Using Variable Rate Models to Identify Genes Under Selection in Sequence Pairs: Their Validity and Limitations for EST Sequences

Using likelihood-based variable selection models, we determined if positive selection was acting on 523 EST sequence pairs from two lineages of sunflower and lettuce. Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates. However, previous studies have shown that the likelihood ratio test (LRT) is reliable for detecting positive selection, even with low numbers of sequences. These analyses identified 56 genes that show a signature of selection, of which 75% were not identified by simpler models that average selection across codons. Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs. We discuss the validity and limitations of using variable rate models for comparisons of sequence pairs, as well as the limitations of using ESTs for identification of positively selected genes. [Reviewing Editor: Dr. Rasmus Nielsen]     

Variation in multiple paternity in natural populations of a free-spawning marine invertebrate

For free-spawning marine invertebrates, fertilization processes control the genetic diversity of offspring. Each egg can potentially be fertilized by a sperm from a different male, and hence genetic diversity within a brood varies with levels of multiple paternity. Yet, few studies have characterized the frequency of multiple paternity in natural spawns. We analysed patterns of multiple paternity in two populations of the colonial ascidian Botryllus schlosseri using microsatellites. Because previous studies have shown that at moderate to high population densities, competition among male-phase B. schlosseri colonies results in the nearest male dominating the paternity of a brood, we specifically tested the effect of population density on patterns of paternity. Paternity was estimated using three multilocus indices: minimum number of fathers, counts of sperm haplotypes, and effective paternity (K(E)). Multiple paternity was evident in more than 92% of the broods analysed, but highly variable, with a few broods displaying unequal contributions of different males. We found no effect of population density on multiple paternity, suggesting that other factors may control paternity levels. Indirect benefits from increasing the genetic diversity of broods are a possible explanation for the high level of multiple paternity in this species.     

Coordination of leaf N,anatomy, photosynthetic capacity,and hydraulics enhances evergreen expansive potential

Key message

Reduced leaf longevity, N-fixation, and enhanced hydraulic capacity combined support greater shifts in seasonal photosynthetic capacity of an expansive understory evergreen woody species relative to co-occurring less expansive evergreen species.

Abstract

Physiological functioning typically declines with increased leaf life span. While an evergreen leaf habit is generally associated with reduced leaf N, physiological capacity, and slower growth, most expansive woody species are evergreens and/or N fixers. An evergreen leaf habit enables year-round activity and less investment in carbon and nutrients, while N-fixation enhances photosynthetic capacity. Our objective was to compare anatomy and physiology of three woody evergreens Ilex opaca Aiton (Aquifoliaceae), Kalmia latifolia L. (Ericaceae), and Myrica cerifera (Myricaceae) of varying leaf longevity, N-fixation capability, and known expansive potential in a deciduous forest understory to determine if seasonal physiological performance integrated these factors. We hypothesized that I. opaca (non-expansive) and K. latifolia (moderately expansive), which have longer leaf longevities, would have reduced physiological performance compared to M. cerifera (expansive), which has shorter leaf longevity, and symbiotically fixes atmospheric N. Stomatal conductance to water vapor, photosynthetic and hydraulic capacities, specific leaf area, and leaf %N decreased with increasing leaf life span; however, trends among species were not consistent seasonally. While hydraulic capacity remained constant throughout the year, photosynthetic capacity did not. During the growing season, M. cerifera displayed photosynthetic capacity similar to deciduous species, yet, during the winter, photosynthetic capacity was similar to the slower-growing evergreens. Reduced leaf life span, enhanced hydraulic capacity, and nitrogen fixation support the seasonal shift in photosynthetic capacity observed in M. cerifera. This “hybrid” strategy enables M. cerifera to maximize productivity during months of optimal conditions, thereby promoting rapid growth and expansion in the understory.     

Emerging roles for phospholipase A2 enzymes in cancer

Phospholipase A₂ (PLA₂) enzymes (EC3.1.4.4) regulate the release of biologically active fatty acids and lysophospholipids from membrane phospholipid pools. These lipids are also substrates for intracellular biochemical pathways that generate potent autocrine and paracrine lipid mediators such as the eicosanoids and platelet activating factor. These factors, in turn, regulate cell proliferation, survival, differentiation, motility, tissue vascularisation, and immune surveillance in virtually all tissues, functions that are subverted by cancer cells for tumour growth and metastasis. Thus the relevance of PLA₂-dependent pathways to the genesis and progression of cancer has been of interest since their discovery and with recent technological advances, their role in tumourigenesis has become more tractable experimentally. Limited human genetic studies have not yet identified PLA₂ enzymes as classical mutated oncogenes or tumour suppressor genes. However, there is strong evidence that of the 22 identified human PLA₂ enzymes, ten of which have been studied in cancer to date, most are aberrantly expressed in a proportion of tumours derived from diverse organs. Correlative and functional studies implicate the expression of some secreted enzymes (sPLA₂s), particularly the best studied enzyme Group IIA sPLA₂ in either tumour promotion or inhibition, depending on the organ involved and the biochemical microenvironment of tumours. As in immune-mediated inflammatory pathologies, genetic deletion studies in mice, supported by limited studies with human cells and tissues, have identified an important role for Group IVA PLA₂ in regulating certain cancers. Pharmacological intervention studies in prostate cancer suggest that hGIIA-dependent tumour growth is dependent on indirect regulation of Group IVA PLA₂. Group VI calcium-independent PLA₂ enzymes have also been recently implicated in tumourigenesis with in vitro studies suggesting multiple possible roles for these enzymes. Though apparently complex, further characterization of the regulatory relationships amongst PLA₂ enzymes, lipid mediator biosynthetic enzymes and the lipid mediators they produce during tumour progression is required to define the biochemical context in which the enzymes modulate cancer growth and development.     

Oncology drug discovery applications using the FMAT 8100 HTS system

High-throughput screening (HTS) for potential anticancer agents requires a broad portfolio of assay platforms that may include kinase enzyme assays, protein-protein binding assays, and functional cell-based apoptosis assays. The authors have explored the use of fluorometric microvolume assay technology (the FMAT 8100 HTS System) in three distinct homogeneous HTS assays: (1). a Src tyrosine kinase enzyme assay, (2). a Grb2-SH2 protein-peptide interaction assay, and (3). an annexin V binding apoptosis assay. Data obtained from all three assays suggest that the FMAT system should facilitate the implementation of homogeneous assays for a wide variety of molecular targeted and cell-based screens.     

Thinning Jeffrey pine stands to reduce susceptibility to bark beetle infestations in California,U.S.A.

• 1 Bark beetles (Coleoptera: Curculionidae, Scolytinae) are commonly recognized as important tree mortality agents in coniferous forests of the western U.S.A.
• 2 High stand density is consistently associated with bark beetle infestations in western coniferous forests, and therefore thinning has long been advocated as a preventive measure to alleviate or reduce the amount of bark beetle‐caused tree mortality.
• 3 The present study aimed to determine the effectiveness of thinning to reduce stand susceptibility to bark beetle infestations over a 10‐year period in Pinus jeffreyi forests on the Tahoe National Forest, California, U.S.A. Four treatments were replicated three times within 1‐ha square experimental plots. Treatments included thinning from below (i.e. initiating in the smallest diameter classes) to a residual target basal area (cross‐sectional area of trees at 1.37 m in height) of: (i) 18.4 m²/ha (low density thin); (ii) 27.6 m²/ha (medium density thin); (iii) 41.3 m²/ha (high density thin); and (iv) no stand manipulation (untreated control).
• 4 Throughout the present study, 107 trees died as a result of bark beetle attacks. Of these, 71% (75 trees) were Abies concolor killed by Scolytus ventralis; 20.6% (22 trees) were Pinus ponderosa killed by Dendroctonus ponderosae; 4.7% (five trees) were P. jeffreyi killed by Dendroctonus jeffreyi; 1.8% (two trees) were P. jeffreyi killed by Ips pini; 0.9% (one tree) were P. jeffreyi killed by Orthotomicus (= Ips) latidens; 0.9% (one tree) were P. ponderosa killed by both Dendroctonus brevicomis and D. ponderosae; and 0.9% (one tree) were P. jeffreyi killed by unknown causes.
• 5 In the low density thin, no pines were killed by bark beetles during the 10‐year period. Significantly fewer trees (per ha/year) were killed in the low density thin than the high density thin or untreated control. No significant treatment effect was observed for the percentage of trees (per year) killed by bark beetles.

     

Why clinically used tazobactam and sulbactam are poor inhibitors of OXA-10 beta-lactamase: Raman crystallographic evidence

The clinically used inhibitors tazobactam and sulbactam are effective in the inhibition of activity of class A beta-lactamases, but not for class D beta-lactamases. The two inhibitors exhibit a complex multistep profile for their chemistry of inhibition with class A beta-lactamases. To compare the inhibition profiles for class A and D enzymes, the reactions were investigated within OXA-10 beta-lactamase (a class D enzyme) crystals using a Raman microscope. The favored reaction pathway appears to be distinctly different from that for class A beta-lactamases. In contrast to the case of class A enzymes that favor the formation of a key enamine species, the OXA-10 enzyme forms an alpha,beta-unsaturated acrylate (acid or ester). Quantum mechanical calculations support the likely product as the adduct of Ser115 to the acrylate. Few enamine-like species are formed by sulbactam or tazobactam with this enzyme. Taken together, our results show that the facile conversion of the initial imine, formed upon acylation of the active site Ser67, to the cis- and/or trans-enamine is disfavored. Instead, there is a significant population of the imine that could either experience cross-linking to a second nucleophile (e.g., Ser115) or give rise to the alpha,beta-unsaturated product and permanent inhibition. Alternatively, the imine can undergo hydrolysis to regenerate the catalytically active OXA-10 enzyme. This last process is the dominant one for class D beta-lactamases since the enzyme is not effectively inhibited. In contrast to sulbactam and tazobactam, the reactions between oxacillin or 6alpha-hydroxyisopropylpenicillinate (both substrates) and OXA-10 beta-lactamase appear much less complex. These compounds lead to a single acyl-enzyme species, the presence of which was confirmed by Raman and MALDI-TOF experiments.     

Activation of the phosphatidylinositol 3-kinase Vps34 by a G protein alpha subunit at the endosome

In the yeast Saccharomyces cerevisiae, the G protein beta gamma subunits are essential for pheromone signaling. The Galpha subunit Gpa1 can also promote signaling, but the effectors in this pathway are not well characterized. To identify candidate Gpa1 effectors, we expressed the constitutively active Gpa1(Q323L) mutant in each of nearly 5000 gene-deletion strains and measured mating-specific responses. Our analysis reveals a requirement for both the catalytic (Vps34) and regulatory (Vps15) subunits of the sole phosphatidylinositol 3-kinase in yeast. We demonstrate that Gpa1 is present at endosomes, where it interacts directly with both Vps34 and Vps15 and stimulates increased production of phosphatidylinositol 3-phosphate. Notably, Vps15 binds to GDP-bound Gpa1 and is predicted to have a seven-WD repeat structure similar to that of known G protein beta subunits. These findings reveal two new components of the pheromone signaling pathway. More remarkably, these proteins appear to comprise a preformed effector-G beta subunit assembly and function at the endosome rather than at the plasma membrane.