Recovery plan for Kootenai River white sturgeon (Acipenser transmontanus)

The white sturgeon ( Acipenser transmontanus ) of the Kootenai River was listed as endangered on September 6, 1994 by the United States Fish and Wildlife Service. This transboundary population, residing in Kootenay Lake and Kootenay River in Canada, and the Kootenai River in the US, has been in general decline since the mid-1960's. There has been very little recruitment to this population in the last 20 years.
This population became isolated from other white sturgeon populations of the Columbia River basin during the last ice age of approximately 10,000 years ago. The population adapted to the pre-development conditions of the Kootenai system, with a high spring freshet and extensive side channel and low-lying delta marshlands. Modification of the Kootenai River by human activities, such as industrial developments, floodplain dyking, and dam construction has changed the hydrograph of the Kootenai River, altering sturgeon spawning, incubation and rearing habitats and reducing overall biological productivity.
A Kootenai River white sturgeon draft recovery plan was prepared by the US Fish and Wildlife Service in cooperation with other agencies in the US and Canada. The plan was peer reviewed and there was a parallel public consultation process, where public commentary was invited from both sides of the international border. The short-term recovery objectives of the recovery plan are to prevent extinction and re-establish successful natural recruitment. The identified long-term objectives are the re-establishment of a self sustaining population and the restoration of productive habitat, in order to downlist to threatened status and subsequently delist this population when recovery is well established. Specific actions needed for recovery include spring flow augmentation during the reproduction period; a conservation aquaculture program to prevent near-term extinction; habitat restoration, and research and monitoring programs to evaluate recovery progress.     

Calreticulin, PDI, Grp94 and BiP chaperone proteins are associated with retained COMP in pseudoachondroplasia chondrocytes.

Cartilage oligomeric matrix protein (COMP), a large pentameric glycoprotein and member of the thrombospondin (TSP) group of extracellular proteins, is found in the territorial matrix surrounding chondrocytes. More than 50 unique COMP mutations have been identified as causing two skeletal dysplasias: pseudoachondroplasia (PSACH); and multiple epiphyseal dysplasia (EDM1). Recent studies suggest that calcium-binding and calcium-induced protein folding differ between wild type and mutant proteins, and abnormal processing of the mutant COMP protein contributes to the characteristic enlarged lamellar appearing rER cisternae in PSACH and EDMI chondrocytes in vivo and in vitro. Towards the goal of delineating the pathogenesis of PSACH and EDM1, in-vivo PSACH growth plate and in-vitro PSACH chondrocytes cultured in alginate beads were examined to identify and localize the chaperone proteins participating in the processing of the retained extracellular matrix proteins in the PSACH rER. Aggrecan was localized to both the rER cisternae and matrix while COMP and type IX collagen were only found in the rER. Type II collagen was solely found in the ECM suggesting that it is processed and transported differently from other retained ECM proteins. Five chaperone proteins: BiP (Grp78); calreticulin (CRT); protein disulfide (PDI); ERp72; and Grp94, demonstrated immunoreactivity in the enlarged PSACH cisternae and the short rER channels of chondrocytes from both in-vivo and in-vitro samples. The chaperone proteins cluster around the electron dense material within the enlarged rER cisternae. CRT, PDI and GRP94 AB-gold particles appear to be closely associated with COMP. Immunoprecipitation and Western blot, and Fluorescence Resonance Energy Transfer (FRET) analyses indicate that CRT, PDI and GRP94 are in close proximity to normal and mutant COMP and BiP to mutant COMP. These results suggest that these proteins play a role in the processing and transport of wild type COMP in normal chondrocytes and in the retention of mutant COMP in PSACH chondrocytes.     

Multiple molecular forms of xanthine dehydrogenase and related enzymes. IV. The relationship of aldehyde oxidase to xanthine dehydrogenase

Variants of the enzyme aldehyde oxidase in Drosophila melanogaster are described. In addition to electrophoretic variants, a mutant that causes low levels of the enzyme has been found by screening more than 80 strains for aldehyde oxidase levels. The locus of the mutation maps on the third chromosome near lpo and aldox. The existence of the ry, lpo, and aldox mutants and of the new mutant indicates that xanthine dehydrogenase, pyridoxal oxidase, and aldehyde oxidase are under a separate genetic control, in addition to a common genetic control by ma-l and lxd. The genetic separation is shown to be accompanied by physical separation of the enzymes with DEAE-cellulose column chromatography and (NH ₄)₂SO₄fractionation. Further data on the metabolism of aldehydes by xanthine dehydrogenase and aldehyde oxidase are presented. Although xanthine dehydrogenase requires NAD or a similar cofactor to metabolize purine and pteridine substrates, aldehyde oxidase oxidizes salicylaldehyde to salicylic acid without dissociable cofactors and with the uptake of oxygen.This work was supported in part by Research Grant GM-08202, by a Predoctoral Fellowship (J.C.) and a Genetics Training Grant (J.C. and E.D.), and by a Research Career Development Award (E.G.), all from the National Institutes of Health. Part of this work was submitted by J.C. to the University of North Carolina at Chapel Hill in partial fulfillment of the degree of Doctor of Philosophy.     

Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling

Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a trial sequence of putative activated protein Z (PZa) by identifying amino acid mutations in the SP-like domain that might reasonably resurrect the serine protease catalytic activity of PZ. The structure of the activated form was then modeled based on the proposed sequence using homology modeling and solvent-equilibrated molecular dynamics simulations. In silico docking of inhibitors of FVIIa and FXa to the putative active site of equilibrated PZa, along with structural comparison with its homologous proteins, suggest that the designed PZa can possibly act as a serine protease.     

Substituted benzothiadizine inhibitors of Hepatitis C virus polymerase

The synthesis and optimisation of HCV NS5B polymerase inhibitors with improved potency versus the existing compound 1 is described. Substitution in the benzothiadiazine portion of the molecule, furnishing improvement in potency in the high protein Replicon assay, is highlighted, culminating in the discovery of 12h, a highly potent oxyacetamide derivative.     

Ecophysiological responses of salt cedar (Tamarix spp. L.) to the northern tamarisk beetle (Diorhabdacarinulata Desbrochers) in a controlled environment

The northern tamarisk beetle (Diorhabda carinulata Desbrochers) was released in several western states as a biocontrol agent to suppress Tamarix spp. L. which has invaded riparian ecosystems; however, effects of beetle herbivory on Tamarix physiology are largely undocumented and may have ecosystem ramifications. Herbivory by this insect produces discoloration of leaves and premature leaf drop in these ecosystems, yet the cause of premature leaf drop and the effects of this leaf drop are still unknown. Insect herbivory may change leaf photosynthesis and respiration and may affect a plant’s ability to regulate water loss and increase water stress. Premature leaf drop may affect plant tissue chemistry and belowground carbon allocation. We conducted a greenhouse experiment to understand how Tamarix responds physiologically to adult beetle and larvae herbivory and to determine the proximate cause of premature leaf drop. We hypothesized that plants experiencing beetle herbivory would have greater leaf and root respiration rates, greater photosynthesis, increased water stress, inefficient leaf nitrogen retranslocation, lower root biomass and lower total non-structural carbohydrates in roots. Insect herbivory reduced photosynthesis rates, minimally affected respiration rates, but significantly increased water loss during daytime and nighttime hours and this produced increased water stress. The proximate cause for premature leaf drop appears to be desiccation. Plants exposed to herbivory were inefficient in their retranslocation of nitrogen before premature leaf drop. Root biomass showed a decreasing trend in plants subjected to herbivory. Stress induced by herbivory may render these trees less competitive in future growing seasons.     

Measuring succession: methods for establishing long-term vegetation monitoring sites

Successional stages are often characterized by dominant plant species (species with the highest cover) and their effect on the structure and function of an area through time. However, the plant species determining the ecosystem properties and plant community dynamics may not be the dominant, especially when it is exotic. Understanding plant community dynamics in ecosystems that are uncharacterized and/or affected by invasive plant species requires a data-driven approach and proper placement of monitoring plots. To generate robust datasets on vegetation change through time, monitoring plot placement must consider the scale of ecological variation for both vegetation and soils and plots would ideally be replicated within similar ecological site types to quantify the consistency of successional transitions. We characterized soil and vegetation across and within seven floodplains affected by Russian olive (Elaeagnus angustifolia L.) along the Yellowstone River in southeastern Montana, USA. Using modern Classification and Regression Trees (CART) and multivariate net differentiation, we identified five distinct plant community types, or classes, characterized by their tertiary woody plant cover, not the primary species, Russian olive. Our findings indicate that Russian olive communities differ across space, and these riparian areas can be classified into distinct plant community types. Characterizing plant community types via this analytical approach should allow practitioners to modify management decisions and forecast succession within relevant plant communities.     

Focus on Weed Control: Natural Compounds as Next-Generation Herbicides

Herbicides with new modes of action (MOAs) are badly needed due to the rapidly evolving resistance to commercial herbicides, but a new MOA has not been introduced in over 20 years. The greatest pest management challenge for organic agriculture is the lack of effective natural product herbicides. The structural diversity and evolved biological activity of natural phytotoxins offer opportunities for the development of both directly used natural compounds and synthetic herbicides with new target sites based on the structures of natural phytotoxins. Natural phytotoxins are also a source for the discovery of new herbicide target sites that can serve as the focus of traditional herbicide discovery efforts. There are many examples of strong natural phytotoxins with MOAs other than those used by commercial herbicides, which indicates that there are molecular targets of herbicides that can be added to the current repertoire of commercial herbicide MOAs.The evolutionary forces driving the survival of species include chemical interactions between organisms, which function in positive interactions such as mutualistic and symbiotic relationships and negative interactions such as competitive and parasitic relationships. These processes have led to the emergence of novel secondary metabolic pathways (often through gene duplication), producing a vast array of structurally diverse and biologically active molecules (Moore and Purugganan, 2005; Ober, 2005; Flagel and Wendel, 2009; Jiang et al., 2013). This evolutionary process is similar to a high-throughput screen. However, unlike conventional in vitro screens, which test many compounds on a single biochemical target over a very short period of time, this natural high-throughput process selects molecules based on their whole-organism activities, involving numerous chemical interactions between countless organisms and target sites over millions of years. To date, approximately 200,000 secondary metabolites have been identified (Tulp and Bohlin, 2005), with many more expected to be discovered. Few of these compounds have been examined for phytotoxicity, and the modes or mechanisms of action (MOAs) of even fewer known phytotoxins have been elucidated.The negative chemical interactions between organisms are often characterized using anthropomorphic language, such as chemical warfare, referring to the production of phytotoxins used by plant pathogens to invade their host plants (Maor and Shirasu, 2005), and the novel weapons hypothesis, which is associated with the chemical-based advantage of some invasive plant species over native plant populations (Callaway and Aschehoug, 2000; Callaway and Ridenour, 2004; Callaway and Maron, 2006; Cappuccino and Arnason, 2006; Callaway et al., 2008). While simplistic, this terminology illustrates how these toxin-based interactions exploit biochemical weaknesses between an organism and its host or enemy/competitor to enhance its own survival (Verhoeven et al., 2009). In fact, these interactions can even be multitrophic, such as when exotic plants enhance their invasiveness by promoting the growth of certain native soil pathogens noxious to native plants (Mangla et al., 2008; Barto et al., 2011).As humans evolved from a nomadic hunter-gatherer subsistence existence to an agricultural lifestyle, they learned to utilize certain biologically active secondary metabolites to manage agricultural pests. Indeed, the concept that nature is an excellent source of natural pesticides is captured in the following ancient Lithica poem (circa 400 B.C.): “All the pests that out of earth arise, the earth itself the antidote supplies” (Ibn et al., 1781). Less than a century later, Greek and Roman treatises described practices to control agricultural pests that include the use of essential oils. Similar documents are found in Chinese literature, such as a survey describing plant species used to control plant pests (Yang and Tang, 1988). The mid-20th century ushered in the use of synthetic pesticides, which have revolutionized agriculture. Like pharmaceuticals (Harvey, 1999, 2008; Newman and Cragg, 2012), many pesticides are based on natural compounds. However, natural products have not played a major role in herbicide discovery (Copping and Duke, 2007; Hüter, 2011).