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Yersinia pestis , the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis . Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis -specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis . In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis . Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis . These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.

Picosecond infrared spectroscopy in the mid-IR has been applied to the study of laser–material interactions on an ultrafast time scale. We excite the sample with one pulse at 1064 or 266 nm and probe some time later in the mid IR (2900–1400 cm −1 ). We study photochemical reactions by exciting the sample directly in the UV. Alternatively, we initiate thermal reactions by exciting a `heater' dye at 1.064 μ m, which quickly converts the photon energy into heat. The potential of this technique to study reactions in the solid state was demonstrated for the photochemically induced (266 nm) Wolff rearrangement in a polymer matrix. This reaction is the basis of most positive photoresists. We were able to assign the key intermediate (ketene) in real time at room temperature for the first time. Thermal initiation also resulted in Wolff rearrangement. The position, amplitude and width of the product bands changed, probably due to additional side reactions and temperature effects.

Time-resolved infrared (TRIR) techniques have been employed to study the reactions of carbon monoxide with the cytochrome alpha 3-Cu(B) site of cytochrome c oxidase (CcO). The ligation dynamics immediately following photodissociation have been investigated using picosecond TRIR spectroscopy and linear dichroism. The rate of photoinitiated transfer of CO from cytochrome alpha 3 to CuB was measured directly by monitoring the development of the transient CuBCO absorption. In less than 1 ps, a stationary CuBCO spectrum develops, which together with the CO infrared linear dichroism is constant until the CO dissociates from CuB on a microsecond time scale. These observations indicate that the CO is transferred between metals and reaches its equilibrium conformation in less than 1 ps. This unprecedented ligand transfer rate has profound implications with regard to the structure and dynamics of the cytochrome alpha 3-CuB site, the functional architecture of the protein, and coordination dynamics in general.

A combined experimental and computational approach utilizing CO2 infrared gas lasers and chemometric multivariate analysis was employed to detect chemicals and their concentrations in the open atmosphere under controlled release conditions. Absorption spectra of four organic gases were collected in the laboratory by lasing 40 lines of a Synrad 15 W CO2 laser in the 9.3 to 10.8 micron range. Several chemometric calibration models were constructed based on this IR data using the Partial Least Squares computational technique. The chemometric models were used to analyze in near real time the field DIAL data acquired over this exact wavelength range at round trip distances of 7 and 13 km. It will be shown that the ability to predict the chemicals and their respective concentrations depends on a variety of factors. In 39 of the 45 experiments, the identities of the released chemicals were correctly identified without predictions of false positives or false negatives. Under the best field conditions, we achieved predictions of absolute concentrations within 30% of the actual values.© (1996) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Recent advances in ultrafast infrared spectroscopy are described, including experimental details and fundamental limitations. The utility of this technique is illustrated with two recent examples.

Cytochrome c oxidase (CcO), an enzyme which catalyzes the reduction of dioxygen to water in the terminal step of the respiratory chain, combines several fundamental chemical processes in performing its function; electron, proton and ligand transfers.[1] The coordination chemistry and ligation dynamics of the cytochrome a 3-CuB site, where O2 and other small molecules such as CO, NO and isocyanates can bind, are essential to the function of the enzyme.[2] The sensitivity of the vibrational frequencies and bandwidths of small molecules to changes in coordination and environment makes infrared spectroscopy uniquely useful as a probe for those processes, particularly at CUB +, which generally is not observable by other spectroscopies. [1,2] Recent time-resolved infrared (TRIR) and visible absorption measurements have shown that coordination to CuB + is an obligatory mechanistic stop for CO entering the cytochrome a 3 heme site and departing the protein after photodissociation. [2] The timescale (> 10−7 s) of the TRIR measurements, however, precluded observation of the ligation dynamics immediately following photodissociation. Here we report a picosecond timescale TRIR study of these events. The results reveal that the photoinitiated ligand transfer of CO from Fea3 2+ to CuB +, which are believed to lie 4–5 A apart [1], occurs within 1 ps.

Time-resolved electronic absorption, infrared, resonance Raman, and magnetic circular dichroism spectroscopies are applied to characterization of the intermediate which is formed within 20 ps after photodissociation of CO from cytochrome a3 of reduced cytochrome oxidase. This intermediate decays with the same halflife (ca. 1 microsecond(s)) as the post- photodissociation CuB+-CO species previously observed by time-resolved infrared. The transient UV-Vis spectra, kinetics, infrared, and Raman evidence suggest that an endogenous ligand is transferred from CuB to Fea3 when CO binds to CuB, forming a cytochrome a3 species with axial ligation which differs from the reduced unliganded enzyme. The time-resolved magnetic circular dichroism results suggest that this transient is high spin and therefore five coordinate. Thus it is inferred that the ligand from CuB binds on the distal side of cytochrome a3 and displaces the proximal histidine imidazole. This remarkable mechanistic feature is an additional aspect of the previously proposed 'ligand shuttle' activity of the CuB/Fea3 pair. The authors suggest that the ligand shuttle may play a functional role in redox-linked proton translocation by the enzyme. More detail on this work is presented elsewhere.© (1991) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Time-resolved infrared spectroscopy (TRIRS) has been employed to study the reactions of small molecules with the cytochrome a3-CuB site of cytochrome c oxidase (CcO). All phases of these reactions have been investigated, from ultrafast phenomena (hundreds of femtoseconds) to relatively slow processes (milliseconds). The ligation dynamics immediately following photodissociation have been studied using a TRIRS technique with time resolution of less than 1 ps. The rate of photoinitiated transfer of CO from Fea32+ to CuB+ was measured directly by monitoring the development of the transient CuB+-CO absorption. The development of a stationary CuB+ spectrum which is constant until the CO dissociates from CuB+ occurs in less than 1 ps, indicating that the photoinitiated transfer of CO is remarkably fast. This unprecedented ligand transfer rate has profound implications with regard to the structure and dynamics of the cytochrome a3-CuB site, the functional architecture of the protein and coordination dynamics in general. The photodissociation and recombination of CN- has also been studied using a real-time TRIR technique. The CN- recombination rate of 430 s-1 is consistent with a recombination pathway similar to the one we have previously proposed for CO, in which a long-lived barrier to recombination is formed by the binding of an endogenous ligand L to Fea32+. The authors suggest the rate determining step for CN- recombination is the thermal dissociation of the Fea32+-L bond.

As part of a program to develop diagnostics for laser-driven reaction in polymer matrices, we have investigated the photoinduced decomposition of 5-diazo-2,2-dimethyl-1,3-dioxane-4,6-dione (5-diazo Meldrum`s acid, DM) in a PMMA matrix. This particular diazoketone is sensitive to deep UV (200-260nm), making it suitable for high-resolution lithographic applications. It has historically been difficult to study the chemistry of such resists as many of the intermediates are short-lived and absorb only in the UV. Recent advances in ultrafast infrared spectroscopy, however, now allow us to directly examine the initial steps occurring in UV photoresists with infrared spectroscopy. Herein, we describe the first room temperature observation of intermediates in the photochemistry of DM with utlrafast infrared spectroscopy. In summary, these experiments have provided the first example of how ultrafast infrared spectroscopy may be used to examine laser-driven reactions in polymeric matrices. We have determined that the photoinduced Wolff rearrangement of DM in a PMMA matrix is complete within 20 ps. The IR band assignable to the ketene is centered at 2161 cm{sup -1} and has a width of 29 cm{sup -1}. The rapid formation of the ketene is a key element of the high quantum yield of carboxylic acid formation and a key elementmore » as well for the use of DM as an ablation sensitizer. 22 refs., 3 figs.« less

A combined experimental and computational approach utilizing tunable CO(2) lasers and chemometric analysis was employed to detect chemicals and their concentrations in the field under controlled release conditions. We collected absorption spectra for four organic gases in the laboratory by lasing 40 lines of the laser in the 9.3-10.8-mum range. The ability to predict properly the chemicals and their respective concentrations depends on the nature of the target, the atmospheric conditions, and the round-trip distance. In 39 of the 45 field experiments, the identities of the released chemicals were identified correctly without predictions of false positives or false negatives.

One of the most technologically important uses of organic photochemistry is in the imaging industry where radiation-sensitive organic monomers and polymers are used in photoresists. A widely-used class of compounds for imaging applications are diazoketones; these compounds undergo a photoinduced Wolff rearrangement to form a ketene intermediate which subsequently hydrolyses to a base-soluble, carboxylic acid. Another use of organic molecules in polymer matrices is for dopant induced ablation of polymers. As part of a program to develop diagnostics for laser-driven reactions in polymer matrices, we have investigated the photo-induced decomposition of 5-diazo-2,2-dimethyl-l,3-dioxane-4,6-dione (5-diazo Meldrum's acid, DM) in a PMMA matrix using picosecond infrared spectroscopy. In particular, irradiation of DM with a 60 ps 266 nm laser pulse results in immediate bleaching of the diazo infrared band (v = 2172 cm-1). Similarly, a new band appears within our instrument response at 2161 cm-1 (FWHM = 29 cm-1) and is stable to greater than 6 ns.; we assign this band to the ketene photoproduct of the Wolff rearrangement. Using deconvolution techniques we estimate a limit for its rate of formation of τ < 20 ps. The linear dependence of the absorbance change with the pump power (266 nm) even above the threshold of ablation suggest that material ejection take place after 6ns.