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 19, 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-actin...
Source: Methods - February 19, 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 19, 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 16, 2020 Category: Molecular Biology Source Type: research

From Laboratory to Clinic: Translation of Extracellular Vesicle Based Cancer Biomarkers
Publication date: Available online 12 February 2020Source: MethodsAuthor(s): Anudeep Yekula, Koushik Muralidharan, Keiko Kang, Lan Wang, Leonora Balaj, Bob S. CarterAbstractThe past decade has witnessed a rapid growth in the field of extracellular vesicle (EV) based biomarkers for the diagnosis and monitoring of cancer. Several studies have reported novel EV based biomarkers, but the technical and clinical validation phase has been hampered by general challenges common to biomedical research field as well as specific challenges inherent to the nanoparticle field. This has led to more common failures than success stories in...
Source: Methods - February 13, 2020 Category: Molecular Biology Source Type: research

Lactobionamide-based fluorinated detergent for functional and structural stabilization of membrane proteins
We report herein the use of a fluorinated lactobionamide-based detergent named FLAC6 for functional and structural stabilization of membrane proteins. We first demonstrated that FLAC6 efficiently solubilized three membrane proteins i.e. the native adenosine receptor A2AR, a G protein-coupled receptor, and two native transporters AcrB and BmrA. The resulting affinity purified MPs were highly pure, homogenous and aggregates free. Furthermore, the functionality of each MP was well maintained. Finally, striking overstabilization features were observed. Indeed, the Tm of native A2AR, AcrB and BmrA could be improved by 7, ∼9...
Source: Methods - February 13, 2020 Category: Molecular Biology Source Type: research

SpineJ: A software tool for quantitative analysis of nanoscale spine morphology
We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ offers an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology. (Source: Methods)
Source: Methods - February 8, 2020 Category: Molecular Biology Source Type: research

Assessment of separation methods for extracellular vesicles from human and mouse brain tissues and human cerebrospinal fluids
Publication date: Available online 5 February 2020Source: MethodsAuthor(s): Satoshi Muraoka, Weiwei Lin, Mei Chen, Samuel W. Hersh, Andrew Emili, Weiming Xia, Tsuneya IkezuAbstractExtracellular vesicle (EV) is a unified terminology of membrane-enclosed vesicular species ubiquitously secreted by almost every cell type and present in all body fluids. They carry a cargo of lipids, metabolites, nucleic acids and proteins for their clearance from cells as well as for cell-to-cell communications. The exact composition of EVs and their specific functions are not well understood due to the underdevelopment of the separation protoc...
Source: Methods - February 6, 2020 Category: Molecular Biology Source Type: research

Using inverse finite element analysis to identify spinal tissue behaviour in situ
Publication date: Available online 6 February 2020Source: MethodsAuthor(s): Mengoni MarlèneAbstractIn computational modelling of musculoskeletal applications, one of the critical aspects is ensuring that a model can capture intrinsic population variability and not only representative of a “mean” individual. Developing and calibrating models with this aspect in mind is key for the credibility of a modelling methodology. This often requires calibration of complex models with respect to 3D experiments and measurements on a range of specimens or patients. Most Finite Element (FE) software’s do not have...
Source: Methods - February 6, 2020 Category: Molecular Biology Source Type: research

Biological and chemical approaches to understanding protein arginine methylation
Publication date: Available online 4 February 2020Source: MethodsAuthor(s): Adam Frankel (Source: Methods)
Source: Methods - February 5, 2020 Category: Molecular Biology Source Type: research

Continuum Mechanical Parameterisation of Cytoplasmic Dynein from Atomistic Simulation
Publication date: Available online 30 January 2020Source: MethodsAuthor(s): Benjamin S. Hanson, Shinji Iida, Daniel J. Read, Oliver G. Harlen, Genji Kurisu, Haruki Nakamura, Sarah A. HarrisAbstractCytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of ...
Source: Methods - February 1, 2020 Category: Molecular Biology Source Type: research

Quick and Facile Preparation of Histone Proteins from the Green Microalga Chlamydomonas reinhardtii and Other Photosynthetic Organisms
Publication date: Available online 31 January 2020Source: MethodsAuthor(s): Amanda L. Wong, Nicholas N. Totah, Anthony T. Iavarone, James J. PesaventoAbstractThe development of universal, broadly applicable methods for histone extraction from animal cells and tissues has unlocked the ability to compare these epigenetic-influencing proteins across tissue types, healthy and diseased states, and cancerous versus normal cells. However, for plants and algae, a quick and easily implemented histone extraction method has yet to be developed. In this paper, we report an optimized method that provides a unified approach to extract h...
Source: Methods - February 1, 2020 Category: Molecular Biology Source Type: research

Application of CE-MS for the analysis of histones and histone modifications
Publication date: Available online 31 January 2020Source: MethodsAuthor(s): Klaus Faserl, Bettina Sarg, Herbert H. LindnerAbstractThe analysis, identification and quantification of histones and their post-translational modifications plays a central role in chromatin research and in studying epigenetic regulations during physiological processes. In the last decade analytical strategies based on mass spectrometry have been greatly improved for providing a global view of single modification abundances or to determine combinatorial patterns of modifications. Presented here is a newly developed strategy for histone protein anal...
Source: Methods - February 1, 2020 Category: Molecular Biology Source Type: research

PET Image Reconstruction Using Physical and Mathematical Modelling For Time of Flight PET-MR Scanners in the STIR Library
Publication date: Available online 30 January 2020Source: MethodsAuthor(s): Palak Wadhwa, Kris Thielemans, Nikos Efthimiou, Kristen Wangerin, Nicholas Keat, Elise Emond, Timothy Deller, Ottavia Bertolli, Daniel Deidda, Gaspar Delso, Michel Tohme, Floris Jansen, Roger N. Gunn, William Hallett, Charalampos TsoumpasAbstractThis work demonstrates how computational and physical modelling of the positron emission tomography (PET) image acquisition process for a state-of-the-art integrated PET and magnetic resonance imaging (PET-MR) system can produce images comparable to the manufacturer. The GE SIGNA PET/MR scanner is manufactu...
Source: Methods - January 30, 2020 Category: Molecular Biology Source Type: research

Observing protein interaction dynamics to chemically defined chromatin fibers by colocalization single-molecule fluorescence microscopy
Publication date: Available online 28 January 2020Source: MethodsAuthor(s): Maxime Mivelaz, Beat FierzAbstractIn eukaryotic cells, the genome is packaged into chromatin and exists in different states, ranging from open euchromatic regions to highly condensed heterochromatic regions. Chromatin states are highly dynamic and are organized by an interplay of histone post-translational modifications and effector proteins, both of which are central in the regulation of gene expression. For this, chromatin effector proteins must first search the nucleus for their targets, before binding and performing their role. A key question i...
Source: Methods - January 29, 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 PapanastasiouAbstractThe N-terminal regions of histone proteins (tails) are dynamic elements that protrude from the nucleosome and are involved in many aspects of chromatin organization. Their epigenetic role is well-established, and post-translational modifications (PTMs) present on these regions contribute to transcriptional regulation. While hydrogen/deuterium exchange mass spectrometry (HX-MS) is well-suited for the analysis of dynamic structures, it has seldom b...
Source: Methods - January 29, 2020 Category: Molecular Biology Source Type: research

Antisense probing of dynamic RNA structures
Publication date: Available online 25 January 2020Source: MethodsAuthor(s): Alexandra J. Lukasiewicz, Lydia M. ContrerasAbstractRNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target. We observe changes in signal that qualitatively match prior traditional DMS footprinting experiments. Importantly, we have shown that application of this technique can elucidate new RNA information given its sensitivity for detecting rare in...
Source: Methods - January 26, 2020 Category: Molecular Biology Source Type: research

In Silico Trials: Verification, Validation And Uncertainty Quantification Of Predictive Models Used In The Regulatory Evaluation Of Biomedical Products
Publication date: Available online 25 January 2020Source: MethodsAuthor(s): Marco Viceconti, Francesco Pappalardo, Blanca Rodriguez, Marc Horner, Jeff Bischoff, Flora Musuamba TshinanuAbstractHistorically, the evidences of safety and efficacy that companies provide to regulatory agencies as support to the request for marketing authorization of a new medical product have been produced experimentally, either in vitro or in vivo. More recently, regulatory agencies started receiving and accepting evidences obtained in silico, i.e. through modelling and simulation. However, before any method (experimental or computational) can ...
Source: Methods - January 26, 2020 Category: Molecular Biology Source Type: research

Multi-scale approaches for the simulation of cardiac electrophysiology: II - tissue-level structure and function
Publication date: Available online 25 January 2020Source: MethodsAuthor(s): Alan P. Benson, Harley J. Stevenson-Cocks, Dominic G. Whittaker, Ed White, Michael A. ColmanAbstractComputational models of the heart, from cell-level models, through one-, two- and three-dimensional tissue-level simplifications, to biophysically-detailed three-dimensional models of the ventricles, atria or whole heart, allow the simulation of excitation and propagation of this excitation, and have provided remarkable insight into the normal and pathological functioning of the heart. In this article we present equations for modelling cellular excit...
Source: Methods - January 25, 2020 Category: Molecular Biology Source Type: research

Comprehensive Analysis of Histone-binding Proteins with Multi-Angle Light Scattering
Publication date: Available online 25 January 2020Source: MethodsAuthor(s): Prithwijit Sarkar, Noushin Akhavantabib, Sheena D'ArcyAbstractInteractions between histones and their binding partners are an important aspect of chromatin biology. Determining the stoichiometry of histone-containing complexes is an important pre-requisite for performing in vitro biochemical, biophysical and structural analyses. In this article, we detail how Size Exclusion Chromatography (SEC) coupled to Multi-Angle Light Scattering (MALS) can be used to study histone chaperones and their complexes. Our protocol details system setup, sample prepar...
Source: Methods - January 25, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 15 January 2020Source: Methods, Volume 171Author(s): (Source: Methods)
Source: Methods - January 24, 2020 Category: Molecular Biology Source Type: research

An in silico hybrid continuum-/agent-based procedure to modelling cancer development: interrogating the interplay amongst glioma invasion, vascularity and necrosis
Publication date: Available online 23 January 2020Source: MethodsAuthor(s): Jean de Montigny, Alexandros Iosif, Lukas Breitwieser, Marco Manca, Roman Bauer, Vasileios VavourakisAbstractThis paper develops a three-dimensional in silico hybrid model of cancer, which describes the multi-variate phenotypic behaviour of tumour and host cells. The model encompasses the role of cell migration and adhesion, the influence of the extracellular matrix, the effects of oxygen and nutrient availability, and the signalling triggered by chemical cues and growth factors. The proposed in silico hybrid modelling framework combines successful...
Source: Methods - January 23, 2020 Category: Molecular Biology Source Type: research

Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods
Publication date: Available online 20 January 2020Source: MethodsAuthor(s): Anita Kotar, Hannah N. Foley, Kirk M. Baughman, Sarah C. KeaneAbstractNMR spectroscopy is a key technique that has significantly advanced our understanding of RNA structure and dynamics. However, determination of large RNA structures by NMR spectroscopy remains a significant technical challenge. In this review, we highlight advances that facilitate NMR studies of large RNAs, including methods for sample preparation, isotope labeling strategies, and data acquisition. In addition, we review hybrid approaches that have been instrumental in the structu...
Source: Methods - January 21, 2020 Category: Molecular Biology Source Type: research

Unraveling the Mechanisms that Specify Molecules for Secretion in Extracellular Vesicles
Publication date: Available online 21 January 2020Source: MethodsAuthor(s): Andrew M. Leidal, Jayanta DebnathAbstractExtracellular vesicles (EVs) are small membrane-bound organelles naturally released from cells and potentially function as vehicles of intercellular communication. Cells release numerous sub-species of EVs, including exosomes and microvesicles, which are formed via distinct cellular pathways and molecular machineries and contain specific proteins, RNAs and lipids. Accumulating evidence indicates that the repertoire of molecules packaged into EVs is shaped by both the physiological state of the cell and the E...
Source: Methods - January 21, 2020 Category: Molecular Biology Source Type: research

Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper
Publication date: Available online 21 January 2020Source: MethodsAuthor(s): Rebecca Kirsch, Ole N. Jensen, Veit SchwämmleAbstractVisualization of large-scale, multi-dimensional omics data is a major challenge. Experimental study designs in proteomics research produce multiple data layers, e.g. relationships between hundreds of proteins, their interactions and abundances as a function of time or perturbation, as well as dynamics of post-translational modifications (PTMs) and allelic variants (proteoforms). These different levels and types of information of proteins and proteoforms complicate data analysis and generatio...
Source: Methods - January 21, 2020 Category: Molecular Biology Source Type: research

PET/CT radiomics in breast cancer: mind the step
Publication date: Available online 21 January 2020Source: MethodsAuthor(s): Martina Sollini, Luca Cozzi, Gaia Ninatti, Lidija Antunovic, Lara Cavinato, Arturo Chiti, Margarita KirienkoAbstractThe aim of the present review was to assess the current status of positron emission tomography/computed tomography (PET/CT) radiomics research in breast cancer, and in particular to analyze the strengths and weaknesses of the published papers in order to identify challenges and suggest possible solutions and future research directions. Various combinations of the terms “breast”, “radiomic”, “PET”, &...
Source: Methods - January 21, 2020 Category: Molecular Biology Source Type: research

Methods for characterizing, applying, and teaching CRISPR-Cas systems
Publication date: Available online 16 January 2020Source: MethodsAuthor(s): Chase L. Beisel (Source: Methods)
Source: Methods - January 17, 2020 Category: Molecular Biology Source Type: research

Cutting Edge Approaches for Rapid Characterization of Airway Exosomes
Publication date: Available online 14 January 2020Source: MethodsAuthor(s): Kenneth P. Hough, Jessy S. DeshaneAbstractExosomes have been described as promising biomarkers for understanding disease progression and prognosis. These lipid membrane nanoparticles derived from airway cells have been shown to have immunomodulatory effects, such as driving inflammatory responses in asthma. These emerging evidences demonstrating an important pathophysiological role of exosomes warrants the development of novel approaches for isolation and rapid characterization of exosomes, which would be applicable for both translational and clini...
Source: Methods - January 15, 2020 Category: Molecular Biology Source Type: research

Multiscale network-based approaches in bioinformatics and biomedicine
Publication date: Available online 8 January 2020Source: MethodsAuthor(s): Huiru (Jane) Zheng, Xiaohua (Tony) Hu (Source: Methods)
Source: Methods - January 9, 2020 Category: Molecular Biology Source Type: research

Methods for loading therapeutics into extracellular vesicles and generating extracellular vesicles mimetic-nanovesicles
Publication date: Available online 7 January 2020Source: MethodsAuthor(s): Amirmohammad Nasiri Kenari, Lesley Cheng, Andrew F. HillAbstractExtracellular vesicles (EVs) are membrane bound vesicles released into the extracellular environment by eukaryotic and prokaryotic cells. EVs are enriched in active biomolecules and they can horizontally transfer the cargo to distant recipient cells. In recent years EVs have demonstrated promising clinical applications due to their theragnostic potential. Although EVs have promising therapeutic potential, there are several challenges associated with using EVs before transition from the ...
Source: Methods - January 7, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 1 January 2020Source: Methods, Volume 170Author(s): (Source: Methods)
Source: Methods - January 5, 2020 Category: Molecular Biology Source Type: research

Decellularization and recellularization strategies for translational medicine
Publication date: Available online 28 December 2019Source: MethodsAuthor(s): Masoud Mozafari, James J. Yoo (Source: Methods)
Source: Methods - December 29, 2019 Category: Molecular Biology Source Type: research

Recent trends in cell membrane-cloaked nanoparticles for therapeutic applications
Publication date: Available online 24 December 2019Source: MethodsAuthor(s): Bogyu Choi, Wooram Park, Sung-Bin Park, Won-Kyu Rhim, Dong Keun HanAbstractSynthetic nanoparticles are extensively utilized in various biomedical engineering fields because of their unique physicochemical properties. However, their exogenous characteristics result in synthetic nanosystem invaders that easily induce the passive immune clearance mechanism, thereby increasing the retention effect caused by reticuloendothelial system (RES), resulting in low therapeutic efficacy and toxic effects. Recently, a cell membrane cloaking has been emerging te...
Source: Methods - December 24, 2019 Category: Molecular Biology Source Type: research

Clip for studying protein-RNA interactions that regulate virus replication
Publication date: Available online 22 November 2019Source: MethodsAuthor(s): Christian Shema Mugisha, Kasyap Tenneti, Sebla B. KutluayAbstractViral and cellular RNA-binding proteins regulate numerous key steps in the replication of diverse virus genera. Viruses efficiently co-opt the host cell machinery for purposes such as transcription, splicing and subcellular localization of viral genomes. Though viral RNAs often need to resemble cellular RNAs to effectively utilize the cellular machinery, they still retain unique sequence and structural features for recognition by viral proteins for processes such as RNA polymerizatio...
Source: Methods - December 21, 2019 Category: Molecular Biology Source Type: research

PAQMAN: Protein-nucleic acid Affinity Quantification by MAss spectrometry in Nuclear extracts
Publication date: Available online 16 December 2019Source: MethodsAuthor(s): Cathrin Gräwe, Matthew M. Makowski, Michiel VermeulenAbstractIn recent years, various mass spectrometry-based approaches have been developed to determine global protein-DNA binding specificities using DNA affinity purifications from crude nuclear extracts. However, these assays are semi-quantitative and do not provide information about interaction affinities. We recently developed a technology that we call Protein-nucleic acid Affinity Quantification by MAss spectrometry in Nuclear extracts or PAQMAN, that can be used to determine apparent af...
Source: Methods - December 16, 2019 Category: Molecular Biology Source Type: research

A method for assessing histone surface accessibility genome-wide
Publication date: Available online 9 December 2019Source: MethodsAuthor(s): Luke Marr, David J. Clark, Jeffrey J. HayesAbstractThe assembly of DNA into nucleosomes and higher order chromatin structures serves not only as a means of compaction but also organizes the genome to facilitate crucial processes such as cell division and regulation of gene expression. Chromatin structure generally limits access to DNA, with the accessibility of DNA in chromatin being regulated through post translational modification of the histone proteins as well as the activity of chromatin remodeling proteins and architectural chromatin factors....
Source: Methods - December 11, 2019 Category: Molecular Biology Source Type: research

A practical guide for analysis of histone post-translational modifications by mass spectrometry: best practices and pitfalls
Publication date: Available online 7 December 2019Source: MethodsAuthor(s): Sydney P. Thomas, Spencer A. Haws, Laura E. Borth, John M. DenuAbstractAdvances in mass spectrometry (MS) have revolutionized the ability to measure global changes in histone post-translational modifications (PTMs). The method routinely quantifies over 60 modification states in a single sample, far exceeding the capabilities of traditional western blotting. Thus, MS-based histone analysis has become an increasingly popular tool for understanding how genetics and environmental factors influence epigenetic states. However, histone proteomics experime...
Source: Methods - December 7, 2019 Category: Molecular Biology Source Type: research

Chemical Probes for Protein Arginine Methyltransferases
Publication date: Available online 3 December 2019Source: MethodsAuthor(s): Alice Shi Ming Li, Fengling Li, Mohammad S. Eram, Albina Bolotokova, Carlo C. dela Seña, Masoud VedadiAbstractProtein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups to specific arginine residues of their substrates using S-adenosylmethionine as a methyl donor, contributing to regulation of many biological processes including transcription, and DNA damage repair. Dysregulation of PRMT expression is often associated with various diseases including cancers. Different methods have been used to characterize the activit...
Source: Methods - December 4, 2019 Category: Molecular Biology Source Type: research

Nano-Ghosts: Biomimetic Membranal Vesicles, Technology and Characterization
Publication date: Available online 30 November 2019Source: MethodsAuthor(s): Jacopo Oieni, Lior Levy, Nitzan Letko Khait, Liat Yosef, Beth Schoen, Miguel Fliman, Hagit Shalom-Luxenburg, Natali Malkah Dayan, Domenico D'Atri, Noa Cohen Anavy, Marcelle MachlufAbstractCurrently, nano-carriers for anti-cancer drug delivery are complex systems, which struggle with immunogenicity and enhanced permeability effect (EPR)-related problems that halt the clinical translation of many therapeutics. Consequently, a rapidly growing field of research has been focusing on biomimetic nano-vesicles (BNVs) as an effective delivery alternative. ...
Source: Methods - December 1, 2019 Category: Molecular Biology Source Type: research

Using Affinity Purification Coupled with Stable Isotope Labeling by Amino Acids in Cell Culture Quantitative Mass Spectrometry to Identify Novel Interactors/Substrates of Protein Arginine Methyltransferases
Publication date: Available online 30 November 2019Source: MethodsAuthor(s): Alan Morettin, Julie Bourassa, Kohila Mahadevan, Laura Trinkle-Mulcahy, Jocelyn CoteAbstractThe protein arginine methyltransferase family (PRMT) is known as being the catalytic driving force for arginine methylation. This specific type of post translational modification is extensively used in biological processes, and therefore is highly relevant in the pathology of a profusion of diseases. Since altered PRMT expression or deregulation has been shown to contribute to a vast range of those diseases including cancer, their study is of great interest...
Source: Methods - December 1, 2019 Category: Molecular Biology Source Type: research

Methods – Progress in super-resolution fluorescence microscopy
Publication date: Available online 29 November 2019Source: MethodsAuthor(s): (Source: Methods)
Source: Methods - November 30, 2019 Category: Molecular Biology Source Type: research

Generation, Purification and Engineering of Extracellular Vesicles and Their Biomedical Applications
Publication date: Available online 30 November 2019Source: MethodsAuthor(s): Jin Gao, Xinyue Dong, Zhenjia WangAbstractExtracellular vesicles (EVs), derived from cell membranes, demonstrate the potential to be excellent therapeutics and drug carriers. Although EVs are promising, the process to develop high-quality and scalable EVs for their translation is demanding. Within this research, we analyzed the production of EVs, their purification and their post-bioengineering, and we also discussed the biomedical applications of EVs. We focus on the developments of methods in producing EVs including biological, physical, and che...
Source: Methods - November 30, 2019 Category: Molecular Biology Source Type: research

Spring Model – chromatin modeling tool based on OpenMM
Publication date: Available online 30 November 2019Source: MethodsAuthor(s): Michal Kadlof, Julia Rozycka, Dariusz PlewczynskiAbstractChromatin structures modeling is a rapidly developing field. Parallel to the enormous growth of available experimental data, there is a growing need of building and visualizing 3D structures of nuclei, chromosomes, chromatin domains, and single loops associated with particular genes locus. Here we present a tool for chromatin domain modeling. It is available as a webservice and standalone python script. Our tool is based on molecular mechanics. It uses OpenMM engine for building models. In t...
Source: Methods - November 30, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 1 October 2019Source: Methods, Volume 169Author(s): (Source: Methods)
Source: Methods - November 25, 2019 Category: Molecular Biology Source Type: research

Somatic mutations – Evolution within the individual
Publication date: Available online 8 November 2019Source: MethodsAuthor(s): Satoshi OotaAbstractWith the rapid advancement of sequencing technologies over the last two decades, it is becoming feasible to detect rare variants from somatic tissue samples. Studying such somatic mutations can provide deep insights into various senescence-related diseases, including cancer, inflammation, and sporadic psychiatric disorders. While it is still a difficult task to identify true somatic mutations, relentless efforts to combine experimental and computational methods have made it possible to obtain reliable data. Furthermore, state-of...
Source: Methods - November 25, 2019 Category: Molecular Biology Source Type: research

Identifying the rna targets of rna binding proteins with clip
Publication date: Available online 22 November 2019Source: MethodsAuthor(s): Christian Shema Mugisha, Kasyap Tenneti, Sebla B. KutluayAbstractViral and cellular RNA-binding proteins regulate numerous key steps in the replication of diverse virus genera. Viruses efficiently co-opt the host cell machinery for purposes such as transcription, splicing and subcellular localization of viral genomes. Though viral RNAs often need to resemble cellular RNAs to effectively utilize the cellular machinery, they still retain unique sequence and structural features for recognition by viral proteins for processes such as RNA polymerizatio...
Source: Methods - November 22, 2019 Category: Molecular Biology Source Type: research

Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses
Publication date: Available online 20 November 2019Source: MethodsAuthor(s): Muhammad Arif, Sagheer Atta, Muhammad Amjad Bashir, Ansar Hussain, Muhammad Ifnan Khan, Shahid Farooq, Abdul Hanan, Saif ul Islam, Ummad ud din Umar, Mehran Khan, Wenzhong Lin, Mohamed Hashem, Saad Alamri, Zujian WuAbstractGeminiviruses constitute a family of plant viruses with characteristic twinned quasi-icosahedral virions and a small circular DNA genome. Geminiviruses, especially begomoviruses, cause substantial economic losses in tropical and subtropical regions globally. Geminiviruses use the host’s transcriptional mechanisms to synthe...
Source: Methods - November 21, 2019 Category: Molecular Biology Source Type: research

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
Publication date: Available online 18 November 2019Source: MethodsAuthor(s): Anke Busch, Mirko Brüggemann, Stefanie Ebersberger, Kathi ZarnackAbstractPrecise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understanding the complex post-transcriptional regulation of gene expression. This information can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. Here, we present a complete data analysis workflow to reliably detect RBP binding sites from iCLIP data. The workflow covers all steps from the initial quality control of the sequencin...
Source: Methods - November 19, 2019 Category: Molecular Biology Source Type: research

A Lipid Mixing Assay to Accurately Quantify the Fusion of Outer Membrane Vesicles
Publication date: Available online 17 November 2019Source: MethodsAuthor(s): Yehou M. D. Gnopo, David PutnamAbstractThe intermixing of phospholipids from opposing bilayers, or membrane fusion, is a naturally occurring process that can be leveraged to produce hybrid vesicle systems. Optimizing the production of these hybrid vesicles requires accurate, sensitive and quantitative methods of the lipid mixing that occurs during fusion. A fluorescence-based assay that uses octadecyl-rhodamine B chloride to measure lipid mixing, or R18 assay, was developed by Hoekstra to investigate viral entry almost four decades ago. However, t...
Source: Methods - November 18, 2019 Category: Molecular Biology Source Type: research