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PubMedDate not supplied

Desert ecosystems: similarities, characteristics, and health benefits.

Salty bodies of water in desert zones are known worldwide. The Salton Sea in California, USA, and the Dead Sea between Israel and Jordan are located in arid areas at approximately the same latitude, which might explain some similarities. Both the Salton and Dead Seas have ecosystems consisting of a singular saline sea/hot desert interface. The Salton Sea, the largest inland body of water in California, is a saline lake in the Coachella and Imperial Valleys. The Imperial Valley is one of the 10 top agricultural areas in the United States. Several thermoelectric plants exploiting geothermal wells operate around the Salton Sea, and some areas comprise a National Wildlife Refuge. The Dead Sea (Sea of Salt in Hebrew), the lowest saline lake on earth, contains high concentrations of salts and is a reservoir of minerals with a unique evaporation regime. The Dead Sea salts are the raw materials for the production of several chemical and health products. Magnesium salts and sulfur-containing mud are used for treating human skin disorders, allergies, arthritis, and respiratory diseases. After visiting both zones, we recorded, analyzed, and compared the similarities and differences between the areas. Some differences were found in the geographic, orographic, hydraulic, and climatic properties, but the main difference is in the economic-industrial aspect. The characteristics and health aspects are described in this report.

Animals↗

PubMed1996

Docking enzyme-inhibitor complexes using a preference-based free-energy surface.

We present a docking scheme that utilizes both a surface complementarity screen as well as an energetic criterion based on surface area burial. Twenty rigid enzyme/inhibitor complexes with known coordinate sets are arbitrarily separated and reassembled to an average all-atom rms (root mean square) deviation of 1.0 A from the native complexes. Docking is accomplished by a hierarchical search of geometrically compatible triplets of surface normals on each molecule. A pruned tree of possible bound configurations is built up using successive consideration of larger and larger triplets. The best scoring configurations are then passed through a free-energy screen where the lowest energy member is selected as the predicted native state. The free energy approximation is derived from observations of surface burial by atom pairs across the interface of known enzyme/inhibitor complexes. The occurrence of specific atom-atom surface burial, for a set of complexes with well-defined secondary structure both in the bound and unbound states, is parameterized to mimic the free energy of binding. The docking procedure guides the inhibitor into its native state using orientation and distance-dependent functions that reproduce the ideal model of free energies with an average rms deviation of 0.9 kcal/mol. For all systems studied, this docking procedure identifies a single, unique minimum energy configuration that is highly compatible with the native state.

Enzyme Inhibitors↗

PubMed1994

Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution.

The structure of pig pancreatic alpha-amylase has been determined by X-ray diffraction analysis using multiple isomorphous replacement in a crystal of space group P2(1)2(1)2(1) (a = 70.6 A, b = 114.8 A, c = 118.8 A) containing nearly 75% solvent. The structure was refined by simulated annealing and Powell minimization, as monitored by 2Fo-Fc difference Fourier syntheses, to a conventional R of 0.168 at 2.1 A resolution. The final model consists of all 496 amino acid residues, a chloride and a calcium ion, 145 water molecules and an endogenous disaccharide molecule that contiguously links protein molecules related by the 2(1) crystallographic operator along x. The protein is composed of a large domain (amino acid residues 1 to 403) featuring a central alpha ta-barrel of eight parallel strands and connecting helices with a prominent excursion between strand beta 3 and helix alpha 3 (amino acid residues 100 to 168). The final 93 amino acid residues at the carboxyl terminus form a second small domain consisting of a compact Greek key beta-barrel. The domains are tightly associated through hydrophobic interfaces. The beta 3/alpha 3 excursion and portions of the central alpha/beta-barrel provide four protein ligands to the tightly bound Ca ion; three water molecules complete the coordination. The Cl- ion is bound within one end of the alpha/beta-barrel by two arginine residues in a manner suggesting a plausible mechanism for its allosteric activation of the enzyme. A crystalline complex of the pancreatic alpha-amylase with alpha-cyclodextrin, a cyclic substrate analog of six glucose residues, reveals, in difference Fourier maps, three unique binding sites. One of the alpha-cyclodextrin sites is near the center of the long polysaccharide binding cleft that traverses one end of the alpha/beta-barrel, another is at the extreme of this cleft. By symmetry this can also be considered as two half sites located at the extremes of the active site cleft. This latter alpha-cyclodextrin displaces the endogenous disaccharide when it binds and, along with the first sugar ring, delineates the extended starch binding site. The third alpha-cyclodextrin binds at an "accessory site" near the edge of the protein and is quite distant from the polysaccharide binding cleft. Its presence explains the multivalency of alpha-amylase binding to dextrins in solution. The extended active site cleft is formed by large, sweeping, connecting loops at one end of the alpha/beta-barrel. These include three sequence segments that are highly conserved among alpha-amylases.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMedDate not supplied

Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.

Three-dimensional image reconstructions of large-scale protein aggregates are routinely determined by electron microscopy (EM). We combine low-resolution EM data with high-resolution structures of proteins determined by x-ray crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient and robust method for the localization of protein subunits in low-resolution data. Topology-representing neural networks are employed to vector-quantize and to correlate features within the structural data sets. Microtubules decorated with kinesin-related ncd motors are used as model aggregates to demonstrate the utility of this package of routines. The precision of the docking has allowed for the extraction of unique conformations of the macromolecules and is limited only by the reliability of the underlying structural data.

Animals↗

PubMed2006

An impulse-driven liquid-droplet deposition interface for combining LC with MALDI MS and MS/MS.

A simple and robust impulse-driven droplet deposition system was developed for off-line liquid chromatography matrix-assisted laser desorption ionization mass spectrometry (LC-MALDI MS). The system uses a solenoid operated with a pulsed voltage power supply to generate impulses that dislodge the hanging droplets from the LC outlet directly to a MALDI plate via a momentum transfer process. There is no contact between the LC outlet and the collection surface. The system is compatible with solvents of varying polarity and viscosity, and accommodates the use of hydrophobic and hydrophilic MALDI matrices. MALDI spots are produced on-line with the separation, and do not require further processing before MS analysis. It is shown that high quality MALDI spectra from 5 fmol of pyro-Glu-fibrinopeptide deposition after LC separation could be obtained using the device, indicating that there was no sample loss in the interface. To demonstrate the analytical performance of the system as a proteome analysis tool, a range of BSA digest concentrations covering about 3 orders of magnitude, from 5 fmol to 1 pmol, were analyzed by LC-MALDI quadrupole time-of-flight MS, yielding 6 and 57% amino acid sequence coverage, respectively. In addition, a complex protein mixture of an E. coli cell extract was tryptically digested and analyzed by LC-MALDI MS, resulting in the detection of a total of 409 unique peptides from 100 fractions of 15-s intervals.

Chromatography, Liquid↗

PubMed2000

Gradient elution techniques for capillary electrochromatography.

Capillary electrochromatography (CEC) is a rapidly maturing technique, but still in need of further instrumental development and in need of unique applications that are not possible by traditional pressure-driven LC. We review the development of gradient elution schemes for CEC, beginning with pH gradients initially developed for capillary electrophoresis. Step gradients are the most easily instrumentally implemented, but provide less flexibility in separation than continuous gradients. Pressure-assisted CEC is easily adapted to gradient elution schemes, but does not offer the advantages of very high column efficiency provided by totally electro-driven mobile phases. The development of flow-injection interfaces allows a true solvent gradient to be generated by micro-LC pumps, with the mobile phase drawn into the separation capillary by pure electroosmotic flow. While requiring both a CEC instrument and a traditional pump or pumps capable of generating the gradient, this method offers advantages of greatly reduced column handling, prolonging column lifetimes, and allows simple autosampling. We also discuss voltage gradients, which provide a mobile phase velocity gradient.

Buffers↗

PubMed2002

The three-dimensional model of Dictyostelium discoideum racE based on the human rhoA-GDP crystal structure.

The three-dimensional structure of racE was modeled using several homologous small G proteins, and the best model obtained using the human rhoA as modeling template is reported. The three-dimensional fold of the racE model is remarkably similar to the cellular form of human ras p21 crystal structure. Its secondary structure consists of six alpha-helices, six beta-strands and three 3(10) helices. The model retains its secondary structure after a 300 K, 300 ps molecular dynamics (MD) simulation. Important domains of the protein include its effector loop (residues 34-46), the insertion domain (residues 121-136), and the polybasic motif (between 210 and 220) not modeled in the current structure. The effector loop is inherently flexible and the structure docked with GDP exhibits the effector loop moving significantly closer to the nucleotide binding pocket, forming a tighter complex with the bound GDP. The mobility of the effector loop is conferred by a single residue 'hinge' point at residue 34Asp, also allowing the Switch I region, immediately preceding the effector loop, to be equally mobile. In comparison, the Switch II region shows average mobility. The insertion domain is highly flexible, with the insertion taking the form of a helical domain, with several charged residues forming a complex charged interface over the entire insertion region. While the GDP moiety is loosely held in the active site, the metal cation is extensively co-ordinated. The critical residue 38Thr exhibits high mobility, and is seen interacting directly with the metal ion at a distance of 2.64 A, and indirectly via an intervening water molecule. 64Gln, a key residue involved in GTP hydrolysis in ras, is seen facing the beta-phosphate group and the metal ion. Certain residues (i.e. 51Asn, 38Thr and 65Glu) exhibit unique characteristics and these residues, together with 158Val, may play important roles in the maintenance of the protein's integrity and function. There is strong consensus of secondary structural elements between models generated using various templates, such as h-rac1, h-rhoA and h-cdc42 bound to RhoGDI, all sharing only 50-55% sequence identity with racE, which suggests that this model is in all probability an accurate prediction of the true tertiary structure of racE.

Amino Acid Sequence↗

PubMed2004

Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs.

Basic region-leucine zipper (B-ZIP) proteins are a class of dimeric sequence-specific DNA-binding proteins unique to eukaryotes. We have identified 67 B-ZIP proteins in the Arabidopsis thaliana genome. No A.thaliana B-ZIP domains are homologous with any Homo sapiens B-ZIP domains. Here, we predict the dimerization specificity properties of the 67 B-ZIP proteins in the A.thaliana genome based on three structural properties of the dimeric alpha-helical leucine zipper coiled coil structure: (i) length of the leucine zipper, (ii) placement of asparagine or a charged amino acid in the hydrophobic interface and (iii) presence of interhelical electrostatic interactions. Many A.thaliana B-ZIP leucine zippers are predicted to be eight or more heptads in length, in contrast to the four or five heptads typically found in H.sapiens, a prediction experimentally verified by circular dichroism analysis. Asparagine in the a position of the coiled coil is typically observed in the second heptad in H.sapiens. In A.thaliana, asparagine is abundant in the a position of both the second and fifth heptads. The particular placement of asparagine in the a position helps define 14 families of homodimerizing B-ZIP proteins in A.thaliana, in contrast to the six families found in H.sapiens. The repulsive interhelical electrostatic interactions that are used to specify heterodimerizing B-ZIP proteins in H.sapiens are not present in A.thaliana. Instead, we predict that plant leucine zippers rely on charged amino acids in the a position to drive heterodimerization. It appears that A.thaliana define many families of homodimerizing B-ZIP proteins by having long leucine zippers with asparagine judiciously placed in the a position of different heptads.

Amino Acid Sequence↗

PubMed2004

Friction and second-order phase transitions.

A microscopic model is studied numerically to describe wearless dry friction without thermal fluctuations between atomically flat contact interfaces. The analysis is based on a double-chain model with a Lennard-Jones interaction between the chains which are the respective upper flexible monolayers of the rigid bulk systems. Whereas below a critical interaction strength epsilon(c) the system exhibits a frictionless state, it offers static friction above epsilon(c) . Introducing an appropriate order parameter function we demonstrate the analogy of the critical behavior to a phase transition of second order. The order parameter is related to a hull function describing uniquely the incommensurate ground state of the model. The breakdown of analyticity of the hull function is identified with the phase transition. Critical exponents are calculated and the validity of finite-size scaling is displayed.

Journal Article↗

PubMed1983

Inter- and intra-examiner reliability of leg-length differential measurement: a preliminary study.

The phenomenon of "short leg" has long been used and debated clinically. A uniquely chiropractic measurement technique was not studied in any of the few studies of reliability of measurement which have been reported. An inter- and intra-examiner reliability study was therefore performed to validate a prone leg length-differential test. Naive students (n = 40) were called, in random order, into three adjacent examining rooms where three experienced chiropractic clinicians measured differential leg lengths. Using standard placement a tape measure was read to the nearest mm to detect inequalities at the shoe-sole interface. The leg length differences were recorded, for both the straight and flexed legs prone positions, twice by each of the three clinicians. Intraclass correlations were significant for the two independent readings for all three examiners, indicating high reliability of the test. Good agreement among examiners was indicated as well by significant intraclass correlation in two of the three possible examiner combinations. These results argue strongly for the reality of the leg length inequality phenomenon and also that it can be reliably measured.

Adult↗

PubMed2005

Crystal structure of the conserved hypothetical protein Rv1155 from Mycobacterium tuberculosis.

With the aim of elucidating the biological function of hypothetical proteins unique amongst the Actynomyces sub-group of bacteria, we have solved the crystal structure of the conserved hypothetical protein Rv1155 from Mycobacterium tuberculosis at 1.8 A resolution. Rv1155 is a homodimer both in the crystal structure and in solution and folds into two separate domains consisting of a six-stranded anti-parallel beta-barrel fold flanked by two alpha-helices and a helix-turn-helix domain. Both domains contribute to the formation of two deep clefts at the dimer interface. The overall fold of Rv1155 strikingly resembles that of flavin mononucleotide-binding protein and pyridoxamine 5'-phosphate oxydase, but the architecture of the putative binding pocket is markedly different, consistent with the lack of color of Rv1155 and its inability to bind FMN. Rv1155 thus appears to belong to a group of proteins with stringent conservation of the binding cleft, having evolved towards a new binding function.

Amino Acid Sequence↗

PubMed2001

LINUCS: linear notation for unique description of carbohydrate sequences.

The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form.

Algorithms↗

PubMed2003

Advances in objective assessment of hand function and outcome assessment of the musician's hand.

Doctors have made great strides in the past 20 years in the analysis of musicians' medical problems; we realize they suffer the same medical conditions as the general population but the manifestations may be different and hence the diagnosis more difficult; we realize that many of the conditions glibly attributed to overuse and repetition are no more common in this group than the general public engaged in much less repetitive activity; we realize that many of musicians' symptoms may not represent inflammation or injury but are a manifestation of misuse or mismatch to the instrument and of fatigue; we realize many of these symptoms may be related to technical problems alone; we realize that as a group musicians respond well to appropriate care and that surgery does not inevitably end a musician's career. To diagnose and treat this group properly requires a complete and full analysis of the musician, the interface, and the instrument from the outset. Anything less produces an incorrect or incomplete analysis and the poor results that have bedeviled musicians' medical care to date. Such analysis requires a basic understanding of musicians' problems, detailed knowledge of many of the specific syndromes they suffer, and time for a complete and thorough assessment. It is this lack of time and the lack of facilities to examine the musician while playing that currently causes the greatest number of mistakes in the medical care of this unique and demanding group of individuals.

Disability Evaluation↗

PubMed2004

Staphylococcus aureus IsdG and IsdI, heme-degrading enzymes with structural similarity to monooxygenases.

Heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. All mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. Here we describe the crystal structures of IsdG and IsdI, two heme-degrading enzymes from Staphylococcus aureus. The structures of both enzymes resemble the ferredoxin-like fold and form a beta-barrel at the dimer interface. Two large pockets found on the outside of the barrel contain the putative active sites. Sequence homologs of IsdG and IsdI were identified in multiple Gram-positive pathogens. Substitution of conserved IsdG amino acid residues either reduced or abolished heme degradation, suggesting a common catalytic mechanism. This mechanism of IsdG-mediated heme degradation may be similar to that of the structurally related monooxygenases, enzymes involved in the synthesis of antibiotics in Streptomyces. Our results imply the evolutionary adaptation of microbial enzymes to unique environments.

Amino Acid Sequence↗

PubMed1998

Electron microscopic characterization of filiform papillae in the normal human tongue.

The fine structure of filiform papillae on the normal human tongue was examined level by level, from the basal layer to the surface, in specimens taken from the dorsal side of the lingual body. Human lingual epithelia showed three distinct regions: epithelia on the anterior and on the posterior sides of filiform papillae and an interpapillary epithelium. While the basal and the squamous cell layers were similar throughout these three regions, differences were noted in the granular and the horny layers. The interpapillary epithelium actually lacked both the granular and the horny layers. The epithelium on the anterior side of filiform papillae was characterized by alternating layers of granular cells and of cornified cells. Granular cells possessed three types of keratohyaline-like granules within their cytoplasm: uniformly electron dense, relatively less electron dense, and a heterogeneous type. While the number of the keratohyaline-like granules was remarkably diminished in the epithelium on the posterior side of filiform papillae, a considerable amount of tonofibrils was present in the cytoplasm. In the uppermost portion of the anterior side of filiform papillae, coherence between adjacent epithelial cells depended mainly on the interlocking of cytoplasmic villi and poorly developed desmosomes on villi. On the other hand, epithelial cells on the posterior side of filiform papillae appeared to be more tightly adhesive compared with those on the anterior side. This was due to focal thickening of the plasma membrane and to desmosomes at the interface between the granular and cornified cells, and to the formation of a marginal band and increased intercellular cement presumably derived from lamellar bodies in the horny layer. These findings demonstrate distinct differences between the anterior and the posterior sides of filiform papillae in the human tongue with respect to keratinization patterns, structures associated with cell-to-cell adhesion and the strength of cellular cohesion in the uppermost portion, and the turnover of cornified cells. These differences may contribute to the formation of the unique external configurations of filiform papillae.

Adult↗

PubMed1984

Electron microscopic and hydrodynamic studies of protein A-immunoglobulin G soluble complexes.

The soluble complexes formed by reacting staphylococcal protein A (SpA) with rabbit immunoglobulin G (IgG) antibodies were characterized by hydrodynamic and electron microscopic methods. In moderate SpA excess, equilibrium mixtures of SpA and rabbit IgG formed four discrete complexes that sedimented at approximately 7, 10, 13, and 15S. The putative complexes were visible by electron microscopy and appeared to contain one, two, three, and approximately five molecules of IgG. Probably because of its elongated shape, SpA was not clearly visible in these mixtures or in control preparations of SpA alone. Both native IgG and IgG modified by cleavage of its single-hinge disulfide bond formed similar complexes on interaction with SpA. It was possible to resolve heterogeneous mixtures of IgG-SpA complexes by using an analytical ultracentrifuge equipped with a photoelectric scanner interfaced to a small computer. The relative concentrations and sedimentation velocities of different complexes in a mixture were determined from computer-generated integral and derivative plots. Both hydrodynamic and electron microscopic methods revealed that the distribution of complexes was sensitive to the IgG to SpA molar ratio. The relative amounts of faster complexes increased as the IgG to SpA molar ratio was increased. Surprisingly, when the IgG to SpA molar ratio was greater than or equal to 2, the complexes were converted into a unique 17S complex. This rather unprecedented transformation was reversible: the addition of excess SpA caused the dissociation of the 17S complex into a mixture of the 7, 10, 13, and 15S structures. The average translational diffusion coefficient of the 17S complex was 2.62 +/- 0.13 Ficks. In the electron microscope, the complex appeared to be exceptionally compact with an average diameter of 287 A. The stoichiometry of the 17S complex, together with sedimentation equilibrium, diffusion, and electron microscopic measurements, indicated that it is composed of four molecules of IgG and two molecules of SpA.

Animals↗

PubMed2004

siRNA Selection Server: an automated siRNA oligonucleotide prediction server.

The Whitehead siRNA (short interfering RNA) Selection Web Server (http://jura.wi.mit.edu/bioc/siRNA) automates the design of short oligonucleotides that can specifically 'knock down' expression of target genes. These short sequences are about 21 nt in length, and when synthesized as double stranded RNA and introduced into cell culture, can reduce or eliminate the function of the target gene. Depending on the length of a gene, there are potentially numerous combinations of possible 21mers. Some experimental evidence has already shown that not all 21mers in a gene have the same effectiveness at silencing gene function. Our tool incorporates published design rules and presents the scientist with information about uniqueness of the 21mers within the genome, thermodynamic stability of the double stranded RNA duplex, GC content, presence of SNPs and other features that may contribute to the effectiveness of a siRNA.

Algorithms↗

PubMedDate not supplied

Comparison of a virtual reality simulator and simulated limbs for phlebotomy training.

The current study compared the CathSim virtual reality simulator with simulated limbs for phlebotomy training. In the first experiment, medical students completed two 1-hour training sessions using 1 of the 2 methods. Afterward, the students' performance was assessed with both simulated limbs and genuine patients. The results showed that students trained with the simulated limbs achieved higher scores on both the posttest and the field test with actual patients than those trained on the CathSim system. In the second study, graduate students practiced with the CathSim system for 5 hours. The results showed a significant improvement in scores from pretest to posttest for these students. However, even after extended practice, their final scores did not differ from those of the medical students in the first experiment. Critical differences in design characteristics between the 2 systems may explain these findings. Although the authors observed a clear advantage for simulated limbs over the CathSim system, neither system faithfully represents all of steps needed to perform the procedure. Thus, training decisions may require that the unique advantages afforded by each system be considered.

Adult↗