Single file ion diffusion and the Schmoluchowski equation

The Schmoluchowski equation is introduced into the problem of single file ion diffusion in a channel. The ions mutually interact due to coulomb repulsion and are also subject to a single ion potential due to the channel. The positions of the ions are represented by a continuous co-ordinate. The problem is reduced to the solution of a pair of transfer integral equations. The resistivity of finite and infinite channels is calculated for various dielectric constants and mean ionic separations. The ionic density for finite channels is also calculated. The results clearly demonstrate that strong coulomb interaction leads to a co-operative motion of the ions across channels.     

Ultrastructure of apyrene and eupyrene spermatozoa from the seminal vesicle of Euptoieta hegesia (Lepidoptera: Nymphalidae)

The ultrastructure of the seminal vesicle's spermatozoa of the butterfly Euptoieta hegesia was analyzed. The apyrene spermatozoa measure about 300 microm in length and swim freely in a secretion. The anterior end consists in a cap with a cylindrical extension and a globular structure. The flagellum has a 9+9+2 axoneme, two mitochondrial derivatives with paracrystalline matrices and an external coat formed by concentric layers. The eupyrene spermatozoa measure about 550 microm in length and are grouped into bundles. The anterior end consists in an amorphous globule. Posterior to this globule, a coat with a dense material covers the spermatozoon where an acrosome and a nucleus appear. The flagellum has a 9+9+2 axoneme and two mitochondrial derivatives. External to the coat and attached to the dense material, there is a reticular appendage, which has a paracrystalline core and extends to the distal tip of the spermatozoon.     

Fine structure of the spermatozoa of Chiton marginatus (mollusca: Amphineura), with special reference to nucleus maturation

The spermatozoon of Chiton marginatus is a long uniflagellate cell displaying structural features of “modified sperm.” The nucleus presents a conical shape with a long apical cylindrical extension. The chromatin is homogeneously dense. Scattered inside the condensed nucleus, a few nuclear lacunae are visible. The acrosomal complex is lacking. Some mitochondria are located in a laterofrontal structure side by side with the nucleus. The typical midpiece is absent. The cytoplasm forms a thin layer around the nucleus and the mitochondria. The proximal centriole is in a basal nuclear indent. The distal centriole serves to form the axoneme tail with the usual microtubular pattern. During nuclear maturation, the early spermatid nucleus is spherical and contains fine granular chromatin patches. The nuclear envelope shows a deposit of dense material at the base of the nucleus, forming a semicircular invagination occupied by a flocculent mass. In middle spermatid stage, the chromatin gets organized in filaments, coiled as a hank, attached over the inner surface of the basal thickening of the nuclear envelope. The nucleus starts to elongate anteroposteriorly. At the pointed apical portion of the spermatid, a group of microtubules is observed seeming to impose external pressure to the nucleus giving rise to the long apical nuclear point. The mitochondria have a basal position. Late spermatids have an elongated conical nucleus. The chromatin filaments are further condensed, and lacunae appear inside the nucleus. Some mitochondria migrate to a lateral position.     

Symmetric building blocks and combinatorial functional group transformation as versatile strategies in combinatorial chemistry

A combination of symmetric building blocks and combinatorial functional group transformation for synthesis of pyrimidines was investigated. The purpose of the study was to maximize the return on invested synthetic efforts of reaction development for libraries. A representative set of symmetric diacids was coupled onto deprotected TentaGel Rink Amide resin. The amino function served as a model of a chemical process providing a functional group for additional synthetic steps, while the symmetric building blocks served as a model to connect synthesis protocols and to switch to a different synthesis paradigm consecutively. The reaction sequence was continued in a noncombinatorial step by coupling a bifunctional reagent (3-aminoacetophenone) to the remaining carboxy function of the symmetric diacid. The ketone served as a model of a reagent prepared for combinatorial functional group transformation. The arylmethylketone was reacted with a set of aryl- and heteroarylaldehydes to give alpha,beta-unsaturated ketones. Subsequently, guanidine, alkyl-, and arylcarboxamidines were introduced in combinatorial synthesis of substituted pyrimidines by reaction with the alpha, beta-unsaturated ketone functionality. The combination of symmetric building blocks and combinatorial functional group transformation created a versatile reaction sequence ideally suited for production of libraries from libraries with added diversity.     

Nucleotide sequences of the sfuA, sfuB, and sfuC genes of Serratia marcescens suggest a periplasmic-binding-protein-dependent iron transport mechanism.

The cloned sfu region of the Serratia marcescens chromosome confers the ability to grow on iron-limited media to an Escherichia coli K-12 strain that is unable to synthesize a siderophore. This DNA fragment was sequenced and found to contain three genes termed sfuA, sfuB, and sfuC, arranged and transcribed in that order. The sfuA gene encoded a periplasmic polypeptide with calculated molecular weights of 36,154 for the precursor and 33,490 for the mature protein. The sfuB gene product was a very hydrophobic protein with a molecular weight of 56,589. The sfuC gene was found to encode a rather polar but membrane-bound protein with a molecular weight of 36,671 which exhibited strong homology to consensus sequences of nucleotide-binding proteins. The number, structural characteristics, and locations of the SfuABC proteins were typical of a periplasmic-binding-protein-dependent transport mechanism. How Fe3+ is solubilized and taken up across the outer membrane remains an enigma.     

Substrate specificity of nuclease TT1 from Thermus thermophilus HB8

The substrate and the action mechanism of a nuclease named nuclease TT1, from the culture broth of an extreme thermophile, Thermus thermophilus HB8, were investigated. The enzyme is nonspecific for the sugar moiety and cleaves both single- and double-stranded DNAs, rRNA, tRNA and oligonucleotides irrespective of chain length to produce 5'-mononucleotides exonucleolitically. The action mechanism is processive and the enzyme shows no porality of degradation. The minimal unit as a substrate is a 5'-dinucleotide. The rate of hydrolysis is independent of a terminal phosphate group. The substrate lacking a 5'-phosphoryl group is degraded to leave the 5'-terminus and the penultimate nucleotide (NpN) as a core. The substrate possessing a 3'-phosphoryl group is degraded to leave the mononucleoside 5',3'-diphosphates (pNp). However, NpN and pNp are gradually degraded by a large dose of the enzyme to produce a 5'-mononucleotide. The enzyme is free from nonspecific phosphatase and phosphodiesterase activities. Application of this enzyme to determine the sequence of oligonucleotides is shown.     

An autonomous fueled machine that replicates catalytic nucleic acid templates for the amplified optical analysis of DNA

Here we describe a protocol for the amplified detection of a target DNA using a DNA/FokI-based replicating cutting machine. The protocol is based on the design of a sensing hairpin oligonucleotide that is opened upon hybridization with the analyte DNA. The endonuclease FokI binds to the double-stranded complex and cleaves it to a "cutter" unit. The "cutter" unit reacts with a fuel oligonucleotide to generate and amplify the signal. The fuel molecule is an oligonucleotide in a hairpin configuration with a fluorophore/quencher pair attached to the 5' and 3' ends. Formation of the duplex between the cutter and the fuel leads to the scission of the duplex by FokI, leading to a second, replicated "cutter", a fluorescent waste product, and to the regeneration of the original "cutter" unit. The autonomous replication of the "cutter" unit, as a result of the primary recognition of the analyte DNA, leads to the amplified fluorescent detection of the analyte DNA with a sensitivity limit of 1 x 10(-14) M. The operation of the machine and the sensing process are monitored by the fluorescence generated by the waste product. Here we apply the protocol, which takes about 2 h to complete, to analyze a Tay-Sachs genetic disorder mutant DNA.     

Fine structure of spermatozoa in the gilthead sea bream (Sparus aurata Linnaeus, 1758) (Perciformes, Sparidae)

Scanning and transmission electron microscopy were used to investigate the fine structure of the sperm of the sparid fish Sparus aurata L. The mature spermatozoon of gilthead sea bream belongs, like that of the other sparid fish, to a "type I" as defined by Mattei (1970). It has a spherical head which lacks an acrosome, a short, irregularly-shaped midpiece and a long cylindrical tail. The nucleus reveals a deep invagination (nuclear fossa) in which the centriolar complex is located. The two centrioles are approximately perpendicular to each other and show a conventional "9+0" pattern. The proximal centriole is associated with a cross-striated cylindrical body lying inside a peculiar satellite nuclear notch which appears as a narrow invagination of the nuclear fossa. The distal centriole is attached to the nuclear envelope by means of a lateral plate and radial fibres made of an electron-dense material. The short midpiece houses one mitochondrion. The flagellum is inserted perpendicularly into the base of the nucleus and contains the conventional 9+2 axoneme.     

Constraints for joint angle control of the human arm

The targeting movements of a human arm were examined when restricted to a horizontal plane. The three joints at shoulder, elbow, and wrist are allowed to move. Thus, the system is redundant and needs constraints. A model calculation using a simple form of constraint is found to describe the experimental results: a cost function is applied to each joint. The constraint consists in minimizing the sum of the costs of all three joints. The cost functions might be interpreted as to describing the energy cost necessary to move the joint and/or represent a mechanism which avoids singularities.     

Purification and properties of an endo-1,4-beta-glucanase translated from a Clostridium josui gene in Escherichia coli.

An endoglucanase encoded by a gene of Clostridium josui was expressed in Escherichia coli and purified. The homogeneous enzyme, with a molecular weight of 39,000, revealed maximum endoglucanase activity at pH 7.2 to 7.5 and a temperature of 65 to 70 degrees C. The enzyme was stable at a temperature lower than 45 degrees C (the growth temperature of the bacterium) in the range of pH 4.5 to 9.0. The amino acid sequence of the enzyme at the N terminus was Val-Glu-Glu-Asp-Ser-Ser-His-Leu-Ile-Thr-Asn-Gln-Ala-Lys-Lys----. The enzyme hydrolyzed cellotetraose to cellobiose and then transferred cellobiose to the residual cellotetraose. The resulting cellohexaose was cleaved to cellotriose.     

Computational simulation of internal bone remodelling around dental implants: a sensitivity analysis

This study aimed to predict the distribution of bone trabeculae, as a density change per unit time, around a dental implant based on applying a selected mathematical remodelling model. The apparent bone density change as a function of the mechanical stimulus was the base of the applied remodelling model that describes disuse and overload bone resorption. The simulation was tested in a finite element model of a screw-shaped dental implant in an idealised bone segment. The sensitivity of the simulation to different mechanical parameters was investigated; these included element edge length, boundary conditions, as well as direction and magnitude of the implant loads. The alteration in the mechanical parameters had a significant influence on density distribution and model stability, in particular at the cortical bone region. The remodelling model could succeed to achieve trabeculae-like structure around osseointegrated dental implants. The validation of this model to a real clinical case is required.     

Determination of the three-dimensional structure of iberiotoxin in solution by 1H nuclear magnetic resonance spectroscopy.

The solution structure of chemically synthesized iberiotoxin, a scorpion toxin that blocks Ca(2+)-activated K+ channels, has been determined using 2D 1H NMR spectroscopy. Analysis of the NOEs, coupling constants, and HN-DN exchange rates indicates the structure consists of an antiparallel beta-sheet from residues 25 to 36, with a type 1 turn at residues 30-31, and a helix from residues 13 to 21. The carboxyl-terminal residues form a short, and distorted, third strand of the sheet. The NMR data are consistent with disulfide bonds from residues 7 to 28, 13 to 33, and 17 to 35. The disulfide bridging presents the same profile as in other scorpion toxins, where a Cys-X-Cys sequence in a strand of sheet forms two disulfide bonds to a Cys-X-X-X-Cys sequence in a helix. Three-dimensional structures were generated using the torsion angle space program PEGASUS. The best ten structures had an average rmsd over all pairwise comparisons of 1.49 A. The average rmsd to a calculated average structure is 1.0 A. The resulting structures appear very similar to those of charybdotoxin, a related scorpion toxin.     

Simulation of the human airways using virtual topology tools and meshing optimization

A method is proposed to improve the quality of the three-dimensional airway geometric models using a commercial software, checking the number of elements, meshing time, and aspect ratio and skewness parameters. The use of real and virtual topologies combined with patch-conforming and patch-independent meshing algorithms results in four different models being the best solution the combination of virtual topology and patch-independent algorithm, due to an excellent aspect ratio and skewness of the elements, and minimum meshing time. The result is a reduction in the computational time required for both meshing and simulation due to a smaller number of cells. The use of virtual topologies combined with patch-independent meshing algorithms could be extended in bioengineering because the geometries handling is similar to this case. The method is applied to a healthy person using their computed tomography images. The resulting numerical models are able to simulate correctly a forced spirometry.     

Stages of the cerebral mechanisms of deceptive responses

Cerebral mechanisms of perceiving and telling lies were studied by recording event-related potentials (ERPs) both after an actual deceptive response and during the time interval when the subject decided to tell a lie. Ten healthy volunteers participated in the study. The test consisted of their playing a game against a computer. The subjects could choose between deceptive and truthful answers so as to win the game. The subjects gave a deceptive answer intentionally, the structure of the test ensuring equal numbers of deceptive and truthful answers. The relaxation times in the cases of truthful and deceptive answers did not differ significantly from each other. The comparison of ERPs accompanying deceptive and truthful answers showed the existence of a negativity with a latent period of 90 ms in the regions of the right frontal, central, and right parietal derivations. This negativity indicated that the brain reacted to a deceptive answer even if this a priori “erroneous” act ensured reaching the goal and, in this sense, was subjectively relevant. In terms of the cerebral error detector mechanism, this phenomenon may be regarded as a special case of a general response of the brain to giving an incorrect (deceptive) answer, rather than a response to a lie per se. The interval of time when, presumably, the decision on a deceptive answer was being made was found to contain the late positive component P540, which is most likely to be involved in the preparation of the deceptive answer and the intention to tell a lie.     

Temperature dependence of photovoltages generated by bacteriorhodopsin.

The temperature dependence of the photovoltage developed by a model membrane containing bacteriorhodopsin (BR) is studied. The model membrane is formed by first coating a thin Teflon sheet with lipid and then fusing BR vesicles to it. The time course of the photoresponse is resolved down to 1 microsecond. The photoresponse is taken to be a sum of exponentials. Exponential time constants and amplitudes are determined by an analysis of the photoresponse with a photovoltage vs. log time plot, correlation filter, and nonlinear least-squares routine. The photovoltage is taken to be the sum of three exponentials but only two of the three time constants are resolved. Both are temperature dependent and indicate a thermally activated transport process. The corresponding activation energies are 55 kJ/mol and 62 kJ/mol. Since the photovoltage is proportional to charge times displacement the corresponding charge displacements are 11 and 34 A assuming a total displacement of 45 A. The remaining exponential term corresponds to a small negative transient in the photovoltage that has a rise time less than 1 microsecond even at -20 degrees C. The calculated charge displacement is estimated to be less than 2 A.     

Theory of transverse surface electromagnetic waves propagating along a plasma-metal boundary with a finite radius of curvature in a magnetic field

The spectra of electromagnetic waves propagating perpendicular to the axis of a plasma-filled metal waveguide in a magnetic field are studied with allowance for the effects exerted upon the wave frequency by the radial plasma density variation and by the emission of waves through a narrow axial slit in a waveguide wall. The case of wave propagation along the boundary between a plasma and a cylindrical metal waveguide wall with a periodically varying radius of curvature is also considered. The electromagnetic properties of the plasma are described by a dielectric tensor in the hydrodynamic approximation. The spatial distribution of the wave field is determined by the method of successive approximations. Results are presented from both analytical and numerical investigations. Analytical expressions for the corrections to the wave frequency due to the emission of the wave energy from the waveguide and due to the slight corrugation of the waveguide wall are obtained. The rates of wave damping due to the emission of the wave energy through a narrow axial slit and due to collisions between the plasma particles are found. The correction to the frequency that comes from the periodic variation of the radius of curvature of the plasma surface is calculated to within terms proportional to the square of the small parameter describing the azimuthal corrugation of the waveguide wall. The effect of the radial plasma density variation on the dispersion of the surface modes is examined both analytically and numerically.     

The Sustainable Process Index a new dimension in ecological evaluation

The Sustainable Process Index (SPI) is a measure developed to evaluate the viability of processes under sustainable economic conditions. Its advantages are its universal applicability, its scientific basis, the possibility of adoption in process analyses and syntheses, the high sensitivity for sustainable qualities, and the capability of aggregation to one measure. It has proved to be useful in industrial strategic planning. The concept of the SPI is based on the assumption that in a truly sustainable society the basis of economy is the sustainable flow of solar exergy. The conversion of the solar exergy to services needs area. Thus, area becomes the limiting factor of a sustainable economy. The SPI evaluates the areas needed to provide the raw materials and energy demands and to accommodate by-product flows from a process in a sustainable way. It relates these areas to the area available to a citizen in a given geographical (from regional to global) context. The data necessary to calculate the SPI are usually known at an early stage in process development. The result of the computation is the ratio between the area needed to supply a citizen with a given service and the area needed to supply a citizen with all possible services. Thus, it is a measure of the expense of this service in an economy oriented towards sustainability.     

Bayesian Estimation of Small Effects in Exercise and Sports Science

The aim of this paper is to provide a Bayesian formulation of the so-called magnitude-based inference approach to quantifying and interpreting effects, and in a case study example provide accurate probabilistic statements that correspond to the intended magnitude-based inferences. The model is described in the context of a published small-scale athlete study which employed a magnitude-based inference approach to compare the effect of two altitude training regimens (live high-train low (LHTL), and intermittent hypoxic exposure (IHE)) on running performance and blood measurements of elite triathletes. The posterior distributions, and corresponding point and interval estimates, for the parameters and associated effects and comparisons of interest, were estimated using Markov chain Monte Carlo simulations. The Bayesian analysis was shown to provide more direct probabilistic comparisons of treatments and able to identify small effects of interest. The approach avoided asymptotic assumptions and overcame issues such as multiple testing. Bayesian analysis of unscaled effects showed a probability of 0.96 that LHTL yields a substantially greater increase in hemoglobin mass than IHE, a 0.93 probability of a substantially greater improvement in running economy and a greater than 0.96 probability that both IHE and LHTL yield a substantially greater improvement in maximum blood lactate concentration compared to a Placebo. The conclusions are consistent with those obtained using a ‘magnitude-based inference’ approach that has been promoted in the field. The paper demonstrates that a fully Bayesian analysis is a simple and effective way of analysing small effects, providing a rich set of results that are straightforward to interpret in terms of probabilistic statements.     

Sex-structured HIV/AIDS model to analyse the effects of condom use with application to Zimbabwe

We present a sex-structured model for heterosexual transmission of HIV/AIDS in a community. The model is formulated using integro-differential equations, which are shown to be equivalent to delay differential equations with a time delay due to incubation period. The sex-structured HIV/AIDS model divides the population into a two sex-structure consisting of females and males. The threshold and equilibria for the model are determined and stabilities are examined. We extend the model to focus on the effects of condom use as a single-strategy approach in HIV prevention in the absence of any treatment. Initially we model the use of male condoms and further extend the model to incorporate the use of both female and male condoms. The model includes two primary factors in condom use to control HIV that are condom efficacy and compliance. The exposure risk of infection after each intervention is obtained. Basic reproductive numbers for these models are computed and compared to assess the effectiveness of male and female condom use in a community. The models are numerically analysed to assess the effectiveness of condom use on the transmission dynamics of HIV/AIDS using demographic and epidemiological parameters for Zimbabwe. The study demonstrates the use of sex-structured HIV/AIDS models in assessing the effectiveness of female and male condom use as a preventative strategy in a heterosexually active population. Z. Mukandavire would like to acknowledge financial support given by the National University of Science and Technology through a Staff Development Scholarship. The authors are grateful to Eagle Insurance Company of Zimbabwe for financial support.     

Modeling and experimental studies on intermittent starch feeding and citrate addition in simultaneous saccharification and fermentation of starch to flavor compounds

Simultaneous saccharification and fermentation (SSF) is a combined process of saccharification of a renewable bioresource and fermentation process to produce products, such as lactic acid and ethanol. Recently, SSF has been extensively used to convert various sources of cellulose and starch into fermentative products. Here, we present a study on production of buttery flavors, namely diacetyl and acetoin, by growing Lactobacillus rhamnosus on a starch medium containing the enzyme glucoamylase. We further develop a structured kinetics for the SSF process, which includes enzyme and growth kinetics. The model was used to simulate the effect of pH and temperature on the SSF process so as to obtain optimum operating conditions. The model was experimentally verified by conducting SSF using an initial starch concentration of 100 g/L. The study demonstrated that the developed kinetic was able to suggest strategies for improved productivities. The developed model was able to accurately predict the enhanced productivity of flavors in a three stage process with intermittent addition of starch. Experimental and simulations demonstrated that citrate addition can also lead to enhanced productivity of flavors. The developed optimal model for SSF was able to capture the dynamics of SSF in batch mode as well as in a three stage process. The structured kinetics was also able to quantify the effect of multiple substrates present in the medium. The study demonstrated that structured kinetic models can be used in the future for design and optimization of SSF as a batch or a fed-batch process. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.