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  1. AU="Kamali Kakhki, Reza"
  2. AU=Mortele Koenraad J
  3. AU="Skaarup, Søren H"
  4. AU="Lin, Li-Er"
  5. AU=Goulard Marie
  6. AU=Rosner Mitchell H
  7. AU="Murphy, Bríd"
  8. AU="Tsuneyoshi, Isao"
  9. AU="Tram, Le Thi Hong"
  10. AU="Veli-Pekka Jaakola"
  11. AU="Erduğan, Hüseyin"

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  1. Artikel: A New Specific DNA Target Sequence for Identification of

    Khoshbakht, Reza / Zare, Hosna / Kamali Kakhki, Reza / Neshani, Alireza / Arfaatabar, Maryam

    Avicenna journal of medical biotechnology

    2022  Band 14, Heft 3, Seite(n) 216–222

    Abstract: Background: Staphylococcus epidermidis (S. epidermidis): Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect : Results: The 400 : Conclusion: The Se400 sequence can be considered as a ... ...

    Abstract Background: Staphylococcus epidermidis (S. epidermidis)
    Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect
    Results: The 400
    Conclusion: The Se400 sequence can be considered as a specific target for detecting
    Sprache Englisch
    Erscheinungsdatum 2022-08-19
    Erscheinungsland Iran
    Dokumenttyp Journal Article
    ZDB-ID 2520683-7
    ISSN 2008-4625 ; 2008-2835
    ISSN (online) 2008-4625
    ISSN 2008-2835
    DOI 10.18502/ajmb.v14i3.9828
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of

    Kamali Kakhki, Reza / Aryan, Ehsan / Meshkat, Zahra / Sankian, Mojtaba

    Reports of biochemistry & molecular biology

    2020  Band 8, Heft 4, Seite(n) 383–393

    Abstract: Background: The line probe assay (LPA) is one of the most accurate diagnostic tools for detection of different : Methods: One pair of biotinylated primers and 15 designed DNA oligonucleotide probes were used based on multiple aligned internal ... ...

    Abstract Background: The line probe assay (LPA) is one of the most accurate diagnostic tools for detection of different
    Methods: One pair of biotinylated primers and 15 designed DNA oligonucleotide probes were used based on multiple aligned internal transcribed spacer (ITS) sequences. Specific binding of the PCR-amplified products to the probes immobilized on nitrocellulose membrane strips was evaluated by the hybridization method. Experiments were performed three times on separate days to evaluate the assay's repeatability. The PCR-LPA was evaluated directly on nine clinical samples and their cultivated isolates.
    Results: All 15 probes used in this study hybridized specifically to ITS sequences of the corresponding standard species. Results were reproducible for all the strains on different days. Mycobacterium species of the nine clinical specimens and their cultivated isolates were correctly identified by PCR-LPA and confirmed by sequencing.
    Conclusion: In this study, we describe a PCR-LPA that is readily applicable in the clinical laboratory. The assay is fast, cost-effective, highly specific, and requires no radioactive materials.
    Sprache Englisch
    Erscheinungsdatum 2020-06-04
    Erscheinungsland Iran
    Dokumenttyp Journal Article
    ZDB-ID 2743890-9
    ISSN 2322-3480
    ISSN 2322-3480
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay.

    Kamali Kakhki, Reza / Najafzadeh, Mohammad Javad / Kachuei, Reza / Ghazvini, Kiarash

    European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

    2020  Band 39, Heft 8, Seite(n) 1535–1542

    Abstract: The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, ... ...

    Abstract The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.
    Mesh-Begriff(e) Aspergillus/genetics ; Aspergillus/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchopneumonia/diagnosis ; Cryptococcus/genetics ; Cryptococcus/isolation & purification ; Humans ; Multiplex Polymerase Chain Reaction ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Nocardia/genetics ; Nocardia/isolation & purification ; Sensitivity and Specificity ; Streptomyces/genetics ; Streptomyces/isolation & purification ; Tuberculosis, Pulmonary/diagnosis
    Sprache Englisch
    Erscheinungsdatum 2020-04-06
    Erscheinungsland Germany
    Dokumenttyp Evaluation Study ; Journal Article
    ZDB-ID 603155-9
    ISSN 1435-4373 ; 0934-9723 ; 0722-2211
    ISSN (online) 1435-4373
    ISSN 0934-9723 ; 0722-2211
    DOI 10.1007/s10096-020-03879-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: Antibacterial Activity of

    Roointan, Amir / Kamali-Kakhki, Reza / Fathalipour, Mohammad / Hashemi, Zohreh / Zarshenas, Mohammad Mehdi / Soleimani, Mohammad / Mirjani, Ruhola

    Iranian journal of medical sciences

    2020  Band 45, Heft 6, Seite(n) 444–450

    Abstract: Background: Burn wound infection and sepsis are serious medical conditions requiring prompt intervention. Plants are a good natural source for the development of novel, safe, and cost-effective antibacterial agents. The objective of the present study ... ...

    Abstract Background: Burn wound infection and sepsis are serious medical conditions requiring prompt intervention. Plants are a good natural source for the development of novel, safe, and cost-effective antibacterial agents. The objective of the present study was to assess the antibacterial potential of aqueous, chloroform, and methanol extracts of the
    Methods: The present experimental study was conducted at Shiraz University of Medical Sciences (Shiraz, Iran) during 2018-2019. The antibacterial activity of the total plant extract was assayed using the broth microdilution method. Fractionation was performed using a separation funnel and solvents with different polarities. Broth microdilution and agar well diffusion assays were performed to determine the antibacterial potential of the obtained fractions. Quantitative and qualitative phytochemical analyses were performed to confirm the presence of secondary metabolites in both the total extract and the fractions.
    Results: Methanolic extract of
    Conclusion: For the first time, we demonstrated the antibacterial activity of the
    Sprache Englisch
    Erscheinungsdatum 2020-12-03
    Erscheinungsland Iran
    Dokumenttyp Journal Article
    ZDB-ID 603872-4
    ISSN 1735-3688 ; 0253-0716
    ISSN (online) 1735-3688
    ISSN 0253-0716
    DOI 10.30476/ijms.2019.82071
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.B 1634: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  5. Artikel ; Online: Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example.

    Neshani, Alireza / Kamali Kakhki, Reza / Sankian, Mojtaba / Zare, Hosna / Hooshyar Chichaklu, Amin / Sayyadi, Mahsa / Ghazvini, Kiarash

    BMC infectious diseases

    2018  Band 18, Heft 1, Seite(n) 517

    Abstract: Background: The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we ... ...

    Abstract Background: The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test.
    Methods: A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity.
    Results: The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter.
    Conclusions: Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.
    Mesh-Begriff(e) DNA, Bacterial/chemistry ; DNA, Bacterial/isolation & purification ; DNA, Bacterial/metabolism ; Databases, Genetic ; Genome, Bacterial ; Genomics/methods ; Humans ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Polymerase Chain Reaction/methods ; Tuberculosis/diagnosis ; Tuberculosis/microbiology
    Chemische Substanzen DNA, Bacterial
    Sprache Englisch
    Erscheinungsdatum 2018-10-12
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-018-3417-x
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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