Confirmation of the Dietary Background of Beef from its Stable Isotope Signature

End of project reportConsumers are increasingly demanding information on the authenticity and source of the food they purchase. Molecular DNA-based technology allows animal identification, but without certification or a “paper-trail” but does not provide information about feed history or the production system under which the animal was reared. The stable isotopes of chemical elements (e.g.13C/12C, 15N/14N) are naturally present in animal tissue and reflect the isotopic composition of the diet. The overall aim of this project was to determine the feasibility of using the stable isotopic composition as an intrinsic, biochemical marker to gain information about feed components used in the production of beef. Factors likely to affect the isotopic signature such as source of tissue, duration of feeding and production systems were examined. It is expected that this highly innovative and original technique will permit the identification of country of origin and dietary history of beef and so greatly assist efforts to market Irish beef, particularly in lucrative European markets. Sequential sampling and stable isotope analysis of bovine tail hair and hoof revealed that the two tissues can provide a detailed and continuous record of animal dietary history. Because hair can be sampled repeatedly and noninvasively, we anticipate that this approach will also prove useful for the investigation of short-term wildlife movements and changes in dietary preferences

Southern hemispheric halon trends and global halon emissions, 1978–2011

The atmospheric records of four halons, H-1211 (CBrClF2), H-1301 (CBrF3), H-2402 (CBrF2CBrF2) and H-1202 (CBr2F2), measured from air collected at Cape Grim, Tasmania, between 1978 and 2011, are reported. Mixing ratios of H-1211, H-2402 and H-1202 began to decline in the early to mid-2000s, but those of H-1301 continue to increase up to mid-2011. These trends are compared to those reported by NOAA (National Oceanic and Atmospheric Administration) and AGAGE (Advanced Global Atmospheric Experiment). The observations suggest that the contribution of the halons to total tropospheric bromine at Cape Grim has begun to decline from a peak in 2008 of about 8.1 ppt. An extrapolation of halon mixing ratios to 2060, based on reported banks and predicted release factors, shows this decline becoming more rapid in the coming decades, with a contribution to total tropospheric bromine of about 3 ppt in 2060. Top-down global annual emissions of the halons were derived using a two-dimensional atmospheric model. The emissions of all four have decreased since peaking in the late 1980s–mid-1990s, but this decline has slowed recently, particularly for H-1301 and H-2402 which have shown no decrease in emissions over the past five years. The UEA (University of East Anglia) top-down model-derived emissions are compared to those reported using a top-down approach by NOAA and AGAGE and the bottom-up estimates of HTOC (Halons Technical Options Committee). The implications of an alternative set of steady-state atmospheric lifetimes are discussed. Using a lifetime of 14 yr or less for H-1211 to calculate top-down emissions estimates would lead to small, or even negative, estimated banks given reported production data. Finally emissions of H-1202, a product of over-bromination during the production process of H-1211, have continued despite reported production of H-1211 ceasing in 2010. This raises questions as to the source of these H-1202 emissions

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)

Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.

Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. 

Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. 

MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.

MTB is supported by NCI grant CA089713

Prior chemotherapy does not prevent effective mobilisation by G-CSF of peripheral blood progenitor cells.

In this study we demonstrate that the hemopoietic growth factor, G-CSF successfully mobilised progenitor cell populations into the peripheral blood in a population of patients despite intensive pretreatment with chemotherapy. Administration of G-CSF increased the numbers of peripheral blood progenitor cells (PBPC) by a median of 76-fold above basal levels. Maximal levels of PBPC were observed on days 5 and 6 after G-CSF treatment. In two patients a second cycle of G-CSF mobilised PBPC to levels comparable with those seen after the first cycle of G-CSF treatment. An earlier hemopoietic cell population (pre-CFC's) was also mobilised with levels increased up to 50-fold above basal levels. Using a standard mononuclear cell leukapheresis technique the PBPC were collected extremely efficiently (essentially 100%) and could be further successfully enriched by separation using a Ficoll gradient. For patients who underwent the optimal collection protocol (i.e. leukapheresis on days 5, 6 and 7) a total of 32 +/- 6 x 10(4) GM-CFC kg-1 were collected. The ability to mobilise PBPC using G-CSF alone and to successfully and efficiently harvest these cells has important implications for the future of transplantation and high dose chemotherapy procedures

Strained tetragonal states and Bain paths in metals

Paths of tetragonal states between two phases of a material, such as bcc and fcc, are called Bain paths. Two simple Bain paths can be defined in terms of special imposed stresses, one of which applies directly to strained epitaxial films. Each path goes far into the range of nonlinear elasticity and reaches a range of structural parameters in which the structure is inherently unstable. In this paper we identify and analyze the general properties of these paths by density functional theory. Special examples include vanadium, cobalt and copper, and the epitaxial path is used to identify an epitaxial film as related uniquely to a bulk phase.Comment: RevTeX, 4 pages, 4 figures, submitted to Phys. Rev. Let

White-Tailed Deer are a Biotic Filter During Community Assembly, Reducing Species and Phylogenetic Diversity

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H′), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H′ and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly

Structural and Magnetic Properties of Trigonal Iron

First principles calculations of the electronic structure of trigonal iron were performed using density function theory. The results are used to predict lattice spacings, magnetic moments and elastic properties; these are in good agreement with experiment for both the bcc and fcc structures. We find however, that in extracting these quantities great care must be taken in interpreting numerical fits to the calculated total energies. In addition, the results for bulk iron give insight into the properties of thin iron films. Thin films grown on substrates with mismatched lattice constants often have non-cubic symmetry. If they are thicker than a few monolayers their electronic structure is similar to a bulk material with an appropriately distorted geometry, as in our trigonal calculations. We recast our bulk results in terms of an iron film grown on the (111) surface of an fcc substrate, and find the predicted strain energies and moments accurately reflect the trends for iron growth on a variety of substrates.Comment: 11 pages, RevTeX,4 tar'd,compressed, uuencoded Postscript figure

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm⁵U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G₁ and G₂, and that mcm⁵U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm⁵U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9Δ cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9Δ cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.National Institute of Environmental Health Sciences (R01 ES015037)National Institute of Environmental Health Sciences (R01 ES017010)National Institute of Environmental Health Sciences (P30 ES002109)Massachusetts Institute of Technology (Westaway Fund)Singapore-MIT Alliance for Research and Technolog

The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA

BACKGROUND: Upon exposure to agents that damage DNA, Saccharomyces cerevisiae undergo widespread reprogramming of gene expression. Such a vast response may be due not only to damage to DNA but also damage to proteins, RNA, and lipids. Here the transcriptional response of S. cerevisiae specifically induced by DNA damage was discerned by exposing S. cerevisiae to a panel of three "radiomimetic" enediyne antibiotics (calicheamicin γ(1)(I), esperamicin A1 and neocarzinostatin) that bind specifically to DNA and generate varying proportions of single- and double-strand DNA breaks. The genome-wide responses were compared to those induced by the non-selective oxidant γ-radiation. RESULTS: Given well-controlled exposures that resulted in similar and minimal cell death (~20–25%) across all conditions, the extent of gene expression modulation was markedly different depending on treatment with the enediynes or γ-radiation. Exposure to γ-radiation resulted in more extensive transcriptional changes classified both by the number of genes modulated and the magnitude of change. Common biological responses were identified between the enediynes and γ-radiation, with the induction of DNA repair and stress response genes, and the repression of ribosomal biogenesis genes. Despite these common responses, a fraction of the response induced by gamma radiation was repressed by the enediynes and vise versa, suggesting that the enediyne response is not entirely "radiomimetic." Regression analysis identified 55 transcripts with gene expression induction associated both with double- or single-strand break formation. The S. cerevisiae "DNA damage signature" genes as defined by Gasch et al. [1] were enriched among regulated transcripts associated with single-strand breaks, while genes involved in cell cycle regulation were associated with double-strand breaks. CONCLUSION: Dissection of the transcriptional response in yeast that is specifically signaled by DNA strand breaks has identified that single-strand breaks provide the signal for activation of transcripts encoding proteins involved in the DNA damage signature in S. cerevisiae, and double-strand breaks signal changes in cell cycle regulation genes