The Polymerases for V(D)J Recombination

DNA transactions of a wide variety generally require three major types of enzymatic activities: nucleases, polymerases, and ligases. V(D)J recombination is no exception. In this issue, Bertocci et al. (2006) have provided new insight by generating mice deficient in one or more of the polymerases

Word frequency distributions and lexical semantics

This paper addresses the relation between meaning, lexical productivity, and frequency of use. Using density estimation as a visualization tool, we show that differences in semantic structure can be reflected in probability density functions estimated for word frequency distributions. We call attention to an example of a bimodal density, and suggest that bimodality arises when distributions of well-entrenched lexical tems, which appear to be lognormal, are mixed with distributions of productively reated nonce formation

First-principles study of the Young's modulus of Si <001> nanowires

We report the results of first-principles density functional theory calculations of the Young's modulus and other mechanical properties of hydrogen-passivated Si nanowires. The nanowires are taken to have predominantly {100} surfaces, with small {110} facets. The Young's modulus, the equilibrium length and the residual stress of a series of prismatic wires are found to have a size dependence that scales like the surface area to volume ratio for all but the smallest wires. We analyze the physical origin of the size dependence, and compare the results to two existing models.Comment: 5 pages, 3 figure

Architecture of the Short External Rotator Muscles of the Hip.

BackgroundMuscle architecture, or the arrangement of sarcomeres and fibers within muscles, defines functional capacity. There are limited data that provide an understanding of hip short external rotator muscle architecture. The purpose of this study was thus to characterize the architecture of these small hip muscles.MethodsEight muscles from 10 independent human cadaver hips were used in this study (n = 80 muscles). Architectural measurements were made on pectineus, piriformis, gemelli, obturators, quadratus femoris, and gluteus minimus. Muscle mass, fiber length, sarcomere length, and pennation angle were used to calculate the normalized muscle fiber length, which defines excursion, and physiological cross-sectional area (PCSA), which defines force-producing capacity.ResultsGluteus minimus had the largest PCSA (8.29 cm2) followed by obturator externus (4.54 cm2), whereas superior gemellus had the smallest PCSA (0.68 cm2). Fiber lengths clustered into long (pectineus - 10.38 cm and gluteus minimus - 10.30 cm), moderate (obturator internus - 8.77 cm and externus - 8.04 cm), or short (inferior gemellus - 5.64 and superior gemellus - 4.85). There were no significant differences among muscles in pennation angle which were all nearly zero. When the gemelli and obturators were considered as a single functional unit, their collective PCSA (10.00 cm2) exceeded that of gluteus minimus as a substantial force-producing group.ConclusionsThe key findings are that these muscles have relatively small individual PCSAs, short fiber lengths, and low pennation angles. The large collective PCSA and short fiber lengths of the gemelli and obturators suggest that they primarily play a stabilizing role rather than a joint rotating role

First-principles calculation of mechanical properties of Si <001> nanowires and comparison to nanomechanical theory

We report the results of first-principles density functional theory calculations of the Young's modulus and other mechanical properties of hydrogen-passivated Si nanowires. The nanowires are taken to have predominantly {100} surfaces, with small {110} facets according to the Wulff shape. The Young's modulus, the equilibrium length and the constrained residual stress of a series of prismatic beams of differing sizes are found to have size dependences that scale like the surface area to volume ratio for all but the smallest beam. The results are compared with a continuum model and the results of classical atomistic calculations based on an empirical potential. We attribute the size dependence to specific physical structures and interactions. In particular, the hydrogen interactions on the surface and the charge density variations within the beam are quantified and used both to parameterize the continuum model and to account for the discrepancies between the two models and the first-principles results.Comment: 14 pages, 10 figure

Impact of DNA ligase IV on the fidelity of end joining in human cells

A DNA ligase IV (LIG4)‐null human pre‐B cell line and human cell lines with hypomorphic mutations in LIG4 are significantly impaired in the frequency and fidelity of end joining using an in vivo plasmid assay. Analysis of the null line demonstrates the existence of an error‐prone DNA ligase IV‐independent rejoining mechanism in mammalian cells. Analysis of lines with hypomorphic mutations demonstrates that residual DNA ligase IV activity, which is sufficient to promote efficient end joining, nevertheless can result in decreased fidelity of rejoining. Thus, DNA ligase IV is an important factor influencing the fidelity of end joining in vivo. The LIG4‐defective cell lines also showed impaired end joining in an in vitro assay using cell‐free extracts. Elevated degradation of the terminal nucleotide was observed in a LIG4‐defective line, and addition of the DNA ligase IV–XRCC4 complex restored end protection. End protection by DNA ligase IV was not dependent upon ligation. Finally, using purified proteins, we demonstrate that DNA ligase IV–XRCC4 is able to protect DNA ends from degradation by T7 exonuclease. Thus, the ability of DNA ligase IV–XRCC4 to protect DNA ends may contribute to the ability of DNA ligase IV to promote accurate rejoining in vivo

Atomic layer deposition of ZnS nanotubes

We report on growth of high-aspect-ratio ($\gtrsim300$) zinc sulfide nanotubes with variable, precisely tunable, wall thicknesses and tube diameters into highly ordered pores of anodic alumina templates by atomic layer deposition (ALD) at temperatures as low as 75 $^{\circ}$C. Various characterization techniques are employed to gain information on the composition, morphology, and crystal structure of the synthesized samples. Besides practical applications, the ALD-grown tubes could be envisaged as model systems for the study of a certain class of size-dependent quantum and classical phenomena.Comment: 1 LaTeX source file, 8 eps figures, and the manuscript in PDF forma

Probing Single- to Multi-Cell Level Charge Transport in Geobacter Sulfurreducens DL-1

Microbial fuel cells, in which living microorganisms convert chemical energy into electricity, represent a potentially sustainable energy technology for the future. Here we report the single-bacterium level current measurements of Geobacter sulfurreducens DL-1 to elucidate the fundamental limits and factors determining maximum power output from a microbial fuel cell. Quantized stepwise current outputs of 92(±33) and 196(±20) fA are generated from microelectrode arrays confined in isolated wells. Simultaneous cell imaging/tracking and current recording reveals that the current steps are directly correlated with the contact of one or two cells with the electrodes. This work establishes the amount of current generated by an individual Geobacter cell in the absence of a biofilm and highlights the potential upper limit of microbial fuel cell performance for Geobacter in thin biofilms.Chemistry and Chemical Biolog