275 research outputs found
Drag on particles in a nematic suspension by a moving nematic-isotropic interface
We report the first clear demonstration of drag on colloidal particles by a moving nematic-isotropic
interface. The balance of forces explains our observation of periodic, strip-like structures that are produced by the movement of these particles
Identification of QTLs controlling gene expression networks defined a priori
BACKGROUND: Gene expression microarrays allow the quantification of transcript accumulation for many or all genes in a genome. This technology has been utilized for a range of investigations, from assessments of gene regulation in response to genetic or environmental fluctuation to global expression QTL (eQTL) analyses of natural variation. Current analysis techniques facilitate the statistical querying of individual genes to evaluate the significance of a change in response, also known as differential expression. Since genes are also known to respond as groups due to their membership in networks, effective approaches are needed to investigate transcriptome variation as related to gene network responses. RESULTS: We describe a statistical approach that is capable of assessing higher-order a priori defined gene network response, as measured by microarrays. This analysis detected significant network variation between two Arabidopsis thaliana accessions, Bay-0 and Shahdara. By extending this approach, we were able to identify eQTLs controlling network responses for 18 out of 20 a priori-defined gene networks in a recombinant inbred line population derived from accessions Bay-0 and Shahdara. CONCLUSION: This approach has the potential to be expanded to facilitate direct tests of the relationship between phenotypic trait and transcript genetic architecture. The use of a priori definitions for network eQTL identification has enormous potential for providing direction toward future eQTL analyses
Natural Variation in Seed Very Long Chain Fatty Acid Content Is Controlled by a New Isoform of KCS18 in Arabidopsis thaliana
Abstract Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR.2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the b-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR.2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants
Defect structures and torque on an elongated colloidal particle immersed in a liquid crystal host
Combining molecular dynamics and Monte Carlo simulation we study defect
structures around an elongated colloidal particle embedded in a nematic liquid
crystal host. By studying nematic ordering near the particle and the
disclination core region we are able to examine the defect core structure and
the difference between two simulation techniques. In addition, we also study
the torque on a particle tilted with respect to the director, and modification
of this torque when the particle is close to the cell wall
Simulating Particle Dispersions in Nematic Liquid-Crystal Solvents
A new method is presented for mesoscopic simulations of particle dispersions
in nematic liquid crystal solvents. It allows efficient first-principle
simulations of the dispersions involving many particles with many-body
interactions mediated by the solvents. A simple demonstration is shown for the
aggregation process of a two dimentional dispersion.Comment: 5 pages, 5 figure
A Modular Class of Fluorescent Difluoroboranes: Synthesis, Structure, Optical Properties, Theoretical Calculations and Applications for Biological Imaging.
Ten borylated bipyridines (BOBIPYs) have been synthesized and selected structural modifications have been made that allow useful structure-optical property relationships to be gathered. These systems have been further investigated using DFT calculations and spectroscopic measurements, showing blue to green fluorescence with quantum yields up to 41 %. They allow full mapping of the structure to determine where selected functionalities can be implemented, to tune the optical properties or to incorporate linking groups. The best derivative was thus functionalised with an alkyne linker, which would enable further applications through click chemistry and in this optic, the stability of the fluorophores has been evaluated
The scale of population structure in Arabidopsis thaliana
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales
Direct measurements of the effects of salt and surfactant on interaction forces between colloidal particles at water-oil interfaces
The forces between colloidal particles at a decane-water interface, in the
presence of low concentrations of a monovalent salt (NaCl) and of the
surfactant sodium dodecylsulfate (SDS) in the aqueous subphase, have been
studied using laser tweezers. In the absence of electrolyte and surfactant,
particle interactions exhibit a long-range repulsion, yet the variation of the
interaction for different particle pairs is found to be considerable. Averaging
over several particle pairs was hence found to be necessary to obtain reliable
assessment of the effects of salt and surfactant. It has previously been
suggested that the repulsion is consistent with electrostatic interactions
between a small number of dissociated charges in the oil phase, leading to a
decay with distance to the power -4 and an absence of any effect of electrolyte
concentration. However, the present work demonstrates that increasing the
electrolyte concentration does yield, on average, a reduction of the magnitude
of the interaction force with electrolyte concentration. This implies that
charges on the water side also contribute significantly to the electrostatic
interactions. An increase in the concentration of SDS leads to a similar
decrease of the interaction force. Moreover the repulsion at fixed SDS
concentrations decreases over longer times. Finally, measurements of three-body
interactions provide insight into the anisotropic nature of the interactions.
The unique time-dependent and anisotropic interactions between particles at the
oil-water interface allow tailoring of the aggregation kinetics and structure
of the suspension structure.Comment: Submitted to Langmui
Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis
Quantitative Trait Loci (QTL) analyses in immortal populations are a powerful method for exploring the genetic mechanisms that control interactions of organisms with their environment. However, QTL analyses frequently do not culminate in the identification of a causal gene due to the large chromosomal regions often underlying QTLs. A reasonable approach to inform the process of causal gene identification is to incorporate additional genome-wide information, which is becoming increasingly accessible. In this work, we perform QTL analysis of the shade avoidance response in the Bayreuth-0 (Bay-0, CS954) x Shahdara (Sha, CS929) recombinant inbred line population of Arabidopsis. We take advantage of the complex pleiotropic nature of this trait to perform network analysis using co-expression, eQTL and functional classification from publicly available datasets to help us find good candidate genes for our strongest QTL, SAR2. This novel network analysis detected EARLY FLOWERING 3 (ELF3; AT2G25930) as the most likely candidate gene affecting the shade avoidance response in our population. Further genetic and transgenic experiments confirmed ELF3 as the causative gene for SAR2. The Bay-0 and Sha alleles of ELF3 differentially regulate developmental time and circadian clock period length in Arabidopsis, and the extent of this regulation is dependent on the light environment. This is the first time that ELF3 has been implicated in the shade avoidance response and that different natural alleles of this gene are shown to have phenotypic effects. In summary, we show that development of networks to inform candidate gene identification for QTLs is a promising technique that can significantly accelerate the process of QTL cloning
A Modular Class of Fluorescent Difluoroboranes: Synthesis, Structure, Optical Properties, Theoretical Calculations and Applications for Biological Imaging
- …