The impact of metabolism on stable isotope dynamics: a theoretical framework

Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of molecules occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of atoms occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.     

Improving adherence to medication in stroke survivors (IAMSS): a randomised controlled trial: study protocol

Background  

Adherence to therapies is a primary determinant of treatment success, yet the World Health Organisation estimate that only 50% of patients who suffer from chronic diseases adhere to treatment recommendations. In a previous project, we found that 30% of stroke patients reported sub-optimal medication adherence, and this was associated with younger age, greater cognitive impairment, lower perceptions of medication benefits and higher specific concerns about medication. We now wish to pilot a brief intervention aimed at (a) helping patients establish a better medication-taking routine, and (b) eliciting and modifying any erroneous beliefs regarding their medication and their stroke.     

A novel primary immunodeficiency with specific natural-killer cell deficiency maps to the centromeric region of chromosome 8

We describe four children with a novel primary immunodeficiency consisting of specific natural-killer (NK) cell deficiency and susceptibility to viral diseases. One child developed an Epstein-Barr virus-driven lymphoproliferative disorder; two others developed severe respiratory illnesses of probable viral etiology. The four patients are related and belong to a large inbred kindred of Irish nomadic descent, which suggests autosomal recessive inheritance of this defect. A genomewide scan identified a single 12-Mb region on chromosome 8p11.23-q11.21 that was linked to this immunodeficiency (maximum LOD score 4.51). The mapping of the disease-causing genomic region paves the way for the identification of a novel pathway governing NK cell differentiation in humans.     

Synthesis, characterization and electrochemistry of bis(3-aryl-6,6-dimethylcyclohexadienyl)ruthenium complexes

Five bis(3-aryl-6,6-dimethylcyclohexadienyl)ruthenium complexes (4a-4e) are prepared by reactions between di-μ-chlorodichlorobis[(1-3η:6-8η)-2,7-dimethyl-octadienyl]diruthenium and the corresponding dienes. The larger aryl substituents increase the barrier to rotation in 4a-4e relative to bis(3-methyl-6,6-cyclohexadienyl)ruthenium (5b). The activation parameters were determined by line-shape analysis for the exchange process in 4a: ΔG^† (183 K), 8.0 ± 0.2 kcal/mol; ΔH^†, 10.3 kcal/mol; and ΔS^†, 13 cal/mol/K. The electronic effect of the aryl substituents on the cyclohexadienyl ligand on the oxidation potential of the complex are compared to the effect of methyl substituents.     

eEF1B: At the dawn of the 21st century

Translational regulation of gene expression in eukaryotes can rapidly and accurately control cell activity in response to stimuli or when rapidly dividing. There is increasing evidence for a key role of the elongation step in this process. Elongation factor-1 (eEF1), which is responsible for aminoacyl-tRNA transfer on the ribosome, is comprised of two entities: a G-protein named eEF1A and a nucleotide exchange factor, eEF1B. The multifunctional nature of eEF1A, as well as its oncogenic potential, is currently the subject of a number of studies. Until recently, less work has been done on eEF1B. This review describes the macromolecular complexity of eEF1B, its multiple phosphorylation sites and numerous cellular partners, which lead us to suggest an essential role for the factor in the control of gene expression, particularly during the cell cycle.     

Sequencing and functional validation of the JGI Brachypodium distachyon T‐DNA collection

Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T‐DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T‐DNA collection by 21 078, bringing the overall total to 26 112. Thirty‐seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T‐DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T‐DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/ .     

Conversion of a cyclodextrin glucanotransferase into an alpha-amylase: assessment of directed evolution strategies

Glycoside hydrolase family 13 (GH13) members have evolved to possess various distinct reaction specificities despite the overall structural similarity. In this study we investigated the evolutionary input required to effeciently interchange these specificities and also compared the effectiveness of laboratory evolution techniques applied, i.e., error-prone PCR and saturation mutagenesis. Conversion of our model enzyme, cyclodextrin glucanotransferase (CGTase), into an alpha-amylase like hydrolytic enzyme by saturation mutagenesis close to the catalytic core yielded a triple mutant (A231V/F260W/F184Q) with the highest hydrolytic rate ever recorded for a CGTase, similar to that of a highly active alpha-amylase, while cyclodextrin production was virtually abolished. Screening of a much larger, error-prone PCR generated library yielded far less effective mutants. Our results demonstrate that it requires only three mutations to change CGTase reaction specificity into that of another GH13 enzyme. This suggests that GH13 members may have diversified by introduction of a limited number of mutations to the common ancestor, and that interconversion of reaction specificites may prove easier than previously thought.     

Slow growth phenotype - A possible approach to improved plasmid maintenance in Saccharomyces cerevisiae

Summary Transformation-induced slow growth phenotype (SGP) in yeast is repressed in the presence of 2m plasmids. A full 2m-sequence-based recombinant plasmid (pJB502) was found to be more stable in a 2m-free- [cir] strain of Saccharomyces cerevisiae than in a cir⁺ strain. This could not be attributed to differences in growth rate calculated from kinetic analysis of plasmid loss, but transformed [cir] isolates, which had lost the recombinant plasmid, exhibited varying degrees of SGP in batch culture. One of these isolates was outcompeted in chemostat culture by the recombinant-plasmid-containing strain, suggesting that improved plasmid maintenance can result from SGP in cir hosts.