Fixed and random effects selection in linear and logistic models

We address the problem of selecting which variables should be included in the fixed and random components of logistic mixed effects models for correlated data. A fully Bayesian variable selection is implemented using a stochastic search Gibbs sampler to estimate the exact model-averaged posterior distribution. This approach automatically identifies subsets of predictors having nonzero fixed effect coefficients or nonzero random effects variance, while allowing uncertainty in the model selection process. Default priors are proposed for the variance components and an efficient parameter expansion Gibbs sampler is developed for posterior computation. The approach is illustrated using simulated data and an epidemiologic example.     

Perturbation approaches for integral projection models

Perturbation analysis of population models is fundamental to elucidating mechanisms of population dynamics and examining scenarios of change. The use of integral projection models (IPMs) has increased in the last decade, and while many of the tools and approaches developed for matrix models remain relevant, the nature of IPMs expands the framework of perturbation analysis, with different approaches often requiring important considerations. This article provides a review of – and practical guide to – different perturbation approaches for IPMs, formalizes methodologies for perturbing IPM size transition probabilities, and highlights areas where researchers should be particularly careful and critical when conducting and interpreting perturbation analysis. I use a simulated dataset to compare five hierarchical perturbation approaches for IPMs found within 63 published studies, and apply a combination of approaches to the example of an invasive perennial plant. Other perturbation approaches for IPMs are also highlighted. Most perturbation analyses for IPMs to date have focused on the response of the asymptotic population growth rate (λ) to changes in elements of the discretized projection kernel and/or the growth– survival and reproduction– recruitment sub‐kernels. Perturbations to vital rate functions and regression predictions underlying these kernels provide mechanistic insight, but are less common and can require important considerations regarding the perturbation of size transitions separate from survival and the nature of the state variable (used to represent size). The second most common approach is more specific to IPMs and examines the influence of vital rate regression parameters, each of which can have broad influence on the population growth rate. Researchers using IPMs have many perturbation options available and should carefully consider which approach or combination of approaches is most applicable and interpretable for their specific questions.     

Discovery of GlyT1 inhibitors with improved pharmacokinetic properties

Glycine transporter 1 (GlyT1) represents a novel target for the treatment of schizophrenia via the potentiation of glutamatergic NMDA receptors. The discovery of 4,4-disubstituted piperidine inhibitors of GlyT1 which exhibit improved pharmacokinetic properties, including oral bioavailability, is discussed.     

Functional Characterization of Phospholipid N-Methyltransferases from Arabidopsis and Soybean

Phospholipid N-methyltransferase (PLMT) enzymes catalyze the S-adenosylmethionine-dependent methylation of ethanolamine-containing phospholipids to produce the abundant membrane lipid phosphatidylcholine (PtdCho). In mammals and yeast, PLMT activities are required for the de novo synthesis of the choline headgroup found in PtdCho. PLMT enzyme activities have also been reported in plants, yet their roles in PtdCho biosynthesis are less clear because most plants can produce the choline headgroup entirely via soluble substrates, initiated by the methylation of free ethanolamine-phosphate. To gain further insights into the function of PLMT enzymes in plants, we isolated PLMT cDNAs from Arabidopsis and soybean (Glycine max) based upon primary amino acid sequence homology to the rat PLMT, phosphatidylethanolamine N-methyltransferase. Using a heterologous yeast expression system, it was shown that plant PLMTs methylate phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine but cannot utilize phosphatidylethanolamine as a substrate. Identification of an Arabidopsis line containing a knock-out dissociator transposon insertion within the single copy AtPLMT gene allowed us to investigate the consequences of loss of PLMT function. Although the accumulation of the PLMT substrates phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine was considerably elevated in the atplmt knock-out line, PtdCho levels remained normal, and no obvious differences were observed in plant morphology or development under standard growth conditions. However, because the metabolic routes through which PtdCho is synthesized in plants vary greatly among differing species, it is predicted that the degree with which PtdCho synthesis is dependent upon PLMT activities will also vary widely throughout the plant kingdom.Phosphatidylcholine (PtdCho)2 is the most abundant phospholipid in most non-plastid membranes of eukaryotes. PtdCho biosynthesis has been studied intensively in plants not only because of its importance as a structural membrane lipid, but also because of its role as a precursor to important lipid-based signaling molecules, such as phosphatidic acid, and phospholipase A₂-derived free fatty acids (1). The choline headgroup of PtdCho serves multiple functions as well. In addition to being an essential human nutrient (2), in many plant species choline can be oxidized to produce the potent osmoprotectant glycine betaine (3, 4).For over 2 decades it has been apparent that there are fundamental differences between the manner in which PtdCho is produced in plants versus how it is synthesized in mammals and fungi. In the latter two systems, PtdCho can be formed through two distinct pathways as follows: (a) the “nucleotide pathway” in which free choline is incorporated in PtdCho using CDP-choline as an intermediate, and (b) the “methylation pathway” whereby PtdCho is produced directly from phosphatidylethanolamine (PtdEtn) via three sequential methylation reactions using S-adenosylmethionine (AdoMet) as the methyl donor (5, 6). In contrast, PtdCho biosynthesis in plants occurs through a branched pathway that utilizes components of both the nucleotide and methylation pathways (7). The greatest distinction between the contrasting mechanisms of PtdCho biosynthesis can be attributed to the presence of plant enzymes that are capable of converting ethanolamine headgroups to choline at the phospho-base level, activities that are absent in mammals and yeast. Conversely, mammals and fungi possess methylation enzymes that act directly on PtdEtn, a reaction that cannot be detected in most plant systems investigated (reviewed in Ref. 7).A diagram of the most widely accepted model of phosphoamino alcohol biosynthesis in plants is shown in Fig. 1. Similar to animals and yeast, free choline can be directly incorporated into PtdCho via nucleotide pathway enzymes in plants. In the absence of choline, however, the methylation of Etn-phosphate represents the first committed step in PtdCho biosynthesis. The resulting monomethylethanolamine-phosphate (MMEtn-P) metabolite can be further methylated at the phospho-base level to produce Cho-P. Alternatively, MMEtn-P can be incorporated into phosphatidylmonomethylethanolamine (PtdMMEtn) via the cytidylyltransferase and amino alcohol phosphotransferase activities of the nucleotide pathway and then methylated at the phosphatidyl-base level to complete the synthesis of PtdCho (Fig. 1). The extent with which PtdCho is formed by the flow of metabolites through phospho-bases as opposed to phosphatidyl-bases varies greatly among different plant species. In most higher plants, it is likely that the methylation of the phosphoamino alcohol headgroups involves the flow of metabolites through both branches of the pathway, as has been shown in species such as barley, carrot, and tobacco (3, 8, 9). Nevertheless, examples have also been reported where only one of the branches appears to be utilized. In Lemna paucicostata, for example, the methylation steps in PtdCho biosynthesis were shown to occur almost exclusively at the phospho-base level (10). At the other end of the spectrum is soybean, where all methylations beyond the initial formation of MMEtn-P were reported to occur on phosphatidyl-bases (8, 11). The tremendous variability observed among plants with regard to PtdCho formation is also exemplified by a study conducted by Williams and Harwood (12) where it was shown that the predominant route of PtdCho synthesis in olive culture cells involved the first two methylation reactions taking place at the phospho-base level (producing dimethylethanolamine phosphate) and the final methylation occurring on a phosphatidyldimethylethanolamine (PtdDMEtn) substrate.Open in a separate windowFIGURE 1.Phosphatidylcholine biosynthetic pathways. Steps common to plants, mammals, and yeast are indicated by black arrows. Dashed arrows indicate pathways specific to plants. Methylation of PtdEtn, which occurs in mammals and yeast, is indicated by on open arrow. Enzymes catalyzing phosphoamino alcohol methylation reactions in plants, mammals, and yeast are indicated.Our understanding on the mechanisms by which plants synthesize PtdCho and regulate its accumulation has been further enhanced as the genes encoding the various steps of the phosphoamino alcohol pathway have been isolated and characterized. For example, molecular characterizations led to the conclusion that all of the amino alcohol phosphotransferase reactions depicted in Fig. 1 can be mediated by the product of a single gene (designated AAPT1) that displays a broad substrate specificity (13, 14). Similarly, it was the isolation of the phosphoethanolamine methyltransferase (PEAMT) genes from Arabidopsis and spinach that led to the discovery that all three phospho-base methylation reactions could be catalyzed by a single enzyme (15, 16). Inhibition of PEAMT gene function in Arabidopsis through T-DNA insertion or co-suppression revealed unexpected associations between the phosphoamino alcohol pathway and root development, salt hypersensitivity, and male sterility (17, 18).Although most of the reactions depicted in Fig. 1 have been characterized at the molecular genetic level, conspicuously absent is information on the plant genes/enzymes responsible for the methylation reactions conducted at the phosphatidyl-base level. In contrast, these reactions are among the most well characterized in animals and yeast, catalyzed by enzymes commonly referred to as phospholipid N-methyltransferases (PLMTs). In mammals, the 18-kDa integral membrane protein phosphatidylethanolamine N-methyltransferase (PEMT) is a PLMT that is expressed primarily in the liver (19). PEMT catalyzes all three of the methylation reactions needed to convert PtdEtn to PtdCho. Yeast uses two distinct PLMT enzymes to catalyze the three methylation reactions as follows: Cho2p/Pem1p that mediates the direct methylation of PtdEtn to produce PtdMMEtn (20, 21), and Opi3p/Pem2p, an enzyme homologous to the mammalian PEMT, that primarily catalyzes the methylation of PtdMMEtn to PtdDMEtn and PtdDMEtn to PtdCho, the final two steps of the methylation pathway (20, 22). PLMT activities are critical in both of these systems. Mice possessing pemt knock-out mutations are completely dependent on dietary choline for survival, and they display abnormal levels of choline metabolites within the liver and develop hepatic steatosis even when fed diets supplemented with choline (23). Yeast lacking PLMT activities (cho2/opi3 double mutants) are obligate choline auxotrophs, unable to synthesize PtdCho de novo in the absence of exogenous choline.To gain a greater understanding of the specific function of PLMT reactions in higher plants, and their contribution toward PtdCho biosynthesis, we cloned and characterized PLMT homologs from Arabidopsis and soybean. By expressing the candidate cDNAs in yeast, we were able to confirm that they encoded functional PLMT activities as well as to establish their substrate specificities. We also identified a mutant Arabidopsis line containing a knock-out allele in the single copy PLMT gene found in the Arabidopsis genome, allowing us to characterize the consequences of loss of gene function in this model species.     

The Influence of Physical Habitat,Pyrethroids, and Metals on Benthic Community Condition in an Urban and Residential Stream in California

This study was designed to characterize benthic communities and physical habitat in both an urban (Kirker Creek) and residential (Pleasant Grove Creek) stream in California in late spring of 2006 and 2007. Concurrent water quality evaluations, physical sediment parameters, pyrethroids, bulk metals, and SEM/AVS ratios were also measured during both years of this study. The relationship of various benthic metrics to physical habitat metrics, pyrethroids, and metals was evaluated for each stream using stepwise multiple linear regressions with both years combined for each stream, as well as both years and both streams combined, to increase the statistical power for determining significant relationships. Physical habitat was determined to be poor in each stream during both years of sampling. More than 100 benthic taxa were reported annually for both streams based on 2006 and 2007 sampling. A significant result from the stepwise regression analysis combining data for 2 years across both streams is that when habitat metrics and to a lesser degree metals are considered in the statistical models pyrethroids do not display any significant relationships to the benthic metrics. In summary, it is apparent from this analysis that the health of benthic communities in both streams is primarily affected by habitat metrics.     

Skewed X Chromosome Inactivation and Trisomic Spontaneous Abortion: No Association

Several studies suggest that highly skewed X chromosome inactivation (HSXI) is associated with recurrent spontaneous abortion. We hypothesized that this association reflects an increased rate of trisomic conceptions due to anomalies on the X chromosome that lead both to HSXI and to a diminished oocyte pool. We compared the distribution of X chromosome inactivation (XCI) skewing percentages (range: 50%–100%) among women with spontaneous abortions in four karyotype groups—trisomy (n = 154), chromosomally normal male (n = 43), chromosomally normal female (n = 38), nontrisomic chromosomally abnormal (n = 61)—to the distribution for age-matched controls with chromosomally normal births (n = 388). In secondary analyses, we subdivided the nontrisomic chromosomally abnormal group, divided trisomies by chromosome, and classified women by reproductive history. Our data support neither an association of HSXI with all trisomies nor an association of HSXI with chromosomally normal male spontaneous abortions. We also find no association between HSXI and recurrent abortion (n = 45).     

The deubiquitinase CYLD targets Smad7 protein to regulate transforming growth factor β (TGF-β) signaling and the development of regulatory T cells

CYLD is a lysine 63-deubiquitinating enzyme that inhibits NF-κB and JNK signaling. Here, we show that CYLD knock-out mice have markedly increased numbers of regulatory T cells (Tregs) in peripheral lymphoid organs but not in the thymus. In vitro stimulation of CYLD-deficient naive T cells with anti-CD3/28 in the presence of TGF-β led to a marked increase in the number of Foxp3-expressing T cells when compared with stimulated naive control CD4(+) cells. Under endogenous conditions, CYLD formed a complex with Smad7 that facilitated CYLD deubiquitination of Smad7 at lysine 360 and 374 residues. Moreover, this site-specific ubiquitination of Smad7 was required for activation of TAK1 and p38 kinases. Finally, knockdown of Smad7 or inhibition of p38 activity in primary T cells impaired Treg differentiation. Together, our results show that CYLD regulates TGF-β signaling function in T cells and the development of Tregs through deubiquitination of Smad7.