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Items 1 to 10 of about 911
1. Jensen SI, Nielsen AT: Multiplex Genome Editing in Escherichia coli. Methods Mol Biol; 2018;1671:119-129
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Multiplex Genome Editing in Escherichia coli.
  • Lambda Red recombineering is an easy and efficient method for generating genetic modifications in Escherichia coli.
  • For gene deletions, lambda Red recombineering is combined with the use of selectable markers, which are removed through the action of, e.g., flippase (Flp) recombinase.
  • This PCR-based engineering method has also been applied to a number of other bacteria.
  • In this chapter, we describe a recently developed one plasmid-based method as well as the use of a strain with genomically integrated recombineering genes, which significantly speeds up the engineering of strains with multiple genomic alterations.

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  • (PMID = 29170956.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Flippase recombinase / Genome editing / Industrial biotechnology / Lambda Red recombineering / Synthetic biology / pSIJ8
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4. Maura D, Bandyopadhaya A, Rahme LG: Animal Models for Pseudomonas aeruginosa Quorum Sensing Studies. Methods Mol Biol; 2018;1673:227-241
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Animal Models for Pseudomonas aeruginosa Quorum Sensing Studies.
  • Quorum sensing (QS) systems play global regulatory roles in bacterial virulence.
  • They synchronize the expression of multiple virulence factors and they control and modulate bacterial antibiotic tolerance systems and host defense mechanisms.
  • Therefore, it is important to obtain knowledge about QS modes of action and to test putative therapeutics that may interrupt QS actions in the context of infections.
  • This chapter describes methods to study bacterial pathogenesis in murine acute and persistent/relapsing infection models, using the Gram-negative bacterial pathogen Pseudomonas aeruginosa as an example.
  • These infection models can be used to probe bacterial virulence functions and in mechanistic studies, as well as for the assessment of the therapeutic potential of antibacterials, including anti-virulence agents.

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  • (PMID = 29130177.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Abdominal burn infection / Antibiotic tolerance / Back burn infection / Lung infection / Open wound infection / Persistence / Pseudomonas aeruginosa
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6. Saragadam T, Punekar NS: Novel Route for Agmatine Catabolism in Aspergillus niger: 4-Guanidinobutyrase Assay. Methods Mol Biol; 2018;1694:163-172
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Novel Route for Agmatine Catabolism in Aspergillus niger: 4-Guanidinobutyrase Assay.
  • The enzyme 4-guanidinobutyrase (GBase) catalyzes the hydrolysis of 4-guanidinobutyric acid (GB) to 4-aminobutyric acid (GABA) and urea.
  • Here we describe methods to estimate urea and GABA that were suitably adapted from the published literature.
  • The urea is determined by colorimetric assay using modified Archibald's method.
  • However, the low sensitivity of this method often renders it impractical to perform fine kinetic analysis.
  • To overcome this limitation, a high sensitive method for detecting GABA is exploited that can even detect 1 μM of GABA in the assay mixture.
  • The samples are deproteinized by perchloric acid (PCA) and potassium hydroxide treatment prior to HPLC analysis of GABA.
  • The method involves a pre-column derivatization with o-phthalaldehyde (OPA) in combination with the thiol 3-mercaptopropionic acid (MPA).
  • The fluorescent GABA derivative is then detected after reversed phase high performance liquid chromatography (RP-HPLC) using isocratic elution.
  • The protocols described here are broadly applicable to other biological samples involving urea and GABA as metabolites.

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  • (PMID = 29080167.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; 3-Mercaptopropionic acid / 4-Guanidinobutyrase / 4-Guanidinobutyric acid / Agmatine / GABA / Isocratic / Reversed phase HPLC / Urea / o-Phthalaldehyde
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7. Kaneta T: Determination of Polyamines by Capillary Electrophoresis Using Salicylaldehyde-5-Sulfonate as a Derivatizing Reagent. Methods Mol Biol; 2018;1694:61-68
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Determination of Polyamines by Capillary Electrophoresis Using Salicylaldehyde-5-Sulfonate as a Derivatizing Reagent.
  • Here we describe a protocol for the determination of polyamines using capillary electrophoresis with ultraviolet absorbance detection.
  • Aliphatic polyamines were derivatized with salicylaldehyde-5-sulfonate (SAS) which formed Schiff base with amino groups, resulting in anionic derivatives.
  • The derivatization of polyamines, including putrescine (PUT), cadaverine (CAD), spermidine (SPD), and spermine (SPM), was conducted in 10 mM HEPES buffer with pH 7.8 containing 5 mM SAS in a mixed solvent of water and ethanol.
  • The SAS derivatives were separated using a background electrolyte composed of 10 mM phosphate buffer with pH 7.8.
  • Calibration curves were linear over a concentration range of 20-200 μM for CAD, PUT, SPD, and SPM, and the limits of detection (LOD) were several μM for all polyamines.
  • Furthermore, solid phase extraction was coupled with the CE method to improve the LOD to sub-μM levels, and the calibration curves were linear over a concentration range of 1-20 μM for CAD, PUT, and SPD.

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  • (PMID = 29080155.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Capillary electrophoresis / Polyamines / Salicylaldehyde-5-sulfonate
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8. Savino W, Pinto-Mariz F, Mouly V: Flow Cytometry-Defined CD49d Expression in Circulating T-Lymphocytes Is a Biomarker for Disease Progression in Duchenne Muscular Dystrophy. Methods Mol Biol; 2018;1687:219-227
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Flow Cytometry-Defined CD49d Expression in Circulating T-Lymphocytes Is a Biomarker for Disease Progression in Duchenne Muscular Dystrophy.
  • Duchenne muscular dystrophy (DMD) affects 1:3500-1:5000 male births, and is caused by X-linked mutations in the dystrophin gene, manifested by progressive muscle weakness and wasting due to the absence of dystrophin protein, leading to degeneration of skeletal muscle.
  • DMD patients are clinically heterogeneous and the functional phenotype often cannot be correlated with the genotype.
  • Therefore, defined reliable noninvasive biomarkers aiming at predicting if a given DMD child will progress more or less rapidly will be instrumental to better design inclusion of defined patients for future therapeutic assays.
  • We recently showed that CD49d expression levels in blood-derived T-cell subsets can predict disease progression in DMD patients.
  • Herein we describe in detail the methodology to be applied for defining, through four-color flow cytometry, the membrane expression levels of the CD49d (the α4 chain of the integrins α4β1 and α4β7) in circulating CD4<sup>+</sup> and CD8<sup>+</sup> T cell subsets.
  • Since we have also shown that this molecule can also be placed as a potential target for therapeutics in DMD, we also describe the cell migration functional assay that can be applied to test potential CD49d inhibitors that can modulate their ability to cross endothelial or extracellular matrix (ECM) barriers.

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  • (PMID = 29067667.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Biomarker / Flow cytometry / Immunotherapy / Inflammation / Integrins / Muscular dystrophy / T lymphocytes / VLA-4
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9. Harrison JM, Friese CR, Barton DL, Janz NK, Pressler SJ, Davis MA: Heart Failure and Long-Term Survival Among Older Women With Breast Cancer. Oncol Nurs Forum; 2018 01 02;45(1):A1-A11
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Heart Failure and Long-Term Survival Among Older Women With Breast Cancer
  • Objectives: To evaluate the association between heart failure and overall survival up to 10 years after breast cancer diagnosis.
  • Sample & Setting: Women aged 65 years or older diagnosed with invasive breast cancer, with and without self-reported heart failure, were examined for this retrospective cohort study using Surveillance, Epidemiology, and End Results cancer registries in the United States.
  • Methods & Variables: Cox proportional hazards regression was used to examine the association between heart failure status and mortality, adjusting for comorbidity and other clinical or sociodemographic differences.
  • Associations were examined overall and stratified by cancer stage.
  • Results: In adjusted models, having heart failure was associated with increased likelihood of death up to 10 years after cancer diagnosis.
  • In adjusted subanalyses by cancer stage, heart failure was associated with increased likelihood of death up to 10 years after cancer diagnosis in women with stage I or II cancer but not in women with stage III/IV cancer.
  • Implications for Nursing: Although early-stage breast cancer is generally associated with better prognosis, the competing mortality risk of heart failure was greater for this group than for women with advanced cancer.
  •  Prevention and management of cardiovascular disease should be prioritized for this patient subgroup.

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  • [Copyright] 2018 Oncology Nursing Society
  • (PMID = 29039180.001).
  • [ISSN] 1538-0688
  • [Journal-full-title] Oncology nursing forum
  • [ISO-abbreviation] Oncol Nurs Forum
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; breast cancer (major topic) / heart failure (major topic) / comorbidities (major topic) / survivorship (major topic) / late effects (major topic)
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10. Vunsh R: Methods for Functional Transgenics: Development of Highly Efficient Transformation Protocol in Brachypodium and Its Suitability for Advancing Brachypodium Transgenics. Methods Mol Biol; 2018;1667:101-117
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Methods for Functional Transgenics: Development of Highly Efficient Transformation Protocol in Brachypodium and Its Suitability for Advancing Brachypodium Transgenics.
  • Plant transformation is an invaluable technique in plant genomics by which an extra foreign DNA sequence is introduced into a plant genome.
  • Changing the plant genome is leading to owning new genetic characteristics.
  • Model plant is a keystone in a study of the comprehensive plant phylum.
  • Here, I describe an efficient method to transform the plant species Brachypodium distachyon which, due to its characters, is developing to be an important plant model.

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  • (PMID = 29039007.001).
  • [ISSN] 1940-6029
  • [Journal-full-title] Methods in molecular biology (Clifton, N.J.)
  • [ISO-abbreviation] Methods Mol. Biol.
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] United States
  • [Keywords] NOTNLM ; Agrobacterium tumefaciens / Brachypodium distachyon / Embryonic callus / Transformation
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