDOI
TL;DR: It is demonstrated, using Drosophila melanogaster and D. pseudoobscura flies, that the temperature of rearing, preadult density, and level of consanguinity, can all produce differences in mating propensity between genetically equivalent flies.
Abstract: Sexual isolation inDrosophila is typically measured by multiple-choice mating tests. While many environmental variables during such tests are controlled by the researcher, there are some factors that are usually uncontrolled. We demonstrate, usingDrosophila melanogaster andD. pseudoobscura flies, that the temperature of rearing, preadult density, and level of consanguinity, can all produce differences in mating propensity between genetically equivalent flies. These differences in mating propensity, in turn, can give rise to statistically significant results in multiple-choice mating tests, leading to positive isolation values and the artifactual inference of sexual isolation between populations. This fact agrees with a nonrandom excess of significant positive tests found in a review of the literature ofDrosophila intraspecific mating choice. An overestimate of true cases of sexual isolation inDrosophila in the literature can, therefore, not be ruled out.