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DNA insertions in the 'silent' regions of the 2 microns plasmid of Saccharomyces cerevisiae influence plasmid stability.

The 2 microns plasmid of the yeast Saccharomyces cerevisiae is in principle a suitable vector for expression of foreign genes, due to its high copy number and extreme stability. However, the cloning of genes into 2 microns often results in a reduced copy number and/or reduced stability. One reason for this observed instability could be that the inserts in general were made in one of the several open reading frames (ORFs) of the plasmid. Therefore we studied the effect on stability of insertions in the silent regions of 2 microns without interrupting any known essential regions or ORFs. Using the SnaBI site, a yeast-integrating plasmid (Yip5) was introduced into the region between the ARS and STB locus in two possible orientations. The resulting plasmids could be stably maintained in the cells without the need for complementation by the wild-type 2 microns plasmid. However, the stability of these plasmids in a cir. host was still one to two orders of magnitude lower (0.2% and 0.8% respectively) as reported for the wild-type 2 microns (0.01%). Removal of 2 kb of the bacterial sequences from Yip5 did not increase stability. The stability was dependent on the orientation of the insert. We found that in the less stable orientation, transcription originating from the insert was running into the STB region. DNA inserted in the XmaIII site located outside the ORFs in the REP2/FLP intergenic region influenced both stability and copy number of the plasmid. These effects are strongly dependent on the size of the insert. Insertion of a 2 kb DNA fragment increased the copy number, probably through an effect on FLP expression.

Blotting, Northern↗

Intracellular stability of alpha fragments of beta-galactosidase: effects of amino-terminally fused polypeptides.

Intracellular stability of alpha fragments of beta-galactosidase in Escherichia coli has been studied by pulse-chase/immunoprecipitation experiments. An alpha fragment encoded by the pUC118 vector was relatively stable with an estimated half-life of about 12 min at 37 degrees C, whereas another vector, pSTV28, encoded a less stable alpha fragment that had a different carboxy-terminal sequence. Stability of the fragment was found to be affected markedly by amino-terminal attachment of other sequences. An amino-terminal fusion of a sequence derived from cytoplasmic domain 4 of the SecY protein shortened the half-life of the alpha fragment to less than 1 min. In contrast, an amino-terminal sequence from the NusG protein had no apparent effect on the stability of the fragment. In a fusion protein in which the intact SecY protein was fused to the alpha fragment, stabilization of the SecY part by overproduction of the partner SecE protein resulted in an increased alpha complementation activity of beta-galactosidase. These results indicate that stability of alpha fragment can be dictated by the stability of the fused protein. The alpha fragment of beta-galactosidase, which is unique in that it is largely unstructured but can be "active" in alpha complementation, may be used as an in vivo indicator of stability of proteins attached to it.

Amino Acid Sequence↗

Nonlinear Stability of an Electrified Interface Supporting Surface Charges between Two Viscous Fluids.

The charged boundary between two viscous fluid media is taken to be under the influence of a vertical constant electric field producing surface charges. We illustrate the solution of the nonlinear perturbation using the method of multiple scales. In the neutral stability the relation between surface charge density and surface viscous force is obtained. Because the viscosity ratio has the same value as the dielectric constant ratio a singularity in the nonlinear coefficient of Schrödinger equation is observed and gradually creates a growth in the instability. Previous works have failed to recognize this singularity by not including the effects of viscosity. The absence of surface viscous force leads to decay in the surface charge density and a growth in the stability occurs. Global stability and local instability are observed in the stability diagrams. The duality mechanism is observed for the electric field, the surface charge density, and the stratified kinematic viscosity. Further, the behavior away from neutral stability is explained by examination of the dynamical system. It is observed that the stabilizing or destabilizing role for the surface charge density has been related to the destabilizing or stabilizing role of the density influence. Copyright 1999 Academic Press.

Journal Article↗

Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis.

Bovine pancreatic trypsin inhibitor (BPTI) serves as an important model system for the examination of almost all aspects of protein structure. Systematic studies of the effects of mutation on the thermodynamic stability of BPTI, however, have been limited by the extreme stability of the protein. A derivative of BPTI containing only the 5-55 disulfide bond, termed [5-55]Ala, has been shown previously to fold into a structure very similar to that of native BPTI and to be a functional trypsin inhibitor. [5-55]Ala undergoes a reversible thermal unfolding transition with a melting temperature of 39 degrees C, and is therefore well suited for stability studies. Using an alanine-scanning mutagenesis approach, we have examined the contribution to stability of each side-chain in the [5-55]Ala derivative of BPTI. These studies demonstrate the importance of the two hydrophobic cores composed largely of clusters of aromatic residues, as well as the internal hydrogen-bonding network, in stabilizing BPTI. Overall, there is a strong relationship between change in buried surface area and stability for both polar and hydrophobic residues, with proportionality constants of 50 and 20 cal/A2, respectively. None of the alanine substitutions substantially stabilized [5-55]Ala. Nonetheless, approximately 60% (28/46) of the alanine mutants were destabilized by less than 10 degrees C, suggesting that a form of BPTI with up to half of its residues being alanine could fold into a stable structure resembling the native one.

Alanine↗

Thermodynamic stability of the molten globule states of apomyoglobin.

Whereas horse apomyoglobin is fully unfolded at pH 2 in the absence of salt, addition of a salt such as sodium chloride or sodium trichloroacetate stabilizes the molten globule state. Thermal unfolding of the salt-stabilized molten globule states of horse apomyoglobin at pH 2 measured by far-UV circular dichroism occurs not only on heating (i.e. heat-denaturation) but also on cooling (i.e. cold-denaturation). This demonstrates that a hydrophobic interaction contributes to the stability of the molten globule state and suggests that the unfolding transition can be represented by a cooperative two-state mechanism. To clarify the mechanism of conformational transition, we investigated the thermal unfolding of the chloride-stabilized molten globule state by differential scanning calorimetry. We observed a broad but distinct excess heat capacity peak, which is consistent with the unfolding transition measured by circular dichroism. To further characterize the molten globule states, we examined by far-UV circular dichroism the denaturant-induced unfolding transitions of the molten globule states stabilized by sodium chloride or sodium trichloroacetate. The urea-induced unfolding transitions of the molten globule states were explained by the two-state mechanism. The guanidine-hydrochloride-induced unfolding experiments clarified that the trichloroacetate-stabilized molten globule state is distinct from the chloride-stabilized one and that the former involves additional helical segment(s). These results support a view that the thermal unfolding of the molten globule states at pH 2 can be approximated by a two-state transition. However, several results suggested that a combined mechanism incorporating the two-state transition and a gradual structural change would be more general in describing the conformational transition of the molten globule states.

Animals↗

Salt effects on protein stability: two-stranded alpha-helical coiled-coils containing inter- or intrahelical ion pairs.

An investigation into the role of surface-accessible ion pairs in protein stability was carried out by determining the effects of added salt (KCl, MgCl2 and LaCl3) at neutral and acidic pH on the stability of de novo designed two-stranded alpha-helical coiled-coils. The effects of salt on the stability of coiled-coils containing interhelical i to i' + 5 or intrahelical i to i + 4 and i to i + 3 Lys-Glu ion pairs were compared to the effects on the stability of a control coiled-coil, which contained no intra- or interhelical ion pair. These studies indicate that ionic interactions contribute to coiled-coil stability. The results show that added salt can have complex effects on protein stability, involving stabilizing and destabilizing contributions with the net effect depending on the nature of the charged residues and ionic interactions present in the protein.

Amino Acid Sequence↗

The structural stability of the co-chaperonin GroES.

The structural stability of the co-chaperonin GroES has been studied by high sensitivity differential scanning calorimetry and circular dichroism under different solvent conditions. The thermal folding/unfolding of GroES is a spontaneous reversible process involving a highly cooperative transition between folded heptamers and unfolded monomers. During the denaturation process folded monomers are energetically unfavourable and consequently never become populated to an appreciable degree. Analysis of the high resolution structure indicates that isolated folded monomers of GroES bury a significantly smaller fraction of their total surface than typical globular proteins of similar molecular mass. For this reason the intramolecular interactions within each GroES monomer appear not to be sufficient for thermodynamic stabilization. The stabilization of the heptameric structure is due primarily to intersubunit interactions rather than intrasubunit interactions. These interactions favor oligomerization both enthalpically and entropically. Despite the high density of charged residues, the stability of GroES shows no measurable dependence on salt concentration at pH 7. On the other hand, millimolar concentrations of magnesium stabilize GroES, presumably by specific binding. The stabilization elicited by Mg2+ is consistent with a dissociation constant of the order of 0.5 mM and approximately three binding sites per heptamer. These results emphasize the role of quaternary structure in the stabilization of small oligomeric proteins.

Calorimetry, Differential Scanning↗

In the absence of translation, RNase E can bypass 5' mRNA stabilizers in Escherichia coli.

In Bacilli, ribosomes or 30 S ribosomal subunits that are stalled or bound on mRNAs can stabilize downstream regions, hence the view that the degradation machinery scans mRNAs from their 5' end. In E. coli, several mRNAs can also be stabilized by secondary structures involving their 5' end. To test whether a bound 30 S subunit can act as a 5' stabilizer in E. coli, we compare here the stabilities of two untranslated variants of the lacZ mRNA, the decay of which is controlled by RNase E. In the first variant, a 35 nt region including the Ribosome Binding Site (RBS) is deleted, whereas in the second it is replaced by an 11 nt-long Shine-Dalgarno (SD) sequence lacking an associated start codon. In the latter variant, an 80 nt fragment encompassing the SD and extending up to the mRNA 5' end was stable in vivo (t1/2>one hour), reflecting 30 S binding. Yet, the full-length message was not more stable than when the SD was absent, although two small decay intermediates retaining the 5' end appear somewhat stabilized. A third variant was constructed in which the RBS is replaced by an insert which can fold back onto the lac leader, creating a putative hairpin involving the mRNA 5' end. The fragment corresponding to this hairpin was stable but, again, the full-length message was not stabilized. Thus, the untranslated lacZ mRNA cannot be protected against RNase E by 5' stabilizers, suggesting that mRNA scanning is not an obligate feature of RNase E-controlled degradation. Altogether, these results suggest important differences in mRNA degradation between E. coli and B. subtilis. In addition, we show that mRNA regions involved in stable hairpins or Shine-Dalgarno pairings can be metabolically stable in E. coli.

Base Sequence↗

Six-year stability of parent-reported problem behavior in an epidemiological sample.

An epidemiological sample of 936 Dutch children originally aged 4-11 years was assessed at 2-year intervals over a 6-year period. Parents completed the Child Behavior Checklist (CBCL) on all four occasions. Stability coefficients computed for eight CBCL syndromes, Internalizing and Externalizing dimensions, and total problems revealed considerable long-term stability. There was no significant difference in the 6-year stability of internalizing vs. externalizing scores. This finding was at odds with reports of considerably lower stability of internalizing behavior, and was consistent with findings suggesting that the stability of internalizing problems should not be underestimated. The magnitude and specificity of the long-term stability of internalizing and externalizing scores lends support to the validity of these behavioral dimensions as tapped by the CBCL. No significant sex or age differences in the stability of problem behaviors were found.

Age Factors↗

Effects of 16, 16-dimethyl prostaglandin E2 on lysosomal membrane stability in rat stomach.

The lysosomal membrane encloses numerous hydrolytic enzymes and prevents the cytoplasm from being damaged by these enzymes. It is possible that the fragility of this membrane may be implicated in the pathogenesis of gastric mucosal damage. We investigated the effects of 16,16-dimethyl prostaglandin E2 (dmPGE2), which is known to protect the gastric mucosa from various noxious agents, on lysosomal membrane stability in the rat stomach. Sodium taurocholate (TC) was used as the damaging agent. To assess lysosomal membrane stability in the gastric mucosa, we assayed acid phosphatase released from lysosomes isolated from a gastric mucosal homogenate. To assess lysosomal membrane stability in gastric surface epithelial cells, we used laser scanning confocal microscopy to observe the fading of red fluorescence in living cells vitally stained with acridine orange. Exogenous dmPGE2 enhanced lysosomal membrane stability in the gastric mucosa, whereas TC decreased it. In gastric surface epithelial cells, exogenous dmPGE2 protected the cells against TC-induced damage and prevented TC-induced decreased lysosomal membrane stability. It was concluded that a decrease in lysosomal membrane stability seemed to be closely involved in the pathogenesis of gastric mucosal damage. Moreover, it appears that stabilization of the lysosomal membrane by exogenous dmPGE2 may contribute to its protective effect in the gastric mucosa, both at the level of gastric surface epithelial cells and in regard to the entire gastric mucosa.

Acid Phosphatase↗

[Dynamic radioulnar convergence after Darrach operation, soft tissue stabilizing operations of the distal ulna and ulnar head prosthesis implantation--an experimental biomechanical study].

The most common method of treating the arthrotic distal radioulnar joint (DRUJ) is resection of the entire ulnar head (Darrach procedure). Complications related to instability of the distal forearm resulting from loss of the ulnar head are usually manifested by pain and weak grip strength and have remained the drawbacks of this procedure. In an attempt to mechanically stabilize the distal forearm, an endoprosthesis was developed to replace the ulnar head after Darrach resection. The purpose of this study was to: 1) evaluate the dynamic effects of the Darrach procedure on radioulnar convergence; and 2) evaluate the mechanical efficacy of two soft tissue stabilizing techniques (Pronator quadratus advancement flap and ECU/FCU tenodesis) for the unstable distal ulnar stump and 3) the stability after the implantation of an ulnar head endoprosthesis following a Darrach resection on radioulnar convergence. With a dynamic PC-controled forearm simulator the rotation of 7 fresh-frozen cadaver upper extremities was actively and passively performed while loading relevant muscles. Resultant total forearm torque and the 3-dimensional kinematics of the ulna, radius and third metacarpal were recorded simultaneously. The implantation of the ulnar head endoprosthesis effectively restored the stability of the DRUJ. There were significantly better results after the implantation of the prosthesis compared with the Darrach and the soft tissue stabilization procedures. This study provides laboratory validity to the option of implanting an ulnar head endoprosthesis as an attempt to stabilize the distal forearm after Darrach resection in lieu of performing soft tissue stabilization techniques.

Biomechanical Phenomena↗

Adaptive control of gait stability in reducing slip-related backward loss of balance.

The properties of adaptation within the locomotor and balance control systems directed towards improving one's recovery strategy for fall prevention are not well understood. The purpose of this study was to examine adaptive control of gait stability to repeated slip exposure leading to a reduction in backward loss of balance (and hence in protective stepping). Fourteen young subjects experienced a block of slips during walking. Pre- and post-slip onset stability for all slip trials was obtained as the shortest distance at touchdown (slipping limb) and lift-off (contralateral limb), respectively, between the measured center of mass (COM) state, that is, position and velocity relative to base of support (BOS) and the mathematically predicted threshold for backward loss of balance. An improvement in pre- and post-slip onset stability correlated with a decrease in the incidence of balance loss from 100% (first slip) to 0% (fifth slip). While improvements in pre-slip stability were affected by a proactive anterior shift in COM position, the significantly greater post-slip onset improvements resulted from reductions in BOS perturbation intensity. Such reactive changes in BOS perturbation intensity resulted from a reduction in the demand on post-slip onset braking impulse, which was nonetheless influenced by the proactive adjustments in posture and gait pattern (e.g., the COM position, step length, flat foot landing and increased knee flexion) prior to slip onset. These findings were indicative of the maturing process of the adaptive control. This was characterized by a shift from a reliance on feedback control for postural correction to being influenced by feedforward control, which improved pre-slip stability and altered perturbation intensity, leading to skateover or walkover (>0.05 m or <0.05 m displacement, respectively) adaptive strategies. Finally, the stability at contralateral limb lift-off was highly predictive of balance loss occurrence and its subsequent rapid reduction, supporting the notion of the internal representations of stability limits that could be modified and updated, as a key component in the adaptive control.

Adaptation, Physiological↗

The effect of time to peak ankle torque on balance stability boundary: experimental validation of a biomechanical model.

Pai and Patton (1997), using a biomechanical model, determined a set of feasible center of mass (CM) velocity-position combinations (balance stability boundary) that guarantee upright stability. In their study, the magnitude of the restoring ankle torque was used to study the subject's ability to recover balance. Recent studies have suggested that the ability to maintain a stable posture depends not only on the magnitude of the restoring torque but also on the time to generate this torque. The objectives of the present study were: (1) to build a biomechanical model that predicts the balance stability boundary which includes time to peak ankle torque, (2) to determine the capability of the model to predict successful and failed experimental balance recovery trials, and (3) to compare the predictive capability of the biomechanical model with that of a statistical model (logistic regression). A single-link-plus-foot biomechanical model was used to determine a set of balance stability boundaries, computed from the combination of maximum CM velocity and related CM position, for various times to peak ankle torque. An experiment was conducted to validate the biomechanical model. The participants self-initiated a forward destabilization and were asked to regain balance using an ankle feet-in-place strategy. Also, a forward stepwise logistic regression (predictors: CM position and velocity and time to peak ankle torque) was used to discriminate between successful and failed experimental trials. (1) The outcomes of the biomechanical model confirmed that the time to peak ankle torque drastically constrained the stability boundaries. (2) The biomechanical model predicted 79.9% of the failed experimental trials and 74.5% of the successful experimental trials. (3) The stepwise logistic regression included all independent variables and predicted 57.2% of the failed and 93.7% of the successful experimental trials. Hence, the biomechanical model showed better predictive capability than the statistical model for identifying unsuccessful balance recovery. It is noteworthy that the balance stability boundaries constrained by the speed of ankle torque development predicted the outcome of the experimental trial earlier in the time series than balance stability boundary constrained by constant ankle torque. Overall, the present biomechanical model may serve as an assessment tool to develop specific interventions towards improving a patient's speed of ankle torque development and to possibly reduce falling frequency.

Accidental Falls↗

Evolutionary and dynamic stability in continuous population games.

Asymptotic stability under the replicator dynamics over a continuum of pure strategies is shown to crucially depend on the choice of topology over the space of mixed population strategies, namely probability measures over the real line. Thus, Strong Uninvadability, proved by Bomze (1990) to be a sufficient condition for asymptotic stability under the topology of variational distance between probability measures, implies convergence to fixation over a pure strategy x(*) only when starting from a population strategy which assigns to x(*) a probability sufficiently close to one. It does not imply convergence to x(*) when starting from a distribution of small deviations from x(*), regardless of how small these deviations are. It is, therefore, suggested that when a metric space of pure strategies is involved, another topology, hence another stability condition, may prove more relevant to the process of natural selection. Concentrating on the case of a one dimensional continuous quantitative trait, we resort to the natural Maximum Shift Topology in which an epsilon -vicinity of the fixation on a pure strategy x(*) consists of all mixed population strategies with support which includes x(*) and is in the epsilon -neighborhood of x(*). Under this topology, a relatively simple necessary and sufficient condition for replicator asymptotic stability, namely Continuous Replicator Stability (CRSS), is demonstrated. This condition is closely related to the static stability condition of Neighbor Invadability (Apaloo 1997), and slightly stronger than the condition of Continuous Stability (Eshel and Motro 1981).

Biological Evolution↗

Stability in legged locomotion.

Stability is a key element in a gait synthesis. Static stability margins are widely adopted in crawlers, while no similar approach has been developed for dynamically stable systems. Utilizing an analytical approach, we developed a set of easy-to-calculate stability indices to describe instantaneous static and dynamic (In)stability for a certain group of walking systems. The analysis is based on a thorough analysis of the interaction between ground reaction forces and the walking system. The indices are applicable to walking systems regardless of the number of legs or mechanical/biological design. We show that static and dynamic stability are independent of each other. We suggest a possible categorization of gait modes based on stability. Stability characteristics are analyzed in a healthy and highly pathological human gait. Finally, we discuss the applicability of the proposed methods.

Gait↗

Relative phase dynamics in perturbed interlimb coordination: stability and stochasticity.

Various stability features of bimanual rhythmic coordination, including phase transitions, have been modeled successfully by means of a one-dimensional equation of motion for relative phase obeying a gradient dynamics, the Haken-Kelso-Bunz model. The present study aimed at assessing pattern stability for stationary performance and estimating the model parameters (a, b, and Q) for the stochastic extension of this model. Estimates of a and b allowed for reconstruction of the potential defining the gradient dynamics. Two coordination patterns between the forearms (in-phase, antiphase) were performed at seven different frequencies. Model parameters were estimated on the basis of an exponential decay parameter describing the relaxation behavior of continuous relative phase following a mechanical perturbation. Variability of relative phase and relaxation time provided measures of pattern stability. Although the predicted inverse relation between pattern stability and movement frequency was observed for the lower tempo conditions, it was absent for the higher tempos, reflecting the influence of task constraints. No statistically significant differences in stability were observed between the two coordination modes, indicating the influence of intention. The reconstructed potential reflected the observed stability features, underscoring the adequacy of the parameter estimations. The relaxation process could not be captured adequately by means of a simple exponential decay function but required an additional oscillatory term. In accordance with previous assumptions, noise strength Q did not vary as a function of movement frequency. However, systematic differences in Q were observed between the two coordination modes. The advantages and (potential) pitfalls of using stationary performance of single patterns to examine the stability features of a bistable potential were discussed.

Computer Simulation↗

Three-dimensional stabilization provided by the external spinal fixator compared to two internal fixation devices: a biomechanical in vitro flexibility study.

We performed an in vitro study to investigate the stabilization (i.e. motion reduction) provided by the external spinal fixator (ESF), and to compare the three configurations of the ESF with two internal fixation techniques. Six human cadaveric lumbar spine specimens (L3-S1) were subjected to multidirectional flexibility testing in six configurations: (1) intact, (2) ESF in neutral, (3) ESF in distraction, (4) ESF in compression, (5) translaminar facet screw fixation, and (6) internal transpedicular fixation. Both the ESF and the internal fixation systems stabilized the specimens from L4 to S1. In each testing configuration, pure bending moments of flexion-extension, bilateral axial rotation, and bilateral lateral bending were applied to the uppermost vertebra stepwise to a maximum of 10 Nm. The rigid body motion between the vertebrae was measured using an optoelectronic camera system, and custom software was used to calculate the intervertebral rotations. For each applied motion in all testing configurations, the total range of motion (ROM) of L4-S1 is reported. All three ESF configurations stabilized the spine significantly when compared to the intact specimen. The ESF in compression provided significantly more stabilization in flexion-extension than the two other ESF configurations, but no other significant differences were found between the three ESF modes. In flexion-extension the ESF stabilized the spine significantly when compared with the two internal fixation devices. Only in bilateral lateral bending was the ESF inferior to internal transpedicular fixation in providing stabilization. The results of the present study suggest that the ESF provides a high degree of stabilization for preoperative assessment of selected low back pain patients. Whether other non-mechanical factors affect the pain relief experienced by the patients remains unknown.

Adult↗

Characteristics of an extended internal fixation system for polysegmental transpedicular reduction and stabilization of the thoracic, lumbar, and lumbosacral spine.

The Kluger internal fixator, with its artificial fulcrum outside the operative site, had to be extended for multisegmental use. Three different prototypes, called Central Bar (CB), Double Bar I (DB I) and Double Bar II (DB II) were designed, which were fully compatible with the existing reduction system. To evaluate the ability of these newly developed systems to provide primary stability in a destabilized spine, their stiffness characteristics and stabilizing effects were investigated in multidirectional biomechanical stability tests and compared with those of the clinically well-known Cotrel-Dubousset (CD) system. The investigations were performed on a spine tester using freshly prepared calf spines. The model tested was that of an intact straight spine followed by a defined three-column lesion simulating the most destabilizing type of injury. Pure moments of up to 7.5 Nm were continuously applied to the top of each specimen in flexion/extension, left/right axial rotation, and left/right lateral bending. Segmental motion was measured using a three-dimensional goniometric linkage system. Range of motion and stiffness within the neutral zone were calculated from obtained load-displacement curves. The DB II attained 112.5% (P = 0.26) of the absolute stiffness of the CD system in flexion and enhanced its stability in extension by up to 144.3% (P = 0.004). In axial rotation of the completely destabilized spine, this system achieved 183.3% of the stiffness of the CD system (P < 0.001), and in lateral bending no motion was measured in the most injured specimens stabilized by the DB II. The DB I, which was the first to be designed and was considered to provide high biomechanical stability, did not attain the stiffness standard set by the CD system in either flexion/extension or axial rotation of the most injured spine. The study confirms that it is worthwhile to evaluate in vitro the biomechanical properties of a newly developed implant before its use in patients, in order to refine weak construction points and help to reduce device-related complications and to better evaluate its efficacy in stabilizing the spine.

Animals↗