Influence of Parental Age on Endoreduplication of Giant Chromosomes and Some Quantitative Traits in Drosophila melanogaster Descendants

We studied the influence of parental age on the degree of polyteny of giant chromosomes and expressivity of mutation eyeless in Drosophila melanogaster descendants. The parental age equal to six days exerted an adverse effect on the function of endoreduplication of giant chromosomes in straineyeless. The highest degree of polyteny was observed in descendants of four- and ten-day imago. The maximum reduction of eye facets was observed in descendants of four-day imago, while in the progeny of older parents, the mutation expressivity was sharply reduced. Relations between the changes in chromosome polyteny, expressivity of mutation eyeless, and earlier studied components of adaptation were statistically analyzed in descendants of aging parents of this Drosophila strain.     

The Effect of the Genotype on the Expressiveness of Character vestigial and Polyteny of Giant Chromosomes in Drosophila melanogaster Meig.

The effects of the Bar (B) andwhite (w) mutations on the expressiveness of the character vestigial (vg) and the degree of polyteny of salivary gland giant chromosomes were studied in Drosophila melanogaster.Either mutation changed both the expressiveness of vestigial and the degree of chromosome polyteny. A negative association between the vg expressiveness and the degree of chromosome polyteny was revealed and proved to be stronger in females than in males. The parameters under study were shown to differ between females and males.     

不同温度条件下果蝇染色体结构的变化

将黑腹果蝇Drosophila melanogaster置于不同温度环境下培养,应用改良苯酚品红染色法制片.发现其唾腺染色体在不同的温度培养条件下,分布于染色体上的膨松区域有明显变化,在15℃和27℃下染色体的变化区域明显较19℃和23℃下的多,这些区域都与机体调控和表达的基因相关.这可能是机体对不适生存条件采取的保护措施所引起更多的染色体或基因发生变化的结果.对不同温度条件下部分染色体膨松区域的特殊基因作了简单讨论.     

Endoreduplication in Drosophila melanogaster progeny after exposure to acute γ-irradiation

Radiation and Environmental Biophysics - The purpose of this investigation was to study the effect of acute γ-irradiation of parent adults on the endoreduplication of giant chromosomes in F1...     

Genomic Consequences of Background Effects on scalloped Mutant Expressivity in the Wing of Drosophila melanogaster

We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project–Centre d''Etude du Polymorphisme Humain (HGDP–CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was investigated around all of them, and full resequence data were examined for 9 genes (5 from public sources and 4 from new data sets). For 7 of the genes, genotyping errors were responsible for an artifactual signal of high population differentiation and for 2, the population differentiation did not exceed our significance threshold. For the 18 genes with confirmed high population differentiation, 3 showed evidence of positive selection as measured by unusually extended haplotypes within a population, and 7 more did in between-population analyses. The 9 genes with resequence data included 7 with high population differentiation, and 5 showed evidence of positive selection on the haplotype carrying the nonsynonymous SNP from skewed allele frequency spectra; in addition, 2 showed evidence of positive selection on unrelated haplotypes. Thus, in humans, high population differentiation is (apart from technical artifacts) an effective way of enriching for recently selected genes, but is not an infallible pointer to recent positive selection supported by other lines of evidence.IN the last 50,000–100,000 years (KY), humans have expanded from being a rare species confined to parts of Africa and the Levant to their current numbers of >6 billion with a worldwide distribution (Jobling et al. 2004). Paleontological and archaeological evidence suggests that key aspects of modern human behavior developed ∼100–50 KYA in Africa (Henshilwood et al. 2002) and behaviorally modern humans then expanded out of Africa ∼60–40 KYA (Mellars 2006). The physical and biological environments encountered outside Africa would have been very different from those inside and included climatic deterioration reaching a glacial maximum ∼20 KYA and subsequent amelioration that permitted the development of agricultural and pastoral lifestyles in multiple independent centers after ∼10 KYA. Neolithic lifestyles would have led to further changes including higher population densities, close contact with animals, and novel foods, in turn leading to new diseases (Jobling et al. 2004). It is likely that genetic adaptations accompanied many of these events.Adaptation, or positive natural selection, leaves an imprint on the pattern of genetic variation found in a population near the site of selection. This pattern can be identified by comparing the DNA variants in multiple individuals from the same and different populations and searching for signals such as unusually extended haplotypes (extended haplotype homozygosity, EHH) (Voight et al. 2006; Sabeti et al. 2007; Tang et al. 2007), high levels of population differentiation (International Hapmap Consortium 2005; Barreiro et al. 2008; Myles et al. 2008), or skewed allele frequency spectra (Carlson et al. 2005). These signals become detectable at different times after the start of selection and are all transient, being gradually eroded by both molecular processes such as mutation, recombination, or further selection and population processes such as migration or demographic fluctuations, with the survival order extended haplotypes < population differentiation < allele frequency spectra (Sabeti et al. 2006). The absolute timescales of survival are not well understood, but extended haplotype tests typically detect selection within the last 10 KY (Sabeti et al. 2006) while unusual allele frequency spectra may detect much older selection. For example, it has been suggested that the signal associated with the FOXP2 gene (Enard et al. 2002) may predate the modern human–Neanderthal split ∼300–400 KYA (Krause et al. 2007), although such an interpretation has been questioned (Coop et al. 2008). However, despite significant uncertainties and limitations, population-genetic analyses are well placed to provide insights into many of the important events within the timescale of recent human evolution.In principle, it should be possible to survey the genome for sites of selection and then interpret this catalog in the light of archaeological, climatic, and other records. Progress toward such a goal has, however, been limited: many factors can confound the detection of selection and only genotype data from previously ascertained SNPs, rather than full resequence data, have thus far been available throughout the whole genome. In practice, the strategy used has therefore been to search the genome for signals that can be detected in available genotype data, such as extended haplotypes or population differentiation, and evaluate the significance of the regions identified by comparing them with empirical distributions of the same statistic, models that incorporate information about the demography, or biological expectations (McVean and Spencer 2006). However, it remains unclear how effective this strategy is: What false positive and false negative rates are associated with its applications? Further evaluation is desirable.The International HapMap Project has carried out the highest-resolution study so far of genetic variation in a set of human populations. In an article published in 2005, genotypes of >1 million SNPs were reported from 270 individuals with ancestry from Africa (Yoruba in Ibadan, Nigeria: YRI), Europe (Utah residents with ancestry from northern and western Europe: CEU), China (Han Chinese in Beijing, China: CHB), and Japan (Japanese in Tokyo, Japan: JPT) (International HapMap Consortium 2005). This article highlighted 32 SNPs from 27 genes that showed particular evolutionary interest because of a combination of two factors: they were nonsynonymous, that is, they changed an amino acid within a protein-coding gene and thus were likely to alter biological function, and they also exhibited a high level of population differentiation equal to or exceeding that of rs2814778, a SNP that is associated with strong biological evidence for population-specific selection. This SNP underlies the FY*0 (Duffy blood group negative) phenotype; FY*0 homozygotes do not express the Duffy blood group antigen on red blood cells and are consequently highly resistant to infection by the malarial parasite, Plasmodium vivax. The *0 allele is nearly fixed in Africa and rare outside, and it is widely believed that this is due to selection for resistance to vivax malaria.However, a number of studies have emphasized that large differences in allele frequency between populations can arise without positive selection: for example, a highly differentiated SNP in the Neuregulin I gene was not accompanied by unusual patterns in adjacent SNPs (Gardner et al. 2007), and large frequency differences can be quite common in empirical data sets, particularly in comparisons between Africa or America and the rest of the world, where population bottlenecks and “allele surfing” may have occurred during the exit from and entrance to these continents, respectively (Hofer et al. 2009). We wished to measure the extent to which the high population differentiation observed at the 27 HapMap genes might have resulted from positive selection and the extent to which it reflected other origins such as demographic factors, chance, or errors. We therefore retyped the same SNPs in the HapMap samples and in a large additional set of human populations and applied alternative tests for selection, either based on long-range haplotypes or based on full resequence data. For the latter, sequence data for 5 of the genes were available from public sources, and four new data sets were generated for this project. We found that, while genotyping errors led to some artifactual high differentiation signals, population differentiation was a useful but by no means infallible guide to recent selection detected by other methods.     

DNA Supercoiling Factor Localizes to Puffs on Polytene Chromosomes in Drosophila melanogaster

DNA supercoiling factor (SCF) was first identified in silkworm as a protein that generates negative supercoils in DNA in conjunction with eukaryotic topoisomerase II. To analyze the in vivo role of the factor, we cloned a cDNA encoding Drosophila melanogaster SCF. Northern analysis revealed 1.6- and 1.8-kb mRNAs throughout development. The longer mRNA contains an open reading frame that shares homology with mouse reticulocalbin whereas the shorter one encodes a truncated version lacking the N-terminal signal peptide-like sequence. An antibody against SCF detected a 45-kDa protein in the cytoplasmic fraction and a 30-kDa protein in the nuclear fraction of embryonic extracts. Immunoprecipitation suggests that the 30-kDa protein interacts with topoisomerase II in the nucleus, and hence that it is a functional form of SCF. Immunostaining of blastoderm embryos showed that SCF is present in nuclei during interphase but is excluded from mitotic chromosomes. In larvae, the antibody stained the nuclei of several tissues including a posterior part of the salivary gland. This latter staining was associated with natural or ecdysteroid-induced puffs on polytene chromosomes. Upon heat treatment of larvae, the staining on the endogenous puffs disappeared, and strong staining appeared on heat shock puffs. These results implicate SCF in gene expression.     

Cohesin Complexes in Polytene Chromosomes of Drosophila melanogaster Are Located in Interbands

The distribution of cohesin complex in polytene chromosomes of Drosophila melanogaster was studied. Cohesin is a complicated protein complex which is regulated by the DRAD21 subunit. Using immunostaining for DRAD21p, the cohesins were shown to be preferentially located in the interband regions. This specificity was not characteristic for puffs, where uniform staining was observed. The presence of a few brightly fluorescent regions (five to ten per chromosome arm) enriched with cohesin complexes was shown. Some of these regions had permanent location, and the others, variable location. No antibody binding was detected in the chromocenter. Immunostaining of interphase nuclei of neuroblasts revealed large cohesin formations. On the polytene chromosomes of D. melanogaster, the Drad21 gene was mapped to the chromocentric region (81) of the L arm of chromosome 3.     

Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes in Drosophila melanogaster

We designed a system to determine whether dicentric chromosomes in Drosophila melanogaster break at random or at preferred sites. Sister chromatid exchange in a Ring-X chromosome produced dicentric chromosomes with two bridging arms connecting segregating centromeres as cells divide. This double bridge can break in mitosis. A genetic screen recovered chromosomes that were linearized by breakage in the male germline. Because the screen required viability of males with this X chromosome, the breakpoints in each arm of the double bridge must be closely matched to produce a nearly euploid chromosome. We expected that most linear chromosomes would be broken in heterochromatin because there are no vital genes in heterochromatin, and breakpoint distribution would be relatively unconstrained. Surprisingly, approximately half the breakpoints are found in euchromatin, and the breakpoints are clustered in just a few regions of the chromosome that closely match regions identified as intercalary heterochromatin. The results support the Laird hypothesis that intercalary heterochromatin can explain fragile sites in mitotic chromosomes, including fragile X. Opened rings also were recovered after male larvae were exposed to X-rays. This method was much less efficient and produced chromosomes with a strikingly different array of breakpoints, with almost all located in heterochromatin. A series of circularly permuted linear X chromosomes was generated that may be useful for investigating aspects of chromosome behavior, such as crossover distribution and interference in meiosis, or questions of nuclear organization and function.     

Genotype of Wolbachia pipientis Endosymbiont Affects Octopamine Metabolism in Drosophila melanogaster Females

Russian Journal of Genetics - The effect of the genotype of the endosymbiont Wolbachia pipientis on the metabolism of octopamine (one of the main biogenic amines in insects) was studied in young...     

Modeling of Dark Puffs Using P Transposons in Polytene Chromosomes of Drosophila melanogaster

Modeling of morphologically unusual dark puffs was conducted using Drosophila melanogaster strains transformed by construct P[ry; Prat:bw], in which gene brown is controlled by the promoter of the housekeeping gene Prat. In polytene chromosomes, insertions of this type were shown to form structures that are morphologically similar to small puffs. By contrast, the Broad-Complex (Br-C) locus, which normally produce a dark puff in the 2B region of the X chromosome, forms a typical light-colored puff when transferred to the 99B region of chromosome 3R using P[hs-BRC-z1]. A comparison of transposon-induced puffs with those appearing during normal development indicates that these puff types are formed via two different mechanisms. One mechanism involves decompaction of weakly transcribed bands and is characteristic of small puffs. The other mechanism is associated with contacts between bands adjacent to the puffing zone, which leads to mixing of inactive condensed and actively transcribed decondensed material and forming of large dark puffs.     

Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

Segregation Distorter (SD) is a selfish, coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD⁺ males sire almost exclusively SD-bearing progeny. Fifty years of genetic, molecular, and theory work have made SD one of the best-characterized meiotic drive systems, but surprisingly the details of its evolutionary origins and population dynamics remain unclear. Earlier analyses suggested that the SD system arose recently in the Mediterranean basin and then spread to a low, stable equilibrium frequency (1–5%) in most natural populations worldwide. In this report, we show, first, that SD chromosomes occur in populations in sub-Saharan Africa, the ancestral range of D. melanogaster, at a similarly low frequency (~2%), providing evidence for the robustness of its equilibrium frequency but raising doubts about the Mediterranean-origins hypothesis. Second, our genetic analyses reveal two kinds of SD chromosomes in Africa: inversion-free SD chromosomes with little or no transmission advantage; and an African-endemic inversion-bearing SD chromosome, SD-Mal, with a perfect transmission advantage. Third, our population genetic analyses show that SD-Mal chromosomes swept across the African continent very recently, causing linkage disequilibrium and an absence of variability over 39% of the length of the second chromosome. Thus, despite a seemingly stable equilibrium frequency, SD chromosomes continue to evolve, to compete with one another, or evade suppressors in the genome.     

A New Construct for Cloning DNA and Modeling the Structure of Drosophila melanogaster Polytene Chromosomes

Modification of P-element-based transformation vector pCaSpeR3 yielded a new construct, pICon, which contains the structural region of the Escherichia coli lacZ, the adjacent 5 and 3 regulatory regions of hsp70, pUC19, and two tandem FRTs. Owing to the hsp70 promoter, the pICon insertion site may be located on polytene chromosomes after heat shock by light or electron microscopy. The pUC19 sequence with a polylinker allows cloning of the genomic sequence adjacent to the 3 end of pICon by P-target rescue. Functional FRTs allow insertion or deletion of various DNA fragments. The construct is large (22,046 bp), forms easily detectable structures in polytene chromosomes, and may be used to study the structural and functional organization of the Drosophila melanogaster genome, in particular, to elucidate the causes of banding pattern formation. To map the molecular boundaries of interband 3C6/C7, the DNA sequence of this region was cloned between the two FRTs.     

Influence of diphenyl diselenide on chlorpyrifos-induced toxicity in Drosophila melanogaster

Exposure to chlorpyrifos (CPF) poses several harmful effects to human and animal health. The present study investigated the influence of diphenyl diselenide (DPDS) on CPF-induced toxicity in Drosophila melanogaster. Firstly, the time course lethality response of virgin flies (2- to 3-day-old) to CPF (0.075–0.6 μg/g) and DPDP (5–40 μmol/kg) in the diet for 28 consecutive days were investigated. Subsequently, the protective effect of DPDS (10, 20 and 40 μmol/kg) on CPF (0.15 μg/g)-induced mortality, locomotor deficits, neurotoxicity and oxidative stress was assessed in a co-exposure paradigm for 7 days. Results showed that CPF exposure significantly decreased the percent live flies in a time- and concentration-dependent manner, whereas the percent live flies with DPDS treatment was not statistically different from control following 28 days of treatment. In the co-exposure study, CPF significantly increased flies mortality while the survivors exhibited significant locomotor deficits with decreased acetylcholinesterase (AChE) activity. Dietary supplementation with DPDS was associated with marked decrease in mortality, improvement in locomotor activity and restoration of AChE activity in CPF-exposed flies. Moreover, CPF exposure significantly decreased catalase and glutathione-S-transferase activities, total thiol level with concomitant significant elevation in the levels of reactive oxygen species and thiobarbituric acid reactive substances in the head and body regions of the treated flies. Dietary supplementation with DPDS significantly improved the antioxidant status and prevented CPF-induced oxidative stress, thus demonstrating the protective effect of DPDS in CPF-treated flies.     

Surprising Differences in the Variability of Y Chromosomes in African and Cosmopolitan Populations of Drosophila melanogaster

The nonrecombining Drosophila melanogaster Y chromosome is heterochromatic and has few genes. Despite these limitations, there remains ample opportunity for natural selection to act on the genes that are vital for male fertility and on Y factors that modulate gene expression elsewhere in the genome. Y chromosomes of many organisms have low levels of nucleotide variability, but a formal survey of D. melanogaster Y chromosome variation had yet to be performed. Here we surveyed Y-linked variation in six populations of D. melanogaster spread across the globe. We find surprisingly low levels of variability in African relative to Cosmopolitan (i.e., non-African) populations. While the low levels of Cosmopolitan Y chromosome polymorphism can be explained by the demographic histories of these populations, the staggeringly low polymorphism of African Y chromosomes cannot be explained by demographic history. An explanation that is entirely consistent with the data is that the Y chromosomes of Zimbabwe and Uganda populations have experienced recent selective sweeps. Interestingly, the Zimbabwe and Uganda Y chromosomes differ: in Zimbabwe, a European Y chromosome appears to have swept through the population.     

Evolution of the Ribosomal DNA Spacers of Drosophila melanogaster : Different Patterns of Variation on X and Y Chromosomes

Length variation of the ribosomal gene spacers of Drosophila melanogaster was studied. Analysis of 47 X chromosomal and 47 Y chromosomal linked rDNA arrays collected from five continents indicates that the arrays on the two chromosomes differ qualitatively. The Y-linked arrays from around the world share little or no similarity for either their overall length or the organization of their spacers. Most of the X-linked arrays do, however, share a major length spacer of 5.1 kb. In addition, those X-linked arrays that have a major 5.1-kb band have similar spacer organization as demonstrated by genomic DNA digestions with several restriction enzymes. These data strongly support the hypothesis that spacer length patterns on only X-linked genes are maintained primarily by natural selection.