The role of endogenous retroviruses in the human body.

Endogenous retroviruses (ERVs) are genetic elements that were integrated into the host genome more than 100 million years ago. Their integration took place in germ cells, ensuring their vertical transmission in the human population. They are currently thought to make up to 8 % of the human genome. During evolution, various mutations have accumulated in endogenous retroviruses, leading to their dysfunction, and were therefore considered as junk DNA in the past. However, in recent years it has turned out that they are not completely dysfunctional. With more data becoming available from human genome analyses, their potential roles in the human body are being revealed.

A survey on murine gammaherpesvirus 68 in ticks collected in Slovakia.

Murine gammaherpesvirus 68 (MHV-68) is a natural pathogen that infects murid rodents which serve as hosts for Dermacentor reticulatus and Ixodes ricinus ticks. For the first time, MHV-68 was detected in immature I. ricinus ticks feeding on lizards trapped in Slovakia. Later on, MHV-68 infection was detected in D. reticulatus and Haemaphysalis concinna ticks collected on vegetation, which supported the idea that ticks can acquire the virus from feeding on infected hosts. Here, we report MHV-68 infection, which was detected by nested PCR, in D. reticulatus and I. ricinus adult ticks and I. ricinus nymphs collected in five geographically isolated localities, in west, southwest, south and central Slovakia. Viral incidence in ticks was 46.7% (121/259) without considering the season, site of collection and tick species and their life stage. MHV-68 infection was detected in all five localities investigated and in both tick species. Here, for the first time, we report MHV-68 infection in I. ricinus nymphs collected from the vegetation. The finding of virus in ticks from five separated localities suggested that ticks became infected with MHV-68 via feeding on infected rodents; thus, this virus might be a newfound natural pathogen in ticks.

Development of a new method for the preparation of an acellular allodermis, quality control and cytotoxicity testing.

Demand for use of acellular allodermis is high but commercially appropriate products are not used routinely because of very high price and limited availability. These facts did motivate us to prepare acellular allodermis using a new, simple and less expensive method. We have developed a original method for preparation of acellular allogeneic dermis based on action of a proteolytic enzyme in combination with distilled water. Hypotonic environment in comparison with SDS or Triton ansure no toxicity of the final product. Trials for determination of optimal trypsin concentrations, temperature and time of action were performed. According to our results, the use of 2.5% trypsin/EDTA solution overnight at +4 °C was proving to be optimal. The histology confirmed absence of cells in the prepared dermis. No toxicity of final acellular dermis was confirmed by three independent tests (agar diffusion test contact cytotoxicity test and grow curve). The prepared acellular dermis seems to be suitable not only for direct clinical use, but it can be used as a scaffold for cell cultivation as well.

Interferon lambda induces antiviral response to herpes simplex virus 1 infection.

Lambda interferons (IFN-λ) are known to induce potent antiviral response in a wide variety of target cells. They activate the same intracellular signalling pathways and have similar biological activities as IFN-α/ß, including antiviral activity, but signal via distinct receptor complex, which is expressed in a cell- and species-specific manner. IFN-λ was reported to induce in vitro marked antiviral activity against various RNA viruses, but corresponding data on DNA viruses are sparse. Therefore we examined the IFN-λ1 induced antiviral activity against two strains of herpes simplex virus 1, a highly pathogenic ANGpath and moderately pathogenic KOS. The antiviral response was determined in vitro in Vero cells, known as deficient in production of type I IFNs and in Vero E6 cells, responding to viral infection with abundant IFN-λ production, although deficient in production of type I IFNs. The results showed that IFN-λ1 induced in Vero cells higher antiviral activity against ANGpath strain than against KOS strain. In Vero E6 cells endogenous IFN-λ induced higher antiviral activity against ANGpath strain than against KOS strain, but because of the virus induction of IFN-λ expression the antiviral activity was detected later. The observed differences between the IFN-λ1-induced antiviral activities against viral strains of various pathogenicity suggest that virus attributes may play role in the antiviral state of cells induced by IFN-λ.

Future water resources for food production in five South Asian river basins and potential for adaptation--a modeling study.

The Indian subcontinent faces a population increase from 1.6 billion in 2000 towards 2 billion around 2050. Therefore, expansion of agricultural area combined with increases in productivity will be necessary to produce the food needed in the future. However, with pressure on water resources already being high, and potential effects of climate change still uncertain, the question rises whether there will be enough water resources available to sustain this production. The objective of this study is to make a spatially explicit quantitative analysis of water requirements and availability for current and future food production in five South Asian basins (Indus, Ganges, Brahmaputra, Godavari and Krishna), in the absence or presence of two different adaptation strategies: an overall improvement in irrigation efficiency, and an increase of reservoir storage capacity. The analysis is performed by using the coupled hydrology and crop production model LPJmL. It is found that the Godavari and Krishna basins will benefit most from an increased storage capacity, whereas in the Ganges and the Indus water scarcity mainly takes place in areas where this additional storage would not provide additional utility. Increasing the irrigation efficiency will be beneficial in all basins, but most in the Indus and Ganges, as it decreases the pressure on groundwater resources and decreases the fraction of food production that would become at risk because of water shortage. A combination of both options seems to be the best strategy in all basins. The large-scale model used in this study is suitable to identify hotspot areas and support the first step in the policy process, but the final design and implementation of adaptation options requires supporting studies at finer scales.

Interferons lambda, new cytokines with antiviral activity.

Interferons (IFNs) are key cytokines in the establishment of a multifaceted antiviral response. Three distinct types of IFNs are now recognized (type I, type II, and type III) based on their receptor usage, structural features and biological activities. Although all IFNs are important mediators of antiviral protection, their roles in antiviral defence vary. Interferon lambda (IFN-λ) is a recently discovered group of small helical cytokines capable of inducing an antiviral response both in vitro as well as in vivo. They were discovered independently in 2003 by the groups of Sheppard and Kotenko. This family consists of three structurally related IFN-λ subtypes called IFN-λ1 (IL-29), IFN-λ2 (IL-28A), and IFN-λ3 (IL-28B). In this study we investigate the antiviral activities of IFN-λ1, λ2, and λ3 on some medically important viruses, influenza viruses, herpes viruses and lymphocytic choriomeningitis virus.

Skin explant cultures as a source of keratinocytes for cultivation.

Cultivated human keratinocytes can be used successfully in the treatment of burn patients, but efforts to heal burns and other wounds can be hampered by the very small skin biopsies available for cultivation of transplantable keratinocyte sheets. A small biopsy (and correspondingly small number of enzymatically isolated keratinocytes for use in classical cultivation techniques) can lead to a low yield of multilayer sheets for clinical application or unacceptably long cultivation times. One way of addressing this is to make use of skin remnants remaining after enzymatic digestion and culture cells migrating out of these skin explants. Sufficient numbers of explant-derived keratinocytes can be obtained to facilitate additional routine cultivation of these cells. Biopsy remnants can be used to initiate explant cultures repeatedly (we were able to re-use pieces of skin 10 times and still obtain useful numbers of keratinocytes) and this "passaging" yields substantially more cells for classical cultivation than would be available from conventional methodology alone, and in a comparable timeframe. Another advantage of this method is that it does not require additional biopsies to be procured from already-compromised patients and overcomes problems associated with contamination of skin samples with resistant hospital-acquired bacterial infections common during prolonged hospitalization.

Diverse Mariner-like elements in fig wasps.

Mariner transposable elements are widespread and diverse in insects. We screened 10 species of fig wasps (Hymenoptera: Agaonidae) for mariner elements. All 10 species harbour a large diversity of mariner elements, most of which have interrupted reading frames in the transposase gene region, suggesting that they are inactive and ancient. We sequenced two full-length mariner elements and found evidence to suggest that they are inserted in the genome at a conserved region shared by other hymenopteran taxa. The association between mariner elements and fig wasps is old and dominated by vertical transmission, suggesting that these 'selfish genetic elements' have evolved to impart only very low costs to their hosts.

Therapy-induced antibodies to interferon-alpha 2a recognise its receptor-binding site.

Fifty-eight patients with chronic hepatitis B (HB) or C (HC) were treated with recombinant human interferon (rIFN)-alpha 2 and their sera were assayed for antibodies to rIFN-alpha 2c. Twelve of these patients produced low titres and two high titres of the antibodies. We localized the region which was recognised by the high-titre therapy-induced antibodies on the IFN molecule by testing the antibodies with a set of murine monoclonal antibodies (MoAbs) to IFN-alpha 2 in a competitive radioimmune assay (RIA). Only MoAbs with epitopes located in the amino-terminal portion of IFN-alpha 2 could inhibit the binding of radiolabelled IFN-alpha 2 by patients' sera. Our data indicate that the therapy-induced antibodies were directed to the receptor-binding domain of IFN-alpha 2 formed by amino acids (aa) 30-53. In accordance with this observation, human anti-IFN sera inhibited the binding of rIFN-alpha 2 to human cells.

Human endogenous retrovirus HC2 is a new member of the S71 retroviral subgroup with a full-length pol gene.

We have isolated and characterized a new human endogenous provirus, which is closely related to the human retrovirus S71, but unlike S71 has a full-length pol gene. Two degenerate oligonucleotide primers based on highly conserved motifs within the active sites of two retroviral proteins (the protease and reverse transcriptase) were designed and used for PCR. An amplified product of 847 bp in length, which showed significant homology to protease and reverse transcriptase of several retroviruses, was used for high stringency hybridization with a human genomic library. The MuLV-related endogenous retrovirus sequence, designated HC2, was isolated and completely sequenced. HC2 is a provirus with complete gag and pol genes and a 3' LTR; the 5' LTR and env gene are missing. The gag and pol genes appear complete, since they contain sequences homologous to the matrix protein, capsid protein, and nucleocapsid protein of gag and to the protease, reverse transcriptase, tether, RNase H, and integrase of pol. Phylogenetic analysis suggests that although HC2 and S71 are MuLV-related retroviruses, their characters are quite distinct, being placed outside of a clade containing most of the previously characterized MuLV-related retroviruses such as GaLV, FeLV, BaEV, and SSV/SSAV.

Characterization of a novel murine leukemia virus-related subgroup within mammals.

The murine leukemia virus (MuLV)-related retroviruses are one of seven genera which together constitute the family Retroviridae. They are widespread as both endogenous and exogenous agents within vertebrates and have been associated with a variety of malignancies and other disorders. We isolated and characterized 12 endogenous representatives of this genus from a number of mammalian hosts. Subsequent sequence analysis revealed that the isolated viruses cluster into two clearly distinct groups. All of the exogenous MuLV-related retroviruses which have been isolated to date, as well as several endogenous examples, fall into the first group, whereas the second group is represented solely by endogenous representatives, including human endogenous retrovirus type E (HERV.E). The two groups are widespread within mammals, with both often present within one animal species. Despite this, there is no evidence to date that recombination between members of the different groups has occurred. Genetic distances and several other properties of the HERV.E genome suggest that if exogenous members of this subgroup exist, they are likely to have biological properties different from those of the other exogenous viruses of this genus. Several of these viruses are known to have been integrated within their hosts' genomes for a long period of time, and a most recent divergence date for the MuLV and HERV.E subgroups can thus be proposed. This date, approximately 30 million years ago, is the most recent date possible, and it is probable that the actual period of time since their divergence is significantly longer.

Easel, a gypsy LTR-retrotransposon in the Salmonidae.

Despite the close similarities between retroviruses and the gypsy/Ty3 group of LTR-retrotransposons their host ranges are largely distinct: the retroviruses are found only in vertebrates, whereas the gypsy LTR-retrotransposons are almost exclusively restricted to invertebrates, plants and fungi. Here we report the amplification by PCR, and characterisation, of one of the first LTR-retrotransposons to be discovered in vertebrates--in several members of the piscine family Salmonidae. Phylogenetic analysis of this retroelement, termed easel, indicates that it is probably a phylogeneticaly basal member of the gypsy group of LTR-retrotransposons and occurs in some of the same species from which retroviruses have previously been isolated. Thus some members of the Salmonidae are the first organisms known to harbour both retroviral branch elements and the gypsy LTR-retrotransposon branch elements. This creates an overlap in the host ranges of the two retroelement families.

Interferon alpha2b is the predominant subvariant detected in human genomic DNAs.

Chromosomal DNAs isolated from eight individuals from the Slovak population and from lymphoblastoid Namalwa cells were analyzed for the presence of genes coding for three subvariants of human interferon-alpha 2 (IFN-alpha 2), namely a, b, and c. The respective genes are regarded allelic, because they differ in the coding nucleotide sequence only at the position 137 (a:A, b/c:G) and/or at the position 171 (a/b:A, c:G). IFN-alpha 2 sequences in genomes were selectively amplified using polymerase chain reaction (PCR). Resulting "consensus" PCR-product (the total mixture of PCR-derived clones) was sequenced and the subvariant-specific nucleotides at position 137 and 171 were determined. In one placental genomic DNA and in a mixture of genomic DNAs from leukocytes of seven donors only nucleotides specific for subvariant IFN-alpha 2b could be detected. This suggests that the placental DNA contained only genes coding for IFN-alpha 2b and these alleles were at least prevailing in donor's genomes. On the other hand, the majority of genomic alpha 2-sequences in Namalwa cells (from which IFN-alpha 2c was originally derived), seems to be corresponding to subvariant IFN-alpha 2c.