Selecting representative model micro-organisms

Background  

Micro-biological research relies on the use of model organisms that act as representatives of their species or subspecies, these are frequently well-characterized laboratory strains. However, it has often become apparent that the model strain initially chosen does not represent important features of the species. For micro-organisms, the diversity of their genomes is such that even the best possible choice of initial strain for sequencing may not assure that the genome obtained adequately represents the species. To acquire information about a species' genome as efficiently as possible, we require a method to choose strains for analysis on the basis of how well they represent the species.     

Cell wall residues in yeast protoplast preparations

Protoplast preparations made from Saccharomyces cerevisiae by prolonged treatment with snail digestive juice contained fibrils and chitinous bud-scar residues from the original cell wall.     

Characterization of different B-F (MHC class I) molecules in the chicken

B-F alloantisera recognized distinct 45-Kd molecules on peripheral red blood cells (RBC) from embryonic chickens and heterogeneous molecules of approximately 40 to 44 Kd on peripheral RBC from adult chickens, provisionally referred to as type 1 and type 2, respectively. Type 2 molecules migrated to the basic end of isoelectric focusing gels, exhibited multiple isomorphic variants, and were associated with a smaller polypeptide of approximately 11 to 12 Kd assumed to be beta-2-microglobulin. Type 1 molecules migrated to the acidic end of isoelectric focusing gels, exhibited limited heterogeneity, and were not associated with a smaller polypeptide. Type 1 and type 2 molecules were also shown to be distinct by peptide mapping and serological analyses. In addition, two distinct molecular-weight forms of the type 2 molecules were distinguished, provisionally referred to as 2A (45 Kd) and 2B (42 Kd). In vivo-derived avian erythroblastosis virus (AEV)-transformed erythroleukemia cells expressed type 2A molecules. In vitro-derived AEV-transformed erythroleukemia cells expressed very low levels of B-F molecules; however, they expressed type 2B molecules when induced to differentiate. Normal bursa-derived lymphoid cells expressed type 2A molecules, whereas normal thymus-derived lymphoid cells expressed type 2B molecules. Cloned reticuloendotheliosis virus (REV)-transformed immature lymphoid cells expressed either type 2A or type 2B molecules.     

Natural course of penicillamine nephropathy: a long term study of 33 patients

To elucidate the natural course of the nephropathy associated with penicillamine and thereby facilitate its clinical management 33 patients with rheumatoid arthritis who developed proteinuria during treatment with oral penicillamine were studied in detail throughout their renal illness. Renal biopsies were performed, and creatinine clearance and proteinuria were measured serially for 74 months (range 16-148 months). Fourteen patients developed proteinuria within six months after the start of treatment and 27 within 12 months. When treatment was stopped the proteinuria reached a median peak of 4·2 g/24 h (range 0·3-15·0 g/24 h) at one month (range 0-7 months) before resolving spontaneously by six months (12 patients), 12 months (21), or 18 months (29). In all patients but one, who developed carcinoma of the renal pelvis, proteinuria resolved by 21 months and its median duration was eight months. The median first and last measurements of creatinine clearance showed no appreciable change (80 ml/min and 78 ml/min), and no patient died from or needed treatment for renal failure. The HLA-B8 or HLA-DR3 alloantigen, or both, were identified in 10 patients. Renal biopsy specimens showed membranous glomerulonephritis in 29 patients, minimal change nephropathy in two, and electron dense deposits in the mesangial regions in two.In all the patients whose nephropathy was due solely to treatment with penicillamine the proteinuria resolved completely when the drug was withdrawn; renal function did not deteriorate, and corticosteroids were unnecessary.     

Multiple sequence alignment

A method has been developed for aligning segments of several sequences at once. The number of search steps depends only polynomially on the number of sequences, instead of exponentially, because most alignments are rejected without being evaluated explicitly. A data structure herein called the "heap" facilitates this process. For a set of n sequence segments, the overall similarity is taken to be the sum of all the constituent segment pair similarities, which are in turn sums of corresponding residue similarity scores from a Table. The statistical models that test alignments for significance make it possible to group sequences objectively, even when most or all of the interrelationships are weak. These tests are very sensitive, while remaining quite conservative, and discourage the addition of "misfit" sequences to an existing set. The new techniques are applied to a set of five DNA-binding proteins, to a group of three enzymes that employ the coenzyme FAD, and to a control set. The alignment previously proposed for the DNA-binding proteins on the basis of structural comparisons and inspection of sequences is supported quite dramatically, and a highly significant alignment is found for the FAD-binding proteins.     

1-Methyl-4-phenylpyridine (MPP+) induces oxidative stress in the rodent

MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) produces an irreversible parkinsonism in primates. Recent evidence suggests metabolism of MPTP to 1-methyl-4-phenylpyridine (MPP+) is required for toxicity. We have proposed that MPP+ may play a central role in the toxicity of MPTP, but direct assessment of the effects of MPP+ in brain is difficult. Therefore, we have sought to define the mechanism of peripheral MPP+ toxicity in the rat and mouse. Systemically administered MPP+ produced its major pathology in the lung and was typified by perivascular edema. An increase in plasma glutathione disulfide concentrations also resulted, suggesting that MPP+ in analogy to paraquat produces oxidative stress. In addition, the lethality of MPP+ in the mouse was increased by dietary selenium deficiency. These results define in both pathological and chemical terms the potent systemic toxicity of MPP+ and suggest that MPP+, because of its high concentration in primate brain, has the potential to play an important role in the CNS toxicity of MPTP.     

Studies directed toward testing the "channeling" hypothesis--ribonucleotides----DNA in leukemia L1210 cells

Experiments were carried out to test for the presence of "channeling" in L1210 cells. L1210 cells were incubated in culture in the presence of labeled cytidine and "cold" deoxycytidine and conversely, in the presence of labeled deoxycytidine and "cold" cytidine. Cytidine did not inhibit the incorporation of [14C]deoxycytidine into DNA while deoxycytidine decreased the incorporation of [14C]cytidine into DNA. Further, in L1210 cells there was not a coordinate inhibition of thymidylate synthetase when either DNA polymerase was inhibited (aphidicolin) or ribonucleotide reductase was inhibited (hydroxyurea). These data indicate that leukemia L1210 cells do not selectively channel ribonucleotides to DNA through a tightly coupled enzyme complex.     

Ascorbate-Stimulated Lipid Peroxidation in Human Brain Is Dependent on Iron but Not on Hydroxyl Radical

Abstract: The time dependence of N -acetyl-aspartate (NAA) concentrations relative to lactate and pyruvate in the injured rat spinal cord was investigated. Segments of spinal cord from regions rostral, caudal, and at the epicenter of the injury were analyzed. NAA concentrations were determined by gas chromatography-mass spectrometry and lactate and pyruvate concentrations were determined by UV spectroscopy at 20 min, 60 min, 2 h, 8 h, 24 h, 3 days, and 1 week after injury. NAA levels fell most significantly at the epicenter of the injury, reaching 30% of basal levels within 24 h. In all segments, lactate levels increased significantly shortly after injury, peaking at two to five times normal basal levels between 20 and 60 min after injury. Rostral and caudal to the injury site, lactate elevations and NAA reductions were less dramatic. Pyruvate concentrations were not significantly altered in any of the sections after injury. The temporal and spatial relationships of NAA and lactate changes indicated that ischemic conditions due to injury in the upper thoracic rat spinal cord were distributed asymmetrically. Acute ischemia was more severe caudal to the injury site, and NAA concentrations were more severely impaired in the rostral direction. The results suggest that the extent of neuronal degeneration due to spinal cord injury does not correlate directly with acute ischemic severity as measured by the lactate/pyruvate ratio, and may be more closely related to secondary changes in the neuronal environment.     

Histocompatibility antigen(s) linked to Rfp-Y (Mhc-like) genes in the chicken

 Major histocompatibility complex (Mhc) genes influencing transplantation rejections were first described in mice within the H2 complex and secondly in chickens within the B complex. In chickens, Rfp-Y haplotypes have recently been identified which contain class I and class II Mhc-like genes that assort independently of the B complex. Three Rfp-Y haplotypes have been defined in a closed breeding flock of line N chickens. In this study, progeny were obtained from line N Rfp-Y heterozygous matings to establish the role of Rfp-Y in transplantation immunity. Rfp-Y incompatibility did not induce significant one-way mixed lymphocyte responses. However, Rfp-Y-incompatible skin grafts were rejected more frequently and at a faster rate than Rfp-Y-compatible grafts by two-week-old chicks. The control Mhc B-incompatible grafts were rejected faster than the Rfp-Y-incompatible grafts; the latter were rejected at speeds that resemble rejection of minor histocompatibility antigens. We conclude that Rfp-Y class I and II Mhc-like genes are linked to the expression of minor histocompatibility antigens in chickens. Received: 21 June 1996 / Revised: 23 July 1996     

Predicting badger sett numbers: evaluating methods in East Sussex

Abstract. One way in which a species' numbers may be estimated without direct counting is to predict their dispersion and density from more readily available habitat measures, such as landscape variables measured from maps or vegetation variables measured in the field. We compare the power of ordination and regression techniques for predicting badger ( Meles meles L.) numbers at a local scale, using a land class system, map-read landscape variables and field-derived vegetation variables. Sett density was used as a surrogate of badger density. Multiple linear regression using vegetation and landscape variables together gave the most accurate prediction of sett density, while ordination techniques were of lesser value. The addition of vegetation variables to landscape variables did not substantially improve the power of ordination. Outlier Sett Density was predicted more accurately, and by different variables, to Main Sett Density. The relationship between badger ecology and habitat variables that were useful in predicting sett density is discussed.