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As biomedical research becomes increasingly data-intensive, it is increasingly essential to integrate genomic-scale datasets, so as to generate a more holistic picture of complex biological processes. The systems biology paradigm may differ in strategy from traditional reductionist scientific methods, but the goal remains the same: to generate tenable hypotheses driving the experimental elucidation of biological mechanisms. Intracellular pathogens provide an excellent opportunity for systems analysis, as many of these organisms are amenable to genetic manipulation, allowing their biology to be played off against that of the host. Moreover, many of the most fundamental biological properties of these microbes (host cell invasion, immune escape, intracellular replication, long-term persistence) are directly linked to pathogenesis and readily quantifiable using genomic-scale technologies. In this review, we summarize and discuss some of the available and foreseeable functional genomics datasets pertaining to host-pathogen interactions and suggest that the host-pathogen interface represents a promising, tractable challenge for systems biological analysis. Success will require developing and leveraging new technologies, expanding data acquisition, and increasing public access to comprehensive datasets, in order to assemble quantitative and testable models of the host-pathogen relationship.

Background Prurigo nodularis (PN) is a chronic inflammatory skin disease with nodular itching lesions. UV therapy – both PUVA and NUVB – are known to clear up PN temporarily due to the antipruritic effect of UV light. However, relapse after treatment is common in PN, which means that either long-term therapy is necessary or the treatment protocols have to be optimized to minimize side-effects. Objective The aim of this study was to evaluate the effect that combining bath PUVA and targeted UVB 308 nm excimer radiation has on recalcitrant nodular prurigo. Methods In a prospective trial, 22 patients with PN were treated with either PUVA alone or with a combination of PUVA and excimer UVB. The end point was complete or almost complete remission of PN. Results Adding a 308-nm excimer UVB to the treatment of the pruritic nodules sped up the healing process; 30% less PUVA radiation was needed. Conclusion The combination of PUVA and excimer UVB in PN appears to be very efficacious. Reducing psoralen UVA doses by 30% offered long-term benefits in phototherapy of chronic recalcitrant diseases like PN.

Although a quantitative relationship between sequence similarity and structural similarity has long been established, little is known about the impact of orthology on the relationship between protein sequence and structure. Among homologs, orthologs (derived by speciation) more frequently have similar functions than paralogs (derived by duplication). Here, we hypothesize that an orthologous pair will tend to exhibit greater structural similarity than a paralogous pair at the same level of sequence similarity. To test this hypothesis, we used 284,459 pairwise structure-based alignments of 12,634 unique domains from SCOP as well as orthology and paralogy assignments from OrthoMCL DB. We divided the comparisons by sequence identity and determined whether the sequence-structure relationship differed between the orthologs and paralogs. We found that at levels of sequence identity between 30 and 70%, orthologous domain pairs indeed tend to be significantly more structurally similar than paralogous pairs at the same level of sequence identity. An even larger difference is found when comparing ligand binding residues instead of whole domains. These differences between orthologs and paralogs are expected to be useful for selecting template structures in comparative modeling and target proteins in structural genomics.

— Hepatitis delta virus (HDV) superinfection of woodchuck chronic carriers of woodchuck hepatitis virus (WHV) results in acute and chronic disease. The different courses of disease mimicked the outcome of human HDV superinfection, making woodchucks valuable models for clinical studies of HDV. Ten of 11 woodchuck chronic carriers of WHV superinfected with HDV developed acute HDV infection with markers of viral replication in the serum and liver. One animal (DW128) had no serological markers of acute HDV infection. Nine of 11 (82%) superinfected animals developed chronic HDV infection. An unusual course of chronic HDV infection occurred in one woodchuck (DW128): no serum markers of acute or chronic HDV infection appeared but HDV RNA was detected in the liver, indicating that chronic HDV infection can occur without serological markers.

To gain more information on the mechanism of lubrication in articular joints, the superficial layer of bovine articular cartilage was mechanically removed in a sheet of ice that formed on freezing the cartilage. Freeze-dried samples contained low concentrations of chondroitin sulphate and protein. Analysis of the protein by SDS PAGE showed that the composition of the sample was comparable to that of synovial fluid (SF). Attenuated total reflection infrared (ATR-IR) spectroscopy of the dried residue indicated that the sample contained mostly hyaluronan. Moreover, ATR-IR spectroscopy of the upper layer of the superficial layer, adsorbed onto silicon, showed the presence of phospholipids. A gel could be formed by mixing hyaluronan and phosphatidylcholine in water with mechanical properties similar to those of the superficial layer on cartilage. Much like the superficial layer of natural cartilage, the surface of this gel became hydrophobic on drying out. Thus, it is proposed that the superficial layer forms from hyaluronan and phospholipids, which associate by hydrophobic interactions between the alkyl chains of the phospholipids and the hydrophobic faces of the disaccharide units in hyaluronan. This layer is permeable to material from the SF and the cartilage, as shown by the presence of SF proteins and chondroitin sulphate. As the cartilage dries out after removal from the joint, the phospholipids migrate towards the surface of the superficial layer to reduce the surface tension. It is also proposed that the highly efficient lubrication in articular joints can, at least in part, be attributed to the ability of the superficial layer to adsorb and hold water on the cartilage surface, thus creating a highly viscous boundary protection.

Pyrimethamine resistance in the malaria parasite Plasmodium falciparum is characterized by specific point mutations in the dihydrofolate reductase (DHFR) domain of the bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene. We have previously explored the effect of these mutations by engineering homologous alleles of Toxoplasma gondii DHFR-TS, which can readily be expressed as recombinant protein for enzymatic studies, or as allelic replacements in transgenic parasites. In order to directly assess the costs of pyrimethamine-resistance in vivo, we have carried out competition studies between mixtures of T. gondii tachyzoites harbouring wild-type or mutant DHFR-TS alleles, both in tissue culture and in mice. Arg59+Asn108 mutants (using the P. falciparum numbering system) exhibit no significant fitness defects in vitro, but a fitness defect of 1.8% per generation in mice. Arg59+Ser223 mutants exhibit fitness defects of >2.8% per generation both in vitro and in vivo, which may explain why this highly pyrimethamine-resistant allele has not been observed in the field. It is important to note that long-term propagation of parasites in vitro or in vivo can produce adaptations affecting fitness by >3.7% per generation, necessitating careful attention to background in head-to-head competition studies. A sensitive PCR-based assay permits different growth rates to be assessed even in the absence of a drug resistance marker that can be scored by plaque assay.

Two forms of the protozoan parasite Toxoplasma gondii are associated with intermediate hosts such as humans: rapidly growing tachyzoites are responsible for acute illness, whereas slowly dividing encysted bradyzoites can remain latent within the tissues for the life of the host. In order to identify genetic factors associated with parasite differentiation, we have used a strong bradyzoite-specific promoter (identified by promoter trapping) to drive the expression of T. gondii hypoxanthine-xanthine-guanine phosphoribosyltransferase (HXGPRT) in stable transgenic parasites, providing a stage-specific positive/negative selectable marker. Insertional mutagenesis has been carried out on this parental line, followed by bradyzoite induction in vitro and selection in 6-thioxanthine to identify misregulation mutants. Two different mutants fail to induce the HXGPRT gene efficiently during bradyzoite differentiation. These mutants are also defective in other aspects of differentiation: they replicate well under bradyzoite growth conditions, lysing the host cell monolayer as effectively as tachyzoites. Expression of the major bradyzoite antigen BAG1 is reduced, and staining with Dolichos biflorus lectin shows reduced cyst wall formation. Microarray hybridizations show that these mutants behave more like tachyzoites at a global level, even under bradyzoite differentiation conditions.

Interleukin (IL)-10 is an inhibitor of cell mediated immunity and an antagonist of the development of protective immune responses associated with resistance to T. gondii. These observations led to the hypothesis that the production of IL-10 could contribute to the ability of T. gondii to replicate and survive in an immune competent host. To determine whether the production of IL-10 affects the ability of the RH strain of T. gondii to cause a lethal infection in mice, we compared the immune response to RH in IL-10+/+ and IL-10-/- BALB/c mice. Both groups of mice produced comparable amounts of IL-12 and interferon (IFN)-gamma and had similar mortality curves and parasite burdens. The use of green fluorescent protein-labelled parasites allowed us to infect IL-10+/+ and IL-10-/- mice and use a fluorescence-activated cell sorter to distinguish infected and uninfected populations of macrophages and compare their expression of CD80, CD86 and major histocompatibility complex (MHC) class II. Although infected cells expressed higher overall levels of these molecules than uninfected cells, there were no differences between cells isolated from IL-10+/+ and IL-10-/- mice. Taken together, these results indicate that IL-10 is not required for the virulence of the RH strain of T. gondii, nor is it involved in the regulation of the CD80, CD86 and MHC class II molecules during RH-infection.

Rhoptry associated protein 1 (RAP1) and 2 (RAP2), together with a poorly described third protein RAP3, form the low molecular weight complex within the rhoptries of Plasmodium falciparum. These proteins are thought to play a role in erythrocyte invasion by the extracellular merozoite and are important vaccine candidates. We used gene-targeting technology in P.falciparum blood-stage parasites to disrupt the RAP1 gene, producing parasites that express severely truncated forms of RAP1. Immunoprecipitation experiments suggest that truncated RAP1 species did not complex with RAP2 and RAP3. Consistent with this were the distinct subcellular localizations of RAP1 and 2 in disrupted RAP1 parasites, where RAP2 does not traffic to the rhoptries but is instead located in a compartment that appears related to the lumen of the endoplasmic reticulum. These results suggest that RAP1 is required to localize RAP2 to the rhoptries, supporting the hypothesis that rhoptry biogenesis is dependent in part on the secretory pathway in the parasite. The observation that apparently host-protective merozoite antigens are not essential for efficient erythrocyte invasion has important implications for vaccine design.

Cryoablation has recently become a useful procedure for the treatment of prostatic and hepatic tumors, primarily because of advances in the ability to monitor visually the freezing process with ultrasound. Success of the procedure depends in large part on how well the ice front can be positioned to destroy pathologic tissue, while sparing healthy tissue. This study describes a cryogen delivery system that can be used in conjunction with magnetic resonance (MR) image-guided cryoablation, and an automatic control system that uses MR image guidance in a feedback loop to control the ice front trajectory. Edge-detected MR images are used to determine the current ice front location at each time interval, providing feed-back to an automatic control system that adjusts the flow of cryogen to the cryoprobe. Numerical simulations and experimental results demonstrate that an ice front with cylindrical symmetry can be accurately controlled using this MR image-guided feedback control scheme.

Conventional constant angular velocity sampling of the surface of a sphere results in a higher sampling density near the two poles relative to the equatorial region. More samples, and hence longer sampling time, are required to achieve a given sampling density in the equatorial region when compared with uniform sampling. This paper presents a simple expression for a continuous sample path through a nearly uniform distribution of points on the surface of a sphere. Sampling of concentric spherical shells in k-space with the new strategy is used to design 3D selective inversion and spin-echo pulses. These new 3D selective pulses have been implemented and verified experimentally.

A high frequency solution of the electromagnetic field produced by a circular surface coil adjacend to a homogenous conducting, dielectric sphere is used to predict the attainable signal to noise ratio (S/N) and specific absorption rate (SAR) for in vivo1H NMR spec troscopy experiments from 200 to 430 MHz (4.7–10T). Above 200 MHz the S/N increases more rapidly with frequency and the SAR increases less rapidly compared with the respective S/N and SAR frequency dependence below 200 MHz. The difference in frequency dependence is due to dielectric resonances of the magnetic field inside the sphere at frequencies above 200 MHz. It is predicted that surface coil 1H NMR experiments may be performed on a head-sized sphere, having conductivity and relative dielectric constant of brain, at frequencies up to 430 MHz without exceeding 8 W/kg local SAR and 3.2 W/kg SAR. The calculations of the S/N and SAR are used to determine optimum surface coil geometries for NMR experments. The power radited by the surface coil in the absence of shielding and asymmetries in the received signal with respect to the plane defined by the surface coil axix and the direction of the static magnetic field are significant at high frequency. Experimental measurements of the magnetic field inside a head-sized sphere verfy the presence of dielectric resonances at frequencies above 200 MHz. © 1991 Academic Press, Inc.

The changes in hydrostatic pressure and electrical potentials across vessels in the human vasculature in the presence of a large static magnetic field are estimated to determine the feasibility of in vivo NMR spectroscopy at fields as high as 10 T. A 10-T magnetic field changes the vascular pressure in a model of the human vasculature by less than 0.2%. An exact solution to the magnetohydrodynamic equations describing a conducting fluid flowing transverse to a static magnetic field in a nonconducting, straight, circular tube is used. This solution is compared to an approximate solution that assumes that no magnetic fields are induced in the fluid and that has led previous investigators to predict significant biological effects from static magnetic fields. Experimental results show that the exact solution accurately predicts the magnetohydrodynamic slowing of 15% NaCl flowing transverse to 2.3- and 4.7-T magnetic fields for fluxes below 0.5 liter/min while the approximate solution predicts a much more retarded flow. © 1990 Academic Press, Inc.

Ice was grown by accretion on rotating embryos at air temperatures of −6, −12 and −24°C while the liquid water content ranged approximately between 1 and 4 g m−3. The air speed in the wind tunnel and the modal droplet diameter were, respectively, 20 m s−1 and 13 μm. Details of the structure of the spongy ice were studied in thin sections after elimination of internal liquid water by centrifuging. Sponginess occurred in radial zones associated with surface protuberances but did not necessarily coincide with the indentations between them. Radial striations and tangential microlayers of some 200 μm thickness were found and point to a complex original ice-water interface. About half of the spongy specimens were allowed to freeze undisturbed. The subsequent transparent ice contained patches of air bubbles mostly of some 20 μm in diameter showing distinctive arrangements and a log-normal size distribution. Crystals were elongated in the growth direction while optic axes tended to lie normal to it, 67° being the average value of the angle between the projection of the c-axis on the plane of the hailstone section and the growth direction. This tendency confirms epitaxial growth during the later stages of freezing.

The deuterium content of more than 400 samples cut from 34 hailstones was determined. These hailstones came from three storms the structures of which were studied by radar. the range in values of deuterium excess (δD) of about 60‰ (extending as low as −86‰) was compatible with the moist adiabatic model only if a significant increase in δD of atmospheric vapour occurred at some stage. Individual growth layers were concluded isotopically uniform. Opaque ice was associated with relatively low δD, especially for the bulk of the hailstones beyond the embryo stage. the correlation found between SD and crystal size was used to derive the relationship between δD and ambient temperature. It was hence concluded that embryos mostly grew between 6 and 7km above ground level. Hailstones of all sizes acquired most of their mass between 7 and 8 km (−20 to −25°C) during the early stages of the severe storms when radar echo tops reached up to 16km. However, during later stages most of the growth occurred during descent. Hailstones from places no more than a few kilometres apart in one storm were concluded 10 have grown in very different conditions: while some must have experienced updraughts in which the speed in the environment of the hailstone increased steadily with time, others encountered an updraught that pulsated with a period of about 8min. Updraught maxima often occurred at about 7.5km, approaching values of 40ms−1.

The relationship between emotional stress and infertility was investigated in a study of 59 infertile female patients. Comparisons were made between a functional group (n = 22), an organic group (n = 32) and a fertile group (n = 5). No significant differences in basal pulse volume, heart rate, skin resistance and muscle tension were found. The normal group showed significantly higher heart rate reactivity to sound stimulation than the functional group. It was concluded that the functional group (contrary to expectations) did not show increased tension and lability in smooth and skeletal musculature.

This study examines slice selection and diffusion as sources of systematic error in T2 estimates obtained from imaging experiments. The selective refocusing pulses in a multislice, two-echo, spin-warp experiment cause slice profiles of sequential echoes to change in shape. This results in bias in T2 images calculated from the two-echo data set. A method to correct the bias is presented. The effect of diffusion on T2 images obtained with typical two-echo imaging sequences was found to be negligible. © 1987 Academic Press, Inc.