Knowledge-based simulation of DNA metabolism: prediction of enzyme action

We have developed a knowledge-based simulation of DNA metabolismthat accurately predicts the actions of enzymes on DNA undera large number of environmental conditions. Previous simulationsof enzyme systems rely predominantly on mathematical models.We use a frame-based representation to model enzymes, substratesand conditions. Interactions between these objects are expressedusing production rules and an underlying truth maintenance system.The system performs rapid inference and can explain its reasoning.A graphical interface provides access to all elements of thesimulation, including object representations and explanationgraphs. Predicting enzyme action is the first step in the developmentof a large knowledge base to envision the metabolic pathwaysof DNA replication and repair. Received on February 1, 1990; accepted on October 2, 1990     

Seismic and auditory tuning curves from bullfrog saccular and amphibian papular axons

We present seismic and auditory frequency tuning curves of individual bullfrog, Rana catesbeiana, saccular and amphibian papilla axons that responded to both seismic and auditory stimuli. In this study we found: 1) most saccular axons respond well to auditory stimuli with moderate signal strength (50-70 dB SPL) as well as to seismic stimuli; 2) most amphibian papilla axons respond well to seismic stimuli as well as to auditory stimuli, and their seismic sensitivities are comparable to those of saccular axons (responding to sinusoidal stimuli with peak accelerations in the range 0.001 to 0.1 cm/S2); 3) the responses to both seismic and auditory stimuli from both saccule and amphibian papilla are tuned, i.e. the strength of the response varies with the frequency of the stimulus; and this tuning is clearly not the result of second order resonance; 4) in individual axons the tuning properties for seismic stimuli often are not the same as those for auditory stimuli, a fact that may provide clues about how the stimulus signal energy is transferred to the hair cells in each case.     

Autochthonous outer ramp sedimentation: The Alamogordo Member of the Lake Valley Formation,New Mexico

Summary Paleozoic carbonate ramp sedimentation has generally been described in terms of downlapping clinoforms composed of allochthonous sediment derived from shallower environments. However, during transgressive episodes when carbonate sediment production is low and down slope sediment transport by gravity becomes inactive, autochthonous carbonate sediment accumulates in vertical stacks of essentially in situ sediment. Autochthonous outer ramp deposition is probably a part of many Paleozoic ramp strata, but has heretofore not been recognized because of the general absence of adequate exposures. Evidence of autochthonous, in situ deposition and preservation of sediments in a starved setting is well displayed in the Alamogordo Member of the Lake Valley Formation in south central New Mexico. This evidence includes: 1) beds and bed sets that are individually continuous and traceable along ramp slope for 32 km, 2) down-ramp sequential distributions of depth-sensitive organisms and assemblages but patchy distribution of rock types, 3) lack of sedimentary structures indicative of transport, 4) well preserved, unabraded fossils, 5) the common occurrence of fossils in life position, 6) beds traceable into and through mounds 7) bed thickness trends ascribed to biotic productivity, and 8) geopetal structures in original position. Integrated paleontologic, sedimentologic, and stratigraphic data provide information about depositional processes and setting. The depositional slope was approximately 0.5^o based on the distribution of fossil algae; this is comparable to dips reported for other Mississippian homoclinal ramps. An oxygen minimum zone may have impinged on the ramp during a major flooding event. Shifts in biotic gradients from bed to bed reveal transgressive-regressive patterns that would not be resolvable without detailed paleontological evidence. The Alamogordo Member formed as a result of transgressive and early highstand starved carbonate sedimentation along a narrow, homoclinal outer ramp. The surface of maximum flooding and the boundary between the TST and HST are within the Alamogordo Member.     

Trachypogon plumosus (Poaceae,Andropogoneae): ancient thatch and more from the ceren site,El Salvador

Paleoethnobotanical studies in the Zapotitdn Valley of north-central El Salvador revealed that a species of grass,Trachypogon plumosus, was in common use as a thatch material at the Ceren site, a small mesoamerican farming community inundated by volcanic ash circaa.d. 590. Although the grass must have been common in Precolumbian times, repeated attempts to collect fresh specimens from the modern valley were unsuccessful. A survey of the major herbaria with collections from El Salvador likewise demonstrated a lack of modern specimens from the Zapotitdn Valley. The elimination of theT. plumosus from this area and its characteristic savanna habitat probably occurred as a result of the introduction of competing Old World grasses and excessive herbivory. This finding demonstrates why conservationists working in the tropics should be concerned not only with the extinction of rain forest habitats, but with the elimination of other habitats as well.     

Effect of very low calorie diet on body composition and exercise response in sedentary women.

The effect of very low calorie diet (VLCD) on fat-free mass (FFM) and physiological response to exercise is a topic of current interest. Ten moderately obese women (aged 23-57 years) received VLCD (1695 kJ.day-1) for 6 weeks. FFM, estimated by four conventional techniques, and heart rate (fc), blood lactate (la(b)), mean arterial pressure (MAP), respiratory exchange ratio (R) and rating of perceived exertion (RPE) were measured during a submaximal cycle ergometry test 1 week before, in the 2nd and 6th week, and 1 week after VLCD treatment. Strength and muscular endurance of the quadriceps and hamstrings were tested by isokinetic dynamometry. The 11.5-kg reduction in body mass was approximately 63% fat and 37% FFM. The latter was attributed largely to the loss of water associated with glycogen. Whilst exercise fc increased by 9-14 beats.min-1 (P < 0.01), there were substantial decreases (P < 0.01) in submaximal MAP (1.07-1.73 kPa), la(b) (0.75-1.00 mmol.l-1 and R (0.07-0.09) during VLCD. R and fc returned to normal levels after VLCD. Gross strength decreased (P < 0.01) by 9 and 13% at 1.05 rad.s-1 and 3.14 rad.s-1, respectively. Strength expressed relative to body mass (Nm.kg-1) increased (P < 0.01) at the lower contraction velocity, but there was no change at the faster velocity. Muscular endurance also decreased (P < 0.01) by 62 and 82% for the hamstrings and quadriceps, respectively. We concluded that the strength decrease was a natural adaptation to the reduction in body mass as the ratio of strength to FFM was maintained.(ABSTRACT TRUNCATED AT 250 WORDS)     

Rabies Virus Envelope Glycoprotein Targets Lentiviral Vectors to the Axonal Retrograde Pathway in Motor Neurons

Rabies pseudotyped lentiviral vectors have great potential in gene therapy, not least because of their ability to transduce neurons following their distal axonal application. However, very little is known about the molecular processes that underlie their retrograde transport and cell transduction. Using multiple labeling techniques and confocal microscopy, we demonstrated that pseudotyping with rabies virus envelope glycoprotein (RV-G) enabled the axonal retrograde transport of two distinct subtypes of lentiviral vector in motor neuron cultures. Analysis of this process revealed that these vectors trafficked through Rab5-positive endosomes and accumulated within a non-acidic Rab7 compartment. RV-G pseudotyped vectors were co-transported with both the tetanus neurotoxin-binding fragment and the membrane proteins thought to mediate rabies virus endocytosis (neural cell adhesion molecule, nicotinic acetylcholine receptor, and p75 neurotrophin receptor), thus demonstrating that pseudotyping with RV-G targets lentiviral vectors for transport along the same pathway exploited by several toxins and viruses. Using motor neurons cultured in compartmentalized chambers, we demonstrated that axonal retrograde transport of these vectors was rapid and efficient; however, it was not able to transduce the targeted neurons efficiently, suggesting that impairment in processes occurring after arrival of the viral vector in the soma is responsible for the low transduction efficiency seen in vivo, which suggests a novel area for improvement of gene therapy vectors.