Showing papers in "Genetica in 1999"

Genomes were forged by massive bombardments with retroelements and retrosequences.

Abstract: Retroposition is an efficient route to move coding regions around the genome ‘in search’ of novel regulatory elements and to shotgun regulatory elements into the genome ‘in search’ of new target genes. The templates for such retrogenes are mRNAs, and for regulatory retronuons (nuon = any definable nucleic acid sequence) usually small non-mRNAs (snmRNAs). An example in support of the ‘master gene’ model for SINEs (short interspersed repetive elements) is provided with neuronal BC1 RNA. Furthermore, an alternative explanation of LINE (long interspersed repetive elements) involvement in the generation of SINEs is given. I will also argue that the status of transposable elements with respect to the host resembles more symbiosis than parasitiasis and that host defense is often lenient as if even to ‘tolerate or support’ retronuons. Finally the paradox of evolution’s lack of foresight and the future exaptive use of retronuons is being dealt with by referring to W.F. Doolittle’s ‘Hierarchical Approaches to Genome Evolution’.

Sure facts, speculations, and open questions about the evolution of transposable element copy number

Abstract: Transposable elements (TEs) are sequences capable of multiplying in their host’s genome. They survive by increasing copy numbers due to transpositions, and natural selection washes them out because hosts with heavier loads of TEs have lower fitness. The available phylogenetic evidence supports the view that TEs have existed in living organisms for hundreds of millions of years. A fundamental question facing the field is how can an equilibrium be attained between transposition and selection which allows these parasitic genetic elements to persist for such a long time period? To answer this question, it is necessary to understand how the rate of TE transposition is controlled and to describe the mechanisms with which natural selection opposes TE accumulation. Perhaps the best models for such a study are copia and gypsy retrotransposons in Drosophila. Their average rate of transposition in nature is between 10−5 – 10−4 transpositions per copy per generation. Unlike nature, transposition rates vary widely, from zero to 10−2, between laboratory lines. This variability in transposition rate is controlled by host genes. It is probable that in nature TE site heterogeneity is caused by frequent transpositions in rare flies with permissive alleles, and no transpositions happen in the rest of flies. The average rate of TE transposition in nature may thus depend on the frequency of permissive alleles, which is a function of the rate of mutation from restrictive to permissive alleles, the mechanism and the strength of selection opposing TE multiplication, and population size. Thus, evolution of the frequency of permissive alleles of genes controlling transposition must be accounted for to understand evolution of TE copy numbers.

Molecular paleontology of transposable elements from Arabidopsis thaliana.

Abstract: We report results of a comprehensive computer-assisted analysis of new transposable elements (TEs) from Arabidopsis thaliana. Our analysis revealed several previously unknown pogo- and En/Spm-like families and two novel superfamilies of DNA transposons, Arnold and Harbinger. One of the En/Spm-like families (Atenspm) was found to be involved in generating satellite arrays in paracentromeric regions. Of the two superfamilies reported, Harbinger is distantly related to bacterial IS5-like insertion elements, and Arnold contains DNA transposons without terminal inverted repeats (TIRs), which were never reported in eukaryotes before. Furthermore, we report a large number of young and diverse copia-like autonomous and nonautonomous retroelements and discuss their potential evolutionary relationship with mammalian retroviruses. The A. thaliana genome harbors copia-like retroelements which encode a putative env-like protein reported previously in the SIRE-1 retrotransposon from soybean. Finally, we demonstrate a nonrandom chromosomal distribution of the most abundant A. thaliana TEs clustered in the first half of chromosome II, which includes the centromeric region. The families of TEs from A. thaliana are relatively young, extremely diverse and much smaller than those from mammalian genomes. We discuss the potential factors determining similarities and differences in the evolution of TEs in mammals and A. Thaliana.

Left-handed Z-DNA: structure and function

Abstract: Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-stranded RNA adenosine deaminase type I (ADAR1) has motifs specific for the Z-DNA conformation Editing by ADAR1 requires a double-stranded RNA substrate In the cases known, the substrate is formed by folding an intron back onto the exon that is targeted for modification The use of introns to direct processing of exons requires that editing occurs before splicing Recognition of Z-DNA by ADAR1 may allow editing of nascent transcripts to be initiated immediately after transcription, ensuring that editing and splicing are performed in the correct sequence Structural characterization of the Z-DNA binding domain indicates that it belongs to the winged helix-turn-helix class of proteins and is similar to the globular domain of histone-H5

Transposon dynamics and the breeding system

Abstract: The selfish DNA hypothesis predicts that natural selection is responsible for preventing the unregulated build up of transposable elements in organismal genomes. Accordingly, between-species differences in the strength and effectiveness of selection against transposons should be important in driving the evolution of transposon activity and abundance. We used a modeling approach to investigate how the rate of self-fertilization influences the population dynamics of transposable elements. Contrasting effects of the breeding system were observed under selection based on transposon disruption of gene function versus selection based on element-mediated ectopic exchange. This suggests that the comparison of TE copy number in organisms with different breeding systems may provide a test of the relative importance of these forces in regulating transposon multiplication. The effects of breeding system also interacted with population size, particularly when there was no element excision. The strength and effectiveness of selection against transposons was reflected not only in their equilibrium abundance, but also in the per-site element frequency of individual insertions and the coefficient of variation in copy number. These results are discussed in relation to evidence on transposon abundance available from the literature, and suggestions for future data collection.

Recently integrated human Alu repeats: finding needles in the haystack.

Abstract: Alu elements undergo amplification through retroposition and integration into new locations throughout primate genomes. Over 500,000 Alu elements reside in the human genome, making the identification of newly inserted Alu repeats the genomic equivalent of finding needles in the haystack. Here, we present two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine the human genomic DNA sequence databases in order to identify recently integrated Alu elements. The second method is based on an anchor-PCR technique which we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements are selectively amplified from anchored DNA generating a display or 'fingerprint' of recently integrated Alu elements. Alu insertion polymorphisms are then detected by comparison of the DNA fingerprints generated from different samples. Here, we explore the utility of these methods by applying them to the identification of members of the smallest previously identified subfamily of Alu repeats in the human genome termed Ya8. This subfamily of Alu repeats is composed of about 50 elements within the human genome. Approximately 50% of the Ya8 Alu family members have inserted in the human genome so recently that they are polymorphic, making them useful markers for the study of human evolution.

Molecular domestication — more than a sporadic episode in evolution

Abstract: Transposable elements are short but complex pieces of DNA or RNA containing a streamlined minimal-genome with the capacity for its selfish replication in a foreign genomic environment. Cis-regulatory sections within the elements orchestrate tempo and mode of TE expression. Proteins encoded by TEs mainly direct their own propagation within the genome by recruitment of host-encoded factors. On the other hand, TE-encoded proteins harbor a very attractive repertoire of functional abilities for a cell. These proteins mediate excision, replication and integration of defined DNA fragments. Furthermore, some of these proteins are able to manipulate important host factors by altering their original function. Thus, if the host genome succeeds in domesticating such TE-encoded proteins by taming their ‘anarchistic behavior,’ such an event can be considered as an important evolutionary innovation for its own benefit. In fact, the domestication of TE-derived cis-regulatory modules and protein coding sections took place repeatedly in the course of genome evolution. We will present prominent cases that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time. Furthermore, we will propose that molecular domestication might be considered as a resumption of the same evolutionary process that drove the transition from ‘primitive genomes’ to ‘modern’ ones at the early dawn of life, that is, the adaptive integration of a short piece of autonomous DNA into a complex regulatory network.

Micro-Mechanical Measurement of the Torsional Modulus of DNA

Abstract: The torsional modulus C of DNA is determined from the difference between the work of stretching a single overwound molecule and the work done stretching one underwound by the same number of turns. The value obtained C/k B T = 86 ± 10 nm is within the range (75 ± 25 nm) estimated by more indirect methods

DNA repeats in the human genome

Abstract: Repetitive DNA sequences, interspersed through out the human genome, are capable of forming a wide variety of unusual DNA structures with simple and complex loopfolding patterns The hairpin formed by the fragile X repeat, (CCG)n, and the bipartite triplex formed by the Friedreich’s ataxia repeat, (GAA)n/(TTC)n, show simple loopfolding On the other hand, the doubly folded hairpin formed by the human centromeric repeat, (AATGG)n, the hairpin G-quartet formed by (TTAGGG)n at the 3’ telomere overhang, and the hairpin G-quartet, and hairpin C+•C paired i-motif formed by the insulin minisatellite \( {\left({\begin{array}{*{20}{c}} {ACA{G_4}}{TGT{G_4}}\\ {TGT{C_4}}{ACA{C_4}} \end{array}}\right)_n}, \) show multiple and complex loopfoldingWe have performed high resolution nuclear magnetic resonance (NMR) spectroscopy and in vitro replication to show that unique base-pairing and loopfolding render stability to these unusual structures under physiological conditions The formation of such stable structures offers a mechanism of unwinding which is advantageous during transcription For example, the formation of the hairpin G-quartet, and hairpin C+•C paired i-motif upstream of the insulin gene may facilitate transcription These unusual DNA structures also provide unique “protein recognition motifs” quite different from a Watson-Crick double helix For example, the hairpin G-quartet formed by (TTAGGG)n at the 3’ telomere overhang is specifically recognized and yeast homologue, may stabilize the human telomere by binding to the multiply folded hairpin G-quartet structures

Transposable elements as the key to a 21st century view of evolution

Abstract: Cells are capable of sophisticated information processing. Cellular signal transduction networks serve to compute data from multiple inputs and make decisions about cellular behavior. Genomes are organized like integrated computer programs as systems of routines and subroutines, not as a collection of independent genetic ‘units’. DNA sequences which do not code for protein structure determine the system architecture of the genome. Repetititve DNA elements serve as tags to mark and integrate different protein coding sequences into coordinately functioning groups, to build up systems for genome replication and distribution to daughter cells, and to organize chromatin. Genomes can be reorganized through the action of cellular systems for cutting, splicing and rearranging DNA molecules. Natural genetic engineering systems (including transposable elements) are capable of acting genome-wide and not just one site at a time. Transposable elements are subject to regulation by cellular signal transduction/computing networks. This regulation acts on both the timing and extent of DNA rearrangements and (in a few documented cases so far) on the location of changes in the genomes. By connecting transcriptional regulatory circuits to the action of natural genetic engineering systems, there is a plausible molecular basis for coordinated changes in the genome subject to biologically meaningful feedback.

Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms

Abstract: The analysis of transgene silencing effects in plants and other eukaryotic organisms has revealed novel mechanisms of epigenetic regulation that are based on recognition of nucleic acid sequence homology. These homology- dependent gene silencing phenomena are characterized by an inverse relationship between copy number of a particular sequence and expression levels. Depending on whether promoter regions or transcribed sequences are repeated, silencing occurs at the transcriptional or post-transcriptional level, respectively. Different silencing effects involving DNA-DNA or RNA-DNA associations in the nucleus, and RNA-RNA interactions in the cytoplasm appear to reflect distinct host defense responses to parasitic sequences, including transposable elements (TEs), viroids and RNA viruses. Natural epigenetic phenomena that resemble transgene silencing effects often involve endogenous genes comprising recognizable TE sequences or rearrangements generated by TEs and can thus be interpreted in terms of host defense systems. A genome defense that inactivates TEs by methylation might have been recruited during evolution to regulate the transcription of plant and vertebrate genes that contain remnants of TE insertions in promoter regions.

Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.

Abstract: Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses--the area of research often referred to as 'functional genomics'--aims at deciphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function. This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution. Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed. A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at http:@www.ncbi.nlm.nih.gov/COG). This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism. Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size-parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives. Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function. An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle.

Nature and distribution of constitutive heterochromatin in fishes, genus Hypostomus (Loricariidae).

Abstract: Some Hypostomus species were studied concerning the features of the karyotype structure and the constitutive heterochromatin. The karyotype of sp. F from the Sao Francisco river (Minas Gerais state, Brazil) is now described for the first time. A diversity in the diploid number, ranging from 2n=68 to 2n=80, as well as in the karyotype formulae, is evident in this fish group. Two types of heterochromatin, GC- and AT-rich, could be identified with the use of base-specific fluorochromes. In some species heterochromatic bands are mainly located on the centromeric and telomeric chromosomal regions, while in other species they are also observed at interstitial locations. Hypotheses concerning this heterochromatic distribuition in Hypostomus karyotypes are discussed. A case of supernumerary heterochromatic segment and a centric fusion appear to be related with two variant karyotypic formulae observed among specimens from the Mogi-Guacu and Sao Francisco rivers, respectively. The available data permit us to characterize a divergent karyotypic evolution among the Hypostomus species already analyzed, both at the macro- and microstructural levels, that is, their general karyotype organization and particular features related to chromosomal banding or staining, respectively.

Sex brings transposons and genomes into conflict.

Abstract: Given that transposons are so abundant in mammalian genomes, it is natural to assume that through their maintenance the host gains some net benefit. This need not be true; sexual reproduction allows a transposon to go to fixation if the reduction in fitness of the host is anything less than two-fold. Obligate outcrossing sexual reproduction therefore favors the evolution of aggressive transposons, which in turn select for the evolution of host mechanisms that suppress transposon activity. Hosts that have asexual or self-fertilizing generations will select for transposons that are more benign and self-limiting than those of obligate sexuals, and obligate asexuals and uniparental organelle genomes will be free of active transposons if these impose any fitness penalty. We are interested in host mechanisms that suppress transposons in sexuals and have found that mammals (all of which are obligate sexuals) control their large populations of potentially active retroposons by methylating the five position of cytosine residues within promoter elements. This causes strong transcriptional repression and assembly of the affected sequences into the condensed state. Methylation also causes permanent inactivation in the germline by driving C→T transition mutations at methylated sites. It is now known that methylation remains in place for the large majority of the life of germ cells and is essential for control of the very large transposon burden. There is pressure on transposons to evolve mechanisms that overcome host suppression, and over evolutionary time, the balance swings back and forth between parasite and host. The ability of the mammalian genome to absorb and accumulate additional transposons has caused the amount of reverse transcriptase coding sequence in the human genome to far exceed the sum total of all cellular coding sequence. While transposons could, in principle, contribute functions useful to the host, the fact that asexual species and uniparental organelle genomes lack transposons is strong evidence that transposons have a net deleterious effect even in genomes that might be thought to require an additional source of plasticity. The abundance of transposons in many genomes cannot be taken as evidence of a mutualistic relationship, and the conflict between transposons and genomes may have actually retarded rather than accelerated evolution. It is suggested that the relationship between sex and transposons is as follows: (i) Obligate sexuals will tend to harbor aggressive transposons limited largely by host suppressive mechanisms, which in mammals involve methylation of transposon promoters. (ii) The aggressiveness of transposons in facultative sexuals and self-fertilizing sexuals will be in part self-limited and will be proportional to the relative frequency of asexual and outcrossing sexual generations. (iii) Obligate asexuals and organelles transmitted in a uniparental manner will have no active transposons if these have a net negative effect on host fitness.

Structure, functionality, and evolution of the BARE-1 retrotransposon of barley

Abstract: The BARE-1 retrotransposon is a major, active component of the genome of barley (Hordeum vulgare L.) and other Hordeum species. Copia-like in its organization, it consists of 1.8-kb long terminal repeats bounding an internal domain of 5275 bp which encodes a predicted polyprotein of 1301 residues. The polyprotein contains the key residues, structural motifs, and conserved regions associated with retroviral and retrotransposon GAG, aspartic proteinase, integrase, reverse transcriptase, and RNaseH polypeptides. BARE-1 is actively transcribed and translated. As part of our effort to understand the evolution and function of BARE-1, we have examined its copy number and localization. Full-length members of the BARE-1 family constitute 2.8% of the barley genome. Globally, they are dispersed throughout the genome, excepting the centromeric, telomeric, and NOR regions. Locally, BARE- 1 occurs more commonly in repetitive DNA than in coding regions, forming clusters of nested insertions. Both barley and other Hordeum genomes contain a high proportion of BARE-1 solo LTRs. New techniques have been developed which exploit the insertion site polymorphism generated by BARE-1 integration to produce molecular markers for breeding, biodiversity, and mapping applications.

Distribution of transposable elements in Drosophila species.

Abstract: We present a global analysis of the distribution of 43 transposable elements (TEs) in 228 species of the Drosophila genus from our data and data from the literature. Data on chromosome localization come from in situ hybridization and presence/absence of the elements from southern analyses. This analysis shows great differences between TE distributions, even among closely related species. Some TEs are distributed according to the phylogeny of their host specie; others do not entirely follow the phylogeny, suggesting horizontal transfers. A higher number of insertion sites for most TEs in the genome of D. melanogaster is observed when compared with that in D. simulans. This suggests either intrinsic differences in genomic characteristics between the two species, or the influence of differing effective population sizes, although biases due to the use of TE probes coming mostly from D. melanogaster and to the way TEs are initially detected in species cannot be ruled out. Data on TEs more specific to the species under consideration are necessary for a better understanding of their distribution in organisms and populations.

Functional Genomics and Enzyme Evolution

Abstract: Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses — the area of research often referred to as “functional genomics” - aims at decyphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at http://wwwncbinlmnihgov/COG) This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size -parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle

Size and shape heritability in natural populations of Drosophila mediopunctata: temporal and microgeographical variation.

Abstract: 'Traditional morphometrics' allows us to decompose morphological variation into its major independent sources, identifying them usually as size and shape. To compare and investigate the properties of size and shape in natural populations of Drosophila mediopunctata, estimating their heritabilities and analysing their temporal and microgeographic changes, we carried out collections on seven occasions in Parque Nacional do Itatiaia, Brazil. In one of these collections, we took samples from five different altitudes. Measurements were taken from wild caught inseminated females and up to three of their laboratory-reared daughters. Through a principal component analysis, three major sources of variation were identified as due to size (the first one) and shape (the remaining two). The overall amount of variation among laboratory flies was about half of that observed among wild flies and this reduction was primarily due to size. Shape variation was about the same under natural and artificial conditions. A genetic altitudinal cline was detected for size and shape, although altitude explained only a small part of their variation. Differences among collections were detected both for size and shape in wild and laboratory flies, but no simple pattern emerged. Shape variation had high heritability in nature, close to or above 40% and did not vary significantly temporally. Although on the overall size heritability (18 +/- 6%) was significant its estimates were not consistent along months--they were non-significant in all but one month, when it reached a value of 51 +/- 11%. Overall, this suggests that size and shape have different genetic properties.

The skeletal function of non-genic nuclear DNA: new evidence from ancient cell chimaeras.

Abstract: DNA can be divided functionally into three categories: (1) genes, which code for proteins or specify non-messenger RNAs; (2) semons, short specific sequences involved in the replication, segregation, recombination or specific attachments of chromosomes, or chromosome regions (e.g. loops or domains) or selfish genetic elements; (3) secondary DNA which does not function by means of specific sequences. Probably more than 90% of DNA in the biosphere is secondary DNA in the nuclei of plants and phytoplankton. The amount of genic DNA is related to the complexity of the organism, whereas the amount of secondary DNA increases proportionally with cell volume, not with complexity. This correlation is most simply explained by the skeletal DNA hypothesis, according to which nuclear DNA functions as the basic framework for the assembly of the nucleus and the total genomic DNA content functions (together with relatively invariant folding rules) in determining nuclear volumes. Balanced growth during the cell cycle requires that the cytonuclear ratio is basically constant irrespective of cell volume; thus nuclear volumes, and therefore the overall genome size, has to be evolutionarily adjusted to changing cell volumes for optimal function. Since bacteria, mitochondria, chloroplasts and viruses have no nuclear envelope, the skeletal DNA hypothesis simply explains why secondary DNA is essentially absent from them but present in large cell nuclei. Hitherto it has been difficult to refute the alternative hypothesis that nuclear secondary DNA accumulates merely by mutation pressure (whether “junk” or selfish DNA), and that selection for economy is not strong enough to eliminate it, whereas accumulation in mitochondria and plastids is prevented by intracellular replicative competition between their multiple genomes. New data that and nuclear genome sizes; mutation, though the essential physical basis for changes in genome size, does not directly determine it as is assumed by junk and selfish DNA theories — mutation pressure cannot explain the scaling laws

Plasticity of Drosophila melanogaster wing morphology: effects of sex, temperature and density.

Abstract: In this paper we use an adjusted ellipse to the contour of the wings of Drosophila as an experimental model to study phenotypic plasticity. The geometric properties of the ellipse describe the wing morphology. Size is the geometric mean of its two radii; shape is the ratio between them; and, the positions of the apexes of the longitudinal veins are determined by their angular distances to the major axis of the ellipse. Flies of an inbred laboratory strain of Drosophila melanogaster raised at two temperatures (16.5°C and 25°C) and two densities (10 and 100 larvae per vial) were used. One wing of at least 40 animals of each sex and environmental condition were analyzed (total = 380), a measurement of thorax length was also taken. Wing size variation could be approximately divided into two components: one related to shape variation and the other shape independent. The latter was influenced primarily by temperature, while the former was related to sex and density. A general pattern could be identified for the shape dependent variation: when wings become larger they become longer and the second, fourth and fifth longitudinal veins get closer to the tip of the wing.

Origin, functions and chemistry of H‐2 regulated odorants

Abstract: Genes located within the major histocompatibility complex (MHC) of mice are responsible for individual differences in body odor (odortypes). In this review we suggest that the MHC genes themselves are responsible for odor differences among MHC‐congenic mice. Recent studies indicating that volatile carboxylic acids are at least in part responsible for the individual odors and what this finding implies about the pathway from gene to odorant are also reviewed. We suggest that odorants or their precursors are bound directly by MHC products and are released into serum and concentrated in urine. Finally, possible functions of MHC odortypes in mice are enumerated and important future research questions are raised.

Transposable elements as activators of cryptic genes in E. coli.

Abstract: The concept of transposable elements (TEs) as purely selfish elements is being challenged as we have begun to appreciate the extent to which TEs contribute to allelic diversity, genome building, etc. Despite these long-term evolutionary contributions, there are few examples of TEs that make a direct, positive contribution to adaptive fitness. In E. coli cryptic (silent) catabolic operons can be activated by small TEs called insertion sequences (IS elements). Not only do IS elements make a direct contribution to fitness by activating cryptic operons, they do so in a regulated manner, transposing at a higher rate in starving cells than in growing cells. In at least one case, IS elements activate an operon during starvation only if the substrate for that operon is present in the environment. It appears that E. coli has managed to take advantage of IS elements for its own benefit.

RAPD divergence caused by microsite edaphic selection in wild barley

Abstract: Random amplified polymorphic DNA polymerase chain reaction (RAPDPCR) was used to assess genetic diversity in four subpopulations (86 individuals) of wild barley, Hordeum spontaneum, sampled from Tabigha microsite near the Sea of Galilee, Israel. The microsite consists of two 100 m transects that are topographically separated by 100 m, each equally subdivided into 50 m of basalt and terra rossa soil types. Despite the same macroclimate characterizing the area around the Sea of Galilee, the microsite offers two edaphically different microhabitats, with basalt being a more ecologically heterogeneous and broader-niche than the relatively drier but more homogeneous and narrow-niche terra rossa. Analysis of 118 putative loci revealed significant (P<0.05) genetic differentiation in polymorphism (P0.05) between the two soils across the transects with P being higher in the more heterogeneous basalt (mean P0.05 = 0.902), than in terra rossa (mean P0.05 = 0.820). Gene diversity (He) was higher in basalt (mean He=0.371), than in terra rossa (mean He=0.259). Furthermore, unique alleles were confined to one soil type, either in one or both transects. Rare alleles were observed more frequently in terra rossa than basalt, and in transect II only. Gametic phase disequilibria showed a larger multilocus association of alleles in basalt than terra rossa, and in transect I than II. Spearman rank correlation (rs) revealed a strong association between specific loci and soil types, and transects. Also, analysis of multilocus organization revealed soil-specific multilocus-genotypes. Therefore, our results suggest an edaphically differentiated genetic structure, which corroborates the niche width-variation hypothesis, and can be explained, in part, by natural selection. This pattern of RAPD diversity is in agreement with allozyme and hordein protein diversities in the same subpopulations studied previously.

Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay.

Abstract: Long Interspersed Nuclear Elements (L1s or LINEs) are the most abundant retrotransposons in the human genome, and they comprise approximately 17% of DNA. L1 retrotransposition can be mutagenic, and deleterious insertions both in the germ-line and in somatic cells have resulted in disease. Recently, an assay was developed to monitor L1 retrotransposition in cultured human cells. This assay, for the first time, now allows for a systematic study of L1 retrotransposition at the molecular level. Here, I will review progress made in L1 biology during the past three years. In general, I will limit the discussion to studies conducted on human L1s. However, interesting parallels to rodent L1s and other non-LTR retrotransposons also will be discussed.

Is the evolution of transposable elements modular

Abstract: The evolution of transposable element structures can be analyzed in populations and species and by comparing the functional domains in the main classes of elements. We begin with a synthesis of what we know about the evolution of the mariner elements in the Drosophilidae family in terms of populations and species. We suggest that internal deletion does not occur at random, but appears to frequently occur between short internal repeats. We compared the functional domains of the DNA and/or amino acid sequences to detect similarities between the main classes of elements. This included the gag, reverse transcriptase, and envelope genes of retrotransposons and retroviruses, and the integrases of retrotransposons and retroviruses, and transposases of class II elements. We find that each domain can have its own evolutionary history. Thus, the evolution of transposable elements can be seen to be modular.

The protein data bank. Bridging the gap between the sequence and 3D structure world.

Abstract: The protein data bank (PDB), at Brookhaven National Laboratory, is a database containing information on experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules, with approximately 9000 entries. The PDB has a 27-year history of service to a global community of researchers, educators, and students in a wide variety of scientific disciplines. Data are easily submitted via PDB's WWW-based tool AutoDep, in either PDB or mmCIF format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser. Collaborative centers have been, and continue to be, established worldwide to assist in data deposition, archiving, and distribution.

Chromatin control of HIV‐1 gene expression

Abstract: Upon infection of susceptible cells, the RNA genome of the human immunodeficiency virus type 1 (HIV-1) is reverse transcribed into double-stranded DNA, which can be subsequently integrated into the cellular genome. After integration, the viral long terminal repeat (LTR) promoter is present in a nucleosome-bound conformation and is transcriptionally silent in the absence of stimulation. Activation of HIV-I gene expression is concomitant with an acetylation-dependent rearrangement of the nucleosome positioned at the viral transcription start site. Thus, similar to most cellular genes, the transcriptional state of the integrated HIV-I provirus is closely linked to histone acetylation. This enzymatic activity results from the function of histone-specific nuclear acetyltransferase (HAT) enzymes. Efficient viral transcription is strongly dependent on the virally-encoded Tat protein. The mechanism by which Tat increases the rate of transcriptional initiation has been recently demonstrated and involves the interaction of Tat with the transcriptional coactivator p300 and the closely related CREB-binding protein (CBP), having histone acetyltransferase activity

Age- and sex-distribution of the mutation load.

Abstract: We investigate the age and sex distribution of genetic fitness under mutation-selection balance by means of simple one-locus two-allele models We find that the extent of age and sex variation in the mutation load is very dependent on the average effect of new mutations If the average heterozygote selective effect of new mutations is large, then age and sex differences may constitute a significant fraction of the total load, and be significant as compared to standing genetic variation Whether the mutation load will increase or decrease with age depends on the age- and sex-specific effects of the new mutations, and on the rate of accumulation of mutations in the germ line as individuals age We argue that the load will most likely increase with age in animals with continuous germ-cell division throughout life, and that this will occur even when mutations have unconditionally deleterious effects We show that a male-biased mutation rate is likely to result in both a male-biased mutation load and a load that increases with male age

Modelling DNA Stretching for Physics and Biology

Abstract: We have used internal coordinate molecular mechanics calculations to study how the DNA double helix deforms upon stretching. Results obtained for polymeric DNA under helical symmetry constraints suggest that two distinct forms, a unwound ribbon and a narrow fibre, can be formed as a function of which ends of the duplex are pulled. Similar results are also obtained with DNA oligomers. These experiments lead to force curves which exhibit a plateau as the conformational transition occurs. This is behaviour is confirmed by applying an increasing force to DNA and observing a sudden length increase at a critical force value. It is finally shown some DNA binding proteins can also stretch DNA locally, leading to conformations related to those created by nanomanipulation

NOR polymorphism in the Iberian species Chondrostoma lusitanicum (Pisces: Cyprinidae)--re-examination by FISH.

Abstract: Chromosomal polymorphism regarding the number of chromosomal NOR sites in the cyprinid fish Chondrostoma lusitanicum reported previously (Rodrigues & Collares-Pereira, 1996) was re-examined using fluorescence in situ hybridization (FISH) with a ribosomal DNA (rDNA) probe. All positive CMA3-bands contained ribosomal DNA documented by either two or four FISH positive signals in the respective karyotypes. This polymorphism suggests the occurrence of structural rearrangements of translocation type in rDNA region from one ancestral NOR-bearing chromosome pair ubiquitous among leuciscine cyprinid fishes to another pair. The absence of individuals heterozygous for this polymorphism is discussed.