A simplified inventory approach for estimating carbon in coarse woody debris in high-biomass forests

Forests carrying large quantities of live and dead wood are important carbon (C) stores. Here, we investigate how the inventory of coarse woody debris (CWD) and its embedded C (CWD-C) may be designed efficiently at the scale of logs, plots, and the landscape in Tasmanian tall Eucalyptus obliqua forests, which have very high levels of CWD (here 375–1085 m³ ha–1). From a set of 12 sites representing different times since disturbance, a thorough census of dead wood >10 cm in diameter was carried out at five sites using a fixed-plot (50 × 50 m) approach. This showed that 90% of the volume can be captured by recording only CWD logs >40 cm in diameter. Based on this approach and on the known density and C content of five different decay-classes, volume, mass, and CWD-C was determined for all 12 sites. To obtain an accurate estimate of CWD-C at the landscape scale, it was found to be sufficient to allocate entire individual logs to single decay-classes and to use one global value for C content instead of decay-class-specific values. The most decayed logs, which are difficult to measure, could be ignored. However, at the plot level, no relationships were found between CWD mass and either standing or downed CWD or standing-tree biomass, limiting the utility of these proxies for assessing CWD volume

Nebulin regulates the assembly and lengths of the thin filaments in striated muscle

In many tissues, actin monomers polymerize into actin (thin) filaments of precise lengths. Although the exact mechanisms involved remain unresolved, it is proposed that “molecular rulers” dictate the lengths of the actin filaments. The giant nebulin molecule is a prime candidate for specifying thin filament lengths in striated muscle, but this idea has never been proven. To test this hypothesis, we used RNA interference technology in rat cardiac myocytes. Live cell imaging and triple staining revealed a dramatic elongation of the preexisting thin filaments from their pointed ends upon nebulin knockdown, demonstrating its role in length maintenance; the barbed ends were unaffected. When the thin filaments were depolymerized with latrunculin B, myocytes with decreased nebulin levels reassembled them to unrestricted lengths, demonstrating its importance in length specification. Finally, knockdown of nebulin in skeletal myotubes revealed its involvement in myofibrillogenesis. These data are consistent with nebulin functioning as a thin filament ruler and provide insight into mechanisms dictating macromolecular assembly

Expanding Cosmologies in Brane Geometries

Five dimensional gravity coupled, both in the bulk and on a brane, to a scalar Liouville field yields a geometry confined to a strip around the brane and with time dependent scale factors for the four geometry. In various limits known models can be recovered as well as a temporally expanding four geometry with a warp factor falling exponentially away from the brane. The effective theory on the brane has a time dependent Planck mass and ``cosmological constant''. Although the scale factor expands, the expansion is not an acceleration.Comment: 7 pages, LaTex/RevTex

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase

Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown

The Genetic Drift Inventory: A Tool for Measuring What Advanced Undergraduates Have Mastered about Genetic Drift

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures upper-division students’ understanding of this concept. We used an iterative approach that included extensive interviews and field tests involving 1723 students across five different undergraduate campuses. The GeDI consists of 22 agree–disagree statements that assess four key concepts and six misconceptions. Student scores ranged from 4/22 to 22/22. Statements ranged in mean difficulty from 0.29 to 0.80 and in discrimination from 0.09 to 0.46. The internal consistency, as measured with Cronbach\u27s alpha, ranged from 0.58 to 0.88 across five iterations. Test–retest analysis resulted in a coefficient of stability of 0.82. The true–false format means that the GeDI can test how well students grasp key concepts central to understanding genetic drift, while simultaneously testing for the presence of misconceptions that indicate an incomplete understanding of genetic drift. The insights gained from this testing will, over time, allow us to improve instruction about this key component of evolution

Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity

Changing a highly conserved amino acid in motif A of any of the four yeast family B DNA polymerases, DNA polymerase α, δ, ɛ or ζ, results in yeast strains with elevated mutation rates. In order to better understand this phenotype, we have performed structure–function studies of homologous mutants of RB69 DNA polymerase (RB69 pol), a structural model for family B members. When Leu415 in RB69 pol is replaced with phenylalanine or glycine, the mutant polymerases retain high-catalytic efficiency for correct nucleotide incorporation, yet have increased error rates due to increased misinsertion, increased mismatch extension and inefficient proofreading. The Leu415Phe mutant also has increased dNTP insertion efficiency opposite a template 8-oxoG and opposite an abasic site. The 2.5 Å crystal structure of a ternary complex of RB69 L415F pol with a correctly base-paired incoming dTTP reveals that the phenylalanine ring is accommodated within a cavity seen in the wild-type enzyme, without steric clash or major change in active site geometry, consistent with retention of high-catalytic efficiency for correct incorporation. In addition, slight structural differences were observed that could be relevant to the reduced fidelity of L415F RB69 pol

Nebulin regulates actin filament lengths by a stabilization mechanism

The nebulin molecular ruler hypothesis is challenged as a truncated form of nebulin can stabilize actin filaments that are longer than the mini-nebulin itself

Charge conservation and time-varying speed of light

It has been recently claimed that cosmologies with time dependent speed of light might solve some of the problems of the standard cosmological scenario, as well as inflationary scenarios. In this letter we show that most of these models, when analyzed in a consistent way, lead to large violations of charge conservation. Thus, they are severly constrained by experiment, including those where $c$ is a power of the scale factor and those whose source term is the trace of the energy-momentum tensor. In addition, early Universe scenarios with a sudden change of $c$ related to baryogenesis are discarded.Comment: 4 page