Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach

AbstractBacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ∼3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains’ phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics.

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Impact of Raw Materials and Processing Techniques on The Microbiological Quality of Egyptian Domiati Cheese

International Journal of Veterinary Science ◽

10.37422/ijvs/20.060 ◽

2020 ◽

Keyword(s):

Raw Materials ◽

Microbiological Quality ◽

Raw Milk ◽

Plate Count ◽

E Coli ◽

Fresh Cheese ◽

Processing Techniques ◽

The Impact ◽

Total Yeast

Domiati cheese is the most popular brand of cheese ripened in brine in the Middle East in terms of consumed quantities. This study was performed to investigate the impact of the microbiological quality of the used raw materials, the applied traditional processing techniques and ripening period on the quality and safety of the produced cheese. Three hundred random composite samples were collected from three factories at Fayoum Governorate, Egypt. Collected samples represent twenty-five each of: raw milk, table salt, calf rennet, microbial rennet, water, environmental air, whey, fresh cheese, ripened cheese & swabs from: worker hands; cheese molds and utensils; tanks. All samples were examined microbiologically for Standard Plate Count (SPC), coliforms count, Staphylococcus aureus (S. aureus) count, total yeast & mould count, presence of E. coli, Salmonellae and Listeria monocytogenes (L. monocytogenes). The mean value of SPC, coliforms, S. aureus and total yeast & mould counts ranged from (79×102 CFU/m3 for air to 13×108 CFU/g for fresh cheese), (7×102 MPN/ cm2 for tank swabs to 80×106 MPN/ml for raw milk), (9×102 CFU/g for salt to 69×106 CFU/g for fresh cheese) and (2×102 CFU/cm2 for hand swabs to 60×104 CFU/g for fresh cheese), respectively. Whereas, E. coli, Salmonella and L. monocytogenes failed to be detected in all examined samples. There were significant differences in all determined microbiological parameters (p ≤0.05) between fresh and ripened cheese which may be attributed to different adverse conditions such as water activity, pH, salt content and temperature carried out to improve the quality of the product.

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KUALITAS AIR SUNGAI DI KAWASAN WISATA PANTAI PETITENGET, KEROBOKAN KABUPATEN BADUNG BALI

ECOTROPHIC Jurnal Ilmu Lingkungan (Journal of Environmental Science) ◽

10.24843/ejes.2018.v12.i02.p11 ◽

2018 ◽

Vol 12 (2) ◽

pp. 226

Author(s):

Wayan Budiarsa Suyasa ◽

Sri Kunti Pancadewi G. A ◽

Iryanti E. Suprihatin ◽

Dwi Adi Suastuti G. A.

Keyword(s):

Water Quality ◽

Structural Changes ◽

Pollution Index ◽

Basic Structure ◽

Physical Damage ◽

E Coli ◽

Pollutant Source ◽

Quality Category ◽

Index Value ◽

The Impact

In order to maintain the environmental carrying capacity of coastal tourism, this research was conducted to determine the condition of river water environmental pollution in the Petitenget beach area and pollutant source activities. Determination of water quality is carried out by analyzing the water quality taken at several sampling points in the four rivers that lead to the Petitenget beach. Determined the pollution index value (IP) of the physical chemical and biological pollution parameters. The results showed that the four rivers that flow into the Petitenget Beach area had been contaminated with indications of pH, BOD, COD, ammonia, Coliform and E. coli which exceeded water quality category III class quality (PerGub Bali No 16 Year 2016). The four rivers are included in the criteria of severe contamination. The four rivers have experienced physical damage or structural changes that have very high discharge fluctuations both in quantity and quality. Slimy basic structure, smelly and slum aesthetic waters. While the indication of the impact of pollution is waste water which is directly discharged into the river from hotels, restaurants, homestays, commercial centers and settlements.

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Stochastic simulation for determining the design flood of cascade reservoir systems

Hydrology Research ◽

10.2166/nh.2011.002 ◽

2012 ◽

Vol 43 (1-2) ◽

pp. 54-63 ◽

Cited By ~ 6

Author(s):

Baohong Lu ◽

Huanghe Gu ◽

Ziyin Xie ◽

Jiufu Liu ◽

Lejun Ma ◽

...

Keyword(s):

Simulation Model ◽

Stochastic Simulation ◽

Southern China ◽

Flow Simulation ◽

Simulation Method ◽

Simulation Approach ◽

Design Flood ◽

Design Values ◽

Stochastic Simulation Model ◽

The Impact

Stochastic simulation is widely applied for estimating the design flood of various hydrosystems. The design flood at a reservoir site should consider the impact of upstream reservoirs, along with any development of hydropower. This paper investigates and applies a stochastic simulation approach for determining the design flood of a complex cascade of reservoirs in the Longtan watershed, southern China. The magnitude of the design flood when the impact of the upstream reservoirs is considered is less than that without considering them. In particular, the stochastic simulation model takes into account both systematic and historical flood records. As the reliability of the frequency analysis increases with more representative samples, it is desirable to incorporate historical flood records, if available, into the stochastic simulation model. This study shows that the design values from the stochastic simulation method with historical flood records are higher than those without historical flood records. The paper demonstrates the advantages of adopting a stochastic flow simulation approach to address design-flood-related issues for a complex cascade reservoir system.

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Association of Genetic Polymorphisms in Oxidative Stress and Inflammation Pathways with Glaucoma Risk and Phenotype

Journal of Clinical Medicine ◽

10.3390/jcm10051148 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1148

Author(s):

Makedonka Atanasovska Velkovska ◽

Katja Goričar ◽

Tanja Blagus ◽

Vita Dolžan ◽

Barbara Cvenkel

Keyword(s):

Oxidative Stress ◽

Ocular Hypertension ◽

Gene Deletion ◽

Open Angle Glaucoma ◽

Protective Role ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Gstm1 Gene ◽

Stress Genes ◽

The Impact

Oxidative stress and neuroinflammation are involved in the pathogenesis and progression of glaucoma. Our aim was to evaluate the impact of selected single-nucleotide polymorphisms in inflammation and oxidative stress genes on the risk of glaucoma, the patients’ clinical characteristics and the glaucoma phenotype. In total, 307 patients with primary open-angle glaucoma or ocular hypertension were enrolled. The control group included 339 healthy Slovenian blood donors. DNA was isolated from peripheral blood. Genotyping was performed for SOD2 rs4880, CAT rs1001179, GPX1 rs1050450, GSTP1 rs1695, GSTM1 gene deletion, GSTT1 gene deletion, IL1B rs1143623, IL1B rs16944, IL6 rs1800795 and TNF rs1800629. We found a nominally significant association of GSTM1 gene deletion with decreased risk of ocular hypertension and a protective role of IL1B rs16944 and IL6 rs1800629 in the risk of glaucoma. The CT and TT genotypes of GPX1 rs1050450 were significantly associated with advanced disease, lower intraocular pressure and a larger vertical cup–disc ratio. In conclusion, genetic variability in IL1B and IL6 may be associated with glaucoma risk, while GPX and TNF may be associated with the glaucoma phenotype. In the future, improved knowledge of these pathways has the potential for new strategies and personalised treatment of glaucoma.

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The Location of Substitutions and Bacterial Genome Arrangements

Genome Biology and Evolution ◽

10.1093/gbe/evaa260 ◽

2020 ◽

Author(s):

Daniella F Lato ◽

G Brian Golding

Keyword(s):

Sinorhizobium Meliloti ◽

Bacterial Genome ◽

Evolutionary Analysis ◽

Origin Of Replication ◽

Ancestral Reconstruction ◽

Molecular Change ◽

E Coli ◽

A Genome ◽

The Impact ◽

Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

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The Protein Interactome of Glycolysis in Escherichia coli

Proteomes ◽

10.3390/proteomes9020016 ◽

2021 ◽

Vol 9 (2) ◽

pp. 16

Author(s):

Shomeek Chowdhury ◽

Stephen Hepper ◽

Mudassir K. Lodi ◽

Milton H. Saier ◽

Peter Uetz

Keyword(s):

Escherichia Coli ◽

Protein Interactions ◽

Allosteric Regulation ◽

Glycolytic Enzymes ◽

Protein Protein Interactions ◽

Post Translational Modification ◽

Interacting Protein ◽

E Coli ◽

Protein Interactome ◽

The Impact

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

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