Chromatin structure analysis enables detection of DNA insertions into the mammalian nuclear genome

BackgroundGenetically modified organisms (GMOs) have numerous biomedical, agricultural and environmental applications. Development of accurate methods for the detection of GMOs is a prerequisite for the identification and control of authorized and unauthorized release of these engineered organisms into the environment and into the food chain. Current detection methods are unable to detect uncharacterized GMOs, since either the DNA sequence of the transgene or the amino acid sequence of the protein must be known for DNA-based or immunological-based detection, respectively.MethodsHere we describe the application of an epigenetics-based approach for the detection of mammalian GMOs via analysis of chromatin structural changes occurring in the host nucleus upon the insertion of foreign or endogenous DNA.ResultsImmunological methods combined with DNA next generation sequencing enabled direct interrogation of chromatin structure and identification of insertions of various size foreign (human or viral) DNA sequences, DNA sequences often used as genome modification tools (e.g. viral sequences, transposon elements), or endogenous DNA sequences into the nuclear genome of a model animal organism.ConclusionsThe results provide a proof-of-concept that epigenetic approaches can be used to detect the insertion of endogenous and exogenous sequences into the genome of higher organisms where the method of genetic modification, the sequence of inserted DNA, and the exact genomic insertion site(s) are unknown.General significanceMeasurement of chromatin dynamics as a sensor for detection of genomic manipulation and, more broadly, organism exposure to environmental or other factors affecting the epigenomic landscape are discussed.     

An LTC4 binding site in gastric mucosa is shared with glutathione

Recent results from our laboratory and others have suggested a possible physiological functional role(s) for leukotrienes in gastric mucosa. In the present study 3H-LTC4 binds to washed rabbit gastric mucosal membranes at 4 degrees C with a Kd of 5 nM and a Bmax of 31.3 pmol/mg protein. Leukotrienes D4, E4, B4, oxidized glutathione (GSSG), cysteine, and mercaptoethanol were unable to displace 3H-LTC4 at 1 microM concentrations, while GSH inhibited binding with a Ki of 47 nM. Differential centrifugation of the membrane preparation to remove mitochondria resulted in Ki values for LTC4 and GSH of 14 and 23 nM, respectively. The similar binding affinities and competitive receptor binding kinetics for GSH and LTC4, the low affinity for other leukotrienes, and a Ki of 7 microM for hematin, a substrate for glutathione S-transferase, suggest that 3H-LTC4 binds to a GSH site which does not discriminate between LTC4 and GSH. Membranes fractionated to remove mitochondria were assayed for glutathione peroxidase, gamma-glutamyltranspeptidase, and glutathione S-transferase as possible binding sites for LTC4. We were unable to detect enzyme activity for any of the three enzymes. The binding of LTC4 in gastric mucosa differs from other tissues with respect to the high affinity for GSH, and thus becomes an appropriate tissue in which to investigate the relationships between LTC4 and GSH.     

Estimating global "blue carbon" emissions from conversion and degradation of vegetated coastal ecosystems

Recent attention has focused on the high rates of annual carbon sequestration in vegetated coastal ecosystems-marshes, mangroves, and seagrasses-that may be lost with habitat destruction ('conversion'). Relatively unappreciated, however, is that conversion of these coastal ecosystems also impacts very large pools of previously-sequestered carbon. Residing mostly in sediments, this 'blue carbon' can be released to the atmosphere when these ecosystems are converted or degraded. Here we provide the first global estimates of this impact and evaluate its economic implications. Combining the best available data on global area, land-use conversion rates, and near-surface carbon stocks in each of the three ecosystems, using an uncertainty-propagation approach, we estimate that 0.15-1.02 Pg (billion tons) of carbon dioxide are being released annually, several times higher than previous estimates that account only for lost sequestration. These emissions are equivalent to 3-19% of those from deforestation globally, and result in economic damages of $US 6-42 billion annually. The largest sources of uncertainty in these estimates stems from limited certitude in global area and rates of land-use conversion, but research is also needed on the fates of ecosystem carbon upon conversion. Currently, carbon emissions from the conversion of vegetated coastal ecosystems are not included in emissions accounting or carbon market protocols, but this analysis suggests they may be disproportionally important to both. Although the relevant science supporting these initial estimates will need to be refined in coming years, it is clear that policies encouraging the sustainable management of coastal ecosystems could significantly reduce carbon emissions from the land-use sector, in addition to sustaining the well-recognized ecosystem services of coastal habitats.     

Antibodies designed as effective cancer vaccines

Antigen/antibody complexes can efficiently target antigen presenting cells to allow stimulation of the cellular immune response. Due to the difficulty of manufacture and their inherent instability complexes have proved inefficient cancer vaccines. However, anti-idiotypic antibodies mimicking antigens have been shown to stimulate both antibody and T cell responses. The latter are due to T cell mimotopes expressed within the complementarity-determining regions (CDRs) of antibodies that are efficiently presented to dendritic cells in vivo. Based on this observation we have designed a DNA vaccine platform called ImmunoBody™, where cytotoxic T lymphocyte (CTL) and helper T cell epitopes replace CDR regions within the framework of a human IgG1 antibody. The ImmunoBody™ expression system has a number of design features which allow for rapid production of a wide range of vaccines. The CDR regions of the heavy and light chain have been engineered to contain unique restriction endonuclease sites, which can be easily opened, and oligonucleotides encoding the T cell epitopes inserted. The variable and constant regions of the ImmunoBody™ are also flanked by restriction sites, which permit easy exchange of other IgG subtypes. Here we show a range of T cell epitopes can be inserted into the ImmunoBody™ vector and upon immunization these T cell epitopes are efficiently processed and presented to stimulate high frequency helper and CTL responses capable of anti-tumor activity.Key words: DNA vaccines, cancer vaccines, melanoma, CTL, helper T cells     

Decreased DNA repair rates and protection from heat induced apoptosis mediated by electromagnetic field exposure

In this study, we demonstrate that electromagnetic field (EMF) exposure results in protection from heat induced apoptosis in human cancer cell lines in a time dependent manner. Apoptosis protection was determined by growing HL-60, HL-60R, and Raji cell lines in a 0.15 mT 60 Hz sinusoidal EMF for time periods between 4 and 24 h. After induction of apoptosis, cells were analyzed by the neutral comet assay to determine the percentage of apoptotic cells. To discover the duration of this protection, cells were grown in the EMF for 24 h and then removed for 24 to 48 h before heat shock and neutral comet assays were performed. Our results demonstrate that EMF exposure offers significant protection from apoptosis (P<.0001 for HL-60 and HL-60R, P<.005 for Raji) after 12 h of exposure and that protection can last up to 48 h after removal from the EMF. In this study we further demonstrate the effect of the EMF on DNA repair rates. DNA repair data were gathered by exposing the same cell lines to the EMF for 24 h before damaging the exposed cells and non-exposed cells with H2O2. Cells were allowed to repair for time periods between 0 and 15 min before analysis using the alkaline comet assay. Results showed that EMF exposure significantly decreased DNA repair rates in HL-60 and HL-60R cell lines (P<.001 and P<.01 respectively), but not in the Raji cell line. Importantly, our apoptosis results show that a minimal time exposure to an EMF is needed before observed effects. This may explain previous studies showing no change in apoptosis susceptibility and repair rates when treatments and EMF exposure were administered concurrently. More research is necessary, however, before data from this in vitro study can be applied to in vivo systems.     

The Troyer syndrome (SPG20) protein spartin interacts with Eps15

The hereditary spastic paraplegias comprise a group of inherited neurological disorders in which the primary manifestation is spastic weakness of the lower extremities. Troyer syndrome is an autosomal recessive form of spastic paraplegia caused by a frameshift mutation in the spartin (SPG20) gene. Currently, neither the localization nor the functions of the spartin protein are known. In this study, we generated anti-spartin antibodies and found that spartin is both cytosolic and membrane-associated. Using a yeast two-hybrid approach, we screened an adult human brain library for binding partners of spartin. We identified Eps15, a protein known to be involved in endocytosis and the control of cell proliferation. This interaction was confirmed by fusion protein "pull-down" experiments as well as a cellular redistribution assay. Our results suggest that spartin might be involved in endocytosis, vesicle trafficking, or mitogenic activity, and that impairment in one of these processes may underlie the long axonopathy in patients with Troyer syndrome.     

The dinucleotide (CA) repeat polymorphism of estrogen receptor beta but not the dinucleotide (TA) repeat polymorphism of estrogen receptor alpha is associated with venous ulceration

Venous ulcers are the predominant form of chronic wound in the elderly, accounting for around 70% of all cases. The steroid sex hormone estrogen plays a crucial role in normal human skin maintenance and during cutaneous wound repair following injury. Estrogen can reverse age-related impaired wound healing by dampening the inflammatory response and increasing matrix deposition at the wound site. The molecular actions of estrogen are mediated through two nuclear sex steroid hormone receptors, estrogen receptor alpha (ERalpha) and beta (ERbeta). We have conducted a case-control study to investigate whether dinucleotide repeat polymorphisms in the estrogen receptor genes are associated with venous ulceration in the UK Caucasian population. Genomic fragments containing the ERalpha dinucleotide (TA)(n) repeat polymorphism or the ERbeta dinucleotide (CA)(n) repeat polymorphism were amplified by polymerase chain reaction in subject DNA samples and genotyped according to fragment length by capillary electrophoresis. There was no evidence to suggest that the TA repeat polymorphism of ERalpha was associated with venous ulceration. However, the CA*18 allele of the ERbeta CA repeat polymorphism was significantly associated with venous ulceration (n = 120, OR = 1.8, 95% CI = 1.1-2.8, P = 0.02). When the CA repeats alleles were grouped together into either low (L < or = 18) or high (H > 18) numbers of CA repeats, the low (L) repeat allele was significantly associated with venous ulceration (OR = 1.5, 95% CI = 1.0-2.2, P = 0.03). Our results show that a specific ERbeta variant is associated with impaired healing in the elderly, predisposing individuals to venous ulceration.     

Factors affecting seed germination and seedling establishment of a long-lived desert shrub (<Emphasis Type="Italic">Coleogyne ramosissima</Emphasis>: Rosaceae)

Long-lived desert shrubs exhibit infrequent, episodic recruitment from seed. In spite of this long time scale, selection on life history attributes that affect seedling recruitment should be strong. We studied factors affecting germination phenology and seedling establishment for Coleogyne ramosissima, a dominant shrub species in the ecotone between warm and cold deserts in western North America. We also examined ecotypic differentiation in establishment strategy in response to selection regimes in two contrasting habitats. We followed patterns of dormancy loss, germination, emergence, and survival in reciprocal field experiments at warm winter Mojave Desert and cold winter Colorado Plateau study sites. Seed germination took place in late winter, under winter rain conditions at the warm desert site and under snow at the cold desert site. Distinctive germination phenologies for the two seed populations at contrasting field sites followed predictions based on laboratory germination experiments. There was no seed bank carryover across years. Seedling survival at the end of three growing seasons was remarkably high (mean survival 54%). Most seedling mortality was due to sprout predation by rodents early the first spring in unprotected caches. Emergence and establishment at each site were significantly higher for seeds from the local population, supporting the idea of ecotypic differentiation in establishment strategy. Establishment success was an order of magnitude greater overall at the Colorado Plateau site, which represents the leading edge of an upward elevational shift in distribution for this species under the current climatic regime. The Mojave Desert site is on the trailing edge of this shift, and recruitment there is apparently a much less frequent occurrence.