journal
MENU ▼
Read by QxMD icon Read
search

Methods: a Companion to Methods in Enzymology

journal
https://www.readbyqxmd.com/read/28723583/label-free-high-resolution-3-d-imaging-of-gold-nanoparticles-inside-live-cells-using-optical-diffraction-tomography
#1
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
#2
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
https://www.readbyqxmd.com/read/28716511/an-ensemble-predictive-modeling-framework-for-breast-cancer-classification
#3
Radhakrishnan Nagarajan, Meenakshi Upreti
Molecular changes often precede clinical presentation of diseases and can be useful surrogates with potential to assist in informed clinical decision making. Recent studies have demonstrated the usefulness of modeling approaches such as classification that can predict the clinical outcomes from molecular expression profiles. While useful, a majority of these approaches implicitly use all molecular markers as features in the classification process often resulting in sparse high-dimensional projection of the samples often comparable to that of the sample size...
July 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28716510/evaluation-of-in-vivo-and-in-vitro-models-of-toxicity-by-comparison-of-toxicogenomics-data-with-the-literature
#4
Katerina Taškova, Jean-Fred Fontaine, Ralf Mrowka, Miguel A Andrade-Navarro
Toxicity affecting humans is studied by observing the effects of chemical substances in animal organisms (in vivo) or in animal and human cultivated cell lines (in vitro). Toxicogenomics studies collect gene expression profiles and histopathology assessment data for hundreds of drugs and pollutants in standardized experimental designs using different model systems. These data are an invaluable source for analyzing genome-wide drug response in biological systems. However, a problem remains that is how to evaluate the suitability of heterogeneous in vitro and in vivo systems to model the many different aspects of human toxicity...
July 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28711565/new-aspects-of-molecular-imaging-in-prostate-cancer
#5
Francesco Ceci, Paolo Castellucci, Juliano J Cerci, Stefano Fanti
Nowadays several new imaging modalities are available for investigating prostate cancer (PCa) such as magnet resonance imaging (MRI) in the form of whole body MRI and pelvic multiparametric MRI and positron emission tomography (PET) using choline as radiotracers. Nevertheless, these modalities proved sub-optimal accuracy for detecting PCa metastases, particularly in the recurrence setting. A new molecular probe targeting the prostate specific membrane antigen (PSMA) has been recently developed for PET imaging...
July 12, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28710010/local-network-component-analysis-for-quantifying-transcription-factor-activities
#6
Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu, Luonan Chen
Transcription factors (TFs) could regulate physiological transitions or determine stable phenotypic diversity. The accurate estimation on TF regulatory signals or functional activities is of great significance to guide biological experiments or elucidate molecular mechanisms, but still remains challenging. Traditional methods identify TF regulatory signals at the population level, which masks heterogeneous regulation mechanisms in individuals or subgroups, thus resulting in inaccurate analyses. Here, we propose a novel computational framework, namely Local Network Component Analysis (LNCA), to exploit data heterogeneity and automatically quantify accurate transcription factor activity (TFA) in practical terms, through integrating the partitioned expression sets (i...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28710009/mrna-interactome-capture-in-mammalian-cells
#7
Nicolai Kastelic, Markus Landthaler
Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28710008/identifying-synthetic-lethal-targets-using-crispr-cas9-system
#8
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28705470/hypoxia-and-hypoxia-response-associated-molecular-markers-in-esophageal-cancer-a-systematic-review
#9
REVIEW
Jurgen Peerlings, Lien Van De Voorde, Cristina Mitea, Ruben Larue, Ala Yaromina, Sebastian Sandeleanu, Linda Spiegelberg, Ludwig Dubois, Philippe Lambin, Felix M Mottaghy
PURPOSE: In this systematic review, the existing evidence of available hypoxia-associated molecular response biomarkers in esophageal cancer (EC) patients is summarized and set into the context of the role of hypoxia in the prediction of esophageal cancer, treatment response and treatment outcome. METHODS: A systematic literature search was performed in Web of Science, MEDLINE, and PubMed databases using the keywords: hypoxia, esophagus, cancer, treatment outcome and treatment response...
July 10, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28698070/surgical-preparation-of-rats-and-mice-for-intravital-microscopic-imaging-of-abdominal-organs
#10
George J Rhodes
Intravital microscopy is a powerful research tool that can provide insight into cellular and subcellular events that take place in organs in the body. However, meaningful results can only be obtained from animals whose physiology is preserved during the process of microscopy. Here I discuss the importance of preserving the overall state of health of the animal, methods of anesthesia, surgical techniques for intravital microscopy of various abdominal organs, methods to maintain and monitor the physiology of the animal during microscopy and associated peri- and post-operative recovery considerations...
July 8, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28698069/theranostic-and-nanotheranostic-probes-in-nuclear-medicine
#11
REVIEW
Natascha Drude, Lena Tienken, Felix M Mottaghy
In nuclear medicine, a theranostic probe describes a substance that combines diagnostic and therapeutic capabilities by radiolabeling it with different radionuclides. Next to a brief description of the different emitters (α, β(+), β(-), γ) used for imaging and/or therapy, the aim of this review is to summarize the most commonly used theranostic probes in nuclear medicine. Another goal is to give an idea which chemical requirements need to be fulfilled for radiolabeling with either therapeutic and/ or diagnostic relevant nuclides...
July 8, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28694065/the-power-of-bioluminescence-imaging-in-understanding-host-pathogen-interactions
#12
REVIEW
Natalie Suff, Simon N Waddington
Infectious diseases are one of the leading causes of death worldwide. Modelling and understanding human infection is imperative to developing treatments to reduce the global burden of infectious disease. Bioluminescence imaging is a highly sensitive, non-invasive technique based on the detection of light, produced by luciferase-catalysed reactions. In the study of infectious disease, bioluminescence imaging is a well-established technique; it can be used to detect, localize and quantify specific immune cells, pathogens or immunological processes...
July 8, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28694066/disease-gene-classification-with-metagraph-representations
#13
Sezin Ata Kircali, Yuan Fang, Min Wu, Xiao-Li Li, Xiaokui Xiao
Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to exploit biological properties of individual proteins. More specifically, we integrate keywords describing protein properties into the PPI network, and construct a novel PPI-Keywords (PPIK) network consisting of both proteins and keywords as two different types of nodes...
July 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28694064/rna-fluorescence-in-situ-hybridization-for-high-content-screening
#14
Emmanuelle Querido, Lynda Dekakra-Bellili, Pascal Chartrand
Single molecule RNA imaging using fluorescent in situ hybridization (FISH) can provide quantitative information on mRNA abundance and localization in a single cell. There is now a growing interest in screening for modifiers of RNA abundance and/or localization. For instance, microsatellite expansion within RNA can lead to toxic gain-of-function via mislocalization of these transcripts into RNA aggregate and sequestration of RNA-binding proteins. Screening for inhibitors of these RNA aggregate can be performed by high-throughput RNA FISH...
July 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28684341/near-perfect-protein-multi-label-classification-with-deep-neural-networks
#15
Balázs Szalkai, Vince Grolmusz
Biological sequences can be considered as data items of high-, non-fixed dimensions, corresponding to the length of those sequences. The comparison and the classification of biological sequences in their relations to large databases are important areas of research today. Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successful applications in image- and sound processing and classification problems. ANNs have also been applied for predicting the family or function of a protein, knowing its residue sequence...
July 3, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28684340/modeling-tumor-progression-via-the-comparison-of-stage-specific-graphs
#16
Serene W H Wong, Chiara Pastrello, Max Kotlyar, Christos Faloutsos, Igor Jurisica
Can we use graph mining algorithms to find patterns in tumor molecular mechanisms? Can we model disease progression with multiple time-specific graph comparison algorithms? In this paper, we will focus on this area. Our main contributions are 1) we proposed the Temporal-Omics (Temp-O) workflow to model tumor progression in non-small cell lung cancer (NSCLC) using graph comparisons between multiple stage-specific graphs, and 2) we showed that temporal structures are meaningful in the tumor progression of NSCLC...
July 3, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28684339/-identification-isolation-quantification-and-systems-approach-towards-cd34-a-biomarker-present-in-the-progenitor-stem-cells-from-diverse-lineages
#17
P Sudheer Shenoy, Bipasha Bose
Mesenchymal stem cells (MSCs) constitute the diverse progenitor populations in almost every tissue and are of immense importance in the field of regenerative medicine. CD34 is a cell surface glycoprotein identified first as a marker for the MSCs of hematopoietic origin. CD34 is now known to be expressed in cells of diverse lineages (tissues of non-hematopoietic origin) such as ectoderm, mesoderm and endoderm and is considered as a general marker for progenitor cells. Here, we present detailed protocols to obtain pure populations of MSCs from three diverse lineages such as skeletal muscle, skin, and liver from mouse tissues...
July 3, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28669867/radical-probing-of-spliceosome-assembly
#18
Charnpal S Grewal, Oliver A Kent, Andrew M MacMillan
Here we describe the synthesis and use of a directed hydroxyl radical probe, tethered to a pre-mRNA substrate, to map the structure of this substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly. This methodology may be adapted to the synthesis of a wide variety of modified RNAs for use as probes of RNA structure and RNA-protein interaction.
June 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28669866/procedures-and-applications-of-long-term-intravital-microscopy
#19
REVIEW
Chloé Prunier, Na Chen, Laila Ritsma, Nienke Vrisekoop
Intravital microscopy (IVM) is increasingly used in biomedical research to study dynamic processes at cellular and subcellular resolution in their natural environment. Long-term IVM especially can be applied to visualize migration and proliferation over days to months within the same animal without recurrent surgeries. Skin can be repetitively imaged without surgery. To intermittently visualize cells in other organs, such as liver, mammary gland and brain, different imaging windows including the abdominal imaging window (AIW), dermal imaging window (DIW) and cranial imaging window (CIW) have been developed...
June 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28669865/molecular-signatures-in-breast-cancer
#20
REVIEW
Samir Lal, Amy E McCart Reed, Xavier M de Luca, Peter T Simpson
The use of molecular signatures to add value to standard clinical and pathological parameters has impacted clinical practice in many cancer types, but perhaps most notably in the breast cancer field. This is, in part, due to the considerable complexity of the disease at the clinical, morphological and molecular levels. The adoption of molecular profiling of DNA, RNA and protein continues to reveal important differences in the intrinsic biology between molecular subtypes and has begun to impact the way patients are managed...
June 29, 2017: Methods: a Companion to Methods in Enzymology
journal
journal
31806
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"