Ensembl 2004.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Protein losses in ion-exchange and hydrophobic interaction high-performance liquid chromatography.

Protein losses in ion-exchange and hydrophobic interaction HPLC were examined. The supports were all non-porous, packed in columns of identical dimensions. Two ion-exchange chromatography (IEC), anion and cation, as well as a hydrophobic interaction chromatography (HIC) columns were tested. Proteins included cytochrome c, bovine serum albumin (BSA), immunoglobulin G and fibrinogen. Temperature effects on HIC supports were studied for cytochrome c and BSA. Both retention times and recoveries of the proteins were measured. The influence of column residence time on the recovery of proteins was also investigated. We found a linear relationship between the amount of protein recovered and the log of the molecular mass. Retention times also generally increased with temperature for both HIC and IEC. Other trends in retention behavior and recoveries are discussed.

Antilisterial immunity includes specificity to listeriolysin O (LLO) and non-LLO-derived determinants.

Subclinical infection of BALB/c mice with virulent Listeria monocytogenes leads to the generation of Listeria-specific T-cell populations required for the expression of protective immunity. The L. monocytogenes-produced hemolysin listeriolysin O (LLO) is a virulence factor which appears to be crucial for the induction of protective antilisterial immunity. Analysis of the specificity of antilisterial cytotoxic cells from Listeria-immune BALB/c donors has shown a dominant response to an epitope corresponding to amino acids 91 to 99 of LLO. Demonstration of antilisterial T cells with specificity to non-LLO-derived epitopes has been difficult to achieve because of the requirement of LLO in facilitating escape of the bacteria to the cytoplasm of the host cell and the apparent dominance of an anti-LLO response in antilisterial immunity. In this study we show that antilisterial immunity also includes specificity to non-LLO-derived determinants. We used as an immunogen an LLO- mutant of L. monocytogenes which expresses the hemolysin perfringolysin O (PFO). The LLO- PFO+ L. monocytogenes mutant possesses invasive properties similar to those of wild-type L. monocytogenes and escape from the phagocytic vacuole because of the activity of PFO. We found that J774 target cells infected with the LLO- PFO+ L. monocytogenes mutant were lysed by antilisterial cytotoxic T cells obtained from BALB/c mice immunized with wild-type L. monocytogenes. In addition, BALB/c mice immunized with the LLO- PFO+ L. monocytogenes mutant were immune to challenge with LLO+ wild-type L. monocytogenes, a finding indicative of protective antilisterial immunity specific to Listeria-derived epitopes other than LLO. Spleen cells from BALB/c mice immunized with the LLO- PFO+ L. monocytogenes mutant adoptively transferred antilisterial protection to a subsequent challenge with wild-type L. monocytogenes. This splenocyte population also contained cytotoxic cells which lysed target cells infected with either the LLO- PFO+ L. monocytogenes mutant or wild-type LLO+ L. monocytogenes but did not lyse target cells infected with an LLO-expressing Bacillus subtilis transformant. These results establish that during the immune response to L. monocytogenes, immune splenocytes with specificity for LLO and other, non-LLO-derived epitopes develop. These non-LLO epitopes serve as targets for antilisterial cytotoxic cells and for lymphocytes which adoptively transfer antilisterial immunity.

Parasite lactate dehydrogenase as an assay for Plasmodium falciparum drug sensitivity.

This report compares the use of the lactate dehydrogenase (pLDH) assay with 3H-hypoxanthine incorporation and Giemsa microscopy for the evaluation of anti-malaria drug inhibition of the growth of P. falciparum in vitro. The inhibition profiles and IC50 determinations of the pLDH assay were directly comparable to those determined by the radioactive uptake and microscopic methods. Furthermore, the pLDH culture sensitivity assay is reproducible, easily interpreted, rapid and inexpensive to perform, suggesting field applicability.

Listeriolysin O is a target of the immune response to Listeria monocytogenes.

The immunologic mechanism of protective immunity to the intracellular parasite Listeria monocytogenes (Lm) is not well understood, however, antilisterial immunity can be adoptively transferred with T lymphocytes from Lm-immune donors. The Lm-immune cells are believed to produce macrophage-activating lymphokines, which leads to the eventual macrophage-dependent eradication of the bacterium. Increasing evidence suggests that immunity to Lm resides exclusively within the CD8+ T cell subset. It is possible that the Lm-immune CD8+ T cells function to release sequestered Lm from nonprofessional phagocytes to awaiting activated macrophage populations. This study was conducted to determine if listeriolysin O (LLO), which is an essential determinant of Lm pathogenicity, is also a target of the antilisterial immune response. We have found that target cells infected with a LLO+ Lm strain are lysed by Lm-immune cytotoxic cells, whereas target cells infected with a LLO- Lm mutant, or pulsed with a heat-killed Lm preparation, are not lysed by the Lm-immune effector cells. We have used a Bacillus subtilis (Bs) construct that expresses the LLO gene product and found that target cells infected with the LLO+ Bs construct are lysed by antilisterial cytotoxic cells. The antilisterial cytotoxic response is targeted against LLO, in that we have also used a Bs construct that expresses the perfringolysin (PLO) gene product and found that target cells infected with the PLO+ Bs are not lysed by antilisterial cytotoxic effector cells. These data strongly suggest that LLO is a target antigen of antilisterial immunity and may represent the dominant target during the expression of the immune response to Lm.

Laboratory diagnosis of malaria.

Diagnostic procedures for the detection of malaria differ considerably depending on the aims of evaluation. The current requirements of any laboratory procedure for general application to the detection and diagnosis of malaria include: sensitivity, specificity, simplicity in application, unambiguous interpretation, and rapid turn-around time. Presently the differential stained thick and thin blood smear, examined under the microscope, remains the most reliable and definitive test for diagnosis of malaria.

Allogeneic marrow transplantation in non-Hodgkin's lymphoma.

Nine individuals between 15 and 43 years of age with non-Hodgkin's lymphoma underwent allogeneic marrow transplantation following busulfan 16 mg/kg and cyclophosphamide 120 mg/kg. These individuals were not considered optimal candidates for autologous transplantation chiefly because of marrow involvement or resistance to chemotherapy. All patients engrafted and eight achieved complete remission. Three patients relapsed; one patient died of transplant-related complications. Five individuals are disease-free survivors between 103 and 1169 days following transplantation. Of three individuals with relapsed Burkitt's lymphoma none experienced a sustained disease-free interval following transplantation. Three of four individuals with large cell or lymphoblastic lymphoma are surviving 585 to 1169 days following transplantation. Allogeneic marrow transplantation following busulfan and cyclophosphamide appears reasonably safe and is effective in selected patients with non-Hodgkin's lymphoma who are not good candidates for autologous marrow transplantation.

The influence of parturition on peripheral blood mononuclear phagocyte subpopulations in pregnant women.

Mononuclear phagocytes (MPs) from human peripheral blood were separated on discontinuous Percoll gradients into two subpopulations. A high density population was isolated which contained less mature MPs, while the MPs in the low density population were more mature cells. The proportion of high density MPs was found to increase sharply in conjunction with the peripheral blood monocytosis associated with parturition in women. The data show that there is a measurable response in the circulating MP pool to this acute inflammatory stimulus and that this response is manifested as an increase in absolute numbers of both total and high density MPs. No significant change was found in the number of low density MPs.

The response of human peripheral blood mononuclear phagocytes to rheumatoid arthritis.

The maturity of peripheral blood mononuclear phagocytes (B-MPs) from patients with rheumatoid arthritis (RA), osteoarthritis (OA), and reference ("normal") subjects was compared. Mononuclear cell isolates from peripheral blood were separated on discontinuous gradients of Percoll into low density (more mature) and high density (less mature) subpopulations. Contrary to expectations, the proportion of immature B-MPs in RA patients was found to be significantly lower than that in reference subjects. In RA patients with synovial effusions the proportion of immature B-MPs approached but did not exceed those found in reference subjects, despite the fact that 31% of these patients displayed a peripheral blood monocytosis. It was concluded that the bone marrow precursor population had adapted to the long-term demand for B-MPs in the course of this chronic inflammatory disease.

Mitogen stimulation of whole blood microcultures from patients with rheumatic disease.

In this study the lymphocyte function of therapy matched rheumatoid and non-rheumatoid patients in the mitogen mediated in vitro whole blood microculture system has been analyzed. Normal responses to phytohemagglutinin (PHA) and poke weed mitogen (PWM) and depressed responses to concanavalin A (Con A) were found. The PHA and Con A responses were influenced by drug therapy. Differences in the relative activity of PHA to Con A among the groups studied further supports the contention that rheumatoid arthritis (RA) patients have functional abnormalities in their T cell subpopulations. These differences were not due to a decrease in circulating lymphocytes or in the ratio of T lymphocyte numbers but likely reflects a disproportionate representation of Con A reactive T cells in the circulating T cell pool of RA patients.

Ibuprofen and diflunisal in rheumatoid arthritis: a double-blind comparative trial.

Both diflunisal (750 mg/day) and ibuprofen (1600 mg/day) were shown to be superior to placebo in the treatment of rheumatoid arthritis in a double-blind cross-over trial. Neither drug affected lymphocyte transformation to plant mitogens. Diflunisal scored better than ibuprofen at the dose levels chosen but the differences did not reach significance.

A terminal labelling assay using 3H-uridine to measure cell-mediated cytotoxic responses against parainfluenza type 3 infected target cells.

The standardisation of a terminal labelling cytotoxicity assay which used the incorporation of 3H-uridine to measure target cell survival of the effector phase is described. This assay was applied to a preliminary study of the cell-mediated responses of sheep following intravenous inoculation of Pi-3 virus. The assay provided a simple, accurate, and reproducible method to measure cytotoxic responses against Pi-3 infected target cells. The experimental data did not require mathematical corrections for non-specific effects as in the 51Cr-release assay. When cytotoxicity could be detected in uninfected target cell cultures it was low and statistically insignificant.

A single-blind crossover trial of the anti-inflammatory drug sodium meclofenamate and placebo, including an evaluation of hand grip and of lymphocyte responsiveness.

A single-blind crossover trial was carried out in 21 patients with active rheumatoid arthritis to assess the effectiveness and tolerance of sodium meclofenamate (300 mg per day) compared with placebo. After a 1-week washout period patients had two periods of active medication, each of 2 weeks, separated by 1 week on placebo. Morning stiffness, walking speed, pain score, patient impression of response, joint tenderness and power, work and maximum grip strength achieved by hand grip were all improved by sodium meclofenamate and an anti-inflammatory effect of the drug was demonstrated, with some reduction in the swelling of PIP joints. There was no advantage in assessing pain on full movement of the small joints of the hands in addition to direct tenderness. Power, work and rate of grip release achieved during hand grip provided more information about hand function than maximum grip strength alone. Lymphocyte transformation to non-specific mitogens was enhanced by the drug. Twelve patients had some form of gastro intestinal complaint during the study and it is suggested that diarrhoea is likely to prove to be the major limiting factor of acceptance by some patients.