Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region

Although hyperdiverse groups like terrestrial arthropods are almost certainly severely impacted by habitat fragmentation and destruction, few studies have formally documented such effects. In this paper, we summarize the results of a multifaceted research approach to assess the magnitude and importance of anthropogenic population extinction on the narrowly endemic trapdoor spider genus Apomastus . We used geographical information systems modeling to reconstruct the likely historical distribution of Apomastus , and used molecular phylogeographic data to discern population genetic structure and detect genetic signatures of population extinction. In combination, these complementary lines of inference support direct observations of population extinction, and lead us to conclude that population extinction via urbanization has played an important role in defining the modern-day distribution of Apomastus species. This population loss implies coincident loss of genetic and adaptive diversity within this genus, and more generally, suggests a loss of ground-dwelling arthropod population diversity throughout the Los Angeles Basin. Strategies for minimizing this loss are proposed.     

Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): conflict and agreement with the current system of classification

Mygalomorph spiders, which include the tarantulas, trapdoor spiders, and their kin, represent one of three main spider lineages. Mygalomorphs are currently classified into 15 families, comprising roughly 2500 species and 300 genera. The few published phylogenies of mygalomorph relationships are based exclusively on morphological data and reveal areas of both conflict and congruence, suggesting the need for additional phylogenetic research utilizing new character systems. As part of a larger combined evidence study of global mygalomorph relationships, we have gathered approximately 3.7 kb of rRNA data (18S and 28S) for a sample of 80 genera, representing all 15 mygalomorph families. Taxon sampling was particularly intensive across families that are questionable in composition-Cyrtaucheniidae and Nemesiidae. The following primary results are supported by both Bayesian and parsimony analyses of combined matrices representing multiple 28S alignments: (1) the Atypoidea, a clade that includes the families Atypidae, Antrodiaetidae, and Mecicobothriidae, is recovered as a basal lineage sister to all other mygalomorphs, (2) diplurids and hexathelids form a paraphyletic grade at the base of the non-atypoid clade, but neither family is monophyletic in any of our analyses, (3) a clade consisting of all sampled nemesiids, Microstigmata and the cyrtaucheniid genera Kiama, Acontius, and Fufius is consistently recovered, (4) other sampled cyrtaucheniids are fragmented across three separate clades, including a monophyletic North American Euctenizinae and a South African clade, (5) of the Domiothelina, only idiopids are consistently recovered as monophyletic; ctenizids are polyphyletic and migids are only weakly supported. The Domiothelina is not monophyletic. The molecular results we present are consistent with more recent hypotheses of mygalomorph relationship; however, additional work remains before mygalomorph classification can be formally reassessed with confidence-increased taxonomic sampling and the inclusion of additional character systems (more genes and morphology) are required.     

Quantitative assessment of the structural bias in protein-protein interaction assays

With recent publications of several large-scale protein-protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset.     

Perlecan inhibits smooth muscle cell adhesion to fibronectin: role of heparan sulfate

Smooth muscle cell migration, proliferation, and deposition of extracellular matrix are key events in atherogenesis and restenosis development. To explore the mechanisms that regulate smooth muscle cell function, we have investigated whether perlecan, a basement membrane heparan sulfate proteoglycan, modulates interaction between smooth muscle cells and other matrix components. A combined substrate of fibronectin and perlecan showed a reduced adhesion of rat aortic smooth muscle cells by 70-90% in comparison to fibronectin alone. In contrast, perlecan did not interfere with cell adhesion to laminin. Heparinase treated perlecan lost 60% of its anti-adhesive effect. Furthermore, heparan sulfate as well as heparin reduced smooth muscle cell adhesion when combined with fibronectin whereas neither hyaluronan nor chondroitin sulfate had any anti-adhesive effects. Addition of heparin as a second coating to a preformed fibronectin matrix did not affect cell adhesion. Cell adhesion to the 105- and 120 kDa cell-binding fragments of fibronectin, lacking the main heparin-binding domains, was also inhibited by heparin. In addition, co-coating of fibronectin and (3)H-heparin showed that heparin was not even incorporated in the substrate. Morphologically, smooth muscle cells adhering to a substrate prepared by co-coating of fibronectin and perlecan or heparin were small, rounded, lacked focal contacts, and showed poorly developed stress fibers of actin. The results show that the heparan sulfate chains of perlecan lead to altered interactions between smooth muscle cells and fibronectin, possibly due to conformational changes in the fibronectin molecule. Such interactions may influence smooth muscle cell function in atherogenesis and vascular repair processes.     

Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus

Aptostichus simus is a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6-12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. If a time-limited genealogical perspective is employed, A. simus would be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.     

Fibronectin promotes cell cycle entry in smooth muscle cells in primary culture

Smooth muscle cell proliferation after arterial injury is regulated by growth factors and components of the extracellular matrix. We have previously demonstrated that fibronectin promotes a phenotypic modulation of freshly isolated rat smooth muscle cells from a contractile to a synthetic phenotype in primary culture and supports the ability of the cells to respond to growth factors. Here, we analyzed if fibronectin promotes cell cycle entry in freshly isolated rat aortic smooth muscle cells during primary culture. Cell cycle analysis showed that cells seeded on fibronectin remained in the G(0)/G(1) phase of the cell cycle during the first 6 days of culture. During this period, there was an increased expression of cyclin D1 and p27(KIP1) in the absence of exogenous growth factors. Addition of serum was followed by enhanced cyclin D1 expression, decreased p27(KIP1) levels, hyperphosphorylation of Rb protein, induction of cyclin A and cyclin D3 expression, and cell cycle progression into S phase. The results indicate that fibronectin initiates cell cycle entry in freshly isolated smooth muscle cells by promoting the induction of cyclin D1 and thereby facilitates further cell cycle progression together with growth factors.     

A novel, extraneuronal role for cyclin-dependent protein kinase 5 (CDK5): modulation of cAMP-induced apoptosis in rat leukemia cells

A number of cyclin-dependent protein kinase (CDK) inhibitors were tested for the ability to protect IPC-81 rat leukemic cells against cAMP-induced apoptosis. A near perfect proportionality was observed between inhibitor potency to protect against cAMP-induced apoptosis and to antagonize CDK5, and to a lesser extent, CDK2 and CDK1. Enforced expression of dominant negative CDK5 (but not CDK1-dn or CDK2-dn) protected against death, indicating that CDK5 activity was necessary for cAMP-induced apoptosis. The CDK inhibitors failed to protect the cells against daunorubicine-, staurosporine-, or okadaic acid-induced apoptosis. The inhibition of CDK5 prevented the cleavage of pro-caspase-3 in cAMP-treated cells. The cells could be saved closer to the moment of their onset of death by inhibitors of caspases than by inhibitors of CDK5. This suggested that the action of CDK5 was upstream of caspase activation. The cAMP treatment resulted in a moderate increase of the level of CDK5 mRNA and protein in IPC-81 wild-type cells. Such cAMP induction of CDK5 was not observed in cells expressing the inducible cAMP early repressor. The cAMP-induced increase of CDK5 contributed to apoptosis since cells overexpressing CDK5-wt were more sensitive for cAMP-induced death. These results demonstrate the first example of a proapoptotic CDK action upstream of caspase activation and of an extra-neuronal effect of CDK5.     

Original Articles: Nitrogen Mineralization in Two Unpolluted Old-Growth Forests of Contrasting Biodiversity and Dynamics

Studies in unpolluted, old-growth forests in the coastal range of southern Chile (42°30′S) can provide a baseline for understanding how forest ecosystems are changing due to the acceleration of nitrogen (N) inputs that has taken place over the last century. Chilean temperate forests, in contrast to their northern hemisphere counterparts, exhibit extremely low losses of inorganic N to stream waters. The objectives of this study were (a) to determine whether low inorganic N outputs in these forests were due to low rates of N mineralization or nitrification, and (b) to examine how biodiversity (defined as number of dominant tree species) and forest structure influence N mineralization and overall patterns of N cycling. Studies were conducted in a species-poor, conifer-dominated (Fitzroya cupressoides) forest with an even-aged canopy, and in a mixed-angiosperm (Nothofagus nitida) forest with a floristically more diverse and unstable canopy. Nitrogen mineralization rates measured in laboratory assays varied seasonally, reaching 6.0 μg N/g DW/day in both forests during late summer. Higher values were related to higher microbial activity, larger pools of labile inorganic N, and increased fine litter inputs. Field assays, conducted monthly, indicated positive net flux from N mineralization mainly from December to January in both forests. Annual net flux of N from mineralization varied from 20 to 23 kg/ha/year for the Fitzroya forest and from 31 to 37 kg/ha/year for the Nothofagus forest. Despite low losses of inorganic N to streams, N mineralization and nitrification are not inhibited in these forests, implying the existence of strong sinks for NO₃ ⁻ in the ecosystem. Field N mineralization rates were two times higher in the Nothofagus forest than in the Fitzroya forest, and correlated with greater N input via litterfall, slightly higher soil pH, and narrower carbon (C)–nitrogen ratios of soils and litter in the former. Differences in N mineralization between the two forest types are attributed to differences in biotic structure, stand dynamics, and site factors. Median values of net N mineralization rates in these southern hemisphere forests were lower than median rates for forests in industrialized regions of North America, such as the eastern and central USA. We suggest that these high N mineralization rates may be a consequence of enhanced atmospheric N deposition.     

Purification and characterization of hormone-regulated isoforms of the regulatory subunit of type II cAMP-dependent protein kinase from rat ovaries

The regulatory subunit (R-II) of cAMP-dependent protein kinase type II is induced in rat ovarian granulosa cells by the synergistic actions of estradiol and follicle-stimulating hormone. The R-II from rat ovaries was compared with R-II from rat heart, rat brain, bovine heart, and bovine brain using immunological methods, 8-N3[32P]cAMP photoaffinity labeling and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Three isoforms of R-II were identified in rat ovarian cell extract (R-II54 Mr = 54,000, R-II52 Mr = 52,000, R-II51 Mr = 51,000), two isoforms of R-II in rat brain cell extract (Mr = 54,000, Mr = 52,000), and one isoform of R-II in rat heart cell extract (Mr = 54,000). Rat ovarian R-II54, heart R-II, and brain R-II (Mr = 54,000) were recognized by antiserum against rat heart R-II, whereas rat ovarian R-II52/R-II51 and rat brain R-II (Mr = 52,000) were not. In contrast, an antiserum raised against bovine heart R-II recognized all three isoforms of ovarian R-II as well as the lower molecular weight form of rat brain R-II. Ovarian types R-II52 and R-II51 but not R-II54 were increased selectively in granulosa cells by estradiol and follicle-stimulating hormone. In addition: 1) ovarian R-II52/51 subunits were purified to homogeneity and shown to recombine with C subunit from bovine heart to form a cAMP-dependent protein kinase; 2) pure R-II52/51 were not interconvertible to a higher molecular weight form by C subunit-dependent phosphorylation; 3) pure rat heart R-II (Mr = 54,000) and ovarian R-II52/51 exhibited distinct differences based on one- and two-dimensional peptide mapping; and 4) by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis pure R-II52/51 were resolved as three (rather than two) isoelectric variants which were clearly different from pure rat heart R-II54. Thus, the hormone-regulated form of R-II in rat ovarian granulosa cells appears to represent a gene product distinct from R-II54 in rat heart.