Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes

Recent evidence suggests that the genes an organism needs to survive in an environment drastically differ when alone or in a community. However, it is not known if there are universal functions that enable microbes to persist in a community and if there are functions specific to interactions between microbes native to the same (sympatric) or different (allopatric) environments. Here, we ask how the essential functions of the oral pathogen Aggregatibacter actinomycetemcomitans change during pairwise coinfection in a murine abscess with each of 15 microbes commonly found in the oral cavity and 10 microbes that are not. A. actinomycetemcomitans was more abundant when coinfected with allopatric than with sympatric microbes, and this increased fitness correlated with expanded metabolic capacity of the coinfecting microbes. Using transposon sequencing, we discovered that 33% of the A. actinomycetemcomitans genome is required for coinfection fitness. Fifty-nine “core” genes were required across all coinfections and included genes necessary for aerobic respiration. The core genes were also all required in monoinfection, indicating the essentiality of these genes cannot be alleviated by a coinfecting microbe. Furthermore, coinfection with some microbes, predominately sympatric species, induced the requirement for over 100 new community-dependent essential genes. In contrast, in other coinfections, predominately with nonoral species, A. actinomycetemcomitans required 50 fewer genes than in monoinfection, demonstrating that some allopatric microbes can drastically alleviate gene essentialities. These results expand our understanding of how diverse microbes alter growth and gene essentiality within polymicrobial infections.

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Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

Molecular Genetics and Genomics ◽

10.1007/s00438-015-1154-z ◽

2016 ◽

Vol 291 (2) ◽

pp. 905-912 ◽

Cited By ~ 12

Author(s):

Xiaowen Yang ◽

Yajie Li ◽

Juan Zang ◽

Yexia Li ◽

Pengfei Bie ◽

...

Keyword(s):

Essential Genes ◽

The Core ◽

Pan Genome ◽

Core Genes

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A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

F1000Research ◽

10.12688/f1000research.51873.2 ◽

2021 ◽

Vol 10 ◽

pp. 286

Author(s):

Granger Sutton ◽

Gary B. Fogel ◽

Bradley Abramson ◽

Lauren Brinkac ◽

Todd Michael ◽

...

Keyword(s):

Essential Genes ◽

Considerable Time ◽

The Core ◽

Pan Genome ◽

A Genome ◽

Low Penetrance Genes ◽

Almost All ◽

Bioinformatic Approach ◽

Core Genes ◽

Broad Understanding

Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.

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A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

F1000Research ◽

10.12688/f1000research.51873.1 ◽

2021 ◽

Vol 10 ◽

pp. 286

Author(s):

Granger Sutton ◽

Gary B. Fogel ◽

Bradley Abramson ◽

Lauren Brinkac ◽

Todd Michael ◽

...

Keyword(s):

Essential Genes ◽

Considerable Time ◽

The Core ◽

Pan Genome ◽

A Genome ◽

Low Penetrance Genes ◽

Almost All ◽

Bioinformatic Approach ◽

Core Genes ◽

Broad Understanding

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Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽

10.1186/s12864-021-07702-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Seth Commichaux ◽

Kiran Javkar ◽

Padmini Ramachandran ◽

Niranjan Nagarajan ◽

Denis Bertrand ◽

...

Keyword(s):

Public Health ◽

Public Health Response ◽

High Quality ◽

Short Read ◽

Short Reads ◽

The Core ◽

Long Reads ◽

Health Response ◽

Long Read ◽

Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

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Large-scale structural analysis of the core promoter in mammalian and plant genomes

Nucleic Acids Research ◽

10.1093/nar/gki737 ◽

2005 ◽

Vol 33 (13) ◽

pp. 4255-4264 ◽

Cited By ~ 75

Author(s):

K. Florquin

Keyword(s):

Structural Analysis ◽

Large Scale ◽

Core Promoter ◽

Plant Genomes ◽

The Core

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A large-scale whole-genome sequencing analysis reveals false positives of bacterial essential genes

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11702-3 ◽

2021 ◽

Author(s):

Yuanhao Li ◽

Bo Jiang ◽

Weijun Dai

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

False Positives ◽

Essential Genes ◽

Whole Genome ◽

Sequencing Analysis

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Identification of CCNB2 expression in triple-negative breast cancer based on bioinformatics results

10.21203/rs.3.rs-506326/v1 ◽

2021 ◽

Author(s):

jintao cao ◽

SHUAI SUN ◽

RAN LI ◽

RUI MIN ◽

XINGYU FAN ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Triple Negative Breast Cancer ◽

Protein Complex ◽

Triple Negative ◽

Expression Profiles ◽

Pathway Enrichment Analysis ◽

Analysis Tool ◽

The Core ◽

Core Genes

Abstract Background The current epidemiology shows that the incidence of breast cancer is increasing year by year and tends to be younger. Triple-negative breast cancer is the most malignant of breast cancer subtypes. The application of bioinformatics in tumor research is becoming more and more extensive. This study provided research ideas and basis for exploring the potential targets of gene therapy for triple-negative breast cancer (TNBC). Methods We analyzed three gene expression profiles (GSE64790、GSE62931、GSE38959) selected from the Gene Expression Omnibus (GEO) database. The GEO2R online analysis tool was used to screen for differentially expressed genes (DEGs) between TNBC and normal tissues. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to identify the pathways and functional annotation of DEGs. Protein–protein interaction network of these DEGs were visualized by the Metascape gene-list analysis tool so that we could find the protein complex containing the core genes. Subsequently, we investigated the transcriptional data of the core genes in patients with breast cancer from the Oncomine database. Moreover, the online Kaplan–Meier plotter survival analysis tool was used to evaluate the prognostic value of core genes expression in TNBC patients. Finally, immunohistochemistry (IHC) was used to evaluated the expression level and subcellular localization of CCNB2 on TNBC tissues. Results A total of 66 DEGs were identified, including 33 up-regulated genes and 33 down-regulated genes. Among them, a potential protein complex containing five core genes was screened out. The high expression of these core genes was correlated to the poor prognosis of patients suffering breast cancer, especially the overexpression of CCNB2. CCNB2 protein positively expressed in the cytoplasm, and its expression in triple-negative breast cancer tissues was significantly higher than that in adjacent tissues. Conclusions CCNB2 may play a crucial role in the development of TNBC and has the potential as a prognostic biomarker of TNBC.

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Progressive Evolution of the Core of the Fast Breeder Test Reactor

18th International Conference on Nuclear Engineering: Volume 1 ◽

10.1115/icone18-29404 ◽

2010 ◽

Author(s):

S. Varatharajan ◽

K. V. Sureshkumar ◽

K. V. Kasiviswanathan ◽

G. Srinivasan

Keyword(s):

Fast Reactor ◽

Large Scale ◽

Power Reactor ◽

Test Bed ◽

Fast Breeder Test Reactor ◽

The Core ◽

Linear Heat ◽

Mox Fuel ◽

Test Reactor ◽

Carbide Fuel

The second stage of Indian nuclear programme envisages the deployment of fast reactors on a large scale for the effective use of India’s limited uranium reserves. The Fast Breeder Test Reactor (FBTR) at Kalpakkam is a loop type, sodium cooled fast reactor, meant as a test bed for the fuels and structural materials for the Indian fast reactor programme. The reactor was made critical with a unique high plutonium MK-I carbide fuel (70% PuC+30%UC). Being a unique untested fuel of its kind, it was decided to test it as a driver fuel, with conservative limits on Linear Heat Rating and burn-up, based on out-of-pile studies. FBTR went critical in Oct 1985 with a small core of 23 MK-I fuel subassemblies. The Linear Heat Rating and burn-up limits for the fuel were conservatively set at 250 W/cm & 25 GWd/t respectively. Based on out-of-pile simulation in 1994, it was possible to raise the LHR to 320 W/cm. It was decided that when the fuel reaches the target burn-up of 25 GWd/t, the MK-I core would be progressively replaced with a larger core of MK-II carbide fuel (55% PuC+45%UC). Induction of MK-II subassemblies was started in 1996. However, based on the Post-Irradiation Examination (PIE) of the MK-I fuel at 25, 50 & 100 GWd/t, it became possible to enhance the burn-up of the MK-I fuel to 155 GWd/t. More than 900 fuel pins of MK-I composition have reached 155 GWd/t without even a single failure and have been discharged. One subassembly (61 pins) was taken to 165 GWd/t on trial basis, without any clad failure. The core has been progressively enlarged, adding MK-I subassemblies to compensate for the burn-up loss of reactivity and replacement of discharged subassemblies. The induction of MK-II fuel was stopped in 2003. One test subassembly simulating the composition of the MOX fuel (29% PuO2) to be used in the 500 MWe Prototype Fast Breeder Reactor was loaded in 2003. It is undergoing irradiation at 450 W/cm, and has successfully seen a burn-up of 92.5 GWd/t. In 2006, it was proposed to test high Pu MOX fuel (44% PuO2), in order to validate the fabrication and fuel cycle processes developed for the power reactor MOX fuel. Eight MOX subassemblies were loaded in FBTR core in 2007. The current core has 27 MK-I, 13 MK-II, eight high Pu MOX and one power reactor MOX fuel subassemblies. The reactor power has been progressively increased from 10.5 MWt to 18.6 MWt, due to the progressive enlargement of the core. This paper presents the evolution of the core based on the progressive enhancement of the burn-up limit of the unique high Pu carbide fuel.

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Performance of Core Exit Thermocouple for PWR Accident Management Action in Vessel Top Break LOCA Simulation Experiment at OECD/NEA ROSA Project

Volume 4: Structural Integrity; Next Generation Systems; Safety and Security; Low Level Waste Management and Decommissioning; Near Term Deployment: Plant Designs, Licensing, Construction, Workforce and Public Acceptance ◽

10.1115/icone16-48754 ◽

2008 ◽

Author(s):

Mitsuhiro Suzuki ◽

Takeshi Takeda ◽

Hideo Nakamura

Keyword(s):

Time Delay ◽

Large Scale ◽

Simulation Experiment ◽

Three Dimensional ◽

Test Facility ◽

Large Temperature ◽

Energy Agency ◽

Pressurized Water ◽

The Core ◽

Accident Management

Presented are experiment results of the Large Scale Test Facility (LSTF) conducted at the Japan Atomic Energy Agency (JAEA) with a focus on core exit thermocouple (CET) performance to detect core overheat during a vessel top break loss-of-coolant accident (LOCA) simulation experiment. The CET temperatures are used to start accident management (AM) action to quickly depressurize steam generator (SG) secondary sides in case of core temperature excursion. Test 6-1 is the first test of the OECD/NEA ROSA Project started in 2005, simulating withdraw of a control rod drive mechanism penetration nozzle at the vessel top head. The break size is equivalent to 1.9% cold leg break. The AM action was initiated when CET temperature rose up to 623K. There was no reflux water fallback onto the CETs during the core heat-up period. The core overheat, however, was detected with a time delay of about 230s. In addition, a large temperature discrepancy was observed between the CETs and the hottest core region. This paper clarifies the reasons of time delay and temperature discrepancy between the CETs and heated core during boil-off including three-dimensional steam flows in the core and core exit. The paper discusses applicability of the LSTF CET performance to pressurized water reactor (PWR) conditions and a possibility of alternative indicators for earlier AM action than in Test 6-1 is studied by using symptom-based plant parameters such as a reactor vessel water level detection.

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