The Arabidopsis transposable element Tag1 is widely distributed among Arabidopsis ecotypes

Tag1 is an autonomous transposable element (3.3 kb in length) first identified as an insertion in the CHL1 (NRT1) gene of Arabidopsis thaliana. Tag1 has been found in the Landsberg erecta ecotype of A. thaliana but not in Columbia or WS. In this paper, 41 additional ecotypes were examined for the presence of Tag1. Using an internal Tag1 fragment as probe, we found that DNA from 19 of the 41 ecotypes strongly hybridized to Tag1. Almost all of the Tag1-containing ecotypes had only one or two copies of Tag1 per haploid genome, as determined by Southern blot analysis. The only exception, Bf-1 from Bretagny-sur-Orge, France, had four copies. Two ecotypes, Di-G and S96, gave identical Southern blot patterns to that of Landsberg erecta and were subsequently shown to contain Tag1 at the same two positions found in Landsberg erecta (loci designated as Tag1-2 and Tag1-3). Two other ecotypes, Ag-0 and Lo-1, had a Tag1 element located at Tag1-2 but not at Tag1-3. The distance between these two loci was determined to be 0.37 cM. Analysis of DNA from two related species, A. griffithiana and A. pumila, showed that both species contain sequences that hybridize to Tag1 and that could be amplified with an oligonucleotide specific to the terminal inverted repeats of Tag1. These results show that Tag1 and related elements are present, and may be useful for insertional mutagenesis, in many A. thaliana ecotypes and several Arabidopsis species. Received: 18 August 1997 / Accepted: 9 October 1997     

LAP5 and LAP6 Encode Anther-Specific Proteins with Similarity to Chalcone Synthase Essential for Pollen Exine Development in Arabidopsis

Pollen grains of land plants have evolved remarkably strong outer walls referred to as exine that protect pollen and interact with female stigma cells. Exine is composed of sporopollenin, and while the composition and synthesis of this biopolymer are not well understood, both fatty acids and phenolics are likely components. Here, we describe mutations in the Arabidopsis (Arabidopsis thaliana) LESS ADHESIVE POLLEN (LAP5) and LAP6 that affect exine development. Mutation of either gene results in abnormal exine patterning, whereas pollen of double mutants lacked exine deposition and subsequently collapsed, causing male sterility. LAP5 and LAP6 encode anther-specific proteins with homology to chalcone synthase, a key flavonoid biosynthesis enzyme. lap5 and lap6 mutations reduced the accumulation of flavonoid precursors and flavonoids in developing anthers, suggesting a role in the synthesis of phenolic constituents of sporopollenin. Our in vitro functional analysis of LAP5 and LAP6 using 4-coumaroyl-coenzyme A yielded bis-noryangonin (a commonly reported derailment product of chalcone synthase), while similar in vitro analyses using fatty acyl-coenzyme A as the substrate yielded medium-chain alkyl pyrones. Thus, in vitro assays indicate that LAP5 and LAP6 are multifunctional enzymes and may play a role in both the synthesis of pollen fatty acids and phenolics found in exine. Finally, the genetic interaction between LAP5 and an anther gene involved in fatty acid hydroxylation (CYP703A2) demonstrated that they act synergistically in exine production.Pollen grains of land plants are surrounded by complex cell walls that are divided into three layers: (1) an outer exine, itself a multilayered structure, primarily made of sporopollenin; (2) an inner intine, made primarily of cellulose; and (3) a lipid- and protein-rich pollen coat in the crevices of exine. The exine is morphologically diverse, provides protection against environmental stresses and bacterial and fungal attacks, and plays a role in species-specific adhesion (Zinkl et al., 1999; Edlund et al., 2004).Several studies indicate that sporopollenin is a complex polymer composed of fatty acids and phenolic compounds (Guilford et al., 1988; Ahlers et al., 1999; Wiermann et al., 2001). Sporopollenin is remarkably strong and chemically resistant, making it difficult to determine its precise composition by direct chemical analysis. Ozonolysis has yielded simple straight- and branched-chain monocarboxylic acids, typical of fatty acid breakdown (Shaw, 1971), as well as phenolic acids, such as p-hydroxybenzoic, m-hydroxybenzoic, and protocatechuic acids. Additional evidence for phenolic compounds came from degradation experiments or studies showing the incorporation of radiolabeled Phe and p-coumaric acid into sporopollenin (Shulze Osthoff and Wiermann, 1987; Rittscher and Wiermann, 1988; Gubatz et al., 1993), while immunolocalization studies with anti-p-coumaric acid antibodies demonstrated the occurrence of phenols in exines of different plant species (Niester-Nyveld et al., 1997).While a growing number of genes have been identified that are important for exine development, still relatively little is known about the genetic network that governs the formation of this structure, and the pathways that lead to its biosynthesis are far from being understood. In recent years, the importance of fatty acid-derived components in sporopollenin composition has been revealed through the identification of several Arabidopsis (Arabidopsis thaliana) genes, such as MALE STERILITY2 (MS2; Aarts et al., 1997), cytochrome P450 CYP703A2 (Morant et al., 2007), cytochrome P450 CYP704B1 (Dobritsa et al., 2009), and ACYL-CoA SYNTHETASE5 (ACOS5; de Azevedo Souza et al., 2009), which are important for exine production and involved in fatty acid metabolism. Less is known concerning the role of phenolics in sporopollenin biosynthesis, and the key synthetic and regulatory genes specifically associated with this aspect of sporopollenin biosynthesis are absent from the literature.Phenolic compounds are a large class of secondary metabolites that play a variety of biological roles (Hahlbrock and Scheel, 1989). Most plant phenolics are products of phenylpropanoid metabolism, including lignins, coumarins, stilbenes, and flavonoids. A well-characterized biosynthetic pathway leads to the biosynthesis of flavonoids (Supplemental Fig. S1). Chalcone synthase (CHS) catalyzes the first committed step in this pathway using 4-coumaroyl-CoA provided by 4-coumaroyl:CoA ligase as a substrate. Flavonoids are important for pollen germination and plant fertility in several plant species (Coe et al., 1981; Taylor and Jorgensen, 1992; van der Meer et al., 1992; Fischer et al., 1997; Napoli et al., 1999), while a null mutation in the Arabidopsis CHS gene, TRANSPARENT TESTA4 (TT4), results in plants with normal fertility and an absence of flavonoids in the mature stamens (Burbulis et al., 1996; Ylstra et al., 1996). This suggests that flavonoids are either not required for Arabidopsis male fertility or that TT4-independent flavonoid synthesis occurs in anthers, perhaps transiently and at an earlier developmental stage, through a mechanism that has not been detected in previous experiments.Recently, an anther-specific gene, ACOS5, was described that is essential for exine production and sporopollenin biosynthesis (de Azevedo Souza et al., 2009). ACOS5 is related to a phenylpropanoid enzyme, 4-coumaroyl:CoA ligase, but encodes a novel medium- to long-chain fatty acyl-CoA synthetase. In this study, we describe the identification and characterization of two highly conserved anther-specific genes that are involved in pollen exine development, likely participate in sporopollenin biosynthesis, and, similar to ACOS5, are related to, yet distinct from, an enzyme of the phenylpropanoid pathway. Our results provide further insight into the mechanism that leads to the formation of sporopollenin.     

O-linked glycans mediate apical sorting of human intestinal sucrase-isomaltase through association with lipid rafts.

The plasma membrane of polarised epithelial cells is characterised by two structurally and functionally different domains, the apical and basolateral domains. These domains contain distinct protein and lipid constituents that are sorted by specific signals to the correct surface domain [1]. The best characterised apical sorting signal is that of glycophosphatidylinositol (GPI) membrane anchors [2], although N-linked glycans on some secreted proteins [3] and O-linked glycans [4] also function as apical sorting signals. In the latter cases, however, the underlying sorting mechanisms remain obscure. Here, we have analysed the role of O-glycosylation in the apical sorting of sucrase-isomaltase (SI), a highly polarised N- and O-glycosylated intestinal enzyme, and the mechanisms underlying this process. Inhibition of O-glycosylation by benzyl-N-acetyl-alpha-D-galactosaminide (benzyl-GalNAc) was accompanied by a dramatic shift in the sorting of SI from the apical membrane to both membranes. The sorting mechanism of SI involves its association with sphingolipid- and cholesterol-rich membrane rafts because this association was eliminated when O-glycosylation was inhibited by benzyl-GaINAc. The results demonstrate for the first time that O-linked glycans mediate apical sorting through association with lipid rafts.     

Evaluating range‐expansion models for calculating nonnative species' expansion rate

Species range shifts associated with environmental change or biological invasions are increasingly important study areas. However, quantifying range expansion rates may be heavily influenced by methodology and/or sampling bias. We compared expansion rate estimates of Roesel''s bush-cricket (Metrioptera roeselii, Hagenbach 1822), a nonnative species currently expanding its range in south-central Sweden, from range statistic models based on distance measures (mean, median, 95^th gamma quantile, marginal mean, maximum, and conditional maximum) and an area-based method (grid occupancy). We used sampling simulations to determine the sensitivity of the different methods to incomplete sampling across the species'' range. For periods when we had comprehensive survey data, range expansion estimates clustered into two groups: (1) those calculated from range margin statistics (gamma, marginal mean, maximum, and conditional maximum: ˜3 km/year), and (2) those calculated from the central tendency (mean and median) and the area-based method of grid occupancy (˜1.5 km/year). Range statistic measures differed greatly in their sensitivity to sampling effort; the proportion of sampling required to achieve an estimate within 10% of the true value ranged from 0.17 to 0.9. Grid occupancy and median were most sensitive to sampling effort, and the maximum and gamma quantile the least. If periods with incomplete sampling were included in the range expansion calculations, this generally lowered the estimates (range 16–72%), with exception of the gamma quantile that was slightly higher (6%). Care should be taken when interpreting rate expansion estimates from data sampled from only a fraction of the full distribution. Methods based on the central tendency will give rates approximately half that of methods based on the range margin. The gamma quantile method appears to be the most robust to incomplete sampling bias and should be considered as the method of choice when sampling the entire distribution is not possible.     

Chimpanzee (Pan troglodytes) Precentral Corticospinal System Asymmetry and Handedness: A Diffusion Magnetic Resonance Imaging Study

Background

Most humans are right handed, and most humans exhibit left-right asymmetries of the precentral corticospinal system. Recent studies indicate that chimpanzees also show a population-level right-handed bias, although it is less strong than in humans.

Methodology/Principal Findings

We used in vivo diffusion-weighted and T1-weighted magnetic resonance imaging (MRI) to study the relationship between the corticospinal tract (CST) and handedness in 36 adult female chimpanzees. Chimpanzees exhibited a hemispheric bias in fractional anisotropy (FA, left>right) and mean diffusivity (MD, right>left) of the CST, and the left CST was centered more posteriorly than the right. Handedness correlated with central sulcus depth, but not with FA or MD.

Conclusions/Significance

These anatomical results are qualitatively similar to those reported in humans, despite the differences in handedness. The existence of a left>right FA, right>left MD bias in the corticospinal tract that does not correlate with handedness, a result also reported in some human studies, suggests that at least some of the structural asymmetries of the corticospinal system are not exclusively related to laterality of hand preference.     

Automatic layout and visualization of biclusters

Background  

Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these algorithms may output a very large number of biclusters with varying degrees of overlap. There are no systematic methods that create a two-dimensional layout of the computed biclusters and display overlaps between them.     

A two‐step approach to map quantitative trait loci for meat quality in connected porcine F2 crosses considering main and epistatic effects

The aim of this study was to map QTL for meat quality traits in three connected porcine F₂ crosses comprising around 1000 individuals. The three crosses were derived from the founder breeds Chinese Meishan, European Wild Boar and Pietrain. The animals were genotyped genomewide for approximately 250 genetic markers, mostly microsatellites. They were phenotyped for seven meat quality traits (pH at 45 min and 24 h after slaughter, conductivity at 45 min and 24 h after slaughter, meat colour, drip loss and rigour). QTL mapping was conducted using a two‐step procedure. In the first step, the QTL were mapped using a multi‐QTL multi‐allele model that was tailored to analyse multiple connected F₂ crosses. It considered additive, dominance and imprinting effects. The major gene RYR1:g.1843C>T affecting the meat quality on SSC6 was included as a cofactor in the model. The mapped QTL were tested for pairwise epistatic effects in the second step. All possible epistatic effects between additive, dominant and imprinting effects were considered, leading to nine orthogonal forms of epistasis. Numerous QTL were found. The most interesting chromosome was SSC6. Not all genetic variance of meat quality was explained by RYR1:g.1843C>T. A small confidence interval was obtained, which facilitated the identification of candidate genes underlying the QTL. Epistasis was significant for the pairwise QTL on SSC12 and SSC14 for pH24 and for the QTL on SSC2 and SSC5 for rigour. Some evidence for additional pairwise epistatic effects was found, although not significant. Imprinting was involved in epistasis.