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PubMed1996

The NASA OCEAN project--an ocean-space analog

An advanced life support system (ALS) with bioregenerative components may one day be required for long-term, deep space exploration, in extended missions to Mars or in establishing long-term bases on the moon. Intensive research programs on such ALS systems have been ongoing throughout the National Aeronautics and Space Administration (NASA) since 1988. Notably, projects have been initiated at the John F. Kennedy Space Center (KSC), Ames Research Center (ARC), and the Lyndon B. Johnson Space Center (JSC). The KSC ALS work has been named the "Breadboard Project" because of its approach developing the components and combining them into a breadboard to understanding the bioregenerative ALS picture [also called a Controlled Ecological Life Support System (CELSS)] in smaller pieces, similar to an electronic "breadboard." The Breadboard Project has been involved for 7 years in the study of higher crops grown in a 113 m3 chamber--the longest operating and largest such closed, controlled growth chamber in the world. This chamber has proven itself to be very successful in growing a wide variety of crops from seedlings to harvest and in helping researchers understand the complex biological cycle of such edible plants in closed, environmentally controlled environments. Because the system's ultimate use will be a more challenging environment, moving a specially designed piece of the system into extreme conditions was an important test. Engineers at KSC developed a compact, portable, functional plant module for testing in the world's only fixed seafloor laboratory at Key Largo, FL. The laboratory, called MarineLab, is operated out of the facilities of the Marine Resources Development Foundation in a lagoon of some 10 m depth. The project was called the OCEAN project (Ocean CELSS Experimental Analog NASA).

Ecological Systems, Closed↗
PubMed2005

Effects of operating conditions on the adhesive strength of Pseudomonas fluorescens biofilms in tubes.

Understanding the mechanical properties of biofilms, especially the force required to disrupt them and remove them from substrata is very important to development of antibiofouling strategies. In this work, a novel micromanipulation technique with a specially designed T-shaped probe has been developed to serve as an experimental means to measure directly the adhesive strength of biofouling deposits on the surface of a glass test stud. The basic principle of this novel technique is to pull away a whole biofilm accumulated on the surface of a glass test stud with T-shaped probe, and to measure simultaneously the force imposed on the biofilm. The adhesive strength between the biofilms and the surface to which they are attached, is defined as the work per unit area required to remove the biofilms from the surface. The biofouling experiments were performed on an elaborate design of a simulated heat exchanger system. A monoculture of Pseudomonas fluorescens was chosen as the fouling microorganism for the laboratory studies. Results indicate that the adhesive strength of the biofilm was affected by the conditions of operation, such as biofilm age, nutrient concentration, suspended cell concentration, pH, surface roughness of the substratum and fluid velocity. As noted, the effect of fluid velocity on the biofilm adhesive strength seemed to overwhelm other factors. At the same operating conditions, the biofilm adhesive strength increased as the fluid velocity increased within the range of 0.6-1.6m/s. In addition, the flow-related biofilm structures were observed that biofilms generally grew as a more compact pattern at the higher fluid velocity. Apparently, the fluid velocity can affect the biofilm structure, which in turn determines the biofilm adhesive strength. The knowledge of the biofilm adhesive strength with associated influences of the operating conditions may be used to define better cleaning procedures.

Bacterial Adhesion↗
PubMed1998

Morphology of porcine cumulus-oocyte-complexes depends on the stage of preovulatory maturation.

The aim of this investigation was to determine the relationship between the morphology of the cumulus-oocyte-complexes (COCs) and the meiotic configuration of oocytes as an LH peak mimicked by hCG. Estrus was synchronized in a total of 29 crossbred Landrace gilts by feeding Regumate for 15 d and administering 1000 IU PMSG. The LH peak was simulated by treatment with 500 IU hCG at 80 h after PMSG. Endoscopic oocyte recovery was carried out 2 h before and 10, 22 and 34 h after hCG. Only macroscopically healthy follicles with a diameter of more than 5 mm were punctured. Altogether, 410 follicles from 57 ovaries were punctured and 251 COCs were aspirated. Oocyte recovery rate increased from 48.5% (P < 0.01) of the early, not yet preovulatory follicles (2 h before hCG) to 80.8% of late preovulatory follicles (34 h after hCG). Cumulus morphology in COCs recovered 2 h before and 10 h after hCG was heterogeneous, with most (72.9 to 57.4%; P < 0.01) showing a compact or slightly expanded cumulus. Starting at about 22 h after hCG, COC morphology changed dramatically (86.7% of COCs with expanded cumulus; P < 0.01), and 34 h after hCG, 98.3% of the COCs had only an expanded cumulus. The percentage of oocytes with a mature meiotic configuration increased (11.2; 7.1; 41.4 and 70.2%, respectively, n = 238 oocytes; P < 0.01) as the interval post hCG increased (-2, 10, 22, 34 h, respectively). Meiotic configuration was related to COC morphology: compact COCs--88.9% diplotene, expanded COCs--53.8% metaphase II (M-II), and denuded oocytes--69.2% degenerated chromatin. These results indicate that there is a relationship between oocyte recovery rate, COC morphology, and meiotic configuration and preovulatory follicle maturation after the application of hCG.

Animals↗
PubMed2000

HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

We describe a hidden Markov model, HMMSTR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear hidden Markov models used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the protein database and, by representing overlapping motifs in a much more compact form, achieves a great reduction in parameters. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.3 %, backbone torsion angles better than any previously reported method and the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction.

Amino Acid Motifs↗
PubMed2006

Modelling sequential protein folding under kinetic control.

MOTIVATION: This study presents a novel investigation of the effect of kinetic control on cotranslational protein folding. We demonstrate the effect using simple HP lattice models and show that the cotranslational folding of proteins under kinetic control has a significant impact on the final conformation. Differences arise if nature is not capable of pushing a partially folded protein back over a large energy barrier. For this reason we argue that such constraints should be incorporated into structure prediction techniques. We introduce a finite surmountable energy barrier which allows partially formed chains to partly unfold, and permits us to enumerate exhaustively all energy pathways. RESULTS: We compare the ground states obtained sequentially with the global ground states of designing sequences (those with a unique global ground state). We find that the sequential ground states become less numerous and more compact as the surmountable energy barrier increases. We also introduce a probabilistic model to describe the distribution of final folds and allow partial settling to the Boltzmann distribution of states at each stage. As a result, conformations with the highest probability of final occurrence are not necessarily the ones of lowest energy. AVAILABILITY: Software available on request.

Amino Acid Sequence↗
PubMed2004

Half-soliton interaction of population taxis waves in predator-prey systems with pursuit and evasion.

In this paper, we use numerical simulations to demonstrate a half-soliton interaction of waves in a mathematical model of a "prey-predator" system with taxis when of two colliding waves, one annihilates and the other continues to propagate. We show that this effect depends on the "ages" or, equivalently, "widths" of the colliding waves. In two spatial dimensions we demonstrate that the type of interaction, i.e., annihilation, quasisoliton, or half-soliton, depends not only on curvature and width of the colliding waves, but also on the angle of the collision. When conditions of collision are varying in such a way that only a part of a wave survives the collision, then "taxitons," compact pieces of solitary waves, may form, which can exist for a significant time.

Adaptation, Physiological↗
PubMed2005

The characterization of plasma membrane Ca2+-ATPase in rich sphingomyelin-cholesterol domains.

According to the raft hypothesis, sphingolipid-cholesterol (CHOL) microdomains are involved in numerous cellular functions. Here, we have prepared liposomes to simulate the lipid composition of rafts/caveolae using phosphatidylchone, sphingomyelin (SPM)-CHOL in vitro. Experiments of both 1,6-diphenyl-1,3,5-hexatriene and merocyanine-540 fluorescence showed that a phase transition from l(d) to l(o) can be observed clearly. In particular, we investigated the behavior of a membrane protein, plasma membrane Ca(2+)-ATPase (PMCA), in lipid rafts (l(o) phase). Three complementary approaches to characterize the physical appearance of PMCA were employed in the present study. Tryptophan intrinsic fluorescence increase, fluorescence quenching by both acrylamid and hypocrellin B decrease, and MIANS fluorescence decrease, indicate that the conformation of PMCA embedded in lipid l(o) phase is more compact than in lipid l(d) phase. Also, our results showed that PMCA activity decreased with the increase of SPM-CHOL content, in other words, with the increase of l(o) phase. This suggests that the specific domains containing high SPM-CHOL concentration are not a favorable place for PMCA activity. Finally, a possible explanation about PMCA molecules concentrated in caveolae/rafts was discussed.

Acrylamide↗
PubMed1990

Theory for protein mutability and biogenesis.

Using an elementary physical model for protein folding, of self-avoiding short copolymer chains on two-dimensional square lattices, we address two questions regarding the evolution and origins of globular proteins. (i) How will protein native structures and stabilities be affected by single-and double-site mutations? (ii) What is the probability that a randomly chosen sequence of amino acids will be compact and globular under folding conditions? For a large number of different sequences, we search the conformational space exhaustively to find unequivocally the "native" conformation(s), of global minimum free energy, for each sequence. We find that replacing nonpolar residues in the core by polar residues is generally destabilizing, that surface sites are less sensitive than core sites, that some mutations increase the degeneracy of native states, and that overall it is most probable that a mutation will be neutral, having no effect on the native structure. These results support a "Continuity Principle," that small changes in sequence seldom have large effects on structure or stability of the native state. The simulations also show that (i) the number of "convergent" sequences (different sequences coding for the same native structure) is extremely large and (ii) most sequences become quite dense under folding conditions. This implies that the probability of formation of a globular protein from a random sequence of amino acids by prebiotic or mutational methods is significantly greater than zero.

Amino Acid Sequence↗
PubMed2002

Random walk with memory enhancement and decay.

A model of random walk with memory enhancement and decay was presented on the basis of the characteristics of the biological intelligent walks. In this model, the movement of the walker is determined by the difference between the remaining information at the jumping-out site and jumping-in site. The amount of the memory information s(i)(t) at a site i is enhanced with the increment of visiting times to that site, and decays with time t by the rate e(-beta(t)), where beta is the memory decay exponent. When beta=0, there exists a transition from Brownian motion (BM) to the compact growth of walking trajectory with the density of information energy u increasing. But for beta>0, this transition does not appear and the walk with memory enhancement and decay can be considered as the BM of the mass center of the cluster composed of remembered sites in the late stage.

Animals↗
PubMed2004

In silico protein design by combinatorial assembly of protein building blocks.

Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring folds with low homology to existing proteins. A selected protein is first partitioned into its building blocks based on their compactness, degree of isolation from the rest of the structure, and hydrophobicity. Next, the protein building blocks are substituted by fragments taken from other proteins with overall low sequence identity, but with a similar hydrophobic/hydrophilic pattern and a high structural similarity. These criteria ensure that the designed protein has a similar fold, low sequence identity, and a good hydrophobic core compared with its native counterpart. Here, we have selected two proteins for engineering, protein G B1 domain and ubiquitin. The two engineered proteins share approximately 20% and approximately 25% amino acid sequence identities with their native counterparts, respectively. The stabilities of the engineered proteins are tested by explicit water molecular dynamics simulations. The algorithm implements a strategy of designing a protein using relatively stable fragments, with a high population time. Here, we have selected the fragments by searching for local minima along the polypeptide chain using the protein building block model. Such an approach provides a new method for engineering new proteins with similar folds and low homology.

Amino Acid Sequence↗
PubMedDate not supplied

Use of influence diagrams to structure medical decisions.

Influence diagrams are compact representations of decision problems that are mathematically equivalent to decision trees. The authors present five important principles for structuring a decision as an influence diagram: 1) start at the value node and work back to the decision nodes; 2) draw the arcs in the direction that makes the probabilities easiest to assess; 3) use informational arcs to specify which events will have been observed at the time each decision is made; 4) ensure that missing arcs reflect intentional assertions about conditional independence and the timing of observations; and 5) ensure that there are no cycles in the influence diagram. They then build an influence diagram for the problem of staging non-small-cell lung cancer as an illustration. Influence diagrams offer several strengths for structuring medical decisions. They represent graphically and compactly the probabilistic relationships between parameters in the model. Influence diagrams also allow the model to be structured in a fashion that eases the necessary probability assessments, regardless of whether the assessments are based on available evidence or on expert judgment. Influence diagrams provide an important complement to decision trees, especially for representing probabilistic relationships among variables in a decision model.

Carcinoma, Non-Small-Cell Lung↗
PubMed2007

Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation.

The contraction process of an electroactive actuator constituted by calix[4]arene units and quaterthiophene segments has been investigated at the microscopic level by using atomistic molecular dynamics simulations in dichloromethane solution using explicit solvent molecules. Results derived from a 1 mus trajectory of the oxidized and deprotonated actuator indicate that the contraction occurs through a non-concerted mechanism in which each actuating units present in the system behave independently. The efficiency of the contraction process can be reduced by the presence of secondary conformational transitions in the calix[4]arene scaffolds. Accordingly, the drastic reduction of the molecular length expected during the contraction process can be limited by such transitions, which involve the rotational isomerism of a phenolate ring. However, such type of conformational transitions does not compromise the actuator power due to its intrinsic capacity to adopt compact molecular arrangements. On the other hand, the rate of the contraction process is influenced by the presence of solvent molecules, which have been found to reduce it by a factor of about 1000.

Calixarenes↗
PubMed2000

A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent.

This study documents the feasibility of switching to an aprotic medium in sugar receptor research. The solvent change offers additional insights into mechanistic details of receptor--carbohydrate ligand interactions. If a receptor retained binding capacity in an aprotic medium, solvent-exchangeable protons of the ligand would not undergo transfer and could act as additional sensors, thus improving the level of reliability in conformational analysis. To probe this possibility, we first focused on hevein, the smallest lectin found in nature. The NMR-spectroscopic measurements verified complexation, albeit with progressively reduced affinity by more than 1.5 orders of magnitude, in mixtures of up to 50% dimethyl sulfoxide (DMSO). Since hevein lacks the compact beta-strand arrangement of other sugar receptors, such a structural motif may confer enhanced resistance to solvent exchange. Two settings of solid-phase activity assays proved this assumption for three types of alpha- and/or beta-galactoside-binding proteins, that is, a human immunoglobulin G (IgG) subfraction, the mistletoe lectin, and a member of the galectin family of animal lectins. Computer-assisted calculations and NMR experiments also revealed no conspicuous impact of the solvent on the conformational properties of the tested ligands. To define all possible nuclear Overhauser effect (NOE) contacts in a certain conformation and to predict involvement of exchangeable protons, we established a new screening protocol applicable during a given molecular dynamics (MD) trajectory and calculated population densities of distinct contacts. Experimentally, transferred NOE (tr-NOE) experiments with IgG molecules and the disaccharide Gal'alpha1-3Galbeta1-R in DMSO as solvent disclosed that such an additional crosspeak, that is, Gal'OH2--GalOH4, was even detectable for the bound ligand under conditions in which spin diffusion effects are suppressed. Further measurements with the plant lectin and galectins confirmed line broadening of ligand signals and gave access to characteristic crosspeaks in the aprotic solvent and its mixtures with water. Our combined biochemical, computational, and NMR-spectroscopical strategy is expected to contribute notably to the precise elucidation of the geometry of ligands bound to compactly folded sugar receptors and of the role of water molecules in protein--ligand (carbohydrate) recognition, with relevance to areas beyond the glycosciences.

Antimicrobial Cationic Peptides↗
PubMed2005

Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy.

Feature selection is an important problem for pattern classification systems. We study how to select good features according to the maximal statistical dependency criterion based on mutual information. Because of the difficulty in directly implementing the maximal dependency condition, we first derive an equivalent form, called minimal-redundancy-maximal-relevance criterion (mRMR), for first-order incremental feature selection. Then, we present a two-stage feature selection algorithm by combining mRMR and other more sophisticated feature selectors (e.g., wrappers). This allows us to select a compact set of superior features at very low cost. We perform extensive experimental comparison of our algorithm and other methods using three different classifiers (naive Bayes, support vector machine, and linear discriminate analysis) and four different data sets (handwritten digits, arrhythmia, NCI cancer cell lines, and lymphoma tissues). The results confirm that mRMR leads to promising improvement on feature selection and classification accuracy.

Algorithms↗
PubMed2004

Conformational states of the Rapana thomasiana hemocyanin and its substructures studied by dynamic light scattering and time-resolved fluorescence spectroscopy.

Hemocyanins are dioxygen-transporting proteins freely dissolved in the hemolymph of mollusks and arthropods. Dynamic light scattering and time-resolved fluorescence measurements show that the oxygenated and apo-forms of the Rapana thomasiana hemocyanin, its structural subunits RtH1 and RtH2, and those of the functional unit RtH2e, exist in different conformations. The oxygenated respiratory proteins are less compact and more asymmetric than the respective apo-forms. Different conformational states were also observed for the R. thomasiana hemocyanin in the absence and presence of an allosteric regulator. The results are in agreement with a molecular mechanism for cooperative dioxygen binding in molluscan hemocyanins including transfer of conformational changes from one functional unit to another.

Animals↗
PubMed2000

Measurement and Network Modeling of Liquid Permeation into Compacted Mineral Blocks.

A microbalance has been used to measure the rate of uptake of a wetting fluid, 1,3-propandiol, into a cube of compacted calcium carbonate. The cube had sides 12 mm long, with a wax band applied to the outer perpendicular edges of one basal plane to prevent external surface uptake, and the liquid was applied in a highly controlled manner at this single face only. The percolation characteristics of an identical sample were measured by mercury porosimetry. A three-dimensional void structure was generated with the same percolation characteristics using a software package called "Pore-Cor." The wetting of 1,3-propandiol into this model structure was then calculated using an extended Lucas-Washburn equation, developed by Bosanquet, which includes viscous, inertial, and capillary force effects. Neither the experimental nor the simulated wetting can be explained in terms of an "hydraulic stream tube" or "effective hydraulic radius" model. A mathematical function is presented which compensates for the differences in the boundary conditions between the simulation and the experiment. The wetting is found to be initially slowed by inertial flow, then speeded up to a t(0.8) dependence by the connectivity of the three-dimensional void network. The effect of the inertial flow is most pronounced for larger pores. Copyright 2000 Academic Press.

Journal Article↗
PubMed2006

A compact highly efficient and low hemolytic centrifugal blood pump with a magnetically levitated impeller.

A magnetically levitated (maglev) centrifugal blood pump (CBP), intended for use as a ventricular assist device, needs to be highly durable and reliable for long-term use without any mechanical failure. Furthermore, maglev CBPs should be small enough to be implanted into patients of various size and weight. We have developed a compact maglev CBP employing a two-degree-of-freedom controlled magnetic bearing, with a magnetically suspended impeller directly driven by an internal brushless direct current (DC) motor. The magnetic bearing actively controls the radial motion of the impeller and passively supports axial and angular motions using a permanent magnet embedded in the impeller. The overall dimensions of the maglev CBP are 65 mm in diameter and 40 mm in height. The total power consumption and pump efficiency for pumping 6 L/min against a head pressure of 105 mm Hg were 6.5 W and 21%, respectively. To evaluate the characteristics of the maglev CBP when subjected to a disturbance, excitation of the base, simulating the movement of the patient in various directions, and the sudden interception of the outlet tube connected with the pump in a mock circulatory loop, simulating an unexpected kink and emergent clamp during a heart surgery, were tested by monitoring the five-degree-of-freedom motion of the impeller. Furthermore, the hemolytic characteristics of the maglev CBP were compared with those of the Medtronic Biomedicus BPX-80, which demonstrated the superiority of the maglev CBP.

Animals↗
PubMed2000

Electrostatic properties of bovine beta-lactoglobulin.

Bovine beta-Lactoglobulin (BLG) has been studied for many decades, but only recently structural data have been obtained, making it possible to simulate its molecular properties. In the present study, electrostatic properties of BLG are investigated theoretically using Poisson-Boltzmann calculations and experimentally following pH titration via NMR. Electrostatic properties are determined for several structural models, including an ensemble of NMR structures obtained at low pH. The changes in electrostatic forces upon changes in ionic strength, solvent dielectric constant, and pH are calculated and compared with experiments. pK(a)s are computed for all titratable sites and compared with NMR titration data. The analysis of theoretical and experimental results suggests that (1) there may be more than one binding sites for negatively charged ligands; (2) at low pH the core of the molecule is more compact than observed in the structures obtained via restrained molecular dynamics from NMR data, but loop and terminal regions must be disordered.

Amino Acid Sequence↗