Editorial Board
Publication date: 1 February 2020Source: Methods, Volume 172Author(s): (Source: Methods)
Source: Methods - March 9, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 15 February 2020Source: Methods, Volume 173Author(s): (Source: Methods)
Source: Methods - March 9, 2020 Category: Molecular Biology Source Type: research

Extracellular vesicles as a platform to study cell-surface membrane proteins
Publication date: Available online 7 March 2020Source: MethodsAuthor(s): Vincent Delauzun, Beatrice Amigues, Anais Gaubert, Philippe Leone, Magali Grange, Laurent Gauthier, Alain Roussel (Source: Methods)
Source: Methods - March 8, 2020 Category: Molecular Biology Source Type: research

“RNA-Seq: Methods and applications”
Publication date: Available online 6 March 2020Source: MethodsAuthor(s): (Source: Methods)
Source: Methods - March 7, 2020 Category: Molecular Biology Source Type: research

Direct RNA sequencing approach to compare non-model mitochondrial transcriptomes: an application to a cephalopod host and its mesozoan parasite
Publication date: Available online 6 March 2020Source: MethodsAuthor(s): Hiroki Ono, Masa-aki Yoshida (Source: Methods)
Source: Methods - March 7, 2020 Category: Molecular Biology Source Type: research

From tumour perfusion to drug delivery and clinical translation of in silico cancer models
Publication date: Available online 5 March 2020Source: MethodsAuthor(s): Myrianthi Hadjicharalambous, Peter A. Wijeratne, Vasileios Vavourakis (Source: Methods)
Source: Methods - March 6, 2020 Category: Molecular Biology Source Type: research

Extracellular vesicles (EVs): Comprehensive packages with promises and complications for clinical translation and commercialization
Publication date: Available online 4 March 2020Source: MethodsAuthor(s): Young Jik Kwon (Source: Methods)
Source: Methods - March 4, 2020 Category: Molecular Biology Source Type: research

Multi-scale approaches for the simulation of cardiac electrophysiology: I - sub-cellular and stochastic calcium dynamics from cell to organ
Publication date: Available online 29 February 2020Source: MethodsAuthor(s): Michael A. Colman, Maxx Holmes, Dominic G. Whittaker, Izzy Jayasinghe, Alan P. Benson (Source: Methods)
Source: Methods - March 1, 2020 Category: Molecular Biology Source Type: research

Functional analyses of mammalian virus 5′UTR-derived, small RNAs that regulate virus translation
Publication date: Available online 17 February 2020Source: MethodsAuthor(s): Mei-Ling Li, Gary Brewer (Source: Methods)
Source: Methods - March 1, 2020 Category: Molecular Biology Source Type: research

Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS
Publication date: Available online 28 January 2020Source: MethodsAuthor(s): James Mullahoo, Terry Zhang, Karl Clauser, Steven A. Carr, Jacob D. Jaffe, Malvina Papanastasiou (Source: Methods)
Source: Methods - February 27, 2020 Category: Molecular Biology Source Type: research

Atomistic and Coarse-Grained Simulations of Membrane Proteins: A Practical Guide
This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions. (Source: Methods)
Source: Methods - February 19, 2020 Category: Molecular Biology Source Type: research

The fine art of preparing membrane transport proteins for biomolecular simulations: concepts and practical considerations
Publication date: Available online 17 February 2020Source: MethodsAuthor(s): Hana Shiref, Shana Bergman, Sophie Clivio, Michelle A. SahaiAbstractMolecular dynamics (MD) simulations have developed into an invaluable tool in bimolecular research, due to the capability of the method in capturing molecular events and structural transitions that describe the function as well as the physiochemical properties of biomolecular systems. Due to the progressive development of more efficient algorithms, expansion of the available computational resources, as well as the emergence of more advanced methodologies, the scope of computationa...
Source: Methods - February 18, 2020 Category: Molecular Biology Source Type: research

Functional analyses of mammalian virus 5’UTR-derived, small RNAs that regulate virus translation
Publication date: Available online 17 February 2020Source: MethodsAuthor(s): Mei-Ling Li, Gary BrewerAbstractEnterovirus A71 (EV-A711) RNA contains an internal ribosomal entry site (IRES) to direct cap-independent translation. IRES-dependent translation requires the host’s translation initiation factors and IRES-associated trans-acting factors (ITAFs). We previously showed that hnRNP A1, the mRNA stability factor HuR, and the RISC subunit Argonaute 2 (Ago2) are ITAFs that associate with stem loop II (SL-II) of the IRES and promote IRES-dependent translation. By contrast, the mRNA decay factor AUF1 is a negative-acting IT...
Source: Methods - February 18, 2020 Category: Molecular Biology Source Type: research

Differential fluorescence nanoparticle tracking analysis for enumeration of the extracellular vesicle content in mixed particulate solutions
ConclusionDifferential NTA/F-NTA facilitates determination of the percentage of EV marker protein-positive nanoparticles within a mixed particulate solution. The set of markers can be extended to other MSC-EV positive and negative surface proteins in order to establish F-NTA-based profiling as a supporting method for the quantification of EVs. (Source: Methods)
Source: Methods - February 18, 2020 Category: Molecular Biology Source Type: research

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis
Publication date: Available online 15 February 2020Source: MethodsAuthor(s): Mariel Coradin, Mariel R. Mendoza, Simone Sidoli, Andrew J. Alpert, Congcong Lu, Benjamin A. GarciaAbstractMiddle-down proteomics has emerged as the method of choice to study combinatorial histone post translational modifications (PTMs). In the common bottom-up workflow, histones are digested into relatively short peptides (4-20 aa), separated using reversed-phase chromatography and analyzed using typical proteomics methods in mass spectrometry. In middle-down, histones are cleaved into longer polypeptides (50-60 aa) mostly corresponding to their ...
Source: Methods - February 15, 2020 Category: Molecular Biology Source Type: research