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PubMed1994

Molecular recognition of antigenic polysaccharides: a conformational comparison of capsules from Streptococcus pneumoniae serogroup 9.

Aqueous solution conformations of three antigenic bacterial capsular polysaccharides (CPS) from S. pneumoniae serogroup 9 were determined using a combination of NMR data (NOE build-up rates and conformation-dependent chemical shifts), simulated annealing, and molecular dynamics simulations. Each polymer adopts a flexible extended ribbon conformation in solution. Conformations of structural elements shared by each PS are indistinguishable. Differences in conformations are minor and localised at the sites of structural variations; there is no evidence of long-range stabilisation of a secondary structure. It is likely that antigenic specificity of Group 9 PS is dominated by local structural variation rather than by conformational differences.

Bacterial Capsules↗

PubMed1981

Biophysical responses of red cell-membrane systems to very low concentrations of inorganic mercury.

Changes in red blood cell size, deformability, and osmotic fragility are indicators of altered condition and/or altered regulatory processes at the whole cell and membrane levels. An agent, such as HgCl2, that brings about specific changes of this kind can therefore serve as a selective probe of such cell condition and regulatory state. Conversely, for a health-threatening agent "active" in this way, the cell-membrane responses serve to clarify the more fundamental bases of its toxicity, as well as to permit identification and characterization of its early and low-level actions on living systems. Taking advantage of recent advances in the technique of "resistive pulse spectroscopy," we present a coordinated study of these three interrelated biophysical properties for the interactions of HgCl2 with human red cells. We thereby are able to extend previous studies of this kind into domains of shorter time (instantaneous exposures), lower level exposures (down to 10(-9) M, well below the level of acute human toxicity), as well as to additional kinds of responses (e.g., "dynamic osmotic hemolysis"). For conditions ranging from 10(-4) to 10(-9) M in HgCl2, for instantaneous to 90-min-incubated exposures, for medium osmolarities from 120 to 300, the matrix of observed cell responses includes relative swelling as well as shrinkage, changes in deformability, and both enhancement of and protection against osmotic hemolysis. Some unexpected short-term effects of time and temperature of storage of blood cell stock samples, with respect to increasing and decreasing osmotic fragility, are also reported. These apparently disparate results are interpreted in terms of mercury interactions with cell and membrane SH groups, and a reasonable rationale is presented for most of the responses in terms of disruption of passive and active Na+-K+, gradient controls, plus interactions with cellular proteins.

Adult↗

PubMed1988

The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study.

The solution conformation of the antibacterial polypeptide cecropin A from the Cecropia moth is investigated by nuclear magnetic resonance (NMR) spectroscopy under conditions where it adopts a fully ordered structure, as judged by previous circular dichroism studies [Steiner, H. (1982) FEBS Lett. 137, 283-287], namely, 15% (v/v) hexafluoroisopropyl alcohol. By use of a combination of two-dimensional NMR techniques the 1H NMR spectrum of cecropin A is completely assigned. A set of 243 approximate interproton distance restraints is derived from nuclear Overhauser enhancement (NOE) measurements. These, together with 32 distance restraints for the 16 intrahelical hydrogen bonds identified on the basis of the pattern of short-range NOEs, form the basis of a three-dimensional structure determination by dynamical simulated annealing [Nilges, M., Clore, G.M., & Gronenborn, A.M. (1988) FEBS Lett. 229, 317-324]. The calculations are carried out starting from three initial structures, an alpha-helix, an extended beta-strand, and a mixed alpha/beta structure. Seven independent structures are computed from each starting structure by using different random number seeds for the assignments of the initial velocities. All 21 calculated structures satisfy the experimental restraints, display very small deviations from idealized covalent geometry, and possess good nonbonded contacts. Analysis of the 21 converged structure indicates that there are two helical regions extending from residues 5 to 21 and from residues 24 to 37 which are very well defined in terms of both atomic root mean square differences and backbone torsion angles. For the two helical regions individually the average backbone rms difference between all pairs of structures is approximately 1 A. The long axes of the two helices lie in two planes, which are at an angle of 70-100 degrees to each other. The orientation of the helices within these planes, however, cannot be determined due to the paucity of NOEs between the two helices.

Anti-Bacterial Agents↗

PubMed2025

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.

The Klebsiella pneumoniae species complex inhabits a wide variety of hosts and environments, and is a major cause of antimicrobial resistant infections. Genomics has revealed the population comprises multiple species/sub-species and hundreds of distinct co-circulating sub-lineage (SLs) that are associated with distinct gene complements. A substantial fraction of the pan-genome is predicted to be involved in metabolic functions and hence these data are consistent with metabolic differentiation at the SL level. However, this has so far remained unsubstantiated because in the past it was not possible to explore metabolic variation at scale. Here, we used a combination of comparative genomics and high-throughput genome-scale metabolic modeling to systematically explore metabolic diversity across the K. pneumoniae species complex (n = 7,835 genomes). We simulated growth outcomes for each isolate using carbon, nitrogen, phosphorus, and sulfur sources under aerobic and anaerobic conditions (n = 1,278 conditions per isolate). We showed that the distributions of metabolic genes and growth capabilities are structured in the population, and confirmed that SLs exhibit unique metabolic profiles. In vitro co-culture experiments demonstrated reciprocal commensalistic cross-feeding between SLs, effectively extending the range of conditions supporting individual growth. We propose that these substrate specializations may promote the existence and persistence of co-circulating SLs by reducing nutrient competition and facilitating commensal interactions. Our findings have implications for understanding the eco-evolutionary dynamics of K. pneumoniae and for the design of novel strategies to prevent opportunistic infections caused by this World Health Organization priority antimicrobial resistant pathogen.

Klebsiella pneumoniae↗

PubMed1977

Pulmonary mechanics in normal rats.

A versatile, whole-body pressure, or volume plethysmographic system for the study of pulmonary mechanics in anesthetized, tracheotomized rats has been described. Lung volumes and lung compliance values were in good agreement with those previously reported. Pulmonary resistance and chest wall compliance values were lower than those previously reported. Total dynamic compliance remained independent of respiratory frequency between 40 and 320 breaths/min. Flow-limiting behavior was demonstrated from a series of imposed forced expiratory maneuvers of graded effort. With a deflation pressure of 30 cmH2O, the effort-independent range of maximum flow extended to 40-50% of vital capacity. Maximal flow-static recoil pressure relationships were essentially linear over the effort independent portion of the flow-volume curve. Substitution of a low-density gas mixture (80% He-20% O2) for air resulted in increased forced expiratory flow rates but the magnitude of the response was considerably less than that which has been reported in man.

Airway Resistance↗

PubMed1992

Automatic focus correction for spot-scan imaging of tilted specimens.

The variation in defocus within an image of a highly tilted specimen can be a serious source of artifact. Spot-scan imaging can be combined with dynamic focusing to greatly reduce this range of defocus. A protocol is described for determining the parameters required for the automatic focus compensation during the recording of a spot-scan image. Images of a gold test specimen demonstrate the efficacy of this procedure in extending the area of the image that contains high-quality data. In case the tilt angle or resolution is high enough that the height difference of the specimen within each small illuminated area is larger than the depth of field, the image must be treated to compensate for the focus variation. The same principle is used as was developed for compensation of conventional images of tilted specimens.

Artifacts↗

PubMed1976

Force-velocity relations and fiber composition in human knee extensor muscles.

Standardized measurements of dynamic strength of the kneee extensor muscles were performed in 25 healthy male subjects (17-37 yr) by means of isokinetic contractions, i.e., knee extensions with constant angular velocities. Overall variation between double determinations of maximal torque throughout the 90 degrees arc of motion (0 degrees = fully extended leg) averaged 10% for the different constant velocities chosen. At any given angle of the knee the torque produced was higher for isometric than for dynamic contractions. Dynamic torque decreased gradually with increased speed of shortening. Peak dynamic torque was reached at knee angles in the range: 55-66 degrees, with a displacement toward smaller knee angles with higher angular velocities. Correlations were demonstrated between peak torque produced at the highest speed of muscle shortening and percent as well as relative area of fast twitch fibers in the contracting muscle. In addition muscles with a high percentage of fast twitch fibers had the highest maximal contraction speeds. These observations on intact human skeletal muscle are consistent with earlier findings in animal skeletal muscle preparations.

Adolescent↗

PubMed1992

Pantalar and tibiotalocalcaneal arthrodesis for post-traumatic osteoarthrosis of the ankle and hindfoot.

Twenty-one patients had a unilateral extended arthrodesis of the ankle and hindfoot (a tibiotalocalcaneal procedure in thirteen patients and a pantalar procedure in eight) for post-traumatic osteoarthrosis or deformity, or both. The operation was performed through a transfibular extended lateral approach, and autogenous bone graft and rigid internal fixation was used. A final alignment of 0 to 5 degrees of valgus, 0 to 5 degrees of calcaneus, and external rotation equal to that of the contralateral side was sought. Subjective and objective evaluation, including a personal interview, physical examination, and radiographic and dynamic pedobarographic analysis, was performed at a mean interval of thirty-two months (range, twenty-four to fifty-four months) after the operation. A solid fusion was achieved in eighteen (86 per cent) of the twenty-one patients. There were five malunions (24 per cent) and two superficial wound problems (10 per cent). Of the seventeen patients who were not retired from work, eleven returned to work: nine to an occupation that involved standing and two to a sedentary occupation. Although seventeen (81 per cent) of the twenty-one patients reported that they were much improved, twenty (95 per cent) had some pain, and most benefited from modifications in shoe-wear. Patients who had had a tibiotalocalcaneal arthrodesis were more mobile and functioned at a higher level than those who had had a pantalar arthrodesis. Extended arthrodesis of the ankle and hindfoot is a complex, technically demanding procedure, and should be regarded as a salvage operation capable of producing a satisfactory result and usually providing a reasonable alternative to amputation.

Adult↗

PubMed1991

Nuclear magnetic resonance investigations of calcium antagonist drugs. II: Conformational and dynamic features of verapamil in [2H6]DMSO.

Conformational features of verapamil in [2H6]DMSO have been delineated by measuring 13C and 1H NMR parameters. Spin-lattice relaxation rates were interpreted within the frame of an extended alkane chain with segmental motions hampered by the aromatic substituents at both ends. The effective correlation times were all evaluated in the range 0.16-0.22 ns at 293 K. The aromatic rings were found to lie somewhat out-of-plane with the alkane chain. The NMR data were used to construct a Dreiding model of the most probable spatial arrangement and a molecular modeling system was utilized to represent the "preferred" conformation of verapamil in solution.

Calcium Channel Blockers↗

PubMed1995

Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2.

There is a region of well-ordered structure in the transition state of folding of chymotrypsin inhibitor 2 (CI2) that consists of N-terminal residues in the unique alpha-helix (residues 12 to 24) plus some long range interactions, in particular those of Ala16 with Ile57 and Leu49 in the hydrophobic core. This is proposed to be a nucleation site. A crucial question for understanding the initiation of protein folding is: when is the nucleation site formed? Is the alpha-helix pre-formed in the nominally unfolded state, or does it require long-range interactions to be stabilized? To answer this question, we have characterized a series of N-terminal fragments of CI2, each containing an increasing number of subsets of the regular secondary structure. Four small fragments have been examined by circular dichroism and two-dimensional 1H and 15N NMR spectroscopy. The smallest, [1-5], comprises the sequence corresponding to the first beta-strand of the intact protein; the second, [1-13], contains also a type III reverse turn, the second beta-strand, and a type II reverse turn; the third [1-25], consists additionally of the sequence corresponding to the alpha-helix (residues 12 to 24); the fourth, [1-28], contains, in addition, the turn following the alpha-helix. All the fragments have disordered, non-compact structure in aqueous solution. In the structure-promoting co-solvent, trifluoroethanol, alpha-helical structure is stabilized in [1-25] and [1-28] in the region corresponding to the alpha-helix in the intact protein; however, the helix is frayed at both ends and is only fractionally populated, being in dynamic equilibrium with extended conformations. These observations indicate that there is little drive for independent formation of local secondary structure in CI2, and this is reflected in the highly concerted nature of the folding reaction of this protein. The nucleation site of folding of CI2 does not accumulate in the starting state for the folding reaction, but remains embryonic until there are sufficient long range interactions to stabilize it.

Amino Acid Sequence↗

PubMed1993

Social organization in a wild population of Callithrix jacchus. I. Group composition and dynamics.

Data are presented on group dynamics in a wild population of the common marmoset, Callithrix jacchus, in northeastern Brazil. Three marked and habituated groups were observed, and composition noted, for at least 5 days a month over 12-18 consecutive months. Group sizes ranged from 5 to 15 individuals, and changes in group composition were the result of births, immigrations, and disappearances. No immigrations into the main study groups were observed throughout the study period. None of the three known emigrants was known to join an established or incipient group for up to 10 weeks after their departure. One group contained only breeding individuals and their offspring. Observations of recruitment and loss in the other two groups suggest that they, too, were extended family groups. The group dynamics described in studies of other populations of Callithrix suggest that extended family groups, or at least groups consisting of breeding individuals and their close relatives, may be characteristic of those populations.

Animals↗

PubMed2026

Engineering the Vero Cell Lineage: Toward a Programmable Vaccine Manufacturing Platform.

Vero cells remain an indispensable continuous substrate for human viral vaccine manufacturing. Despite decades of empirical process optimization, intrinsic genomic instability, including segmental aneuploidy and dynamic chromatin rearrangements, continues to limit the durability of engineered phenotypes under sustained viral burden and bioreactor stress. Here, we review the expanding engineering toolkit for the Vero lineage across a three-layered functional framework: the membrane interface, cytoplasmic foundry, and nuclear blueprint, evaluating translational prospects at each level. Receptor transplantation and morphological reprogramming have broadened viral entry range and enabled suspension-adapted culture formats, while metabolic flux management and temporally controlled apoptosis modulation have addressed intracellular production bottlenecks, albeit often with trade-offs between productivity, biosafety, and long-term population stability. At the genomic level, targeted perturbations of transcriptional regulators and emerging epigenetic interventions offer more durable gains, yet expression drift, clonal heterogeneity, and karyotypic instability during extended passaging highlight the need for locus-level precision rather than constitutive trait installation. Looking forward, infection-responsive dynamic logic circuits and the systematic identification of Vero-specific genomic safe harbors could shift the paradigm toward a conditionally responsive manufacturing architecture. Collectively, these advances suggest a pathway for transitioning the Vero lineage from a passive, empirically optimized biological substrate into a conditionally responsive, genomically stable, and programmable platform for modern vaccine preparedness.

Vero cells↗

PubMed1993

13C-NMR determination of the molecular dynamics of cholesterol in dimyristoylphosphatidylcholine vesicles.

Using 13C-NMR measurements of T1, T2 and the nuclear Overhauser enhancement factor at 50.32, 90.56 and 150.87 MHz, we have measured the dynamics of cholesterol in dimyristoylphosphatidylcholine (DMPC) vesicles from 28 to 50 degrees C. Using the model-free approach of Lipari and Szabo, we have found that at 37 degrees C the motion of the rigid steroid ring can be described by an equal contribution from two effective motions with correlation times of 63 and 0.85 ns. The C26 and C27 carbon atoms of cholesterol were found to have an effective correlation time of 8 +/- 2 ps and a value for the square of the generalised order parameter of 0.03 +/- 0.01. The corresponding values for the C25 carbon atom were 17 +/- 4 ps and 0.09 +/- 0.02, showing slower motion and greater order for this carbon atom, which is nearer to the rigid steroid ring. Apart from the effect of vesicle size on T2, no concentration dependence of the dynamics of cholesterol was detected over the cholesterol concentration range 2-30 mol%. The order parameters and correlation times from the present 13C-NMR experiments are shown to be compatible with those from 2H-NMR experiments. This establishes the validity of the present approach, which we are currently extending to low concentrations of cholesteryl oleate in DMPC vesicles.

Carbon Isotopes↗

PubMed1991

A 1H NMR study of human calcitonin in solution.

Human calcitonin (hCT) has been investigated by NMR at 400 MHz in DMSOd6 and in an 85% DMSOd6-15% 1H2O (v/v) cryoprotective mixture. All backbone and side-chain resonances have been assigned, and the secondary structure has been determined in both solvents. In DMSOd6, the simultaneous presence of d alpha N, dNN, and some specific weak medium-range nuclear Overhauser effects, together with the amide temperature coefficients and the analysis of the NH-alpha CH spin-spin coupling constants, indicates that hCT is highly flexible but with three domains (comprising segments Asn3-Gly10, Gln14-Thr21, and Thr25-Ala31) in extended conformations which dynamically transform into isolated beta turns in the N- and C-terminal regions and into adjacent tight turns, resembling a 3(10) helix structure, in the central part. The DMSO-water mixture rigidifies the polypeptide chain, favoring an ordered, extended conformation. NOESY data indicate the presence of a short double-stranded antiparallel beta sheet in the central region made by residues 16-21 and connected by a two-residue hairpin loop formed by residues 18 and 19. Two tight turns, formed by residues 3-6 and 28-31, were also identified. The central beta sheet does not favor an amphipathic distribution of the residues as found for salmon calcitonin [Motta, A., Castiglione Morelli, M. A., Goud, N., & Temussi, P. A. (1989) Biochemistry 28, 7998-8002]. This is in agreement with the smaller tendency of hCT to form the amphipathic alpha helix, postulated to be responsible for the interaction of hCT with lipids. The possible role of the cis-trans isomerism of Pro is discussed.

Amino Acid Sequence↗

PubMed1994

Evaluation of patellar tracking in patients with suspected patellar malalignment: cine MR imaging vs arthroscopy.

OBJECTIVE: The purpose of this study was to compare results of motion-triggered cine MR imaging of active extension of the knee with arthroscopic findings in cases of suspected femoropatellar malalignment. SUBJECTS AND METHODS: Twenty patients with clinically proved or suspected patellar subluxation or dislocation were examined prospectively with motion-triggered cine MR imaging to analyze patellar tracking from 30 degrees of flexion to full extension during active extension of the knee. The patellar tracking pattern was evaluated by measuring the following: bisect offset and lateral patellar displacement to assess lateralization of the patella and the patellar tilt angle to assess tilting of patella. The slopes of the linear regression lines of the MR findings vs the knee angle position, representing the patellar tracking, and the position of the patella at 30 degrees and 0 degrees of flexion were correlated with a semiquantitative arthroscopic classification of patellar tracking that had four categories ranging from normal to highly abnormal. RESULTS: The results showed a significant correlation between the semiquantitative arthroscopic findings of patellar tracking and the slopes of the linear regression lines of the bisect offset, lateral patellar displacement, and patellar tilt angle, as measured with cine MR imaging (p < .01). The arthroscopic findings also correlated significantly with the position of the patella when the knee was extended (p < .01), but not with the knee flexed 30 degrees. CONCLUSION: We conclude that motion-triggered cine MR imaging of active extension of the knee enables the dynamic evaluation of patellar bracing and is therefore suitable for noninvasive analysis of patellar tracking.

Adult↗

PubMed1992

Intracellular HRP study of nociceptive neurons within the ventrobasal complex of the cat thalamus.

Locations and morphological characteristics of nociceptive specific (NS) and wide dynamic range (WDR) neurons of the ventrobasal (VB) thalamic complex were studied using an intracellular HRP injection technique in cats anesthetized with urethane and chloralose. Both NS and WDR neurons were found within the marginal zone of the VB complex. Their somata were confined to the VB complex, but dendrites were extended into the structures of the thalamus surrounding the VB complex. NS neurons were found in the caudal part of the VB complex, whereas WDR neurons were found more rostrally. Examinations of their locations within the marginal zone of the VB complex confirmed the somatotopic organization, as found previously. We also confirmed the previous reports that there are 3 different types of low-threshold mechanoreceptive (LTM) neurons within the VB complex. They are type I, type II and type III neurons. Both NS and WDR neurons were either type I or type II neurons. Obvious morphological differences were not found between LTM neurons and two classes of nociceptive VB neurons investigated.

Animals↗

PubMedDate not supplied

Controlled deposition of tantalum powder in a cast of the human airways: applications for aerosol bronchography.

A hollow latex cast of the human larynx and tracheobronchial tree extending to 2 mm diameter airways "inhaled" tantalum powder (mass median aero-dynamic diameter equals 9.2 mum, omicron-g equals 1.41) at 8 liters/min. Tantalum deposited within the cast as predicted by preliminary deposition calculations. These calculations predicted deposition surface densities among greater than 2 mm diam. airways to have a range of similar to 2:1, and also predicted less than 5% alveolar deposition. A deposition surface density of 8 mg/cm-2 provided good bronchographic visualization. Single rice grains located within some airways were distinctly outlined. The small amount of tantalum needed to outline the airways be a simulated voluntary inhalation indicates that tantalum may be suitable for use as a bronchographic contrast medium when administered under strictly controlled exposure conditions.

Aerosols↗

PubMed1991

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.

Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.

Computer Simulation↗