Effect of deuteration on the phase behaviour and structure of lamellar phases of phosphatidylcholines - Deuterated lipids as proxies for the physical properties of native bilayers.

Deuteration of phospholipids is a common practice to elucidate membrane structure, dynamics and function, by providing selective visualisation in neutron scattering, nuclear magnetic resonance and vibrational spectroscopy. It is generally assumed that the properties of the deuterated lipids are identical to those of the protiated lipids, and while a number of papers have compared the properties of different forms, to date this has been no systematic study of the effects over a range of conditions. Here we present a study of the effects of deuteration on the organisation and phase behaviour of four common phospholipids (DSPC, DPPC, DMPC, DOPC), observing the effect of chain deuteration and headgroup deuteration on lipid structure and phase behaviour. For saturated lipids in excess water the gel-fluid phase transition temperature is 4.3 ± 0.1 °C lower for lipids with deuterated chains compared to protiated chains, consistent with previous work. Despite this significant change, well away from the transition structural changes as measured by powder small angle X-ray scattering are small and within errors. To investigate this further, measurements were carried out on oriented multilamellar stacks of DOPC in the fluid phase at reduced hydration. Neutrons are used in conjunction with contrast variation to elucidate the role of the deuteration explicitly. It is found that deuterated chains cause a reduction in the lamellar repeat spacing and bilayer thickness, but deuterated headgroups cause an increase. Consequences for the interpretation of Neutron Scattering data with deuterated lipids are discussed.

Mixed-Metal Hybrid Polyoxometalates with Amino Acid Ligands: Electronic Versatility and Solution Properties.

Eight new members of a family of mixed-metal (Mo,W) polyoxometalates (POMs) with amino acid ligands have been synthesized and investigated in the solid state and solution using multiple physical techniques. While the peripheral POM structural framework is conserved, the different analogues vary in nuclearity of the central metal-oxo core, overall redox state, metal composition, and identity of the zwitterionic α-amino acid ligands. Structural investigations reveal site-selective substitution of Mo for W, with a strong preference for Mo to occupy the central metal-oxo core. This core structural unit is a closed tetrametallic loop in the blue reduced species and an open trimetallic loop in the colorless oxidized analogues. Density functional theory calculations suggest the core as the favored site of reduction and reveal that the corresponding molecular orbital is much lower in energy for a tetra- versus trimetallic core. The reduced species are diamagnetic, each with a pair of strongly antiferromagnetically coupled MoV centers in the tetrametallic core, while in the oxidized complexes all Mo is hexavalent. Solution small-angle X-ray scattering and circular dichroism (CD) studies indicate that the hybrid POM is stable in aqueous solution on a time scale of days within defined concentration and pH ranges, with the stability enhanced by the presence of excess amino acid. The CD experiments also reveal that the amino acid ligands readily exchange with other α-amino acids, and it is possible to isolate the products of amino acid exchange, confirming retention of the POM framework. Cyclic voltammograms of the reduced species exhibit an irreversible oxidation process at relatively low potential, but an equivalent reductive process is not evident for the oxidized analogues. Despite their overall structural similarity, the oxidized and 2e-reduced hybrid POMs are not interconvertible because of the respective open- versus closed-loop arrangement in the central metal-oxo cores.

Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross.

Cryptic genetic variants that do not typically influence traits can interact epistatically with each other and mutations to cause unexpected phenotypes. To improve understanding of the genetic architectures and molecular mechanisms that underlie these interactions, we comprehensively dissected the genetic bases of 17 independent instances of the same cryptic colony phenotype in a yeast cross. In eight cases, the phenotype resulted from a genetic interaction between a de novo mutation and one or more cryptic variants. The number and identities of detected cryptic variants depended on the mutated gene. In the nine remaining cases, the phenotype arose without a de novo mutation due to two different classes of higher-order genetic interactions that only involve cryptic variants. Our results may be relevant to other species and disease, as most of the mutations and cryptic variants identified in our study reside in components of a partially conserved and oncogenic signalling pathway.

Multi-locus Genotypes Underlying Temperature Sensitivity in a Mutationally Induced Trait.

Determining how genetic variation alters the expression of heritable phenotypes across conditions is important for agriculture, evolution, and medicine. Central to this problem is the concept of genotype-by-environment interaction (or 'GxE'), which occurs when segregating genetic variation causes individuals to show different phenotypic responses to the environment. While many studies have sought to identify individual loci that contribute to GxE, obtaining a deeper understanding of this phenomenon may require defining how sets of loci collectively alter the relationship between genotype, environment, and phenotype. Here, we identify combinations of alleles at seven loci that control how a mutationally induced colony phenotype is expressed across a range of temperatures (21, 30, and 37 °C) in a panel of yeast recombinants. We show that five predominant multi-locus genotypes involving the detected loci result in trait expression with varying degrees of temperature sensitivity. By comparing these genotypes and their patterns of trait expression across temperatures, we demonstrate that the involved alleles contribute to temperature sensitivity in different ways. While alleles of the transcription factor MSS11 specify the potential temperatures at which the trait can occur, alleles at the other loci modify temperature sensitivity within the range established by MSS11 in a genetic background- and/or temperature-dependent manner. Our results not only represent one of the first characterizations of GxE at the resolution of multi-locus genotypes, but also provide an example of the different roles that genetic variants can play in altering trait expression across conditions.

Transcriptional Derepression Uncovers Cryptic Higher-Order Genetic Interactions.

Disruption of certain genes can reveal cryptic genetic variants that do not typically show phenotypic effects. Because this phenomenon, which is referred to as 'phenotypic capacitance', is a potential source of trait variation and disease risk, it is important to understand how it arises at the genetic and molecular levels. Here, we use a cryptic colony morphology trait that segregates in a yeast cross to explore the mechanisms underlying phenotypic capacitance. We find that the colony trait is expressed when a mutation in IRA2, a negative regulator of the Ras pathway, co-occurs with specific combinations of cryptic variants in six genes. Four of these genes encode transcription factors that act downstream of the Ras pathway, indicating that the phenotype involves genetically complex changes in the transcriptional regulation of Ras targets. We provide evidence that the IRA2 mutation reveals the phenotypic effects of the cryptic variants by disrupting the transcriptional silencing of one or more genes that contribute to the trait. Supporting this role for the IRA2 mutation, deletion of SFL1, a repressor that acts downstream of the Ras pathway, also reveals the phenotype, largely due to the same cryptic variants that were detected in the IRA2 mutant cross. Our results illustrate how higher-order genetic interactions among mutations and cryptic variants can result in phenotypic capacitance in specific genetic backgrounds, and suggests these interactions might reflect genetically complex changes in gene expression that are usually suppressed by negative regulation.

Higher-order genetic interactions and their contribution to complex traits.

The contribution of genetic interactions involving three or more loci to complex traits is poorly understood. These higher-order genetic interactions (HGIs) are difficult to detect in genetic mapping studies, therefore, few examples of them have been described. However, the lack of data on HGIs should not be misconstrued as proof that this class of genetic effect is unimportant. To the contrary, evidence from model organisms suggests that HGIs frequently influence genetic studies and contribute to many complex traits. Here, we review the growing literature on HGIs and discuss the future of research on this topic.

Modular molecules: site-selective metal substitution, photoreduction, and chirality in polyoxometalate hybrids.

The first members of a promising new family of hybrid amino acid-polyoxometalates have emerged from a search for modular functional molecules. Incorporation of glycine (Gly) or norleucine (Nle) ligands into an yttrium-tungstoarsenate structural backbone, followed by crystallization with p-methylbenzylammonium (p-MeBzNH3(+)) cations, affords (p-MeBzNH3)6K2(GlyH)[As(III)4(Y(III)W(VI)3)W(VI)44Y(III)4O159(Gly)8(H2O)14]⋅47 H2O (1) and enantiomorphs (p-MeBzNH3)15(NleH)3[As(III)4(Mo(V)2Mo(VI)2)W(VI)44Y(III)4O160(Nle)9(H2O)11][As(III)4(Mo(VI)2W(VI)2)W(VI)44Y(III)4O160(Nle)9(H2O)11] (generically designated 2: L-Nle, 2 a; D-Nle, 2 b). An intensive structural, spectroscopic, electrochemical, magnetochemical and theoretical investigation has allowed the elucidation of site-selective metal substitution and photoreduction of the tetranuclear core of the hybrid polyanions. In the solid state, markedly different crystal packing is evident for the compounds, which indicates the role of noncovalent interactions involving the amino acid ligands. In solution, mass spectrometric and small-angle X-ray scattering studies confirm maintenance of the structure of the polyanions of 2, while circular dichroism demonstrates that the chirality is also maintained. The combination of all of these features in a single modular family emphasizes the potential of such hybrid polyoxometalates to provide nanoscale molecular materials with tunable properties.

Genetic interactions involving five or more genes contribute to a complex trait in yeast.

Recent research suggests that genetic interactions involving more than two loci may influence a number of complex traits. How these 'higher-order' interactions arise at the genetic and molecular levels remains an open question. To provide insights into this problem, we dissected a colony morphology phenotype that segregates in a yeast cross and results from synthetic higher-order interactions. Using backcrossing and selective sequencing of progeny, we found five loci that collectively produce the trait. We fine-mapped these loci to 22 genes in total and identified a single gene at each locus that caused loss of the phenotype when deleted. Complementation tests or allele replacements provided support for functional variation in these genes, and revealed that pre-existing genetic variants and a spontaneous mutation interact to cause the trait. The causal genes have diverse functions in endocytosis (END3), oxidative stress response (TRR1), RAS-cAMP signalling (IRA2), and transcriptional regulation of multicellular growth (FLO8 and MSS11), and for the most part have not previously been shown to exhibit functional relationships. Further efforts uncovered two additional loci that together can complement the non-causal allele of END3, suggesting that multiple genotypes in the cross can specify the same phenotype. Our work sheds light on the complex genetic and molecular architecture of higher-order interactions, and raises questions about the broader contribution of such interactions to heritable trait variation.

RNA-driven genetic changes in bacteria and in human cells.

As recently demonstrated in the yeast Saccharomyces cerevisiae model organism using synthetic RNA-containing oligonucleotides (oligos), RNA can serve as a template for DNA synthesis at the chromosomal level during the process of double-strand break (DSB) repair. Herein we show that the phenomenon of RNA-mediated DNA modification and repair is not limited to yeast cells. A tract of six ribonucleotides embedded in single-strand DNA oligos corresponding to either lagging or leading strand sequences could serve as a template to correct a defective lacZ marker gene in the chromosome of the bacterium Escherichia coli. In order to test the capacity of RNA to modify DNA in mammalian cells, we utilized DNA oligos containing an embedded tract of six ribonucleotides, as well as oligos mostly made of RNA. These oligos were designed to repair a chromosomal break generated within a copy of the green fluorescent protein (GFP) gene randomly integrated into the genome of human HEK-293 cells. We show that these RNA-containing oligos can serve as templates to repair a DSB in human cells and can introduce base changes into genomic or plasmid DNA. In both E. coli and human cells, the strand bias of chromosomal gene correction by the single-strand RNA-containing oligos was the same as that obtained for the corresponding DNA molecules. Therefore, the RNA-containing oligos are not converted into a cDNA before annealing with complementary DNA. Overall, we demonstrate that in both bacterial and human cells, as in yeast, RNA sequences can have a direct role in DNA genetic modification and remodeling.