ALBERT

Description: SUMMARY We present forward and adjoint spectral-element simulations of coupled acoustic and (an)elastic seismic wave propagation on fully unstructured hexahedral meshes. Simulations benefit from recent advances in hexahedral meshing, load balancing and software optimization. Meshing may be accomplished using a mesh generation tool kit such as CUBIT, and load balancing is facilitated by graph partitioning based on the SCOTCH library. Coupling between fluid and solid regions is incorporated in a straightforward fashion using domain decomposition. Topography, bathymetry and Moho undulations may be readily included in the mesh, and physical dispersion and attenuation associated with anelasticity are accounted for using a series of standard linear solids. Finite-frequency Fréchet derivatives are calculated using adjoint methods in both fluid and solid domains. The software is benchmarked for a layercake model. We present various examples of fully unstructured meshes, snapshots of wavefields and finite-frequency kernels generated by Version 2.0 ‘Sesame’ of our widely used open source spectral-element package SPECFEM3D.

Description: SUMMARY The Central Iran plateau appears aseismic during the last few millenniums based on instrumental and historical seismic records. Nevertheless, it is sliced by several strike-slip faults that are hundreds of kilometres long. These faults display along-strike, horizontal offsets of intermittent gullies that suggest the occurrence of earthquakes in the Holocene. Establishing this is crucial for accurately assessing the regional seismic hazard. The first palaeoseismic study performed on the 200-km long, NS striking Anar fault shows that this right-lateral fault hosted three large ( M w ≈ 7) earthquakes during the Holocene or possibly Uppermost Pleistocene for the older one. These three seismic events are recorded within a sedimentary succession, which is not older than 15 ka, suggesting an average recurrence of at most 5 ka. The six optically stimulated luminescence ages available provide additional constraints and allow estimating that the three earthquakes have occurred within the following time intervals: 4.4 ± 0.8, 6.8 ± 1 and 9.8 ± 2 ka. The preferred age of the more recent event, ranging between 3600 and 5200 yr, suggests that the fault is approaching the end of its seismic cycle and the city of Anar could be under the threat of a destructive earthquake in the near future. In addition, our results confirm a previous minimum slip rate estimate of 0.8 ± 0.1 mm yr −1 for the Anar fault indicating that the westernmost prominent right-lateral faults of the Central Iran plateau are characterized by slip rates close to 1 mm yr −1 . These faults, which have repeatedly produced destructive earthquakes with large magnitudes and long recurrence interval of several thousands of years during the Holocene, show that the Central Iran plateau does not behave totally as a rigid block and that its moderate internal deformation is nonetheless responsible for a significant seismic hazard.

Description: Background: In agricultural regions, streamside forests have been reduced in age and extent, or removed entirely to maximize arable cropland. Restoring and reforesting such riparian zones to mature forest, particularly along headwater streams (which constitute 90% of stream network length) would both increase carbon storage and improve water quality. Age and management-related cover/condition classes of headwater stream networks can be used to rapidly inventory carbon storage and sequestration potential if carbon storage capacity of conditions classes and their relative distribution on the landscape are known. Results: Based on the distribution of riparian zone cover/condition classes in sampled headwater reaches, current and potential carbon storage was extrapolated to the remainder of the North Carolina Coastal Plain stream network. Carbon stored in headwater riparian reaches is only about 40% of its potential capacity, based on 242 MgC/ha stored in sampled mature riparian forest (forest 〉 50 y old). The carbon deficit along 57,700 km of headwater Coastal Plain streams is equivalent to about 25TgC in 30-m-wide riparian buffer zones and 50 TgC in 60-m-wide buffer zones. Conclusions: Estimating carbon storage in recognizable age-and cover-related condition classes provides a rapid way to better inventory current carbon storage, estimate storage capacity, and calculate the potential for additional storage. In light of the particular importance of buffer zones in headwater reaches in agricultural landscapes in ameliorating nutrient and sediment input to streams, encouraging the restoration of riparian zones to mature forest along headwater reaches worldwide has the potential to not only improve water quality, but also simultaneously reduce atmospheric CO2.

Description: The University of California Santa Cruz (UCSC) Genome Browser ( http://genome.ucsc.edu ) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation ‘tracks’ are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

Description: Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes ~15–18 Ma. Extant lineages radiated rapidly 6–10 Ma and are organized into four genera ( Hylobates , Hoolock , Symphalangus , and Nomascus ) consisting of 12–19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock , with the Nomascus–Hoolock clade sister to Hylobates . Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species.

Description: Multiple visual pigments, prerequisites for color vision, are found in arthropods, but the evolutionary origin of their diversity remains obscure. In this study, we explore the opsin genes in five distantly related species of Onychophora, using deep transcriptome sequencing and screening approaches. Surprisingly, our data reveal the presence of only one opsin gene (onychopsin) in each onychophoran species, and our behavioral experiments indicate a maximum sensitivity of onychopsin to blue–green light. In our phylogenetic analyses, the onychopsins represent the sister group to the monophyletic clade of visual r-opsins of arthropods. These results concur with phylogenomic support for the sister-group status of the Onychophora and Arthropoda and provide evidence for monochromatic vision in velvet worms and in the last common ancestor of Onychophora and Arthropoda. We conclude that the diversification of visual pigments and color vision evolved in arthropods, along with the evolution of compound eyes—one of the most sophisticated visual systems known.

Description: Background: In interferon-gamma-stimulated cells, the dimeric transcription factor STAT1 (signal transducer and activator of transcription 1) recognizes semi-palindromic motifs in the promoter regions of cytokine-driven target genes termed GAS (gamma-activated sites). However, the molecular steps that facilitate GAS binding and the subsequent liberation of STAT1 homodimers from these promoter elements are not well understood. Results: Using a mutational approach, we identified two critical glutamyl residues within the DNA-binding domain adjacent to the phosphodiester backbone of DNA which efficiently release phospho-STAT1 from DNA. The release of STAT1 dimers from DNA enhances transcriptional activity on both interferon-driven reporter and endogenous target genes. A substitution of either of the two glutamic acid residues broadens the repertoire of putative binding sites on DNA and enhances binding affinity to GAS sites. However, despite elevated levels of tyrosine phosphorylation and a prolonged nuclear accumulation period, the STAT1 DNA-binding mutants show a significantly reduced transcriptional activity upon stimulation of cells with interferon-gamma. This reduced transcriptional response may be explained by the deposition of oligomerized STAT1 molecules outside GAS sites. Conclusions: Thus, two negatively charged amino acid residues in the DNA-binding domain are engaged in the liberation of STAT1 from DNA, resulting in a high dissociation rate from non-GAS sites as a key feature of STAT1 signal transduction, which positively regulates cytokine-dependent gene expression probably by preventing retention at transcriptionally inert sites.

Description: Background: Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Results: Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio omega that varies linearly with RSA provides a better model fit than an RSA-independent omega or an omega that is estimated separately in individual RSA bins. We further show that the branch length t and the transition--transverion ratio kappa also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between omega and RSA, and gene expression level affects both the intercept and the slope. Conclusions: Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between omega and RSA implies that genes are better characterized by their omega slope and intercept than by just their mean omega.

Description: Mitochondria lack the ability to repair certain helix-distorting lesions that are induced at high levels in mitochondrial DNA (mtDNA) by important environmental genotoxins and endogenous metabolites. These lesions are irreparable and persistent in the short term, but their long-term fate is unknown. We report that removal of such mtDNA damage is detectable by 48 h in Caenorhabditis elegans , and requires mitochondrial fusion, fission and autophagy, providing genetic evidence for a novel mtDNA damage removal pathway. Furthermore, mutations in genes involved in these processes as well as pharmacological inhibition of autophagy exacerbated mtDNA damage-mediated larval arrest, illustrating the in vivo relevance of removal of persistent mtDNA damage. Mutations in genes in these pathways exist in the human population, demonstrating the potential for important gene–environment interactions affecting mitochondrial health after genotoxin exposure.

Description: Horizontal gene transfer (HGT) has been recognized to be an important mechanism that shaped the evolution and genomes of prokaryotes and unicellular eukaryotes. However, HGT is regarded to be exceedingly rare among eukaryotes. We discovered massive transfers of a DNA transposon, a Tc1 element encoding a transposase, between multiple teleost fishes and lampreys that last shared a common ancestor over 500 Ma. Members of this group of Tc1 elements were found to exhibit a mosaic phylogenetic distribution, yet their sequences were highly similar even between distantly related lineages (95%–99% identity). Our molecular phylogenetic analyses suggested that horizontal transfers of this element happened repeatedly, involving multiple teleost fishes that are phylogenetically only distantly related. Interestingly, almost all the affected teleost lineages are also known to be subject to lamprey parasitism, suggesting that the horizontal transfers between vertebrates might have occurred through parasite–host interaction. The genomes of several northern hemisphere lamprey species, including that of the sea lamprey ( Petromyzon marinus ), were found to contain thousands of copies of the foreign elements. Impact of this event is discussed in relation to other peculiar genomic features of lampreys.