DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women

Background

High frequency of physical aggression is the central feature of severe conduct disorder and is associated with a wide range of social, mental and physical health problems. We have previously tested the hypothesis that differential DNA methylation signatures in peripheral T cells are associated with a chronic aggression trajectory in males. Despite the fact that sex differences appear to play a pivotal role in determining the development, magnitude and frequency of aggression, most of previous studies focused on males, so little is known about female chronic physical aggression. We therefore tested here whether or not there is a signature of physical aggression in female DNA methylation and, if there is, how it relates to the signature observed in males.

Methodology/Principal Findings

Methylation profiles were created using the method of methylated DNA immunoprecipitation (MeDIP) followed by microarray hybridization and statistical and bioinformatic analyses on T cell DNA obtained from adult women who were found to be on a chronic physical aggression trajectory (CPA) between 6 and 12 years of age compared to women who followed a normal physical aggression trajectory. We confirmed the existence of a well-defined, genome-wide signature of DNA methylation associated with chronic physical aggression in the peripheral T cells of adult females that includes many of the genes similarly associated with physical aggression in the same cell types of adult males.

Conclusions

This study in a small number of women presents preliminary evidence for a genome-wide variation in promoter DNA methylation that associates with CPA in women that warrant larger studies for further verification. A significant proportion of these associations were previously observed in men with CPA supporting the hypothesis that the epigenetic signature of early life aggression in females is composed of a component specific to females and another common to both males and females.     

Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast

Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAs. We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ribosome, is formed between the 5′-end of 25S and the 3′-end of 5.8S rRNAs. Previously we demonstrated that formation of this structure was critical for pre-rRNA processing in yeast. Here we show that there are no sequence-specific recognition elements within the ITS2-proximal stem, rather the structure of this stem is critical for processing. This stem cannot exceed a specific length, but there are different length restrictions for different regions within this tripartite stem. Neither the conserved unpaired nucleotides within the stem nor the sequence of the mature rRNA at the processing sites are required for processing. Collectively, these results suggest a measuring model whereby initial cleavage within ITS2 at the C2 processing site and termination of subsequent exonuclease activity yielding the mature termini are affected by the relative position of sequence and structural elements within the ITS2-proximal stem.     

Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order

A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N/RBP56), alpha-2-plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi-directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-NPEPPS-TAF2N-SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.     

Importance of factors determining the effective lifetime of a mass, long-lasting, insecticidal net distribution: a sensitivity analysis

Background

Long-lasting insecticidal nets (LLINs) reduce malaria transmission by protecting individuals from infectious bites, and by reducing mosquito survival. In recent years, millions of LLINs have been distributed across sub-Saharan Africa (SSA). Over time, LLINs decay physically and chemically and are destroyed, making repeated interventions necessary to prevent a resurgence of malaria. Because its effects on transmission are important (more so than the effects of individual protection), estimates of the lifetime of mass distribution rounds should be based on the effective length of epidemiological protection.

Methods

Simulation models, parameterised using available field data, were used to analyse how the distribution's effective lifetime depends on the transmission setting and on LLIN characteristics. Factors considered were the pre-intervention transmission level, initial coverage, net attrition, and both physical and chemical decay. An ensemble of 14 stochastic individual-based model variants for malaria in humans was used, combined with a deterministic model for malaria in mosquitoes.

Results

The effective lifetime was most sensitive to the pre-intervention transmission level, with a lifetime of almost 10 years at an entomological inoculation rate of two infectious bites per adult per annum (ibpapa), but of little more than 2 years at 256 ibpapa. The LLIN attrition rate and the insecticide decay rate were the next most important parameters. The lifetime was surprisingly insensitive to physical decay parameters, but this could change as physical integrity gains importance with the emergence and spread of pyrethroid resistance.

Conclusions

The strong dependency of the effective lifetime on the pre-intervention transmission level indicated that the required distribution frequency may vary more with the local entomological situation than with LLIN quality or the characteristics of the distribution system. This highlights the need for malaria monitoring both before and during intervention programmes, particularly since there are likely to be strong variations between years and over short distances. The majority of SSA's population falls into exposure categories where the lifetime is relatively long, but because exposure estimates are highly uncertain, it is necessary to consider subsequent interventions before the end of the expected effective lifetime based on an imprecise transmission measure.     

Interaction with functional membrane proteins--a common mechanism of toxicity for lipophilic environmental chemicals?

1. The effects of several phenols, anilines and aliphatic alcohols on yeast plasma membrane H(+)-ATPase and purine transport system as well as on Na+, K(+)-ATPase and adenosine uptake by Chinese hamster ovary cells (CHO) were investigated. 2. In all cases an inhibition was observed, which could be correlated with the octanol/water partition coefficients of the substances tested, thus making quantitative structure-activity predictions possible. 3. The observed effects correlated well with the influence of the chemicals on cell growth. 4. The results suggest a common mechanism of toxicity by the action of hydrophobic xenobiotics on biomembranes.     

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Background

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Results

Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3.

Conclusions

The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1597-y) contains supplementary material, which is available to authorized users.     

An improved neutral landscape model for recreating real landscapes and generating landscape series for spatial ecological simulations

Many studies have assessed the effect of landscape patterns on spatial ecological processes by simulating these processes in computer‐generated landscapes with varying composition and configuration. To generate such landscapes, various neutral landscape models have been developed. However, the limited set of landscape‐level pattern variables included in these models is often inadequate to generate landscapes that reflect real landscapes. In order to achieve more flexibility and variability in the generated landscapes patterns, a more complete set of class‐ and patch‐level pattern variables should be implemented in these models. These enhancements have been implemented in Landscape Generator (LG), which is a software that uses optimization algorithms to generate landscapes that match user‐defined target values. Developed for participatory spatial planning at small scale, we enhanced the usability of LG and demonstrated how it can be used for larger scale ecological studies. First, we used LG to recreate landscape patterns from a real landscape (i.e., a mountainous region in Switzerland). Second, we generated landscape series with incrementally changing pattern variables, which could be used in ecological simulation studies. We found that LG was able to recreate landscape patterns that approximate those of real landscapes. Furthermore, we successfully generated landscape series that would not have been possible with traditional neutral landscape models. LG is a promising novel approach for generating neutral landscapes and enables testing of new hypotheses regarding the influence of landscape patterns on ecological processes. LG is freely available online.     

Unidirectional Movement of Cellulose Synthase Complexes in Arabidopsis Seed Coat Epidermal Cells Deposit Cellulose Involved in Mucilage Extrusion,Adherence, and Ray Formation

CELLULOSE SYNTHASE5 (CESA5) synthesizes cellulose necessary for seed mucilage adherence to seed coat epidermal cells of Arabidopsis (Arabidopsis thaliana). The involvement of additional CESA proteins in this process and details concerning the manner in which cellulose is deposited in the mucilage pocket are unknown. Here, we show that both CESA3 and CESA10 are highly expressed in this cell type at the time of mucilage synthesis and localize to the plasma membrane adjacent to the mucilage pocket. The isoxaben resistant1-1 and isoxaben resistant1-2 mutants affecting CESA3 show defects consistent with altered mucilage cellulose biosynthesis. CESA3 can interact with CESA5 in vitro, and green fluorescent protein-tagged CESA5, CESA3, and CESA10 proteins move in a linear, unidirectional fashion around the cytoplasmic column of the cell, parallel with the surface of the seed, in a pattern similar to that of cortical microtubules. Consistent with this movement, cytological evidence suggests that the mucilage is coiled around the columella and unwinds during mucilage extrusion to form a linear ray. Mutations in CESA5 and CESA3 affect the speed of mucilage extrusion and mucilage adherence. These findings imply that cellulose fibrils are synthesized in an ordered helical array around the columella, providing a distinct structure to the mucilage that is important for both mucilage extrusion and adherence.The epidermal cells of Arabidopsis (Arabidopsis thaliana) seed coats produce two distinct secondary cell walls: pectin-rich mucilage and cellulose-rich columellae (Western et al., 2000). When seeds are hydrated, mucilage expands rapidly, rupturing the outer tangential cell wall and forming a mucilage capsule that surrounds the seed. Seed coat mucilage is composed primarily of rhamnogalacturonan I (RG I) and also contains homogalacturonan (HG), hemicelluloses (such as xylans and glucomannans), and cellulose (for review, see Haughn and Western, 2012). Extruded mucilage consists of an outer, nonadherent fraction and an inner, adherent fraction (Western et al., 2000, 2001; Macquet et al., 2007a). The adherent and nonadherent mucilage layers differ in the amount of methylesterified HG (Rautengarten et al., 2008; Saez-Aguayo et al., 2013; Voiniciuc et al., 2013), galactans (Dean et al., 2007; Macquet et al., 2007b), arabinans (Arsovski et al., 2009), mannans (Yu et al., 2014), and cellulose (Harpaz-Saad et al., 2011; Mendu et al., 2011; Sullivan et al., 2011), all of which influence the physical properties of the layers.Adherent mucilage has a distinct structure, which can be examined using cell wall dyes and antibodies. When treated with cellulose-specific dyes, densely stained rays extend from the top of each columella to the outer edge of the adherent layer, many cell lengths above the seed surface (Mendu et al., 2011; Sullivan et al., 2011). Cytological evidence indicates that cellulose, pectins, and mannans are components of the ray (Haughn and Western, 2012; Griffiths et al., 2014; North et al., 2014; Yu et al., 2014), although the exact manner in which they are assembled is unknown.Cellulose is abundant in mucilage rays and mediates adherence. Loss-of-function mutations in CELLULOSE SYNTHASE5 (CESA5) result in reduced cellulose levels and increased detachment of mucilage from the seed (Harpaz-Saad et al., 2011; Mendu et al., 2011; Sullivan et al., 2011; Griffiths et al., 2014). How a reduction in cellulose results in a loss of adherence is still unknown, but it likely involves interaction with other mucilage components such as pectin and arabinogalactan proteins (Griffiths et al., 2014). Since cesa5 mutants still have some cellulose in the rays of the adherent mucilage halo (Mendu et al., 2011; Sullivan et al., 2011), additional cellulose synthases must be involved in mucilage cellulose biosynthesis.The Arabidopsis genome encodes 10 different CESAs (Delmer, 1999; Richmond and Somerville, 2000). Multiple lines of evidence suggest that three different CESAs are required to form one active cellulose synthase complex (CSC; for review, see Somerville, 2006). CSCs are membrane-bound protein complexes that synthesize cellulose microfibrils in the apoplast (for review, see Somerville, 2006; Endler and Persson, 2011; Lei et al., 2012). CESA1, CESA3, and CESA6 are considered the core components of the primary wall CSC (Desprez et al., 2007; Persson et al., 2007). CESA2, CESA5, and CESA9 are partially redundant to CESA6 in primary wall biosynthesis, and genetic evidence suggests that each of these CESA polypeptides can form a functional CSC with CESA3 and CESA1 (Desprez et al., 2007; Persson et al., 2007). CESA10 is expressed in young plants, stems, floral tissue, and the base of rosette leaves (Beeckman et al., 2002; Doblin et al., 2002), but its function in cellulose biosynthesis is unclear. Other cesa mutant lines have been examined for altered mucilage phenotypes (cesa1, radially swollen1 [Burn et al., 2002; Sullivan et al., 2011], cesa2, cesa6, and cesa9 [Mendu et al., 2011]; CESA3, je5 [Sullivan et al., 2011] and cesa10-1 [Sullivan et al., 2011]); to date, only CESA5 has been shown to be required for cellulose biosynthesis during mucilage deposition.Two mutant alleles of CESA3, isoxaben resistant1-1 (ixr1-1) and ixr1-2, were isolated in a screen for resistance to the herbicide isoxaben (Scheible et al., 2001). Isoxaben inhibits the incorporation of Glc into the emerging cellulose polymer and is considered a potent and specific inhibitor of cellulose biosynthesis (Heim et al., 1990). Homozygous ixr1-1 and ixr1-2 lines show increased resistance to the herbicide, and the mutations causing this resistance were mapped to the genomic locus of CESA3 (Heim et al., 1990; Scheible et al., 2001). The ixr1-1 and ixr1-2 mutations cause amino acid substitutions near the C terminus of the CESA3 protein. ixr1-1 causes a Gly-to-Asn substitution (G998A) located in a transmembrane domain, while ixr1-2 contains a Thr-to-Ile substitution (T942I) in an apoplastic region of the protein between two transmembrane domains (Scheible et al., 2001). Recently, the ixr1-2 allele was shown to affect the velocity of CSCs in the plasma membrane, which consequently modifies cellulose crystallinity in the cell wall (Harris et al., 2012). It is not exactly clear how the ixr1-1 mutation affects cellulose biosynthesis. The effects of either of these mutations on seed coat mucilage have not been investigated.Since mucilage is composed primarily of pectins with smaller amounts of cellulose, seed coat epidermal cells represent an excellent system to study cellulose biosynthesis and interactions between cellulose and other wall components in muro. In this study, we investigated how cellulose is synthesized and deposited in seed coat epidermal cells. We show that at least three different CESA proteins are highly expressed in the seed coat epidermis during mucilage biosynthesis. These CESAs are oriented and move in a linear fashion around the cytoplasmic column of each cell in an identical pattern to cortical microtubules. In addition, we provide evidence that the adherent mucilage has a helical structure that expands and unwinds during extrusion to form the mucilage ray. We propose that during seed coat epidermal cell development, the biosynthesis of cellulose predetermines the structure of rays in the adherent mucilage layer.     

Expression of the mammalian mitochondrial genome. Role for membrane potential in the production of mature translation products

Protein synthesis was investigated in isolated mitochondria under conditions which either inhibited electron transport or uncoupled oxidative phosphorylation. In a medium containing an exogenous source of ATP and oligomycin, an inhibitor of the ATP synthase complex, incorporation of [35S]methionine into proteins is stimulated in the presence of inhibitors of the electron transport chain; substituting uncouplers of oxidative phosphorylation for the latter leads, in contrast, to a decrease in the rate of incorporation of the labeled amino acid into mitochondrial translation products. Studies on the metabolic stability of mitochondrial translation products revealed that "mature" polypeptides made in isolated mitochondria are stable as indicated by the absence of degradation during a 50 min "chase" period. Under conditions which reduce or dissipate the membrane potential, 50-60% of the newly made polypeptides (pulse) are degraded within 50 min. The kinetics of the degradation process for individual mitochondrial gene products reveal that the largest proportion of polypeptides degraded to an acid-soluble form during the chase period are abnormal proteins, likely the result of premature chain termination. Emerging as a common denominator in these studies is a role for a transmembrane potential across the inner membrane in the production of mature "stable" mitochondrial gene products.