Functional Compensation of Primary and Secondary Metabolites by Duplicate Genes in Arabidopsis thaliana

It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic products, the relative roles of the two mechanisms have been extensively studied in yeast but not in any multi-cellular organisms. Here, to address the functional compensation of metabolic products by duplicate genes, we quantified 35 metabolic products from 1,976 genes in knockout mutants of Arabidopsis thaliana by a high-throughput Liquid chromatography-Mass spectrometer (LC-MS) analysis. We found that knocking out either a singleton gene or a duplicate gene with distant paralogs in the genome tends to induce stronger metabolic effects than knocking out a duplicate gene with a close paralog in the genome, indicating that only duplicate genes with close paralogs play a significant role in functional compensation for metabolic products in A. thaliana. To extend the analysis, we examined metabolic products with either high or low connectivity in a metabolic network. We found that the compensatory role of duplicate genes is less important when the metabolite has a high connectivity, indicating that functional compensation by alternative pathways is common in the case of high connectivity. In conclusion, recently duplicated genes play an important role in the compensation of metabolic products only when the number of alternative pathways is small

Chemogenetic fingerprinting by analysis of cellular growth dynamics

<p>Abstract</p> <p>Background</p> <p>A fundamental goal in chemical biology is the elucidation of on- and off-target effects of drugs and biocides. To this aim chemogenetic screens that quantify drug induced changes in cellular fitness, typically taken as changes in composite growth, is commonly applied.</p> <p>Results</p> <p>Using the model organism <it>Saccharomyces cerevisiae </it>we here report that resolving cellular growth dynamics into its individual components, growth lag, growth rate and growth efficiency, increases the predictive power of chemogenetic screens. Both in terms of drug-drug and gene-drug interactions did the individual growth variables capture distinct and only partially overlapping aspects of cell physiology. In fact, the impact on cellular growth dynamics represented functionally distinct chemical fingerprints.</p> <p>Discussion</p> <p>Our findings suggest that the resolution and quantification of all facets of growth increases the informational and interpretational output of chemogenetic screening. Hence, by facilitating a physiologically more complete analysis of gene-drug and drug-drug interactions the here reported results may simplify the assignment of mode-of-action to orphan bioactive compounds.</p

Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses

When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pairs in the Caenorhabditis elegans genome. Remarkably, in contrast to expectations, we find that phenotype masking makes only a minor contribution to the low knockdown phenotype rate for duplicate genes. Instead, we find that non-essential genes are highly over-represented among duplicates, leading to a low observed loss-of-function phenotype rate. We further find that duplicate pairs derived from essential and non-essential genes have contrasting evolutionary dynamics: whereas non-essential genes are both more often successfully duplicated (fixed) and lost, essential genes are less often duplicated but upon successful duplication are maintained over longer periods. We expect the fundamental evolutionary duplication dynamics presented here to be broadly applicableclose9

Need-based up-regulation of protein levels in response to deletion of their duplicate genes.

Many duplicate genes maintain functional overlap despite divergence over long evolutionary time scales. Deleting one member of a paralogous pair often has no phenotypic effect, unless its paralog is also deleted. It has been suggested that this functional compensation might be mediated by active up-regulation of expression of a gene in response to deletion of its paralog. However, it is not clear how prevalent such paralog responsiveness is, nor whether it is hardwired or dependent on feedback from environmental conditions. Here, we address these questions at the genomic scale using high-throughput flow cytometry of single-cell protein levels in differentially labeled cocultures of wild-type and paralog-knockout Saccharomyces cerevisiae strains. We find that only a modest fraction of proteins (22 out of 202) show significant up-regulation to deletion of their duplicate genes. However, these paralog-responsive proteins match almost exclusively duplicate pairs whose overlapping function is required for growth. Moreover, media conditions that add or remove requirements for the function of a duplicate gene pair specifically eliminate or create paralog responsiveness. Together, our results suggest that paralog responsiveness in yeast is need-based: it appears only in conditions in which the gene function is required. Physiologically, such need-based responsiveness could provide an adaptive mechanism for compensation of genetic, environmental, or stochastic perturbations in protein abundance

THE PHYSIOLOGICAL DISPOSITION OF AEROSOLIZED 4-[(3-(4-ACETYL-3-HYDROXY-2- PROPYLPHENOXY)PROPYL)SULFONYL]-y-OXOBENZENEBUTANOATE (L-648,05 1) IN

&apos; C-labeIed 4-[(3-(4-acetyl-3-hydroxy-2-propylphenoxy)propyl)

A comparison in precision and accuracy of the conventional syringe to the Suh precision syringe

PurposeTo compare the accuracy and precision of a conventional intraocular syringe to the Suh precision syringe (SPS), a new injection device designed to decrease operator error and to reduce adverse outcomes by providing a more ergonomic technique for periocular and intraocular injections.MethodsParticipants were instructed to inject a specified quantity of water into a 0.2&nbsp;mL polymerase chain reaction (PCR) tube and a sheep eye, first with the conventional syringe, and then with the SPS. The degree of needle movement during injection was video recorded and analyzed for forward-retraction movement and variability in movement. The volume of water injected into the PCR tube was also documented. Data was analyzed using a Wilcoxon signed-rank test.ResultsAs compared to the conventional syringe, the SPS had significantly less forward-retraction movement when injecting into the sheep eye (P=0.04). Similarly, the forward-retraction movement of the needle when injecting into the PCR tube was less while using the SPS compared with the conventional syringe; however, this was not statistically significant (P=0.09). There was no significant difference in the volume of water expelled from both syringes (P=0.28).ConclusionThe SPS demonstrates significant potential to decrease the overall risk involved with injections through reduction of forward-retraction movement during device operation. This new syringe design also provides better control with injection depth and drug injection volume. With its more ergonomic design, the SPS has the potential to decrease risks associated with intraocular injections by improving the accuracy and precision of the injection

The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

peer-reviewedThis study was supported by Science Foundation Ireland grants to MAF under two programs: the President of Ireland Young Researcher Award (04/YI1/M518) and the Research Frontiers Program (10/RFP/GEN2685). The study of distribution of mutations in duplicates and their possible effects on fitness was supported by a grant from the Ministerio de Ciencia e Innovacion (BFU2009-12022) to MAF. CT is supported by a long-term postdoctoral EMBO fellowship (EMBO ALTF 730-2011).Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be retained than small-scale duplications (SSDs), though their relative contribution to the functional fate of duplicates remains unexplored. Using the map of genetic interactions and the re-sequencing of 27 Saccharomyces cerevisiae genomes evolving for 2,200 generations we show that SSD-duplicates lead to neo-functionalization while WGD-duplicates partition ancestral functions. This conclusion is supported by: (a) SSD-duplicates establish more genetic interactions than singletons and WGD-duplicates; (b) SSD-duplicates copies share more interaction-partners than WGD-duplicates copies; (c) WGDduplicates interaction partners are more functionally related than SSD-duplicates partners; (d) SSD-duplicates gene copies are more functionally divergent from one another, while keeping more overlapping functions, and diverge in their subcellular locations more than WGD-duplicates copies; and (e) SSD-duplicates complement their functions to a greater extent than WGD–duplicates. We propose a novel model that uncovers the complexity of evolution after gene duplicationScience Foundation IrelandMinisterio de Ciencia e InnovacionEuropean Molecular Biology Organizatio

Thigh-length compression stockings and DVT after stroke

Controversy exists as to whether neoadjuvant chemotherapy improves survival in patients with invasive bladder cancer, despite randomised controlled trials of more than 3000 patients. We undertook a systematic review and meta-analysis to assess the effect of such treatment on survival in patients with this disease

Contaminants, pollution and potential anthropogenic impacts in chagos/BIOT

A broad range of chemical contaminants and pollutants have been measured within the Chagos Archipelago. Contamination is amongst the lowest in the world. Whilst much data is in the open literature, the chapter also includes details of extensive pollution monitoring for the atoll Diego Garcia which hosts a military facility. Hydrocarbons present are primarily of a natural origin with negligible evidence of contamination from petroleum or combustion origins. Tar balls, however, have been reported on several beaches in the Archipelago. Analyses of faecal steroids provide negligible evidence of sewage contamination. ‘Persistent organic pollutants’ (POPs), including PCBs and pesticides, were generally below analytical detection limits, as were polyfluorinated compounds, brominated, chlorinated and organo-phosphorous flame retardants, fluorinated tensides, and surfactants (PFOS). Antifouling biocides and herbicides in Diego Garcia show negligible contamination. Metal concentrations are very low. Levels of most contaminants are typically comparable to those recorded in environments perceived to be pristine, for example, the Antarctic. In Diego Garcia, extensive monitoring includes regular analyses in accredited US laboratories of over one hundred metals and organic contaminants. Results generally reveal concentrations below detection limits. This is in agreement with the open literature surveys. These legislated assessments are designed to ensure both environmental and human health preservation. Whilst many detection limits are higher than those of the independent surveys, they generally confirm the pristine nature of the Archipelago. Beach surveys, however, revealed a surprisingly high number of pieces of debris throughout the Archipelago, mainly plastics of South East Asian origin. The number of litter pieces in Diego Garcia was less than in the other atolls, reductions being attributed to beach clean-up events. Microplastic contamination is shown to be both widespread and relatively high compared to other locations on a global scale, and there were significantly more microplastics at uninhabited atolls compared to the Diego Garcia, showing the potential for microplastics to accumulate in remote locations. Holothurian (sea cucumber) poaching has been another significant environmental pressure on the coral reefs of Chagos and is included in this review, in view of the reported ecological benefits of the group to reef health and resilience