Recombination-induced variants of Clostridium acetobutylicum ATCC 824 with increased solvent production

Three sporulation-specific genes (orfA, sigE, sigG) from clostridium acetobutylicum ATCC 824 are arranged in a cluster, encoding the putative sigma E-processing enzyme, sigma E, and sigma sigma G respectively. When they were transformed into Clostridium acetobutylicum while on a plasmid functional in this organism, transformants did not survive. Three kinds of recombinations were then attempted with nonreplicative plasmids: duplication of orfA and sigE, replacement of all of the three genes, and inactivation of orfA. While the wild-type strain ceased to grow and produce solvents in batch cultures after approximately 24 h, mutant strains were isolated that showed sustained growth for a much longer time and produced a threefold increase in acetone and butanol in test tube cultures. In addition, one of the derived strains showed a significantly higher growth rate. Features of the restriction maps of the recombinants did not correlate with expected maps, indicating possible complications occurring during the recombination events.     

Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens

The rapid identification of mycobacterial DNA in clinical samples by PCR can be useful in the diagnosis of tuberculous infections, but several large studies have found that the sensitivity of this approach is not better than that of culture. In order to improve the sensitivity of detection of mycobacterial DNA in clinical specimens from patients with paucibacillary forms of tuberculosis, we have developed a procedure permitting the specific capture of mycobacterial DNA in crude samples prior to amplification, thereby concentrating the target sequences and removing irrelevant DNA and other potential inhibitors of the amplification reaction (sequence capture-PCR). By using this approach to capture and amplify two different sequences specific for organisms of the Mycobacterium tuberculosis complex (IS6110 and the direct repeat region), it was possible to detect as little as one genome of mycobacterial DNA in samples containing up to 750 micrograms of total DNA, representing a 10- to 100-fold increase in sensitivity compared with that obtained by purifying total DNA prior to amplification. Detection of the IS6110 sequence in pleural fluid samples from patients with tuberculous pleurisy by sequence capture-PCR gave positive results in 13 of 17 cases, including 3 of 3 culture-positive samples and 10 of 14 culture-negative samples. In contrast, when total DNA was purified from these samples by adsorption to a silica matrix prior to amplification, only the three culture-positive samples were positive by PCR. The sensitivity of detection of the direct repeat sequence in these samples by sequence capture-PCR was similar to that of IS6110 and, in addition, permitted immediate typing of the strains from some patients. We conclude that sequence capture-PCR improves the sensitivity of detection of mycobacterial DNA in paucibacillary samples. This approach should be useful in detecting rare target sequences from organisms implicated in other pathologic processes.     

Tunable wavelength filters based on nonlinear optical interactionsin semiconductor amplifiers

A novel class of narrow-band tunable wavelength filters is proposed and evaluated. Wavelength selectivity of the proposed filters Is derived from the finite time response of an optical nonlinearity. The nonlinearity is gain saturation in semiconductor optical amplifier structures. The filters are shown to have very narrow passbands tunable over the entire semiconductor gain bandwidth. The key to filter implementation is a device configuration in which the wave-mixing products can be isolated from the amplified inputs. Three integrated optics compatible configurations are considered and shown to have high filter throughputs 34 to 180% and subangstrom bandwidths     

Low-temperature phase transformation in Li-10 at. % Mg

It is not known whether impaired hematopoiesis noted during human immunodeficiency virus (HIV) infection results from infection of stem/progenitor cells or of cells of the bone marrow microenvironment. Normal adherent primary stromal layers were exposed to HIV to determine which of this mixture of endothelial cells, fibroblasts, and macrophages are susceptible to the virus. Viral p24 in supernatants was noted with monocytotropic HIV-1Ada, HIV-1Ba-L, and HIV-1JR-FL but not with lymphotropic HIV-1LAI nor HIV-1MN strain, and only stromal macrophages expressed the viral antigens. Coculture of the layers with PHA-activated normal lymphocytes failed to rescue lymphotropic virus. No p24 was produced when macrophage-depleted stromal cells were exposed to either HIV-1Ba-L or HIV-1LAI; proviral DNA was then amplified by PCR in cells exposed to either virus, though coculture with lymphocytes rescued only HIV-1Ba-L. Altogether, these data indicate that macrophages are the major targets of HIV in cultured stromal layers. As virus replication in macrophages did not affect the profile of major cytokines involved in regulating hematopoiesis, HIV infection could alter hematopoiesis by other as yet unspecified mechanisms.     

Monitoring systems and determination of actual fatigue usage

At GKN, fatigue monitoring of important components has been conducted since 1979. The monitoring methods depend on the mechanisms of damage; quasi-static loads are regarded as well as dynamic loads. The components were selected for monitoring on the basis of a system analysis. The data resulting from monitoring are used to optimise operation mode steadily. Experience shows that the use of monitoring data as input for fatigue assessment is the most realistic and cost-effective way. This fatigue assessment uses global and local sensitivity studies to evaluate the load-stress relation for each component. These relations can be programmed to produce stress vs. time curves. These are processed according to ASME rules to give a realistic fatigue usage.     

A new monitoring system for piping systems in fossil fired power plants

A CEC-funded project has been performed to tackle the problem of producing an advanced Life Monitoring System (LMS) which would calculate the creep and fatigue damage experienced by high temperature pipework components. Four areas were identified where existing Life Monitoring System technology could be improved:

1. 1. the inclusion of creep relaxation

2. 2. the inclusion of external loads on components

3. 3. a more accurate method of calculating thermal stresses due to temperature transients

4. 4. the inclusion of high cycle fatigue terms.

The creep relaxation problem was solved using stress reduction factors in an analytical in-elastic stress calculation. The stress reduction factors were produced for a number of common geometries and materials by means of non-linear finite element analysis. External loads were catered for by producing influence coefficients from in-elastic analysis of the particular piping system and using them to calculate bending moments at critical positions on the pipework from load and displacement measurements made at the convenient points at the pipework. The thermal stress problem was solved by producing a completely new solution based on Green's Function and Fast Fourier transforms. This allowed the thermal stress in a complex component to be calculated from simple non-intrusive thermocouple measurements made on the outside of the component. The high-cycle fatigue problem was dealt with precalculating the fatigue damage associated with standard transients and adding this damage to cumulative total when a transient occurred.

The site testing provided good practical experience and showed up problems which would not otherwise have been detected.     

Study of photosensitive mixtures of TMAE and helium, hydrocarbon or CF4-based carrier gases

Among the photocathodes used for particle identification based on the Cherenkov Ring Imaging technique, the TMAE molecule is still the best in terms of quantum efficiency. Despite the fact that TMAE gaseous photocathodes have already been used in a number of large experiments, one still seeks answers to many detailed questions. We present a systematic study of gaseous photocathodes based on TMAE mixed with helium, hydrocarbon and CF₄-based gases at normal pressure. The study includes a measurement of the electron drift velocity, gas quenching properties, single electron pulse height spectra and anode wire aging. The paper makes recommendations for carrier gas mixtures to obtain the best quenching, and suggests how to manage TMAE wire aging. This study was motivated by a specific particle identification detector proposal, the Fast Drift CRID proposed for the B-factory at SLAC.     

Nitric oxide reduction and carbon monoxide oxidation over carbon-supported copper-chromium catalysts

Carbon supported copper-chromium catalysts are shown to be very active for both the reduction of nitric oxide with carbon monoxide and the oxidation of carbon monoxide with oxygen. Mixed copper-chromium oxide active phases have good activity in the simultaneous removal of nitric oxide and carbon monoxide from exhaust gases. The influence of several catalyst variables has been investigated. The activity per volume of catalyst increases with increasing loading, while the intrinsic activity shows a maximum around C/M=100−50. An optimum catalyst for nitric oxide reduction and carbon monoxide oxidation has a copper/chromium ratio of 2/1. The apparent activation energy for the carbon monoxide oxidation over carbon supported copper-chromium catalysts is 77 kJ/mol, suggesting that the Cu---O bond rupture is the rate-limiting process. The reduction of nitric oxide takes place at higher temperatures. Since all catalysts have a low selectivity for molecular nitrogen formation at lower temperatures, the dissociation of nitric oxide is probably rate determining, resulting in a slightly reduced catalyst system. In an excess of carbon monoxide the reaction is first-order in nitric oxide and zero-order in carbon monoxide. Moisture inhibits the reaction by reversible competitive adsorption, whereas carbon dioxide does not. Oxygen completely inhibits the reduction of nitric oxide due to the more rapid reoxidation of the catalytic sites compared to nitric oxide. Therefore, the reduction of nitric oxide takes place only when all oxygen has been converted and, hence, is shifted to higher temperatures. As a possible consequence, the production of nitrous oxide is reduced. Nitric oxide and molecular oxygen react preferentially with carbon monoxide, so, in an excess of oxidizing component, gasification of the carbon support occurs at higher temperatures after carbon monoxide has been completely consumed.     

Afterburner [network-independent card for protocols]

Many current implementations of protocols such as the Transmission Control Protocol/Internet Protocol (TCP/IP) are inefficient because data are often accessed more frequently than necessary. Three techniques that reduce the need for memory bandwidth are proposed. The techniques are copy-on-write, page remapping, and single-copy. Afterburner, a network-independent card that provides the services that are necessary for a single-copy protocol stack, is described. The card has 1 MByte of local buffers and provides a simple interface to a variety of network link adapters, including HIPPI and asynchronous transfer mode (ATM). Afterburner can support transfers to and from the link adapter card at rates up to 1 Gbit/s. An implementation of TCP/IP that uses the features provided by Afterburner to reduce the movement of data to a single copy is discussed. Measurements of the end-to-end performance of Afterburner and the single-copy implementation of TCP/IP are presented     

The evolution of custom microarray manufacture

Given the enormous size of the genome and that there are potentially many other types of measurements we need to do to understand it, it has become necessary to pick and choose one's targets to measure because it is still impossible to evaluate the entire genome all at once. What has emerged is a need to have rapidly customizable microarrays. There are two dominant methods to accomplish custom microarray synthesis, Affymetrix-like microarrays manufactured using light projection rather than semiconductor-like masks used by Affymetrix to mass manufacture their GeneChip/sup TM/ arrays now, or the ink-jet printing method employed by Agilent. The manufacture of these custom Affymetrix-like microarrays can now be done on a digital optical chemistry (DOC) machine developed at the University of Texas Southwestern Medical Center, and this method offers much higher feature numbers and feature density than is possible with ink-jet printed arrays. On a microarray, each feature contains a single genetic measurement. The initial DOC prototype has been described in several publications, but that has now led to a second-generation machine. This machine reliably produces a number of arrays daily, has been deployed against a number of biomedical questions, is being used in new ways and has also led to a number of spin-off technologies.