Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: Evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes. (c) 2007 Elsevier Ltd. All rights reserved.

Cytogenetic Mapping of the Retroelements Rex1, Rex3 and Rex6 among Cichlid Fish: New Insights on the Chromosomal Distribution of Transposable Elements

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations

The P transposable element copy numbers and the KP/full-sized P element ratios were determined in eight Brazilian strains of Drosophila melanogaster. Strains from tropical regions showed lower overall P element copy numbers than did strains from temperate regions. Variable numbers of full-sized and defective elements were detected, but the full-sized P and KP elements were the predominant classes of elements in all strains. The full-sized P and KP element ratios were calculated and compared with latitude. The northernmost and southernmost Brazilian strains showed fewer full-sized elements than KP elements per genome, and the strains from less extreme latitudes had many more full-sized P than KP elements. However, no clinal variation was observed. Strains from different localities, previously classified as having P cytotype, displayed a higher or a lower proportion of KP elements than of full-sized P elements, as well as an equal number of the two element types, showing that the same phenotype may be produced by different underlying genomic components of the P-M system.

Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Hydrothermal rare earth elements mineralization in the Barra do Itapirapua carbonatite, southern Brazil: behaviour of selected trace elements and stable isotopes (C, O)

The Bura do Itapira pua carbonatite is located in southern Brazil and belongs to the Cretaceous Ponta Grossa alkaline-carbonatitic province related to the opening of the South Atlantic. The carbonatite complex is emplaced in Proterozoic granites and is mainly composed of plutonic magnesio- to ferrocarbonatite, with smaller amounts of subvolcanic magnesiocarbonatite. Hydrothermal alteration of the carbonatite has led to the formation of quartz, apatite, fluorite, rue earth fluorocarbonates, barite and sulfides in variable proportions. Trace element data, delta(13)C and delta(18)O are presented here, with the aim of better understanding the geochemical nature of hydrothermal alteration related to rare earth elements (REE) mineralization. The non-overprinted plutonic carbonatite shows the lowest REE contents, and its primitive carbon and oxygen stable isotopic composition places it in the field of primary igneous carbonatites. Two types of hydrothermally overprinted plutonic carbonatites can be distinguished based on secondary minerals and geochemical composition. Type I contains mainly quartz, rare earth fluorocarbonates and apatite as hydrothermal secondary minerals, and has steep chondrite normalized REE patterns, with Sigma(REE+Y) of up to 3 wt.% (i.e., two orders of magnitude higher than in fresh plutonic samples). In contrast, the Type II overprint contains apatite, fluorite and barite as dominant hydrothermal minerals, and is characterized by heavy REE enrichment relative to the fresh samples, with flat chondrite normalized REE patterns. Carbon and oxygen stable isotope ratios of Types I and II are elevated (delta(18)O + 8 to + 12 parts per thousand; delta(13)C - 6 to - 2 parts per thousand) relative to the fresh samples. Hydrothermally overprinted carbonatites exposed to weathering show even higher delta(18)O values (delta(18)O 13 to 25 parts per thousand) but no additional REE enrichment. The subvolcanic carbonatite has anomalously high delta(13)C of up to + 1 parts per thousand, which suggests crustal contamination through interaction with carbonate-bearing metasediments. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Preference ratios for mercury and other chemical elements in the Madeira River, Brazil

Samples of water, suspended solids, and bottom sediments from the Madeira River, Rondonia state, Brazil, were physically and chemically analyzed to investigate the actual Hg mobilization in the aquatic environment and compare it with that of other heavy metals and elements in the area. Two dimensionless Hg preference ratios were defined, expressing (1) the ratio of Hg and other elements in the liquid phase divided by the ratio of Hg and other elements in bottom sediments (P(l.phase)) and (2) the ratio of Hg and other elements in the particulate matter divided by the ratio of Hg and other elements in bottom sediments (P(s.solids)). These preference ratios are useful for comparing Hg transport in three different phases (liquid, particulate matter, and bottom sediments). They also were applicable to any analyzed elementin the area studied, because they generated an almost constant value when the maximum calculated was divided by the minimum (P(l.phase) = 2931; P(s.solids) = 84) and because of their sensitivity to the dominance of sorption processes by Fe oxides and hydroxides. Mercury could be transported preferentially to other analyzed elements in the particulate phase only if its concentration reached values at least 10(4)-fold higher than those expected or quantified in the area. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Simultaneous Determination of Two Groups of Elements in Milk by Electrothermal Atomic Absorption Spectrometry: Evaluation of Ruthenium Modifiers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Characterization of two full-sized P elements from Drosophila sturtevanti and Drosophila prosaltans

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Distribution and insertion numbers of transposable elements in species of the Drosophila saltans group

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Stress induced ordering due to interstitial elements in Nb and Ta by frequency analysis

It is well known that the interstitial elements present in solid solution in metals interact with the matrix by a relaxation process known as stress induced ordering. Traditionally this relaxation process is observed in the internal friction measurements. It is a common practice that researchers present the results of the frequency together with internal friction without giving any analysis. In this work we apply an expression which relates the variation of frequency with temperature and analyse the experimental results cited in the literature of the relaxation process due to the stress induced ordering of oxygen and nitrogen present in niobium and tantalum.

Genomic organization of the Neurospora crassa gsn gene: possible involvement of the STRE and HSE elements in the modulation of transcription during heat shock

Glycogen synthase, an enzyme involved in glycogen biosynthesis, is regulated by phosphorylation and by the allosteric ligand glucose-6-phosphate (G6P). In addition, enzyme levels can be regulated by changes in gene expression. We recently cloned a cDNA for glycogen synthase (gsn) from Neurospora crassa, and showed that gsn transcription decreased when cells were exposed to heat shock (shifted from 30degreesC to 45degreesC). In order to understand the mechanisms that control gsn expression, we isolated the gene, including its 5' and 3' flanking regions, from the genome of N. crassa. An ORF of approximately 2.4 kb was identified, which is interrupted by four small introns (II-V). Intron I (482 bp) is located in the 5'UTR region. Three putative Transcription Initiation Sites (TISs) were mapped, one of which lies downstream of a canonical TATA-box sequence (5'-TGTATAAA-3'). Analysis of the 5'-flanking region revealed the presence of putative transcription factor-binding sites, including Heat Shock Elements (HSEs) and STress Responsive Elements (STREs). The possible involvement of these motifs in the negative regulation of gsn transcription was investigated using Electrophoretic Mobility Shift Assays (EMSA) with nuclear extracts of N. crassa mycelium obtained before and after heat shock, and DNA fragments encompassing HSE and STRE elements from the 5'-flanking region. While elements within the promoter region are involved in transcription under heat shock, elements in the 5'UTR intron may participate in transcription during vegetative growth. The results thus suggest that N. crassa possesses trans-acting elements that interact with the 5'-flanking region to regulate gsn transcription during heat shock and vegetative growth.

The contribution of transposable elements to Bos taurus gene structure

In an effort to identify the contribution of TEs to bovine genome evolution, the abundance, distribution and insertional orientation of TEs were examined in all bovine nuclear genes identified in sequence build 2.1 (released October 11, 2005). Exons, introns and promoter segments (3 kb upstream the transcription initiation sites) were screened with the RepeatMasker program. Most of the genes analyzed contained TE insertions, with an average of 18 insertions/gene. The majority of TE insertions identified were classified as retrotransposons and the remainder classified as DNA transposons. TEs were inserted into exons and promoter segments infrequently, while insertion into intron sequences was strikingly more abundant. The contribution of TEs to exon sequence is of great interest because TE insertions can directly influence the phenotype by altering protein sequences. We report six cases where the entire exon sequences of bovine genes are apparently derived from TEs and one of them, the insertion of Charlie into a bovine transcript similar to the zinc finger 452 gene is analyzed in detail. The great similarity of the TE-cassette sequence to the ZNF452 protein and phylogenetic relationship strongly suggests the occurrence of Charlie 10 DNA exaptation in the mammalian zinc finger 452 gene. (c) 2006 Published by Elsevier B.V.

Effects of trophic poisoning with methylmercury on the appetitive elements of the agonistic sequence in fighting-fish (Betta splendens)

The aggressive display in Betta splendens is particularly prominent, and vital to its adaptation to the environment. Methylmercury is an organic variation of Hg that presents particularly pronounced neuro-behavioral effects. The present experiments aim to test the effect of acute and chronic poisoning with methylmercury on the display in Bettas. The animals were poisoned by trophic means in both experiments (16 ug/kg in acute poisoning; 16 ug/kg/day for chronic poisoning), and tested in agonistic pairs. The total frequency of the display was recorded, analyzing the topography of the agonistic response. The methylmercury seems to present a dose- and detoxification-dependent effect on these responses, with a more pronounced effect on motivity in acute poisoning and on emotionality in the chronic poisoning. It is possible that this effect could be mediated by alteration in the mono-amino-oxidase systems.