scholarly journals Solvent quality and chromosome folding in Escherichia coli

2020 ◽  
Author(s):  
Yingjie Xiang ◽  
Ivan V. Surovtsev ◽  
Yunjie Chang ◽  
Sander K. Govers ◽  
Bradley R. Parry ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Electron Tomography ◽  
Mesh Size ◽  
Bacterial Cells ◽  
Solvent Quality ◽  
Ribosome Density ◽  
Live Bacteria ◽  
Dna Density ◽  
Poor Solvent

SummaryAll cells must fold their genomes, including bacterial cells where the chromosome is compacted into a domain-organized meshwork called nucleoid. Polymer conformation depends highly on the quality of the solvent. Yet, the solvent quality for the DNA polymer inside cells remains unexplored. Here, we developed a method to assess this fundamental physicochemical property in live bacteria. By determining the DNA concentration and apparent average mesh size of the nucleoid, we provide evidence that the cytoplasm is a poor solvent for the chromosome in Escherichia coli. Monte Carlo simulations showed that such a poor solvent compacts the chromosome and promotes spontaneous formation of chromosomal domains connected by lower-density DNA regions. Cryo-electron tomography and fluorescence microscopy revealed that the (poly)ribosome density within the nucleoid is spatially heterogenous and correlates negatively with DNA density. These findings have broad implications to our understanding of chromosome folding and intracellular organization.

Genetic engineering: possibilities and prospects for its application in industrial microbiology

1980 ◽  
Vol 290 (1040) ◽  
pp. 369-386 ◽  
Keyword(s):  
Escherichia Coli ◽  
Genetic Engineering ◽  
Detailed Analysis ◽  
Bacterial Cells ◽  
Bacterial Enzymes ◽  
Distant Future ◽  
Cells In Culture ◽  
Wide Range ◽  
Hybrid Dna

A wide range of techniques is now available for the construction of hybrid DNA molecules comprising components from disparate species. Transfer of segments of DNA from other organisms, and especially eukaryotes, to Escherichia coli permits their preparation in quantities sufficient for detailed analysis of their structure and mechanism of expression. This information could be exploited to enhance the quantity or quality of polypeptide products from bacterial cells. Greatly increased yields of bacterial enzymes have been obtained in this way in several instances. The approaches that have been pioneered with bacteria are currently being applied to higher organisms. Much work is in progress with yeasts, in which transformation has been successfully demonstrated, with animal viruses and cells in culture and with some plant systems and offers the promise of wider applications of genetic engineering in the not too distant future.

scholarly journals Morphological peculiarities of DNA-protein complexes in dormant Escherichia coli cells, subjected to prolonged starvation Condensation of DNA in dormant cells of Escherichia coli

2020 ◽  
Author(s):  
Natalia Loiko ◽  
Yana Danilova ◽  
Andrey Moiseenko ◽  
Vladislav Kovalenko ◽  
Ksenia Tereshkina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Liquid Crystalline ◽  
Environmental Changes ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Bacterial Cells ◽  
Ordered Structures ◽  
Extreme Stress ◽  
Different Types ◽  
Dps Protein

AbstractOne of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of Dps protein is tightly bound to nucleoid DNA. We demonstrated that the population of the dormant cell is structurally heterogeneous, which allows cells to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

Mechanisms involved in effects of antimicrobial peptides, bactenectins ChBac3.4, ChBac5, and mini-ChBac7.5Nb, on bacterial cells

2017 ◽  
pp. 43-50
Author(s):  
О.В. Шамова ◽  
М.С. Жаркова ◽  
П.М. Копейкин ◽  
Д.С. Орлов ◽  
Е.А. Корнева
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Activity ◽  
Innate Immunity ◽  
Infectious Diseases ◽  
Metabolic Activity ◽  
Capra Hircus ◽  
Bacterial Cells ◽  
Antibiotic Resistant ◽  
Resistant Strains

Антимикробные пептиды (АМП) системы врожденного иммунитета - соединения, играющие важную роль в патогенезе инфекционных заболеваний, так как обладают свойством инактивировать широкий спектр патогенных бактерий, обеспечивая противомикробную защиту живых организмов. В настоящее время АМП рассматриваются как потенциальные соединения-корректоры инфекционной патологии, вызываемой антибиотикорезистентными бактериями (АБР). Цель данной работы состояла в изученим механизмов антибактериального действия трех пептидов, принадлежащих к семейству бактенецинов - ChBac3.4, ChBac5 и mini-ChBac7.5Nb. Эти химически синтезированные пептиды являются аналогами природных пролин-богатых АМП, обнаруженных в лейкоцитах домашней козы Capra hircus и проявляющих высокую антимикробную активность, в том числе и в отношении грамотрицательных АБР. Методы. Минимальные ингибирующие и минимальные бактерицидные концентрации пептидов (МИК и МБК) определяли методом серийных разведений в жидкой питательной среде с последующим высевом на плотную питательную среду. Эффекты пептидов на проницаемость цитоплазматической мембраны бактерий для хромогенного маркера исследовали с использованием генетически модифицированного штамма Escherichia coli ML35p. Действие бактенецинов на метаболическую активность бактерий изучали с применением маркера резазурина. Результаты. Показано, что все исследованные пептиды проявляют высокую антимикробную активность в отношении Escherichia coli ML35p и антибиотикоустойчивых штаммов Escherichia coli ESBL и Acinetobacter baumannii in vitro, но их действие на бактериальные клетки разное. Использован комплекс методик, позволяющих наблюдать в режиме реального времени динамику действия бактенецинов в различных концентрациях (включая их МИК и МБК) на барьерную функцию цитоплазматической мембраны и на интенсивность метаболизма бактериальных клеток, что дало возможность выявить различия в характере воздействия бактенецинов, отличающихся по структуре молекулы, на исследуемые микроорганизмы. Установлено, что действие каждого из трех исследованных бактенецинов в бактерицидных концентрациях отличается по эффективности нарушения целостности бактериальных мембран и в скорости подавления метаболизма клеток. Заключение. Полученная информация дополнит существующие фундаментальные представления о механизмах действия пролин-богатых пептидов врожденного иммунитета, а также послужит основой для биотехнологических исследований, направленных на разработку на базе этих соединений новых антибиотических препаратов для коррекции инфекционных заболеваний, вызываемых АБР и являющимися причинами тяжелых внутрибольничных инфекций. Antimicrobial peptides (AMPs) of the innate immunity are compounds that play an important role in pathogenesis of infectious diseases due to their ability to inactivate a broad array of pathogenic bacteria, thereby providing anti-microbial host defense. AMPs are currently considered promising compounds for treatment of infectious diseases caused by antibiotic-resistant bacteria. The aim of this study was to investigate molecular mechanisms of the antibacterial action of three peptides from the bactenecin family, ChBac3.4, ChBac5, and mini-ChBac7.5Nb. These chemically synthesized peptides are analogues of natural proline-rich AMPs previously discovered by the authors of the present study in leukocytes of the domestic goat, Capra hircus. These peptides exhibit a high antimicrobial activity, in particular, against antibiotic-resistant gram-negative bacteria. Methods. Minimum inhibitory and minimum bactericidal concentrations of the peptides (MIC and MBC) were determined using the broth microdilution assay followed by subculturing on agar plates. Effects of the AMPs on bacterial cytoplasmic membrane permeability for a chromogenic marker were explored using a genetically modified strain, Escherichia coli ML35p. The effect of bactenecins on bacterial metabolic activity was studied using a resazurin marker. Results. All the studied peptides showed a high in vitro antimicrobial activity against Escherichia coli ML35p and antibiotic-resistant strains, Escherichia coli ESBL and Acinetobacter baumannii, but differed in features of their action on bacterial cells. The used combination of techniques allowed the real-time monitoring of effects of bactenecin at different concentrations (including their MIC and MBC) on the cell membrane barrier function and metabolic activity of bacteria. The differences in effects of these three structurally different bactenecins on the studied microorganisms implied that these peptides at bactericidal concentrations differed in their capability for disintegrating bacterial cell membranes and rate of inhibiting bacterial metabolism. Conclusion. The obtained information will supplement the existing basic concepts on mechanisms involved in effects of proline-rich peptides of the innate immunity. This information will also stimulate biotechnological research aimed at development of new antibiotics for treatment of infectious diseases, such as severe in-hospital infections, caused by antibiotic-resistant strains.

Microbiological quality of residues from drinking water preparation

1995 ◽  
Vol 31 (5-6) ◽  
pp. 75-79 ◽  
Author(s):  
M. Würzer ◽  
A. Wiedenmann ◽  
K. Botzenhart
Keyword(s):  
Waste Water ◽  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Drinking Water ◽  
Water Treatment ◽  
Pathogenic Bacteria ◽  
Waste Water Treatment ◽  
Microbiological Quality ◽  
Detection Limits

In Germany the application of procedures such as flocculation and filtration in the preparation of drinking water results in the annual production of an estimated 500,000 t of sediments and sludges. Some of these residues have a potential for being reused, for example in agriculture, forestry, brickworks or waste water treatment. To assess the microbiological quality of residues from waterworks methods for the detection of enterobacteria, Escherichia coli, Salmonella, Pseudomonas aeruginosa, Legionella, poliovirus, Ascaris suis eggs and Cryptosporidium have been evaluated regarding their detection limits and were applied to various residues from German waterworks. Results show that sediments and sludges may contain pathogenic bacteria, viruses and protista. When residues from waterworks are intended to be reused in agriculture or forestry the microbiological quality should therefore be considered.

Crystallization of Isotactic Poly(propylene) in Solution as Followed by Slow Calorimetry

1995 ◽  
Vol 60 (11) ◽  
pp. 1905-1924 ◽  
Author(s):  
Hong Phuong-Nguyen ◽  
Geneviève Delmas
Keyword(s):  
Molecular Weight ◽  
Crystal Growth ◽  
High Temperature ◽  
Heat Of Fusion ◽  
Complete Dissolution ◽  
Polymer Molecular Weight ◽  
Solvent Quality ◽  
Temperature Ramp ◽  
Poly Propylene

Dissolution, crystallization and second dissolution traces of isotactic poly(propylene) have been obtained in a slow temperature ramp (3 K h-1) with the C80 Setaram calorimeter. Traces of phase-change, in presence of solvent, are comparable to traces without solvent. The change of enthalpy on heating or cooling, ∆Htotal, over the 40-170 °C temperature range, is the sum of two contributions, ∆HDSC and ∆Hnetwork. The change ∆HDSC is the usual heat obtained in a fast temperature ramp and ∆Hnetwork is associated with a physical network whose disordering is slow and subject to superheating due to strain. When dissolution is complete, ∆Htotal is equal to ∆H0, the heat of fusion of perfect crystals. The values of ∆Htota for nascent and recrystallized samples are compared. Dissolution is the tool to evaluate the quality of the crystals. The repartition of ∆Htotal, into the two endotherms, reflects the quality of crystals. The crystals grown more rapidly have a higher fraction of network crystals which are stable at high T in the solvents. A complete dissolution, i.e. a high temperature (170 °C or more) is necessary to obtain good crystals. The effect of concentration, polymer molecular weight and solvent quality on crystal growth is analyzed.

Microbiological Quality of Fresh Blue Crabmeat, Clams and Oysters

1983 ◽  
Vol 46 (11) ◽  
pp. 978-981 ◽  
Author(s):  
B. A. WENTZ ◽  
A. P. DURAN ◽  
A. SWARTZENTRUBER ◽  
A. H. SCHWAB ◽  
R. B. READ
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Microbiological Quality ◽  
Fecal Coliforms ◽  
Geometric Means ◽  
Colony Forming Units ◽  
Plate Counts ◽  
The Mean ◽  
Eastern Oysters

The microbiological quality of fresh blue crabmeat, soft- and hardshell clams and shucked Eastern oysters was determined at the retail (crabmeat, oysters) and wholesale (clams) levels. Geometric means of aerobic plate counts incubated at 35°C were: blue crabmeat 140,000 colony-forming units (CFU)/g, hardshell clams, 950 CFU/g, softshell clams 680 CFU/g and shucked Eastern oysters 390,000 CFU/g. Coliform geometric means ranged from 3,6/100 g for hardshell clams to 21/g for blue crabmeat. Means for fecal coliforms or Escherichia coli ranged from <3/100 g for clams to 27/100 g for oysters, The mean Staphylococcus aureus count in blue crabmeat was 10/g.

Effect of Gamma Radiation on the Reduction of Salmonella strains, Listeria monocytogenes, and Shiga Toxin–Producing Escherichia coli and Sensory Evaluation of Minimally Processed Spinach (Tetragonia expansa)

2014 ◽  
Vol 77 (10) ◽  
pp. 1768-1772 ◽  
Author(s):  
ANA CAROLINA B. REZENDE ◽  
MARIA CRYSTINA IGARASHI ◽  
MARIA TERESA DESTRO ◽  
BERNADETTE D. G. M. FRANCO ◽  
MARIZA LANDGRAF
Keyword(s):  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
Gamma Radiation ◽  
Shiga Toxin ◽  
Radiation Doses ◽  
Minimally Processed ◽  
Tetragonia Expansa ◽  
Effects Of Irradiation On ◽  
Spinach Leaves

This study evaluated the effects of irradiation on the reduction of Shiga toxin–producing Escherichia coli (STEC), Salmonella strains, and Listeria monocytogenes, as well as on the sensory characteristics of minimally processed spinach. Spinach samples were inoculated with a cocktail of three strains each of STEC, Salmonella strains, and L. monocytogenes, separately, and were exposed to gamma radiation doses of 0, 0.2, 0.4, 0.6, 0.8, and 1.0 kGy. Samples that were exposed to 0.0, 1.0, and 1.5 kGy and kept under refrigeration (4°C) for 12 days were submitted to sensory analysis. D10-values ranged from 0.19 to 0.20 kGy for Salmonella and from 0.20 to 0.21 for L. monocytogenes; for STEC, the value was 0.17 kGy. Spinach showed good acceptability, even after exposure to 1.5 kGy. Because gamma radiation reduced the selected pathogens without causing significant changes in the quality of spinach leaves, it may be a useful method to improve safety in the fresh produce industry.

scholarly journals The Functional Quality of Soluble Recombinant Polypeptides Produced in Escherichia coli Is Defined by a Wide Conformational Spectrum

2008 ◽  
Vol 74 (23) ◽  
pp. 7431-7433 ◽  
Author(s):  
Mónica Martínez-Alonso ◽  
Nuria González-Montalbán ◽  
Elena García-Fruitós ◽  
Antonio Villaverde
Keyword(s):  
Escherichia Coli ◽  
Green Fluorescent Protein ◽  
Recombinant Proteins ◽  
Fluorescent Protein ◽  
Native Structure ◽  
Functional Quality ◽  
Soluble Aggregates ◽  
Recombinant Polypeptides ◽  
Green Fluorescent

ABSTRACT We have observed that a soluble recombinant green fluorescent protein produced in Escherichia coli occurs in a wide conformational spectrum. This results in differently fluorescent protein fractions in which morphologically diverse soluble aggregates abound. Therefore, the functional quality of soluble versions of aggregation-prone recombinant proteins is defined statistically rather than by the prevalence of a canonical native structure.

scholarly journals PARALLEL DELAUNAY REFINEMENT: ALGORITHMS AND ANALYSES

2007 ◽  
Vol 17 (01) ◽  
pp. 1-30 ◽  
Author(s):  
DANIEL A. SPIELMAN ◽  
SHANG-HUA TENG ◽  
ALPER ÜNGÖR
Keyword(s):  
Mesh Size ◽  
Constant Factor ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Delaunay Refinement ◽  
Steiner Points ◽  
Input Domain ◽  
Set Of Points ◽  
Refinement Algorithm

We present a parallel Delaunay refinement algorithm for generating well-shaped meshes in both two and three dimensions. Like its sequential counterparts, the parallel algorithm iteratively improves the quality of a mesh by inserting new points, the Steiner points, into the input domain while maintaining the Delaunay triangulation. The Steiner points are carefully chosen from a set of candidates that includes the circumcenters of poorly-shaped triangular elements. We introduce a notion of independence among possible Steiner points that can be inserted simultaneously during Delaunay refinements and show that such a set of independent points can be constructed efficiently and that the number of parallel iterations is O( log 2Δ), where Δ is the spread of the input — the ratio of the longest to the shortest pairwise distances among input features. In addition, we show that the parallel insertion of these set of points can be realized by sequential Delaunay refinement algorithms such as by Ruppert's algorithm in two dimensions and Shewchuk's algorithm in three dimensions. Therefore, our parallel Delaunay refinement algorithm provides the same shape quality and mesh-size guarantees as these sequential algorithms. For generating quasi-uniform meshes, such as those produced by Chew's algorithms, the number of parallel iterations is in fact O( log Δ). To the best of our knowledge, our algorithm is the first provably polylog(Δ) time parallel Delaunay-refinement algorithm that generates well-shaped meshes of size within a constant factor of the best possible.

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