Dynamic filtration of the expression pattern variability of Drosophila zygotic segmentation genes

Analysis of the quantitative data obtained by processing the confocal images showed that the initial variability of the expression pattern of Drosophila zygotic segmentation genes was strongly reduced by the onset of gastrulation. The following variability components were studied: the range of gene expression intensity in different embryos, the time and succession of the formation of expression domain, types of formation, and domain positioning. At the level of zygotic genes, the positioning error proved to be dynamically filtered with time.     

Registration of the expression patterns of Drosophila segmentation genes by two independent methods

MOTIVATION: To construct an integrated map of Drosophila segmentation gene expression from partial data taken from individual embryos. RESULTS: Spline and wavelet based registration techniques were developed to register Drosophila segmentation gene expression data. As ground control points for registration we used the locations of extrema on gene expression patterns, represented in 1D. The registration method was characterized by unprecedented high accuracy. A method for constructing the integrated pattern of gene expression at cellular resolution was designed. These patterns were constructed for 9 segmentation genes belonging to gap and pair-rule classes.     

Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method

In order to reconstruct the establishment of the body pattern over time in Drosophila embryos, we have developed automated methods for detecting the age of an embryo on the basis of knowledge about its gene expression patterns. In this paper we perform temporal classification of confocal images of expression patterns of genes controlling segmentation by means of a neural network based on multi-valued neurons (MVN). MVN are artificial neural processing elements with complex-valued weights and high functionality, which proved to be efficient for solving the image recognition problems. The results obtained by this method confirm its efficiency for image recognition and indicate that the method can detect characteristic features of expression patterns which mark their development over time.     

Evolutionary fate and expression patterns of chimeric new genes in Drosophila melanogaster

Origin and evolution of new genes contribute a lot to genome diversity. New genes usually form chimeric gene structures through DNA-based exon shuffling and generate proteins with novel functions. We investigated polymorphism of 14 chimeric new genes in Drosophila melanogaster populations and found that eight have premature stop codons in some individuals while six are intact in the population, four of which are under negative selection, suggesting the two evolutionary fates of new chimeric genes after origination: accumulate premature stop codons and pseudolize, or acquire functions and get fixed by natural selection. Different from new genes originated through RNA-based duplication (retroposition) which are usually testis-specific or male-specific expressed, the expression patterns of these new genes through DNA-based exon shuffling are temporally and spatially diverse, implying that they may have the potential to evolve various biological functions despite that they may become pseudogenes or non-protein-coding RNA genes.     

黒腹果蝇中嵌合新基因的进化命运和表达模式

新基因的起源和进化对基因组多样性的产生具有重要的贡献.新基因起源常常通过外显子重排而形成嵌合的基因结构,以产生具有新功能的蛋白质.该文调查了在黒腹果蝇中的14个新起源的嵌合基因在群体中的多态性,发现其中8个在群体中的核苷酸多态性会引起提前终止子,而其他6个在群体中编码框都完整且其中4个受到负选择.研究结果表明,嵌合新基因起源后可能存在两种命运:积累提前终止子突变而假基因化,或者表现出一定功能而受自然选择固定下来.基因表达的数据显示,与RNA介导外显子重排(逆转座)形成的新基因不一样,这些由DNA水平外显子重排产生的新基因没有精巢或者雄性特异性表达模式,而是表现出更为多样性的时空表达模式,这提示尽管通过DNA水平外显子重排产生的新基因可能正在变成假基因或者非蛋白质编码的RNA基因,但它们依然可能具有进化出广泛的生物学功能的潜力.     

Dominant maternal interactions with Drosophila segmentation genes

Summary A systematic search for X chromosome loci showing a dominant maternal interaction with the segmentation genes Krüppel, hunchback, knirps and hairy was performed using deficiencies spanning 65% of the X chromosome. No interaction with the knirps gene was observed, but five regions of the X chromosome showed a maternal dominant interaction with the Krüppel gene. Two of these regions also show a maternal dominant interaction with either hunchback (region 10A7–10A8) or hairy (region 10E1–10F3). In all of these interactions dead embryos were observed which showed the same defects as embryos homozygous for the segmentation gene tested. These results suggest that a complex repartition of maternal products necessary for subsequent segmentation may occur in the Drosophila egg.     

Drosophila segmentation genes and blastoderm cell identities

The formation of the segmentation pattern in Drosophila embryos provides an excellent model for investigating the process of pattern formation in multicellular organisms. Several genes required in an embryo for normal segmentation have been analyzed by classical and molecular genetic and morphological techniques. A detailed consideration of these results suggests that these segmentation genes are combinatorially involved in translating the positional identities of individual cells at an early stage in Drosophila development.     

The role of maternal and zygotic Gprk2 expression in Drosophila development

G protein-coupled receptor activity is controlled by a number of factors including phosphorylation by the family of G protein-coupled receptor kinases. This phosphorylation is an important first step in desensitization of the receptor. The role of G protein-coupled receptor kinases in cellular physiology has been extensively studied, but less is known about their role in development. A Drosophila G protein-coupled receptor kinase mutant (gprk2(6936)) has developmental defects throughout the life cycle of the fly. This allows the opportunity to address G protein-coupled receptor kinase's function in vivo. Using a series of transgenic flies in which the wild type Gprk2 gene is expressed under the control of the hsp70 or germline-specific promoter, in combination with germline mosaic analysis, we have made a detailed analysis of the developmental stages in which Gprk2 expression is required and the tissues that must express Gprk2 for rescue of the gprk2(6936) mutant. These studies have shown that Gprk2 expression is required in the germline for proper formation of the anterior egg structures and for early embryogenesis. In the absence of maternal Gprk2 activity, zygotic expression affords partial rescue of egg hatching, suggesting that Gprk2 also plays an important role in late embryogenesis.     

Interactions of the Drosophila gap gene giant with maternal and zygotic pattern-forming genes.

The Drosophila gene giant (gt) is a segmentation gene that affects anterior head structures and abdominal segments A5-A7. Immunolocalization of the gt product shows that it is a nuclear protein whose expression is initially activated in an anterior and a posterior domain. Activation of the anterior domain is dependent on the maternal bicoid gradient while activation of the posterior domain requires maternal nanos gene product. Initial expression is not abolished by mutations in any of the zygotic gap genes. By cellular blastoderm, the initial pattern of expression has evolved into one posterior and three anterior stripes of expression. The evolution, position and width of these stripes are dependent on interactions between gt and the other gap genes. In turn, gt activity in these domains affects the expression of the other gap genes. These interactions, typical of the cross-regulation previously observed among gap genes, confirm that gt is a member of the gap gene class whose function is necessary to establish the overall pattern of gap gene expression. After cellular blastoderm, gt protein continues to be expressed in the head region in parts of the maxillary and mandibular segments as well as in the labrum. Expression is never detected in the labial or thoracic segment primordia but persists in certain head structures, including the ring gland, until the end of embryonic development.     

Embryonic expression patterns of Drosophila ACS family genes related to the human sialin gene

The anion/cation symporter (ACS) family is a large subfamily of the major facilitator superfamily (MFS) of transporters. ACS family permeases are widely distributed in nature and transport either organic or inorganic anions in response to chemiosmotic cation gradients. The only protein in the ACS family to which a human disease has been linked, is sialin, the proton-driven lysosomal carrier for sialic acid. Genetic defects in sialin cause a lysosomal storage disease in humans. Here we have identified a group of conserved Drosophila ACS family genes related to sialin and studied their expression patterns throughout embryogenesis. Drosophila sialin-related genes are expressed in a wide variety of tissues. Expression is frequently observed throughout various parts of the intestinal tract, including Malpighian tubules and salivary glands. Additionally, some genes are expressed in vitellophages (yolk nuclei), nervous system, respiratory tract and a number of other embryonic tissues. These data will aid the establishment of a fruitfly model of human lysosomal storage disorders, the most common cause of neurodegeneration in childhood.     

Organ-specific patterns of gene expression in the reproductive tract of Drosophila are regulated by the sex-determination genes

The sex-determination genes of Drosophila act to repress the developmental pathway for the internal somatic reproductive organs of the opposite sex. By misregulating this pathway during preadult development, the organ-specific expression pattern of the glucose dehydrogenase gene (Gld) in the reproductive tract of adult flies has been changed without a concomitant sexual transformation of the reproductive organs. Misregulation of the tra, tra-2, and dsx genes leads to very similar patterns of ectopic expression of Gld. The induced ectopic patterns of Gld expression at the adult stage occur in a small subset of organs which all normally express the Gld gene during their morphogenesis. These ectopic patterns are irrevocably set during late larval-early pupal development. The normal pattern of Gld expression in several other Drosophila species is quite similar to the ectopic patterns which we have generated in D. melanogaster, suggesting that the interspecific variation in Gld expression may result from variation in the expression of the sex-determination genes.     

Zygotically active genes that affect the spatial expression of the fushi tarazu segmentation gene during early Drosophila embryogenesis

The establishment of the segmental body pattern of Drosophila requires the coordinated functions of three classes of zygotically active genes early in development. We have examined the effects of mutations in these genes on the spatial expression of the fushi tarazu (ftz) pair-rule segmentation gene. Mutations in four gap loci and in three pair-rule loci dramatically affect the initial pattern of transverse stripes of ftz-containing nuclei. Five other pair-rule genes and several other loci that affect the larval cuticular pattern do not detectably affect ftz expression. No simple regulatory relationships can be deduced. Rather, expression of the ftz gene depends upon the interactions among the different segmentation genes active at each position along the anterior-posterior axis of the early embryo.     

Maternal-effect genes as the recording genes of Turing-Child patterns: sequential compartmentalization in Drosophila

The early embryo is often a two-dimensional surface. The fate map is the subdivision of this surface into regions which give rise to parts of the phenotype. It is shown for Drosophila that the fate map is generated by the spontaneous and sequential formation of Turing-Child (TC) eigenfunction patterns. These patterns are recorded by the maternal-effect genes. The addition of the nodal lines of the TC patterns yields the correct number, positions, sequences and symmetries of regional boundaries. A simplest nontrivial 'homeotic transformation' is suggested and explained. A single mutation converts a region in one end of the fate map to a mirror-symmetric image of a nonadjacent region in the other end of the fate map, and this is attributed to the geometry of the TC patterns. This geometry also determines the initial shape of the zygotic gene expression. The vision of William Bateson that biological form is shaped like Chladni's patterns in acoustics and music is justified. A similar sequence of TC patterns occurs in the normal development of all organisms, and it is suggested that artificial intervention which completes the full sequence of TC patterns can be useful in the context of regenerative medicine and this is illustrated with the sea urchin.     

GCPReg package for registration of the segmentation gene expression data in Drosophila

In modern functional genomics registration techniques are used to construct reference gene expression patterns and create a spatiotemporal atlas of the expression of all the genes in a network. In this paper we present a software package called GCPReg, which can be used to register the expression patterns of segmentation genes in the early Drosophila embryo. The key task which this package performs is the extraction of spatially localized characteristic features of expression patterns. To facilitate this task, we have developed an easy-to-use interactive graphical interface. We describe GCPReg usage and demonstrate how this package can be applied to register gene expression patterns in wild-type and mutants. GCPReg has been designed to operate on a UNIX platform and is freely available via the Internet at http://urchin.spbcas.ru/downloads/GCPReg/GCPReg.htm.