Characterization of legumain

The mammalian legumain, also called asparaginyl endopeptidase (AEP), is critically involved in the processing of bacterial antigens for MHC class II presentation. In order to investigate the substrate specificity of AEP in the P1' position, we created a peptide library and digested it with purified pig kidney AEP. Digestion was less efficient only when proline was in the P1' position. Maximum AEP activity was found in lysosomal fractions of different types of antigen presenting cells (APC). When the multiple sclerosis-associated autoantigen myelin basic protein (MBP) was digested with AEP, the immunodominant epitope 83-99 was destroyed. Myoglobin as an alternative substrate was AEP resistant. These results suggest an important, but not necessarily critical role for AEP in lysosomal antigen degradation.     

Towards a framework for the evolutionary genomics of Kinetoplastids: what kind of data and how much?

The current status of kinetoplastids phylogeny and evolution is discussed in view of the recent progresses on genomics. Some ideas on a potential framework for the evolutionary genomics of kinetoplastids are presented.     

On the allelic spectrum of human disease

Human disease genes show enormous variation in their allelic spectra; that is, in the number and population frequency of the disease-predisposing alleles at the loci. For some genes, there are a few predominant disease alleles. For others, there is a wide range of disease alleles, each relatively rare. The allelic spectrum is important: disease genes with only a few deleterious alleles can be more readily identified and are more amenable to clinical testing. Here, we weave together strands from the human mutation and population genetics literature to provide a framework for understanding and predicting the allelic spectra of disease genes. The theory does a reasonable job for diseases where the genetic etiology is well understood. It also has bearing on the Common Disease/Common Variants (CD/CV) hypothesis, predicting that at loci where the total frequency of disease alleles is not too small, disease loci will have relatively simple spectra.     

The role of intravascular ultrasound imaging in vascular brachytherapy

Intracoronary brachytherapy has recently emerged as a new therapy to prevent restenosis. Initial experimental work was achieved in animal models and the results were assessed by histomorphometry. Initial clinical trials used angiography to guide dosimetry and to assess efficacy. Intravascular ultrasound (IVUS) permits tomographic examination of the vessel wall, elucidating the true morphology of the lumen and transmural components, which cannot be investigated on the lumenogram obtained by angiography. This paper reviews the use of IVUS in the clinical studies of brachytherapy conducted to date. IVUS allows clinicians to make a thorough assessment of the remodeling of the vessel and appears to have a major role to play in facilitating understanding of the underlying mechanisms of action in this emerging field. The authors propose that state-of-the-art IVUS techniques should be employed to further knowledge of the mechanisms of action of brachytherapy in atherosclerotic human coronary arteries.     

Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase

RsrI [N6-adenine] DNA methyltransferase (M·RsrI), which recognizes GAATTC and is a member of a restriction–modification system in Rhodobacter sphaeroides, was purified to >95% homogeneity using a simplified procedure involving two ion exchange chromatographic steps. Electrophoretic gel retardation assays with purified M·RsrI were performed on unmethylated, hemimethylated, dimethylated or non-specific target DNA duplexes (25 bp) in the presence of sinefungin, a potent inhibitory analog of AdoMet. M·RsrI binding was affected by the methylation status of the DNA substrate and was enhanced by the presence of the cofactor analog. M·RsrI bound DNA substrates in the presence of sinefungin with decreasing affinities: hemimethylated > unmethylated > dimethylated >> non-specific DNA. Gel retardation studies with DNA substrates containing an abasic site substituted for the target adenine DNA provided evidence consistent with M·RsrI extruding the target base from the duplex. Consistent with such base flipping, an ~1.7-fold fluorescence intensity increase was observed upon stoichiometric addition of M·RsrI to hemimethylated DNA containing the fluorescent analog 2-aminopurine in place of the target adenine. Pre-steady-state kinetic and isotope- partitioning experiments revealed that the enzyme displays burst kinetics, confirmed the catalytic competence of the M·RsrI–AdoMet complex and eliminated the possibility of an ordered mechanism where DNA is required to bind first. The equilibrium dissociation constants for AdoMet, AdoHcy and sinefungin were determined using an intrinsic tryptophan fluorescence-quenching assay.     

The Time Value of Leaf Area

When a plant invests in construction of a leaf, the revenue-stream that accrues is shaped by three variables: first, the light-capture area per milligram dry mass invested, analogous to a potential rate of return on investment; second, the longevity of the leaf, analogous to the expected duration of the revenue stream; and third, a time-discount rate, quantifying the fact that light-capture area deployed in the immediate future is more valuable to the plant than the same area deployed at some later time. Recent comparative data make it possible to quantify the cross-species trade-off between the first variable and the second variable. Here we develop an approach through which the consequences of the third variable, the time-discount rate, can be related to the trade-off between the first variable and the second variable. The approach involves an equal-benefit set, the cross-species equivalent of a fitness set. A wide spread of strategies is actually observed to coexist in vegetation, from low to high light capture area per gram and, correspondingly, from high to low leaf longevity. The coexistence suggests that the different observed strategies do not have a clear-cut advantage over the other. The equal-benefit set can be used to investigate what levels of time discount would make it the case that neither the highest-longevity nor the highest light-capture area per milligram strategies would have a clear advantage over the other, with regard to the time-discounted value of the revenue stream generated per milligram invested in leaf.     

Seedbed and moisture availability determine safe sites for early Thuja occidentalis (Cupressaceae) regeneration

Regeneration of many late-successional tree species depends on specialized safe sites. The primary objective was to investigate the roles of seedbed and moisture retention as dimensions of safe sites for the early regeneration of drought-sensitive northern white cedar (Thuja occidentalis). We hypothesized that rates of germination, survival, and growth of T. occidentalis are unlikely to differ among seedbed types under conditions of abundant water, but that differences are likely to emerge as water becomes more limited. In a 67-d greenhouse experiment, cedar seeds were sown on logs, leaf litter, and soil of cedar and paper birch (Betula papyrifera) canopy origin. Seedbeds were subjected to three water treatments. Among the water treatments, highest germination rates occurred within the high water treatment, although germination on cedar litter was comparable to that of the low water treatment. Higher germination and survival rates occurred on decayed logs than other natural seedbeds for medium (P = 0.001) and low (P < 0.0001) water treatments. Germination on birch logs occurred at higher rates than on cedar logs within the low water treatment (P = 0.04). Seedling growth for the medium water treatment was lower on leaf litter than any other type of seedbed (P < 0.01). Results generally demonstrated that the interplay between seedbed and moisture retention is a component of safe sites for T. occidentalis regeneration.     

Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes.

The CCR5-Delta32 deletion obliterates the CCR5 chemokine and the human immunodeficiency virus (HIV)-1 coreceptor on lymphoid cells, leading to strong resistance against HIV-1 infection and AIDS. A genotype survey of 4,166 individuals revealed a cline of CCR5-Delta32 allele frequencies of 0%-14% across Eurasia, whereas the variant is absent among native African, American Indian, and East Asian ethnic groups. Haplotype analysis of 192 Caucasian chromosomes revealed strong linkage disequilibrium between CCR5 and two microsatellite loci. By use of coalescence theory to interpret modern haplotype genealogy, we estimate the origin of the CCR5-Delta32-containing ancestral haplotype to be approximately 700 years ago, with an estimated range of 275-1,875 years. The geographic cline of CCR5-Delta32 frequencies and its recent emergence are consistent with a historic strong selective event (e.g. , an epidemic of a pathogen that, like HIV-1, utilizes CCR5), driving its frequency upward in ancestral Caucasian populations.