scholarly journals In vivo generation of DNA sequence diversity for cellular barcoding

2014 ◽  
Author(s):  
Ian Peikon ◽  
Diana Gizatullina ◽  
Anthony Zador
Keyword(s):  
Dna Sequencing ◽  
Dna Sequence ◽  
Biological Samples ◽  
Biological Systems ◽  
Sequence Diversity ◽  
Bacterial Cells ◽  
Complete Understanding ◽  
Novel Method ◽  
Cellular Barcoding

Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. We demonstrate the feasibility of this technique in bacterial cells. This method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.

scholarly journals In vivo generation of DNA sequence diversity for cellular barcoding

2014 ◽  
Vol 42 (16) ◽  
pp. e127-e127 ◽  
Author(s):  
Ian D. Peikon ◽  
Diana I. Gizatullina ◽  
Anthony M. Zador
Keyword(s):  
Dna Sequence ◽  
Sequence Diversity ◽  
Cellular Barcoding

Development of Synchrotron Footprinting at NSLS and NSLS-II

2019 ◽  
Vol 26 (1) ◽  
pp. 55-60 ◽  
Author(s):  
Jen Bohon
Keyword(s):  
Solvent Accessibility ◽  
Biological Systems ◽  
In Vivo Studies ◽  
Aqueous Samples ◽  
Biological Mechanisms ◽  
Macromolecular Assembly ◽  
Structure And Dynamics ◽  
Synchrotron Light ◽  
Ideal Technique

Background: First developed in the 1990’s at the National Synchrotron Light Source, xray synchrotron footprinting is an ideal technique for the analysis of solution-state structure and dynamics of macromolecules. Hydroxyl radicals generated in aqueous samples by intense x-ray beams serve as fine probes of solvent accessibility, rapidly and irreversibly reacting with solvent exposed residues to provide a “snapshot” of the sample state at the time of exposure. Over the last few decades, improvements in instrumentation to expand the technology have continuously pushed the boundaries of biological systems that can be studied using the technique. Conclusion: Dedicated synchrotron beamlines provide important resources for examining fundamental biological mechanisms of folding, ligand binding, catalysis, transcription, translation, and macromolecular assembly. The legacy of synchrotron footprinting at NSLS has led to significant improvement in our understanding of many biological systems, from identifying key structural components in enzymes and transporters to in vivo studies of ribosome assembly. This work continues at the XFP (17-BM) beamline at NSLS-II and facilities at ALS, which are currently accepting proposals for use.

scholarly journals DNA thermodynamics shape chromosome organization and topology

2013 ◽  
Vol 41 (2) ◽  
pp. 548-553 ◽  
Author(s):  
Andrew A. Travers ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Chromosome Organization ◽  
Topological Properties ◽  
Genetic Organization ◽  
And Topology ◽  
Dna Translocases

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

scholarly journals PLASTID DNA SEQUENCE DIVERSITY IN A WORLDWIDE SET OF GRAPEVINE CULTIVARS (VITIS VINIFERA L. SUBSP. VINIFERA)

2014 ◽  
pp. 609-616 ◽  
Author(s):  
T. Beridze ◽  
I. Pipia ◽  
J. Beck ◽  
S.-C. Hsu ◽  
B. Schaal ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Dna Sequence ◽  
Plastid Dna ◽  
Sequence Diversity ◽  
Vitis Vinifera L

scholarly journals A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2111
Author(s):  
Bo-Wei Zhao ◽  
Zhu-Hong You ◽  
Lun Hu ◽  
Zhen-Hao Guo ◽  
Lei Wang ◽  
...  
Keyword(s):  
Drug Target ◽  
Large Scale ◽  
Computational Models ◽  
Structural Information ◽  
Characteristic Curve ◽  
Representation Learning ◽  
Graph Representation ◽  
Convolutional Network ◽  
Novel Method

Identification of drug-target interactions (DTIs) is a significant step in the drug discovery or repositioning process. Compared with the time-consuming and labor-intensive in vivo experimental methods, the computational models can provide high-quality DTI candidates in an instant. In this study, we propose a novel method called LGDTI to predict DTIs based on large-scale graph representation learning. LGDTI can capture the local and global structural information of the graph. Specifically, the first-order neighbor information of nodes can be aggregated by the graph convolutional network (GCN); on the other hand, the high-order neighbor information of nodes can be learned by the graph embedding method called DeepWalk. Finally, the two kinds of feature are fed into the random forest classifier to train and predict potential DTIs. The results show that our method obtained area under the receiver operating characteristic curve (AUROC) of 0.9455 and area under the precision-recall curve (AUPR) of 0.9491 under 5-fold cross-validation. Moreover, we compare the presented method with some existing state-of-the-art methods. These results imply that LGDTI can efficiently and robustly capture undiscovered DTIs. Moreover, the proposed model is expected to bring new inspiration and provide novel perspectives to relevant researchers.

scholarly journals Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ryan Lusk ◽  
Evan Stene ◽  
Farnoush Banaei-Kashani ◽  
Boris Tabakoff ◽  
Katerina Kechris ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Dna Sequence ◽  
Mammalian Species ◽  
Alternative Polyadenylation ◽  
Sequence Information ◽  
Rna Seq ◽  
Average Precision ◽  
Polyadenylation Sites ◽  
Dna Nucleotide Sequence

AbstractAnnotation of polyadenylation sites from short-read RNA sequencing alone is a challenging computational task. Other algorithms rooted in DNA sequence predict potential polyadenylation sites; however, in vivo expression of a particular site varies based on a myriad of conditions. Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning paradigm to predict expressed polyadenylation sites. Specifically, as input aptardi takes DNA nucleotide sequence, genome-aligned RNA-Seq data, and an initial transcriptome. The program evaluates these initial transcripts to identify expressed polyadenylation sites in the biological sample and refines transcript 3′-ends accordingly. The average precision of the aptardi model is twice that of a standard transcriptome assembler. In particular, the recall of the aptardi model (the proportion of true polyadenylation sites detected by the algorithm) is improved by over three-fold. Also, the model—trained using the Human Brain Reference RNA commercial standard—performs well when applied to RNA-sequencing samples from different tissues and different mammalian species. Finally, aptardi’s input is simple to compile and its output is easily amenable to downstream analyses such as quantitation and differential expression.

scholarly journals Cyclic Voltammetry in Biological Samples: A Systematic Review of Methods and Techniques Applicable to Clinical Settings

Signals ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 138-158
Author(s):  
Hsiang-Wei Wang ◽  
Cameron Bringans ◽  
Anthony J. R. Hickey ◽  
John A. Windsor ◽  
Paul A. Kilmartin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Systematic Review ◽  
Cyclic Voltammetry ◽  
Clinical Setting ◽  
Biological Samples ◽  
Antioxidant Status ◽  
Redox Status ◽  
Electrochemical Technique ◽  
Processing And Storage

Oxidative stress plays a pivotal role in the pathogenesis of many diseases, but there is no accurate measurement of oxidative stress or antioxidants that has utility in the clinical setting. Cyclic Voltammetry is an electrochemical technique that has been widely used for analyzing redox status in industrial and research settings. It has also recently been applied to assess the antioxidant status of in vivo biological samples. This systematic review identified 38 studies that used cyclic voltammetry to determine the change in antioxidant status in humans and animals. It focusses on the methods for sample preparation, processing and storage, experimental setup and techniques used to identify the antioxidants responsible for the voltammetric peaks. The aim is to provide key information to those intending to use cyclic voltammetry to measure antioxidants in biological samples in a clinical setting.

scholarly journals A novel application of bubble-eye strain of Carassius auratus for ex vivo fish immunological studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hiroto Nakajima ◽  
Atsushi Miyashita ◽  
Hiroshi Hamamoto ◽  
Kazuhisa Sekimizu
Keyword(s):  
Inflammatory Cytokines ◽  
Immune Cells ◽  
Ex Vivo ◽  
Large Bubble ◽  
Suitable Model ◽  
Bacterial Cells ◽  
Functional Impairments ◽  
Gene Expressions ◽  
Pro Inflammatory Cytokines

AbstractIn this study, we investigated a new application of bubble-eye goldfish (commercially available strain with large bubble-shaped eye sacs) for immunological studies in fishes utilizing the technical advantage of examining immune cells in the eye sac fluid ex vivo without sacrificing animals. As known in many aquatic species, the common goldfish strain showed an increased infection sensitivity at elevated temperature, which we demonstrate may be due to an immune impairment using the bubble-eye goldfish model. Injection of heat-killed bacterial cells into the eye sac resulted in an inflammatory symptom (surface reddening) and increased gene expression of pro-inflammatory cytokines observed in vivo, and elevated rearing temperature suppressed the induction of pro-inflammatory gene expressions. We further conducted ex vivo experiments using the immune cells harvested from the eye sac and found that the induced expression of pro-inflammatory cytokines was suppressed when we increased the temperature of ex vivo culture, suggesting that the temperature response of the eye-sac immune cells is a cell autonomous function. These results indicate that the bubble-eye goldfish is a suitable model for ex vivo investigation of fish immune cells and that the temperature-induced infection susceptibility in the goldfish may be due to functional impairments of immune cells.

Lowest aqueous picomolar fluoride ions and in vivo aluminum toxicity detection by an aluminum(iii) binding chemosensor

2021 ◽  
Author(s):  
Monojit Das ◽  
Debdeep Maity ◽  
Tusar Kanta Acharya ◽  
Sudip Sau ◽  
Chandan Giri ◽  
...  
Keyword(s):  
Detection Limit ◽  
Aluminum Toxicity ◽  
Biological Systems ◽  
Water Soluble ◽  
Fluoride Ions ◽  
Toxicity Effect

A water-soluble PET-based chemosensor is developed which can detect Al(iii) and F− ions up to nano- and picomolar (lowest detection so far) detection limit, respectively, also utilized to establish aluminum-toxicity effect in biological systems.

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