Showing papers in "Journal of Genetics in 2008"

Genetic landscape of the people of India: A canvas for disease gene exploration

Abstract: Analyses of frequency profiles of markers on disease or drug-response related genes in diverse populations are important for the dissection of common diseases. We report the results of analyses of data on 405 SNPs from 75 such genes and a 5.2 Mb chromosome, 22 genomic region in 1871 individuals from diverse 55 endogamous Indian populations. These include 32 large (>10 million individuals) and 23 isolated populations, representing a large fraction of the people of India. We observe high levels of genetic divergence between groups of populations that cluster largely on the basis of ethnicity and language. Indian populations not only overlap with the diversity of HapMap populations, but also contain population groups that are genetically distinct. These data and results are useful for addressing stratification and study design issues in complex traits especially for heterogeneous populations.

Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in rice grains

Abstract: complex traits that are important in agriculture, including mineral content. In the present study, with a set of 241 recombinant-inbred lines (RILs) derived from a cross be- tween Zhenshan 97 and Minghui 63, mapping of main-effect QTLs and epistatic QTLs for the Fe, Ca, Zn, Mn and Cu content of rice grain was conducted based on field measure- ments.

The Drosophila melanogaster circadian pacemaker circuit

Abstract: As an experimental model system, the fruit fly Drosophila melanogaster has been seminal in shaping our understanding of the circadian clockwork. The wealth of genetic tools at our disposal over the past four decades has enabled discovery of the genetic and molecular bases of circadian rhythmicity. More recently, detailed investigation leading to the anatomical, neuro-chemical and electrophysiological characterization of the various neuronal subgroups that comprise the circadian machinery has revealed pathways through which these neurons come together to act as a neuronal circuit. Thus the D. melanogaster circadian pacemaker circuit presents a relatively simple and attractive model for the study of neuronal circuits and their functions.

Defining fitness in evolutionary models.

Abstract: The analysis of evolutionary models requires an appropriate definition for fitness. In this paper, I review such definitions in relation to the five major dimensions by which models may be described, namely (i) finite versus infinite (or very large) population size, (ii) type of environment (constant, fixed length, temporally stochastic, temporally predictable, spatially stochastic, spatially predictable and social environment), (iii) density-independent or density-dependent, (iv) inherent population dynamics (equilibrium, cyclical and chaotic), and (v) frequency-dependent or independent. In simple models, the Malthusian parameter ‘r’ or the net reproductive rate R 0 may be satisfactory, but once density-dependence or complex population dynamics is introduced the invasion exponent should be used. Defining fitness in a social environment or when there is frequency-dependence requires special consideration.

Phenotypic effects of genetic variability in human clock genes on circadian and sleep parameters

Abstract: Circadian rhythms and sleep are two separate but intimately related processes. Circadian rhythms are generated through the precisely controlled, cyclic expression of a number of genes designated clock genes. Genetic variability in these genes has been associated with a number of phenotypic differences in circadian as well as sleep parameters, both in mouse models and in humans. Diurnal preferences as determined by the selfreported Horne-Ostberg (HO) questionnaire, has been associated with polymorphisms in the human genes CLOCK, PER1, PER2 and PER3. Circadian rhythm-related sleep disorders have also been associated with mutations and polymorphisms in clock genes, with the advanced type cosegrating in an autosomal dominant inheritance pattern with mutations in the genes PER2 and CSNK1D, and the delayed type associating without discernible Mendelian inheritance with polymorphisms in CLOCK and PER3. Several mouse models of clock gene null alleles have been demonstrated to have affected sleep homeostasis. Recent findings have shown that the variable number tandem polymorphism in PER3, previously linked to diurnal preference, has profound effects on sleep homeostasis and cognitive performance following sleep loss, confirming the close association between the processes of circadian rhythms and sleep at the genetic level.

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.).

Abstract: Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China.

Abstract: Genetic diversity of maize (Zea mays L.) plays a key role in maize breeding (William and Michael 2002). Knowledge of the amount and the distribution of genetic variation within and among maize landraces will provide a guide for predicting the degree of inheritance, variation, and level of heterosis, that are essential for maize breeding (Duan et al. 2006). For several decades, maize breeders have focused on short-term breeding. This has resulted in the development of a narrow genetic base for commercial maize hybrids (Darrah and Zuber 1986). A survey that was conducted in late 1970s and mid 1980s on inbred lines showed that some of the inbreds continued to contribute substantially to hybrids marketed in the United States. And the pedigrees of most hybrids are derivatives of 6–8 inbred lines (Darrah and Zuber 1986; James et al. 2002). In China, the parenthood of 91.6% hybrids consists of about 20 elite inbred lines (Li et al. 2002). With such a restrictive base, maize may not contain all the desirable and favourable alleles to maintain selection progress. Wuling mountain region covers Hunan, Hubei, Chongqing, and Guizhou provinces in China, where farmersaved maize landraces are still grown. The development of molecular markers provides a means of assessing genetic diversity at the DNA level (Reif et al. 2003). In particular, SSR markers are potentially useful for large-scale DNA fingerprinting of maize genotypes due to a high level of polymorphism detected (Smith et al. 1997), automated analysis systems (Sharon et al. 1997), and high accuracy and repeatability (Heckenberger et al. 2002). No attempts have been made so far to characterize maize landraces in Wuling mountain region using SSR markers. These original landraces represent a vast array of germplasm, which can be used in maize breeding for improving disease and pest

Is vertical migration in Antarctic krill (Euphausia superba) influenced by an underlying circadian rhythm

Abstract: Antarctic krill (Euphausia superba) is a keystone species in the southern ocean ecosystem where it is the main consumer of phytoplankton and constitutes the main food item of many higher predators. Both food and predators are most abundant at the surface, thus krill hide in the depth of the ocean during the day and migrate to the upper layers at night, to feed at a time when the predatory risk is lowest. Although the functional significance of this diel vertical migration (DVM) is clear and its modulation by environmental factors has been described, the involvement of an endogenous circadian clock in this behaviour is as yet not fully resolved. We have analysed the circadian behaviour of Euphausia superba in a laboratory setting and here we present the first description of locomotor activity rhythms for this species. Our results are in agreement with the hypothesis that the circadian clock plays a key role in DVM. They also suggest that the interplay between food availability, social cues and the light:dark cycle acts as the predominant Zeitgeber for DVM in this species.

Molecular assessment of genetic diversity in mung bean germplasm.

Abstract: RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard’s similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appears to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.

The role of microRNAs (miRNA) in circadian rhythmicity.

Abstract: MicroRNA (miRNA) is a recently discovered new class of small RNA molecules that have a significant role in regulating gene and protein expression. These small RNAs (∼22 nt) bind to 3′ untranslated regions (3′ UTRs) and induce degradation or repression of translation of their mRNA targets. Hundreds of miRNAs have been identified in various organisms and have been shown to play a significant role in development and normal cell functioning. Recently, a few studies have suggested that miRNAs may be an important regulators of circadian rhythmicity, providing a new dimension (posttranscriptional) of our understanding of biological clocks. Here, we describe the mechanisms of miRNA regulation, and recent studies attempting to identify clock miRNAs and their function in the circadian system.

The electroretinogram as a method for studying circadian rhythms in the mammalian retina

Abstract: Circadian clocks are thought to regulate retinal physiology in anticipation of the large variation in environmental irradiance associated with the earth’s rotation upon its axis. In this review we discuss some of the rhythmic events that occur in the mammalian retina, and their consequences for retinal physiology. We also review methods of tracing retinal rhythmicity in vivo and highlight the electroretinogram (ERG) as a useful technique in this field. Principally, we discuss how this technique can be used as a quick and noninvasive way of assessing physiological changes that occur in the retina over the course of the day. We highlight some important recent findings facilitated by this approach and discuss its strengths and limitations.

Energy-responsive timekeeping

Abstract: An essential component of energy homeostasis lies in an organism’s ability to coordinate daily patterns in activity, feeding, energy utilization and energy storage across the daily 24-h cycle. Most tissues of the body contain the molecular clock machinery required for circadian oscillation and rhythmic gene expression. Under normal circumstances, behavioural and physiological rhythms are orchestrated and synchronized by the suprachiasmatic nucleus (SCN) of the hypothalamus, considered to be the master circadian clock. However, metabolic processes are easily decoupled from the primarily light-driven SCN when food intake is desynchronized from normal diurnal patterns of activity. This dissociation from SCN based timing demonstrates that the circadian system is responsive to changes in energy supply and metabolic status. There has long been evidence for the existence of an anatomically distinct and autonomous food-entrainable oscillator (FEO) that can govern behavioural rhythms, when feeding becomes the dominant entraining stimulus. But now rapidly growing evidence suggests that core circadian clock genes are involved in reciprocal transcriptional feedback with genetic regulators of metabolism, and are directly responsive to cellular energy supply. This close interaction is likely to be critical for normal circadian regulation of metabolism, and may also underlie the disruption of proper metabolic rhythms observed in metabolic disorders, such as obesity and type-II diabetes.

Oscillating perceptions: the ups and downs of the CLOCK protein in the mouse circadian system

Abstract: A functional mouse CLOCK protein has long been thought to be essential for mammalian circadian clockwork function, based mainly on studies of mice bearing a dominant negative, antimorphic mutation in the Clock gene. However, new discoveries using recently developed Clock-null mutant mice have shaken up this view. In this review, I discuss how this recent work impacts and alters the previous view of the role of CLOCK in the mouse circadian clockwork.

Evolution of ageing since Darwin

Abstract: In the late 19th century, the evolutionary approach to the problem of ageing was initiated by August Weismann, who argued that natural selection was more important for ageing than any physiological mechanism. In the mid-twentieth century, J. B. S. Haldane, P. B. Medawar and G. C. Williams informally argued that the force of natural selection falls with adult age. In 1966, W. D. Hamilton published formal equations that showed mathematically that two’ forces of natural selection’ do indeed decline with age, though his analysis was not genetically explicit. Brian Charlesworth then developed the required mathematical population genetics for the evolution of ageing in the 1970’s. In the 1980’s, experiments using Drosophila showed that the rate of ageing evolves as predicted by Hamilton’s’ forces of natural selection’. The discovery of the cessation of ageing late in life in the 1990’s was followed by its explanation in terms of evolutionary theory based on Hamilton’s forces. Recently, it has been shown that the cessation of ageing can also be manipulated experimentally using Hamilton’s’ forces of natural selection’. Despite the success of evolutionary research on ageing, mainstream gerontological research has largely ignored both this work and the opportunity that it provides for effective intervention in ageing.

Angiotensin-I converting enzyme gene and I/D polymorphism distribution in the Greek population and a comparison with other European populations

Abstract: Angiotensin-I converting enzyme (ACE) gene is one of the most intensely studied genes because of the key role it plays in the renin–angiotensin system (RAS). ACE catalyses the conversion of angiotensin I to angiotensin II, a vasoactive and aldosterone-stimulating peptide, and inactivates bradykinin (Erdos and Skidgel 1987). ACE gene is located on chromosome 17q23 and consists of 26 exons and 25 introns. The insertion deletion (I/D) polymorphism in this gene refers to an Alu repetitive sequence 287 bp long, in intron 16, resulting in three genotypes,DD and II homozygotes and ID heterozygotes. The I/D polymorphism is reported to determine circulating and tissue ACE levels, such that individuals homozygous for the D allele have higher tissue and plasma ACE concentrations than heterozygotes and II homozygotes (Rigat et al. 1990; Costerousse et al. 1993). The I/D polymorphism is associated with cardiovascular diseases (Cambien et al. 1992; Marian et al. 1993; Schunkert et al. 1994; Kario et al. 1996) as well as chronic renal diseases (Hohenfellner et al. 2001; Ohtomo et al. 2001). However, little is known about the distribution of the ACE gene I/D polymorphism in the general population and the differences it may present among different ethnicities. In this study, we examined the distribution of the ACE I/D polymorphism in a sample of a Greek population. We have also presented a comparision of our data with data for other population in the literature.

The simplest formal argument for fitness optimization

Abstract: The Formal Darwinism Project aims to provide a formal argument linking population genetics to fitness optimization, which of necessity includes defining fitness. This bridges the gulf between those biologists who assume that natural selection leads to something close to fitness optimization and those biologists who believe on theoretical grounds that there is no sense of fitness that can usefully be said to be optimized. The current paper’s main objective is to provide a careful mathematical introduction to the project, and it also reflects on the project’s scope and limitations. The central argument is the proof of close ties between the mathematics of motion, as embodied in the Price equation, and the mathematics of optimization, as represented by optimization programmes. To make these links, a general and abstract model linking genotype, phenotype and number of successful gametes is assumed. The project has begun with simple dynamic models and simple linking models, and its progress will involve more realistic versions of them. The versions given here are fully mathematically rigorous, but elementary enough to serve as an introduction.

Adaptation to different climates results in divergent phenotypic plasticity of wing size and shape in an invasive drosophilid.

Abstract: The phenotypic plasticity of wing size and wing shape of Zaprionus indianus was investigated in relation to growth temperature (17°C to 31°C) in two natural populations living under different climates, equatorial and subtropical. The two populations were clearly distinguished not only by their wing size (the populations from the colder climate being bigger in size), but also by the shape of the response curves to growth temperature i.e., their reaction norms. In this respect, the temperature at which the size of the wing was maximum was about 3°C higher in the equatorial population. Such a difference in size plasticity is already found in two other nonclosely related species, might be a general evolutionary pattern in drosophilids. Wing shape was investigated by calculating an ellipse included into the wing blade, then by considering the ratio of the two axes, and also by analysing the angular position of 10 wing-vein landmarks. For an overall shape index (ratio of the two axes of the ellipse), a regular and almost linear increase was observed with increasing temperature i.e., a more round shape at high temperatures. Wing shape was also analysed by considering the variations of the various angles according to temperature. A diversity of response curves was observed, revealing either a monotonous increase or decrease with increasing temperature, and sometimes a bell shape curve. An interesting conclusion is that, in most cases, a significant difference was observed between the two populations, and the difference was more pronounced at low temperatures. These angular variations are difficult to interpret in an evolutionary context. More comparative studies should be undertaken before reaching some general conclusions.

Eucalyptus microsatellites mined in silico: survey and evaluation.

Abstract: Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.

Minisatellites as DNA markers to classify bermudagrasses (Cynodon spp.): confirmation of minisatellite in amplified products.

Abstract: Hyper variable repetitive DNA sequences such as microsatellites, minisatellites, midisatellites and satellites can be of great value in assessing a high level of polymorphism as they are distributed throughout the genomes. Here we used a polymerase chain reaction (PCR) technique, known as the directed amplification of minisatellite-region DNA (DAMD), an inexpensive, PCR-based method to amplify minisatellite DNA regions of 11 Cynodon species. A total of 10 minisatellite core primer sequences derived from other species, including human, were used as primers in DAMD-PCR to assess polymorphisms within 11 Cynodon species. A total of six bands of amplified products were cloned and sequenced. Results indicated that not all the amplified products contained minisatellites. However, the primers used in the DAMD technique offered highly reproducible and polymorphic DNA markers differentiating all the species of bermudagrasses studied. DNA markers are much valuable tool for the plant breeders and taxonomist because they do not have the disadvantages of isozyme and morphological markers, which are usually affected by environmental conditions and different stages of plant development. DNA markers offer a rapid, cost effective, safe and efficient way to test the genetic purity of the varieties, and are a powerful tools in any genome mapping programme to identify DNA markers linked to economically important quantitative traits (Karaca et al. 2002, 2004). There are several DNA-marker techniques for genetic analyses. The restriction fragment length polymorphism (RFLP) technique, is one of the first DNA methods used in a variety of organisms in mapping and genetic diversity studies (Williams and Clair 1993). However, the RFLP technique has several limitations in comparison to various PCRbased marker techniques. The RFLP technique requires large

Multidimensional analysis of Drosophila wing variation in Evolution Canyon.

Abstract: Environmental stress has been suggested to be a major evolutionary force, both through inducing strong selection and because of its direct impact on developmental buffering processes that alter the evolvability of organisms. In particular, temperature has attracted much attention because of its importance as an ecological feature and the relative ease with which it can be experimentally manipulated in the lab. Evolution Canyon, Lower Nahal Oren, Israel, is a well studied natural site where ecological parameters are suspected to drive evolutionary differentiation. In this study, using Drosophila melanogaster isofemale lines derived from wild flies collected on both slopes of the canyon, we investigated the effect of developmental temperature upon the different components of phenotypic variation of a complex trait: the wing. Combining geometric and traditional morphometrics, we find only limited evidence for a differentiation among slopes. Investigating simultaneously phenotypic plasticity, genetic variation among isofemale lines, variation among individuals and fluctuating asymmetry, we could not identify a consistent effect of the stressful conditions encountered on the south facing slope. The prevailing structuring effect is that of the experimentally manipulated temperature which clearly influences wing mean size and shape. Variability, in contrast, is not consistently affected by temperature. Finally, we investigated the specific relationship between individual variation and fluctuating asymmetry. Using metric multi-dimensional scaling we show that the related patterns of wing shape variation are not identical, supporting the view that the underlying developmental processes are to a certain extent different.

Sexual conflict and environmental change: trade-offs within and between the sexes during the evolution of desiccation resistance

Abstract: Intralocus sexual conflict occurs when males and females experience sex-specific selection on a shared genome. With several notable exceptions, intralocus sexual conflict has been investigated in constant environments to which the study organisms have had an opportunity to adapt. However, a change in the environment can result in differential or even opposing selection pressures on males and females, creating sexual conflict. We used experimental evolution to explore the interaction between intralocus sexual conflict, sexual dimorphism and environmental variation in Drosophila melanogaster. Six populations were selected for adult desiccation resistance (D), with six matched control populations maintained in parallel (C). After 46 generations, the D populations had increased in survival time under arid conditions by 68% and in body weight by 20% compared to the C populations. The increase in size was the result of both extended development and faster growth rate of D juveniles. Adaptation to the stress came at a cost in terms of preadult viability and female fecundity. Because males are innately less tolerant of desiccation stress, very few D males survived desiccation-selection; while potentially a windfall for survivors, these conditions mean that most males’ fitness was determined posthumously. We conjectured that selection for early maturation and mating in males was in conflict with selection for survival and later reproduction in females. Consistent with this prediction, the sexes showed different patterns of age-specific desiccation resistance and resource acquisition, and there was a trend towards increasingly female-biased sexual size dimorphism. However, levels of desiccation resistance were unaffected, with D males and females increasing in parallel. Either there is a strong positive genetic correlation between the sexes that limits independent evolution of desiccation resistance, or fitness pay-offs from the strategy of riding out the stress bout are great enough to sustain concordant selection on the two sexes. We discuss the forces that mould fitness in males under a regimen where trade-offs between survival and reproduction may be considerable.

Meiotic behaviour in three interspecific three-way hybrids between Brachiaria ruziziensis and B. brizantha (Poaceae: Paniceae)

Abstract: The meiotic behaviour of three three-way interspecific promising hybrids (H17, H27, and H34) was evaluated. These hybrids resulted from the crosses between B. ruziziensis × B. brizantha and crossed to another B. brizantha. Two half-sib hybrids (H27 and H34) presented an aneuploid chromosome number (2n = 4x = 33), whereas hybrid H17 was a tetraploid (2n = 4x = 36), as expected. Chromosome paired predominantly as multivalents suggesting that genetic recombination and introgression of specific target genes from B. brizantha into B. ruziziensis can be expected. Arrangement of parental genomes in distinct metaphase plates was observed in H27 and H34, which have different male genitors. Hybrids H17 and H34 have the same male genitor, but did not display this abnormality. In H17, abnormalities were more frequent from anaphase II, when many laggard chromosomes appeared, suggesting that each genome presented a different genetic control for meiotic phase timing. Despite the phylogenetic proximity among these two species, these three hybrids presented a high frequency of meiotic abnormalities, mainly those related to irregular chromosome segregation typical of polyploids, H34, 69.1%; H27, 56.1% and H17, 44.9%. From the accumulated results obtained through cytological studies in Brachiaria hybrids, it is evident that cytogenetical analysis is of prime importance in determining which genotypes can continue in the process of cultivar development and which can be successfully used in the breeding. Hybrids with high frequency of meiotic abnormalities can seriously compromise seed production, a key trait in assuring adoption of a new apomictic cultivar of Brachiaria for pasture formation.

Egg-laying rhythm in Drosophila melanogaster.

Abstract: Extensive research has been carried out to understand how circadian clocks regulate various physiological processes in organisms. The discovery of clock genes and the molecular clockwork has helped researchers to understand the possible role of these genes in regulating various metabolic processes. In Drosophila melanogaster, many studies have shown that the basic architecture of circadian clocks is multi-oscillatory. In nature, different neuronal subgroups in the brain of D. melanogaster have been demonstrated to control different circadian behavioural rhythms or different aspects of the same circadian rhythm. Among the circadian phenomena that have been studied so far in Drosophila, the egg-laying rhythm is unique, and relatively less explored. Unlike most other circadian rhythms, the egg-laying rhythm is rhythmic under constant light conditions, and the endogenous or free-running period of the rhythm is greater than those of most other rhythms. Although the clock genes and neurons required for the persistence of adult emergence and activity/rest rhythms have been studied extensively, those underlying the circadian egg-laying rhythm still remain largely unknown. In this review, we discuss our current understanding of the circadian egg-laying rhythm in D. melanogaster, and the possible molecular and physiological mechanisms that control the rhythmic output of the egg-laying process.

Can simple population genetic models reconcile partial match frequencies observed in large forensic databases

Abstract: A recent study of partial matches in the Arizona offender database of DNA profiles has revealed a large number of nine and ten locus matches. I use simple models that incorporate the product rule, population substructure, and relatedness to predict the expected number of matches in large databases. I find that there is a relatively narrow window of parameter values that can plausibly describe the Arizona results. Further research could help determine if the Arizona samples are congruent with some of the models presented here or whether fundamental assumptions for predicting these match frequencies requires adjustments.

GJB2 and mitochondrial A1555G gene mutations in nonsyndromic profound hearing loss and carrier frequencies in healthy individuals.

Abstract: This study aimed to assess mutations in GJB2 gene (connexin 26), as well as A1555G mitochondrial mutation in both the patients with profound genetic nonsyndromic hearing loss and healthy controls. Ninety-five patients with profound hearing loss (>90 dB) and 67 healthy controls were included. All patients had genetic nonsyndromic hearing loss. Molecular analyses were performed for connexin 26 (35delG, M34T, L90P, R184P, delE120, 167delT, 235delC and IVS1+1 A-->G) mutations, and for mitochondrial A1555G mutation. Twenty-two connexin 26 mutations were found in 14.7% of the patients, which were 35delG, R184P, del120E and IVS1+1 A-->G. Mitochondrial A1555G mutation was not encountered. The most common GJB2 gene mutation was 35delG, which was followed by del120E, IVS1+1 A-->G and R184P, and 14.3% of the patients segregated with DFNB1. In consanguineous marriages, the most common mutation was 35delG. The carrier frequency for 35delG mutation was 1.4% in the controls. 35delG and del120E populations, seems the most common connexin 26 mutations that cause genetic nonsyndromic hearing loss in this country. Nonsyndromic hearing loss mostly shows DFNB1 form of segregation.

The molecular basis of speciation: from patterns to processes, rules to mechanisms

Abstract: The empirical study of speciation has brought us closer to unlocking the origins of life’s vast diversity. By examining recently formed species, a number of general patterns, or rules, become apparent. Among fixed differences between species, sexual genes and traits are one of the most rapidly evolving and novel functional classes, and premating isolation often develops earlier than postmating isolation. Among interspecific hybrids, sterility evolves faster than inviability, the X-chromosome has a greater effect on incompatibilities than autosomes, and hybrid dysfunction affects the heterogametic sex more frequently than the homogametic sex (Haldane’s rule). Haldane’s rule, in particular, has played a major role in reviving interest in the genetics of speciation. However, the large genetic and reproductive differences between taxa and the multi-factorial nature of each rule have made it difficult to ascribe general mechanisms. Here, we review the extensive progress made since Darwin on understanding the origin of species. We revisit the rules of speciation, regarding them as landmarks as species evolve through time. We contrast these ‘rules’ of speciation to ‘mechanisms’ of speciation representing primary causal factors ranging across various levels of organization—from genic to chromosomal to organismal. To explain the rules, we propose a new ‘hierarchical faster-sex’ theory: the rapid evolution of sex and reproduction-related (SRR) genes (faster-SRR evolution), in combination with the preferential involvement of the X-chromosome (hemizygous X-effects) and sexually selected male traits (faster-male evolution). This unified theory explains a comprehensive set of speciation rules at both the prezyotic and postzygotic levels and also serves as a cohesive alternative to dominance, composite, and recent genomic conflict interpretations of Haldane’s rule.

GJB2 mutations in Baluchi population.

Abstract: gene have been reported.Many are ‘private’mutations, having observedin only one orfew pedigrees, although very common alleles have also beenidentified in several populations including the 35delG allelein Caucasians, 167delTallelein AshkenaziJews, 235delCal-lele in east Asian population, and R143W mutation in Ghana(Nance 2003). Although a broad spectrum of recessive deaf-ness mutation in the

α-Thalassaemia in Tunisia: some epidemiological and molecular data

Abstract: Unlike the other haemoglobinopathies, few researches have been published concerning α-thalassaemia in Tunisia. The aim of the present work is to acquire further data concerning α-thalassaemia prevalence and molecular defects spectrum in Tunisia, by collecting and studying several kinds of samples carrying α-thalassaemia. The first survey conducted on 529 cord blood samples using cellulose acetate electrophoresis, have displayed the prevalence of 7.38% Hb Bart’s carriers at birth. Molecular analyses were conducted by PCR and DNA sequencing on 20 families’ cases from the above survey carrying the Hb Bart’s at birth and on 10 Hb H diseased patients. The results showed six α-globin gene molecular defects and were responsible for α-thalassaemia: -α3.7, - -MedI, αTSaudi, α2cd23GAG→Stop, Hb Greone Hart: α1119CCT→TCT corresponding to 11 genotypes out of which two are responsible for Hb H disease (- -Med/-α3.7) and (αTSaudiα/αTSaudiα) and a newly described polymorphism: α+6C→G. The geographical repartition of α-thal carriers showed that the -α3.7 deletion is distributed all over the country, respectively the αHphI and αTSaudi seem to be more frequent in the central region of the northeast region. The haematological and clinical data showed a moderate phenotype with a late age of diagnosis for Hb H disease. This work had permitted, in addition to an overview on α-thalassaemia in the country, the optimization of protocols for α-thalassaemia detection in our lab, allowing further investigations concerning phenotype-genotype correlation in sickle cell disease or β-thalassaemia.

OGG1, MYH and MTH1 gene variants identified in gastric cancer patients exhibiting both 8-hydroxy-2'-deoxyguanosine accumulation and low inflammatory cell infiltration in their gastric mucosa.

Abstract: Introduction 8-Hydroxy-2′-deoxyguanosine (8-OHdG) is one of the main DNA modifications produced by reactive oxygen species (ROS). Because 8-OHdG can pair with cytosine and adenine bases during DNA synthesis, when 8-hydroxyguanine (8-OHG) is present in the DNA template, it causes G:C to T:A transversions (Shibutani et al. 1991), and it induces A:T to C:G transversions when 8-hydroxy-dGTP in the nucleotide pool is incorporated into DNA (Maki and Sekiguchi 1992). Because of these transversions, 8-OHdG accumulation is thought to cause carcinogenesis. 8-OHdG accumulation in mammalian cells is prevented by the base excision repair enzymes OGG1, MYH and NEIL1, and by MTH1, an enzyme that removes 8-hydroxy-dGTP from the intracellular nucleotide pool (Nakabeppu 2001). A variety of factors, including sodium chloride, Helicobacter pylori infection and smoking (Tredaniel et al. 1997; Farinati et al. 1998), induce inflammation in the stomach tissue. A considerable inflammatory cell infiltrate in the gastric mucosa causes the production of ROS (Ernst 1999), and ROS are thought to lead to 8-OHdG accumulation in the gastric mucosa (Farinati et al. 1998), suggesting that the level of inflammatory cell infiltration in the stomach may be one of the factors that determine the 8-OHdG level in the stomach. We, therefore, hypothesized that gastric cancer patients with both 8-OHdG accumulation and low level of inflammatory cell infiltration in their stomach have genetic factors that cause them to have a low ability to repair 8-OHdG. We selected 23 patients exhibiting mild or no neutrophil and mono-

Genetic diversity in Indian FCV and burley tobacco cultivars.

Abstract: Tobacco is an important commercial crop of India. Though it has never been found in wild state, cultivated tobacco is highly polymorphic with wide range of morphological types and diverse uses. Most of the commercial tobaccos produced in the world are Nicotiana tabacum. The only other species used on a limited commercial scale is N. rustica (Goodspeed 1954). India is the only country where many different types of tobacco, viz., flue-cured Virginia (FCV), burley, natu, cigar filler, cigar wrapper, cheroot, hookah, bidi and chewing are grown under different agro-climatic conditions. Among them FCV and burley are exportable tobacco types and are mainly used in cigarette manufacturing. Indian FCV tobacco is famous in the world market for its filling quality in cigarettes, and burley tobacco for cigarette blending. FCV tobacco is mainly grown in Andhra Pradesh (AP) and Karnataka states of India, and burley in AP only. The kind of tobacco grown in an area differs considerably with respect to climatic conditions, nutrient supply and use of the end product. Hence, breeding of tobacco varieties is location-specific, right from the choice of parents to the final stages of evaluation and selection. This approach has resulted in the development of a large number of location specific high yielding tobacco varieties. Varietal diversification is apparent among commercial cultivars of FCV and burley tobaccos grown in India. Assessment of their genetic diversity is of importance for longterm tobacco improvement and reduction of vulnerability of the crop. Prior to the availability of DNA-based markers, most genetic diversity studies in various crops were carried out using morphological markers. Molecular markers have become useful tools to provide a relatively unbiased method of quantifying genetic diversity in plants (Clegg 1990). Genetic diversity has been studied in many crops using