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Items 1 to 10 of about 998
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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5. Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O: A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. Methods Mol Biol; 2018;1702:247-276
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.
  • Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches.
  • The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks.
  • We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling.
  • As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions.
  • Analysis carried out by the workflow revealed that HOXD10, BCL2, and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN, and JUNB are playing a central role.
  • The identified key elements of each network are validated using patient survival analysis.
  • The workflow presented here allows experimentalists to use heterogeneous data sources for the identification of diagnostic and prognostic signatures.

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  • (PMID = 29119509.001).
  • [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 ; Disease signatures / Integrative workflow / Large-scale networks / Mathematical models / Network-based analysis
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6. Li B, Takahashi D, Kawamura Y, Uemura M: Plasma Membrane Proteomics of Arabidopsis Suspension-Cultured Cells Associated with Growth Phase Using Nano-LC-MS/MS. Methods Mol Biol; 2018;1696:185-194
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Plasma Membrane Proteomics of Arabidopsis Suspension-Cultured Cells Associated with Growth Phase Using Nano-LC-MS/MS.
  • Arabidopsis thaliana suspension-cultured cells (T87 line) are important model system for studies of responses to biotic and abiotic stresses at the cellular level in vitro since the cells have certain advantages compared with the whole plant system.
  • However, the physiological and morphological characteristics of the cells are influenced by the progress of the growth phase of cells, which may result in different stress tolerance.
  • To obtain comprehensive proteome profiles of the plasma membrane of Arabidopsis thaliana T87 suspension-cultured cells at the lag, log, or stationary growth phase, a shotgun proteomics method using nano-LC-MS/MS is used.
  • The results obtained indicate that proteome profiles of the plasma membrane with the progress of the growth phase of cells dynamically changed, which may be associated with the physiological and morphological characteristics of the plasma membrane of the suspension-cultured cells.
  • The proteomics results are further applied to explain different responsive patterns in the plasma membrane to cold acclimation and ABA treatment, which lead to understanding of different freezing tolerance associated with the growth phase of the cells.

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  • (PMID = 29086404.001).
  • [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 ; Culture cells / Growth phase / Nano-LC-MS/MS / Plasma membrane / Proteomics
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7. 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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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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