Isolation and regional localization of a large collection (2,000) of single-copy DNA fragments on human chromosome 3 for mapping and cloning tumor suppressor genes

Summary A collection of 2,000 lambda phage-carrying human single-copy inserts (> 700 bp) were isolated from two chromosome-3 flow-sorted libraries. The single-copy DNA fragments were first sorted into 3p and 3q locations and about 700 3p fragments were regionally mapped using a deletion mapping panel comprised of two humanhamster and two-human-mouse cell hybrids, each containing a chromosome 3 with different deletions in the short arm. The hybrids were extensively mapped with a set of standard 3p markers physically localized or ordered by linkage. The deletion mapping panel divided the short arm into five distinct subregions (A-E). The 3p fragments were distributed on 3p regions as follows: region A, 26%; B, 31%; C, 4%; D, 4% and E, 35%. We screened 300 single-copy DNA fragments from the distal part of 3p (regions A and B) with ten restriction endonucleases for their ability to detect restriction fragment length polymorphisms (RFLPs). Of these fragments 110 (36%) were found to detect useful RFLPs: 35% detected polymorphisms with frequency of heterozygosity of 40% or higher, and 25% with frequency of 30% or higher. All polymorphisms originated from single loci and most of them were of the base pair substitution type. These RFLP markers make it possible to construct a fine linkage map that will span the distal part of chromosome 3p and encompasses the von Hippel-Lindau disease locus. The large number of single-copy fragments (2,000) spaced every 100–150 kb on chromosome 3 will make a significant contribution to mapping and sequencing the entire chromosome 3. The 300 conserved chromosome 3 probes will increase the existing knowledge of man-mouse homologies.     

Nuclear localization of TRK-A in liver cells

The liver represents a site of expression of neurotrophins and their receptors. We have characterized the expression and intracellular localization of the nerve growth factor (NGF) receptor, Trk-A, in liver cells in vivo and in vitro. In both normal and fibrotic liver tissue, Trk-A immunostaining was present in different cell types, including parenchymal cells and cells of the inflammatory infiltrate. In hepatocytes and activated stellate cells (HSC), Trk-A showed a predominant nuclear localization, both in the presence and absence of injury. In cultured HSC, Trk-A was found to be functional, because exposure of the cells to recombinant NGF resulted in stimulation of cell migration and activation of intracellular signaling pathways, including Ras-ERK and PI3K/Akt. Remarkably, in cultured HSC, Trk-A staining was found constitutively in the nucleus. In these cells, Trk-A could be stained only by antibodies directed against the intracellular domain but not by those recognizing the extracellular portion of Trk-A suggesting that the intracellular portion of the receptor is the major determinant of nuclear Trk-A staining. In contrast to HSC, freshly isolated hepatocytes did not show any nuclear localization of the intracellular portion of Trk-A. In pheocromocytoma cells, nuclear staining for Trk-A was not present in conditions of serum deprivation, but could be induced by exposure to NGF or to a mixture of soluble mediators. We conclude that nuclear localization of the intracellular domain of Trk-A is observed constitutively in liver cells such as HSC, while in other cell types it could be induced in response to soluble factors.     

Climate change at northern latitudes: rising atmospheric humidity decreases transpiration, N-uptake and growth rate of hybrid aspen

At northern latitudes a rise in atmospheric humidity and precipitation is predicted as a consequence of global climate change. We studied several growth and functional traits of hybrid aspen (Populus tremula L.×P. tremuloides Michx.) in response to elevated atmospheric humidity (on average 7% over the ambient level) in a free air experimental facility during three growing seasons (2008-2010) in Estonia, which represents northern temperate climate (boreo-nemoral zone). Data were collected from three humidified (H) and three control (C) plots, and analysed using nested linear models. Elevated air humidity significantly reduced height, stem diameter and stem volume increments and transpiration of the trees whereas these effects remained highly significant also after considering the side effects from soil-related confounders within the 2.7 ha study area. Tree leaves were smaller, lighter and had lower leaf mass per area (LMA) in H plots. The magnitude and significance of the humidity treatment effect - inhibition of above-ground growth rate - was more pronounced in larger trees. The lower growth rate in the humidified plots can be partly explained by a decrease in transpiration-driven mass flow of NO(3) (-) in soil, resulting in a significant reduction in the measured uptake of N to foliage in the H plots. The results suggest that the potential growth improvement of fast-growing trees like aspens, due to increasing temperature and atmospheric CO(2) concentration, might be smaller than expected at high latitudes if a rise in atmospheric humidity simultaneously takes place.     

Biostimulation and Bioaugmentation of Anaerobic Pentachlorophenol Degradation in Contaminated Soils

The effects of bioaugmentation with a pentachlorophenol (PCP)-adapted consortium and biostimulation with glucose as a carbon source on anaerobic bioremediation of PCP-contaminated soil were investigated in terms of the initial PCP removal rate and the extent of PCP dechlorination and mineralization. Samples from two PCP-contaminated sites were prepared, put into a series of Hungate tubes, inoculated, and fed under different conditions. Chlorophenols in the tubes were monitored over a 4-month period to measure PCP transformation in the soil. In less contaminated soil (10 mg PCP/kg soil), it was found that biostimulation with glucose at 1 g/kg soil or bioaugmentation at 0.14 g volatile suspended solids (VSS)/kg soil could greatly improve PCP degradation. The best PCP degradation was obtained when both bioaugmentation and biostimulation were applied, but higher levels of glucose (2 g/kg soil) or inoculum (0.56 g VSS/kg soil) had little additional effect. The highest initial PCP-removal rate reached 8.1 μmol/kg soil-d, which is almost 20 times greater than in the unamended controls. PCP was dechlorinated to lesser chlorinated phenols with 0.6 chlorine remaining on average, and the extent of mineralization approached 70% in 4 months. In highly PCP-contaminated soil (90 mg PCP/kg soil), PCP degradation was partially inhibited, but the relative effects of augmentation, stimulation, and combined treatments were the same as in the less contaminated soil.     

Characterization, mapping, and distribution of the two XMRV parental proviruses

Xenotropic murine leukemia virus-related virus (XMRV) was previously reported to be associated with human prostate cancer and chronic fatigue syndrome. Our groups recently showed that XMRV was created through recombination between two endogenous murine retroviruses, PreXMRV-1 and PreXMRV-2, during the passaging of a prostate tumor xenograft in nude mice. Here, multiple approaches that led to the identification of PreXMRV-2, as well as the distribution of both parental proviruses among different mouse species, are described. The chromosomal loci of both proviruses were determined in the mouse genome, and integration site information was used to analyze the distribution of both proviruses in 48 laboratory mouse strains and 46 wild-derived strains. The strain distributions of PreXMRV-1 and PreXMRV-2 are quite different, the former being found predominantly in Asian mice and the latter in European mice, making it unlikely that the two XMRV ancestors could have recombined independently in the wild to generate an infectious virus. XMRV was not present in any of the mouse strains tested, and among the wild-derived mouse strains analyzed, not a single mouse carried both parental proviruses. Interestingly, PreXMRV-1 and PreXMRV-2 were found together in three laboratory strains, Hsd nude, NU/NU, and C57BR/cd, consistent with previous data that the recombination event that led to the generation of XMRV could have occurred only in the laboratory. The three laboratory strains carried the Xpr1(n) receptor variant nonpermissive to XMRV and xenotropic murine leukemia virus (X-MLV) infection, suggesting that the xenografted human tumor cells were required for the resulting XMRV recombinant to infect and propagate.     

Extinction debt in a common grassland species: immediate and delayed responses of plant and population fitness

Changes in landscape structure and environmental conditions due to habitat fragmentation can have significant effects on plant populations. Decreasing genetic diversity and changing population structure can reduce plant fitness and influence the long-term persistence of populations. Dry calcareous grasslands in Estonia have witnessed a large decline in area within the last 80 years, but due to extinction debt, the species richness in these grasslands has not yet responded to this decline. In these calcareous grasslands, we studied genetic diversity, phenotypic performance and population characteristics of a common habitat-specialist grass, Briza media. A decrease in genetic diversity was associated with a decrease in plant reproductive output. In addition, we found that some fitness components of B. media showed a delayed response to landscape changes. Specifically, plant height and germination success were related to historical rather than to current landscape parameters, indicating a time-lagged response of plant performance to habitat fragmentation. Dependence on historical landscape structure may thus result in a future decline in population fitness even if habitat loss and fragmentation no longer continue. The documented effect of current environmental conditions, however, shows that fitness-related traits are already slowly adapting to the changing conditions. Our results indicate that even common habitat-specialist species can be susceptible to landscape changes and be threatened by decreased population performance in the future.