Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake

A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper 40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5–10 between their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of nitrogen. Adjustment of Dymond et al.’s assumptions to account for dissolved and suspended nitrogen yields a flux estimate that is consistent with sediment trap measurements and our model.     

Rational metabolic engineering of transgenic plants for biosynthesis of omega-3 polyunsaturates

The health-beneficial effects of long-chain polyunsaturated fatty acids (LC-PUFAs), derived mainly from fish oil, coupled with the growing requirement for an alternative and sustainable source of these compounds, has led to efforts to engineer oilseed crops for their production. LC-PUFA synthesis has been achieved using combinations of heterologous endomembrane desaturases and elongases expressed in model oilseed plants. Two general approaches have been employed that both use endogenous 18 carbon fatty acids as the starting substrates: the Delta6- and Delta8-pathways, which perform desaturation followed by elongation or elongation followed by desaturation, respectively. However, yields above 20% have not yet been realized owing to bottlenecks that become apparent in the endogenous biosynthetic pathways when heterologous genes are expressed. These bottlenecks might be caused partly by inefficient non-native enzymes in the host system or also by suboptimal acyl-exchange mechanisms between the acyl-CoA and lipid class pools. The fine-tuning of the fatty acid flux between the acyl-CoA, phospholipid, and triacylglycerol pools will be essential to maximise polyunsaturated fatty acid yields in seed oils. In addition, efficient substrate channelling and lipid synthesis could depend on specific endoplasmic reticulum subdomain localisation for key endogenous enzymes, and this organization could be compromised in heterologous systems.     

The pygmy hog is a unique genus: 19th century taxonomists got it right first time round

The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenetic analyses of 2316 bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.     

Epigenetic Control of Skeletal Development by the Histone Methyltransferase Ezh2

Epigenetic control of gene expression is critical for normal fetal development. However, chromatin-related mechanisms that activate bone-specific programs during osteogenesis have remained underexplored. Therefore, we investigated the expression profiles of a large cohort of epigenetic regulators (>300) during osteogenic differentiation of human mesenchymal cells derived from the stromal vascular fraction of adipose tissue (AMSCs). Molecular analyses establish that the polycomb group protein EZH2 (enhancer of zeste homolog 2) is down-regulated during osteoblastic differentiation of AMSCs. Chemical inhibitor and siRNA knockdown studies show that EZH2, a histone methyltransferase that catalyzes trimethylation of histone 3 lysine 27 (H3K27me3), suppresses osteogenic differentiation. Blocking EZH2 activity promotes osteoblast differentiation and suppresses adipogenic differentiation of AMSCs. High throughput RNA sequence (mRNASeq) analysis reveals that EZH2 inhibition stimulates cell cycle inhibitory proteins and enhances the production of extracellular matrix proteins. Conditional genetic loss of Ezh2 in uncommitted mesenchymal cells (Prrx1-Cre) results in multiple defects in skeletal patterning and bone formation, including shortened forelimbs, craniosynostosis, and clinodactyly. Histological analysis and mRNASeq profiling suggest that these effects are attributable to growth plate abnormalities and premature cranial suture closure because of precocious maturation of osteoblasts. We conclude that the epigenetic activity of EZH2 is required for skeletal patterning and development, but EZH2 expression declines during terminal osteoblast differentiation and matrix production.     

Discovery of a new class of glucosylceramide synthase inhibitors

A novel series of potent inhibitors of glucosylceramide synthase are described. The optimization of biochemical and cellular potency as well as ADME properties led to compound 23c. Broad tissue distribution was obtained following oral administration to mice. Thus 23c could be another useful tool compound for studying the effects of GCS inhibition in vitro and in vivo.     

A complete skull of an early cretaceous sauropod and the evolution of advanced titanosaurians

Advanced titanosaurian sauropods, such as nemegtosaurids and saltasaurids, were diverse and one of the most important groups of herbivores in the terrestrial biotas of the Late Cretaceous. However, little is known about their rise and diversification prior to the Late Cretaceous. Furthermore, the evolution of their highly-modified skull anatomy has been largely hindered by the scarcity of well-preserved cranial remains. A new sauropod dinosaur from the Early Cretaceous of Brazil represents the earliest advanced titanosaurian known to date, demonstrating that the initial diversification of advanced titanosaurians was well under way at least 30 million years before their known radiation in the latest Cretaceous. The new taxon also preserves the most complete skull among titanosaurians, further revealing that their low and elongated diplodocid-like skull morphology appeared much earlier than previously thought.     

Shoreline urbanization interrupts allochthonous subsidies to a benthic consumer over a gradient of lake size

The role of resource subsidies across ecosystem boundaries has emerged as an important concept in contemporary ecology. For lake ecosystems, this has led to interest in quantifying the contribution of terrestrial allochthonous carbon to aquatic secondary production. An inverse relationship between habitat area and the role of allochthonous subsidies has been documented on marine islands and assumed for lakes, yet there have been no tests of this pattern among benthic (lake bottom) consumers. Here, we used carbon stable isotopes to trace terrestrial allochthonous and benthic autochthonous carbon use by the crayfish Pacifastacus leniusculus over a gradient of lake area, productivity and urbanization. Consistent with findings from terrestrial islands, habitat size dictated the importance of allochthonous subsidies, as P. leniusculus transitioned from using predominantly terrestrial carbon in small lakes to an increased reliance on autochthonous production in larger lakes. However, shoreline urbanization interacted with this pattern, particularly for small lakes where greater urbanization resulted in reduced use of allochthonous resources. As such, we provide, to our knowledge, the first confirmation of the predicted relationship between habitat size and importance of allochthonous subsidies to lake benthic consumers, but found that urbanization can interfere with this pattern.     

Ontogeny, phylogeny, and morphology in anuran larvae: morphometric analysis of cranial development and evolution in Rana tadpoles (Anura: Ranidae)

Comparative studies of chondrocranial morphology in larval anurans are typically qualitative in nature, focusing primarily on discrete variation or gross differences in the size or shape of individual structures. Detailed data on chondrocranial allometry are currently limited to only two species, Rana sylvatica and Bufo americanus. This study uses geometric morphometric and multivariate statistical analyses to examine interspecific variation in both larval chondrocranial shape and patterns of ontogenetic allometry among six species of Rana. Variation is interpreted within the context of hypothesized phylogenetic relationships among these species. Canonical variates analyses of geometric morphometric datasets indicate that species can be clearly discriminated based on chondrocranial shape, even when whole ontogenies are included in the analysis. Ordinations and cluster analyses based on chondrocranial shape data indicate the presence of three primary groupings (R. sylvatica; R. catesbeiana + R. clamitans; and R. palustris + R. pipiens + R. sphenocephala), and patterns of similarity closely reflect phylogenetic relationships. Analysis of chondrocranial allometry reveals that some patterns are conserved across all species (e.g., most measurements scale with negative allometry, those associated with the posterior palatoquadrate tend to scale with isometry or positive allometry). Ontogenetic scaling along similar allometric trajectories, lateral transpositions of individual trajectories, and variable allometric relationships all contribute to shape differences among species. Overall patterns of similarity among ontogenetic trajectories also strongly reflect phylogenetic relationships. Thus, this study demonstrates a tight link between ontogeny, phylogeny, and morphology, and highlights the importance of including both ontogenetic and phylogenetic data in studies of chondrocranial evolution in larval anurans.     

The structure of an antitumor C(H)2-domain-deleted humanized antibody

C(H)2-domain-deleted CC49 (HuCC49DeltaCH2), a recombinant humanized antibody that recognizes the TAG-72 antigen expressed on a variety of human carcinomas, is secreted from cultured cells as a mixture of two homodimeric isoforms. Isoform A contains two covalent interchain disulfide bonds at heavy chain positions 239 and 242, while isoform B fails to develop any interchain disulfide bonds but has 239-242 intrachain disulfide bonds instead. Form A is currently in preclinical development as a therapeutic agent for treating colorectal carcinoma, though form B shows equal efficacy. HuCC49DeltaCH2 form B can be crystallized from sodium formate only in the presence of detergents. X-ray diffraction data were collected on a single cryo-cooled crystal grown with Triton X-100 and the structure was solved by molecular replacement. The model has refined to R=0.246 (R(free)=0.297) for 2.8A data. The antibodies pack in the crystal around crystallographic 2-fold axes as tetramers with approximate 222 symmetry. Atomic force microscopy studies show that this tetrameric structure is the crystal building block and also exists free in the mother liquor. The tetramer is composed of two rings, back-to-back, with a thickness of approximately 83A. Each ring is composed of two antibodies with the complementarity-determining regions (CDR) of the two Fabs of one antibody interacting with the CDR regions of the second antibody in a head-to-head fashion. These rings are approximately 167A long and 112A wide. The C(H)3 domain is inverted with respect to the Fabs when compared to the usual orientation found in conventional antibodies. The polypeptides joining the C(H)3 domains to the Fab portions of the antibody are not seen and are almost certainly disordered. The antigen combining site of HuCC49DeltaCH2 is very similar, but not identical, in topology and charge distribution to that of antibody B72.3, which binds a similar epitope on TAG-72. The combining site consists of a deep cleft, heavily lined with aromatic amino acid side-chains but bounded by numerous charged groups.