Affinity Network Fusion and Semi-supervised Learning for Cancer Patient Clustering
Publication date: Available online 26 May 2018 Source:Methods Author(s): Tianle Ma, Aidong Zhang Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omi...
Source: Methods - May 27, 2018 Category: Molecular Biology Source Type: research

In silico experiment system for testing hypothesis on gene functions using three condition specific biological networks
Publication date: Available online 25 May 2018 Source:Methods Author(s): Chai-Jin Lee, Dongwon Kang, Sangseon Lee, Sunwon Lee, Jaewoo Kang, Sun Kim Determining functions of a gene requires time consuming, expensive biological experiments. Scientists can speed up this experimental process if the literature information and biological networks can be adequately provided. In this paper, we present a web-based information system that can perform in silico experiments of computationally testing hypothesis on the function of a gene. A hypothesis that is specified in English by the user is converted to genes using a literature an...
Source: Methods - May 26, 2018 Category: Molecular Biology Source Type: research

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
Publication date: Available online 24 May 2018 Source:Methods Author(s): Ji Hun Kim, Katelyn R. Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer E. Phillips-Cremins Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due ...
Source: Methods - May 25, 2018 Category: Molecular Biology Source Type: research

Statistical Selection of Biological Models for Genome-Wide Association Analyses
Publication date: Available online 25 May 2018 Source:Methods Author(s): Wenjian Bi, Guolian Kang, Stanley B. Pounds Genome-wide association studies have discovered many biologically important associations of genes with phenotypes. Typically, genome-wide association analyses formally test the association of each genetic feature (SNP, CNV, etc) with the phenotype of interest and summarize the results with multiplicity-adjusted p-values. However, very small p-values only provide evidence against the null hypothesis of no association without indicating which biological model best explains the observed data. Correctly identif...
Source: Methods - May 25, 2018 Category: Molecular Biology Source Type: research

Implementing Fast Photochemical Oxidation of Proteins (FPOP) as a Footprinting Approach to Solve Diverse Problems in Structural Biology
Publication date: Available online 23 May 2018 Source:Methods Author(s): Bojie Zhang, Ming Cheng, Don Rempel, Michael L. Gross Fast photochemical oxidation of proteins (FPOP) is a footprinting technique used in mass spectrometry-based structural proteomics. It has been applied to solve a variety of problems in different areas of biology. A FPOP platform requires a laser, optics, and sample flow path properly assembled to enable fast footprinting. Sample preparation, buffer conditions, and reagent concentrations are essential to obtain reasonable oxidations on proteins. FPOP samples can be analyzed by LC-MS methods to meas...
Source: Methods - May 24, 2018 Category: Molecular Biology Source Type: research

Storage, Visualization, and Navigation of 3D genomics data
Publication date: Available online 22 May 2018 Source:Methods Author(s): Jérôme Waldispühl, Eric Zhang, Alexander Butyaev, Elena Nazarova, Yan Cyr The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art computing technology, as well as the solutions adopted by the platform...
Source: Methods - May 22, 2018 Category: Molecular Biology Source Type: research

Translational –omics: Future Potential and Current Challenges in Precision Medicine
Publication date: Available online 22 May 2018 Source:Methods Author(s): Arsalan Wafi, Reza Mirnezami Rapid advances in computational science and biotechnology are paving the way for precision medicine – a vision in next-generation healthcare that promises to provide a care package uniquely tailored to each individual’s molecular make-up. Until relatively recently, the focus has been firmly centred around the genome; however, over the past two decades there has been a surge in the study of molecular activity within other biological domains (proteome/transcriptome/metabolome) involved in health and pathogenesis...
Source: Methods - May 22, 2018 Category: Molecular Biology Source Type: research

Affinity capillary electrophoresis for studying interactions in life sciences
Publication date: Available online 19 May 2018 Source:Methods Author(s): Mais Olabi, Matthias Stein, Hermann Wätzig Affinity capillary electrophoresis (ACE) analyzes noncovalent interactions between ligands and analytes based on changes in their electrophoretic mobility. This technique has been widely used to investigate various biomolecules, mainly proteins, polysaccharides and hormones. ACE is becoming a technique of choice to validate high throughput screening results, since it is very predictively working in realistic and relevant media, e.g. in body fluids. It is highly recommended to incorporate ACE as a powerf...
Source: Methods - May 20, 2018 Category: Molecular Biology Source Type: research

Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins
Publication date: Available online 18 May 2018 Source:Methods Author(s): Ulrik H. Mistarz, Kasper D. Rand Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by react...
Source: Methods - May 19, 2018 Category: Molecular Biology Source Type: research

POST: a framework for set-based association analysis in high-dimensional data
Publication date: Available online 17 May 2018 Source:Methods Author(s): Xueyuan Cao, E. Olusegun George, Mingjuan Wang, Dale B. Armstrong, Cheng Cheng, Susana Raimondi, Jeffrey E. Rubnitz, James R. Downing, Mondira Kundu, Stanley B. Pounds Evaluating the differential expression of a set of genes belonging to a common biological process or ontology has proven to be a very useful tool for biological discovery. However, existing gene-set association methods are limited to applications that evaluate differential expression across k ⩾ 2 treatment groups or biological categories. This limitation precludes researchers from mo...
Source: Methods - May 18, 2018 Category: Molecular Biology Source Type: research

Evaluating the susceptibility of AGO2-loaded microRNAs to degradation by nucleases in vitro
Publication date: Available online 17 May 2018 Source:Methods Author(s): Reyad Elbarbary, Lynne E. Maquat MicroRNAs (miRNAs) comprise a class of small non-coding RNAs that regulate the stability and/or translatability of most protein-coding transcripts. Steady-state levels of mature miRNAs can be controlled through mechanisms that influence their biogenesis and/or decay rates. Pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We recently described Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay (TumiD) as a cellular pathway that promotes t...
Source: Methods - May 18, 2018 Category: Molecular Biology Source Type: research

Expression of recombinant proteins in insect and mammalian cells
Publication date: Available online 18 May 2018 Source:Methods Author(s): Edward A McKenzie, W Mark Abbott Purified recombinant proteins are key reagents in academic and industrial research. The ability to make these proteins quickly often relies on the availability of higher eukaryotic cell hosts such as insect and mammalian cells where there is a very wide range of post-translational modifications, protein folding and trafficking pathways. This enables the generation of many proteins that cannot be made in microbial hosts. In this article we outline some of the most commonly used methods to express recombinant proteins i...
Source: Methods - May 18, 2018 Category: Molecular Biology Source Type: research

Screening and selection of artificial riboswitches
Publication date: Available online 18 May 2018 Source:Methods Author(s): Svetlana V. Harbaugh, Jennifer Martin, Jenna Weinstein, Grant Ingram, Nancy Kelley-Loughnane Synthetic riboswitches are engineered to regulate gene expression in response to a variety of non-endogenous small molecules, and a challenge to select this engineered response requires robust screening tools. A new synthetic riboswitch can be created by linking an in vitro-selected aptamer library with a randomized expression platform followed by in vivo selection and screening. In order to determine response to analyte, we developed a dual-color reporter co...
Source: Methods - May 18, 2018 Category: Molecular Biology Source Type: research

The fine art of integral membrane protein crystallisation
Publication date: Available online 18 May 2018 Source:Methods Author(s): James Birch, Danny Axford, James Foadi, Arne Meyer, Annette Eckardt, Yvonne Thielmann, Isabel Moraes Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank...
Source: Methods - May 18, 2018 Category: Molecular Biology Source Type: research

Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies
Publication date: Available online 10 May 2018 Source:Methods Author(s): M. Scalabrin, S.M. Dixit, M.M. Makshood, C.E. Krzemien, Daniele Fabris With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the posit...
Source: Methods - May 11, 2018 Category: Molecular Biology Source Type: research

NMR-based investigations into target DNA search processes of proteins
Publication date: Available online 10 May 2018 Source:Methods Author(s): Junji Iwahara, Levani Zandarashvili, Catherine A. Kemme, Alexandre Esadze To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental m...
Source: Methods - May 11, 2018 Category: Molecular Biology Source Type: research

Efficient computation of co-transcriptional RNA-ligand interaction dynamics
We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2’-deoxyguanosine (2’dG)-sensing riboswitch from Mesoplasma florum. (Source: Methods)
Source: Methods - May 5, 2018 Category: Molecular Biology Source Type: research

LC/MS at the whole protein level: Studies of biomolecular structure and interactions using native LC/MS and cross-path reactive chromatography (XP-RC) MS
Publication date: Available online 25 April 2018 Source:Methods Author(s): Igor A. Kaltashov, Jake W. Pawlowski, Wenhua Yang, Khaja Muneeruddin, Honglin Yao, Cedric E. Bobst, Andrei N. Lipatnikov Interfacing liquid chromatography (LC) with electrospray ionization (ESI) to enable on-line MS detection had been initially implemented using reversed phase LC, which in the past three decades remained the default type of chromatography used for LC/MS and LC/MS/MS studies of protein structure. In contrast, the advantages of other types of LC as front-ends for ESI MS, particularly those that allow biopolymer higher order structure...
Source: Methods - May 3, 2018 Category: Molecular Biology Source Type: research

Cryo-electron microscopy of membrane proteins
Publication date: Available online 25 April 2018 Source:Methods Author(s): Nopnithi Thonghin, Vasileios Kargas, Jack Clews, Robert C. Ford Membrane proteins represent a large proportion of the proteome, but have characteristics that are problematic for many methods in modern molecular biology (that have often been developed with soluble proteins in mind). For structural studies, low levels of expression and the presence of detergent have been thorns in the flesh of the membrane protein experimentalist. Here we discuss the use of cryo-electron microscopy in breakthrough studies of the structures of membrane proteins. This ...
Source: Methods - May 1, 2018 Category: Molecular Biology Source Type: research

Iteratively improving Hi-C experiments one step at a time
Publication date: Available online 30 April 2018 Source:Methods Author(s): Rosela Golloshi, Jacob Sanders, Rachel Patton McCord The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role o...
Source: Methods - May 1, 2018 Category: Molecular Biology Source Type: research

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe
Publication date: Available online 30 April 2018 Source:Methods Author(s): Santosh Lamichhane, Partho Sen, Alex M. Dickens, Matej Orešič, Hanne Christine Bertram It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabol...
Source: Methods - May 1, 2018 Category: Molecular Biology Source Type: research

Selective recovery of RNAs from bacterial pathogens after their internalization by human host cells
Publication date: Available online 27 April 2018 Source:Methods Author(s): Simon Raynaud, Hélène LePabic, Brice Felden Selective RNA extractions are required when studying bacterial gene expression within complex mixtures of pathogens and human cells, during adhesion, internalization and survival within the host. New technologies should be developed and implemented to enrich the amount of bacterial RNAs since the majority of RNAs are from the eukaryotic host cells, requiring high read depth coverage to capture the bacterial transcriptomes in dual-RNAseq studies. This will improve our understanding about bact...
Source: Methods - April 28, 2018 Category: Molecular Biology Source Type: research

Multiplex Confounding Factor Correction for Genomic Association Mapping with Squared Sparse Linear Mixed Model
Publication date: Available online 27 April 2018 Source:Methods Author(s): Haohan Wang, Xiang Liu, Yunpeng Xiao, Ming Xu, Eric P. Xing Genome-wide Association Study has presented a promising way to understand the association between human genomes and complex traits. Many simple polymorphic loci have been shown to explain a significant fraction of phenotypic variability. However, challenges remain in the non-triviality of explaining complex traits associated with multifactorial genetic loci, especially considering the confounding factors caused by population structure, family structure, and cryptic relatedness. In this pap...
Source: Methods - April 27, 2018 Category: Molecular Biology Source Type: research

Assessment of microbiota:host interactions at the vaginal mucosa interface
Publication date: Available online 27 April 2018 Source:Methods Author(s): Pamela Pruski, Holly V. Lewis, Yun S. Lee, Julian R. Marchesi, Phillip R. Bennett, Zoltan Takats, David A. MacIntyre There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman’s lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiolog...
Source: Methods - April 27, 2018 Category: Molecular Biology Source Type: research

High-dimensional NMR methods for intrinsically disordered proteins studies
Publication date: Available online 27 April 2018 Source:Methods Author(s): Katarzyna Grudziąż, Anna Zawadzka-Kazimierczuk, Wiktor Koźmiński Intrinsically disordered proteins (IDPs) are getting more and more interest of the scientific community. Nuclear magnetic resonance (NMR) is often a technique of choice for these studies, as it provides atomic-resolution information on structure, dynamics and interactions of IDPs. Nonetheless, NMR spectra of IDPs are typically extraordinary crowded, comparing to those of structured proteins. To overcome this problem, high-dimensional NMR experiments can be used, which allow for a ...
Source: Methods - April 27, 2018 Category: Molecular Biology Source Type: research

Basic Experiments in 2H static NMR for the Characterization of Protein Side-Chain Dynamics
Publication date: Available online 27 April 2018 Source:Methods Author(s): Liliya Vugmeyster, Dmitry Ostrovsky The focus of this review is the basic methodology for applications of static deuteron NMR for studies of dynamics in the side chains of proteins. We review experimental approaches for the measurements of static line shapes and relaxation rates as well as signal enhancement strategies using the multiple echo acquisition scheme. Further, we describe computational strategies for modeling jump and diffusive motions underlying experimental data. Applications are chosen from studies of amyloid fibrils comprising the am...
Source: Methods - April 27, 2018 Category: Molecular Biology Source Type: research

Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies
Publication date: Available online 27 April 2018 Source:Methods Author(s): Haohan Wang, Bryon Aragam, Eric P. Xing A fundamental and important challenge in modern datasets of ever increasing dimensionality is variable selection, which has taken on renewed interest recently due to the growth of biological and medical datasets with complex, non-i.i.d. structures. Naïvely applying classical variable selection methods such as the Lasso to such datasets may lead to a large number of false discoveries. Motivated by genome-wide association studies in genetics, we study the problem of variable selection for datasets arising ...
Source: Methods - April 27, 2018 Category: Molecular Biology Source Type: research

LC/MS at the whole protein level: studies of biomolecular structure and interactionsusing native LC/MS, cross-path reactive chromatography (XP-RC) MS
Publication date: Available online 25 April 2018 Source:Methods Author(s): Igor A. Kaltashov, Jake W. Pawlowski, Wenhua Yang, Khaja Muneeruddin, Honglin Yao, Cedric E. Bobst, Andrei N. Lipatnikov Interfacing liquid chromatography (LC) with electrospray ionization (ESI) to enable on-line MS detection had been initially implemented using reversed phase LC, which in the past three decades remained the default type of chromatography used for LC/MS and LC/MS/MS studies of protein structure. In contrast, the advantages of other types of LC as front-ends for ESI MS, particularly those that allow biopolymer higher order structure...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Cryo-electron microscopy of membrane proteins.
Publication date: Available online 25 April 2018 Source:Methods Author(s): Nopnithi Thonghin, Vasileios Kargas, Jack Clews, Robert C. Ford Membrane proteins represent a large proportion of the proteome, but have characteristics that are problematic for many methods in modern molecular biology (that have often been developed with soluble proteins in mind). For structural studies, low levels of expression and the presence of detergent have been thorns in the flesh of the membrane protein experimentalist. Here we discuss the use of cryo-electron microscopy in breakthrough studies of the structures of membrane proteins. This ...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Mass Spectrometry Approaches to Metabolic Profiling of Microbial Communities within the Human Gastrointestinal Tract
Publication date: Available online 26 April 2018 Source:Methods Author(s): Simon JS Cameron, Zoltán Takáts The interaction between microbial communities and their environment, such as the human gastrointestinal tract, has been an area of microbiology rapidly advanced, by developments in sequencing technology. However, these techniques are largely limited to the detection of the taxonomic composition of a microbial community and/or its genetic functional capacity. Here, we discuss a range of mass spectrometry-based approaches which researchers can employ to explore the host-microbiome interactions at the meta...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Contemporary Hydrogen Deuterium Exchange Mass Spectrometry
Publication date: Available online 26 April 2018 Source:Methods Author(s): Irina Oganesyan, Cristina Lento, Derek J. Wilson Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) emerged as a tool for biochemistry and structural biology around 25 years ago. It has since become a key approach for studying protein dynamics, protein-ligand interactions, membrane proteins and intrinsically disordered proteins (IDPs). In HDX labeling, proteins are exposed to deuterated solvent (usually D2O) for a variable ‘labeling time’, resulting in isotope exchange of unprotected labile protons on the amide backbone and amino ...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions?
Publication date: Available online 26 April 2018 Source:Methods Author(s): Wenjun Tong, Guanbo Wang Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology a...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Resolving biomolecular motion and interactions by R2 and R1 ρ Relaxation Dispersion NMR
Publication date: Available online 26 April 2018 Source:Methods Author(s): Erik Walinda, Daichi Morimoto, Kenji Sugase Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer
Publication date: Available online 26 April 2018 Source:Methods Author(s): Vanessa L. Hale, Patricio Jeraldo, Michael Mundy, Janet Yao, Gary Keeney, Nancy Scott, E. Heidi Cheek, Jennifer Davidson, Megan Green, Christine Martinez, John Lehman, Chandra Pettry, Erica Reed, Kelly Lyke, Bryan A. White, Christian Diener, Osbaldo Resendis-Antonio, Jaime Gransee, Tumpa Dutta, Xuan-Mai Petterson, Lisa Boardman, David Larson, Heidi Nelson, Nicholas Chia Multi-omic data and genome-scale microbial metabolic models have allowed us to examine microbial communities, community function, and interactions in ways that were not available to...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Functional Microbiomics: Evaluation of Gut Microbiota-Bile Acid Metabolism Interactions in Health and Disease
Publication date: Available online 26 April 2018 Source:Methods Author(s): Benjamin H. Mullish, Alexandros Pechlivanis, Grace F. Barker, Mark R. Thursz, Julian R. Marchesi, Julie A.K. McDonald There is an ever-increasing recognition that bile acids are not purely simple surfactant molecules that aid in lipid digestion, but are a family of molecules contributing to a diverse range of key systemic functions in the host. It is now also understood that the specific composition of the bile acid milieu within the host is related to the expression and activity of bacterially-derived enzymes within the gastrointestinal tract, as ...
Source: Methods - April 26, 2018 Category: Molecular Biology Source Type: research

Hidden motions and motion-induced invisibility: dynamics-based spectral editing in solid-state NMR
Publication date: Available online 24 April 2018 Source:Methods Author(s): Irina Matlahov, Patrick C.A. van der Wel Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments’ sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chan...
Source: Methods - April 25, 2018 Category: Molecular Biology Source Type: research

SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data
In this study, we proposed a new method, SigEMD, that combines a data imputation approach, a logistic regression model and a nonparametric method based on the Earth Mover’s Distance, to precisely and efficiently identify DE genes in scRNAseq data. The regression model and data imputation are used to reduce the impact of large amounts of zero counts, and the nonparametric method is used to improve the sensitivity of detecting DE genes from multimodal scRNAseq data. By additionally employing gene interaction network information to adjust the final states of DE genes, we further reduce the false positives of calling DE ...
Source: Methods - April 25, 2018 Category: Molecular Biology Source Type: research

An integrative approach to investigate the association among high-sensitive C-reactive protein, body fat mass distribution, and other cardiometabolic risk factors in young healthy women
Publication date: Available online 24 April 2018 Source:Methods Author(s): Bin Wu, Jingshan Huang, Lihua Zhang, Mohan Vamsi Kasukurthi, Fangwan Huang, Jiang Bian, Keisuke Fukuo, Tsutomu Kazumi Prior research has indicated that as an important biomarker of chronic low-grade inflammation, high-sensitivity C-reactive protein (hs-CRP) can play important roles on the onset of metabolic syndrome and cardiovascular diseases (CVD). We conducted an integrative approach, which combines biological wet-lab experiments, statistical analysis, and semantics-oriented bioinformatics & computational analysis, to investigate the ass...
Source: Methods - April 25, 2018 Category: Molecular Biology Source Type: research

Engineering expression and function of membrane proteins
Publication date: Available online 24 April 2018 Source:Methods Author(s): Min-Kyoung Kang, Danielle Tullman-Ercek Membrane proteins are involved in a diverse array of cellular functions and part of many important metabolic pathways. As such, they are attractive targets in the pharmaceutical and bio-based chemical industries. Despite their great potential, many challenges remain before membrane proteins gain widespread success in biotechnology. The two biggest issues are that expression of membrane proteins leads to inhibition of cellular growth and metabolism, and native membrane proteins often lack a desired function or...
Source: Methods - April 25, 2018 Category: Molecular Biology Source Type: research

Three invariant Hi-C interaction patterns: applications to genome assembly
Publication date: Available online 22 April 2018 Source:Methods Author(s): Sivan Oddes, Aviv Zelig, Noam Kaplan Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three inv...
Source: Methods - April 23, 2018 Category: Molecular Biology Source Type: research

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut
Publication date: Available online 19 April 2018 Source:Methods Author(s): Eleanor Jameson, Mussa Quareshy, Yin Chen The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enz...
Source: Methods - April 20, 2018 Category: Molecular Biology Source Type: research

Folding and stabilizing membrane proteins in amphipol A8-35
Publication date: Available online 18 April 2018 Source:Methods Author(s): Christel Le Bon, Anaïs Marconnet, Sandrine Masscheleyn, Jean-Luc Popot, Manuela Zoonens Membrane proteins (MPs) are important pharmacological targets because of their involvement in many essential cellular processes whose dysfunction can lead to a large variety of diseases. A detailed knowledge of the structure of MPs and the molecular mechanisms of their activity is essential to the design of new therapeutic agents. However, studying MPs in vitro is challenging, because it generally implies their overexpression under a functional form, follow...
Source: Methods - April 18, 2018 Category: Molecular Biology Source Type: research

MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals
Publication date: Available online 18 April 2018 Source:Methods Author(s): Devrishi Goswami, Jun Zhang, Pavel V. Bondarenko, Zhongqi Zhang Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of...
Source: Methods - April 18, 2018 Category: Molecular Biology Source Type: research

How to Run Molecular Dynamics Simulations on Electrospray Droplets and Gas Phase Proteins: Basic Guidelines and Selected Applications
Publication date: Available online 18 April 2018 Source:Methods Author(s): Lars Konermann, Haidy Metwally, Robert G. McAllister, Vlad Popa The ability to transfer intact proteins and protein complexes into the gas phase by electrospray ionization (ESI) has opened up numerous mass spectrometry (MS)-based avenues for exploring biomolecular structure and function. However, many details regarding the ESI process and the properties of gaseous analyte ions are difficult to decipher when relying solely on experimental data. Molecular dynamics (MD) simulations can provide additional insights into the behavior of ESI droplets and ...
Source: Methods - April 18, 2018 Category: Molecular Biology Source Type: research

In silico design of ligand triggered RNA switches
Publication date: Available online 13 April 2018 Source:Methods Author(s): Sven Findeiß, Stefan Hammer, Michael T. Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L. Hofacker This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.,e., knowing its K d and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure repres...
Source: Methods - April 14, 2018 Category: Molecular Biology Source Type: research

Real-time imaging of specific genomic loci in eukaryotic cells using the ANCHOR DNA labelling system
We describe an approach for live cell imaging of a DNA locus during the entire cell cycle in human breast cancer cells. (Source: Methods)
Source: Methods - April 14, 2018 Category: Molecular Biology Source Type: research

Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics
Publication date: Available online 12 April 2018 Source:Methods Author(s): Zhou Gong, Charles D. Schwieters, Chun Tang Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides wit...
Source: Methods - April 13, 2018 Category: Molecular Biology Source Type: research

An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution
Publication date: Available online 12 April 2018 Source:Methods Author(s): John D. Persons, Shahid N. Khan, Rieko Ishima This manuscript presents an NMR strategy to investigate conformational differences in protein-inhibitor complexes, when the inhibitors tightly bind to a protein at sub-nanomolar dissociation constants and are highly analogous to each other. Using HIV-1 protease (PR), we previously evaluated amide chemical shift differences, ΔCSPs, of PR bound to darunavir (DRV) compared to PR bound to several DRV analogue inhibitors, to investigate subtle but significant long-distance conformation changes caused b...
Source: Methods - April 12, 2018 Category: Molecular Biology Source Type: research

Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing C αHα-CαHα bonds in anti-parallel β-sheets
Publication date: Available online 12 April 2018 Source:Methods Author(s): T. Michael Sabo, Vytautas Gapsys, Korvin F.A. Walter, R. Bryn Fenwick, Stefan Becker, Xavier Salvatella, Bert L. de Groot, Donghan Lee, Christian Griesinger Dipole-dipole cross-correlated relaxation (CCR) between two spin pairs is rich with macromolecular structural and dynamic information on inter-nuclear bond vectors. Measurement of short range dipolar CCR rates has been demonstrated for a variety of inter-nuclear vector spin pairs in proteins and nucleic acids, where the multiple quantum coherence necessary for observing the CCR rate is created ...
Source: Methods - April 12, 2018 Category: Molecular Biology Source Type: research

Tumor classification with MALDI-MSI data of tissue microarrays: a case study
Publication date: Available online 12 April 2018 Source:Methods Author(s): Nadine E. Mascini, Jannis Teunissen, Rob Noorlag, Stefan M. Willems, Ron M.A. Heeren With mass spectrometry imaging (MSI) on tissue microarrays (TMAs) a large number of biomolecules can be studied for many patients at the same time, making it an attractive tool for biomarker discovery. Here we investigate whether lymph node metastasis can be predicted from MALDI-MSI data. Measurements are performed on TMAs and then filtered based on spectral intensity and the percentage of tumor cells, after which the resulting data for 122 patients is further prep...
Source: Methods - April 12, 2018 Category: Molecular Biology Source Type: research