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  1. Article ; Online: Environmental DNA transformation resulted in an active phage in Escherichia coli.

    Karaynir, Abdulkerim / Bozdoğan, Bülent / Salih Doğan, Hanife

    PloS one

    2023  Volume 18, Issue 10, Page(s) e0292933

    Abstract: The achievement of an active biological entity from environmental DNA is important in the field of phage. In this study, the environmental DNA extracted from hospital wastewater was transferred into Escherichia coli DH10B and Escherichia coli BL21 with ... ...

    Abstract The achievement of an active biological entity from environmental DNA is important in the field of phage. In this study, the environmental DNA extracted from hospital wastewater was transferred into Escherichia coli DH10B and Escherichia coli BL21 with chemical transformation and electroporation. After transformation, overnight cultures were filtered and used as phage source. The efficacies of the techniques were evaluated with spot test and double-layer agar assay. The emerged phage, named as ADUt, was purified and host-range analysis was performed. Phage DNA was isolated, sequenced and restriction profile was determined. The genome was assembled. The phylogenetic tree was constructed via VipTree. The extracted DNA resulted in active phage by the transformation of E. coli DH10B, but not E. coli BL21. The chemical transformation was found more successful than electroporation. ADUt phage was found to be polyvalent and effective against limited strains of Shigella and Escherichia genera. The phage genome size and GC ratio are 166904 bp and 35.67%, respectively. ADUt is a member of Straboviridae family and Tequatrovirus genus. This is the first study that uses environmental DNA for acquiring active phage, which may be an important source of new phage discovery. The result showed that DNA transformation yields active bacteriophage with both chemical transformation and electroporation.
    MeSH term(s) Bacteriophages/genetics ; Escherichia coli/genetics ; DNA, Environmental ; Phylogeny ; Myoviridae/genetics
    Chemical Substances DNA, Environmental
    Language English
    Publishing date 2023-10-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0292933
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  2. Article ; Online: Two novel phages, Klebsiella phage GADU21 and Escherichia phage GADU22, from the urine samples of patients with urinary tract infection.

    Salih Doğan, Hanife / Karaynir, Abdulkerim / Yilmaz, Ülkü İrem / Başgöz, Bilgin Bahadır / Hoşbul, Tuğrul / Bozdoğan, Bülent

    Virus genes

    2024  Volume 60, Issue 2, Page(s) 208–221

    Abstract: Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate ... ...

    Abstract Phages are found in a wide variety of places where bacteria exist including body fluids. The aim of the present study was to isolate phages from the urine samples of patients with urinary tract infection. The 10 urine samples were cultured to isolate bacteria and also used as phage sources against the isolated bacteria. From 10 urine samples with positive cultures, 3 phages were isolated (33%) and two of them were further studied. The Klebsiella phage GADU21 and Escherichia phage GADU22 phages infected Klebsiella pneumonia and Escherichia coli, respectively. Among the tested 14 species for host range analysis, the Klebsiella phage GADU21 was able to infect two species which are Klebsiella pneumonia and Proteus mirabilis, and Escherichia phage GADU22 was able to infect four species which are Shigella flexneri, Shigella sonnei and Escherichia coli. Among different isolates of the indicator bacteria for each phage, GADU21 infected half of the tested 20 Klebsiella pneumonia isolates while GADU22 infected 85% of the tested 20 E. coli isolates. The genome sizes and GC ratios were 75,968 bp and 44.4%, and 168,023 bp and 35.3% for GADU21 and GADU22, respectively. GADU21 and GADU22 were both lytic and had no antibiotic resistance and virulence genes. GADU21 was homologue with Klebsiella phage vB_KpP_FBKp27 but only 88% of the genome was covered by this phage. The non-covered parts of the GADU21 genome included genes for tail-fiber-proteins and HNH-endonuclease. GADU22 had 94.8% homology with Escherichia phage vB_Eco_OMNI12 and had genes for immunity proteins. Phylogenetic analysis showed GADU21 and GADU22 were members of Schitoviridae family and Efbeekayvirus genus and Straboviridae family and Tevenvirinae genus, respectively. VIRIDIC analysis classified these phages in new species clusters. Our study demonstrated the possibility to use infected body fluids as phage sources to isolate novel phages. GADU21 is the first reported Klebsiella phage isolated from human body fluid. The absence of virulence and antibiotic resistance genes in their genomes makes the phages a potential therapeutic tool against infections.
    MeSH term(s) Humans ; Bacteriophages/genetics ; Escherichia coli/genetics ; Klebsiella/genetics ; Phylogeny ; Urinary Tract Infections/microbiology ; Bacteria ; Klebsiella pneumoniae/genetics ; Pneumonia
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-024-02052-z
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  3. Article ; Online: Characterization, genome analysis and antibiofilm efficacy of lytic Proteus phages RP6 and RP7 isolated from university hospital sewage.

    Ali, Sahd / Karaynir, Abdulkerim / Salih, Hanife / Öncü, Serkan / Bozdoğan, Bülent

    Virus research

    2023  Volume 326, Page(s) 199049

    Abstract: The crystalline formation of biofilms by Proteus blocks the urine flow which often complicates the health care of catheterized patients. Bacteriophages has been highlighted as a promising tool to control biofilm-mediated bacterial infections. Here, we ... ...

    Abstract The crystalline formation of biofilms by Proteus blocks the urine flow which often complicates the health care of catheterized patients. Bacteriophages has been highlighted as a promising tool to control biofilm-mediated bacterial infections. Here, we isolated and characterized two newly isolated lytic phages capable of infecting clinical isolates of P. mirabilis and P. vulgaris. Moreover, insights regarding the biological and molecular characterization were analysed. Both RP6 and RP7 phages showed a Proteus-genus-specific profile, administering no lytic activity against other family of Enterobacteriaceae. The optimal MOI value of the RP6 and RP7 phages were determined as 0.1 and 0.01, respectively. The one-step growth curve showed that RP6 and RP7 phages have a short latent period of 20 min and large burst size of 220-371 PFU/ML per infected host cell. Bacteria growth was reduced immediately after the phages were added, which is shown by the optical density (OD) measurement after 24 hr. Proteus phage RP6 and RP7 were found to eradicate both the planktonic and mature biofilms produced by the Proteus isolates tested. Genome sequence of Proteus phage RP6 was found to be 58,619 bp, and a G-C content of 47%. Also, Proteus phage RP7 genome size was 103,593 bp with G-C ratio of 38.45%. A total of 70 and 172 open reading frame (ORF) was encoded in RP6 and RP7 phage genomes, respectively. Interestingly, there were no tRNA encoded by Proteus phage RP6 genome even though there is a significant G-C content difference between the phage and its host. Additionally, the exhibition of highly lytic activity and absence of virulence and antibiotic-resistant genes in both Proteus RP6 and RP7 phages emphasized that this newly isolated phages are promising for potential therapeutic phages.
    MeSH term(s) Humans ; Bacteriophages/genetics ; Sewage ; Proteus/genetics ; Proteus mirabilis/genetics ; Genome, Viral ; Biofilms ; Hospitals
    Chemical Substances Sewage
    Language English
    Publishing date 2023-01-28
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2023.199049
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  4. Article: Phage-antibiotic combinations in various treatment modalities to manage MRSA infections.

    Loganathan, Archana / Bozdogan, Bulent / Manohar, Prasanth / Nachimuthu, Ramesh

    Frontiers in pharmacology

    2024  Volume 15, Page(s) 1356179

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2024-04-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2024.1356179
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  5. Article ; Online: Isolation and characterization of Brochothrix phage ADU4.

    Karaynir, Abdulkerim / Salih, Hanife / Bozdoğan, Bülent / Güçlü, Özgür / Keskin, Dilek

    Virus research

    2022  Volume 321, Page(s) 198902

    Abstract: B. thermosphacta is a psychrotrophic bacterium that often forms the predominant part ... of the newly isolated lytic Brochothrix phage ADU4, which is capable of infecting the B. thermosphacta ... test analysis showed positivity with B. thermosphacta strains, while no infection was observed ...

    Abstract B. thermosphacta is a psychrotrophic bacterium that often forms the predominant part of the spoilage microflora of aerobically and anaerobically stored meats. Bacteriophages are natural enemies of bacteria and their potential for use in environmentally friendly biocontrol of specific pathogens in food is being intensively studied. In this study, we reported the isolation and characterization of the newly isolated lytic Brochothrix phage ADU4, which is capable of infecting the B. thermosphacta bacterium. For the characterization of Brochothrix phage ADU4; host range, multiplicity of infection values (MOI), phage growth parameters (latent period and burst size), stability at various temperatures and pH, reduction growth of bacteria, effect on biofilm, and molecular characterization were investigated. The spot-test analysis showed positivity with B. thermosphacta strains, while no infection was observed in any other species and genera of bacteria tested. The optimal MOI value of the phage was determined as 0.1. The phage latent period and burst sizes were 40-50 min and 311 PFU/ml per infected host cell, respectively by one-step growth curve analysis. Brochothrix phage ADU4 reduced bacteria immediately after infection, which is shown by optical density (OD) measurement and colony counting (<10 CFU/ml) for 3 days. The degradation of B. thermosphacta in biofilm by Brochothrix phage ADU4 was analyzed and it was found that high titer phage breakdown the existing biofilm and also persistently inhibited biofilm formation. Brochothrix phage ADU4 genome was found to be 127,819 bp, and GC content 41.65%. The genome contains 217 putative open reading frames (ORFs), 4 tRNAs, and additionally, no known virulence and antibiotic resistance genes (AMR) were identified. Brochothrix phage ADU4 showed a high identity (96.09%) to the A9 phage that belongs to the Herelleviridae family. Nevertheless, the assembly module and its around appeared less conserved, and some DNA fragments in Brochothrix phage ADU4 genome were not found in A9 genome and vice versa. A9 contains TnpB, a transposase accessory protein involved in lysogenicity which is absent in Brochothrix phage ADU4. In contrary Brochothrix phage ADU4 had auxiliary metabolic genes (AMG) mostly carried by lytic phages. All these results showed that the Brochothrix phage ADU4 has excellent properties such as strong antibacterial activity, short latent period, high burst size, stability in different conditions, inhibition of biofilms, and absence of virulence and AMR genes. Based on all these features, this newly isolated phage is promising to control B. thermosphacta contamination in meat and meat products, and has the potential to be used alone or in combination with phage cocktails.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; Brochothrix ; Meat/microbiology ; Transposases/metabolism ; Transposases/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Transposases (EC 2.7.7.-)
    Language English
    Publishing date 2022-09-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2022.198902
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  6. Article: Combining Gold Nanoparticles with Other Radiosensitizing Agents for Unlocking the Full Potential of Cancer Radiotherapy.

    Alhussan, Abdulaziz / Bozdoğan, Ece Pinar Demirci / Chithrani, Devika B

    Pharmaceutics

    2021  Volume 13, Issue 4

    Abstract: About half of cancer patients (50%) receive radiotherapy (RT) for the treatment of local tumors. However, one of the main obstacles in RT is the close proximity of adjacent organs at risk, resulting in treatment doses being limited by significant tissue ... ...

    Abstract About half of cancer patients (50%) receive radiotherapy (RT) for the treatment of local tumors. However, one of the main obstacles in RT is the close proximity of adjacent organs at risk, resulting in treatment doses being limited by significant tissue toxicity, hence preventing the necessary dose escalation that would guarantee local control. Effective local cancer therapy is needed to avoid progression of tumors and to decrease the development of systemic metastases which may further increase the possibility of resection. In an effort to do so, radiosensitizing agents are introduced to further increase damage to the tumor while minimizing normal tissue toxicity. Cisplatin and docetaxel (DTX) are currently being used as radiation dose enhancers in RT. Recent research shows the potential of gold nanoparticles (GNPs) as a radiosensitizing agent. GNPs are biocompatible and have been tested in phase I clinical trials. The focus will be on exploring the effects of adding other radiosensitizing agents such as DTX and cisplatin to the GNP-RT platform. Therefore, a combined use of local radiosensitizing agents, such as GNPs, with currently available radiosensitizing drugs could make a significant impact in future RT. The ultimate goal is to develop treatments that have limited or nonexistent side effects to improve the quality of life of all cancer patients.
    Language English
    Publishing date 2021-03-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics13040442
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  7. Article: Bactericidal activity of quinupristin-dalfopristin against strains of Staphylococcus aureus with the MLS(B) phenotype of resistance according to the erm gene type.

    Clarebout, G / Nativelle, E / Bozdogan, B / Villers, C / Leclercq, R

    International journal of antimicrobial agents

    2004  Volume 24, Issue 5, Page(s) 444–449

    Abstract: ... against Staphylococcus aureus strains with characterized phenotypes and genotypes of MLS(B) resistance ... the erm(A), erm(B) or erm(C) genes constitutively expressed and of 13 clinical isolates containing ... these genes inducibly or constitutively expressed were studied. Three of the clinical isolates with erm(B) or ...

    Abstract The bactericidal activity of quinupristin-dalfopristin was assessed by time-kill experiments against Staphylococcus aureus strains with characterized phenotypes and genotypes of MLS(B) resistance. A set of laboratory strains composed of isogenic pairs of S. aureus RN4220 derivatives containing or not the erm(A), erm(B) or erm(C) genes constitutively expressed and of 13 clinical isolates containing these genes inducibly or constitutively expressed were studied. Three of the clinical isolates with erm(B) or erm(A) genes had an unusual inducible MLS(B) cross resistance. The early bactericidal activity of quinupristin-dalfopristin was altered against strains expressing constitutive quinupristin resistance regardless of the erm(A), erm(B) or erm(C) type of gene. We conclude that the bactericidal activity of quinupristin-dalfopristin against staphylococci was dependent on the activity of quinupristin rather than on the erm genotype of the strain.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Genotype ; Methyltransferases/genetics ; Microbial Sensitivity Tests/methods ; Phenotype ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/enzymology ; Virginiamycin/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Virginiamycin (11006-76-1) ; quinupristin-dalfopristin (126602-89-9) ; Methyltransferases (EC 2.1.1.-) ; ErmA protein, Bacteria (EC 2.1.1.184)
    Language English
    Publishing date 2004-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2004.06.016
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  8. Article ; Online: Modeling and analyzing rheological behavior of sour lemon juice concentrate using image processing methods.

    Çavdir, Esra / Akben, Selahaddin B / Bozdoğan, Adnan

    Journal of texture studies

    2020  Volume 51, Issue 5, Page(s) 789–799

    Abstract: In this study, temperature-concentration related rheological behavior of sour lemon juice concentrate (SLJC) were investigated. Lemons were squeezed, and lemon juices were obtained. SLJC samples were produced by two methods: atmospheric and vacuum ... ...

    Abstract In this study, temperature-concentration related rheological behavior of sour lemon juice concentrate (SLJC) were investigated. Lemons were squeezed, and lemon juices were obtained. SLJC samples were produced by two methods: atmospheric and vacuum conditions. The rheological properties of SLJC at 10, 20, 30, 40, and 50°C for each 31, 36, 41, 46, 51 °Bx were measured with rheometer. Firstly, it was determined that the SLJC showed Newtonian flow behavior at measured concentrations and temperatures. Then, viscosity of SLJC produced under vacuum conditions was determined higher than SLJC produced under atmospheric conditions. This difference was calculated statistically significant (p < .05). Furthermore, activation energy values of samples produced under atmospheric and vacuum conditions ranged between 13.6-24.0 kJ/mol and 9.0-17.9 kJ/mol, respectively. Finally, temperature-concentration dependent viscosity variations were modeled by surface equations, and the data predicted were transformed into images to provide visual analysis. It was determined by images that the viscosity change is proportional to concentration while inversely proportional to temperature. Ascorbic acid value was found higher under vacuum conditions than atmospheric conditions. In contrast, the HMF value was detected in low quantities under vacuum conditions.
    MeSH term(s) Citrus ; Fruit ; Fruit and Vegetable Juices ; Hydrogen-Ion Concentration ; Plant Oils ; Rheology ; Taste ; Temperature ; Viscosity
    Chemical Substances Plant Oils ; lemon oil (I9GRO824LL)
    Language English
    Publishing date 2020-07-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 242507-5
    ISSN 1745-4603 ; 0022-4901
    ISSN (online) 1745-4603
    ISSN 0022-4901
    DOI 10.1111/jtxs.12537
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  9. Article: Men's Knowledge and Attitudes Towards Breast Cancer: A Descriptive Study.

    Özaydın, Ayşe Nilüfer / Doğan, Emrah / Bozdoğan, Berk

    European journal of breast health

    2020  Volume 16, Issue 3, Page(s) 183–191

    Abstract: Objective: Breast cancer (BC) is an important disease for women. BC influences both patient's and relatives' lives. Especially, husbands/boyfriends/ lovers are the ones that are affected mostly. In this study, it was aimed to introduce knowledge and ... ...

    Abstract Objective: Breast cancer (BC) is an important disease for women. BC influences both patient's and relatives' lives. Especially, husbands/boyfriends/ lovers are the ones that are affected mostly. In this study, it was aimed to introduce knowledge and attitudes of men toward BC and their sources of information about BC.
    Materials and methods: This descriptive study was conducted with men applied to a University Hospital in Istanbul (Turkey-2018). The ethics permission was obtained from The Clinical Research Ethics Committee. Data regarding socio-demographic characteristics with the knowledge and attitudes towards BC were collected with a questionnaire specific to the research. Statistical significance level was accepted as p<0.05.
    Results: In the study, 240 men (mean age: 36.2±10.6 years,min: 18.0, max: 63.0) were interviewed. Fifty four percent of men declared that they would not marry someone with BC and/or someone who had mastectomy. Thirty four percent of participants thought that a woman with BC should conceal the disease. The mean BC knowledge score was 234.1±128.0 (median: 227.5, min: 0, max: 571.0) among the total which was 600.
    Conclusion: A significant proportion of men did not have sufficient and accurate knowledge about BC. If the BC knowledge scores increase, there was an association with more positive attitudes. Negative attitudes of men related with BC of a woman may be an indicator of stigmatization. If it is aimed to increase support of men for women dealing with BC, it is recommended that BC awareness activities should be prepared to include men in order to increase their knowledge and to change their attitudes into a more positive way.
    Language English
    Publishing date 2020-03-31
    Publishing country Turkey
    Document type Journal Article
    ISSN 2587-0831
    ISSN 2587-0831
    DOI 10.5152/ejbh.2020.5193
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  10. Article: Effects of genes encoding resistance to streptogramins A and B on the activity of quinupristin-dalfopristin against Enterococcus faecium.

    Bozdogan, B / Leclercq, R

    Antimicrobial agents and chemotherapy

    1999  Volume 43, Issue 11, Page(s) 2720–2725

    Abstract: Quinupristin-dalfopristin is a streptogramin combination active against multiply resistant Enterococcus faecium. Among 45 E. faecium isolated from patients in various French hospitals, only two strains were intermediate (MIC = 2 microgram/ml) and one, E. ...

    Abstract Quinupristin-dalfopristin is a streptogramin combination active against multiply resistant Enterococcus faecium. Among 45 E. faecium isolated from patients in various French hospitals, only two strains were intermediate (MIC = 2 microgram/ml) and one, E. faecium HM1032, was resistant (MIC = 16 microgram/ml) to quinupristin-dalfopristin, according to British Society for Antimicrobial Chemotherapy and National Committee for Clinical Laboratory Standards approved breakpoints. The latter strain contained the vgb and satA genes responsible for hydrolysis or acetylation of quinupristin and dalfopristin, respectively, and an ermB gene (also previously referred to as ermAM) encoding a ribosomal methylase. The two intermediate strains had an LS(A) phenotype characterized by resistance to lincomycin (L), increased MICs (>/=8 microgram/ml) of dalfopristin (streptogramin A [S(A)]), and susceptibility to erythromycin and quinupristin. This phenotype was also detected in eight other strains susceptible to quinupristin-dalfopristin. No genes already known and conferring resistance to dalfopristin by acetylation or active efflux were detected in these LS(A) strains. Nineteen other strains resistant to erythromycin but susceptible to the quinupristin-dalfopristin combination displayed elevated MICs of quinupristin after induction (from 16 to >128 microgram/ml) and contained ermB genes. The effects of ermB, vgb, and satA genes on the activity of the streptogramin combination were tested by cloning these genes individually or in various combinations in recipient strains susceptible to quinupristin-dalfopristin, E. faecium HM1070 and Staphylococcus aureus RN4220. The presence of both the satA and vgb genes (regardless of the presence of an ermB gene) was necessary to confer full quinupristin-dalfopristin resistance to the host. The same genetic constructs were introduced into E. faecium BM4107 which displays a LS(A) phenotype. Addition of the satA or vgb gene to this LS(A) background conferred resistance to quinupristin-dalfopristin.
    MeSH term(s) Acetyltransferases/genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Drug Resistance, Microbial ; Enterococcus faecium/drug effects ; Enterococcus faecium/genetics ; Genes, Bacterial/genetics ; Genotype ; Gram-Positive Bacterial Infections/microbiology ; Hemeproteins/genetics ; Humans ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Polymerase Chain Reaction ; Staphylococcus aureus/drug effects ; Virginiamycin/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Hemeproteins ; Vgb protein, Bacteria ; Virginiamycin (11006-76-1) ; quinupristin-dalfopristin (126602-89-9) ; Methyltransferases (EC 2.1.1.-) ; rRNA (adenosine-O-2'-)methyltransferase (EC 2.1.1.230) ; Acetyltransferases (EC 2.3.1.-) ; streptogramin A acetyltransferase, Enterococcus faecium (EC 2.3.1.-)
    Language English
    Publishing date 1999-11
    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.43.11.2720
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