Heating of a Local Region of a Branching Streamer as a Starting Point of a Space Leader and a Negative-Leader Step

Plasma Physics Reports - Localized plasma formations called space leaders are observed in streamer coronas of negative leaders of long laboratory sparks. The main leader completes a step when the...     

Effects of a disease affecting a predator on the dynamics of a predator-prey system

We study the effects of a disease affecting a predator on the dynamics of a predator-prey system. We couple an SIRS model applied to the predator population, to a Lotka-Volterra model. The SIRS model describes the spread of the disease in a predator population subdivided into susceptible, infected and removed individuals. The Lotka-Volterra model describes the predator-prey interactions. We consider two time scales, a fast one for the disease and a comparatively slow one for predator-prey interactions and for predator mortality. We use the classical “aggregation method” in order to obtain a reduced equivalent model. We show that there are two possible asymptotic behaviors: either the predator population dies out and the prey tends to its carrying capacity, or the predator and prey coexist. In this latter case, the predator population tends either to a “disease-free” or to a “disease-endemic” state. Moreover, the total predator density in the disease-endemic state is greater than the predator density in the “disease-free” equilibrium (DFE).     

Biomechanics of a muscular hydrostat: a model of lapping by a reptilian tongue

We have developed a quantitative model of an example of a muscular hydrostat, a reptilian tongue, and have used this model to study a functional movement, protrusion and retrusion, a form of lapping. The model tongue consists of a longitudinal muscle that shortens the tongue when it contracts, and a circumferential muscle wrapped around the longitudinal muscle that lengthens the tongue when it contracts. The anatomy of the model tongue and the pattern of activation of its muscles are based on studies of the tongue of the lizard Tupinambis nigropunctatus (Smith 1984). The mechanics of pressure vessels were used to derive a relationship between the forces in the two muscles. Muscle force production was modelled as the product of length/tension properties, force/velocity properties, and activation due to neural inputs (incorporating both recruitment and firing period). Passive forces were modeled as a force in parallel with the longitudinal muscle. Muscle activation dynamics were modeled as a first order low pass filter. When the model tongue is short, the two muscles can lengthen or shorten it with comparable forces, but as it lengthens, the force that the circumferential muscle can exert drops precipitously. When the tongue is long, it can neither be very stiff, nor can it generate much force. The model also reproduces the kinematics of lapping movements actually observed in Tupinambis.     

Kinetic analysis of protonation of a specific site on a buffered surface of a macromolecular body

The kinetics of protonation of a specific site on a macromolecular structure (micelle) in buffered solution was studied with the purpose of evaluating the effect of buffer on the observed dynamics. The experimental system consisted of the following elements: Brij 58 micelles serving as homogeneous uncharged macromolecular bodies, bromocresol green, a well-adsorbed proton detector, and 2-naphthol-3,6-disulfonate as a proton emitter in the bulk. Imidazole was the mobile buffer while neutral red, which has a high affinity for the micellar surface, served as the immobile buffer. An intensive laser pulse ejects a proton from the proton emitter, and the subsequent proton-transfer reactions are measured by fast spectrophotometric methods. The dynamics of proton pulse in buffered solution are characterized by a very rapid trapping of the discharged protons by the abundant buffer molecules. This event has a major effect on the kinetic regime of the reaction. During the first 200 ns the proton flux is rate limited by free-proton diffusion. After this period, when the free-proton concentration decayed to the equilibrium level, the relaxation of the system is carried out by the diffusion of buffer. Thus in the buffered biochemical system, at neutral pH, most of proton flux between active sites and bulk is carried out by buffer molecules--not by diffusion of free protons. Surface groups on a high molecular weight body exchange protons among them at a very fast rate. This reaction has a major role on proton transfer from a specific site to the bulk.(ABSTRACT TRUNCATED AT 250 WORDS)     

Inactivation of C5a anaphylatoxin by a peptide that is complementary to a region of C5a

PL37 (RAARISLGPRCIKAFTE) is an antisense homology box peptide composed of aa 37-53 of C5a-anaphylatoxin and is considered to be the region essential for C5a function. Using a computer program, we designed the complementary peptides ASGAPAPGPAGPLRPMF (Pep-A) and ASTAPARAGLPRLPKFF (Pep-B). Pep-A bound to PL37 and to C5a with very slow dissociation as determined by analysis using surface plasmon resonance, whereas Pep-B failed to bind at all. C5a was inactivated by concentrations of 7 nM or more of Pep-A, and this concentration of Pep-A inhibited induction of intracellular Ca(2+) influx in neutrophils. Patch clamp electrophysiology experiments also showed the effectiveness of Pep-A in C5aR-expressing neuroblastoma cells. Furthermore, Pep-A administration prevented rats from C5a-mediated rapid lethal shock induced by an Ab to a membrane inhibitor of complement after LPS sensitization.     

Study of hydrodynamic instabilities of a Z-pinch during a high-current explosion of a thin wire

Results are presented from laboratory and numerical experiments on the influence of the core and associated hydrodynamic instabilities on the high-current implosion of a plasma of exploding metal wires. The experimental investigation of the discharge structure was carried out using the multiframe X-ray backlighting technique with high temporal and spatial resolution (<1 ns and 1 μm, respectively); X-pinches were used as small-sized radiation sources. The implosion of a dense Z-pinch was modeled by the free-point method with the use of a two-dimensional radiative MHD code. The onset of instabilities at the corona-core boundary was modeled by the NUTCY Eulerian code. The results show that hydrodynamic processes in the core are primarily responsible for the formation of small bright regions observed in X-rays. After the reflection of a shock wave from the axis, the rapid onset of hydrodynamic instabilities can occur at the corona-core boundary. __________ Translated from Fizika Plazmy, Vol. 26, No. 9, 2000, pp. 797–810. Original Russian Text Copyright ? 2000 by Gus’kov, Ivanenkov, Mingaleev, Nikishin, Pikuz, Rozanov, Stepniewski, Tishkin, Hammer, Shelkovenko.     

Construction of a cultivation system of a yeast single cell in a cell chip microchamber

A novel single cell screening system was constructed using a yeast cell chip in combination with the yeast cell surface engineering [NanoBiotechnology 2005, 1, 105-111]. Enzymes or functional proteins displayed on a yeast cell surface can be used as a protein cluster. To achieve high-throughput screening of protein libraries on the cell surface, a catalytic reaction by a single cell-surface-engineered yeast cell was successfully carried out in the microchamber on the yeast cell chip. After screening, to replicate a target cell for use in measuring of activity, DNA sequencing, and preservation, a novel single cell cultivation system in the yeast cell chip was constructed. To avoid damage of the rapid dry up of medium in the microchamber array, the yeast cell chip was modified with a protection sheet, so that the modified chip was like a micro-culture tank constructed on the yeast cell chip microchamber. As a result, single yeast cell cultivation in the yeast cell chip microchamber was observed, and the modified yeast cell chip was evaluated to be good for a single cell selection. The improvement showed that the single cell screening system coupled with the single cell cultivation using the modified yeast cell chip may be superior to that by a cell sorter for the isolation of a target cell and its practical use.     

Aggregation of a slow-folding mutant of a beta-clam protein proceeds through a monomeric nucleus

Mechanistic understanding of protein aggregation, leading either to structured amyloid fibrils or to amorphous inclusion body-like deposits, should facilitate the identification of potential therapeutic intervention strategies for the devastating amyloid-based diseases. Here we focus on the in vitro aggregation of a slow-folding mutant of the beta-clam protein, cellular retinoic acid-binding protein I (P39A CRABP I), which forms inclusion bodies when expressed in Escherichia coli. Aggregation was monitored by observing the fluorescence of a fluorescein-based biarsenical dye (FlAsH) that ligates to a tetra-Cys motif, here incorporated into a flexible Omega-loop. The fluorescence signal of FlAsH on the tetra-Cys-containing P39A CRABP I is sensitive to whether this protein is native or unfolded, and was used in combination with other techniques to follow aggregate formation. The aggregation time course is compatible with a nucleation-dependent polymerization model, and detailed kinetic analysis showed that the energetically unfavorable nucleus is monomeric. A similar conclusion was reached previously for poly(Gln) species [Chen, S., Ferrone, F. A., and Wetzel, R. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 11884-11889] and points to an unfavorable equilibrium between the misfolded intermediate and the bulk pool of monomers as causative in aggregation. The P39A mutation, which removes a helix-stop signal, may slow closure of the beta-barrel in P39A CRABP I relative to the wild type, leaving it vulnerable to aggregation. Wide-angle X-ray scattering showed that the amorphous aggregates formed by the aggregation-prone intermediates of P39A CRABP I contain predominantly beta-strands structured in a lamellar fashion with 10.03 A spacing between adjacent beta-sheets.     

Determining a maximum-tolerated schedule of a cytotoxic agent

Most phase I clinical trials are designed to determine a maximum-tolerated dose (MTD) for one initial administration or treatment course of a cytotoxic experimental agent. Toxicity usually is defined as the indicator of whether one or more particular adverse events occur within a short time period from the start of therapy. However, physicians often administer an agent to the patient repeatedly and monitor long-term toxicity due to cumulative effects. We propose a new method for such settings. It is based on the time to toxicity rather than a binary outcome, and the goal is to determine a maximum-tolerated schedule (MTS) rather than a conventional MTD. The model and method account for a patient's entire sequence of administrations, with the overall hazard of toxicity modeled as the sum of a sequence of hazards, each associated with one administration. Data monitoring and decision making are done continuously throughout the trial. We illustrate the method with an allogeneic bone marrow transplantation (BMT) trial to determine how long a recombinant human growth factor can be administered as prophylaxis for acute graft-versus-host disease (aGVHD), and we present a simulation study in the context of this trial.     

Some properties of a neutral phosphatase of a bacterium isolated from a trickling filter effluent

Summary The partial purification and some of the properties of a neutral phosphatase from a Gram-negative oxidative bacterium isolated from a sewage works effluent are described. The enzyme is active against a variety of organic and inorganic phosphates and, of a number of ions tested, cadmium, copper, mercury and zinc and tungstate and molybdate were the most powerful inhibitors of enzyme action. Inhibition by phosphate is competitive. The possible significance of bacterial neutral phosphatases in purification processes is discussed.     

Numerical Simulation of Passage of a Neutrophil through a Rectangular Channel with a Moderate Constriction

The authors have previously presented a mathematical model to predict transit time of a neutrophil through an alveolar capillary segment which was modeled as an axisymmetric arc-shaped constriction settled in a cylindrical straight pipe to investigate the influence of entrance curvature of a capillary on passage of the cell. The axially asymmetric cross section of a capillary also influences the transit time because it requires three-dimensional deformation of a cell when it passes through the capillary and could lead to plasma leakage between the cell surface and the capillary wall. In this study, a rectangular channel was introduced, the side walls of which were moderately constricted, as a representative of axially asymmetric capillaries. Dependence of transit time of a neutrophil passing through the constriction on the constriction geometry, i.e., channel height, throat width and curvature radius of the constriction, was numerically investigated, the transit time being compared with that through the axisymmetric model. It was found that the transit time is dominated by the throat hydraulic diameter and curvature radius of the constriction and that the throat aspect ratio little affects the transit time with a certain limitation, indicating that if an appropriate curvature radius is chosen, such a rectangular channel model can be substituted for an axisymmetric capillary model having the same throat hydraulic diameter in terms of the transit time by choosing an appropriate curvature radius. Thus, microchannels fabricated by the photolithography technique, whose cross section is generally rectangular, are expected to be applicable to in vitro model experiments of neutrophil retention and passage in the alveolar capillaries.     

Parameter determination for a computer simulation model of a diver and a springboard

This study used kinematic data on springboard diving performances to estimate viscoelastic parameters of a planar model of a springboard and diver with wobbling masses in the trunk, thigh, and calf segments and spring dampers acting at the heel, ball, and toe of the foot segment. A subject-specific angle-driven eight-segment model was used with an optimization algorithm to determine viscoelastic parameter values by matching simulations to four diving performances. Using the parameters determined from the matching of a single dive in a simulation of another dive resulted in up to 31% difference between simulation and performance, indicating the danger of using too small a set of kinematic data. However, using four dives in a combined matching process to obtain a common set of parameters resulted in a mean difference of 8.6%. Because these four dives included very different rotational requirements, it is anticipated that the combined parameter set can be used with other dives from these two groups.     

Parallel computation of a maximum-likelihood estimator of a physical map

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity that provides the motivation for parallel computing. Parallelization strategies for a maximum-likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails a gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a stochastic optimization algorithm such as simulated annealing or microcanonical annealing. A two-level parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the stochastic optimization algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a distributed-memory multiprocessor cluster running the parallel virtual machine (PVM) environment are presented using simulated and real hybridization data.     

Gulose as a constituent of a glycoprotein.

The aldohexose gulose was identified as a constituent of a hydroxyproline-rich glycopeptide derived from the glycoprotein SSG 185. This glycoprotein is part of the extracellular matrix of the green alga Volvox carteri. The gulose residue occupies a terminal position in the corresponding saccharide.     

Identification of a nuclear variant of MGEA5, a cytoplasmic hyaluronidase and a beta-N-acetylglucosaminidase

MGEA5 was originally identified to be a novel human hyaluronidase, which is immunogenic in meningioma patients. Recently an N-acetylglucosaminidase was reported with identical sequence. Here, we define the origin of a splice variant by determining the genomic organization of the mgea5 gene. We find the splice variant missing a putative acetyltransferase domain of MGEA5. As for evolutionary analysis, we show that the MGEA5 is highly conserved in higher eukaryotes. As for expression analysis, we find both mRNA variants ubiquitously expressed in various human tissues and throughout mouse development. We generated polyclonal antibodies against MGEA5s/5 and identified proteins of 75 and 130 kDa, indicating posttranslational modifications of the larger protein. Cell fractionation revealed the cytoplasmic/cytoskeletal localization of the 130-kDa protein and the nuclear localization of the 75-kDa protein. We propose a model in which MGEA5 functions both as a hyaluronidase and an N-acetylglucosaminidase.     

Vegetation as a component of a non-nested hierarchy: a conceptual model

Abstract. A general conceptual model of vegetation based on hierarchy theory is presented. The model emphasizes that prediction of vegetation requires consideration of both mechanisms of vegetation change and the constraints within which it occurs. The mechanisms of vegetation change are the responses to and effects upon their surroundings of individual plants. The most general constraints upon vegetation are aspects of the environment not affected by vegetation over successional time, and the pool of species within dispersal range. Examples of such environmental factors include macroclimate and soil parent material. In some cases, vegetation may alter important labile environmental factors such as soil nutrient and water availability. Some vegetation compositions appear to be resistant to changes in the general constraints. Due to both sources, there are multiple possible vegetation compositions given the same general constraints. Disturbance is defined as an abrupt change in the constraints on the vegetation resulting in a change in the vegetation's state or dynamics. Both the recognition of disturbance and the distinction between independent and labile environmental factors depend on the spatial and temporal scale of observation. For example, a particular wildfire at a given stand may be a disturbance, whereas at a larger scale of observation the same event may contribute to the wildfire regime, part of the constraints at that scale. Similarly, levels of soil organic matter may constrain vegetation over short time scales, due to influencing availability of water and nutrients. Over long time scales, the vegetation itself is a primary determinant of soil organic matter content. This model contains elements of both the initial, holistic theory of vegetation and recent, reductionistic approaches. It reiterates the need to considerboth mechanisms and constraints, stressed by contemporary and earlier workers. Hierarchy theory provides new insights concerning sufficient conditions for prediction, possible limits on predictability, and appropriate research strategy.     

Death of a trypanosome: a selfish altruism

African trypanosomes and some related parasitic protozoa are affected by a form of programmed cell death (PCD) that shows typical hallmarks of apoptosis. Although it has been speculated that PCD has a function in life-cycle progression and the struggle for survival of these parasites, no satisfactory model has yet been proposed for the molecular mechanism(s) of PCD in protozoa, raising questions about its physiological relevance in these organisms. As we discuss here, the most important point that needs to be addressed is whether a single-celled organism can undertake a process that is considered altruistic.     

Eo: a history of a mutation

Eighteen mouse t haplotype-carrying strains were found not to express cell-surface E molecules controlled by class II genes of the H-2 complex (= Eo strains). Northern and Southern blot analysis of these and other, non-t strains that also fail to express the E molecule, has revealed two kinds of defect. Three strains (CRO437, tw2, and presumably to) were found to transcribe the E alpha gene, but they were not able to convert the message into a functional protein. All other Eo strains fail to transcribe the E alpha gene because of a deletion encompassing the promoter region, the RNA initiation site, and the first exon. The length of the deletion is approximately 650 +/- 50 bp. These two defects closely resemble those found previously in standard inbred strains carrying the H-2f, H-2q (failure of E mRNA to be expressed functionally), H-2b, and H-2s (deletion of a part of the E alpha gene) haplotypes. In particular, the location and length of the E alpha deletion appear to be the same in the strains carrying this mutation. The E alpha deletion is in linkage disequilibrium with certain alleles at other H-2 loci in some of the strains. These observations, combined with the growing evidence that H-2 haplotypes associated with t chromosomes derive from a single ancestral haplotype, suggest that the E alpha deletion is an old mutation and that it has been disseminated in mouse populations by the t chromosomes.     

Geminiviruses: a tale of a plasmid becoming a virus

Background  

Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons.     

Identification of miRNAs in a Liver of a Human Fetus by a Modified Method

Background

miRNAs are 17–25 nucleotides long RNA molecules that have been found to regulate gene expression in human cells. There are studies showing that different groups of miRNAs are involved in development of different tissues. In hepatocytes there are reported particular types of miRNAs that regulate gene expression.

Methods

We established a human fetal liver cDNA library by a modified cloning protocol. Then plasmid isolation from the colonies was performed. After sequencing and database searching, the miRNAs were recognized. RT-PCR and sequencing were carried out to validate the miRNAs detected. Real-time PCR was used to analyze the expression of each miRNA.

Results

One novel miRNA was discovered, together with another 35 previously-known miRNAs in the fetal liver. Some of them existed in variants. The miRNAs identified were validated by RT-PCR and sequencing. Quantitative analysis showed that they have variable expression.

Conclusion

Our results indicate that a special group of miRNAs may play an important role in fetal liver development in a synergistic manner.