Contrast analysis of the composition of ribosomes extracted with different purification procedures

2000 ◽  
Vol 33 (4) ◽  
pp. 1113-1118 ◽  
Author(s):  
Giuseppe Briganti ◽  
Rita Giordano ◽  
Paola Londei ◽  
Francesco Valle
Keyword(s):  
Particle Density ◽  
Buoyant Density ◽  
Bulk Water ◽  
Water Molecules ◽  
Experimental Conditions ◽  
Reliable Technique ◽  
E Coli ◽  
Contrast Analysis ◽  
Definition Of ◽  
Contour Surface

The composition and hydration ofE. coliribosomes isolated with different purification protocols has been analysed by combining two experimental techniques: measurements of small-angle neutron scattering (SANS), for two different isotopic solvent compositions, and refractive index (RI) increments. From the contrast between the solvent and solute scattering densities and the molar polarizability, determined experimentally with SANS and RI measurements, three independent equations are obtained and three unknown quantities are determined: (i) the volume of the solute hydrated skeletonVs, (ii) the material contained in it, namely the biological components, intrinsic (rRNA and proteins) and extrinsic, such as aminoacylsynthetase and elongation factors, (iii) the number of water molecules structurally bound to the ribosome and non-exchangeable with the solvent. From the form factor at infinite contrast, a second definition of the solute volume is obtained, V_s^c, which represents the volume within the contour surface of the ribosome. This value is generally larger thanVsand can include a certain amount of water molecules,i.e.those inside the volume (V_s^c −Vs). Considering the molar volume of this water to be equal to that of the bulk water, it is possible to evaluate its amount. The particle density calculated from the ribosome components in V_s^c, including proteins, RNA, bound and unbound water molecules, corresponds to the buoyant density measured forE. coli70S particles. The two ribosomal preparations display different performances in protein synthesis; hence the results indicate that the optimal condition corresponds to a wider skeleton and contour volume but containing a smaller amount of segregated water molecules. It is believed that the method provides a reliable technique to determine the composition of ribosomes under various experimental conditions.

scholarly journals Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicity

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hsien-Ya Lin ◽  
Chia-Yu Chen ◽  
Ting-Chien Lin ◽  
Lun-Fu Yeh ◽  
Wei-Che Hsieh ◽  
...  
Keyword(s):  
Cancer Metabolism ◽  
Glucuronic Acid ◽  
Intestinal Epithelial Cells ◽  
Primary Treatment ◽  
Water Molecules ◽  
Intestinal Epithelial ◽  
E Coli ◽  
Severe Diarrhea ◽  
Coordinated Water ◽  
Consequent Increase

AbstractIrinotecan inhibits cell proliferation and thus is used for the primary treatment of colorectal cancer. Metabolism of irinotecan involves incorporation of β-glucuronic acid to facilitate excretion. During transit of the glucuronidated product through the gastrointestinal tract, an induced upregulation of gut microbial β-glucuronidase (GUS) activity may cause severe diarrhea and thus force many patients to stop treatment. We herein report the development of uronic isofagomine (UIFG) derivatives that act as general, potent inhibitors of bacterial GUSs, especially those of Escherichia coli and Clostridium perfringens. The best inhibitor, C6-nonyl UIFG, is 23,300-fold more selective for E. coli GUS than for human GUS (Ki = 0.0045 and 105 μM, respectively). Structural evidence indicated that the loss of coordinated water molecules, with the consequent increase in entropy, contributes to the high affinity and selectivity for bacterial GUSs. The inhibitors also effectively reduced irinotecan-induced diarrhea in mice without damaging intestinal epithelial cells.

scholarly journals Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Kingshuk Mukherjee ◽  
Massimiliano Rossi ◽  
Leena Salmela ◽  
Christina Boucher
Keyword(s):  
Single Molecule ◽  
De Bruijn Graph ◽  
Anabas Testudineus ◽  
E Coli ◽  
Genome Wide ◽  
A Genome ◽  
De Bruijn ◽  
Optical Maps ◽  
Definition Of ◽  
Numeric Representation

AbstractGenome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper.

Intercalation Processes in Cobalt Substituted Nickel Oxyhydroxides

1990 ◽  
Vol 210 ◽  
Author(s):  
Claude Delmas
Keyword(s):  
Ir Spectroscopy ◽  
Mechanical Treatment ◽  
Positive Charge ◽  
Van Der Waals ◽  
The Other ◽  
Hydrolysis Reaction ◽  
Water Molecules ◽  
Layered Oxides ◽  
Experimental Conditions ◽  
Cobalt Ions

AbstractChimie douce reactions (hydrolysis and reduction) from layered oxides : NaNiO2, NaxCoO2 and NaNil-xCoxO2 lead to numerous oxyhydroxides and hydroxides which differ by the composition of the intersheet space.According to the experimental conditions of the hydrolysis reaction, the oxyhydroxides can be unhydrated or intercalated with one or two layers of water molecules. From the most hydrated phases, the other ones can be obtained by chemical, thermal and even mechanical treatment.The reduction of Co-substituted nickel oxyhydroxides leads to hydroxides in which nickel and cobalt ions are respectively divalent and trivalent. In order to compensate the excess of positive charge in the (Ni, Co)O2 sheet, anions (OH-, CO32-, SO42-, NO3-) are inserted in the Van der Waals gap.For the highest anion amounts, well ordered α*-type materials are obtained. Water molecules are simultaneously inserted in the interslab space. Their structure is strongly related to the hydrotalcite one. When the amouit of anions in the intersheet space is not sufficient, interstratified materials are obtained. In this case the (Ni,Co)(OH)2 slabs are separated by a layer of CO32- anions and water molecules (α*-type) or by an empty Van der Waals gap (β(II)-type). The amount of α*-type planes in the structure increases with the cobalt amount. All these materials have been characterized by IR spectroscopy which allows to detect the existence of two types of O-H bonds (free in α*-type plane or hydrogen bonded in ²(II)-type plane).

Role of magnetic resonance ventriculography in multiloculated hydrocephalus

2013 ◽  
Vol 11 (6) ◽  
pp. 697-703 ◽  
Author(s):  
Gurpreet S. Gandhoke ◽  
Paolo Frassanito ◽  
Nagesh Chandra ◽  
Bal K. Ojha ◽  
Anoop Singh
Keyword(s):  
Magnetic Resonance ◽  
Endoscopic Treatment ◽  
Ventricular System ◽  
Third Ventriculostomy ◽  
Csf Flow ◽  
Reliable Technique ◽  
Accurate Definition ◽  
Multiloculated Hydrocephalus ◽  
Definition Of ◽  
Complex Cases

Object In this paper the authors' goal was to investigate the clinical usefulness of Gd-enhanced MR ventriculography (MRV) in pediatric patients affected by multiloculated hydrocephalus. Methods Eighteen patients (11 boys and 7 girls, age range 2–14 months) with a diagnosis of multiloculated hydrocephalus were included in the study. After injection of gadodiamide (0.02–0.04 mmol) into the lateral ventricle by tapping the anterior fontanel, sagittal, coronal, and axial T1-weighted MR images were acquired. The location of the septations and the sites of obstruction of CSF flow were assessed. Postoperative MRV was obtained to confirm the results of endoscopic treatment in most complex cases. Results No adverse events were observed after injection of contrast medium into the ventricular system. Preoperative MRV accurately defined the exact morphology of septae and ventricular walls in all cases. In 1 case the diagnosis of multiloculated hydrocephalus was ruled out. Sites of obstruction of CSF flow within the ventricular system were also well established. In 4 cases the multiple compartments were proven to intercommunicate. Postoperative MRV was useful in assessing the functional status of third ventriculostomy, aqueductoplasty, and other endoscopic fenestrations. Conclusions Magnetic resonance ventriculography is a safe, effective, and reliable technique. The accurate definition of the anatomy of the ventricles and the site of obstruction in multiloculated hydrocephalus can help to plan the most appropriate treatment and minimize the number of procedures. Although MRV is also useful during postoperative follow-up to determine the results of endoscopic treatment, it should be limited to particularly complex cases, due to its invasiveness.

scholarly journals Ein Wasserstoffisotopieeffekt im CuSO4 * 5H2O

1969 ◽  
Vol 24 (10) ◽  
pp. 1502-1511
Author(s):  
Karl Heinzinger
Keyword(s):  
Water Vapor ◽  
Aqueous Solutions ◽  
Separation Factor ◽  
Room Temperature ◽  
Copper Ion ◽  
Hydrogen Isotopes ◽  
Bulk Water ◽  
Water Molecules ◽  
Hydration Water ◽  
Sulfate Solutions

Abstract There are two kinds of water in CuSO4·5H2O differing by their binding in the crystal. The oxygen of four water molecules is bonded to the copper ion, that of the fifth molecule is hydrogen bonded. It is shown that the D/H ratios of these two kinds of water differ by 5.7%, the light isotope being enriched in the water molecules coordinated with the copper ion. The results show that there is no exchange of the hydrogen isotopes during the time needed for dehydration at room temperature which takes several days. The assumption has been confirmed that the water coordinated with the copper ion leaves the crystal first on dehydration at temperatures below 50 °C. Additional measurements of the separation factor for the hydrogen isotopes between water vapor and copper sulfate solutions allow conclusions on the fractionation of the hydrogen isotopes between bulk water and hydration water in aqueous solutions.

Distribution of Pathogens in Central Line–Associated Bloodstream Infections among Patients with and without Neutropenia following Chemotherapy Evidence for a Proposed Modification to the Current Surveillance Definition

2013 ◽  
Vol 34 (2) ◽  
pp. 171-175 ◽  
Author(s):  
James P. Steinberg ◽  
Chad Robichaux ◽  
Sheri Chernetsky Tejedor ◽  
Mary Dent Reyes ◽  
Jesse T. Jacob
Keyword(s):  
Bloodstream Infections ◽  
Central Line ◽  
University Hospitals ◽  
Central Venous ◽  
E Coli ◽  
National Healthcare Safety Network ◽  
Proposed Modification ◽  
Definition Of ◽  
Hospital Acquired ◽  
Study Hospital

Objective.Many bloodstream infections (BSIs) occurring in patients with febrile neutropenia following cytotoxic chemotherapy are due to translocation of intestinal microbiota. However, these infections meet the National Healthcare Safety Network (NHSN) definition of central line-associated BSIs (CLABSIs). We sought to determine the differences in the microbiology of NHSN-defined CLABSIs in patients with and without neutropenia and, using these data, to propose a modification of the CLABSI definition.Design.Retrospective review.Setting.Two large university hospitals over 18 months.Methods.All hospital-acquired BSIs occurring in patients with central venous catheters in place were classified using the NHSN CLABSI definition. Patients with postchemotherapy neutropenia (500 neutrophils/mm3or lower) at the time of blood culture were considered neutropenic. Pathogens overrepresented in the neutropenic group were identified to inform development of a modified CLABSI definition.Results.Organisms that were more commonly observed in the neutropenic group compared with the nonneutropenic group includedEscherichia coli(22.7% vs 2.5%;P< .001) but not other Enterobacteriaceae,Enterococcus faecium(18.2% vs 6.1%;P= .002), and streptococci (18.2% vs 0%;P< .001). Application of a modified CLABSI definition (removing BSI with enterococci, streptococci, orE. coli) excluded 33 of 66 neutropenic CLABSIs and decreased the CLABSI rate in one study hospital with large transplant and oncology populations from 2.12 to 1.79 cases per 1,000 line-days.Conclusions.Common gastrointestinal organisms were more common in the neutropenia group, suggesting that many BSIs meeting the NHSN criteria for CLABSI in the setting of neutropenia may represent translocation of gut organisms. These findings support modification of the NHSN CLABSI definition.

scholarly journals Genotypic and Phenotypic Traits That Distinguish Neonatal Meningitis-Associated Escherichia coli from Fecal E. coli Isolates of Healthy Human Hosts

2012 ◽  
Vol 78 (16) ◽  
pp. 5824-5830 ◽  
Author(s):  
Catherine M. Logue ◽  
Curt Doetkott ◽  
Paul Mangiamele ◽  
Yvonne M. Wannemuehler ◽  
Timothy J. Johnson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Group ◽  
Neonatal Meningitis ◽  
Phenotypic Traits ◽  
Healthy Human ◽  
Content Type ◽  
Plasmid Content ◽  
E Coli ◽  
Healthy Humans ◽  
Definition Of

ABSTRACTNeonatal meningitisEscherichia coli(NMEC) is one of the top causes of neonatal meningitis worldwide. Here, 85 NMEC and 204 fecalE. coliisolates from healthy humans (HFEC) were compared for possession of traits related to virulence, antimicrobial resistance, and plasmid content. This comparison was done to identify traits that typify NMEC and distinguish it from commensal strains to refine the definition of the NMEC subpathotype, identify traits that might contribute to NMEC pathogenesis, and facilitate choices of NMEC strains for future study. A large number ofE. colistrains from both groups were untypeable, with the most common serogroups occurring among NMEC being O18, followed by O83, O7, O12, and O1. NMEC strains were more likely than HFEC strains to be assigned to the B2 phylogenetic group. Few NMEC or HFEC strains were resistant to antimicrobials. Genes that best discriminated between NMEC and HFEC strains and that were present in more than 50% of NMEC isolates were mainly from extraintestinal pathogenicE. coligenomic and plasmid pathogenicity islands. Several of these defining traits had not previously been associated with NMEC pathogenesis, are of unknown function, and are plasmid located. Several genes that had been previously associated with NMEC virulence did not dominate among the NMEC isolates. These data suggest that there is much about NMEC virulence that is unknown and that there are pitfalls to studying single NMEC isolates to represent the entire subpathotype.

scholarly journals Proton Transfer in Bulk Water using the Full Adaptive QM/MM Method: Integration of Solute- and Solvent-Adaptive Approaches

2020 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Masayuki Yamada ◽  
Yohichi Suzuki
Keyword(s):  
Proton Transfer ◽  
Control Algorithm ◽  
Adaptive Methods ◽  
Bulk Water ◽  
Water Molecules ◽  
Adaptive Treatment ◽  
Grotthuss Mechanism ◽  
Hydronium Ions ◽  
Method Integration ◽  
Large Systems

<div><div>The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that increases the accessibility of local electronic structures of large systems.</div><div> The technique combines the benefit of accuracy found in the QM method and that of cost efficiency found in the MM method.</div><div> However, it is difficult to directly apply the QM/MM method to the dynamics of solution systems, particularly for proton transfer. </div><div> As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ions and solvent water molecules. </div><div> Hence, when the QM/MM method is applied, an adaptive treatment, namely on-the-fly revisions on molecular definitions, is required for both the solute and solvent. </div><div> Although several solvent-adaptive methods have been proposed, a full adaptive framework, which is an approach that also considers adaptation for solutes, remains untapped. In this paper, we propose a new numerical expression for the coordinates of the excess proton and its control algorithm.</div><div> Furthermore, we confirm that this method can stably and accurately simulate proton transfer dynamics in bulk water.</div></div>

scholarly journals STUDY OF ANTIBACTERIAL ACTIVITY OF THE PREPARATIONS WITH DIOXIDINE AND LEVOFLOXACIN ON MAIN PURULENT-INFLAMMATORY PROCESSES PATHOGENS

2021 ◽  
Vol 74 (9) ◽  
pp. 2109-2111
Author(s):  
Evheniia A. Shtaniuk ◽  
Oleksandra O. Vovk ◽  
Larisa V. Krasnikova ◽  
Yuliia I. Polyvianna ◽  
Tetiana I. Kovalenko
Keyword(s):  
Antibacterial Activity ◽  
Water Soluble ◽  
Diffusion Method ◽  
E Coli ◽  
Mueller Hinton ◽  
Microbiological Methods ◽  
Pure Cultures ◽  
Inflammatory Processes ◽  
Definition Of

The aim: Study of antibacterial activity of the preparations, containing antiseptic dioxidine and antibiotic levofloxacin in vitro on standard strains of main optional-anaerobic pathogens of purulent-inflammatory processes of surgical wounds S. aureus, E. coli, P. aeruginosa and definition of more effective ones on them. Materials and methods: Solutions of dioxidine 1.2 %, dioxidine 1.2% with decamethaxin, Dioxisole, water soluble ointment with dioxidine 1.2% and levofloxacin 0.1% with decamethaxin were used in experiment. Antibacterial activity was studied on standard strains of S. aureus АТСС 25923, E. coli АТСС 25922, P. aeruginosa АТСС 27853. Distinguishing and identification of pure cultures of bacteria was done according to generally accepted microbiological methods. Determination of purulent-inflammatory processes pathogens sensitivity was done by disco-diffuse method on Mueller-Hinton medium. Antibacterial activity of solutions and ointments was studied with the help of agar diffusion method (“well” method) according to methodic recommendations. Each investigation was repeated 6 times. Method of variation statistics was used for the research results analysis. Results: All antibacterial preparations under study are effective and highly effective on S. aureus АТСС 25923, E. coli АТСС 25922, P. aeruginosa АТСС 27853. Solution with 1.2 % dioxidine with decamethaxin and ointment with 0.1 % levofloxacin and decamethaxin have larger growth retardation zones towards S. aureus and P. aeruginosa. E. coli strains are more sensitive to the solution of Dioxisole and ointment with 1.2 % dioxidine. Conclusions: All strains are sensitive, most of them are highly sensitive, up to 5 antibacterial preparations under study in vitro.

scholarly journals Enteroaggregative Escherichia coli: epidemiology, virulence and detection

2007 ◽  
Vol 56 (1) ◽  
pp. 4-8 ◽  
Author(s):  
Andrej Weintraub
Keyword(s):  
Escherichia Coli ◽  
Tissue Culture ◽  
Watery Diarrhoea ◽  
Biological Assays ◽  
E Coli ◽  
The Past ◽  
Sporadic Cases ◽  
Trained Staff ◽  
Definition Of ◽  
Specific Virulence

Enteroaggregative Escherichia coli (EAEC) is a subgroup of diarrhoeagenic E. coli (DEC) that during the past decade has received increasing attention as a cause of watery diarrhoea, which is often persistent. EAEC have been isolated from children and adults worldwide. As well as sporadic cases, outbreaks of EAEC-caused diarrhoea have been described. The definition of EAEC is the ability of the micro-organism to adhere to epithelial cells such as HEp-2 in a very characteristic ‘stacked-brick’ pattern. Although many studies searching for specific virulence factor(s) unique for this category of DEC have been published it is still unknown why the EAEC cause persistent diarrhoea. In addition, the aggregative property of EAEC causes a lot of problems in serotyping due to the cells auto-agglutinating. The gold standard for identification of EAEC includes isolation of the agent and an adherence assay using tissue culture, viz. HEp-2 cells. This assay is in most cases reliable; however, emergence of ‘atypical’ EAEC has been described in several publications. In addition, the HEp-2 assay is time consuming, demands a tissue culture lab and trained staff. Several molecular biological assays have been described, however, none show 100 % specificity.

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