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Biomedical subjects

D N Lee

Publications and source records attributed to D N Lee.

At least 19 recordsLinked to original sources
PubMed1995

Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex.

A central enigma of transcriptional regulation is how the normally efficient transcription elongation complex stops at pause and termination signals. One possibility, raised by the discovery that RNA polymerase sometimes contracts its DNA footprint, is that discontinuous movements contribute to recognizing these signals. We report that E. coli RNA polymerase responds to sequences immediately downstream and upstream from the his leader pause site by changing neither its downstream DNA contact nor its upstream RNA contact for 8 bp preceding the pause. This compressed complex isomerizes to a paused conformation by an approximately 10 bp jump of its downstream DNA contact and simultaneous extrusion of an RNA hairpin that stabilizes the paused conformation. We suggest pausing and termination could be alternative outcomes of a similar isomerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump.

Base Sequence↗
PubMed1995

The functional significance of arm movements in neonates.

Arm movements made by newborn babies are usually dismissed as unintentional, purposeless, or reflexive. Spontaneous arm-waving movements were recorded while newborns lay supine facing to one side. They were allowed to see only the arm they were facing, only the opposite arm on a video monitor, or neither arm. Small forces pulled on their wrists in the direction of the toes. The babies opposed the perturbing force so as to keep an arm up and moving normally, but only when they could see the arm, either directly or on the video monitor. The findings indicate that newborns can purposely control their arm movements in the face of external forces and that development of visual control of arm movement is underway soon after birth.

Arm↗
PubMed1995

Steering by echolocation: a paradigm of ecological acoustics.

1. Flights of three big brown bats (Eptesicus fuscus) landing on a hand and catching a suspended mealworm were video analysed. 2. Results were consistent with the bats using the same basic control procedure in the quite different approach tasks--namely keeping tau (r) = kr and tau (a)/tau (r) = k alpha r. Here r is the current distance to the destination; alpha is the angle between the current direction of the destination and the goal direction of final approach (beta min); tau (r) = r/r, tau (alpha) = alpha/alpha; and kr, k alpha r are constants. 3. The bats were each quite consistent on a particular task (hand or mealworm) in the values they used for the control parameters kr, k alpha r and beta min. However, different values were used in the two tasks, which reflected the different behaviour required at the destination. Flights to hand required twisting and landing upside down and approach angle beta min was closer to vertical and kr was smaller and corresponded to decelerating nearly to a stop. In contrast, the mealworms were caught in mid flight and approach angle beta min was shallower and speed of approach was about constant. 4. tau (r) might be registered acoustically by tau (echo-delay) or by tau (echo-intensity). tau (alpha) might be registered by the bat's directional hearing and gravity sense. 5. The bat's learned the tasks easily, suggesting that the control procedure they used in the experiments was part and parcel of the natural skills they had developed in the wild.

Acoustics↗
PubMed1995

Development of prospective control of catching moving objects in preterm at-risk infants.

Healthy term infants and infants classified as neurologically at-risk because of low birthweight and preterm birth were tested longitudinally between 20 and 48 weeks on the ability to use visual information predictively. Reaching for an object moving at different speeds was assessed; the object was occluded from view by a screen during the last part of its approach. At each infant's first reaching session, gaze anticipated the reappearance of the moving toy; however, onset of reaching and prospective control of gaze and hand varied considerably between the normal and at-risk groups. In addition, some at-risk infants geared their actions not to the time but to the distance that the toy was from the catching place, causing problems with faster-moving toys. The two children who anticipated least well were the only two of the at-risk group who were later diagnosed as having cerebral palsy.

Case-Control Studies↗
PubMed1994

GreA-induced transcript cleavage in transcription complexes containing Escherichia coli RNA polymerase is controlled by multiple factors, including nascent transcript location and structure.

The Escherichia coli GreA and GreB proteins induce cleavage of 3' fragments from nascent transcripts in halted transcription complexes. We have overproduced and purified the GreA protein and tested how it affects initiation, pausing, and termination by E. coli RNA polymerase. Recombinant GreA induced cleavage of two to three nucleotide fragments in two promoter-proximal complexes, whereas an apparently endogenous cleavage removed a single larger fragment. Both types of cleavage stopped once the transcript was shortened to approximately 10 nucleotides. However, during initiation, GreA induced cleavage of transcripts as short as four nucleotides, inhibiting their release as abortive products and stimulating both productive initiation and "primer-shifting" at a weak promoter. GreA induced repetitive cleavage over a long distance in complexes containing a long G-less nascent transcript. However, reverse translocation was inhibited in transcription complexes that contained a G-rich, C-less nascent transcript. Substituting IMP for GMP in the transcript relieved inhibition. Finally, GreA had little effect on transcription through the his and trp leader pause sites or on termination at nine different p-independent terminators. We propose that transcript cleavage and reverse translocation are controlled in part by backsliding of the nascent transcript through an RNA-binding site.

Bacterial Proteins↗
PubMed1994

GreA-induced transcript cleavage is accompanied by reverse translocation to a different transcription complex conformation.

GreA- and GreB-induced transcript cleavage drives reverse translocation of Escherichia coli RNA polymerase on a DNA template in the absence of NTPs (Feng, G.-H., Lee, D. N., Wang, D., Chan, C. L., and Landick, R. (1994) J. Biol. Chem. 269, 22282-22294, accompanying report). During transcript elongation, the sizes of the DNA footprint and the single-stranded transcription bubble vary markedly among transcription complexes halted at different template positions. To test whether transcription complex intermediates formed during transcript cleavage-induced reverse translocation also display heterogeneous conformations at different template positions, we examined the structures of two different transcription complexes before and after GreA treatment. Transcription complexes halted at position +16 after initiation at the T7 A1 promoter or paused at the trpL pause site exhibited strong blocks to transcript cleavage after removal of 6 to 10 nucleotides. In both cases, the down-stream contact between RNA polymerase and DNA moved little during transcript cleavage, thereby increasing its distance from the active site, whereas the upstream DNA contact and the borders of the transcription bubble moved in approximate register with the transcript 3'-end. The backward movements of halted E. coli RNA polymerase are similar to a recently postulated model for discontinuous translocation during transcription, but differ from those reported for arrested RNA polymerase II transcription complexes.

Bacterial Proteins↗
PubMed1994

Where we look when we steer.

Steering a car requires visual information from the changing pattern of the road ahead. There are many theories about what features a driver might use, and recent attempts to engineer self-steering vehicles have sharpened interest in the mechanisms involved. However, there is little direct information linking steering performance to the driver's direction of gaze. We have made simultaneous recordings of steering-wheel angle and drivers' gaze direction during a series of drives along a tortuous road. We found that drivers rely particularly on the 'tangent point' on the inside of each curve, seeking this point 1-2 s before each bend and returning to it throughout the bend. The direction of this point relative to the car's heading predicts the curvature of the road ahead, and we examine the way this information is used.

Automobile Driving↗
PubMed1994

Prospective control in catching by infants.

Catching a moving object requires the ability to predict the future trajectory of the object. To test whether infants can use visual information predictively, reaching for a toy moving at different speeds was investigated in six infants around 11 months of age. The toy was occluded from view by a screen during the last part of its approach. Gaze arrived at the exit side of the screen and the hand started to move forward before the toy had disappeared behind the occluder; these actions were prospectively geared to certain times before the toy would reappear. In addition, hand-movement duration was found to be related to the time of reappearance of the toy--the information used to regulate duration of hand movement being picked up before the toy disappeared behind the occluder. In a longitudinal experiment, the development of predictive reaching was investigated in two infants between the ages of 20 and 48 weeks. At all ages studied, gaze anticipated the reappearance of the moving toy. However, anticipation with hand movement of the disappearance of the toy and the ability to gear actions prospectively to the time (instead of distance) the toy was away from certain points on the track developed relatively late and marked the transition to successfully catching faster-moving toys.

Acceleration↗
PubMed1993

[Disseminated intravascular coagulation--a case report].

A 31 year-old T1PoAoL1 female developed the early Disseminated Intravascular Coagulation (DIC) signs after cesarean section. The patient had recovery completely after transabdomen total hysterectomy (TAH) and blood products transfusion. Case presentation, literature review, possible pathogenetic mechanism and treatment of DIC were discussed.

Adult↗
PubMed1992

Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase.

RNA polymerases pause conspicuously at certain positions on a DNA template. At the well-studied pause sites in the attenuation control regions that precede the trp and his operons, both formation of secondary structure in the nascent transcript and the DNA sequence immediately downstream contribute to pausing. The mechanisms of these effects are unknown. We report here studies on the structure of the RNA and DNA strands in purified trp and his paused transcription complexes in comparison to ten elongation complexes halted by nucleoside triphosphate deprivation. A 14 to 22 nucleotide region of the DNA strands was accessible to modification by KMnO4 or diethylpyrocarbonate in both the paused and halted transcription complexes. However, the region in front of the nucleotide-addition site was reactive only in some halted complexes. In both types of complexes, approximately eight nucleotides on the template strand immediately preceding the 3' end were protected from modification. We also examined the sensitivity of the nascent transcript to RNase A and found that the 3'-proximal eight nucleotide region could be cleaved without complete loss of the potential for elongation. However, a model RNA:DNA hybrid designed to mimic a hybrid in the transcription complex could also be cleaved under similar conditions. Together, the results suggest that the 3'-proximal eight nucleotides of transcript may pair with the DNA template and that this structure is not disrupted by hairpin formation at a pause site. Rather, pausing may result from distinct interactions between RNA polymerase and both the pause RNA hairpin and the downstream DNA sequence.

Base Sequence↗
PubMed1992

Common principle of guidance by echolocation and vision.

1. Using echolocation, bats move as gracefully as birds through the cluttered environment, suggesting common principles of optic and acoustic guidance. We tested the idea by analysing braking control of bats (Macroderma gigas) flying through a narrow aperture with eyes covered and uncovered. 2. Though braking control would seem to require rapid detection of distance and velocity and computation of deceleration, simpler control is possible using the tau function of any sensory variable S that is a power function of distance to aperture. Tau function of S is tau (S) = S/S (the dot means time derivative). Controlled braking is achievable by keeping tau (S) constant. 3. Previous experiments indicated the tau (S) constant procedure is followed by humans and birds in visually controlling braking. Analysis of the bats' flight trajectories indicated they too followed the braking procedure using echolocation. 4. The tau function of echo-delay or of echo-intensity or of angle subtended by directions of echoes from two points on the approach surface could be used to control braking. Aperture size was modulated during flight on some trials in an attempt to test between these possibilities, but the results were inconclusive.

Animals↗
PubMed1992

How do somersaulters land on their feet?

Body movements of trampolinists landing upright from forward somersaults, with eyes open and closed, were analyzed to test a theory of how braking and timing of actions are conjointly controlled. In regulating landing, rotation has to be slowed by extending the body so that it reaches the upright just as the feet hit the trampoline. Extending a theory of visual control of linear braking, it was hypothesized that upright landing is achieved by perceptually regulating body extension so as to keep the ratio angle of body to upright: rate of change of angle (the tau function of the angle) proportional to time-to-landing. The data support the hypothesis, indicate that vision improves precision of control, and argue further for the value of the tau function in the perceptual regulation of action.

Attention↗
PubMed1992

Errors in young children's decisions about traffic gaps: experiments with roadside simulations.

Young children's vulnerability as pedestrians has often been attributed to deficiencies in their decision making about vehicle approach times. Some studies have found a preponderance of risky decisions below the age of eight years. In contrast, studies using a closer simulation of road crossing, known as the pretend road, have found a preponderance of overcautious decisions in young children: traffic gaps of adequate size were frequently rejected (missed opportunities). However, the pretend road has potentially distorting characteristics which may account for this divergent pattern of findings. The experiments reported below show that new simulations that eradicate distortions nevertheless validate the pattern of results produced with the pretend road. Differences between adults and young children were pronounced for missed opportunities, but not for risky decisions. Subsidiary analyses suggest that the risky decisions of the youngest children may have arisen through lapses in attention, rather than deficits in timing. These findings run contrary to the view that attributes young children's pedestrian vulnerability to perceptuo-motor deficiency.

Acceleration↗
PubMed1991

Effect of task on movement control in cerebral palsy: implications for assessment and therapy.

In order to examine the possibility that children with cerebral palsy (CP) find abstract tasks, such as extending the arm as much as possible, more difficult than concrete tasks, such as reaching to grasp an object, nine hemiparetic children with CP and 12 nursery-school children were tested with both a concrete and an abstract task. The children with CP achieved a significantly larger range of movement in the concrete task, whereas the nursery-school children showed no difference between tasks. Thus the CP children's poorer performance on the abstract task did not fully reflect their movement capability. This means that conventional neurological measurements of limb function in cerebral palsy, which mainly use abstract tasks or passive movements, will give an incomplete picture of the child's action capability.

Cerebral Palsy↗
PubMed1990

Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences.

Escherichia coli RNA polymerase pauses immediately after transcription of certain sequences that can form stable secondary structures in the nascent RNA transcript; pausing appears to be essential for several types of bacterial transcription attenuation mechanisms. Because base changes that weaken the RNA secondary structures reduce the half-life of pausing by RNA polymerase, nascent transcript RNA hairpins are thought to cause pausing at these sites. We show here that, for the well characterized trpL pause site, the determinants of transcription pausing are not limited to the RNA hairpin, but include the not-yet-transcribed sequence of DNA immediately downstream from the pause site. We show that this effect extends to bases up to fourteen nucleotides downstream from the pause site, that placement of a oligo(dT) tract in the nontranscribed strand in this region does not convert the pause site to a termination site, and that shifting the position of pausing by one nucleotide downstream almost eliminates pausing. From an analysis of many variants of this downstream sequence, we argue that the effect of downstream sequence is not related simply to its GC content. We suggest that these effects are mediated by altered interactions between RNA polymerase and the DNA template downstream from the enzyme's active site.

Base Sequence↗
PubMed1990

Development of looking with head and eyes.

Research into stabilization of gaze has concentrated on how the eyes counterrotate to compensate for head rotation. There is little information on how head movements function as an integral part of gaze stabilization. The head and eye coordination of six adults and six infants was tested under two conditions: tracking a moving target when the body was stationary; fixating a stationary target when the body was turning. Under each condition, both infants and adults turned their heads more than their eyes in stabilizing gaze. The infants were tested at 3-week intervals between the ages of 11 and 28 weeks. During this period, the precision with which head turning was coupled to their own or the target movement developed to near adult level, showing rapid growth between 11 and 16 weeks. However, the infants' ability to couple the eyes onto the target did not change over the tested period, remaining much less precise than the adults'. These findings have important implications for the assessment of abnormal gaze stabilization, which could facilitate the early diagnosis of perceptuomotor dysfunction.

Arousal↗
PubMed1990

Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination.

Control of transcription at pause and termination sites is common in bacteria. Many transcriptional pause and termination events are thought to occur in response to formation of an RNA hairpin in the nascent transcript. Some mutations in the beta-subunit of Escherichia coli RNA polymerase that confer resistance to the transcription inhibitor rifampicin also alter the response to transcriptional pause and termination signals. Here, we report isolation of termination-altering mutations that do not confer rifampicin resistance and show that such mutations occur predominantly in limited regions of the beta-subunit polypeptide. One region is between amino acid residues 500 and 575, which encompasses the locations of almost all known rifampicin-resistance mutations. Many termination-altering mutations also occur in two other regions: between amino acid residues 740 and 840 and near the carboxyl terminus of the beta-subunit (amino acid residues 1225-1342). Amino acid sequences in these three regions of the beta-subunit are conserved between prokaryotic and eukaryotic beta-subunit homologs. Several mutations that alter transcription termination in vitro affect amino acid residues that are identical in prokaryotic and eukaryotic RNA polymerase beta-subunit homologs, suggesting that they alter an important function common to multisubunit RNA polymerases. We propose that these three regions of the beta-subunit may contact the nascent RNA transcript, the RNA-DNA heteroduplex, or the DNA template in the transcription complex and that mutations in these regions alter transcription pausing and termination by affecting these contacts.

Amino Acid Sequence↗