scholarly journals A large-scale chemical-genetic strategy to design antimicrobial combination chemotherapy forMycobacterium tuberculosis

2019 ◽  
Author(s):  
Eachan O Johnson ◽  
Emma Office ◽  
Tomohiko Kawate ◽  
Marek Orzechowski ◽  
Deborah T Hung
Keyword(s):  
Small Molecule ◽  
Combination Chemotherapy ◽  
Large Scale ◽  
Genetic Interaction ◽  
Resistance Mechanisms ◽  
Screening Strategy ◽  
Chemical Genetic ◽  
Collateral Sensitivity ◽  
Novel Target ◽  
High Level

The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT to the discovery of newMycobacterium tuberculosisinhibitors, which resulted in identification of the small molecule BRD-8000, an inhibitor of a novel target, EfpA. Leveraging the chemical genetic interaction profile of BRD-8000, we identified BRD-9327, another, structurally distinct small molecule EfpA inhibitor. We show that the two compounds are synergistic and display collateral sensitivity because of their distinct modes of action and resistance mechanisms. High-level resistance to one increases the sensitivity to and reduces the emergence of resistance to the other. Thus, the combination of BRD-9327 and BRD-8000 represents a proof-of-concept for the novel strategy of leveraging chemical-genetics in the design of antimicrobial combination chemotherapy in which mutual collateral sensitivity is exploited.

A novel small-molecule screening strategy identifies mitoxantrone as a RhoGTPase inhibitor

2013 ◽  
Vol 450 (1) ◽  
pp. 55-62 ◽  
Author(s):  
Aurélien Bidaud-Meynard ◽  
Daniela Arma ◽  
Said Taouji ◽  
Michel Laguerre ◽  
Jean Dessolin ◽  
...  
Keyword(s):  
Small Molecule ◽  
High Throughput Screening ◽  
Large Scale ◽  
Topoisomerase Ii ◽  
Screening Strategy ◽  
Filamentous Actin ◽  
Library Screen ◽  
Rac1 Gtpase ◽  
Gtpase Activation

RhoGTPases are GDP/GTP molecular switches that control a wide variety of cellular processes, thereby contributing to many diseases, including cancer. As a consequence, there is great interest in the identification of small-molecule inhibitors of RhoGTPases. In the present paper, using the property of GTP-loaded RhoGTPases to bind to their effectors, we describe a miniaturized and robust assay to monitor Rac1 GTPase activation that is suitable for large-scale high-throughput screening. A pilot compound library screen revealed that the topoisomerase II poison MTX (mitoxantrone) is an inhibitor of Rac1, and also inhibits RhoA and Cdc42 in vitro. We show that MTX prevents GTP binding to RhoA/Rac1/Cdc42 in vitro. Furthermore, MTX strongly inhibits RhoGTPase-mediated F-actin (filamentous actin) reorganization and cell migration. Hence, we report a novel biochemical assay yielding the identification of RhoGTPase inhibitors and we present a proof-of-concept validation with the identification of MTX as a novel pan-RhoGTPase inhibitor.

scholarly journals Efficient strategies for screening large-scale genetic interaction networks

2017 ◽  
Author(s):  
Raamesh Deshpande ◽  
Justin Nelson ◽  
Scott W. Simpkins ◽  
Michael Costanzo ◽  
Jeff S. Piotrowski ◽  
...  
Keyword(s):  
Large Scale ◽  
Optimal Algorithm ◽  
Genetic Interaction ◽  
Genetic Screens ◽  
Chemical Genetic ◽  
Genome Wide ◽  
Powerful Approach ◽  
Interaction Screening ◽  
Genetic Interaction Data

Large-scale genetic interaction screening is a powerful approach for unbiased characterization of gene function and understanding systems-level cellular organization. While genome-wide screens are desirable as they provide the most comprehensive interaction profiles, they are resource and time-intensive and sometimes infeasible, depending on the species and experimental platform. For these scenarios, optimal methods for more efficient screening while still producing the maximal amount of information from the resulting profiles are of interest.To address this problem, we developed an optimal algorithm, called COMPRESS-GI, which selects a small but informative set of genes that captures most of the functional information contained within genome-wide genetic interaction profiles. The utility of this algorithm is demonstrated through an application of the approach to define a diagnostic mutant set for large-scale chemical genetic screens, where more than 13,000 compound screens were achieved through the increased throughput enabled by the approach. COMPRESS-GI can be broadly applied for directing genetic interaction screens in other contexts, including in species with little or no prior genetic-interaction data.

scholarly journals Large-Scale Chemical-Genetic Strategy Enables the Design of Antimicrobial Combination Chemotherapy in Mycobacteria

2019 ◽  
Vol 6 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Eachan O. Johnson ◽  
Emma Office ◽  
Tomohiko Kawate ◽  
Marek Orzechowski ◽  
Deborah T. Hung
Keyword(s):  
Combination Chemotherapy ◽  
Large Scale ◽  
Chemical Genetic

scholarly journals Cereal resistance to Fusarium head blight and possibilities of its improvement through breeding

2009 ◽  
Vol 45 (No. 3) ◽  
pp. 87-105 ◽  
Author(s):  
K. Kosová ◽  
J. Chrpová ◽  
V. Šíp
Keyword(s):  
Fusarium Head Blight ◽  
Large Scale ◽  
Phenotypic Selection ◽  
Resistance Mechanisms ◽  
Head Blight ◽  
Cereal Breeding ◽  
Fhb Resistance ◽  
The Individual ◽  
Different Response ◽  
High Level

The aim of this review is to summarize recent information on Fusarium head blight (FHB) in small grain cereals, especially in wheat and barley. Basic information on FHB epidemiology, types of resistance and plant resistance mechanisms is included. Standard methods for the evaluation of the individual types of FHB resistance and the extent of infection are briefly described. Special attention is paid to the sources of FHB resistance of different origin and possibility of their exploitation in cereal breeding. Unfortunately, a high level of FHB resistance was detected in non-adapted germplasm or distant relatives, which is a serious impediment to breeding progress in this field. The present state of breeding for FHB resistance in wheat, barley, rye, triticale and oats was analyzed. It was shown that large-scale QTL detections provide new opportunities for increasing the resistance; however, multi-step phenotypic selection still remains to be the most effective tool. Pedigree analyses indicated that the latest progress reached in this field was obtained through the cumulation of resistance genes coming from heterogeneous sources with different response to FHB.

scholarly journals Systematic Functional Annotation and Visualization of Biological Networks

2015 ◽  
Author(s):  
Anastasia Baryshnikova
Keyword(s):  
Biological Networks ◽  
Large Scale ◽  
Functional Organization ◽  
Genetic Interaction ◽  
Interaction Network ◽  
Functional Enrichment ◽  
Functional Structure ◽  
Cancer Drug ◽  
Functional Connections ◽  
High Level

ABSTRACTLarge-scale biological networks map functional connections between most genes in the genome and can potentially uncover high level organizing principles governing cellular functions. These networks, however, are famously complex and often regarded as disordered masses of tangled interactions (“hairballs”) that are nearly impenetrable to biologists. As a result, our current understanding of network functional organization is very limited. To address this problem, I developed a systematic quantitative approach for annotating biological networks and examining their functional structure. This method, named Spatial Analysis of Functional Enrichment (SAFE), detects network regions that are statistically overrepresented for a functional group or a quantitative phenotype of interest, and provides an intuitive visual representation of their relative positioning within the network. By successfully annotating theSaccharomyces cerevisiaegenetic interaction network with Gene Ontology terms, SAFE proved to be sensitive to functional signals and robust to noise. In addition, SAFE annotated the network with chemical genomic data and uncovered a new potential mechanism of resistance to the anti-cancer drug bortezomib. Finally, SAFE showed that protein-protein interactions, despite their apparent complexity, also have a high level functional structure. These results demonstrate that SAFE is a powerful new tool for examining biological networks and advancing our understanding of the functional organization of the cell.

scholarly journals Large-scale chemical-genetics yields new Mycobacterium tuberculosis inhibitor classes

2018 ◽  
Author(s):  
Eachan O. Johnson ◽  
Emily LaVerriere ◽  
Mary Stanley ◽  
Emma Office ◽  
Elisabeth Meyer ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Large Scale ◽  
Genetic Interactions ◽  
Wild Type ◽  
Chemical Genetic ◽  
Conventional Drug ◽  
Folate Biosynthesis ◽  
New Antibiotics ◽  
Novel Target ◽  
Novel Strategy

New antibiotics are needed to combat rising resistance, with new Mycobacterium tuberculosis (Mtb) drugs of highest priority. Conventional whole-cell and biochemical antibiotic screens have failed. We developed a novel strategy termed PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets) in which we screen compounds against pools of strains depleted for essential bacterial targets. We engineered strains targeting 474 Mtb essential genes and screened pools of 100-150 strains against activity-enriched and unbiased compounds libraries, measuring > 8.5-million chemical-genetic interactions. Primary screens identified >10-fold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insight. We identified > 40 novel compounds targeting DNA gyrase, cell wall, tryptophan, folate biosynthesis, and RNA polymerase, as well as inhibitors of a novel target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating PROSPECT’s ability to yield inhibitors against novel targets which would have eluded conventional drug discovery.

scholarly journals Identification of a Novel Gene Associated with High-Level β-Lactam Resistance in Heterogeneous Vancomycin-IntermediateStaphylococcus aureusStrain Mu3 and Methicillin-ResistantS. aureusStrain N315

2018 ◽  
Vol 63 (2) ◽  
pp. e00712-18 ◽  
Author(s):  
Miki Matsuo ◽  
Norio Yamamoto ◽  
Tomomi Hishinuma ◽  
Keiichi Hiramatsu
Keyword(s):  
Genetic Interaction ◽  
Stringent Response ◽  
Resistance Mechanisms ◽  
Multicopy Plasmid ◽  
Content Type ◽  
Unknown Gene ◽  
Type Gene ◽  
High Level ◽  
Chromosomal Mutations ◽  
Level Resistance

ABSTRACTβ-Lactam resistance levels vary among methicillin-resistantStaphylococcus aureus(MRSA) clinical isolates, mediated by chromosomal mutations and exogenous resistance genemecA. However, MRSA resistance mechanisms are incompletely understood. A P440L mutation in the RNA polymerase β′ subunit (RpoC) in slow-vancomycin-intermediateS. aureus(sVISA) strain V6-5 is associated with conversion of heterogeneous VISA (hVISA) to sVISA. In this study, we found a V6-5-derivative strain (L4) with significantly decreased MICs to oxacillin (OX) and vancomycin. Whole-genome sequencing revealed that L4 has nonsense mutations in two genes,relQ, encoding (p)ppGpp synthetase, an alarmone of the stringent response, and a gene of unknown function.relQdeletion in the hVISA strain Mu3 did not affect OX MIC. However, introducing nonsense mutation of the unknown gene into Mu3 decreased OX MIC, whereas wild-type gene recovered high-level resistance. Thus, mutation of this unknown gene (ehoM) decreased β-lactam resistance in Mu3 and L4. Presence ofrelQin a multicopy plasmid restored high-level resistance in strain L4 but not in theehoMmutant Mu3 strain, indicating a genetic interaction betweenehoMandrelQdepending on the L4 genetic background. While mupirocin (a stringent response inducer) can increase the β-lactam resistance of MRSA, mupirocin supplementation in anehoMdeletion mutant of N315 did not elevate resistance.ehoMexpression in N315 was induced by mupirocin, and the relative amount ofehoMtranscript in Mu3 was higher than in N315 induced by the stringent response. Our findings indicate thatehoMplays an essential role in high-level β-lactam resistance in MRSA via the stringent response.

Social inequality in the evolution of human societies

2019 ◽  
pp. 98-120
Author(s):  
Georgi Derluguian
Keyword(s):  
Social Inequality ◽  
Large Scale ◽  
Human Beings ◽  
Mass Violence ◽  
Public And Private ◽  
Tangible Assets ◽  
Transition To Agriculture ◽  
New Institutions ◽  
High Level ◽  
Political Economic

The author develops ideas about the origin of social inequality during the evolution of human societies and reflects on the possibilities of its overcoming. What makes human beings different from other primates is a high level of egalitarianism and altruism, which contributed to more successful adaptability of human collectives at early stages of the development of society. The transition to agriculture, coupled with substantially increasing population density, was marked by the emergence and institutionalisation of social inequality based on the inequality of tangible assets and symbolic wealth. Then, new institutions of warfare came into existence, and they were aimed at conquering and enslaving the neighbours engaged in productive labour. While exercising control over nature, people also established and strengthened their power over other people. Chiefdom as a new type of polity came into being. Elementary forms of power (political, economic and ideological) served as a basis for the formation of early states. The societies in those states were characterised by social inequality and cruelties, including slavery, mass violence and numerous victims. Nowadays, the old elementary forms of power that are inherent in personalistic chiefdom are still functioning along with modern institutions of public and private bureaucracy. This constitutes the key contradiction of our time, which is the juxtaposition of individual despotic power and public infrastructural one. However, society is evolving towards an ever more efficient combination of social initiatives with the sustainability and viability of large-scale organisations.

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