Development of a RIVPACS-type predictive model for bioassessment of wadeable streams in Wyoming

RIVPACS models produce a community-level measure of biological condition known as O/E, which is derived from a comparison of the observed (O) biota with those expected (E) to occur in the absence of anthropogenic stress. We used benthic macroinvertebrate and environmental data collected at 925 stream monitoring stations, from 1993 to 2001, to develop, validate, and apply a RIVPACS model to assess the biological condition of wadeable streams in Wyoming. From this dataset, 296 samples were identified as reference, 157 of which were used to calibrate the model, 46 to validate it, and 93 to examine temporal variability in reference site O/E-values. We used cluster analyses to group the model development reference sites into biologically similar classes of streams and multiple discriminant function analysis to determine which environmental variables best discriminated among reference groups. A suite of 14 categorical and continuous environmental variables best discriminated among 15 reference groups and explained a large proportion of the natural variability in biota within the reference dataset. Eleven of the predictor variables were derived from GIS. As expected, mean O/E-values for reference sites used in model development and validation were near unity and statistically similar. Temporal variability in O/E-values for reference sites was low. Test site values ranged from 0 to 1.45 (mean = 0.73). The model was accurate in both space and time and precise enough (S.D. of O/E-values for calibration data = 0.17) to detect modest alteration in biota associated with anthropogenic stressors. Our model was comparable in performance to other RIVPACS models developed in the United States and can produce effective assessments of biological condition over a broad, ecologically diverse region. We also provide convincing evidence that RIVPACS models can be developed primarily with GIS-based predictor variables. This framework not only simplifies the extraction of predictor variable information while potentially reducing expenditures of time and money in the collection of predictor variable information, but opens the door for development and/or application of RIVPACS models in regions where there is a paucity of local-scale, abiotic information.     

A perivascular origin for mesenchymal stem cells in multiple human organs

Mesenchymal stem cells (MSCs), the archetypal multipotent progenitor cells derived in cultures of developed organs, are of unknown identity and native distribution. We have prospectively identified perivascular cells, principally pericytes, in multiple human organs including skeletal muscle, pancreas, adipose tissue, and placenta, on CD146, NG2, and PDGF-Rbeta expression and absence of hematopoietic, endothelial, and myogenic cell markers. Perivascular cells purified from skeletal muscle or nonmuscle tissues were myogenic in culture and in vivo. Irrespective of their tissue origin, long-term cultured perivascular cells retained myogenicity; exhibited at the clonal level osteogenic, chondrogenic, and adipogenic potentials; expressed MSC markers; and migrated in a culture model of chemotaxis. Expression of MSC markers was also detected at the surface of native, noncultured perivascular cells. Thus, blood vessel walls harbor a reserve of progenitor cells that may be integral to the origin of the elusive MSCs and other related adult stem cells.     

Family portraits: the enzymes behind benzylisoquinoline alkaloid diversity

Benzylisoquinoline alkaloids (BIAs) are a group of specialized metabolites found predominantly in the plant order Ranunculales. Approximately 2500 naturally occurring BIAs have been identified, many of which possess a variety of potent biological and pharmacological properties. The initial BIA skeleton is formed via condensation by a unique enzyme, norcoclaurine synthase, of the l-tyrosine derivatives dopamine and 4-hydroxyphenylacetaldehyde, yielding (S)-norcoclaurine as a central intermediate. The vast diversity of BIA structures is subsequently derived from (1) transformation of the basic BIA backbone by oxidative enzymes, particularly cytochromes P450 and FAD-linked oxidases, and (2) further structural and functional group modification by tailoring enzymes, which also include various reductases, dioxygenases, acetyltransferases, and carboxylesterases. Most of the biosynthetic enzymes responsible for the biosynthesis of major BIAs (i.e. morphine, noscapine, papaverine, and sanguinarine) in opium poppy (Papaver somniferum), and other compounds (e.g. berberine) in related plants, have been isolated and partially characterized. Diversity in BIA metabolism is driven by the modular and repetitive recruitment, and subsequent neo-functionalization, of a limited number of ancestral enzymes. In this review, BIA biosynthetic enzymes are discussed in the context of their respective families, facilitating exploration of common phylogeny and biochemical mechanisms.     

A structural study of the myristoylated N-terminus of ARF1

The effect of myristoylation on the 15-amino-acid peptide from the membrane-binding N-terminus of ADP ribosylation factor 1 (ARF1) was studied using neutron diffraction and circular dichroism. A previous study on the non-acylated form indicated that the peptide lies parallel to the membrane, at a shallow depth and in the vicinity of the phosphorylcholine headgroups. It was suggested that the helix does not extend past residue 12, an important consequence for the linking region of the ARF1 protein. In this paper, we show that the result of myristoylation is to increase the helical content reaching the peptide's C-terminus, resulting in the formation of a new hydrophobic face. This increased helicity may augment the entire protein's membrane-binding affinity, indicating that ARF1 effectively has two interdependent membrane-binding motifs.     

Large P body-like RNPs form in C. elegans oocytes in response to arrested ovulation, heat shock, osmotic stress, and anoxia and are regulated by the major sperm protein pathway

As Caenorhabditis elegans hermaphrodites age, sperm become depleted, ovulation arrests, and oocytes accumulate in the gonad arm. Large ribonucleoprotein (RNP) foci form in these arrested oocytes that contain RNA-binding proteins and translationally masked maternal mRNAs. Within 65 min of mating, the RNP foci dissociate and fertilization proceeds. The majority of arrested oocytes with foci result in viable embryos upon fertilization, suggesting that foci are not deleterious to oocyte function. We have determined that foci formation is not strictly a function of aging, and the somatic, ceh-18, branch of the major sperm protein pathway regulates the formation and dissociation of oocyte foci. Our hypothesis for the function of oocyte RNP foci is similar to the RNA-related functions of processing bodies (P bodies) and stress granules; here, we show three orthologs of P body proteins, DCP-2, CAR-1 and CGH-1, and two markers of stress granules, poly (A) binding protein (PABP) and TIA-1, appear to be present in the oocyte RNP foci. Our results are the first in vivo demonstration linking components of P bodies and stress granules in the germ line of a metazoan. Furthermore, our data demonstrate that formation of oocyte RNP foci is inducible in non-arrested oocytes by heat shock, osmotic stress, or anoxia, similar to the induction of stress granules in mammalian cells and P bodies in yeast. These data suggest commonalities between oocytes undergoing delayed fertilization and cells that are stressed environmentally, as to how they modulate mRNAs and regulate translation.     

The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins

Carrier proteins (CPs) play a critical role in the biosynthesis of various natural products, especially in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymology, where the CPs are referred to as peptidyl‐carrier proteins (PCPs) or acyl‐carrier proteins (ACPs), respectively. CPs can either be a domain in large multifunctional polypeptides or standalone proteins, termed Type I and Type II, respectively. There have been many biochemical studies of the Type I PKS and NRPS CPs, and of Type II ACPs. However, recently a number of Type II PCPs have been found and biochemically characterized. In order to understand the possible interaction surfaces for combinatorial biosynthetic efforts we crystallized the first characterized and representative Type II PCP member, BlmI, from the bleomycin biosynthetic pathway from Streptomyces verticillus ATCC 15003. The structure is similar to CPs in general but most closely resembles PCPs. Comparisons with previously determined PCP structures in complex with catalytic domains reveals a common interaction surface. This surface is highly variable in charge and shape, which likely confers specificity for interactions. Previous nuclear magnetic resonance (NMR) analysis of a prototypical Type I PCP excised from the multimodular context revealed three conformational states. Comparison of the states with the structure of BlmI and other PCPs reveals that only one of the NMR states is found in other studies, suggesting the other two states may not be relevant. The state represented by the BlmI crystal structure can therefore serve as a model for both Type I and Type II PCPs. Proteins 2014; 82:1210–1218. © 2013 Wiley Periodicals, Inc.     

High-resolution habitat and bathymetry maps for 65,000 sq. km of Earth’s remotest coral reefs

Coral Reefs - With compelling evidence that half the world’s coral reefs have been lost over the last four decades, there is urgent motivation to understand where reefs are located and their...     

Material Spiraling in Stream Corridors: A Telescoping Ecosystem Model

Stream ecosystems consist of several subsystems that are spatially distributed concentrically, analogous to the elements of a simple telescope. Subsystems include the central surface stream, vertically and laterally arrayed saturated sediments (hyporheic and parafluvial zones), and the most distal element, the riparian zone. These zones are hydrologically connected; thus water and its dissolved and suspended load move through all of these subsystems as it flows downstream. In any given subsystem, chemical transformations result in a change in the quantity of materials in transport. Processing length is the length of subsystem required to “process” an amount of substrate equal to advective input. Long processing lengths reflect low rates of material cycling. Processing length provides the length dimension of each cylindrical element of the telescope and is specific to subsystem (for example, the surface stream), substrate (for instance, nitrate), and process (denitrification, for example). Disturbance causes processing length to increase. Processing length decreases during succession following disturbance. The whole stream-corridor ecosystem consists of several nested cylindrical elements that extend and retract, much as would a telescope, in response to disturbance regime. This telescoping ecosystem model (TEM) can improve understanding of material retention in running water systems; that is, their “nutrient filtration” capacity. We hypothesize that disturbance by flooding alters this capacity in proportion to both intensity of disturbance and to the relative effect of disturbance on each subsystem. We would expect more distal subsystems (for example, the riparian zone) to show the highest resistance to floods. In contrast, we predict that postflood recovery of functions such as material processing (that is, resilience) will be highest in central elements and decrease laterally. Resistance and resilience of subsystems are thus both inversely correlated and spatially separated. We further hypothesize that cross-linkages between adjacent subsystems will enhance resilience of the system as a whole. Whole-ecosystem retention, transformation, and transport are thus viewed as a function of subsystem extent, lateral and vertical linkage, and disturbance regime. Received 15 April 1997; accepted 1 September 1997.