Hybrid model for efficient prediction of Poly(A) signals in human genomic DNA
In this study, we developed a novel method for PAS recognition. The method is implemented in a hybrid PAS recognition model (HybPAS), which is based on deep neural networks (DNNs) and logistic regression models (LRMs). One of such models is developed for each of the 12 most frequent human PAS hexamers. DNN models appeared the best for eight PAS types (including the two most frequent PAS hexamers), while LRM appeared best for the remaining four PAS types. The new models use different combinations of signal processing-based, statistical, and sequence-based features as input. The results obtained on human genomic data show th...
Source: Methods - April 15, 2019 Category: Molecular Biology Source Type: research

Rapid High Resolution 3D Imaging of Expanded Biological Specimens with Lattice Light Sheet Microscopy
Publication date: Available online 9 April 2019Source: MethodsAuthor(s): Yun-Chi Tsai, Wei-Chun Tang, Christine Siok Lan Low, Yen-Ting Liu, Jyun-Sian Wu, Po-Yi Lee, Lindsay Quinn Chen, Yi-Ling Lin, Pakorn Kanchanawong, Liang Gao, Bi-Chang ChenAbstractExpansion 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 (...
Source: Methods - April 10, 2019 Category: Molecular Biology Source Type: research

AFM-based single-molecule observation of the conformational changes of DNA structures
Publication date: Available online 9 April 2019Source: MethodsAuthor(s): Masayuki EndoAbstractDirect 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. The DNA origami technology allows precise placement of target molecules in a designed nanostructure...
Source: Methods - April 10, 2019 Category: Molecular Biology Source Type: research

Single-molecule approach for studying RNAP II transcription initiation using magnetic tweezers
Publication date: Available online 18 March 2019Source: MethodsAuthor(s): Eric J. Tomko, Eric A. GalburtAbstractThe 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. In particular, bacterial initiation requires only the formation ...
Source: Methods - April 7, 2019 Category: Molecular Biology Source Type: research

Proteomic navigation using proximity-labeling
Publication date: Available online 4 April 2019Source: MethodsAuthor(s): Marc Gentzel, Mercedes Pardo, Sivaraman Subramaniam, A. Francis Stewart, Jyoti S. ChoudharyAbstractThe 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. Proximity label...
Source: Methods - April 5, 2019 Category: Molecular Biology Source Type: research

A Computational System for Identifying Operons Based on RNA-Seq Data
Publication date: Available online 4 April 2019Source: MethodsAuthor(s): Brian TjadenAbstractAn 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. Thus, accurate identification of operons is important in understanding co-regulation of genes and their functional relationships. Here, we present a computational system that uses RNA-seq data...
Source: Methods - April 5, 2019 Category: Molecular Biology Source Type: research

RNA-based Capture-SELEX for the selection of small molecule-binding aptamers
Publication date: Available online 4 April 2019Source: MethodsAuthor(s): Adrien Boussebayle, Florian Groher, Beatrix SuessAbstractDespite 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. More...
Source: Methods - April 5, 2019 Category: Molecular Biology Source Type: research

Fluorescent carbon dots derived from urine and their application for bio-imaging
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 4.8% and 17.8%, respectively. TEM analysis revealed that UCDs and HUCDs had an average size of 2.5 nm and 5.5 nm, respectively. X-ray photoelectron spectroscopy (XPS) an...
Source: Methods - April 5, 2019 Category: Molecular Biology Source Type: research

How to Benchmark RNA Secondary Structure Prediction Accuracy
Publication date: Available online 2 April 2019Source: MethodsAuthor(s): David H. MathewsAbstractRNA 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. (Source: Methods)
Source: Methods - April 3, 2019 Category: Molecular Biology Source Type: research

Probing RNA structure and interaction dynamics at the single molecule level
Publication date: Available online 3 April 2019Source: MethodsAuthor(s): Adrien Chauvier, Javier Cabello-Villegas, Nils G. WalterAbstractRNA 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 S...
Source: Methods - April 3, 2019 Category: Molecular Biology Source Type: research

Supercritical Angle Fluorescence for Enhanced Axial Sectioning in STED Microscopy
Publication date: Available online 1 April 2019Source: MethodsAuthor(s): Siddharth Sivankutty, Iván Coto Hernández, Nicolas Bourg, Guillaume Dupuis, Sandrine Lévêque-FortAbstractWe 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 em...
Source: Methods - April 2, 2019 Category: Molecular Biology Source Type: research

Studying ribosome dynamics with simplified models
Publication date: Available online 30 March 2019Source: MethodsAuthor(s): Mariana Levi, Jeffrey K. Noel, Paul C. WhitfordAbstractWith 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. Specifically, we focus on applications of the &ldquo...
Source: Methods - March 30, 2019 Category: Molecular Biology Source Type: research

An Extended Dual Graph Library and Partitioning Algorithm Applicable to Pseudoknotted RNA Structures
Publication date: Available online 27 March 2019Source: MethodsAuthor(s): Swati Jain, Sera Saju, Louis Petingi, Tamar SchlickAbstractExploring 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. Here we develop a dual graph enumeration algorithm to generate an expanded library of dual graph topologies for 2 to 9 vertices, and extend our dual graph partitioning algorithm ...
Source: Methods - March 28, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 1 April 2019Source: Methods, Volume 158Author(s): (Source: Methods)
Source: Methods - March 28, 2019 Category: Molecular Biology Source Type: research

Advances in Bead-Based Biomarker Detection
Publication date: 1 April 2019Source: Methods, Volume 158Author(s): Brian K. McFarlin, John H. Curtis (Source: Methods)
Source: Methods - March 28, 2019 Category: Molecular Biology Source Type: research

Reconstitution and Analyses of RNA Interactions with Eukaryotic Translation Initiation Factors and Ribosomal Preinitiation Complexes
Publication date: Available online 26 March 2019Source: MethodsAuthor(s): Xiaozhuo Liu, Peter J. Schuessler, Ansuman Sahoo, Sarah E. WalkerAbstractControl 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 trans...
Source: Methods - March 27, 2019 Category: Molecular Biology Source Type: research

RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns
Publication date: Available online 26 March 2019Source: MethodsAuthor(s): Xuhua XiaAbstractIntrons 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. Mechanistically, SE should depend on signal strength at key splice sites (SS) such as 5'SS, 3'SS and branchpoint site (BPS), i.e., SE = F(5'SS, 3'SS, BPS). However, without...
Source: Methods - March 27, 2019 Category: Molecular Biology Source Type: research

FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data
Publication date: Available online 26 March 2019Source: MethodsAuthor(s): Daniel Quang, Xiaohui XieAbstractDue 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...
Source: Methods - March 27, 2019 Category: Molecular Biology Source Type: research

Rapid enzymatic synthesis of long RNA polymers: a simple protocol to generate RNA libraries with random sequences
Publication date: Available online 26 March 2019Source: MethodsAuthor(s): Irina Randrianjatovo-Gbalou, Marc DelarueAbstractRNA 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 chemi...
Source: Methods - March 27, 2019 Category: Molecular Biology Source Type: research

IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques
In this study, IVS2vec brings many convincing results than Autodock vina in the reverse target searching case of Quercetin. (Source: Methods)
Source: Methods - March 23, 2019 Category: Molecular Biology Source Type: research

Translation imaging of single mRNAs in Established Cell Lines and Primary Cultured Neurons
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): Mallgorzata J. Latallo, Nathan M. Livingston, Bin WuAbstractThe 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. These techniques enabl...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

Advances in optogenetic regulation of gene expression in mammalian cells using cryptochrome 2 (CRY2)
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): Carmen N. Hernández-Candia, Christina L. Wysoczynski, Chandra L. TuckerAbstractSynthetic 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...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

Chemical methods for the modification of RNA
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): Marie Flamme, Luke K McKenzie, Ivo Sarac, Marcel HollensteinAbstractRNA 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 ch...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): Navoun Silué, Endrei Marcantonio, F-X Campbell-ValoisAbstractShigella spp. are enterobacteria that invade human colonic mucosal cells using their Type Three Secretion Apparatus (T3SA). Shigella spp. possess a large plasmid that encodes most of its virulence factors and has been the focus of seminal work that defined the T3SA regulon. Thus, a global assessment of the transcriptional response regulated by the T3SA has been lacking. Herein we used RNA-Seq to identify genes that are differentially expressed when the T3SA is active (on-state) versu...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

Enhancer Prediction with Histone Modification Marks Using a Hybrid Neural Network Model
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): A. Lim, S. Lim, S. KimAbstractEnhancer 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. However, predictions by different tools vary widely and quite a significant portion of enhancer predictions does not agree. Thus, computational methods for enhancer prediction should be further developed. In this paper, a...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

In vitro reconstitution of yeast RNA polymerase II transcription initiation with high efficiency
Publication date: Available online 21 March 2019Source: MethodsAuthor(s): Rina Fujiwara, Kenji MurakamiAbstractTranscription 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...
Source: Methods - March 22, 2019 Category: Molecular Biology Source Type: research

Optimization of fluorogenic RNA-based biosensors using droplet-based microfluidic ultrahigh-throughput screening
Publication date: Available online 19 March 2019Source: MethodsAuthor(s): Alexis Autour, Farah Bouhedda, Roger Cubi, Michael RyckelynckAbstractBiosensors 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 repor...
Source: Methods - March 20, 2019 Category: Molecular Biology Source Type: research

Methods Review: Mass Spectrometry Analysis of RNAPII Complexes
Publication date: Available online 19 March 2019Source: MethodsAuthor(s): Katlyn Hughes Burriss, Amber L. MosleyAbstractRNA 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. This review will focus on how mass spectrometry (MS) met...
Source: Methods - March 20, 2019 Category: Molecular Biology Source Type: research

Single-molecule approach for studying Pol II transcription initiation using magnetic tweezers
Publication date: Available online 18 March 2019Source: MethodsAuthor(s): Eric J. Tomko, Eric A. GalburtAbstractThe 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 Prokaryotes. In particular, while bacterial initiation proceeds spontaneou...
Source: Methods - March 19, 2019 Category: Molecular Biology Source Type: research

Role of Integrative Structural Biology in Understanding Transcriptional Initiation
Publication date: Available online 16 March 2019Source: MethodsAuthor(s): Mike Trnka, Riccardo Pellarin, Philip RobinsonAbstractIntegrative 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 b...
Source: Methods - March 18, 2019 Category: Molecular Biology Source Type: research

MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction
Publication date: Available online 16 March 2019Source: MethodsAuthor(s): Nathan LaPierre, Chelsea J.-T. Ju, Guangyu Zhou, Wei WangAbstractThe 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 num-ber of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been grow-ing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. So...
Source: Methods - March 16, 2019 Category: Molecular Biology Source Type: research

Visualizing mRNA in live mammalian cells
Publication date: Available online 14 March 2019Source: MethodsAuthor(s): Zejun Wang, Wenhan Liu, Chunhai Fan, Nan ChenAbstractmRNAs 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. Live cell imaging and tracking of mRNA remains a challenge due to their relatively short half-life and lack of versatile imaging probes. This review provides an ...
Source: Methods - March 15, 2019 Category: Molecular Biology Source Type: research

Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization
Publication date: Available online 13 March 2019Source: MethodsAuthor(s): Elina Ly, James A. Goodrich, Jennifer F. KugelAbstractRNA 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. Reconstituted in vitro transcription systems are important tools for studying the enzymology and fundamental steps in the transcription reaction. In these systems...
Source: Methods - March 13, 2019 Category: Molecular Biology Source Type: research

Nanoscale exploration of the extracellular space in the live brain by combining single carbon nanotube tracking and super-resolution imaging analysis
Publication date: Available online 9 March 2019Source: MethodsAuthor(s): Chiara Paviolo, Federico N. Soria, Joana S. Ferreira, Antony Lee, Laurent Groc, Erwan Bezard, Laurent CognetAbstractThe 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 fluorescen...
Source: Methods - March 11, 2019 Category: Molecular Biology Source Type: research

Unsupervised Classification of Multi-Omics Data during Cardiac Remodeling using Deep Learning
Publication date: Available online 7 March 2019Source: MethodsAuthor(s): Neo Christopher Chung, Bilal Mirza, Howard Choi, Jie Wang, Ding Wang, Peipei Ping, Wei WangAbstractIntegration 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. To this end, we perfo...
Source: Methods - March 8, 2019 Category: Molecular Biology Source Type: research

Machine Learning Polymer Models of Three-Dimensional Chromatin Organization in Human Lymphoblastoid Cells
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 experi...
Source: Methods - March 8, 2019 Category: Molecular Biology Source Type: research

Exploring semi-supervised variational autoencoders for biomedical relation extraction
We present a novel semi-supervised approach based on variational autoencoder (VAE) for biomedical relation extraction. Our model consists of the following three parts, a classifier, an encoder and a decoder. The classifier is implemented using multi-layer convolutional neural networks (CNNs), and the encoder and decoder are implemented using both bidirectional long short-term memory networks (Bi-LSTMs) and CNNs, respectively. The semi-supervised mechanism allows our model to learn features from both the labeled and unlabeled data. We evaluate our method on multiple public PPI, DDI and CPI corpora. Experimental results show...
Source: Methods - March 5, 2019 Category: Molecular Biology Source Type: research

In vitro assembly and proteomic analysis of RNA polymerase II complexes
Publication date: Available online 4 March 2019Source: MethodsAuthor(s): Yoo Jin Joo, Scott B. Ficarro, Jarrod A. Marto, Stephen BuratowskiAbstractThe 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 template...
Source: Methods - March 5, 2019 Category: Molecular Biology Source Type: research

Base editing the mammalian genome
Publication date: Available online 2 March 2019Source: MethodsAuthor(s): Emma M. Schatoff, Maria Paz Zafra, Lukas E DowAbstractBase 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 (Cas9D10A) 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. In the past 2 years, a vast array of new and mo...
Source: Methods - March 5, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 15 March 2019Source: Methods, Volume 157Author(s): (Source: Methods)
Source: Methods - March 5, 2019 Category: Molecular Biology Source Type: research

Methods in Nuclear Architecture and Transport
Publication date: 15 March 2019Source: Methods, Volume 157Author(s): Bryce M. Paschal (Source: Methods)
Source: Methods - March 5, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 1 March 2019Source: Methods, Volume 156Author(s): (Source: Methods)
Source: Methods - February 28, 2019 Category: Molecular Biology Source Type: research

“Mining the Epitranscriptome: Detection of RNA editing and RNA modifications”
Publication date: 1 March 2019Source: Methods, Volume 156Author(s): Michael F. Jantsch, Matthias R. Schaefer (Source: Methods)
Source: Methods - February 28, 2019 Category: Molecular Biology Source Type: research

Exploring Semi-supervised V ariational Autoencoders for Biomedical Relation Extraction
We present a novel semi-supervised approach based on variational autoencoder (VAE) for biomedical relation extraction. Our model consists of the following three parts, a classifier, an encoder and a decoder. The classifier is implemented using multi-layer convolutional neural networks (CNNs), and the encoder and decoder are implemented using both bidirectional long short-term memory networks (Bi-LSTMs) and CNNs, respectively. The semi-supervised mechanism allows our model to learn features from both the labeled and unlabeled data. We evaluate our method on multiple public PPI, DDI and CPI corpora. Experimental results show...
Source: Methods - February 27, 2019 Category: Molecular Biology Source Type: research

Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest
Publication date: Available online 22 February 2019Source: MethodsAuthor(s): Juntaek Oh, Jun Xu, Jenny Chong, Dong WangAbstractTranscription, 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. Through decades of research on transcriptional pausing, it is widely known that Pol II can distinguish between different types...
Source: Methods - February 23, 2019 Category: Molecular Biology Source Type: research

CRISPR/Cas9-mediated generic protein tagging in mammalian cells
Publication date: Available online 22 February 2019Source: MethodsAuthor(s): Fabian M.B. Thöne, Nina S. Kurrle, Harald von Melchner, Frank SchnütgenAbstractSystematic 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. Although gene targeting efficiency by homologous recom...
Source: Methods - February 23, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: 15 February 2019Source: Methods, Volume 155Author(s): (Source: Methods)
Source: Methods - February 21, 2019 Category: Molecular Biology Source Type: research

Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation
Publication date: 15 February 2019Source: Methods, Volume 155Author(s): Eric J. Wagner, Aaron C. Goldstrohm (Source: Methods)
Source: Methods - February 21, 2019 Category: Molecular Biology Source Type: research

Iridium(III)-based chemosensors for the detection of metal ions
Publication date: Available online 20 February 2019Source: MethodsAuthor(s): Dik-Lung Ma, Suk-Yu Wong, Tian-Shu Kang, Hing-Pan Ng, Quan-Bin Han, Chung-Hang LeungAbstractIn 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...
Source: Methods - February 21, 2019 Category: Molecular Biology Source Type: research

Functional assays for transcription mechanisms in high-throughput
Publication date: Available online 20 February 2019Source: MethodsAuthor(s): Chenxi Qiu, Craig D. KaplanAbstractDramatic 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 studi...
Source: Methods - February 21, 2019 Category: Molecular Biology Source Type: research