We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes …

Fully-stabilized nanometric zirconia samples with varying degrees of porosity and grain sizes were analyzed using the coincidence Doppler broadening mode of the positron annihilation spectroscopy (PAS). A decrease in the low momentum fraction was observed and coincided with a decrease in porosity. In addition to pores, it is proposed that defects in the negatively charges grain boundary space region act as positron trapping centers; their effectiveness decreases with an increase in grain size. It is shown that PAS is sensitive to small grain size differences within the nanometric regime in these oxide materials.

Paternally transmitted chromosomal damage has been associated with pregnancy loss, developmental and morphological defects, infant mortality, infertility, and genetic diseases in the offspring including cancer. There is epidemiological evidence linking paternal exposure to occupational or environmental agents with an increased risk of abnormal reproductive outcomes. There is also a large body of literature on germ cell mutagenesis in rodents showing that treatment of male germ cells with mutagens has dramatic consequences on reproduction producing effects such as those observed in human epidemiological studies. However, we know very little about the etiology, transmission and early embryonic consequences of paternally-derived chromosomal abnormalities. The available evidence suggests that: (1) there are distinct patterns of germ cell-stage differences in the sensitivity of induction of transmissible genetic damage with male postmeiotic cells being the most sensitive; (2) cytogenetic abnormalities at first metaphase after fertilization are critical intermediates between paternal exposure and abnormal reproductive outcomes; and, (3) there are maternally susceptibility factors that may have profound effects on the amount of sperm DNA damage that is converted into chromosomal aberrations in the zygote and directly affect the risk for abnormal reproductive outcomes.

The deep-sea gorgonian octocoral Primnoa resedaeformis is distributed throughout the Atlantic and Pacific Oceans at depths of 65-3200 m. It has a two-part skeleton of calcite and gorgonin. Towards the inside of the axial skeleton gorgonin and calcite are deposited in concentric growth rings, similar to tree rings. Colonies were collected from the Northeast Channel (northwest Atlantic Ocean, southwest of Nova Scotia, Canada) from depths of 250-475 m. Radiocarbon was measured in individual rings isolated from sections of each colony, after dissolution of calcite. Each {Delta}{sup 14}C measurement was paired with a ring age determined by three amateur ring counters. The precision of ring counts averaged better than {+-} 2 years. Accurate reconstruction of 20th century bomb-radiocarbon shows that (1) the growth rings are formed annually, (2) the gorgonin is derived from surface particulate organic matter (POM) and (3) useful environmental data are recorded in the organic endoskeletons of deep-sea octocorals. These results support the use of Primnoa resedaeformis as a long-term, high resolution monitor of surface ocean conditions, particularly in temperate and boreal environments where proxy data are lacking.

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Conventional and high resolution electron microscopy havebeen applied for studying lattice defects in nonpolar a-plane GaN grownon a 4H-SiC substrate with an AlN buffer layer. Samples in plan-view andcross-section configurations have been investigated. Basal and prismaticstacking faults together with Frank and Shockley partial dislocationswere found to be the main defects in the GaN layers. High resolutionelectron microscopy in combination with image simulation supported Drum smodel for the prismatic stacking faults. The density of basal stackingfaults was measured to be ~;1.6_106cm-1. The densities of partialdislocations terminating I1 and I2 types of intrinsic basal stackingfaults were ~;4.0_1010cm-2 and ~;0.4_1010cm-2, respectively. The energyof the I2 stacking fault in GaN was estimated to be (40+-4) erg/cm2 basedon the separation of Shockley partial dislocations. To the best of ourknowledge, the theoretically predicted I3 basal stacking fault in GaN wasobserved experimentally for the first time.