Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase

Vaccinia virus DNA polymerase catalyzes duplex-by-duplex DNA joining reactions in vitro and many features of these recombination reactions are reprised in vivo. This can explain the intimate linkage between virus replication and genetic recombination. However, it is unclear why these apparently ordinary polymerases exhibit this unusual catalytic capacity. In this study, we have used different substrates to perform a detailed investigation of the mechanism of duplex-by-duplex recombination catalyzed by vaccinia DNA polymerase. When homologous, blunt-ended linear duplex substrates are incubated with vaccinia polymerase, in the presence of Mg²⁺ and dNTPs, the appearance of joint molecules is preceded by the exposure of complementary single-stranded sequences by the proofreading exonuclease. These intermediates anneal to form a population of joint molecules containing hybrid regions flanked by nicks, 1–5 nt gaps, and/or short overhangs. The products are relatively resistant to exonuclease (and polymerase) activity and thus accumulate in joining reactions. Surface plasmon resonance (SPR) measurements showed the enzyme has a relative binding affinity favoring blunt-ended duplexes over molecules bearing 3′-recessed gaps. Recombinant duplexes are the least favored ligands. These data suggest that a particular combination of otherwise ordinary enzymatic and DNA-binding properties, enable poxvirus DNA polymerases to promote duplex joining reactions.     

Degradation of extractive-free lignocelluloses by Coriolus versicolor and Poria placenta

Summary The wood-decay fungi Coriolus versicolor, a white-rot fungus, and Poria placenta, a brown-rot fungus, were grown on an extractive-free lignocellulose prepared from quackgrass (Agropyron repens). Their abilities to decompose this lignocellulose were compared to their abilities to decompose softwood (Picea pungens) and hardwood (Acer rubrum) lignocelluloses. The two fungi were grown on malt-extract dampened lignocelluloses at 28°C for up to 12 weeks. Replicate cultures were periodically harvested and lignocellulose decomposition was followed by monitoring substrate weight loss, lignin loss, and carbohydrate loss. Coriolus versicolor decomposed the lignin and carbohydrate components of the grass lignocellulose as efficiently as the softwood and hardwood lignocelluloses. Poria placenta, however, was not an efficient degrader of either lignin or carbohydrate in the grass lignocellulose. Poria placenta readily decomposed carbohydrate components of the softwood lignocellulose but not the hardwood lignocellulose.Paper number 81520 of the Idaho Agricultural Experiment Station     

Hemodynamic consequences of rapid changes in posture in humans.

Tolerance to +G(z) gravitational stress is reduced when +G(z) stress is preceded by exposure to hypogravity (fraction, 0, or negative G(z)). For example, there is an exaggerated fall in eye-level arterial pressure (ELAP) early on during +G(z) stress (head-up tilt; HUT) when this stress is immediately preceded by -G(z) stress (head-down tilt; HDT). The aims of the present study were to characterize the hemodynamic consequences of brief HDT on subsequent HUT and to test the hypothesis that an elevation in leg vascular conductance induced by -G(z) stress contributes to the exaggerated fall in ELAP. Young healthy subjects (n = 3 men and 4 women) were subjected to 30 s of 30 degrees HUT from a horizontal position and to 30 s of 30 degrees HUT when HUT was immediately preceded by 20 s of -15 degrees HDT. Four bouts of HDT-HUT were alternated between five bouts of HUT in a counterbalanced designed to minimize possible time effects of repeated exposure to gravitational stress. One minute was allowed for recovery between tilts. Brief exposure to HDT elicited an exaggerated fall in ELAP during the first seconds of the subsequent HUT (-17.9 +/- 1.4 mmHg) compared with HUT alone (-12.4 +/- 1.2 mmHg, P <0.05) despite a greater rise in stroke volume (Doppler ultrasound) and cardiac output over this brief time period in the HDT-HUT trials compared with the HUT trials (thereafter stroke volume fell under both conditions). The greater fall in ELAP was associated with an exaggerated increase in leg blood flow (femoral artery Doppler ultrasound) and was therefore largely (70%) attributable to an exaggerated rise in estimated leg vascular conductance, confirming our hypotheses. Thus brief exposure to -G(z) stress leads to an exaggerated fall in ELAP during subsequent HUT, owing to an exaggerated increase in estimated leg vascular conductance.     

Chemical modification of the actin binding site of rabbit muscle aldolase by diethylpyrocarbonate

Summary To extend the available information on the significance of the interactions between glycolytic enzymes and the actin component of the cellular ultrastructure, investigations into the compositional characteristics of the actin binding site on one of the major glycolytic enzymes, aldolase, have been undertaken. As the electrostatic nature of the association has been previously reported indicative of a cationic region on the enzyme involved in the binding, these studies have investigated the possibility of the involvement of histidine residues in this binding region. By the use of the histidine specific reagent, diethylpyrocarbonate, we have been able to establish a difference in nature of an actin binding domain and the active site domain which does contain an essential histidine. The results have been discussed in relation to the significance of this finding with respect to the binding of aldolase to subcellular structure.     

Environmental influences on growth and defence responses of the invasive shrub,Lonicera maackii,to simulated and real herbivory in the juvenile stage

Background and Aims

Tolerance and defence against herbivory are among the many mechanisms attributed to the success of invasive plants in their novel ranges. Because tolerance and defence against herbivory differ with the ontogeny of a plant, the effects of herbivore damage on plant fitness vary with ontogenetic stage and are compounded throughout a plant''s lifetime. Environmental stresses such as light and nutrient limitations can further influence the response of the plant. Much is known about the response of plants in the seedling and reproductive adult stages, but less attention has been given to the pre-reproductive juvenile stage.

Methods

Juvenile plants of the North American invasive Lonicera maackii were exposed to simulated herbivory under high and low light and nitrogen availability and growth, allocation patterns and foliar defensive chemistry were measured. In a second experiment, complete nutrient availability and damage type (generalist caterpillar or simulated) were manipulated.

Key Results

Juvenile plants receiving 50 % defoliation had lower total biomass and a higher root^:^shoot ratio than controls for all treatment combinations except low nitrogen/low light. Low light and defoliation increased root^:^shoot ratio. Light, fertilization and defoliation had little impact on foliar defensive chemistry. In the second experiment, there was a reduction in total biomass when caterpillar damage was applied. The root^:^shoot ratio increased under low soil fertility and was not affected by defoliation. Stem-diameter growth rates and specific leaf area did not vary by damage type or fertilization. Foliar protein increased through time, and more strongly in defoliated plants than in controls, while peroxidase activity and total flavonoids decreased with time. Overall, resource limitations were more influential than damage in the growth of juvenile L. maackii plants.

Conclusions

The findings illustrate that even when resources are limited, the tolerance and defence against herbivory of a woody invasive plant in the juvenile stage may contribute to the establishment and persistence of some species in a variety of habitats.     

Mechanism of inactivation gating of human T-type (low-voltage activated) calcium channels

Recovery from inactivation of T-type Ca channels is slow and saturates at moderate hyperpolarizing voltage steps compared with Na channels. To explore this unique kinetic pattern we measured gating and ionic currents in two closely related isoforms of T-type Ca channels. Gating current recovers from inactivation much faster than ionic current, and recovery from inactivation is much more voltage dependent for gating current than for ionic current. There is a lag in the onset of gating current recovery at -80 mV, but no lag is discernible at -120 mV. The delay in recovery from inactivation of ionic current is much more evident at all voltages. The time constant for the decay of off gating current is very similar to the time constant of deactivation of open channels (ionic tail current), and both are strongly voltage dependent over a wide voltage range. Apparently, the development of inactivation has little influence on the initial deactivation step. These results suggest that movement of gating charge occurs for inactivated states very quickly. In contrast, the transitions from inactivated to available states are orders of magnitude slower, not voltage dependent, and are rate limiting for ionic recovery. These findings support a deactivation-first path for T-type Ca channel recovery from inactivation. We have integrated these concepts into an eight-state kinetic model, which can account for the major characteristics of T-type Ca channel inactivation.     

Fingerprinting closely related xanthomonas pathovars with random nonamer oligonucleotide microarrays

Current bacterial DNA-typing methods are typically based on gel-based fingerprinting methods. As such, they access a limited complement of genetic information and many independent restriction enzymes or probes are required to achieve statistical rigor and confidence in the resulting pattern of DNA fragments. Furthermore, statistical comparison of gel-based fingerprints is complex and nonstandardized. To overcome these limitations of gel-based microbial DNA fingerprinting, we developed a prototype, 47-probe microarray consisting of randomly selected nonamer oligonucleotides. Custom image analysis algorithms and statistical tools were developed to automatically extract fingerprint profiles from microarray images. The prototype array and new image analysis algorithms were used to analyze 14 closely related Xanthomonas pathovars. Of the 47 probes on the prototype array, 10 had diagnostic value (based on a chi-squared test) and were used to construct statistically robust microarray fingerprints. Analysis of the microarray fingerprints showed clear differences between the 14 test organisms, including the separation of X. oryzae strains 43836 and 49072, which could not be resolved by traditional gel electrophoresis of REP-PCR amplification products. The proof-of-application study described here represents an important first step to high-resolution bacterial DNA fingerprinting with microarrays. The universal nature of the nonamer fingerprinting microarray and data analysis methods developed here also forms a basis for method standardization and application to the forensic identification of other closely related bacteria.     

Accuracy and direction of error in the sexing of the skeleton: implications for paleodemography

Determinations of sex by subjective assessment of the skulls from a skeletal series of known sex were compared to fully independent assessments based on pelves of the same specimens. Within-sex correlations of cranial and pelvic morphologies measured on an android-gynecoid scale were smaller than expected. Subjective assessment by means of the skull compared favorably to that of the linear discriminant functions of Giles and Elliot; however, the direction of error was similar for both procedures. Of course, estimations based on the pelves were generally superior to both in terms of frequency and overall bias of error. The bias of sex estimation for paleodemographic purposes is contingent upon completeness of skeletal remains.     

The spatial structures of hypolithic communities in the Dry Valleys of East Antarctica

Hypolithic communities represent important reservoirs of microbial life in hyper-arid deserts. A number of studies on the diversity and ecology of these communities from different geographic areas have been reported in the past decade, but the spatial distribution of the different components of these communities is still not understood. Moss- and cyanobacteria-dominated hypolithic community morphotypes from Miers Valley (McMurdo Dry Valleys, East Antarctica) were analyzed by electron microscopy in order to characterize the microscale spatial structure. The two communities showed a high degree of internal organization, but differing according to the biological composition. In moss-dominated hypoliths, the moss plantlets are intermixed with mineral fragments of soil origin. However, in cyanobacteria-dominated hypoliths, a layered spatial organization was structured by filamentous cyanobacteria and associated extracellular polymeric components. While moss cells were lacking in cyanobacteria-dominated communities, biofilms formed by cyanobacteria and heterotrophic bacteria were observed in both community morphotypes. The water-holding capacity of both live and dead moss cells and the associated organic matrix, together with the protective properties of the extracellular polymeric substances, could facilitate the survival and activity of these communities. Similar structural strategies can favor the survival of microbial communities in different extreme environments.