Sequence analysis of rabbit haemorrhagic disease virus (RHDV) in Australia: alterations after its release

Liver samples from rabbits killed by RHDV, collected from five States in Australia in 1996 and 1997 were analysed by RT-PCR. A 398 bp fragment of the capsid protein (VP60) gene was amplified by PCR and directly sequenced. The alignment of the nucleotide and amino acid sequences and their comparison with the original strain of the virus released in Australia indicated genetic changes after two years have been small with 98.2% to 100% identity. The constructed phylogenetic tree suggests slight differences in nucleotide substitutions in various States but there is no clear evidence of clustering of sequences according to their geographic origin. In practical terms, sequencing of viral RNA provides a means of testing the efficacy of further releases and subsequent spread of the virus if such a strategy is employed as a means of enhancing RHD as a biological control of the wild rabbit in Australia.

Algebraic Bethe ansatz for integrable Kondo impurities in the one-dimensional supersymmetric t-J model

An integrable Kondo problem in the one-dimensional supersymmetric t-J model is studied by means of the boundary supersymmetric quantum inverse scattering method. The boundary K matrices depending on the local moments of the impurities are presented as a nontrivial realization of the graded reflection equation algebras in a two-dimensional impurity Hilbert space. Further, the model is solved by using the algebraic Bethe ansatz method and the Bethe ansatz equations are obtained. (C) 1999 Elsevier Science B.V.

Integrability of a t - J model with impurities

A t - J model for correlated electrons with impurities is proposed. The impurities are introduced in such a way that integrability of the model in one dimension is not violated. The algebraic Bethe ansatz solution of the model is also given and it is shown that the Bethe states are highest weight states with respect to the supersymmetry algebra gl(2/1).

A mathematical model for estimating the extent of solute- and water-flux heterogeneity in multiple sample percolation experiments

Multiple sampling is widely used in vadose zone percolation experiments to investigate the extent in which soil structure heterogeneities influence the spatial and temporal distributions of water and solutes. In this note, a simple, robust, mathematical model, based on the beta-statistical distribution, is proposed as a method of quantifying the magnitude of heterogeneity in such experiments. The model relies on fitting two parameters, alpha and zeta to the cumulative elution curves generated in multiple-sample percolation experiments. The model does not require knowledge of the soil structure. A homogeneous or uniform distribution of a solute and/or soil-water is indicated by alpha = zeta = 1, Using these parameters, a heterogeneity index (HI) is defined as root 3 times the ratio of the standard deviation and mean. Uniform or homogeneous flow of water or solutes is indicated by HI = 1 and heterogeneity is indicated by HI > 1. A large value for this index may indicate preferential flow. The heterogeneity index relies only on knowledge of the elution curves generated from multiple sample percolation experiments and is, therefore, easily calculated. The index may also be used to describe and compare the differences in solute and soil-water percolation from different experiments. The use of this index is discussed for several different leaching experiments. (C) 1999 Elsevier Science B.V. All rights reserved.

Integrable Kondo impurities in the one-dimensional supersymmetric U model of strongly correlated electrons

Integrable Kondo impurities in the one-dimensional supersymmetric U model of strongly correlated electrons are studied by means of the boundary graded quantum inverse scattering method. The boundary K-matrices depending on the local magnetic moments of the impurities are presented as non-trivial realizations of the reflection equation algebras in an impurity Hilbert space. Furthermore, the model Hamiltonian is diagonalized and the Bethe ansatz equations are derived. It is interesting to note that our model exhibits a free parameter in the bulk Hamiltonian but no free parameter exists on the boundaries. This is in sharp contrast to the impurity models arising from the supersymmetric t-J and extended Hubbard models where there is no free parameter in the bulk but there is a free parameter on each boundary.

Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins

Retroviral entry into cells depends on envelope glycoproteins, whereby receptor binding to the surface-exposed subunit triggers membrane fusion by the transmembrane protein (TM) subunit. We determined the crystal structure at 2.5-Angstrom resolution of the ectodomain of gp21, the TM from human T cell leukemia virus type 1. The gp21 fragment was crystallized as a maltose-binding protein chimera, and the maltose-binding protein domain was used to solve the initial phases by the method of molecular replacement. The structure of gp21 comprises an N-terminal trimeric coiled coil, an adjacent disulfide-bonded loop that stabilizes a chain reversal, and a C-terminal sequence structurally distinct from HIV type 1/simian immunodeficiency virus gp41 that packs against the coil in an extended antiparallel fashion. Comparison of the gp21 structure with the structures of other retroviral TMs contrasts the conserved nature of the coiled coil-forming region and adjacent disulfide-bonded loop with the variable nature of the C-terminal ectodomain segment. The structure points to these features having evolved to enable the dual roles of retroviral TMs: conserved fusion function and an ability to anchor diverse surface-exposed subunit structures to the virion envelope and infected cell surface. The structure of gp21 implies that the N-terminal fusion peptide is in close proximity to the C-terminal transmembrane domain and likely represents a postfusion conformation.

Population balance model of in vivo neutrophil formation following bone marrow rescue therapy

In this paper, we develop a simple four parameter population balance model of in vivo neutrophil formation following bone marrow rescue therapy. The model is used to predict the number and type of neutrophil progenitors required to abrogate the period of severe neutropenia that normally follows a bone marrow transplant. The estimated total number of 5 billion neutrophil progenitors is consistent with the value extrapolated from a human trial. The model provides a basis for designing ex vivo expansion protocols.

Molecular characterization of Drosophila C virus isolates

Reverse transcription coupled with polymerase chain reaction and restriction enzyme analysis was used to characterize 12 Drosophila C virus isolates from geographically different regions. A 1.2-kb fragment was amplified from cDNA and profiles from digestion with 20 restriction enzymes were generated. Analysis of the restriction fragment data gave estimates of nucleotide divergence of 0-10% between isolates. The isolates were grouped on the basis of genetic distance estimates derived from the restriction data. For the isolates from which a single genotype could be purified, a geographical pattern in the distribution of viral genotypes was identified. The 4 Moroccan isolates were very closely related to each other, differing in only 1 restriction profile. The 2 Australian isolates were each other's closest relatives, as were the 2 isolates first recovered in France. The PCR-RFLP technique used in this study has provided us with a simple procedure which can be used to characterize DCV isolates. A single enzyme, Tag I, generated 5 distinct and diagnostic restriction fragment patterns, which allowed easy assignment of isolates to one of the five viral genotypes identified in this study. (C) 1999 Academic Press.

Phase diagram of a Heisenberg spin-Peierls model with quantum phonons

Using a new version of the density-matrix renormalization group we determine the phase diagram of a model of an antiferromagnetic Heisenberg spin chain where the spins interact with quantum phonons. A quantum phase transition from a gapless spin-fluid state to a gapped dimerized phase occurs at a nonzero value of the spin-phonon coupling. The transition is in the same universality class as that of a frustrated spin chain, to which the model maps in the diabatic limit. We argue that realistic modeling of known spin-Peierls materials should include the effects of quantum phonons.

Human and murine cytomegalovirus evasion of cytotoxic T lymphocyte and natural killer cell-mediated immune responses

Herpesviruses, such as human and murine cytomegalovirus, possess an impressive array of genes believed to assist in virus survival against the host immune response. In this review, we cover the rapidly growing area of cytomegalovirus evasion of cellular immunity, specifically cytotoxic T lymphocytes and natural killer cells. The proposed mechanisms of action of viral proteins involved in blocking peptide presentation to CD8(+) T cells, namely, interference with peptide generation, inhibition of peptide assembly with class I MHC and retention/destabilization of class I MHC complexes, are described. In addition, recent evidence implicating the viral class I MHC-like proteins as inhibitors of natural killer cell-mediated clearance is reviewed, (C) 1998 Academic Press.

Extended integrability regime for the supersymmetric U model

An extension of the supersymmetric U model for correlated electrons is given and integrability is established by demonstrating that the model can he constructed through the quantum inverse scattering method using an R-matrix without the difference property. Some general symmetry properties of the model are discussed and from the Bethe ansatz solution an expression for the energies is presented.

Integrable Kondo impurities in the one-dimensional supersymmetric extended Hubbard model

An integrable Kondo problem in the one-dimensional supersymmetric extended Hubbard model is studied by means of the boundary graded quantum inverse scattering method. The boundary K-matrices depending on the local moments of the impurities are presented as a non-trivial realization of the graded reflection equation algebras in a two-dimensional impurity Hilbert space. Further, the model is solved by using the algebraic Bethe ansatz method and the Bethe ansatz equations are obtained.

On modifications to the long-term survival mixture model in the presence of competing risks

A mixture model for long-term survivors has been adopted in various fields such as biostatistics and criminology where some individuals may never experience the type of failure under study. It is directly applicable in situations where the only information available from follow-up on individuals who will never experience this type of failure is in the form of censored observations. In this paper, we consider a modification to the model so that it still applies in the case where during the follow-up period it becomes known that an individual will never experience failure from the cause of interest. Unless a model allows for this additional information, a consistent survival analysis will not be obtained. A partial maximum likelihood (ML) approach is proposed that preserves the simplicity of the long-term survival mixture model and provides consistent estimators of the quantities of interest. Some simulation experiments are performed to assess the efficiency of the partial ML approach relative to the full ML approach for survival in the presence of competing risks.

Using Lindenmayer systems to model morphogenesis in a tropical pasture legume Stylosanthes scabra

This paper summarizes the processes involved in designing a mathematical model of a growing pasture plant, Stylosanthes scabra Vog. cv. Fitzroy. The model is based on the mathematical formalism of Lindenmayer systems and yields realistic computer-generated images of progressive plant geometry through time. The processes involved in attaining growth data, retrieving useful growth rules, and constructing a virtual plant model are outlined. Progressive output morphological data proved useful for predicting total leaf area and allowed for easier quantification of plant canopy size in terms of biomass and total leaf area.

Computational binding assays of antigenic peptides

Computer models can be combined with laboratory experiments for the efficient determination of (i) peptides that bind MHC molecules and (ii) T-cell epitopes. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures. This requires the definition of standards and experimental protocols for model application. We describe the requirements for validation and assessment of computer models. The utility of combining accurate predictions with a limited number of laboratory experiments is illustrated by practical examples. These include the identification of T-cell epitopes from IDDM-, melanoma- and malaria-related antigens by combining computational and conventional laboratory assays. The success rate in determining antigenic peptides, each in the context of a specific HLA molecule, ranged from 27 to 71%, while the natural prevalence of MHC-binding peptides is 0.1-5%.