Shrubs as ecosystem engineers in a coastal dune: influences on plant populations,communities and ecosystems

Question: How do two shrubs with contrasting life‐history characteristics influence abundance of dominant plant taxa, species richness and aboveground biomass of grasses and forbs, litter accumulation, nitrogen pools and mineralization rates? How are these shrubs – and thus their effects on populations, communities and ecosystems – distributed spatially across the landscape? Location: Coastal hind‐dune system, Bodega Head, northern California. Methods: In each of 4 years, we compared vegetation, leaf litter and soil nitrogen under canopies of two native shrubs –Ericameria ericoides and the nitrogen‐fixing Lupinus chamissonis– with those in adjacent open dunes. Results: At the population level, density and cover of the native forb Claytonia perfoliata and the exotic grass Bromus diandrus were higher under shrubs than in shrub‐free areas, whereas they were lower under shrubs for the exotic grass Vulpia bromoides. In contrast, cover of three native moss species was highest under Ericameria and equally low under Lupinus and shrub‐free areas. At community level, species richness and aboveground biomass of herbaceous dicots was lower beneath shrubs, whereas no pattern emerged for grasses. At ecosystem level, areas beneath shrubs accumulated more leaf litter and had larger pools of soil ammonium and nitrate. Rates of nitrate mineralization were higher under Lupinus, followed by Ericameria and then open dune. At landscape level, the two shrubs – and their distinctive vegetation and soils – frequently had uniform spatial distributions, and the distance separating neighbouring shrubs increased as their combined sizes increased. Conclusions: Collectively, these data suggest that both shrubs serve as ecosystem engineers in this coastal dune, having influences at multiple levels of biological organization. Our data also suggest that intraspecific competition influenced the spatial distributions of these shrubs and thus altered the distribution of their effects throughout the landscape.     

Effect of hypermethylation of CCWGG sequences in DNA of Mesembryanthemum crystallinum plants on their adaptation to salt stress

Under salt stress conditions, the level of CpNpG-methylation (N is any nucleoside) of the nuclear genome of the facultative halophyte Mesembryanthemum crystallinum in the CCWGG sequences (W = A or T) increases two-fold and is coupled with hypermethylation of satellite DNA on switching-over of C3-photosynthesis to the crassulacean acid metabolism (CAM) pathway of carbon dioxide assimilation. The methylation pattern of the CCWGG sequences is not changed in both the 5'-promoter region of the gene of phosphoenolpyruvate carboxylase, the key enzyme of C4-photosynthesis and CAM, and in the nuclear ribosomal DNA. Thus, a specific CpNpG-hypermethylation of satellite DNA has been found under conditions of expression of a new metabolic program. The functional role of the CpNpG-hypermethylation of satellite DNA is probably associated with formation of a specialized chromatin structure simultaneously regulating expression of a large number of genes in the cells of M. crystallinum plants on their adaptation to salt stress and switching-over to CAM metabolism.     

A novel yeast two-hybrid approach to identify CDPK substrates: characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein

Calcium-dependent protein kinases (CDPKs) are sensor-transducer proteins capable of decoding calcium signals in diverse phosphorylation-dependent calcium signaling networks in plants and some protists. Using a novel yeast two-hybrid (YTH) approach with constitutively active and/or catalytically inactive forms of AtCPK11 as bait, we identified AtDi19 as an AtCPK11-interacting protein. AtDi19 is a member of a small family of stress-induced genes. The interaction was confirmed using pull-down assays with in vitro translated AtCPK11 and GST-AtDi19 and localization studies in Arabidopsis protoplasts cotransfected with AtCPK11:GFP and AtDi19:DsRed2 protein fusions. We further showed that the interaction of AtDi19 is specific to both AtCPK4 and AtCPK11, whereas other closely related CPKs from Arabidopsis interacted weakly (e.g., AtCPK12) or did not interact (e.g., AtCPK26, AtCPK5 and AtCPK1) with AtDi19. Deletion analyses showed that a region containing two predicted nuclear localization signals (NLS) and a nuclear export signal (NES) of AtDi19 is essential for interaction with AtCPK11. We further demonstrated that AtDi19 is phosphorylated by AtCPK11 in a Ca(2+)-dependent manner at Thr105 and Ser107 within the AtDi19 bipartite NLS using in vitro kinase assays. Our data suggest that disruption of the autoinhibitor domain leading to the formation of a constitutively active CDPK may stabilize kinase-substrate interactions without affecting specificity.     

Temporal Changes in Native and Exotic Vegetation and Soil Characteristics following Disturbances by Feral Pigs in a California Grassland

Invasive species that increase prevailing disturbance regimes can profoundly alter the composition and structure of ecosystems they invade. Using both comparative and manipulative approaches, we investigated how native and exotic vegetation and soil characteristics at a coastal grassland site in northern California changed through time following disturbances by feral pigs (Sus scrofa). We quantified these successional changes by comparing pig disturbances of varying ages (2, 14, 26+, and 60+ months) during the spring and early summer of 2001. Our results indicate that species richness of native plants increased slowly but steadily through time following disturbances, whereas richness of exotic species rebounded much more rapidly. Percent cover of native perennial grasses also increased steadily through time after pig disturbance, whereas the cover of exotic perennial grasses, annual grasses and forbs initially increased rapidly after disturbance and then remained the same or subsided slightly with time. The cover of native forbs and bulbs either increased weakly through time following disturbance or did not change substantially. Pools of ammonium and nitrate in the soil did not change greatly through time following pig disturbance. Net mineralization rates for ammonium and nitrate also varied little with age since disturbance, although we did find that nitrate mineralization was greater at intermediate ages in one study. Neither organic matter content or particle size varied significantly with disturbance age. In summary, we have shown that native and exotic plants from different functional groups vary greatly in how they recovered from pig disturbances. Exotic taxa were generally able to rapidly colonize and persist in pig disturbances, whereas native taxa usually exhibited a slow but steady rebounding following pig disturbance. Given our results, and those of others from nearby sites, we suggest that the health of coastal grasslands may be enhanced substantially by eliminating or greatly reducing the size of feral pig populations.     

Using peptide arrays to define nuclear carrier binding sites on nucleoporins

In the peptide SPOT array technique, an array of different peptides are synthesized on, and covalently linked to, cellulose membranes. In one usage of this technique, these peptides are screened in an overlay assay to determine which short sequence(s) contains a binding site for an interacting protein. By preparing overlapping peptides that cover the entire sequence of a protein, all of the binding domains on the protein for a second protein can be identified. We have utilized the peptide SPOT array technique to identify the short amino acid sequences within nuclear pore complex proteins (also known as nucleoporins or Nups) that bind the nuclear carrier importin-beta. Crystallization studies by others have indicated that nuclear carriers such as importin-beta bind to phenylalanine-glycine (FG) repeats present in numerous copies in the sequences of a family of nucleoporins. Consistent with this, we found that most (but not all) of the Nup binding sites for importin-beta identified by this technique contain Fx, FG, FxFG, FxFx, or GLFG sequences, although not all such sequences bound importin-beta. Peptide SPOT array substitution studies confirmed a crucial role for the phenylalanine in FG repeats and identified a lysine residue flanking some repeats that is crucial for importin-beta binding to those repeats. In addition to these expected binding sequences for importin-beta, we found multiple instances of a peptide lacking a canonical FG repeat that strongly bound importin-beta, indicating that additional Nup sequences may form binding sites for importin-beta.     

Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis

Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.     

Evaluation of indenoisoquinoline topoisomerase I inhibitors using a hollow fiber assay

The indenoisoquinolines are a novel class of non-camptothecin topoisomerase I (Top1) inhibitors whose mechanism of action involves trapping the covalent complex formed between DNA and Top1 during cellular processes. As an ongoing evaluation of the indenoisoquinolines for Top1 inhibition and anticancer activity, indenoisoquinoline analogs have been screened in the National Cancer Institute's hollow fiber assay (HFA). Some of the derivatives demonstrated significant activity at intraperitoneal and subcutaneous fiber placement sites, along with net cancer cell kill in one or more cell lines.     

Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease

Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are clinical tests commonly used to screen for coagulation-factor deficiencies. One genome-wide association study (GWAS) has been reported previously for aPTT, but no GWAS has been reported for PT. We conducted a GWAS and meta-analysis to identify genetic loci for aPTT and PT. The GWAS for aPTT was conducted in 9,240 individuals of European ancestry from the Atherosclerosis Risk in Communities (ARIC) study, and the GWAS for PT was conducted in 2,583 participants from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS) and the Lothian Birth Cohorts (LBC) of 1921 and 1936. Replication was assessed in 1,041 to 3,467 individuals. For aPTT, previously reported associations with KNG1, HRG, F11, F12, and ABO were confirmed. A second independent association in ABO was identified and replicated (rs8176704, p = 4.26 × 10(-24)). Pooling the ARIC and replication data yielded two additional loci in F5 (rs6028, p = 3.22 × 10(-9)) and AGBL1 (rs2469184, p = 3.61 × 10(-8)). For PT, significant associations were identified and confirmed in F7 (rs561241, p = 3.71 × 10(-56)) and PROCR/EDEM2 (rs2295888, p = 5.25 × 10(-13)). Assessment of existing gene expression and coronary artery disease (CAD) databases identified associations of five of the GWAS loci with altered gene expression and two with CAD. In summary, eight genetic loci that account for ～29% of the variance in aPTT and two loci that account for ～14% of the variance in PT were detected and supported by functional data.     

cdpop: A spatially explicit cost distance population genetics program

Spatially explicit simulation of gene flow in complex landscapes is essential to explain observed population responses and provide a foundation for landscape genetics. To address this need, we wrote a spatially explicit, individual-based population genetics model (cdpop). The model implements individual-based population modelling with Mendelian inheritance and k-allele mutation on a resistant landscape. The model simulates changes in population and genotypes through time as functions of individual based movement, reproduction, mortality and dispersal on a continuous cost surface. This model will be a valuable tool for the study of landscape genetics by increasing our understanding about the effects of life history, vagility and differential models of landscape resistance on the genetic structure of populations in complex landscapes.     

Simulating natural selection in landscape genetics

Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially-explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal panmictic populations in an allopatric setting in their predictions of population structure and frequency of fixation of adaptive alleles. We explore initial applications of a spatially-explicit, individual-based evolutionary landscape genetics program that incorporates all factors--mutation, gene flow, genetic drift and selection--that affect the frequency of an allele in a population. We incorporate natural selection by imposing differential survival rates defined by local relative fitness values on a landscape. Selection coefficients thus can vary not only for genotypes, but also in space as functions of local environmental variability. This simulator enables coupling of gene flow (governed by resistance surfaces), with natural selection (governed by selection surfaces). We validate the individual-based simulations under Wright-Fisher assumptions. We show that under isolation-by-distance processes, there are deviations in the rate of change and equilibrium values of allele frequency. The program provides a valuable tool (cdpop v1.0; http://cel.dbs.umt.edu/software/CDPOP/) for the study of evolutionary landscape genetics that allows explicit evaluation of the interactions between gene flow and selection in complex landscapes.