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Methods: a Companion to Methods in Enzymology

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https://www.readbyqxmd.com/read/28813689/large-scale-machine-learning-of-media-outlets-for-understanding-public-reactions-to-nation-wide-viral-infection-outbreaks
#1
Sungwoon Choi, Jangho Lee, Min-Gyu Kang, Hyeyoung Min, Yoon-Seok Chang, Sungroh Yoon
From May to July 2015, there was a nation-wide outbreak of Middle East respiratory syndrome (MERS) in Korea. MERS is caused by MERS-CoV, an enveloped, positive-sense, single stranded RNA virus belonging to the family Coronaviridae. Despite expert opinions that the danger of MERS might be exaggerated, there was an overreaction by the public according to the Korean mass media, which led to a noticeable reduction in social and economic activities during the outbreak. To explain this phenomenon, we presumed that machine learning-based analysis of media outlets would be helpful and collected a number of Korean mass media articles and short-text comments produced during the 10-week outbreak...
August 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28807723/identifying-consistent-disease-subnetworks-using-dnet
#2
Jiajie Peng, Junya Lu, Xuequn Shang, Jin Chen
It is critical to identify disease-specific subnetworks from the vastly available genome-wide gene expression data for elucidating how genes perform high-level biological functions together. Various algorithms have been developed for disease gene identification. However, the topological structure of the disease networks (or even the fraction of the networks) has been left largely unexplored. In this article, we present DNet, a method for the identification of significant disease subnetworks by integrating both the network structure and gene expression information...
August 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802715/elucidating-virus-entry-using-a-tetracysteine-tagged-virus
#3
REVIEW
Bjorn-Patrick Mohl, Polly Roy
Fluorescent tags constitute an invaluable tool in facilitating a deeper understanding of the mechanistic processes governing virus-host interactions. However, when selecting a fluorescent tag for in vivo imaging of cells, a number of parameters and aspects must be considered. These include whether the tag may affect and interfere with protein conformation or localization, cell toxicity, spectral overlap, photo-stability and background. Cumulatively, these constitute challenges to be overcome. Bluetongue virus (BTV), a member of the Orbivirus genus in the Reoviridae family, is a non-enveloped virus that is comprised of two architecturally complex capsids...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802714/in-silico-structure-based-approaches-to-discover-protein-protein-interaction-targeting-drugs
#4
REVIEW
Woong-Hee Shin, Charles W Christoffer, Daisuke Kihara
A core concept behind modern drug discovery is finding a small molecule that modulates a function of a target protein. This concept has been successfully applied since the mid-1970s. However, the efficiency of drug discovery is decreasing because the druggable target space in the human proteome is limited. Recently, protein-protein interaction (PPI) has been identified as an emerging target space for drug discovery. PPI plays a pivotal role in biological pathways including diseases. Current human interactome research suggests that the number of PPIs ranges from 130,000 to 650,000, and only a small number of them have been targeted as drug targets...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802713/detecting-exact-breakpoints-of-deletions-with-diversity-in-hepatitis-b-viral-genomic-dna-from-next-generation-sequencing-data
#5
Ji-Hong Cheng, Wen-Chun Liu, Ting-Tsung Chang, Sun-Yuan Hsieh, Vincent S Tseng
Many studies have suggested that deletions of Hepatitis B Viral (HBV) are associated with the development of progressive liver diseases, even ultimately resulting in hepatocellular carcinoma (HCC). Among the methods for detecting deletions from next-generation sequencing (NGS) data, few methods considered the characteristics of virus, such as high evolution rates and high divergence among the different HBV genomes. Sequencing high divergence HBV genome sequences using the NGS technology outputs millions of reads...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28790018/variation-in-single-nucleotide-sensitivity-of-eclip-derived-from-reverse-transcription-conditions
#6
REVIEW
Eric L Van Nostrand, Alexander Shishkin, Gabriel A Pratt, Thai B Nguyen, Gene W Yeo
Crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing identifies the binding sites of RNA binding proteins on RNAs. The covalent RNA-amino acid adducts produced by UV irradiation can cause premature reverse transcription termination and deletions (referred to as crosslink-induced mutation sites (CIMS)), which may decrease overall cDNA yield but are exploited in state-of-the-art CLIP methods to identify these crosslink sites at single-nucleotide resolution. Here, we show the ratio of both crosslinked base deletions and read-through versus termination are highly dependent on the identity of the reverse transcriptase enzyme as well as on buffer conditions used...
August 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28790017/detecting-pathway-relationship-in-the-context-of-human-protein-protein-interaction-network-and-its-application-to-parkinson-s-disease
#7
Ying Hu, Yichen Yang, Zhonghai Fang, Yan-Shi Hu, Lei Zhang, Ju Wang
In human physiological conditions like complex diseases, a large number of genes/proteins, as well as their interactions, are involved. Thus, detecting the biochemical pathways enriched in these genes/proteins and identifying the pathway relationships is critical to understand the molecular mechanisms underlying a disease and can also be valuable in selecting the potential molecular targets for further exploration. In this study, we proposed a method to measure the relationship between pathways based on their distribution in the human PPI network...
August 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28790016/tau-imaging-in-neurodegeneration
#8
REVIEW
Gérard N Bischof, Heike Endepols, Thilo van Eimeren, Alexander Drzezga
Pathological cerebral aggregations of proteins are suggested to play a crucial role in the development of neurodegenerative disorders. For example, aggregation of the protein ß-amyloid in form of extracellular amyloid-plaques as well as intraneuronal depositions of the protein tau in form of neurofibrillary tangles represent hallmarks of Alzheimer's disease (AD). Recently, novel tracers for in vivo molecular imaging of tau-aggregates in the brain have been introduced, complementing existing tracers for imaging amyloid-plaques...
August 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28780320/non-invasive-intravital-imaging-of-head-and-neck-squamous-cell-carcinomas-in-live-mice
#9
Panomwat Amornphimoltham, Jamie Thompson, Nicolas Melis, Roberto Weigert
Head and neck squamous cell carcinoma is one of the most common cancers with a 50% 5-year survival rate. Understanding the mechanisms that control development, progression, and spreading of the tumor to distal sites is of paramount importance to develop effective therapies. Here, we describe a minimally invasive procedure, which enables performing intravital microscopy of the mouse tongue in models for oral cancer and provides structural and dynamic information of the tumors at cellular and subcellular level...
August 2, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28778489/clustering-of-rna-seq-samples-comparison-study-on-cancer-data
#10
Pablo Andretta Jaskowiak, Ivan G Costa, Ricardo J G B Campello
RNA-Seq is becoming the standard technology for large-scale gene expression level measurements, as it offers a number of advantages over microarrays. Standards for RNA-Seq data analysis are, however, in its infancy when compared to those of microarrays. Clustering, which is essential for understanding gene expression data, has been widely investigated w.r.t. microarrays. In what concerns the clustering of RNA-Seq data, however, a number of questions remain open, resulting in a lack of guidelines to practitioners...
August 2, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28774682/methods-for-molecular-imaging-of-brain-tumours-in-a-hybrid-mr-pet-context-water-content-t2%C3%A2-diffusion-indices-and-fet-pet
#11
A M Oros-Peusquens, R Loução, M Zimmermann, K-J Langen, N J Shah
The aim of this study is to present and evaluate a multiparametric and multi-modality imaging protocol applied to brain tumours and investigate correlations between these different imaging measures (R1.1). In particular, we describe a method for rapid, non-invasive, quantitative imaging of water content of brain tissue, based on a single multiple-echo gradient-echo (mGRE) acquisition. We include in the processing a method for noise reduction of the multi-contrast data based on Principal Component Analysis (PCA)...
July 31, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28754563/changes-in-gene-expression-variability-reveal-a-stable-synthetic-lethal-interaction-network-in-brca2-ovarian-cancers
#12
Raymund Bueno, Jessica C Mar
Synthetic lethal interactions (SLIs) are robust mechanisms that provide cells with the ability to sustain viability despite having mutations in genes critical to the DNA damage response, a core cellular process. Studies in model organisms such as S. cerevisiae showed that thousands of genes important in maintaining DNA integrity cooperated in a SLI network. Two genes participate in a SLI when mutation in one gene has no effect on the cell, but mutations in both interacting genes are lethal. Furthermore in C...
July 25, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28746829/imaging-chemistry-inside-living-cells-by-stimulated-raman-scattering-microscopy
#13
REVIEW
Hyeon Jeong Lee, Ji-Xin Cheng
Stimulated Raman scattering (SRS) microscopy is a vibrational imaging platform developed to visualize chemical content of a biological sample based on molecular vibrational fingerprints. With high-speed, high-sensitivity, and three-dimensional sectioning capability, SRS microscopy has been used to study chemical distribution, molecular transport, and metabolic conversion in living cells in a label-free manner. Moreover, aided with bio-orthogonal small-volume Raman probes, SRS microscopy allows direct imaging of metabolic activities of small molecules in living cells...
July 23, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28743635/molecular-imaging-in-drug-development-update-and-challenges-for-radiolabeled-antibodies-and-nanotechnology
#14
REVIEW
Ilaria Colombo, Marta Overchuk, Juan Chen, Raymond M Reilly, Gang Zheng, Stephanie Lheureux
Despite the significant advancement achieved in understanding the molecular mechanisms responsible for cancer transformation and aberrant proliferation, leading to novel targeted cancer therapies, significant effort is still needed to "personalize" cancer treatment. Molecular imaging is an emerging field that has shown the ability to characterize in vivo the molecular pathways present at the cancer cell level, enabling diagnosis and personalized treatment of malignancies. These technologies, particularly SPECT and PET also permit the development of novel radiotheranostic probes, which provide capabilities for diagnosis and treatment with the same agent...
July 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28739118/single-cell-based-automated-quantification-of-therapy-response-of-invasive-cancer-spheroids-in-organotypic-3d-culture
#15
Cornelia Veelken, Gert-Jan Bakker, David Drell, Peter Friedl
Organotypic in vitro culture of 3D spheroids in extracellular matrix represent a promising cancer therapy prediction model for personalized medicine screens, due to their controlled experimental conditions and physiological similarities to in vivo models. As in tumors in vivo, 3D invasion cultures identify intratumor heterogeneity of growth, invasion and apoptosis induction by cytotoxic therapy. We here combine in vitro 3D spheroid invasion culture with irradiation and automated nucleus-based segmentation for single cell analysis to quantify growth, survival, apoptosis and invasion response during experimental radiation therapy...
July 21, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28734934/analysis-of-rna-protein-interactions-in-vertebrate-embryos-using-uv-crosslinking-approaches
#16
Vladimir Despic, Mario Dejung, Falk Butter, Karla M Neugebauer
A decade ago, we believed that at least 300 RNA binding proteins (RBPs) were encoded in our genomes based on annotations of known or predicted RNA binding domains. Deciphering the roles of those RBPs in regulated gene expression was a vast frontier awaiting exploration. Since then, the field has developed a number of key tools that navigate the landscape of cellular RNA. These rely principally on UV crosslinking to create covalent bonds between RBPs and target RNAs in vivo, revealing not only target identities but also local binding sites upon RNA-Seq...
July 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28733090/intravital-multiphoton-microscopy-as-a-tool-for-studying-renal-physiology-and-pathophysiology
#17
Ruben M Sandoval, Bruce A Molitoris
The kidney is a complex and dynamic organ with over 40 cell types, and tremendous structural and functional diversity. Intravital multi-photon microscopy, development of fluorescent probes and innovative software, have rapidly advanced the study of intracellular and intercellular processes within the kidney. Researchers can quantify the distribution, behavior, and dynamic interactions of up to four labeled chemical probes and proteins simultaneously and repeatedly in four dimensions (time), with subcellular resolution in near real time...
July 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28733089/a-computational-protocol-for-the-discovery-of-lead-molecules-targeting-dna-unique-to-pathogens
#18
Akhilesh Mishra, Pradeep Pant, Nirotpal Mrinal, B Jayaram
With the rapid emergence of drug resistant pathogens, it has become imperative to develop alternative medications as well as find new drug targets to overcome this crisis. Hence, this has become prime focus of several academic laboratories and pharmaceutical companies. Here, we report a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only...
July 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28723583/label-free-high-resolution-3-d-imaging-of-gold-nanoparticles-inside-live-cells-using-optical-diffraction-tomography
#19
Doyeon Kim, Nuri Oh, Kyoohyun Kim, SangYun Lee, Chan-Gi Pack, Ji-Ho Park, YongKeun Park
Delivery of gold nanoparticles (GNPs) into live cells has high potentials, ranging from molecular-specific imaging, photodiagnostics, to photothermal therapy. However, studying the long-term dynamics of cells with GNPs using conventional fluorescence techniques suffers from phototoxicity and photobleaching. Here, we present a method for 3-D imaging of GNPs inside live cells exploiting refractive index (RI) as imaging contrast. Employing optical diffraction tomography, 3-D RI tomograms of live cells with GNPs are precisely measured for an extended period with sub-micrometer resolution...
July 16, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28723582/overexpression-and-purification-of-dicer-and-accessory-proteins-for-biochemical-and-structural-studies
#20
Niladri K Sinha, Brenda L Bass
The Dicer family of ribonucleases plays a key role in small RNA-based regulatory pathways by generating short dsRNA fragments that modulate expression of endogenous genes, or protect the host from invasive nucleic acids. Beginning with its initial discovery, biochemical characterization of Dicer has provided insight about its catalytic properties. However, a comprehensive understanding of how Dicer's domains contribute to substrate-specific recognition and catalysis is lacking. One reason for this void is the lack of high-resolution structural information for a metazoan Dicer in the apo- or substrate-bound state...
July 16, 2017: Methods: a Companion to Methods in Enzymology
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