Breast cancer risk and heterocyclic amines and effect modification by NAT gene polymorphisms

Breast cancer is the most common cancer in women in the United States and is a leading cause of cancer-related deaths (1). Recently, dietary heterocyclic amines (HCAs) have been proposed to be a risk factor for breast cancer (2). This study uses the data collected for a case-control study conducted at the M.D. Anderson Cancer Center to assess the association between breast cancer risk and HCAs {2-amino-1-methyl-6-phenylimidazole [4,5-b] pyridine (PhIP), 2-amino-3,8-dimethylimidazo [4,5-f] quinoxaline (MeIQx), 2-amino-3,4,8-trimethylimidazo [4,5-f] quinoxaline (DiMeIQx) and mutagenicity of HCAs} and to examine if this association is modified by genetic polymorphisms of N-acetyl transferases (NAT1/NAT2). The NAT1/2 genotype was determined using Taqman technology. HCAs were estimated by using a meat preparation questionnaire on meat type, cooking method, and doneness, combined with a quantitative HCA database. Three hundred and fifty patients with breast cancer attending the Diagnostic Radiology Clinic at M. D. Anderson Cancer Center and fulfilling the eligibility criteria were compared to three hundred and fifty patients attending the same clinic for benign breast lesions to answer these questions. Logistic regression models were used to control for known risk factors and showed no statistically significant association between breast cancer versus benign breast cancer lesions and dietary intake of heterocyclic amines. There was no clear difference in their effect after subgroup analyses in different acetylator strata of NAT1/2 and no statistical interactions were found between NAT1/2 genotypes and HCAs, suggesting no effect modification by NAT1/2 acetylator status. These results suggest the need for further research to analyze if these null associations were because of the benign breast lesions sharing the risk factors with breast cancer or any other factors which haven't been explored yet.^

Modification of mutagen sensitivity by chemopreventive agents {\it in vitro\/}

The clinical application of chemopreventive agents is expected to prevent the appearance of cancer by arresting carcinogenesis or reversing it in the precancerous stages. The hypothesis of the present investigations was that chemopreventive agents (retinoids and antioxidant vitamins) may counteract the clastogenic effects of bleomycin in vitro in both lymphoblastoid cell lines and primary lymphocyte cultures and that a similar phenomenon can be detected in lymphocytes from individuals treated with 13-cis-retinoic acid. The efficacy of 13-cis-retinoic acid, n-(4-hydroxyphenyl)-retinamide, ascorbic acid, n-acetyl-l-cysteine, alpha-tocopherol, and alpha-tocopherol-acid succinate was tested against bleomycin-induced chromosomal breakage.^ The results provided direct evidence of the concentration-related protective effects of these agents against bleomycin-induced clastogenicity in cultures of human lymphoblastoid cell lines in vitro. Similar anticlastogenic protection was demonstrated with 13-cis-retinoic acid, ascorbic acid, n-acetyl-l-cysteine, and alpha-tocopherol-acid succinate in primary lymphocyte cultures in vitro. The in vitro anticlastogenic effect of 13-cis-retinoic acid was also demonstrated in lymphocyte cultures from peripheral blood samples from patients treated with this retinoid.^ An important consideration is that the concentrations used in the present investigations are comparable to those achieved in clinical situations.^ The in vitro anticlastogenic effect of these retinoids and antioxidants may constitute an important element of their chemopreventive properties. The results corroborate the hypothesis that these compounds may be effective in clinical chemoprevention trials. The bleomycin-assay may also be used as a short-term test to evaluate the antimutagenic effects of various agents. ^

2-methylthio-N$\sp6$-dimethylallyl modification of adenosine 37 of tRNAs in {\it Escherichia coli\/} K-12

The hypermodified, hydrophobic 2-methylthio-N$\sp6$-(dimethylallyl)-adenosine (ms${2{\cdot}6}\atop1$A) residue occurs $3\sp\prime$ to the anticodon in tRNA species that read codons beginning with U. The first step (i$\sp6$A37 formation) of this modification is catalyzed by dimethylallyl diphosphate:tRNA dimethyallyltransferase (EC 2.5.1.8), which is the product of the miaA gene. Subsequent steps were proposed to be catalyzed by MiaB and MiaC enzymes to complete the ms${2{\cdot}6}\atop1$A37 modification. The study of functions of the ms${2{\cdot}6}\atop1$A37 is very important because this modified base is one of the best candidates for a role in global control in response to environmental stress. This dissertation describes the further delineation of functions of the ms${2{\cdot}6}\atop1$A37 modification in E. coli K-12 cells. This work provides significant information on functions of tRNA modifications in E. coli cells to adapt to stressful environmental conditions. Three hypotheses were tested in this work.^ The first hypothesis tested was that non-optimal translation processes cause increased spontaneous mutagenesis by the induction of SOS response in starving cells. To test this hypothesis, I measured spontaneous mutation rates of wild type cells and various mutant strains which are defective in tRNA modification, SOS response, or oxidative damage repair. I found that the miaA mutation acts as a mutator that increased Lac$\sp+$ reversion rates and Trp$\sp+$ reversion frequencies of the wild-type cells in starving conditions. However, the lexA3(Ind)(which abolishes the induction of SOS response) mutation abolished the mutator phenotype of the miaA mutant. The recA430 mutation, not other identified SOS genes, decreased the Lac$\sp+$ reversion to a less extent than that of the lexA3(Ind) mutation. These results suggest that RecA together with another unidentified SOS gene product are responsible for the process.^ The second hypothesis tested was that MiaA protein binds to full-length tRNA$\sp{\rm Phe}$ molecules in form of a protein dimer. To test this hypothesis, three versions of the MiaA protein and seven species of tRNA substrates were purified. Binding studies by gel mobility shift assays, filter binding assays and gel filtration shift assays support the hypothesis that MiaA protein binds to full-length tRNA$\sp{\rm Phe}$ as a protein dimer but as a monomer to the anticodon stem-and-loop. These results were further supported by using steady state enzyme kinetic studies.^ The third hypothesis tested in this work was that the miaB gene in E. coli exists and is clonable. The miaB::Tn10dCm insertion mutation of Salmonella typhimurium was transduced to E. coli K-12 cells by using P$\sb1$ and P$\sb{22}$ bacteriophages. The insertion was confirmed by HPLC analyses of nucleotide profiles of miaB mutants of E. coli. The insertion mutation was cloned and DNA sequences adjacent to the transposon were sequenced. These DNA sequences were 86% identical to the f474 gene at 14.97 min chromosome of E. coli. The f474 gene was then cloned by PCR from the wild-type chromosome of E. coli. The recombinant plasmid complemented the mutant phenotype of the miaB mutant of E. coli. These results support the hypothesis that the miaB gene of E. coli exists and is clonable. In summary, functions of the ms${2{\cdot}6}\atop1$A37 modification in E. coli cells are further delineated in this work in perspectives of adaptation to stressful environmental conditions and protein:tRNA interaction. (Abstract shortened by UMI.) ^

Chemical Modification of Partially Hydrogenated Vegetable Oil to Improve its Functional Properties to Replace Petroleum Waxes

A novel, chemically-modified partially hydrogenated vegetable oil (PHVO) is described. The PHVO is produced by a three-step reaction process that includes epoxidation, a ringopening reaction, followed by esterification. The modified PHVO has improved kneadability and, if mixed with fully hydrogenated fat(s ), hardness comparable to umnodified PHVO.

Geochemistry and oxygen and iron isotope ratios of mafic rocks

Recycling of oceanic crust into the deep mantle via subduction is a widely accepted mechanism for creating compositional heterogeneity in the upper mantle and for explaining the distinct geochemistry of mantle plumes. The oxygen isotope ratios (d18O) of some ocean island basalts (OIB) span values both above and below that of unmetasomatised upper mantle (5.5 ± 0.4 per mil) and provide support for this hypothesis, as it is widely assumed that most variations in d18O are produced by near-surface low-temperature processes. Here we show a significant linear relationship between d18O and stable iron isotope ratios (d57Fe) in a suite of pristine eclogite xenoliths. The d18O values of both bulk samples and garnets range from values within error of normal mantle to significantly lighter values. The observed range and correlation between d18O and d57Fe is unlikely to be inherited from oceanic crust, as d57Fe values determined for samples of hydrothermally altered oceanic crust do not differ significantly from the mantle value and show no correlation with d18O. It is proposed that the correlated d57Fe and d18O variations in this particular eclogite suite are predominantly related to isotopic fractionation by disequilibrium partial melting although modification by melt percolation processes cannot be ruled out. Fractionation of Fe and O isotopes by removal of partial melt enriched in isotopically heavy Fe and O is supported by negative correlations between bulk sample d57Fe and Cr content and bulk sample and garnet d18O and Sc contents, as Cr and Sc are elements that become enriched in garnet- and pyroxene-bearing melt residues. Melt extraction could take place either during subduction, where the eclogites represent the residues of melted oceanic lithosphere, or could take place during long-term residence within the lithospheric mantle, in which case the protoliths of the eclogites could be of either crustal or mantle origin. This modification of both d57Fe and d18O by melting processes and specifically the production of low-d18O signatures in mafic rocks implies that some of the isotopically light d18O values observed in OIB and eclogite xenoliths may not necessarily reflect near-surface processes or components.

Geochemistry of recent sediments from the Indian Ocean

During the International Indian Ocean Expedition (1964/65) sediment cores were taken on six profiles off the western coast of the Indian Subcontinent. These profiles run approximately perpendicular to the coast, from the deep-sea over the continental slope to the continental shelf. Additional samples and cores were taken in a dense pattern in front of the delta of the Indus River. This pattern of sampling covered not only marine sediments, but also river and beach sediments in Pakistan. The marine samples were obtained with piston, gravity and box corers and by a Van Veen grab sampler. The longest piston core is about 5 meters long. 1. Distribution of the elements on the sediment surface The area of maximal carbonate values (aprox. 80-100% CaCO3) essentially coincides with the continental shelf. The highest Sr values were observed largely within this area, but only in the vicinity of the Gulf of Cambay. Mainly the aragonitic coprolites are responsible for those high Sr contents. The Mg contents of the carbonates are comparatively low; surprisingly enough the highest Mg concentrations were also measured in the coprolites. The maximum contents of organic matter (Core) were found along the upper part of the continental slope. They coincide with the highest porosity and water content of the sediments. Frequently the decomposition of organic matter by oxydation is responsible for the measured Corg contents. On the other side the quantity of originally deposited organic material is less important in most cases. The enrichment of the "bauxitophile" elements Fe, Ti, Cr and V in the carbonate- and quartz-free portions of the sediments is essentially due to the influence of coarse terrigenous detritus. For the elements Mn, Ni and Cu (in per cent of the carbonateand quartz-free sediment) a strong enrichment was observed in the deep-sea realm. The strong increase in Mn toward the deep-sea is explained by authigenesis of Mn-Fe-concretions. Mn-nodules form only under oxydizing conditions which obviously are possible only at very low rates of deposition. The Mg, B and, probably also Mn contents in the clay minerals increase with increasing distance from the continent. This can be explained by the higher adsorption of those elements from sea water because of increasing duration of the clay mineral transport. The comparison of median contents of some elements in our deep-sea samples with deep-sea sediments described by TUREKIAN & WEDEPOHL (1961) shows that clear differences in concentration exist only in the case of "bauxitophile" elements Cr and Be. The Cr and Be contents show a clear increase in the Indian Ocean deep-sea samples compared to those described by TUREKIAn & WEDEPOHL (1961) which can obviously be attributed to the enrichment in the lateritic and bauxitic parent rocks. The different behaviour of the elements Fe, Ti and Mn during decomposition of the source rocks, transport to the sea and during oxydizing and reducing conditions in the marine environment can be illustrated by Ti02/Fe and MnO/Fe ratios. The different compositions of the sediments off the Indus Delta and those of the remaining part of the area investigated are characterized by a different distribution of the elements Mn and Ti. 2. Chemical inhomogenities in the sediments Most longer cores show 3 intervals defined by chemical and sedimentological differences. The top-most interval is coarse-grained, the intermedial interval is fine grained and the lower one again somewhat coarser. At the same time it is possible to observe differences from interval to interval in the organogenic and detrital constituents. During the formation of the middle interval different conditions of sedimentation from those active during the previous and subsequent periods have obviously prevailed. Looking more closely at the organogenic constituents it is remarkable that during the formation of the finer interval conditions of a more intensive oxydation have prevailed that was the case before and after: Core decreases, whereas P shows a relative increase. This may be explained by slower sedimentation rate or by a vertical migration of the oxygen rich zone of the sea-water. The modifications of the elements from minerals in detrital portion of the sediments support an explanation ascribing this fact to modifications of the conditions of denudation and transportation which can come about through a climatic change or through tectonic causes. The paleontological investigations have shown (ZOBEL, in press) that in some of the cores the middle stratum of fine sedimentation represents optimal conditions for organic life. This fact suggests also oxydizing conditions during the sedimentation of this interval. In addition to the depositional stratification an oxydation zone characterized by Mn-enrichment can be recognized. The thickness of the oxidation zone decreases towards the coast and thins out along the middle part of the continental slope. At those places, where the oxydation zone is extremely thin, enrichment of Mn has its maximum. This phenomenon can probably be attributed to the migration of Mn taking place in its dissociated form within the sediment under reducing conditions. On the other side this Mn-migration in the sediment does not take place in the deep-sea, where oxydizing conditions prevail. 3. Interstitial waters in the sediments Already at very small core depths, the interstitial waters have undergone a distinct modification compared with the overlying sea water. This distinct modification applies both to total salinity and to the individual ions. As to the beginning of diagenesis the following conclusions can be drawn: a) A strong K-increase occurs already at an early stage. It may be attributable to a diffusion barrier or to an exchange of Mg-ions on the clays. Part of this increase may also originate from the decomposition of K-containing silicates (mica and feldspars). A K-decrease owing to the formation of illite (WEAVER 1967), however, occurs only at much greater sediment depth. b) Because of an organic protective coating, the dissolution of carbonate is delayed in recent organogenic carbonates. At the same time some Ca is probably being adsorbed on clay minerals. Consequently the Ca-content of the interstitial water drops below the Ca-content of the sea water. c) Already at an early stage the Mg adsorption on the clays is completed. The adsorbed Mg is later available for diagenetic mineral formations and transformations.

Geochemistry at DSDP Leg 74 Holes

Clay mineralogical and inorganic geochemical data from the Campanian to the Pleistocene provide information bearing on the evolution of both continental and marine paleoenvironments in the Walvis Ridge area. (1) Alteration processes of basalts occurred under subaerial conditions during the Campanian and Maestrichtian and were virtually absent in deeper marine environments. (2) Strong tectonic effects were present during the Campanian and persisted until the early Eocene. (3) Subsidence of this part of the Walvis Ridge became important during the late Maestrichtian and continued into the Paleocene and Eocene. (4) The influence of global climatic cooling was evident from the late Eocene on. (5) Modification of oceanic circulation and the increasing influence of surface and deep water masses on the sedimentation characterized the Cenozoic.

Chemistry of altered basalts from ODP Hole 123-765D

Volcanic basement recovered at Hole 765D is characterized by nonpervasive, oxidative alteration, typical of seafloor weathering. Chilled margins and the mesostasis of the lavas are variably altered to assemblages of celadonite, Fe-oxyhydroxides, zeolites, and calcite with trace saponite. Plagioclase is partially altered to Ca-Na zeolites and/or albite. Well-developed alteration halos parallel fracture surfaces and extend several centimeters into the surrounding rock. These clay-rich halos are enriched in K2O and Fe2O3 relative to the adjacent clay-poor rock. The halos and adjacent rock are characterized by d18O values 2 per mil-3 per mil higher than those of fresh MORB. The "freshness" of the samples and the scarcity of saponite suggest that the duration of seawater circulation was short-lived. Albitization of plagioclase indicates that the volcanic rocks were altered initially at low temperatures and were subsequently reheated off-axis in a closed environment. Reheating did not result in significant modification of the bulk composition of the crust.

Mineral composition and geochemistry of sediments from ODP Leg 127 sites

The lithostratigraphy of Neogene hemipelagic sediments recovered from the Japan Sea during Leg 127 was revised to improve intersite consistency and to remove confusion stemming from diagenetic modification of the lithology through the opal-A to opal-CT transformation. Special emphasis was put on the presence and nature of dark-light cycles in revising the lithostratigraphy. Mineral composition analysis was conducted for samples from Sites 794, 795, and 797. In addition, major element chemical composition analysis was conducted for these same sample sets from Site 794. The result of mineral composition analysis suggests that the detrital component, which consists of such minerals as quartz, plagioclase, illite, and kaolinite plus chlorite, is diluted to various degrees by biogenic silica (opal-A) and its diagenetic equivalents (opal-CT and quartz). Smectite, on the other hand, may be a diagenetic or hydrothermal alteration product of volcanic material, although more study is necessary to confirm its origin. As a whole, vertical variation in the sediment composition is consistent with the revised lithostratigraphy and helps to characterize the redefined lithologic units quantitatively.

Chemical composition of upper Cenozoic at DSDP Leg 70 Holes

The hydrothermal deposits that we analyzed from Leg 70 are composed of ferruginous green clays and fragments of manganese-hydroxide crust. Data from X-ray diffraction, IR-spectroscopy, electron diffraction, and chemical analyses indicate that the hydrothermal green clays are composed of disordered mixed-layer phases of celadonite-nontronite. Electron diffraction shows that the parameters of the unit cells and the degree of three-dimensional ordering of mixed-layer phases with 80% celadonite interlayers are very close to Fe-micas of polymorphic modification IM-celadonite. In some sections, there is a tendency for the number of celadonite layers to increase with depth. The manganese-hydroxide crust fragments are predominantly composed of todorokite (buserite). An essential feature of hydrothermal accumulation is the sharp separation of Fe and Mn. Ba/Ti and Ba/Sr ratios are typical indicators of hydrothermal deposits. Sediments composing the hydrothermal mounds were deposited from moderately heated waters, which had extracted the components from solid basalts in environments where there were considerable gradients of temperature, eH, and pH. The main masses of Fe and Mn were deposited in the late Pleistocene. Postsedimentary alteration of deposited hydrothermal sediments led to their slight recrystallization and, in the green clays, to celadonitization. Further, factor analysis (by Varentsov) of chemical components from these hydrothermal deposits revealed paragenetic assemblages. Green clays corresponding to a definite factor assemblage were formed during the main stage of hydrothermal mineral formation. Manganese hydroxide and associated components were largely accumulated during an early stage and at the end of the main stage.

Impact of elevated levels of CO2 on animal mediated ecosystem function: The modification of sediment nutrient fluxes by burrowing urchins

A mesocosm experiment was conducted to quantify the relationships between the presence and body size of two burrowing heart urchins (Brissopsis lyrifera and Echinocardium cordatum) and rates of sediment nutrient flux. Furthermore, the impact of seawater acidification on these relationships was determined during this 40-day exposure experiment. Using carbon dioxide (CO2) gas, seawater was acidified to pHNBS 7.6, 7.2 or 6.8. Control treatments were maintained in natural seawater (pH = 8.0). Under normocapnic conditions, burrowing urchins were seen to reduce the sediment uptake of nitrite or nitrate whilst enhancing the release of silicate and phosphate. In acidified (hypercapnic) treatments, the biological control of biogeochemical cycles by urchins was significantly affected, probably through the combined impacts of high CO2 on nitrifying bacteria, benthic algae and urchin behaviour. This study highlights the importance of considering biological interactions when predicting the consequences of seawater acidification on ecosystem function.

Modification and Developer Metrics at the Function Level: Metrics for the Study of the Evolution of a Software Project

Software evolution, and particularly its growth, has been mainly studied at the file (also sometimes referred as module) level. In this paper we propose to move from the physical towards a level that includes semantic information by using functions or methods for measuring the evolution of a software system. We point out that use of functions-based metrics has many advantages over the use of files or lines of code. We demonstrate our approach with an empirical study of two Free/Open Source projects: a community-driven project, Apache, and a company-led project, Novell Evolution. We discovered that most functions never change; when they do their number of modifications is correlated with their size, and that very few authors who modify each; finally we show that the departure of a developer from a software project slows the evolution of the functions that she authored.