Structural Organization of the Human Genome: Distribution of Nucleotides,AluRepeats, and Exons in Chromosomes 21 and 22

Analysis of DNA sequences of the human chromosomes 21 and 22 performed using a specially designed MegaGene software allowed us to obtain the following results. Purine and pyrimidine nucleotide residues are unevenly distributed along both chromosomes, displaying maxima and minima (waves) with a period of about 3 Mbp. Distribution of G+C along both chromosomes has no distinct maxima and minima, however, chromosome 21 contains considerably less G+C than chromosome 22. Both exons and Alurepeats are unevenly distributed along chromosome 21: they are scarce in its left part and abundant in the right part, while MIR elements are quite monotonously spread along this chromosome. The Alurepeats show a wave-like distribution pattern similar for both repeat orientations. The number of the Alurepeats of opposite orientations was equal for both studied chromosomes, and this may be considered a new property of the human genome. The positive correlation between the exon and Aludistribution patterns along the chromosome, the concurrent distribution of Alurepeats in both orientations along the chromosome, and the equal copy numbers for Aluin direct and inverted orientations within an individual chromosome point to their important role in the human genome, and do not fit the notion that Alurepeats belong to parasitic (junk) DNA.     

A Novel ZZ/ZW Sex Chromosome System for the Genus Leporinus (Pisces, Anostomidae, Characiformes)

A wide range of sex chromosome mechanisms, including simple and multiple chromosome systems is characteristic of fishes. The Leporinus genus represent a good model to study sex chromosome mechanisms, because an unambiguous ZZ/ZW sex chromosome system was previously described for seven species, while the remaining studied species of the genus do not show differentiated sex chromosomes. The occurrence of sex chromosomes in Leporinus trifasciatus and Leporinus sp2 from the Araguaia river, Amazon basin, Brazil, was here investigated. ZZ/ZW sex chromosomes were detected for both species. The Z and W chromosome morphology of L. trifasciatus is the same as described for other species of the genus Leporinus. However, the Z and W chromosomes of L. sp2 were quite different in their morphology and banding pattern suggesting that the ZW system of this species have originated independently from the ZW system previously described for other Leporinus.     

Nucleotide Sequence, Genomic Organization, and Chromosomal Localization of Genes Encoding the Human NMDA Receptor Subunits NR3A and NR3B

The N-methyl-D-aspartate (NMDA) receptors are glutamate-regulated ion channels that are critically involved in important physiological and pathological functions of the mammalian central nervous system. We have identified and characterized the gene encoding the human NMDA receptor subunit NR3A (GRIN3A), as well as the gene (GRIN3B) encoding an entirely novel subunit that we named NR3B, as it is most closely related to NR3A (57.4% identity). GRIN3A localizes to chromosome 9q34, in the region 13-34, and consists of nine coding exons. The deduced protein contains 1115 amino acids and shows 92.7% identity to rat NR3A. GRIN3B localizes to chromosome 19p13.3 and contains, as does the mouse NR3B gene (Grin3b), eight coding exons. The deduced proteins of human and mouse NR3B contain 901 and 900 amino acid residues, respectively (81.6% identity). In situ hybridization shows a widespread distribution of Grin3b mRNA in the brain of the adult rat.     

Genes for the SMC Family Proteins in a Common Vole Microtus arvalis

Genes for four subfamilies of SMC (structural maintenance of chromosomes) proteins have been isolated from the genome of a common vole Microtus arvalis. The high degree of homology between representatives of each SMC protein subfamily of different classes of organisms has been demonstrated. The full-sized copy of a mammalian gene encoding SMC4 protein has been isolated and analyzed for the first time. The SMC proteins enter into the composition of complexes responsible for cohesion of sister chromatids, formation of mitotic chromosomes, recombination, DNA repair, and regulation of gene expression. We discuss the possible participation of the SMC proteins in inactivation of the X chromosome in mammalian females. Common voles of genus Microtusgroup arvalis serve a unique model for the study of the inactivation process.     

Limits to food intake and fiber utilization in the prairie vole,Microtus ochrogaster: effects of food quality and energy need

We fed prairie voles (Microtus ochrogaster) rat chow diluted with variable amounts of -cellulose to determine 1) how much fiber the voles could tolerate in their diet; 2) changes in food intake and digestibility of dry matter and of fiber; 3) the extent to which voles utilized fiber as an energy source; and 4) whether any of these variables differed between groups of animals maintained at 5 or 22°C. Fiber content of the diets ranged from 20 to 84%. Animals held at 5°C maintained body mass through a diet containing 69% fiber, while animals held at 22°C maintained body mass through the 84% fiber diet. Dry matter intake increased with fiber level from 9.3 to 15.0 g·day^-1 for animals at 5°C and from 5.6 to 14.0 g·day^-1 for animals at 22°C; intake on the highest fiber diet eaten by either group was not different. Dry matter digestibility decreased significantly as the fiber in the diets increased, but was not affected by temperature treatments. Digestible dry matter intake for each group remained constant regardless of diet quality, but on each diet digestible dry matter intake for animals at 5°C was significantly higher than that of the animals held at 22°C. Digestibility of the fiber portion of the experimental diets remained constant as food quality decreased, so the percent of daily energy need met by fiber utilization increased with higher food intake. On the lowest quality diet each group tolerated, fiber digestion provided approximately 42 and 68% of the energy needs of voles at 5 and 22°C, respectively.Abbreviations BM body mass - BMR basal metabolic rate - DE digestible energy - DM dry matter - DMD dry matter digestibility - DDMI digestible dry matter intake - MR metabolic rate - NDF neutral detergent fiber (=cell walls) - NDS neutral detergent solubles (=cell solubles) - SEM standard error of mean - T _a ambient temperature     

Genomic organization and chromosomal localization of a new repeat MS7, specific for heterochromatin of sex chromosomes in Microtus species voles of the arvalis group

The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis [1, 2]. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M. arvalis. It has been shown by analyzing the phage genomic clones that one MS4 copy makes a part of a monomeric unit exceeding 8.5 kb that also includes a new MS7 repeat and, possibly, LINE fragments. MS7 is located together with MS4 in heterochromatin of common vole sex chromosomes, but in a substantially lesser amount. Probably, as a result of an evolutionary transition of an original repeat from euchromatin of the X chromosome to heterochromatin of the Y chromosome, MS4 underwent multiple amplification, and MS7 spread throughout heterochromatin, being surrounded by the MS4 tandem arrays.     

Heterochromatin is not an adequate explanation for close proximity of interphase chromosomes 1--Y, 9--Y, and 16--Y in human spermatozoa

Analysis of human spermatozoa and lymphocytes using C-banding techniques and in situ hybridization has shown a higher order packaging of the human genome. Chromosomes are not distributed entirely at random within the nucleus. In particular, chromosomes 1, 9, and 16, carrying large blocks of pericentromeric heterochromatin, and the Y chromosome, carrying heterochromatin in Yq12, are in close proximity to each other within the nucleus and are involved in somatic pairing with nonhomologous chromosomes. In order to determine whether the close proximity of these chromosomes in any way is attributable to the distribution of heterochromatin, double in situ hybridization was performed on chromosomes 1--Y, 9--Y, and 16--Y as well as on 1--X, 9--X, and 16--X-with chromosome X as the other gonosome carrying less heterochromatin-in human spermatozoa. Each pair was found to have a nonrandom spatial distribution. However, comparison of the arrangement of chromosomes 1--Y versus 1--X and 9--Y versus 9--X revealed that heterochromatin cannot be the only cause for the tendency of chromosome fusion, because only the results of the chromosome pair 1--Y/1--X could support this proposition. In conclusion, the heterochromatin effect cannot be, in itself, an adequate explanation for chromosome association, implicating as well other mechanisms.     

Tandem and Interspersed Repeats Contribute to the Mosaic Structure of Segmental Duplications in the Human Genome

Intrachromosomal and interchromosomal segmental duplications account for more than 5% of the human genome. To analyze the processes resulting in the complex mosaic structure of duplicons, a draft human genome sequence was searched for duplicated segments of a genomic fragment of the pericentric region of the chromosome 21 short arm. The duplicons found consist of modules having paralogs in various genome regions. Module ends are flanked with various tandem or interspersed repeats, which are more unstable as compared with unique sequences. In most cases, the boundaries of duplicated segments exactly coincide with or are in close proximity to hot spots of various rearrangements within repeats or boundaries between repeats and unique sequences or between two different repeats. Homologous recombination between repetitive elements was assumed to be the major mechanism contributing to the mosaic structure of duplicons.     

Determinants of reproductive success in voles: space use in relation to food and litter size manipulation

Spacing behaviour of female mammals is suggested to depend on the distribution and abundance of food. In addition, food limitation has been found to constrain the reproductive success of females. However, whether females maximize their reproductive success by adjusting space use in relation to current food availability and reproductive effort (e.g. litter size) has not been experimentally studied. We examined these questions by manipulating simultaneously food resources (control vs. food supplementation) and litter sizes (control vs. plus two pups) of territorial female bank voles (Clethrionomys glareolus) in large outdoor enclosures. Females with supplementary food had smaller home ranges (foraging area) and home range overlaps than control females, whereas litter size manipulation had no effect on space use. In contrast, the size of territory (exclusive area) was not affected by food supplementation or litter size manipulation. As we have previously shown elsewhere, extra food increases the reproductive success of bank vole females in terms of size and proportion of weaned offspring. According to the present data, greater overlap of female home ranges had a negative effect on reproductive success of females, particularly on survival of offspring. We conclude that higher food availability increases the reproductive success of bank vole females, and this effect may be mediated through lower vulnerability of offspring to direct killing and/or detrimental effects from other females in the population. Moreover, it seems that when density of conspecifics is controlled for, home range sizes of females, but not territoriality, is related to food resources in Clethrionomys voles.     

黑腹果蝇dCAF-1-p55突变引起果蝇发育迟缓和染色体不稳定性

在真核生物中高度保守的染色质装配因子1(chromatin assembly factor 1,CAF-1)是染色质装配过程中的组蛋白分子伴侣之一.dCAF-1-p55是果蝇中CAF-1复合物中的最小亚基,它与另外两个亚基dCAF-1-p180及dCAF-1-p105一起负责将组蛋白H3/H4组装到新合成的DNA上.除了CAF-1复合物,dCAF-1-p55还参与其他多个复合物的形成,如NURF、PRC2及Sin3-HDAC1.dCAF-1-p55的这一广泛参与性提示了其功能的多样性和重要性.为了研究dCAF-1-p55的体内功能,我们利用基因靶向敲除技术制备了果蝇dCAF-1-p55突变体.实验结果表明,dCAF-1-p55的缺失导致果蝇发育迟缓并且最终致死.进一步研究发现,在dCAF-1-p55突变细胞中,中期染色体较为松散,姐妹染色单体连接异常,后期染色体不能正常分离.这些缺陷都是与癌症发生密切相关的染色体不稳定性(chromosome instability,CIN)的典型特征.综上所述,我们的研究表明了dCAF-1-p55在果蝇发育过程及维持染色体稳定性方面的重要作用,同时提示该基因具有保护细胞免遭CIN和癌变的潜在功能.     

Response of Barley Lines with Structural Rearrangements in Chromosomes 5, 6 and 7 to Limited Nitrogen Nutrition

The responses of barley (Hordeum vulgare L.) lines with rebuilt chromosomes 5, 6 and 7 to reduced nitrogen nutrition were evaluated in juvenile growth stages. The material included two series of duplications (D) produced in the short arm of chromosome 6 and of chromosome 7, and in the long arm of chromosome 5 and of chromosome 6; their parental translocation lines (T) - from which analyzed duplications were derived and a standard karyotype cv. Bonus as a control. The translocation lines have break points located in 6_S and 7_S, or 5_L and 6_L. Only the lines with duplicated segments of the short arms of satellited (6 and 7) chromosomes exhibited an improved tolerance to reduced nitrogen supply. No changes relative to cv. Bonus were observed in the T-lines. More tolerant D-lines showed lower stimulation of the root development. Obtained results suggests that the adaptability factors for the low N tolerance at the vegetative growth stage of barley are located in the short arms of 6 and 7 chromosomes. This revised version was published online in July 2006 with corrections to the Cover Date.     

A New Blind Cave Fish Population of Genus Astyanax: Geography, Morphology and Behavior

A new population of blind, cave dwelling tetra fish of the genus Astyanax was discovered in Granadas Cave, in the Balsas drainage, southern México. All blind Mexican tetras previously described are from Tampico and San Luis Potosí, northern México. The discovery of a new blind morph thus represents an independent colonization and convergent adaptation to the cave environment by this fish. Individuals of this population display variability of their troglomorphic features. Some individuals presented asymmetrical degeneration of the eyes, where one was normal, but the other somewhat reduced in size and complexity. Loss of pigmentation and eye reduction, although sometimes correlated, were not always linked; reduced eyes were found on pigmented fish and unpigmented fish often possessed normal eyes. Some individuals had reduced lens size or an absence of lens altogether. Retina is highly modified with photoreceptors sometimes absent. Eye reduction was correlated with a diminished size of the optic lobes and an increase of the prosencephalon. Modifications of the skull involve closing in of the circumorbital series of bones. Certain aspects of behavior are also modified.     

A Large-Insert (130 kbp) Bacterial Artificial Chromosome Library of the Rice Blast FungusMagnaporthe grisea:Genome Analysis, Contig Assembly, and Gene Cloning

Magnaporthe grisea(Hebert) Barr causes rice blast, one of the most devastating diseases of rice (Oryza sativa) worldwide. This fungus is an ideal organism for studying a number of aspects of plant–pathogen interactions, including infection-related morphogenesis, avirulence, and pathogen evolution. To facilitateM. griseagenome analysis, physical mapping, and positional cloning, we have constructed a bacterial artificial chromosome (BAC) library from the rice infecting strain 70-15. A new method was developed for separation of partially digested large-molecular-weight DNA fragments that facilitated library construction with large inserts. The library contains 9216 clones, with an average insert size of 130 kbp (>25 genome equivalents) stored in 384-well microtiter plates that can be double spotted robotically on to a single nylon membrane. Several unlinked single-copy DNA probes were used to screen 4608 clones in the library and an average of 13 (minimum of 6) overlapping BAC clones was found in each case. Hybridization of total genomic DNA to the library and analysis of individual clones indicated that ≈26% of the clones contain single-copy DNA. Approximately 35% of BAC clones contained the retrotransposon MAGGY. The library was used to identify BAC clones containing a adenylate cyclase gene (mac1). In addition, a 550-kbp contig composed of 6 BAC clones was constructed that encompassed two adjacent RFLP markers on chromosome 2. These data show that the BAC library is suitable for genome analysis ofM. grisea.Copies of colony hybridization membranes are available upon request.     

Chromosomal localization and evolution of satellite DNAs and heterochromatin in grasses (Poaceae), especially tribe Aveneae

The physical mapping of three abundant tandemly repeated DNA sequences, CON1, CON2, and COM2, and the distributional pattern of AT- and GC-rich regions in the chromosomes of 32 species of the grass family Poaceae have been established by means of fluorescence in situ hybridization and fluorochrome banding with chromomycin and DAPI. Additionally, locations of 5S, 35S rDNA, and the C-banding pattern were examined. All satellite DNAs (satDNA) tested are situated predominantly subtelomerically in the chromosomes, but occur also colocalized with 35S and 5S ribosomal DNAs (rDNA). Especially, CON2 is most often colocalized with the 5S rDNA, but is evolutionarily not derived from it. Subtelomeric heterochromatin bands are frequently, but not always correlated with satDNA bands. Moreover, the DAPI- or rarely chromomycin-positive stainability of heterochromatin is not caused by these satDNAs as revealed by their sequence organization, showing too few clusters of AT or GC base pairs as required for binding of the fluorochromes. The occurrence of satDNAs is not correlated with that of other components of the heterochromatin. Proportions of satDNAs and other sequences of the heterochromatin relative to the entire genome appear subjected to a much faster evolutionary change than the rather stable proportions of the rDNAs. Heteromorphism in banding patterns found in many species is related in most instances with breeding system and life form. The independent evolution and amplification of different satDNAs is discussed in relation to molecular phylogenetic data. The value and limitations of satDNA data in addressing systematic questions in grasses is exemplified for several grass subfamilies and tribes.     

Molecular Phylogeny of Tuco-Tucos, Genus Ctenomys (Rodentia: Octodontidae): Evaluation of the mendocinus Species Group and the Evolution of Asymmetric Sperm

The phylogenetic relationships among 23 individuals representing 14 species of underground hystricognath rodents of the genus Ctenomys were studied by analyzing variation of complete cytochrome b gene sequences. Maximum parsimony, neighbor joining, and maximum likelihood analyses were performed, using the octodontine genera Octodon and Tympanoctomys as outgroups. Our analyses support previous studies based on chromosomes and skull morphology that suggested a clade comprised of Argentinean and Uruguayan populations of C. rionegrensis. This clade is closely related to one comprised of C. flamarioni and the C. mendocinus species complex. Our analyses provide evidence that the symmetric sperm morph, which is common to other South American hystricognath rodents, is the plesiomorphic character state in Ctenomys and in Hystricognathi. Our analyses do not support the hypothesis that the sperm morphs define two major lineages of tuco-tuco species, because species with asymmetric sperm are diphyletic on the basis of cytochrome b sequences, and this morphology appears to have evolved twice in Ctenomys.     

Morphological Differentiation and Possible Origin of B Chromosomes in Natural Brazilian Population of Astyanax Scabripinnis (PISCES, CHARACIDAE)

Specimens of Astyanax scabripinnisfrom three different altitudes (1920, 1800 and 700?m) along the Ribeirão Grande stream in the Campos do Jordão region (São Paulo State, Brazil) were investigated. The same diploid number, 2n?=?50, was detected in the three populations, with the following karyotypic constitution: 6M, 22SM, 10ST and 12A. The populations located at 1920 and 1800?m altitude presented a high incidence of B chromosomes varying in number (0–2), shape (meta- and submetacentrics), size (large and small) and sex-related frequency (they were more frequent among females). The two morphologically variant B chromosomes probably evolved from a metacentric macrochromosome, which is the most commonly observed B chromosome in several A. scabripinnispopulations.     

Chromosomal organization of simple sequence repeats in the Pacific oyster (<Emphasis Type="Italic">Crassostrea gigas</Emphasis>): (GGAT)<Subscript>4</Subscript>, (GT)<Subscript>7</Subscript> and (TA)<Subscript>10</Subscript> chromosome patterns

Chromosome identification is essential in oyster genomic research. Fluorescence in situ hybridization (FISH) offers new opportunities for the identification of oyster chromosomes. It has been used to locate satellite DNAs, telomeres or ribosomal DNA sequences. However, regarding chromosome identification, no study has been conducted with simple sequence repeats (SSRs). FISH was used to probe the physical organization of three particular SSRs, (GGAT)(4), (GT)(7) and (TA)(10) onto metaphase chromosomes of the Pacific oyster, Crassostrea gigas. Hybridization signals were observed in all the SSR probes, but the distribution and intensity of signals varied according to the oligonucleotide repeat. The intercalary, centromeric and telomeric bands were observed along the chromosomes, and for each particular repeat every chromosome pair presented a similar pattern, allowing karyotypic analysis with all the SSRs tested. Our study is the first in mollusks to show the application of SSR in situ hybridization for chromosome identification and karyotyping. This technique can be a useful tool for oyster comparative studies and to understand genome organization in different oyster taxa.     

A Densovirus of German Cockroach Blattella germanica: Detection,Nucleotide Sequence,and Genome Organization

A new Blattella germanica densovirus (BgDNV, Parvoviridae: Densovirinae, Densovirus) was found. Virus DNA and cockroach tissues infected with BgDNV were examined by electron microscopy. Virus particles about 20 nm in diameter were observed both in the nucleus and in the cytoplasm of infected cells. Virus DNA proved to be a linear molecule sized about 1.2 m. The complete BgDNV genome was sequenced and analyzed. Five ORF were detected: two coded for structural capsid proteins and were on one DNA strand, and three coded for regulatory proteins and were on the other strand. Potential promoters and polyadenylation signals were identified. Structural analysis was performed for terminal inverted repeats containing extended palindromes. The genome structure of BgDNV was compared with that of other Parvoviridae.     

Genomic analysis reveals a duplication of eight rather than seven short consensus repeats in primate CR1 and CR1L: evidence for an additional set shared between CR1 and CR2

We report the discovery of previously unrecognised short consensus repeats (SCRs) within human and chimpanzee CR1 and CR1L. Analysis of available genomic, protein and expression databases suggests that these are actually genomic remnants of SCRs previously reported in other complement control proteins (CCPs). Comparison with the nucleotide motifs of the 11 defined subfamilies of SCRs justifies the designation g-like because of the close similarity to the g subfamily found in CR2 and MCP. To date, we have identified five such SCRs in human and chimpanzee CR1, one in human and chimpanzee CR1L, but none in either rat or mouse Crry in keeping with the number of internal duplications of the long homologous repeat (LHR) found in CR1 and CR1L. In fact, at the genomic level, the ancestral LHR must have contained eight SCRs rather than seven as previously thought. Since g-like SCRs are found immediately downstream of d SCRs, we suggest that there must have been a functional dg set which has been retained by CR2 and MCP but which is degenerate in CR1 or CR1L. Interestingly, dg is also present in the CR2 component of mouse CR1. The degeneration of the g SCR must have occurred prior to the formation of primate CR1L and prior to the duplication events which resulted in primate CR1. In this context, the apparent conservation of g-like SCRs may be surprising and may suggest the existence of mechanisms unrelated to protein coding. These results provide examples of the many processes which have contributed to the evolution of the extensive repertoire of CCPs.     

Chromosomal inversions and genetic control revisited: the use of inversions in sexing systems for higher Diptera

Summary Genetic sexing systems based on sex-linked translocations and deleterious mutations are subject to breakdown from genetic recombination in males. Including inversions in these strains may provide a solution to this problem, by ensuring selective elimination of recombinant products. Inversions could be used either in coupling to or in repulsion to the translocation. The latter system, requiring homozygous-viable inversions, would be more difficult to construct, but would offer several advantages not available with coupled translocation/inversion systems. A system proposed for the blowfly Lucilia cuprina is outlined, which combines homozygous-viable pericentric inversions in repulsion to existing sex-linked translocations. This system should both stabilize the genetic sexing system and increase the suppressive potential of such strains.