ALBERT

Description: 〈span〉〈div〉Abstract〈/div〉Records of post-glacial sea-level change in the Cascadia subduction zone (North American Pacific coast) analyzed using one-dimensional Earth models suggest upper mantle viscosities 〈∼10〈sup〉20〈/sup〉 Pa·s, significantly weaker than those based on observations from cratonic regions in North America. We explore this variability by comparing predictions based on a three-dimensional (3-D) model of the glacial isostatic adjustment process with relative sea-level histories from sites along the Oregon and Washington (USA) and Hudson Bay (northeastern Canada) coasts. We demonstrate that a 3-D mantle viscosity field, with a geometry constrained by seismic tomography and that reflects the tectonic setting of the Cascadia subduction zone, can simultaneously reconcile the rapid rate of late Holocene adjustment observed in central Cascadia and the longer decay times of post-glacial uplift curves in Hudson Bay. Specifically, below the Cascadia subduction zone, this field is characterized by a shallow subduction wedge of low viscosity (〈10〈sup〉20〈/sup〉 Pa·s) and higher viscosity material associated with subduction of the Juan de Fuca plate.〈/span〉

Description: Accurately scaling sap flux observations to tree or stand levels requires accounting for variation in sap flux between wood types and by depth into the tree. However, existing models for radial variation in axial sap flux are rarely used because they are difficult to implement, there is uncertainty about their predictive ability and calibration measurements are often unavailable. Here we compare different models with a diverse sap flux data set to test the hypotheses that radial profiles differ by wood type and tree size. We show that radial variation in sap flux is dependent on wood type but independent of tree size for a range of temperate trees. The best-fitting model predicted out-of-sample sap flux observations and independent estimates of sapwood area with small errors, suggesting robustness in the new settings. We develop a method for predicting whole-tree water use with this model and include computer code for simple implementation in other studies.

Description: For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org ) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users.

Description: The impact of stored water on estimates of transpiration from scaled sap flux measurements was assessed in mature Pinus taeda (L.) at the Duke Free-Air CO 2 Enrichment (FACE) site. We used a simple hydraulic model with measurements of sap flux ( J ) at breast height and the base of the live crown for 26 trees over 6 months to examine the effects of elevated CO 2 (eCO 2 ) and fertilization (N F ) treatments, as well as temporal variation in soil moisture ( M ( t ) ), on estimates of the hydraulic time constant (). At low M ( t ) , there was little (〈12%) difference in of different treatments. At high M ( t ) , differences were much greater, with reductions of 27, 52 and 34% in eCO 2 , N F and eCO 2 x N F respective to the control. Incorporating with these effects into the analysis of a larger data set of previous J measurements at this site (1998–2008) improved agreement between modeled and measured values in 92% of cases. However, a simplified calibration of that neglected treatment and soil moisture effects performed more dependably, improving agreement in 98% of cases. Incorporating had the effect of increasing estimates of reference stomatal conductance at 1 kPa vapor pressure deficit (VPD) and saturating photosynthetic active radiation (PAR) an average of 12–14%, while increasing estimated sensitivities to VPD and PAR. A computationally efficient hydraulic model, such as the one presented here, incorporated into a hierarchical model of stomatal conductance presents a novel approach to including hydraulic time constants in estimates of stomatal responses from long-term sap flux data sets.

Description: In this study, we employ a network of thermal dissipation probes (TDPs) monitoring sap flux density to estimate leaf-specific transpiration ( E L ) and stomatal conductance ( G S ) in Pinus taeda (L.) and Liquidambar styraciflua L. exposed to +200 ppm atmospheric CO 2 levels (eCO 2 ) and nitrogen fertilization. Scaling half-hourly measurements from hundreds of sensors over 11 years, we found that P. taeda in eCO 2 intermittently (49% of monthly values) decreased stomatal conductance ( G S ) relative to the control, with a mean reduction of 13% in both total E L and mean daytime G S . This intermittent response was related to changes in a hydraulic allometry index ( A H ), defined as sapwood area per unit leaf area per unit canopy height, which decreased a mean of 15% with eCO 2 over the course of the study, due mostly to a mean 19% increase in leaf area ( A L ). In contrast, L. styraciflua showed a consistent (76% of monthly values) reduction in G S with eCO 2 with a total reduction of 32% E L , 31% G S and 23% A H (due to increased A L per sapwood area). For L. styraciflua , like P. taeda , the relationship between A H and G S at reference conditions suggested a decrease in G S across the range of A H . Our findings suggest an indirect structural effect of eCO 2 on G S in P. taeda and a direct leaf level effect in L. styraciflua . In the initial year of fertilization, P. taeda in both CO 2 treatments, as well as L. styraciflua in eCO 2 , exhibited higher G S with N F than expected from shifts in A H , suggesting a transient direct effect on G S . Whether treatment effects on mean leaf-specific G S are direct or indirect, this paper highlights that long-term treatment effects on G S are generally reflected in A H as well.

Description: Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial diseases; epidemictyphus, trench fever, and relapsing fever. In order to gain insights into the molecular bases for these differences, we analyzed alternative splicing (AS) using next-generation sequencing data for one strain of head lice and one strain of body lice. We identified a total of 3,598 AS events which were head or body lice specific. Exon skipping AS events were overrepresented among both head and body lice, whereas intron retention events were underrepresented in both. However, both the enrichment of exon skipping and the underrepresentation of intron retention are significantly stronger in body lice compared with head lice. Genes containing body louse-specific AS events were found to be significantly enriched for functions associated with development of the nervous system, salivary gland, trachea, and ovarian follicle cells, as well as regulation of transcription. In contrast, no functional categories were overrepresented among genes with head louse-specific AS events. Together, our results constitute the first evidence for transcript pool differences in head and body lice, providing insights into molecular adaptations that enabled human lice to adapt to clothing, and representing a powerful illustration of the pivotal role AS can play in functional adaptation.

Description: Mitochondrial DNA (mtDNA) mutations cause a variety of mitochondrial disorders for which effective treatments are lacking. Emerging data indicate that selective mitochondrial degradation through autophagy (mitophagy) plays a critical role in mitochondrial quality control. Inhibition of mammalian target of rapamycin (mTOR) kinase activity can activate mitophagy. To test the hypothesis that enhancing mitophagy would drive selection against dysfunctional mitochondria harboring higher levels of mutations, thereby decreasing mutation levels over time, we examined the impact of rapamycin on mutation levels in a human cytoplasmic hybrid (cybrid) cell line expressing a heteroplasmic mtDNA G11778A mutation, the most common cause of Leber's hereditary optic neuropathy. Inhibition of mTORC1/S6 kinase signaling by rapamycin induced colocalization of mitochondria with autophagosomes, and resulted in a striking progressive decrease in levels of the G11778A mutation and partial restoration of ATP levels. Rapamycin-induced upregulation of mitophagy was confirmed by electron microscopic evidence of increased autophagic vacuoles containing mitochondria-like organelles. The decreased mutational burden was not due to rapamycin-induced cell death or mtDNA depletion, as there was no significant difference in cytotoxicity/apoptosis or mtDNA copy number between rapamycin and vehicle-treated cells. These data demonstrate the potential for pharmacological inhibition of mTOR kinase activity to activate mitophagy as a strategy to drive selection against a heteroplasmic mtDNA G11778A mutation and raise the exciting possibility that rapamycin may have therapeutic potential for the treatment of mitochondrial disorders associated with heteroplasmic mtDNA mutations, although further studies are needed to determine if a similar strategy will be effective for other mutations and other cell types.

Description: We present 109–115 GHz (3 mm) wide-field spectral line observations of 12 CO, 13 CO and C 18 O J  = 1–0 molecular emission and 5.5 and 8.8 GHz (6 and 3 cm) radio continuum emission towards the high-mass star-forming complex known as G305. The morphology of G305 is dominated by a large evacuated cavity at the centre of the complex driven by clusters of O stars surrounded by molecular gas. Our goals are to determine the physical properties of the molecular environment and reveal the relationship between the molecular and ionized gas and star formation in G305. This is in an effort to characterize the star-forming environment and constrain the star formation history in an attempt to evaluate the impact of high-mass stars on the evolution of the G305 complex. Analysis of CO emission in G305 reveals 156 molecular clumps with the following physical characteristics; excitation temperatures ranging from 7 to 25 K, optical depths of 0.2–0.9, H 2 column densities of 0.1–4.0 10 22 cm –2 , clump masses ranging from 10 2 to 10 4 M and a total molecular mass of 〉3.5 10 5 M . The 5.5 and 8.8 GHz radio continuum emission reveals an extended low surface brightness ionized environment within which we identify 15 large-scale features with a further eight smaller sources projected within these features. By comparing to mid-infrared emission and archival data, we identify nine H ii regions, seven compact H ii regions, one UC H ii region and four extended regions. The total integrated flux of the radio continuum emission at 5.5 GHz is ~180 Jy corresponding to a Lyman continuum output of 2.4 10 50  photons s –1 . We compare the ionized and molecular environment with optically identified high-mass stars and ongoing star formation, identified from the literature. Analysis of this data set reveals a star formation rate of 0.008–0.016 M yr –1 and efficiency of 7–12 per cent, allows us to probe the star formation history of the region and discuss the impact of high-mass stars on the evolution of G305.

Description: The IEDB, www.iedb.org , contains information on immune epitopes—the molecular targets of adaptive immune responses—curated from the published literature and submitted by National Institutes of Health funded epitope discovery efforts. From 2004 to 2012 the IEDB curation of journal articles published since 1960 has caught up to the present day, with 〉95% of relevant published literature manually curated amounting to more than 15 000 journal articles and more than 704 000 experiments to date. The revised curation target since 2012 has been to make recent research findings quickly available in the IEDB and thereby ensure that it continues to be an up-to-date resource. Having gathered a comprehensive dataset in the IEDB, a complete redesign of the query and reporting interface has been performed in the IEDB 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. We here present this most recent release of the IEDB and describe the user testing procedures as well as the use of external ontologies that have enabled it.

Description: 〈span〉Records of post-glacial sea-level change in the Cascadia subduction zone (North American Pacific coast) analyzed using one-dimensional Earth models suggest upper mantle viscosities 〈~10〈sup〉20〈/sup〉 Pa·s, significantly weaker than those based on observations from cratonic regions in North America. We explore this variability by comparing predictions based on a three-dimensional (3-D) model of the glacial isostatic adjustment process with relative sea-level histories from sites along the Oregon and Washington (USA) and Hudson Bay (northeastern Canada) coasts. We demonstrate that a 3-D mantle viscosity field, with a geometry constrained by seismic tomography and that reflects the tectonic setting of the Cascadia subduction zone, can simultaneously reconcile the rapid rate of late Holocene adjustment observed in central Cascadia and the longer decay times of post-glacial uplift curves in Hudson Bay. Specifically, below the Cascadia subduction zone, this field is characterized by a shallow subduction wedge of low viscosity (〈10〈sup〉20〈/sup〉 Pa·s) and higher viscosity material associated with subduction of the Juan de Fuca plate.〈/span〉