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Article ; Online: Do an Altered Gut Microbiota and an Associated Leaky Gut Affect COVID-19 Severity?

Kim, Heenam Stanley

2021 Volume 12, Issue 1

Abstract: Coronavirus disease 2019 (COVID-19), which has been declared a pandemic, has exhibited a wide range of severity worldwide. Although this global variation is largely affected by socio-medical situations in each country, there is also high individual-level ...

Abstract	Coronavirus disease 2019 (COVID-19), which has been declared a pandemic, has exhibited a wide range of severity worldwide. Although this global variation is largely affected by socio-medical situations in each country, there is also high individual-level variation attributable to elderliness and certain underlying medical conditions, including high blood pressure, diabetes, and obesity. As both elderliness and the aforementioned chronic conditions are often associated with an altered gut microbiota, resulting in disrupted gut barrier integrity, and gut symptoms have consistently been associated with more severe illness in COVID-19 patients, it is possible that dysfunction of the gut as a whole influences COVID-19 severity. This article summarizes the accumulating evidence that supports the hypothesis that an altered gut microbiota and its associated leaky gut may contribute to the onset of gastrointestinal symptoms and occasionally to additional multiorgan complications that may lead to severe illness by allowing leakage of the causative coronavirus into the circulatory system.
MeSH term(s)	COVID-19/complications ; COVID-19/pathology ; COVID-19/virology ; Dysbiosis ; Gastrointestinal Diseases/complications ; Gastrointestinal Diseases/pathology ; Gastrointestinal Diseases/virology ; Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/pathology ; Intestinal Mucosa/virology ; SARS-CoV-2/pathogenicity ; Severity of Illness Index
Language	English
Publishing date	2021-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03022-20
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Two-Component-System-Governed Regulon That Includes a β-Lactamase Gene is Responsive to Cell Envelope Disturbance.

Lee, Dongju / Park, Jongwook / Yi, Hyojeong / Cho, Kwang-Hwi / Kim, Heenam Stanley

mBio

2022 Volume 13, Issue 4, Page(s) e0174922

Abstract: β-Lactamase production facilitates bacterial survival in nature and affects many infection therapies. However, much of its regulation remains unexplored. We used a genetics-based approach to identify a two-component system (TCS) present in a strain of ... ...

Abstract	β-Lactamase production facilitates bacterial survival in nature and affects many infection therapies. However, much of its regulation remains unexplored. We used a genetics-based approach to identify a two-component system (TCS) present in a strain of Burkholderia thailandensis essential for the regulated expression of a class A β-lactamase gene,
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Regulon ; Soil ; beta-Lactamases/genetics ; beta-Lactamases/metabolism ; beta-Lactams/pharmacology
Chemical Substances	Anti-Bacterial Agents ; Soil ; beta-Lactams ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2022-08-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.01749-22
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Article ; Online: Antibiotic Scars Left on the Gut Microbiota from the Stringent Response.

Yi, Hyojeong / Kim, Heenam Stanley

Trends in microbiology

2018 Volume 26, Issue 9, Page(s) 735–737

Abstract: Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene ... ...

Abstract	Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene regulatory system conserved in most gut bacteria, should not be overlooked.
MeSH term(s)	Anti-Bacterial Agents/adverse effects ; Bacteria/drug effects ; Cicatrix/chemically induced ; Cicatrix/microbiology ; Drug Tolerance ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/microbiology ; Guanosine Pentaphosphate ; Humans
Chemical Substances	Anti-Bacterial Agents ; Guanosine Pentaphosphate (38918-96-6)
Language	English
Publishing date	2018-07-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2018.06.003
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Article ; Online: Mutations in ArgS Arginine-tRNA Synthetase Confer Additional Antibiotic Tolerance Protection to Extended-Spectrum-β-Lactamase-Producing Burkholderia thailandensis.

Yi, Hyojeong / Park, Jongwook / Cho, Kwang-Hwi / Kim, Heenam Stanley

Antimicrobial agents and chemotherapy

2020 Volume 64, Issue 6

Abstract: Highly conserved PenI-type class A β-lactamase in pathogenic members ... ...

Abstract	Highly conserved PenI-type class A β-lactamase in pathogenic members of
MeSH term(s)	Amino Acyl-tRNA Synthetases/genetics ; Anti-Bacterial Agents/pharmacology ; Arginine ; Burkholderia/genetics ; Immune Tolerance ; Mutation ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; Arginine (94ZLA3W45F) ; beta-Lactamases (EC 3.5.2.6) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
Language	English
Publishing date	2020-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.02252-19
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Article: Antibiotic Scars Left on the Gut Microbiota from the Stringent Response

Yi, Hyojeong / Heenam Stanley Kim

Trends in microbiology. 2018 Sept., v. 26, no. 9

2018

Abstract	Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene regulatory system conserved in most gut bacteria, should not be overlooked.
Keywords	antibiotics ; intestinal microorganisms ; stress response
Language	English
Dates of publication	2018-09
Size	p. 735-737.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2018.06.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Role of gut-derived bacterial lipopolysaccharide and peripheral TLR4 in immobilization stress-induced itch aggravation in a mouse model of atopic dermatitis.

Cho, Da-Eun / Hong, Joon-Pyo / Kim, Yoongeun / Sim, Ju Yeon / Kim, Heenam Stanley / Kim, Song-Rae / Lee, Bombi / Cho, Hyo-Sung / Cho, Ik-Hyun / Shin, Sooan / Yeom, Mijung / Kwon, Soon-Kyeong / Lee, In-Seon / Park, Hijoon / Kim, Kyuseok / Hahm, Dae-Hyun

Scientific reports

2024 Volume 14, Issue 1, Page(s) 6263

Abstract: Psychological stress and intestinal leakage are key factors in atopic dermatitis (AD) recurrence and exacerbation. Here, we demonstrate the mechanism underlying bacterial translocation across intestinal epithelial barrier damaged due to stress and ... ...

Abstract	Psychological stress and intestinal leakage are key factors in atopic dermatitis (AD) recurrence and exacerbation. Here, we demonstrate the mechanism underlying bacterial translocation across intestinal epithelial barrier damaged due to stress and further aggravation of trimellitic anhydride (TMA)-induced itch, which remain unclear, in AD mice. Immobilization (IMO) stress exacerbated scratching bouts and colon histological damage, and increased serum corticosterone and lipopolysaccharide (LPS). Orally administered fluorescein isothiocyanate (FITC)-dextran and surgically injected (into the colon) Cy5.5-conjugated LPS were detected in the serum and skin after IMO stress, respectively. The relative abundance of aerobic or facultative anaerobic bacteria was increased in the colon mucus layer, and Lactobacillus murinus, E. coli, Staphylococcus nepalensis, and several strains of Bacillus sp. were isolated from the spleens and mesenteric lymph nodes. Oral antibiotics or intestinal permeability blockers, such as lubiprostone (Lu), 2,4,6-triaminopyrimidine (TAP) and ML-7, inhibited IMO stress-associated itch; however, it was reinduced through intradermal or i.p. injection of LPS without IMO stress. I.p. injection of TAK-242 (resatorvid), a TLR4 inhibitor, abrogated IMO stress-associated itch, which was also confirmed in TLR4-KO mice. IMO stress alone did not cause itch in naïve mice. IMO stress-induced itch aggravation in TMA-treated AD mice might be attributed to the translocation of gut-derived bacterial cells and LPS, which activates peripheral TLR4 signaling.
MeSH term(s)	Animals ; Mice ; Dermatitis, Atopic/metabolism ; Dermatitis, Atopic/pathology ; Disease Models, Animal ; Escherichia coli ; Lipopolysaccharides/metabolism ; Pruritus/chemically induced ; Toll-Like Receptor 4/metabolism
Chemical Substances	Lipopolysaccharides ; Toll-Like Receptor 4
Language	English
Publishing date	2024-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56936-z
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Article ; Online: Cell Wall Recycling-Linked Coregulation of AmpC and PenB β-Lactamases through ampD Mutations in Burkholderia cenocepacia.

Hwang, Junghyun / Kim, Heenam Stanley

Antimicrobial agents and chemotherapy

2015 Volume 59, Issue 12, Page(s) 7602–7610

Abstract: In many Gram-negative pathogens, mutations in the key cell wall-recycling enzyme AmpD (N-acetyl-anhydromuramyl-L-alanine amidase) affect the activity of the regulator AmpR, which leads to the expression of AmpC β-lactamase, conferring resistance to ... ...

Abstract	In many Gram-negative pathogens, mutations in the key cell wall-recycling enzyme AmpD (N-acetyl-anhydromuramyl-L-alanine amidase) affect the activity of the regulator AmpR, which leads to the expression of AmpC β-lactamase, conferring resistance to expanded-spectrum cephalosporin antibiotics. Burkholderia cepacia complex (Bcc) species also have these Amp homologs; however, the regulatory circuitry and the nature of causal ampD mutations remain to be explored. A total of 92 ampD mutants were obtained, representing four types of mutations: single nucleotide substitution (causing an amino acid substitution or antitermination of the enzyme), duplication, deletion, and IS element insertion. Duplication, which can go through reversion, was the most frequent type. Intriguingly, mutations in ampD led to the induction of two β-lactamases, AmpC and PenB. Coregulation of AmpC and PenB in B. cenocepacia, and likely also in many Bcc species with the same gene organization, poses a serious threat to human health. This resistance mechanism is of evolutionary optimization in that ampD is highly prone to mutations allowing rapid response to antibiotic challenge, and many of the mutations are reversible in order to resume cell wall recycling when the antibiotic challenge is relieved.
MeSH term(s)	Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Burkholderia cenocepacia/drug effects ; Burkholderia cenocepacia/genetics ; Burkholderia cenocepacia/metabolism ; Cell Wall/drug effects ; Cell Wall/genetics ; Cell Wall/metabolism ; Cephalosporin Resistance/genetics ; Cephalosporins/pharmacology ; DNA Transposable Elements ; Gene Expression Regulation, Bacterial ; Genetic Complementation Test ; Isoenzymes/genetics ; Isoenzymes/metabolism ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutation ; N-Acetylmuramoyl-L-alanine Amidase/genetics ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Polymorphism, Genetic ; Sequence Alignment ; beta-Lactamases/genetics ; beta-Lactamases/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Cephalosporins ; DNA Transposable Elements ; Isoenzymes ; AmpD protein, Bacteria (EC 3.5.1.28) ; N-Acetylmuramoyl-L-alanine Amidase (EC 3.5.1.28) ; AmpC beta-lactamases (EC 3.5.2.6) ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2015-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.01068-15
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Article ; Online: Mutations in MetG (methionyl-tRNA synthetase) and TrmD [tRNA (guanine-N1)-methyltransferase] conferring meropenem tolerance in Burkholderia thailandensis.

Yi, Hyojeong / Lee, Hyeri / Cho, Kwang-Hwi / Kim, Heenam Stanley

The Journal of antimicrobial chemotherapy

2017 Volume 73, Issue 2, Page(s) 332–338

Abstract: Objectives: Although meropenem is widely used to treat Burkholderia infections, the response of Burkholderia pathogens to this antibiotic is largely unexplored.: Methods: Burkholderia thailandensis, a model for Burkholderia spp., particularly ... ...

Abstract	Objectives: Although meropenem is widely used to treat Burkholderia infections, the response of Burkholderia pathogens to this antibiotic is largely unexplored. Methods: Burkholderia thailandensis, a model for Burkholderia spp., particularly Burkholderia mallei and Burkholderia pseudomallei, was challenged with a lethal level of meropenem and survivors were isolated. The genomes of two of the isolates were analysed to identify mutated genes and these genes were then specifically examined in more isolates to profile mutation diversity. Mutants were characterized to investigate the biological basis underlying survival against meropenem. Results: One of two genes associated with tRNA metabolism [metG or trmD, encoding methionyl-tRNA synthetase or tRNA (guanine-N1)-methyltransferase, respectively] was found to be mutated in the two survivors. A single nucleotide substitution and a frameshift mutation were found in metG and trmD, respectively. Five different substitution mutations affecting methionine- or tRNA-binding sites were found in metG during further screening. The mutants exhibited slowed growth and increased tolerance not only to meropenem but also various other antibiotics. This tolerance required intact RelA, a key stringent response. Conclusions: Specific mutations affecting the tRNA pool, particularly those in metG, play a pivotal role in the B. thailandensis response to meropenem challenge. This mechanism of antibiotic tolerance is important because it can reduce the effectiveness of meropenem and thereby facilitate chronic infection by Burkholderia pathogens. In addition, specific mutations found in MetG will prove useful in the effort to develop new drugs to completely inhibit this essential enzyme, while preventing stringent-response-mediated antibiotic tolerance in pathogens.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Burkholderia/drug effects ; Burkholderia/enzymology ; DNA Mutational Analysis ; Drug Tolerance ; Meropenem/pharmacology ; Methionine-tRNA Ligase/genetics ; Mutant Proteins/genetics ; Mutation ; tRNA Methyltransferases/genetics
Chemical Substances	Anti-Bacterial Agents ; Mutant Proteins ; tRNA Methyltransferases (EC 2.1.1.-) ; tRNA (guanine-N1-)-methyltransferase (EC 2.1.1.221) ; Methionine-tRNA Ligase (EC 6.1.1.10) ; Meropenem (FV9J3JU8B1)
Language	English
Publishing date	2017-11-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkx378
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Article ; Online: Non-catalytic-Region Mutations Conferring Transition of Class A β-Lactamases Into ESBLs

Thinh-Phat Cao / Hyojeong Yi / Immanuel Dhanasingh / Suparna Ghosh / Jin Myung Choi / Kun Ho Lee / Seol Ryu / Heenam Stanley Kim / Sung Haeng Lee

Frontiers in Molecular Biosciences, Vol

2020 Volume 7

Abstract: Despite class A ESBLs carrying substitutions outside catalytic regions, such as Cys69Tyr or Asn136Asp, have emerged as new clinical threats, the molecular mechanisms underlying their acquired antibiotics-hydrolytic activity remains unclear. We discovered ...

Abstract	Despite class A ESBLs carrying substitutions outside catalytic regions, such as Cys69Tyr or Asn136Asp, have emerged as new clinical threats, the molecular mechanisms underlying their acquired antibiotics-hydrolytic activity remains unclear. We discovered that this non-catalytic-region (NCR) mutations induce significant dislocation of β3-β4 strands, conformational changes in critical residues associated with ligand binding to the lid domain, dynamic fluctuation of Ω-loop and β3-β4 elements. Such structural changes increase catalytic regions’ flexibility, enlarge active site, and thereby accommodate third-generation cephalosporin antibiotics, ceftazidime (CAZ). Notably, the electrostatic property around the oxyanion hole of Cys69Tyr ESBL is significantly changed, resulting in possible additional stabilization of the acyl-enzyme intermediate. Interestingly, the NCR mutations are as effective for antibiotic resistance by altering the structure and dynamics in regions mediating substrate recognition and binding as single amino-acid substitutions in the catalytic region of the canonical ESBLs. We believe that our findings are crucial in developing successful therapeutic strategies against diverse class A ESBLs, including the new NCR-ESBLs.
Keywords	extended-spectrum β-lactamase ; non-catalytic-region ESBL ; ceftazidime ; antibiotic resistance ; X-ray crystallography ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Non-catalytic-Region Mutations Conferring Transition of Class A β-Lactamases Into ESBLs.

Cao, Thinh-Phat / Yi, Hyojeong / Dhanasingh, Immanuel / Ghosh, Suparna / Choi, Jin Myung / Lee, Kun Ho / Ryu, Seol / Kim, Heenam Stanley / Lee, Sung Haeng

Frontiers in molecular biosciences

2020 Volume 7, Page(s) 598998

Abstract	Despite class A ESBLs carrying substitutions outside catalytic regions, such as Cys69Tyr or Asn136Asp, have emerged as new clinical threats, the molecular mechanisms underlying their acquired antibiotics-hydrolytic activity remains unclear. We discovered that this non-catalytic-region (NCR) mutations induce significant dislocation of β3-β4 strands, conformational changes in critical residues associated with ligand binding to the lid domain, dynamic fluctuation of Ω-loop and β3-β4 elements. Such structural changes increase catalytic regions' flexibility, enlarge active site, and thereby accommodate third-generation cephalosporin antibiotics, ceftazidime (CAZ). Notably, the electrostatic property around the oxyanion hole of Cys69Tyr ESBL is significantly changed, resulting in possible additional stabilization of the acyl-enzyme intermediate. Interestingly, the NCR mutations are as effective for antibiotic resistance by altering the structure and dynamics in regions mediating substrate recognition and binding as single amino-acid substitutions in the catalytic region of the canonical ESBLs. We believe that our findings are crucial in developing successful therapeutic strategies against diverse class A ESBLs, including the new NCR-ESBLs.
Language	English
Publishing date	2020-11-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2020.598998
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