Construction of recombination-deficient strains of Streptococcus gordonii by disruption of the recA gene

Degenerate oligonucleotide primers were used in a polymerase chain reaction (PCR) to amplify a region of the recA sequence of Streptococcus gordonii Challis. The resulting PCR fragment was cloned into the suicide vector pAM6199 and introduced into strain Challis, giving rise to recombination-deficient strains in which the recA gene was specifically inactivated.     

The emerging landscape of bioinformatics software systems

Fusing computing and biology expertise, bioinformatics software provides a powerful tool for organizing and mining the vast amounts of data genetics researchers are accumulating. As life scientists and computational scientists interact to create useful bioinformatics software systems, several themes or lessons recur. We identify seven themes: the nature of biological data; data storage, analysis and retrieval; computational modeling and simulation; biologically meaningful information integration; data mining; image processing and visualization; and closing the loop     

Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments

Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).     

Influence ofAmaranthus hybridus L. allelochemics on oviposition behavior ofSpodoptera exigua andS. eridania (Lepidoptera: Noctuidae)

Common pigweed,Amaranthus hybridus L., is a favorite host of the beet army worm (BAW),Spodoptera exigua L. Chemicals extracted from homogenized pigweed with distilled water, ethanol, or dichloromethane and sprayed back on pigweed deterred oviposition by the BAW. Similarly, water extracts of frass from conspecific larvae or southern armyworm (SAW) larvae,S. eridania (Cramer), fed pigweed leaves and sprayed back on pigweed plants also deterred BAW oviposition, thus confirming that deterrence was due to plant allelochemics rather than specific compounds associated with the metabolic or excretory products of the larvae. Confirmation of the presence of oviposition-deterring chemicals in pigweed was used to explain a previously observed seasonal displacement of BAW by SAW on pigweed in the field.Mention of a commercial or proprietary product does not constitute an endorsement by the USDA.     

Patterns of DSM-III-R alcohol dependence symptom progression in a general population survey

Age of onset reports obtained retrospectively for each symptom of DSM-III-R alcohol dependence (AD) are used to study patterns of lifetime symptom progression in a large general-population survey of people in the United States. It is shown that symptom progression among a substantial majority of respondents can be summarized as movement across three clusters. Cluster A is defined by symptoms of role impairment/hazardous use (A4), use despite social, psychological or physical problems (A6), and drinking larger amounts or over a longer period of time than intended (A1). Cluster B is defined by tolerance (A7) and impaired control (A2, A3). Cluster C is defined by withdrawal (A8, A9) and giving up activities in order to drink (A5). Clusters are shown to follow a time sequence, with at least one symptom in Cluster A usually occurring first, followed by symptoms in Clusters B and C. In all, 83.4% of the symptom cluster transitions estimated from retrospective age of onset reports are consistent with this progression. Progression to AD is differentially predicted by symptom profiles reported at the age of first symptom onset, with persons reporting Cluster C symptoms most likely to progress subsequently to AD. Furthermore, profiles of AD defined by the highest symptom cluster present at AD onset are differentially predicted by prior personal and parental histories of psychopathology and, among men, are predictive of diagnosis persistence.     

Demonstrative Suffering: The Gestural (Re)embodiment of Symptoms

Despite the long-standing interest in emotion and bodily conduct, there remains relatively little research concerned with how gestures are used with talk and within interaction to reveal emotional and personal experience. In this article, the author considers the medical consultation and, in particular, the ways in which patients attempt to reveal their experience of illness to the doctor. The paper examines how gesture and other forms of bodily conduct are used to transform symptoms into suffering; to display, enact, and (re)embody medical problems and difficulties. The analysis is based on videorecordings of primary health care consultations and focuses on the social and interactional organization of demonstrative suffering.     

Railgun performance with a two-stage light-gas gun injector

Results obtained with the HELEOS (hypervelocity experimental launcher for equation of state) railgun, which uses a two-stage light-gas gun (2SLGG) as an injector, are presented. The high-velocity 2SLGG injector preaccelerates projectiles up to ~7 km/s. The high injection velocity reduces the exposure duration of the railgun barrel to the passing high temperature plasma armature, thereby reducing the ablation and subsequent armature growth. The 2SLGG also provides a column of cool, high-pressure hydrogen gas to insulate the rails behind the projectile, thereby eliminating restrike. A means to form an armature behind the injected projectile has been developed. In preliminary tests, the third-stage railgun has successfully increased the projectile velocity by 1.35 km/s. Extensive diagnostics have been used to determine the behavior of the armature and track the launcher's performance. Insome cases, velocity increases in the railgun section have been achieved, which are in close agreement with theoretical predictions, whereas in other experiments deviations from theoretical have been observed. The reasons for and implications of these results are addressed. Recent tests are reported     

Logistic regression analysis of twin data: estimation of parameters of the multifactorial liability-threshold model

This study with the rat evaluated the contribution of omega-conotoxin GVIA-(omega-CgTx) and verapamil-sensitive Ca2+ channels in behavioural, antinociceptive and thermoregulatory responses to intracerebroventricular (i.c.v.) injection of [D-Ala2,NMePhe4,Gly-ol5]enkephalin (DAMGO), [D-Pen2,D-Pen5]enkephalin (DPDPE) and dynorphin A-(1-17), which are selective agonists for putative mu, delta and kappa-opioid receptors, respectively. The rats treated with omega-CgTx (8-32 pmol i.c.v.) showed transient, dose-dependent shaking behaviour, hyperalgesia and hypothermia which gradually disappeared within 4 h. The behaviour of the rats was normal by 24 h. Histological examination of brain sections showed morphological alterations of neurons in the hippocampus, medial-basal hypothalamus and pyriform cortex. antinociception, catalepsy and thermoregulatory responses elicited by DAMGO (0.4 and 2.0 nmol) were significantly prolonged and potentiated by verapamil (20 pmol i.c.v. 15 min before) or omega-CgTx (8 pmol 24 h before). Antinociception and hypothermia induced by DPDPE were antagonized by verapamil and omega-CgTx, whereas only omega-CgTx prevented the behavioural arousal observed after DPDPE. Similarly, hypothermia induced by dynorphin A-(1-17) (5.0 nmol) and by the kappa-opioid receptor agonist U50,488H (215 nmol) was antagonized by the two Ca2+ channel blockers but only omega-CgTx prevented the barrel rolling and bizarre postures caused by the opioid peptide.     

Mechanical properties of biorenewable fiber/plastic composites

Plastic fiber composites, consisting of polypropylene (PP) or polyethylene (PE), and pinewood, big blue stem (BBS), soybean hulls, or distillers dried grain and solubles (DDGS), were prepared by extrusion. Young's modulus, tensile and flexural strengths, melt flow, shrinkage, and impact energy, with respect to the type, amount, and size of fiber on composites, were evaluated. Young's moduli under tensile load of wood, BBS, and soybean‐hull fiber composites, compared with those of pure plastic controls, were either comparable or higher. Tensile strength significantly decreased for all the PP/fiber composites when compared with that of the control. Strength of BBS fiber composites was higher than or comparable to that of wood. When natural fibers were added there was a significant decrease in the melt flow index for both plastic/fiber composites. There was no significant difference in the shrinkage of all fiber/plastic composites compared to that of controls. BBS/PE plastic composites resulted in higher notched impact strength than that of wood or soybean‐hull fiber composites. There was significant reduction in the unnotched impact strength compared to that of controls. BBS has the potential to be used as reinforcing materials for low‐cost composites. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 2484–2493, 2004