4,032 results match your criteria Methods [Journal]


Hybrid model for efficient prediction of Poly(A) signals in human genomic DNA.

Methods 2019 Apr 13. Epub 2019 Apr 13.

King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia. Electronic address:

Polyadenylation signals (PAS) are found in most protein-coding and some non-coding genes in eukaryotes. Their accurate recognition improves understanding gene regulation mechanisms and recognition of the 3'-end of transcribed gene regions where premature or alternate transcription ends may lead to various diseases. Although different methods and tools for in-silico prediction of genomic signals have been proposed, the correct identification of PAS in genomic DNA remains challenging due to a vast number of non-relevant hexamers identical to PAS hexamers. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.04.001DOI Listing
April 2019
2 Reads

Rapid high resolution 3D imaging of expanded biological specimens with lattice light sheet microscopy.

Methods 2019 Apr 9. Epub 2019 Apr 9.

Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan. Electronic address:

Expansion microscopy was invented to surpass the optical diffraction limit by physically expanding biological specimens with swellable polymers. Due to the large sizes of expanded specimens, 3D imaging techniques that are capable to acquire large volumetric data rapidly at high spatial resolution are therefore required for expansion microscopy. Lattice light sheet microscopy (LLSM) was developed to image biological specimens rapidly at high 3D spatial resolution by using a thin lattice light sheet for sample illumination. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.04.006DOI Listing

AFM-based single-molecule observation of the conformational changes of DNA structures.

Authors:
Masayuki Endo

Methods 2019 Apr 9. Epub 2019 Apr 9.

Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

Direct visualization of the biomolecules of interest is a straightforward way to elucidate the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables direct imaging of biomolecules in suitable solution conditions. As AFM visualizes the molecules at a nanometer-scale spatial resolution, a versatile observation platform is required for precise imaging of the molecules in action. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183034
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http://dx.doi.org/10.1016/j.ymeth.2019.04.007DOI Listing
April 2019
1 Read

RNA-based Capture-SELEX for the selection of small molecule-binding aptamers.

Methods 2019 Apr 3. Epub 2019 Apr 3.

Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany. Electronic address:

Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.04.004DOI Listing
April 2019
1 Read

Fluorescent carbon dots derived from urine and their application for bio-imaging.

Methods 2019 Apr 4. Epub 2019 Apr 4.

School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Qinggongyuan 1, Ganjingzi District, Dalian 116034, China. Electronic address:

This study aims to obtain water-soluble fluorescent carbon dots (C-dots) from low-value metabolites through a simple, economical, one-step synthetic route. The urine C-dots (UCDs) and hydrothermally treated urine C-dots (HUCDs) were obtained, respectively, using straightforward Sephadex filtration method from human adults and hydrothermal reaction method. The UCDs and HUCDs emit fluorescence upon being excited with ultraviolet light with a quantum yield of 4. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.04.005DOI Listing
April 2019
1 Read
3.645 Impact Factor

A computational system for identifying operons based on RNA-seq data.

Authors:
Brian Tjaden

Methods 2019 Apr 4. Epub 2019 Apr 4.

Department of Computer Science, Wellesley College, Wellesley, MA 02481, USA. Electronic address:

An operon is a set of neighboring genes in a genome that is transcribed as a single polycistronic message. Genes that are part of the same operon often have related functional roles or participate in the same metabolic pathways. The majority of all bacterial genes are co-transcribed with one or more other genes as part of a multi-gene operon. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.026DOI Listing
April 2019
1 Read

Proteomic navigation using proximity-labeling.

Methods 2019 Apr 3. Epub 2019 Apr 3.

The Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK. Electronic address:

The identification of bona fide protein-protein interactions and the mapping of proteomes was greatly enhanced by protein tagging for generic affinity purification methods and analysis by mass spectrometry (AP-MS). The high quality of AP-MS data permitted the development of proteomic navigation by sequential tagging of identified interactions. However AP-MS is laborious and limited to relatively high affinity protein-protein interactions. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.028DOI Listing

How to Benchmark RNA Secondary Structure Prediction Accuracy.

Authors:
David H Mathews

Methods 2019 Apr 2. Epub 2019 Apr 2.

Center for RNA Biology, Department of Biochemistry & Biophysics, and Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, United States. Electronic address:

RNA secondary structure prediction is widely used. As new methods are developed, these are often benchmarked for accuracy against existing methods. This review discusses good practices for performing these benchmarks, including the choice of benchmarking structures, metrics to quantify accuracy, the importance of allowing flexibility for pairs in the accepted structure, and the importance of statistical testing for significance. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183034
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http://dx.doi.org/10.1016/j.ymeth.2019.04.003DOI Listing
April 2019
3 Reads

Probing RNA structure and interaction dynamics at the single molecule level.

Methods 2019 Apr 3. Epub 2019 Apr 3.

Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

RNA structures and their dynamic fluctuations lie at the heart of understanding key biological process such as transcription, splicing, translation and RNA decay. While conventional bulk assays have proven to identify and characterize key pathway intermediates, the generally dynamic nature of RNA structures renders the information obtained from time and ensemble averaging techniques necessarily lacking in critical details. Here we detail Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS), a method that readily monitors structural fluctuations of single RNA molecules through the repetitive interaction of fluorescent probes with an unlabeled, surface-immobilized RNA target of virtually any length and in any biological context. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183039
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http://dx.doi.org/10.1016/j.ymeth.2019.04.002DOI Listing
April 2019
4 Reads

Supercritical angle fluorescence for enhanced axial sectioning in STED microscopy.

Methods 2019 Apr 1. Epub 2019 Apr 1.

Institut des Sciences Moléculaires d'Orsay, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. Electronic address:

We demonstrate subwavelength axial sectioning on biological samples with a stimulated emission depletion (STED) microscope combined with supercritical angle fluorescence (SAF) detection. SAF imaging is a powerful technique for imaging the membrane of the cell based on the direct exploitation of the fluorophore emission properties. Indeed, only when fluorophores are close to the interface can their evanescent near-field emission become propagative and be detected beyond the critical angle. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.027DOI Listing
April 2019
1 Read

Studying ribosome dynamics with simplified models.

Methods 2019 Mar 29. Epub 2019 Mar 29.

Department of Physics, Northeastern University, Boston MA, and Crystallography, Max Delbrueck Center, Berlin, Germany. Electronic address:

With the broad accessibility of high-performance computing resources, the significance of a molecular dynamics simulation is now rarely limited by hardware and/or software availability. Rather, the scientific value of each calculation is determined by the principles that underly the theoretical model. The current review addresses this topic in the context of simplified models applied to large-scale (∼20-100Å) dynamics in the ribosome. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.023DOI Listing
March 2019
2 Reads

An Extended Dual Graph Library and Partitioning Algorithm Applicable to Pseudoknotted RNA Structures.

Methods 2019 Mar 27. Epub 2019 Mar 27.

Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA; NYU-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, North Zhongshan Road, 3663 Shanghai, China. Electronic address:

Exploring novel RNA topologies is imperative for understanding RNA structure and pursuing its design. Our RNA-As-Graphs (RAG) approach exploits graph theory tools and uses coarse-grained tree and dual graphs to represent RNA helices and loops by vertices and edges. Only dual graphs represent pseudoknotted RNAs fully. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.022DOI Listing
March 2019
1 Read
3.645 Impact Factor

RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns.

Authors:
Xuhua Xia

Methods 2019 Mar 26. Epub 2019 Mar 26.

Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa K1N 6N5, Canada; Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada. Electronic address:

Introns in different genes, or even different introns within the same gene, often have different splice sites and differ in splicing efficiency (SE). One expects mass-transcribed genes to have introns with higher SE than weakly transcribed genes. However, such a simple expectation cannot be tested directly because variable SE for these genes is often not measured. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.019DOI Listing

Rapid enzymatic synthesis of long RNA polymers: A simple protocol to generate RNA libraries with random sequences.

Methods 2019 Mar 26. Epub 2019 Mar 26.

Unit of Structural Dynamics of Biological Macromolecules and CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.

RNA aptamers have several advantages over DNA aptamers due to their propensity to fold into three-dimensional structures. However, the synthesis of large RNA libraries remains a challenge as it requires more precautions to conserve their functional integrity, especially when such libraries are intended for aptamers or ribozymes selection. Here, we present an enzymatic method that enables the rapid synthesis of RNA polymers thanks to the efficient incorporation of ribonucleotides (NTPs) as well as chemically modified ribonucleotides by human DNA polymerase Theta (θ) mutants. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.025DOI Listing

Reconstitution and analyses of RNA interactions with eukaryotic translation initiation factors and ribosomal preinitiation complexes.

Methods 2019 Mar 26. Epub 2019 Mar 26.

Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, United States. Electronic address:

Control of translation initiation plays a critical role in the regulation of gene expression in all organisms, yet the mechanics of translation initiation in eukaryotic organisms are not well understood. Confounding studies of translation are the large number and overlapping functions of many initiation factors in cells, and a lack of cap-dependence in many in vitro systems. To shed light on intricate mechanisms that are often obscured in vivo, we use a fully reconstituted translation initiation system for analyzing RNA interactions with eukaryotic translation initiation factors and complexes from the model organism Saccharomyces cerevisiae. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.024DOI Listing

FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data.

Methods 2019 Mar 26. Epub 2019 Mar 26.

University of California, Department of Computer Science, Irvine, CA 92697, United States. Electronic address:

Due to the large numbers of transcription factors (TFs) and cell types, querying binding profiles of all valid TF/cell type pairs is not experimentally feasible. To address this issue, we developed a convolutional-recurrent neural network model, called FactorNet, to computationally impute the missing binding data. FactorNet trains on binding data from reference cell types to make predictions on testing cell types by leveraging a variety of features, including genomic sequences, genome annotations, gene expression, and signal data, such as DNase I cleavage. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.020DOI Listing

IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques.

Methods 2019 Mar 22. Epub 2019 Mar 22.

Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, PR China. Electronic address:

Inverse Virtual Screening is a powerful technique in the early stage of drug discovery process. This technique can provide important clues for biologically active molecules, which is useful in the following researches of durg discovery. In this work, combining with Word2vec, a natural language processing technique, dense fully connected neural network (DFCNN) algorithm is utilized to build up a prediction model. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.012DOI Listing

RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state.

Methods 2019 Mar 21. Epub 2019 Mar 21.

Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada. Electronic address:

Shigella spp. are enterobacteria that invade human colonic mucosal cells using their Type Three Secretion Apparatus (T3SA). Shigella spp. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.017DOI Listing
March 2019
2 Reads

Chemical methods for the modification of RNA.

Methods 2019 Mar 21. Epub 2019 Mar 21.

Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. Electronic address:

RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183027
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http://dx.doi.org/10.1016/j.ymeth.2019.03.018DOI Listing
March 2019
8 Reads

In vitro reconstitution of yeast RNA polymerase II transcription initiation with high efficiency.

Methods 2019 Mar 21. Epub 2019 Mar 21.

Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

Transcription initiation can be reconstituted from highly purified general transcription factors (GTFs), RNA polymerase II (pol II), and promoter DNA. However, earlier biochemical reconstitution systems had a serious technical limitation, namely very poor initiation efficiency. Due to the poor efficiency of the reaction and trace amounts of proteins involved in the pre-initiation complex (PIC) assembly, detection of transcription and PIC formation was only possible by the synthesis of a radiolabeled transcript and by immunoblotting for PIC components on templates. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.016DOI Listing
March 2019
1 Read

Advances in optogenetic regulation of gene expression in mammalian cells using cryptochrome 2 (CRY2).

Methods 2019 Mar 21. Epub 2019 Mar 21.

Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address:

Synthetic regulation of gene expression provides a powerful approach to reprogram molecular and cellular processes and test the function of specific genes and gene products. In the last decade, optogenetic systems that allow light-dependent gene regulation have become valuable tools, providing tight spatiotemporal control of protein levels. Here we discuss and build on recent optogenetic approaches for regulating gene expression in mammalian cells using cryptochrome 2 (CRY2), a photoreceptor protein from Arabidopsis. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.011DOI Listing

Enhancer prediction with histone modification marks using a hybrid neural network model.

Authors:
A Lim S Lim S Kim

Methods 2019 Mar 21. Epub 2019 Mar 21.

Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea; Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea. Electronic address:

Enhancer is a DNA sequence of a genome that controls transcription of downstream target genes. Enhancers are known to be associated with certain epigenetic signatures. Machine learning tools, such as CSI-ANN, ChromHMM, and RFECS, were developed for predicting enhancers using various epigenetic features. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.014DOI Listing

Translation imaging of single mRNAs in established cell lines and primary cultured neurons.

Methods 2019 Mar 21. Epub 2019 Mar 21.

Johns Hopkins School of Medicine, Department of Biophysics and Biophysical Chemistry, 855 N Wolfe Street Ste. 454, Baltimore, MD 21205, USA; Johns Hopkins School of Medicine, Center for Cell Dynamics, Baltimore, USA; Johns Hopkins School of Medicine, Solomon H. Snyder Department of Neuroscience, Baltimore, USA. Electronic address:

The central dogma of molecular biology reaches a crescendo at its final step: the translation of an mRNA into its corresponding protein product. This process is highly regulated both spatially and temporally, requiring techniques to interrogate the subcellular translational status of mRNAs in both living and fixed cells. Single-molecule imaging of nascent peptides (SINAPs) and related techniques allow us to study this fundamental process for single mRNAs in live cells. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.021DOI Listing

Methods review: Mass spectrometry analysis of RNAPII complexes.

Methods 2019 Mar 19. Epub 2019 Mar 19.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46402, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46402, United States. Electronic address:

RNA Polymerase II (RNAPII) is responsible for transcribing multiple RNA species throughout eukaryotes. A variety of protein-protein interactions occur throughout the transcription cycle for coordinated regulation of transcription initiation, elongation, and/or termination. Taking a proteomics approach to study RNAPII transcription thereby offers a comprehensive view of both RNAPII biology and the variety of proteins that regulate the process itself. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.013DOI Listing

Optimization of fluorogenic RNA-based biosensors using droplet-based microfluidic ultrahigh-throughput screening.

Methods 2019 Mar 19. Epub 2019 Mar 19.

Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France. Electronic address:

Biosensors are biological molecules able to detect and report the presence of a target molecule by the emission of a signal. Nucleic acids are particularly appealing for the design of such molecule since their great structural plasticity makes them able to specifically interact with a wide range of ligands and their structure can rearrange upon recognition to trigger a reporting event. A biosensor is typically made of three main domains: a sensing domain that is connected to a reporting domain via a communication module in charge of transmitting the sensing event through the molecule. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.015DOI Listing

Single-molecule approach for studying RNAP II transcription initiation using magnetic tweezers.

Methods 2019 Mar 18. Epub 2019 Mar 18.

Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, United States. Electronic address:

The initiation of transcription underlies the ability of cells to modulate genome expression as a function of both internal and external signals and the core process of initiation has features that are shared across all domains of life. Specifically, initiation can be sub-divided into promoter recognition, promoter opening, and promoter escape. However, the molecular players and mechanisms used are significantly different in Eukaryotes and Bacteria. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.010DOI Listing

Role of integrative structural biology in understanding transcriptional initiation.

Methods 2019 Mar 16. Epub 2019 Mar 16.

Department of Biological Sciences, Birkbeck University of London, Institute of Structural and Molecular Biology, London, United Kingdom. Electronic address:

Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.009DOI Listing

MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.

Methods 2019 Mar 16. Epub 2019 Mar 16.

Department of Computer Science, University of California at Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.003DOI Listing
March 2019
1 Read

Visualizing mRNA in live mammalian cells.

Methods 2019 Mar 14. Epub 2019 Mar 14.

Department of Chemistry, Shanghai Normal University, Shanghai 200234, China; Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China. Electronic address:

mRNAs play essential role in gene expression and regulation. Direct visualization of specific intracellular mRNAs can provide key information about mRNA distribution and dynamics that accelerating study of their functionality. This highlights the necessity of characterizing mRNA in mammalian cells with good spatial and temporal resolution. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183028
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http://dx.doi.org/10.1016/j.ymeth.2019.03.008DOI Listing
March 2019
5 Reads

Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization.

Methods 2019 Mar 13. Epub 2019 Mar 13.

Department of Biochemistry, University of Colorado, Boulder, 596 UCB, Boulder, CO 80309, USA. Electronic address:

RNA polymerase II (Pol II) transcribes eukaryotic mRNA genes. To initiate transcription, pre-initiation complexes (PICs) containing Pol II and general transcription factors (GTFs) form on the core promoters of target genes. In cells this process is regulated by transcriptional activators, co-activators, and chromatin modifying complexes. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183030
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http://dx.doi.org/10.1016/j.ymeth.2019.03.006DOI Listing
March 2019
4 Reads

Nanoscale exploration of the extracellular space in the live brain by combining single carbon nanotube tracking and super-resolution imaging analysis.

Methods 2019 Mar 9. Epub 2019 Mar 9.

Université de Bordeaux, Laboratoire Photonique Numérique et Nanosciences, UMR 5298, 33400 Talence, France; Institut d'Optique & CNRS, LP2N UMR 5298, 33400 Talence, France. Electronic address:

The brain extracellular space (ECS) is a system of narrow compartments whose intricate nanometric structure has remained elusive until very recently. Understanding such a complex organisation represents a technological challenge that requires a technique able to resolve these nanoscopic spaces and simultaneously characterize their rheological properties. We recently used single-walled carbon nanotubes (SWCNTs) as near-infrared fluorescent probes to map with nanoscale precision the local organization and rheology of the ECS. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.005DOI Listing

Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Methods 2019 Mar 7. Epub 2019 Mar 7.

Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland. Electronic address:

We present machine learning models of human genome three-dimensional structure that combine one dimensional (linear) sequence specificity, epigenomic information, and transcription factor binding profiles, with the polymer-based biophysical simulations in order to explain the extensive long-range chromatin looping observed in ChIA-PET experiments for lymphoblastoid cells. Random Forest, Gradient Boosting Machine (GBM), and Deep Learning models were constructed and evaluated, when predicting high-resolution interactions within Topologically Associating Domains (TADs). The predicted interactions are consistent with the experimental long-read ChIA-PET interactions mediated by CTCF and RNAPOL2 for GM12878 cell line. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.002DOI Listing
March 2019
1 Read

Unsupervised classification of multi-omics data during cardiac remodeling using deep learning.

Methods 2019 Mar 7. Epub 2019 Mar 7.

NIH BD2K Center of Excellence for Biomedical Computing, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA; Scalable Analytics Institute (ScAi), University of California Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

Integration of multi-omics in cardiovascular diseases (CVDs) presents high potentials for translational discoveries. By analyzing abundance levels of heterogeneous molecules over time, we may uncover biological interactions and networks that were previously unidentifiable. However, to effectively perform integrative analysis of temporal multi-omics, computational methods must account for the heterogeneity and complexity in the data. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183035
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http://dx.doi.org/10.1016/j.ymeth.2019.03.004DOI Listing
March 2019
4 Reads
3.645 Impact Factor

In vitro assembly and proteomic analysis of RNA polymerase II complexes.

Methods 2019 Mar 4. Epub 2019 Mar 4.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States. Electronic address:

The RNA polymerase II (RNApII) transcription cycle consists of multiple steps involving dozens of protein factors. Here we describe a useful approach to study the dynamics of initiation and early elongation, comprising an in vitro transcription system in which complexes are assembled on immobilized DNA templates and analyzed by quantitative mass spectrometry. This unbiased screening system allows quantitation of RNApII complex components on either naked DNA or chromatin templates. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.03.001DOI Listing

Base editing the mammalian genome.

Methods 2019 Mar 2. Epub 2019 Mar 2.

Sandra and Edward Meyer Cancer Center, United States; Department of Medicine, United States; Department of Biochemistry, Weill Cornell Medicine, New York 10021, United States. Electronic address:

Base editing is a powerful technology that enables programmable conversion of single nucleotides in the mammalian genome. Base editors consist of a partially active Cas9 nuclease (Cas9) tethered to a natural or synthetic DNA modifying enzyme. Though only recently described, BE has already shown enormous potential for basic and translational research, allowing the creation or repair of disease alleles in a variety of cell types and model organisms. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.022DOI Listing
March 2019
2 Reads

Methods in Nuclear Architecture and Transport.

Authors:
Bryce M Paschal

Methods 2019 Mar;157:1-2

Center for Cell Signaling, University of Virginia School of Medicine, Room 7021 West Complex, Box 800577, 1400 Jefferson Park Avenue, Charlottesville, VA 22908-0577.

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http://dx.doi.org/10.1016/j.ymeth.2019.02.020DOI Listing

Nucleoside analogs in the study of the epitranscriptome.

Methods 2019 Mar 26;156:46-52. Epub 2018 Oct 26.

Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA. Electronic address:

Over 150 unique RNA modifications are now known including several nonstandard nucleotides present in the body of messenger RNAs. These modifications can alter a transcript's function and are collectively referred to as the epitrancriptome. Chemically modified nucleoside analogs are poised to play an important role in the study of these epitranscriptomic marks. Read More

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http://dx.doi.org/10.1016/j.ymeth.2018.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400310PMC

Using mouse models to unlock the secrets of non-synonymous RNA editing.

Methods 2019 Mar 26;156:40-45. Epub 2018 Oct 26.

Missouri State University, Department of Biomedical Sciences, 901 South National Avenue, Springfield, MO 65897, United States. Electronic address:

The deamination of adenosine to inosine by RNA editing is a widespread post-transcriptional process that expands genetic diversity. Selective substitution of inosine for adenosine in pre-mRNA transcripts can alter splicing, mRNA stability, and the amino acid sequence of the encoded protein. The functional consequences of RNA editing-dependent amino acid substitution are known for only a handful of RNA editing substrates. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183018
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http://dx.doi.org/10.1016/j.ymeth.2018.10.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400289PMC
March 2019
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Exploring semi-supervised variational autoencoders for biomedical relation extraction.

Methods 2019 Feb 27. Epub 2019 Feb 27.

National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA. Electronic address:

The biomedical literature provides a rich source of knowledge such as protein-protein interactions (PPIs), drug-drug interactions (DDIs) and chemical-protein interactions (CPIs). Biomedical relation extraction aims to automatically extract biomedical relations from biomedical text for various biomedical research. State-of-the-art methods for biomedical relation extraction are primarily based on supervised machine learning and therefore depend on (sufficient) labeled data. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.021DOI Listing
February 2019

CRISPR/Cas9-mediated generic protein tagging in mammalian cells.

Methods 2019 Feb 22. Epub 2019 Feb 22.

Department of Molecular Hematology and LOEWE Center for Cell and Gene Therapy, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany; Department of Medicine 2, Hematology/Oncology and Frankfurt Cancer Institute, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany.

Systematic protein localization and protein-protein interaction studies to characterize specific protein functions are most effectively performed using tag-based assays. Ideally, protein tags are introduced into a gene of interest by homologous recombination to ensure expression from endogenous control elements. However, inefficient homologous recombination makes this approach difficult in mammalian cells. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.018DOI Listing
February 2019
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Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest.

Methods 2019 Feb 22. Epub 2019 Feb 22.

Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, United States. Electronic address:

Transcription, catalyzed by RNA polymerase II (Pol II) in eukaryotes, is the first step in gene expression. RNA Pol II is a 12-subunit enzyme complex regulated by many different transcription factors during transcription initiation, elongation, and termination. During elongation, Pol II encounters various types of obstacles that can cause transcriptional pausing and arrest. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.019DOI Listing
February 2019

Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation.

Methods 2019 Feb;155:1-2

University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, 6-155 Jackson Hall, 1214A, 321 Church Street S.E., Minneapolis, MN 55455. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.02.012DOI Listing
February 2019

Functional assays for transcription mechanisms in high-throughput.

Methods 2019 Feb 20. Epub 2019 Feb 20.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address:

Dramatic increases in the scale of programmed synthesis of nucleic acid libraries coupled with deep sequencing have powered advances in understanding nucleic acid and protein biology. Biological systems centering on nucleic acids or encoded proteins greatly benefit from such high-throughput studies, given that large DNA variant pools can be synthesized and DNA, or RNA products of transcription, can be easily analyzed by deep sequencing. Here we review the scope of various high-throughput functional assays for studies of nucleic acids and proteins in general, followed by discussion of how these types of study have yielded insights into the RNA Polymerase II (Pol II) active site as an example. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.017DOI Listing
February 2019

Iridium(III)-based chemosensors for the detection of metal ions.

Methods 2019 Feb 20. Epub 2019 Feb 20.

State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China. Electronic address:

In recent years, transition metal complexes with their prominent photophysical properties have emerged as versatile chemosensors to probe different target analytes, including metal ions. By incorporating specific metal ion receptors, various iridium(III) complex-based cation sensors have been developed using different mechanisms. In this review, we survey examples of iridium(III) complex-based metal ion chemosensors that have been reported in the literature. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.013DOI Listing
February 2019
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Imaging-based assays for investigating functions of the RNA polymerase II elongation factor Elongin and the Elongin ubiquitin ligase.

Methods 2019 Feb 19. Epub 2019 Feb 19.

Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, United States; Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States. Electronic address:

Elongin A binds to Elongins B and C to form the RNA polymerase II transcription elongation factor Elongin. It also functions as the substrate recognition subunit of a ubiquitin ligase that is formed by binding of Elongin to Cullin protein CUL5 and RING finger protein RBX2 and that targets RNA polymerase II for ubiquitination. In this article, we describe use of acceptor photobleaching fluorescence resonance energy transfer (AP-FRET) and laser microirradiation-based assays to study regulated assembly of the Elongin ubiquitin ligase and its recruitment to regions of localized DNA damage. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.015DOI Listing
February 2019
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Free energy calculations of RNA interactions.

Methods 2019 Feb 19. Epub 2019 Feb 19.

Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden. Electronic address:

This review discusses the use of molecular dynamics free energy calculations for characterizing RNA interactions, with particular emphasis on molecular recognition events involved in mRNA translation on the ribosome. The general methodology for efficient free energy calculations is outlined and our specific implementation for binding free energy changes due to base mutations in mRNA and tRNA is described. We show that there are a number of key problems related to the accuracy of protein synthesis that can be addressed with this type of computational approach and several such examples are discussed in detail. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.014DOI Listing
February 2019
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Real-time monitoring of protein-induced DNA conformational changes using single-molecule FRET.

Methods 2019 Feb 15. Epub 2019 Feb 15.

B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany. Electronic address:

Apart from being storage devices for genetic information, nucleic acids can provide regulatory structures through evolutionarily optimized sequences. The interaction of proteins binding specifically to such sequences and resulting secondary structures, or the exposure of single-stranded DNA add a versatile regulatory framework for cells. Biochemical and structural biology experiments have revealed important underlying concepts of protein-DNA interactions but are often limited by ensemble averaging or static information. Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.011DOI Listing
February 2019
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Deep-Resp-Forest: A deep forest model to predict anti-cancer drug response.

Methods 2019 Feb 14. Epub 2019 Feb 14.

Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. Electronic address:

The identification of therapeutic biomarkers predictive of drug response is crucial in personalized medicine. A number of computational models to predict response of anti-cancer drugs have been developed as the establishment of several pharmacogenomics screening databases. In our study, we proposed a deep cascaded forest model, Deep-Resp-Forest, to classify the anti-cancer drug response as "sensitive" or "resistant". Read More

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http://dx.doi.org/10.1016/j.ymeth.2019.02.009DOI Listing
February 2019
1 Read