Which transposable elements are active in the human genome?

Although a large proportion (44%) of the human genome is occupied by transposons and transposon-like repetitive elements, only a small proportion (<0.05%) of these elements remain active today. Recent evidence indicates that approximately 35-40 subfamilies of Alu, L1 and SVA elements (and possibly HERV-K elements) remain actively mobile in the human genome. These active transposons are of great interest because they continue to produce genetic diversity in human populations and also cause human diseases by integrating into genes. In this review, we examine these active human transposons and explore mechanistic factors that influence their mobilization.     

What makes transposable elements move in the Drosophila genome?

Transposable elements (TEs), by their capacity of moving and inducing mutations in the genome, are considered important drivers of species evolution. The successful invasions of TEs in genomes, despite their mutational properties, are an apparent paradox. TEs' transposition is usually strongly regulated to low value, but in some cases these elements can also show high transposition rates, which has been associated sometimes to changes in environmental conditions. It is evident that factors susceptible to induce transpositions in natural populations contribute to TE perpetuation. Different factors were proposed as causative agents of TE mobilization in a wide range of organisms: biotic and abiotic stresses, inter- and intraspecific crosses and populational factors. However, there is no clear evidence of the factors capable of inducing TE mobilization in Drosophila, and data on laboratory stocks show contradictory results. The aim of this review is to have an update critical revision about mechanisms promoting transposition of TEs in Drosophila, and to provide to the readers a global vision of the dynamics of these genomic elements in the Drosophila genome.     

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.     

What is the impact of transposable elements on host genome variability?

The spread of a transposable element family through a wild population may be of astonishing rapidity. At least three families of transposable genetic elements have recently invaded Drosophila melanogaster worldwide, including the P element. The mechanism has been a process of effectively replicative transposition, and, for the P element, has occurred notwithstanding the sterility induced by unrestricted movement. This element's invasion into D. melanogaster has been accompanied by the development of heterogeneity between P sequences, most of which now have internal deletions. Increasing evidence suggests that some deleted elements can repress P transposition, thereby protecting the host from the harmful effects of complete elements. Such repressing elements may rise to high frequencies in populations as a result of selection at the level of the host. We here investigate selective sweeps invoked by the spread of P sequences in D. melanogaster populations. Numerous high-frequency sites have been identified on the X chromosome, which differ in frequency between populations, and which are associated with repression of P-element transposition. Unexpectedly, sequences adjacent to high-frequency P-element sites do not show reduced levels of genetic diversity, and DNA variability is in linkage equilibrium with the presence or absence of a P element at the adjacent selected site. This might be explained by multiple insertions or through a selection for recombination analogous to that seen in 'hitchhiking'.     

A sequence similar to bacterial transposable IS elements present in the 5′ untranslated region of the bovine butanediol dehydrogenase cDNA

A sequence similar to prokaryotic transposable elements was identified in the long 5′ untranslated region (5′UTR) of the butanediol dehydrogenase cDNA isolated from a bovine brain λgt11 library. Several observations suggested that this sequence could be related to bacterial IS elements: (a) 58% nucleotide sequence identity, (b) 56% amino acid sequence identity, and (c) the presence of inverted terminal repeats. However, nucleotide sequence analyses of the 5′UTR bovine cDNA showed the presence of chain-terminating nucleotide substitutions that would render it incapable of encoding a functional transposase. Finally, it was observed that different vertebrate genomes have sequences related to this putative transposable element. This revised version was published online in July 2006 with corrections to the Cover Date.     

Excision of a Ds-like maize transposable element (AcΔ) in a transient assay in Petunia is enhanced by a truncated coding region of the transposable element Ac

Summary The excision of a Ds-like transposable element (Ac) is mediated in trans by the transposable element Ac or its derivatives in Petunia protoplasts cotransfected with two plasmid DNAs. Excision restores the activity of the -glucuronidase (GUS) gene that is otherwise shut off by the presence of Ac in its leader sequence. A transient expression assay (histochemical test) is used to detect the -glucuronidase activity at the protoplast level. The number of blue-stained protoplasts is a measure of the excision frequency. With Ac alone a near-zero background of GUS activity is detected, which is weakly enhanced by the presence, in trans, of either the wild-type Ac or the coding region (ORF_a) transcribed from the 2 promoter of Agrobacterium tumefaciens TR-DNA. A strong enhancement is observed when a truncated Ac coding region, also under the control of the 2 promoter, is supplied in trans. The truncated version has ATG₁₀ at codon 103 in frame with ORF_a and is preceded by 7 out-of-frame ATGs. The assay is quick and well suited for detection of excision frequencies above the value obtained with the wild-type Ac. The presence of empty donor sites following excision can be demonstrated by PCR amplification and direct sequencing of the appropriate DNA fragment.     

Variation in the cell cycle time in the crypts of lieberkühn of the mouse

The durations of the phases of the cell cycle were measured at different levels in the jejunal crypts of male Balb/c mice. A mean cell cycle time of 12.3 h was found for the whole crypt. In cell positions 1 and 2, the cell cycle time was 16.7 h, and this time steadily decreased to a value of between 10 and 11 h for cell positions above 11. It is concluded that basally situated crypt cells in the mouse are cycling relatively slowly, and that they form the functional stem cell pool for the crypt. These cells may also compose the potential stem cell pool which repopulates the crypt after death of proliferative cells.     

Change in the power of EEG activity in the α range in response to tonic nociceptive stimulation of the distal joint of the little finger

Examination of 12 healthy volunteers aged 20–56 years was performed to study the EEG changes caused by a tonic squeeze of the distal joint of the little finger of the left and then the right hand. This stimulation caused painful sensations of different intensity (pain on the right was stronger). Spectral power was measured in the ( ₁ (8–10.5 Hz) and (₂ ranges (10.5–13 Hz) under different conditions. Weak pain led to an increase in the power of the (₁ and ₂ ranges in the occipital regions. With strong pain, the power of ₁ waves increased bilaterally in the posterior regions (O ₁, O ₂, T ₆), as well as in the left frontal region (F ₃, F ₇). The powers of the ₁ and ₂ ranges substantially increased relative to the background level after the strong nociceptive stimulation ceased. This finding testified to a latent and inertial character of its effect on the -wave parameters.Translated from Fiziologiya Cheloveka, Vol. 31, No. 2, 2005, pp. 77–84.Original Russian Text Copyright © 2005 by Garkavenko, Gorkovenko, Mankovskaya, Shevko, Lyskov, Kostyukov.     

Zooplankton in the ponds with tropical plants in the greenhouses of the Botanical Garden of the Jagiellonian University in Kraków

The presence of P. tetraurelia was found in the pond in "The Palm-House" greenhouse.     

Methylation of the ß-positions of the furan ring in F-acids

Major incubation products in feeding experiments with the sodium salt of 7-(5-butyl-furan-2-yl)heptanoic acid (3) on suspension cultures of Saccharum spec. are the unusual F-acids (4a) and (4b). They possess in contrast to natural monomethyl substituted F-acids a methyl substituent in the 4-position of the furan ring. Unexpectedly, the dimethyl substituted F-acids (4c) and (4d) were found only in very small amounts. The detection and structure elucidation of the methylation products (4a)–(4d) was achieved predominantly by GC-MS analysis of the corresponding tetrahydrofuran derivatives (5a)–(5d).     

Role of the hydrophobic and charged residues in the 218–226 region of apoA-I in the biogenesis of HDL

We investigated the significance of hydrophobic and charged residues 218–226 on the structure and functions of apoA-I and their contribution to the biogenesis of HDL. Adenovirus-mediated gene transfer of apoA-I[L218A/L219A/V221A/L222A] in apoA-I^−/− mice decreased plasma cholesterol and apoA-I levels to 15% of wild-type (WT) control mice and generated pre-β- and α4-HDL particles. In apoA-I^−/− × apoE^−/− mice, the same mutant formed few discoidal and pre-β-HDL particles that could not be converted to mature α-HDL particles by excess LCAT. Expression of the apoA-I[E223A/K226A] mutant in apoA-I^−/− mice caused lesser but discrete alterations in the HDL phenotype. The apoA-I[218–222] and apoA-I[E223A/K226A] mutants had 20% and normal capacity, respectively, to promote ABCA1-mediated cholesterol efflux. Both mutants had ∼65% of normal capacity to activate LCAT in vitro. Biophysical analyses suggested that both mutants affected in a distinct manner the structural integrity and plasticity of apoA-I that is necessary for normal functions. We conclude that the alteration of the hydrophobic 218–222 residues of apoA-I disrupts apoA-I/ABCA1 interactions and promotes the generation of defective pre-β particles that fail to mature into α-HDL subpopulations, thus resulting in low plasma apoA-I and HDL. Alterations of the charged 223, 226 residues caused milder but discrete changes in HDL phenotype.     

Involvement of binding lipoproteins in the absorption and transport of α-tocopherol in the rat

1. Specific lipoproteins binding alpha-tocopherol but not its known metabolites have been isolated and identified from cytosol of rat intestinal mucosa and from serum. 2. A timestudy of the appearance of the orally administered alpha-[(3)H]tocopherol with these lipoproteins indicates that very-low-density lipoprotein of serum acts as a carrier of the vitamin. 3. The involvement of the mucosal lipoprotein in the absorption of the vitamin from the intestine has been inferred from observations on the amounts of alpha-tocopherol in serum of orotic acid-fed rats where release of lipoproteins from the liver to serum is completely inhibited. A considerable decrease in the association of alpha-tocopherol with serum very-low-density lipoprotein under this condition is interpreted to mean that serum lipoproteins are limiting factors for the transport of the vitamin across the intestine and that this is possibly effected by exchange of alpha-tocopherol between serum very-low-density lipoprotein and mucosal lipoprotein.     

Copy number variation of transposable elements in Triticum–Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization

Key message

Here, we report on copy number variation of transposable elements and on the genome-specific proliferation in wheat. In addition, we report on revolutionary and evolutionary dynamics of transposons.

Abstract

Wheat is a valuable model for understanding the involvement of transposable elements (TEs) in speciation as wheat species (Triticum–Aegilops group) have diverged from a common ancestor, have undergone two events of speciation through allopolyploidy, and contain a very high fraction of TEs. However, an unbiased genome-wide examination of TE variation among these species has not been conducted. Our research utilized quantitative real time PCR to assess the relative copy numbers of 16 TE families in various Triticum and Aegilops species. We found (1) high variation and genome-specificity of TEs in wheat species, suggesting they were active throughout the evolution of wheat, (2) neither Ae. searsii nor Ae. speltoides by themselves can be the only contributors of the B genome to wheat, and (3) nonadditive changes in TE quantities in polyploid wheat. This study indicates the apparent involvement of large TEs in creating genetic variation in revolutionary and evolutionary scales following allopolyploidization events, presumably assisting in the diploidization of homeologous chromosomes.     

Modeling the Role of TGF-β in Regulation of the Th17 Phenotype in the LPS-Driven Immune System

Airway exposure levels of lipopolysaccharide (LPS) are known to determine type I versus type II helper T cell induced experimental asthma. While low doses of LPS derive Th2 inflammatory responses, high (and/or intermediate) LPS levels induce Th1- or Th17-dominant responses. The present paper develops a mathematical model of the phenotypic switches among three Th phenotypes (Th1, Th2, and Th17) in response to various LPS levels. In the present work, we simplify the complex network of the interactions between cells and regulatory molecules. The model describes the nonlinear cross-talks between the IL-4/Th2 activities and a key regulatory molecule, transforming growth factor β (TGF-β), in response to high, intermediate, and low levels of LPS. The model characterizes development of three phenotypes (Th1, Th2, and Th17) and predicts the onset of a new phenotype, Th17, under the tight control of TGF-β. Analysis of the model illustrates the mono-, bi-, and oneway-switches in the key regulatory parameter sets in the absence or presence of time delays. The model also predicts coexistence of those phenotypes and Th1- or Th2-dominant immune responses in a spatial domain under various biochemical and bio-mechanical conditions in the microenvironment.     

Role of vegetation in the variability of water regimes in the Šumava Mts forest

Deviations between observed and simulated discharge in the basins along the borders of the Czech Republic with Austria and Germany provide outputs which enable to follow changes in runoff. The three basins range in area from 100 to 200 km² and the experimental basin Liz with an area of 0.99 km². The selected experimental catchments are situated in or close to the National Park of the ?umava Mts. This region is described also in Tesa? et al. (2006). Results indicate that changes in runoff appear to be related to damages in forest cover caused by wind disasters and insects damages.Daily time series used for simulations are approximately 40 years long and 20 years in the experimental basin. Two different models of the rainfall — runoff process have been used for simulations and the outputs provide comparable results. The models are the conceptual model Sacramento (Burnash, 1995) and the model BROOK’90 (Federer, 1993). The second model distinguishes the details concerning evapotranspiration, including transpiration, rain and snow interception and snow and soil evaporation.The indicated runoff changes seem to be rather complex. After deforestation the volume of runoff generally increases and peak flows of floods are higher, but low flow in rainless periods show complicated courses.