Detection and monitoring of anaerobic rumen fungi using an ARISA method

AIM

To develop an automated ribosomal intergenic spacer region analysis (ARISA) method for the detection of anaerobic rumen fungi and also to demonstrate utility of the technique to monitor colonization and persistence of fungi, and diet-induced changes in community structure.

METHODS AND RESULTS

The method could discriminate between three genera of anaerobic rumen fungal isolates, representing Orpinomyces, Piromyces and Neocallimastix species. Changes in anaerobic fungal composition were observed between animals fed a high-fibre diet compared with a grain-based diet. ARISA analysis of rumen samples from animals on grain showed a decrease in fungal diversity with a dominance of Orpinomyces and Piromyces spp. Clustering analysis of ARISA profile patterns grouped animals based on diet. A single strain of Orpinomyces was dosed into a cow and was detectable within the rumen fungal population for several weeks afterwards.

CONCLUSIONS

The ARISA technique was capable of discriminating between pure cultures at the genus level. Diet composition has a significant influence on the diversity of anaerobic fungi in the rumen and the method can be used to monitor introduced strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Through the use of ARISA analysis, a better understanding of the effect of diets on rumen anaerobic fungi populations is provided.

Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association

DM catalyzes the exchange of peptides bound to Class II major histocompatibility complex (MHC) molecules. Because the dissociation and association components of the overall reaction are difficult to separate, a detailed mechanism of DM catalysis has long resisted elucidation. UV irradiation of DR molecules loaded with a photocleavable peptide (caged Class II MHC molecules) enabled synchronous and verifiable evacuation of the peptide-binding groove and tracking of early binding events in real time by fluorescence polarization. Empty DR molecules generated by photocleavage rapidly bound peptide but quickly resolved into species with substantially slower binding kinetics. DM formed a complex with empty DR molecules that bound peptide with even faster kinetics than empty DR molecules just having lost their peptide cargo. Mathematical models demonstrate that the peptide association rate of DR molecules is substantially higher in the presence of DM. We therefore unequivocally establish that DM contributes directly to peptide association through formation of a peptide-loading complex between DM and empty Class II MHC. This complex rapidly acquires a peptide analogous to the MHC class I peptide-loading complex.

Structural basis of T-cell specificity and activation by the bacterial superantigen TSST-1

Superantigens (SAGs) bind simultaneously to major histocompatibility complex (MHC) and T-cell receptor (TCR) molecules, resulting in the massive release of inflammatory cytokines that can lead to toxic shock syndrome (TSS) and death. A major causative agent of TSS is toxic shock syndrome toxin-1 (TSST-1), which is unique relative to other bacterial SAGs owing to its structural divergence and its stringent TCR specificity. Here, we report the crystal structure of TSST-1 in complex with an affinity-matured variant of its wild-type TCR ligand, human T-cell receptor beta chain variable domain 2.1. From this structure and a model of the wild-type complex, we show that TSST-1 engages TCR ligands in a markedly different way than do other SAGs. We provide a structural basis for the high TCR specificity of TSST-1 and present a model of the TSST-1-dependent MHC-SAG-TCR T-cell signaling complex that is structurally and energetically unique relative to those formed by other SAGs. Our data also suggest that protein plasticity plays an exceptionally significant role in this affinity maturation process that results in more than a 3000-fold increase in affinity.

Small molecules that enhance the catalytic efficiency of HLA-DM

HLA-DM (DM) plays a critical role in Ag presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Large lateral surfaces involved in the DM:HLA-DR (DR) interaction have been defined, but the mechanism of catalysis is not understood. In this study, we describe four small molecules that accelerate DM-catalyzed peptide exchange. Mechanistic studies demonstrate that these small molecules substantially enhance the catalytic efficiency of DM, indicating that they make the transition state of the DM:DR/peptide complex energetically more favorable. These compounds fall into two functional classes: two compounds are active only in the presence of DM, and binding data for one show a direct interaction with DM. The remaining two compounds have partial activity in the absence of DM, suggesting that they may act at the interface between DM and DR/peptide. A hydrophobic ridge in the DMbeta1 domain was implicated in the catalysis of peptide exchange because the activity of three of these enhancers was substantially reduced by point mutations in this area.

Unusual features of self-peptide/MHC binding by autoimmune T cell receptors

Structural studies on T cell receptors (TCRs) specific for foreign antigens demonstrated a remarkably similar topology characterized by a central, diagonal TCR binding mode that maximizes interactions with the MHC bound peptide. However, three recent structures involving autoimmune TCRs demonstrated unusual interactions with self-peptide/MHC complexes. Two TCRs from multiple sclerosis patients bind with unconventional topologies, and both TCRs are shifted toward the peptide N terminus and the MHC class II beta chain helix. A TCR from the experimental autoimmune encephalomyelitis (EAE) model binds in a conventional orientation, but the structure is unusual because the self-peptide only partially fills the binding site. For all three TCRs, interaction with the MHC bound self-peptide is suboptimal, and only two or three TCR loops contact the peptide. Optimal TCR binding modes confer a competitive advantage for antimicrobial T cells during an infection, whereas altered binding properties may permit survival of a subset of autoreactive T cells during thymic selection.

Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor

Autoimmune diseases are caused by self-reactive lymphocytes that have escaped deletion. Here we have determined the structure of the trimolecular complex for a T cell receptor (TCR) from a patient with multiple sclerosis that causes autoimmunity in transgenic mice. The structure showed a TCR topology notably different from that of antimicrobial TCRs. Rather than being centered on the peptide-major histocompatibility complex, this TCR contacted only the N-terminal peptide segment and made asymmetrical interactions with the major histocompatibility complex helices. The interaction was dominated by the hypervariable complementarity-determining region 3 loops, indicating that unconventional topologies are possible because of the unique complementarity-determining region 3 sequences created during rearrangement. This topology reduces the interaction surface with peptide and alters the geometry for CD4 association. We propose that unusual TCR-binding properties can permit autoreactive T cells to escape deletion.

The performance of a variable-flow indirect calorimeter

Indirect calorimetry estimates energy expenditure from measurement of respiratory gas exchange volumes. This paper considers the design and evaluation of an indirect calorimeter, the Europa GEM, suitable for use in nutritional research. The calorimeter is of the ventilated hood, flow-through type and is intended for use with spontaneously breathing patients. Our aim was to develop an accurate, flexible instrument with a high level of automation. Performance was assessed in a laboratory simulation using reference gas injections (n = 24) producing a mean error of 0.3 +/- 2% in oxygen consumption (VO2), 1.8 +/- 1% in carbon dioxide production (VCO2) and 1.4 +/- 1.5% in respiratory quotient (RQ). In order to investigate the effect of FeCO2 on error multiplication a further subdivision (n = 8) of tests at FeCO2 = 0.5%, 0.75% and 1% was made by modulating the air flow through the hood. However, the predicted increase in system accuracy with increasing FeCO2 was not apparent in practice.

Dietary fat in relation to fatty acid composition of red cells and adipose tissue in colorectal cancer

Fatty acids were determined in erthrocytes in 49 patients with colorectal cancer and compared with age and sex-matched controls. Marginally increased levels of stearic acid (P = 0.057) and oleic acid (P = 0.064) and decreased arachidonic acid (P = 0.043) occurred in cancer patients. There was no difference in the stearic to oleic acid ratio between the two groups. Dietary intake, assessed by dietary recall and adipose tissue analysis was also not different. In control subjects the polyunsaturated:saturated (P:S) fatty acid ratio correlated between diet and adipose tissue (P less than 0.01, at least). In contrast cancer patients showed different correlations; in particular dietary and erythrocyte P:S fatty acid ratios correlated (P less than 0.01). These findings may indicate disturbed fat metabolism in cancer patients. The erythrocyte stearic to oleic acid ratio is of no diagnostic value.

Repeatability, reproducibility and sequential use of condition scoring of Bos indicus cattle

There is a scarcity in the literature of statistical analyses of condition score data. This paper assesses the repeatability and reproducibility of a condition scoring system in order to test whether it can be sufficiently reliable for widespread use and statistical treatment. Differences in cow condition resulting from an eight-month dry season, changes in lactational status and watering frequency were used to demonstrate how condition score data can be used sequentially in parallel with weight or heart girth data to monitor changes in body reserves over a prolonged period. The condition scoring system is based on a nine-point scale and its superiority over a six-point scale is demonstrated under the conditions encountered in Africa. An analysis of the trend in condition over time showed that cows watered daily lost condition linearly while cows watered every three days lost condition in a quadratic decline.

Relationships between body weight, condition score and heart girth changes in Boran cattle

Body weight, heart girth and condition score were monitored in 75 Boran cows over an eight-month period. Condition score was highly correlated with both weight and heart girth when these variables were measured at the end of the dry season. Over the whole period the correlation coefficient between weight and condition score was r = 0.76 and the relationship was linear. When the data were broken down by lactation status the correlation between condition score and weight of lactating cows was lower but was improved by adjusting for differences in cow weight. Heart girth and condition score over the whole period were linearly related as was heart girth and weight. A change of one point in a nine-score system was equivalent to a change of about 24 kg.

Successful renal transplantation in patients with T-cell reactivity to donor

A positive crossmatch due to T-cell reactivity against donor cells is considered a strong contraindication to renal transplantation because of the risk of graft loss from rejection. However, the significance of T-cell reactivity before but not at the time of transplantation is unknown. To determine whether transplantation can be successful under these circumstances, graft survival was observed in 15 highly sensitised patients whose T cells were reactive to donor sera before but not at the time of transplantation. All patients have been followed up for at least 1 year post transplant. Immunosuppression was by azathioprine, prednisone, and rabbit antithymocyte sera. 9 (60%) have functioning grafts and a mean serum creatinine of 1.6 mg/dl. Early non-function occurred in 12 patients. One graft was lost to early acute humoral rejection and two other to chronic rejection. 14 of the 15 had a fall in reactivity to a panel of normal lymphocytes before transplant. 4 of the 15 had donor-specific B-cell antibodies at the time of transplantation and 3 of these lost their grafts because of rejection.