scholarly journals Assessment of Phenotype Relevant Amino Acid Residues in TEM-β-Lactamases by Mathematical Modelling and Experimental Approval

2021 ◽  
Vol 9 (8) ◽  
pp. 1726
Author(s):  
Sara Madzgalla ◽  
Helena Duering ◽  
Jana C. Hey ◽  
Svetlana Neubauer ◽  
Karl-Heinz Feller ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
Hydrolytic Activity ◽  
National Database ◽  
Amino Acid Residues ◽  
Antibiotic Resistant ◽  
Cephalosporin Resistance ◽  
Increased Sensitivity ◽  
Almost All ◽  
Inhibitor Resistance ◽  
Mutagenesis Study

Single substitutions or combinations of them alter the hydrolytic activity towards specific β-lactam-antibiotics and β-lactamase inhibitors of TEM-β-lactamases. The sequences and phenotypic classification of allelic TEM variants, as provided by the NCBI National Database of Antibiotic Resistant Organisms, does not attribute phenotypes to all variants. Some entries are doubtful as the data assessment differs strongly between the studies or no data on the methodology are provided at all. This complicates mathematical and bioinformatic predictions of phenotypes that rely on the database. The present work aimed to prove the role of specific substitutions on the resistance phenotype of TEM variants in, to our knowledge, the most extensive mutagenesis study. In parallel, the predictive power of extrapolation algorithms was assessed. Most well-known substitutions with direct impact on the phenotype could be reproduced, both mathematically and experimentally. Most discrepancies were found for supportive substitutions, where some resulted in antagonistic effects in contrast to previously described synergism. The mathematical modelling proved to predict the strongest phenotype-relevant substitutions accurately but showed difficulties in identifying less prevalent but still phenotype transforming ones. In general, mutations increasing cephalosporin resistance resulted in increased sensitivity to β-lactamase inhibitors and vice versa. Combining substitutions related to cephalosporin and β-lactamase inhibitor resistance in almost all cases increased BLI susceptibility, indicating the rarity of the combined phenotype.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Laboratory capability in Europe for foodborne viruses

2002 ◽  
Vol 7 (4) ◽  
pp. 61-65 ◽  
Author(s):  
B A Lopman ◽  
Y van Duynhoven ◽  
F X Hanon ◽  
M Reacher ◽  
M Koopmans ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Polymerase Chain Reaction ◽  
Human Serum ◽  
National Laboratory ◽  
National Database ◽  
Chain Reaction ◽  
Foodborne Viruses ◽  
Food Items ◽  
Polymerase Chain ◽  
Almost All

This report describes a survey of national laboratory capabilities of diagnostics and surveillance databases for foodborne viruses among the "Foodborne Viruses in Europe" consortium. All the countries have laboratories that can test for HAV antibody in human serum. Eight of the ten surveyed European countries maintain a national database of HAV cases. Food can be tested for the presence of HAV in Finland, Italy, Spain, France and Denmark. All surveyed countries have at least one laboratory that tests for Norwalk-like virus (NLV) by reverse transcriptase-polymerase chain reaction and all also have the capability to use electron microscopy. Five countries maintain a national database of NLV cases and nine maintain a national database of NLV outbreaks. Almost all participant countries have laboratories that can test for NLV in food items including shellfish.

scholarly journals Molecular Alterations in the Stomach of Tff1-Deficient Mice: Early Steps in Antral Carcinogenesis

2020 ◽  
Vol 21 (2) ◽  
pp. 644 ◽  
Author(s):  
Eva B. Znalesniak ◽  
Franz Salm ◽  
Werner Hoffmann
Keyword(s):  
Cysteine Residue ◽  
Molecular Forms ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Rt Pcr ◽  
Molecular Alterations ◽  
Protein Levels ◽  
Increased Sensitivity ◽  
A Minor ◽  
Deficient Mice

TFF1 is a peptide of the gastric mucosa co-secreted with the mucin MUC5AC. It plays a key role in gastric mucosal protection and repair. Tff1-deficient (Tff1KO) mice obligatorily develop antropyloric adenoma and about 30% progress to carcinomas. Thus, these mice represent a model for gastric tumorigenesis. Here, we compared the expression of selected genes in Tff1KO mice and the corresponding wild-type animals (RT-PCR analyses). Furthermore, we systematically investigated the different molecular forms of Tff1 and its heterodimer partner gastrokine-2 (Gkn2) in the stomach (Western blot analyses). As a hallmark, a large portion of murine Tff1 occurs in a monomeric form. This is unexpected because of its odd number of seven cysteine residues. Probably the three conserved acid amino acid residues (EEE) flanking the 7th cysteine residue allow monomeric secretion. As a consequence, the free thiol of monomeric Tff1 could have a protective scavenger function, e.g., for reactive oxygen/nitrogen species. Furthermore, a minor subset of Tff1 forms a disulfide-linked heterodimer with IgG Fc binding protein (Fcgbp). Of special note, in Tff1KO animals a homodimeric form of Gkn2 was observed. In addition, Tff1KO animals showed strongly reduced Tff2 transcript and protein levels, which might explain their increased sensitivity to Helicobacter pylori infection.

scholarly journals The P5A ATPase Spf1p is stimulated by phosphatidylinositol 4-phosphate and influences cellular sterol homeostasis

2019 ◽  
Vol 30 (9) ◽  
pp. 1069-1084 ◽  
Author(s):  
Danny Mollerup Sørensen ◽  
Henrik Waldal Holen ◽  
Jesper Torbøl Pedersen ◽  
Helle Juel Martens ◽  
Daniele Silvestro ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Endoplasmic Reticulum ◽  
Marked Change ◽  
Hydrolytic Activity ◽  
Genetic Interactions ◽  
Eukaryotic Cells ◽  
Lipid Bodies ◽  
Increased Sensitivity ◽  
Phosphatidylinositol 4 ◽  
P Type

P5A ATPases are expressed in the endoplasmic reticulum (ER) of all eukaryotic cells, and their disruption results in severe ER stress. However, the function of these ubiquitous membrane proteins, which belong to the P-type ATPase superfamily, is unknown. We purified a functional tagged version of the Saccharomyces cerevisiae P5A ATPase Spf1p and observed that the ATP hydrolytic activity of the protein is stimulated by phosphatidylinositol 4-phosphate (PI4P). Furthermore, SPF1 exhibited negative genetic interactions with SAC1, encoding a PI4P phosphatase, and with OSH1 to OSH6, encoding Osh proteins, which, when energized by a PI4P gradient, drive export of sterols and lipids from the ER. Deletion of SPF1 resulted in increased sensitivity to inhibitors of sterol production, a marked change in the ergosterol/lanosterol ratio, accumulation of sterols in the plasma membrane, and cytosolic accumulation of lipid bodies. We propose that Spf1p maintains cellular sterol homeostasis by influencing the PI4P-induced and Osh-mediated export of sterols from the ER.

scholarly journals Novel Carbapenemases FLC-1 and IMI-2 Encoded by an Enterobacter cloacae Complex Isolated from Food Products

2019 ◽  
Vol 63 (6) ◽  
Author(s):  
Michael S. M. Brouwer ◽  
Kamaleddin H. M. E. Tehrani ◽  
Michel Rapallini ◽  
Yvon Geurts ◽  
Arie Kant ◽  
...  
Keyword(s):  
General Population ◽  
Enterobacter Cloacae ◽  
Hydrolytic Activity ◽  
Resistant Bacteria ◽  
Human Consumption ◽  
The Novel ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Class A ◽  
Enterobacter Cloacae Complex

ABSTRACT Food for human consumption is screened widely for the presence of antibiotic-resistant bacteria to assess the potential for transfer of resistant bacteria to the general population. Here, we describe an Enterobacter cloacae complex isolated from imported seafood that encodes two carbapenemases on two distinct plasmids. Both enzymes belong to Ambler class A β-lactamases, the previously described IMI-2 and a novel family designated FLC-1. The hydrolytic activity of the novel enzyme against aminopenicillins, cephalosporins, and carbapenems was determined.

scholarly journals Mechanisms of Resistance to Ceftolozane/Tazobactam in Pseudomonas aeruginosa: Results of the GERPA Multicenter Study

2020 ◽  
Author(s):  
Damien Fournier ◽  
Romain Carrière ◽  
Maxime Bour ◽  
Emilie Grisot ◽  
Pauline Triponney ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Hydrolytic Activity ◽  
Resistance Mechanisms ◽  
Group 3 ◽  
High Production ◽  
Resistant Strains ◽  
Recycling Pathway ◽  
French Hospital ◽  
Almost All ◽  
Moderately Resistant

Resistance mechanisms of Pseudomonas aeruginosa to ceftolozane/tazobactam (C/T) were assessed on a collection of 420 nonredundant strains non-susceptible to ceftazidime (MIC > 8 μg/ml) and/or imipenem (> 4 μg/ml), collected by 36 French hospital laboratories over a one month period (GERPA study). Rates of C/T resistance (MIC > 4/4 μg/ml) were equal to 10% in this population (42/420 strains), and 23.2% among the isolates resistant to both ceftazidime and imipenem (26/112). A first group of 21 strains (50%) was found to harbor various extended-spectrum β-lactamases (1 OXA-14; 2 OXA-19; 1 OXA-35; 1 GES-9; 3 PER-1), carbapenemases (2 GES-5; 1 IMP-8; 8 VIM-2), or both (1 VIM-2/OXA-35; 1 VIM-4/SHV-2a). All the strains of this group belonged to widely distributed epidemic clones (ST111, ST175, CC235, ST244, ST348, ST654), and were highly resistant to almost all the antibiotics tested except colistin. A second group was composed of 16 (38%) isolates moderately resistant to C/T (MIC from 8/4 to 16/4 μg/ml), of which 7 were related to international clones (ST111, ST253, CC274, ST352, ST386). As demonstrated by targeted mass spectrometry, cloxacillin-based inhibition tests and gene blaPDC deletion experiments, this resistance phenotype was correlated to an extremely high production of cephalosporinase PDC. In part accounting for this strong PDC upregulation, genomic analyses revealed the presence of mutations in regulator AmpR (D135N/G in 6 strains) and enzymes of the peptidoglycan recycling pathway such as AmpD, PBP4, and Mpl (9 strains). Finally, all the 5 (12%) remaining C/T resistant strains (group 3) appeared to encode PDC variants with mutations known to improve the hydrolytic activity of the β-lactamase to ceftazidime and C/T (F147L, ΔL223-Y226, E247K, N373I). Collectively, our results highlight the importance of both intrinsic and transferable mechanisms in C/T resistant P. aeruginosa. Which mutational events lead some clinical strains to massively produce the natural cephalosporinase PDC remains incompletely understood.

scholarly journals TEM-89 β-Lactamase Produced by a Proteus mirabilis Clinical Isolate: New Complex Mutant (CMT 3) with Mutations in both TEM-59 (IRT-17) and TEM-3

2001 ◽  
Vol 45 (12) ◽  
pp. 3591-3594 ◽  
Author(s):  
Catherine Neuwirth ◽  
Stephanie Madec ◽  
Eliane Siebor ◽  
Andre Pechinot ◽  
Jean-Marie Duez ◽  
...  
Keyword(s):  
Amino Acid ◽  
Clinical Isolate ◽  
Amino Acid Substitution ◽  
Proteus Mirabilis ◽  
Hydrolytic Activity ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid ◽  
Clinical Strain ◽  
Almost All

ABSTRACT TEM-89 (CMT-3) is the first complex mutant β-lactamase produced by a clinical strain of Proteus mirabilis (strain Pm 631). This new enzyme, which has a pI of 6.28, is derived from TEM-3 and has a single amino acid substitution also encountered in TEM-59 (inhibitor-resistant TEM β-lactamase IRT-17): Ser-130 to Gly. TEM-89 hydrolyzed penicillins to the same extent that TEM-3 did but lost almost all hydrolytic activity for cephalosporins and, like TEM-59, was highly resistant to inhibitors.

scholarly journals Molecular Characterization of a Novel Plasmid-Encoded Cefotaximase (CTX-M-12) Found in Clinical Klebsiella pneumoniae Isolates from Kenya

2001 ◽  
Vol 45 (7) ◽  
pp. 2141-2143 ◽  
Author(s):  
S. Kariuki ◽  
J. E. Corkill ◽  
G. Revathi ◽  
R. Musoke ◽  
C. A. Hart
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gel Electrophoresis ◽  
Direct Sequencing ◽  
Hydrolytic Activity ◽  
Pulsed Field Gel Electrophoresis ◽  
Chromosomal Dna ◽  
National Hospital ◽  
Cephalosporin Resistance ◽  
M 12

ABSTRACT Nine Klebsiella pneumoniae isolates, six from blood and three from cerebrospinal fluid of newborn babies at Kenyatta National Hospital, Nairobi, Kenya, were analyzed for the mechanism of cephalosporin resistance. By using pulsed-field gel electrophoresis ofXbaI-digested chromosomal DNA, all the nine isolates were found to be clonal. PCR and direct sequencing revealed a novel extended-spectrum β-lactamase, which we designated CTX-M-12. It has a more potent hydrolytic activity against cefotaxime than against ceftazidime and a pI of 9.0 and is encoded on a large self-transferable ca. 160-kbp plasmid.

scholarly journals LuxS-Mediated Signaling in Streptococcus mutans Is Involved in Regulation of Acid and Oxidative Stress Tolerance and Biofilm Formation

2004 ◽  
Vol 186 (9) ◽  
pp. 2682-2691 ◽  
Author(s):  
Zezhang T. Wen ◽  
Robert A. Burne
Keyword(s):  
Streptococcus Mutans ◽  
Response Regulator ◽  
Regulatory Protein ◽  
Protein A ◽  
Signal Recognition Particle ◽  
Northern Hybridization ◽  
Wild Type ◽  
Increased Sensitivity ◽  
Mutant Phenotypes ◽  
Almost All

ABSTRACT LuxS-mediated quorum sensing has recently been shown to regulate important physiologic functions and virulence in a variety of bacteria. In this study, the role of luxS of Streptococcus mutans in the regulation of traits crucial to pathogenesis was investigated. Reporter gene fusions showed that inactivation of luxS resulted in a down-regulation of fructanase, a demonstrated virulence determinant, by more than 50%. The LuxS-deficient strain (TW26) showed increased sensitivity to acid killing but could still undergo acid adaptation. Northern hybridization revealed that the expression of RecA, SmnA (AP endonuclease), and Nth (endonuclease) were down-regulated in TW26, especially in early-exponential-phase cells. Other down-regulated genes included ffh (a signal recognition particle subunit) and brpA (biofilm regulatory protein A). Interestingly, the luxS mutant showed an increase in survival rate in the presence of hydrogen peroxide (58.8 mM). The luxS mutant formed less biofilm on hydroxylapatite disks, especially when grown in biofilm medium with sucrose, and the mutant biofilms appeared loose and hive-like, whereas the biofilms of the wild type were smooth and confluent. The mutant phenotypes were complemented by exposure to supernatants from wild-type cultures. Two loci, smu486 and smu487, were identified and predicted to encode a histidine kinase and a response regulator. The phenotypes of the smu486 smu487 mutant were, in almost all cases, similar to those of the luxS mutant, although our results suggest that this is not due to AI-2 signal transduction via Smu486 and Smu487. This study demonstrates that luxS-dependent signaling plays critical roles in modulating key virulence properties of S. mutans.

scholarly journals Phylogenetic, Expression, and Bioinformatic Analysis of theABC1Gene Family inPopulus trichocarpa

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Zhanchao Wang ◽  
Haizhen Zhang ◽  
Jingli Yang ◽  
Yunlin Chen ◽  
Xuemei Xu ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Signal Transduction Pathway ◽  
Bioinformatic Analysis ◽  
Wood Formation ◽  
Cellulose Synthesis ◽  
Amino Acid Residues ◽  
Element Analysis ◽  
Aba Signal Transduction ◽  
Almost All

We studied 17ABC1genes inPopulus trichocarpa, all of which contained anABC1domain consisting of about 120 amino acid residues. Most of theABC1gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19Populuschromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap,PtrABC1P14was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promotercis-element analysis indicated that almost all of theABC1genes contained one or twocis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promotercis-element analysis.

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