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.     

Flexible Ion‐Conducting Composite Membranes for Lithium Batteries

The use of metallic lithium anodes enables higher energy density and higher specific capacity Li‐based batteries. However, it is essential to suppress lithium dendrite growth during electrodeposition. Li‐ion‐conducting ceramics (LICC) can mechanically suppress dendritic growth but are too fragile and also have low Li‐ion conductivity. Here, a simple, versatile, and scalable procedure for fabricating flexible Li‐ion‐conducting composite membranes composed of a single layer of LICC particles firmly embedded in a polymer matrix with their top and bottom surfaces exposed to allow for ionic transport is described. The membranes are thin (<100 μm) and possess high Li‐ion conductance at thicknesses where LICC disks are mechanically unstable. It is demonstrated that these membranes suppress Li dendrite growth even when the shear modulus of the matrix is lower than that of lithium. It is anticipated that these membranes enable the use of metallic lithium anodes in conventional and solid‐state Li‐ion batteries as well as in future Li? S and Li? O₂ batteries.     

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Most notably, recent approaches based on counting de novo mutations in family pedigrees have yielded significantly smaller values than classical methods based on sequence divergence. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.61 ± 0.13 × 10⁻⁸ mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.