scholarly journals Antibody Arrays: Technical Considerations and Clinical Applications in Cancer

2006 ◽  
Vol 52 (9) ◽  
pp. 1651-1659 ◽  
Author(s):  
Marta Sanchez-Carbayo
Keyword(s):  
Cancer Research ◽  
Cancer Progression ◽  
High Throughput ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Clinical Applications ◽  
Antibody Concentration ◽  
Antibody Array ◽  
Antibody Arrays

Abstract Antibody arrays represent one of the high-throughput techniques that are able to detect multiple proteins simultaneously. One of the main advantages of this technology over other proteomic approaches is that the identities of the measured proteins are known or can be readily characterized, allowing a biological interpretation of the results. Features such as lower sample volume and antibody concentration requirements, higher format versatility, and reproducibility support the increasing use of antibody arrays in cancer research. Clinical applications include disease marker discovery for diagnosis, prognosis, and drug response, characterization of signaling and protein pathways, and modifications associated with disease development and progression. This report presents an overview of technical issues of the main antibody array formats and various applications in cancer research. Antibody arrays are high-throughput tools that improve the functional characterization of molecular bases for disease. Furthermore, identification and validation of protein expression patterns, characteristic of cancer progression, and tumor subtypes may intervene and improve tailored therapies in the clinical management of cancer patients.

Functional characterization of RNA fragments using high-throughput interactome screening

2019 ◽  
Vol 193 ◽  
pp. 173-183 ◽  
Author(s):  
Paulina Jackowiak ◽  
Angelika Lis ◽  
Magdalena Luczak ◽  
Ireneusz Stolarek ◽  
Marek Figlerowicz
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
Rna Fragments

scholarly journals Formulation, High Throughput In Vitro Screening and In Vivo Functional Characterization of Nanoemulsion-Based Intranasal Vaccine Adjuvants

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126120 ◽  
Author(s):  
Pamela T. Wong ◽  
Pascale R. Leroueil ◽  
Douglas M. Smith ◽  
Susan Ciotti ◽  
Anna U. Bielinska ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
In Vitro Screening ◽  
Vaccine Adjuvants ◽  
Intranasal Vaccine

scholarly journals All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS

2018 ◽  
Vol 10 (6) ◽  
pp. 1991-2004 ◽  
Author(s):  
Evangelos Kiskinis ◽  
Joel M. Kralj ◽  
Peng Zou ◽  
Eli N. Weinstein ◽  
Hongkang Zhang ◽  
...  
Keyword(s):  
Motor Neuron ◽  
High Throughput ◽  
Neuron Model ◽  
Functional Characterization ◽  
All Optical ◽  
Human Ipsc

scholarly journals Genome-wide identification, phylogeny, and expression profile of the sucrose transporter multigene family in tobacco

2019 ◽  
Vol 99 (3) ◽  
pp. 312-323
Author(s):  
Shanshan Wang ◽  
Jun Yang ◽  
Xiaodong Xie ◽  
Feng Li ◽  
Mingzhu Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Nicotiana Sylvestris ◽  
Multiple Roles ◽  
Functional Conservation ◽  
Sucrose Transporters ◽  
Genome Wide ◽  
Pi Starvation ◽  
Profiling Analysis

The transportation and distribution of sucrose in plants is mediated by sucrose transporters (SUTs), which also participate in various plant developmental and resistance processes. However, no such study of the tobacco SUT family has been reported yet. In the present study, 11, 5, and 4 SUT genes were identified from the genomes of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis, respectively. The exon–intron structures of the tobacco SUT genes were highly conserved in the three tobacco species. Gene loss, duplication, and chromosome exchange occurred in the NtSUT family during the formation of allotetraploid common tobacco. Expression profiling analysis revealed that the expression patterns of the NtSUT genes in common tobacco were closer to those in N. sylvestris plants. The NtSUT2s and NtSUT4 genes were ubiquitously expressed in various tobacco tissues, while the NtSUT1s gene was highly expressed in the maturing leaves, indicating their functional conservation and differentiation. The transcriptions of the NtSUT2t, NtSUT3s, NtSUT4, and NtSUT5s genes in tobacco plants were dramatically induced under Pi starvation, drought, and salinity stresses, but their highest expression levels occurred in different tissues, suggesting the multiple roles of NtSUTs in plant resistance to various abiotic stresses. This study provides useful information for the further functional characterization of SUT genes in tobacco.

scholarly journals Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

2016 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefano Campanaro ◽  
Laura Treu ◽  
Panagiotis G. Kougias ◽  
Davide De Francisci ◽  
Giorgio Valle ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
Shotgun Sequencing ◽  
Metagenomic Analysis

scholarly journals Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

2021 ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Stress ◽  
Protein Motif ◽  
Genome Wide

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors

2019 ◽  
Author(s):  
Johan O. L. Andreasson ◽  
Michael R. Gotrik ◽  
Michelle J. Wu ◽  
Hannah K. Wayment-Steele ◽  
Wipapat Kladwang ◽  
...  
Keyword(s):  
High Throughput ◽  
Online Community ◽  
Large Scale ◽  
Functional Characterization ◽  
New Paradigm ◽  
Molecular Sensors ◽  
Rna Switches ◽  
Rna Sensors ◽  
Rna Design

AbstractInternet-based scientific communities promise a means to apply distributed, diverse human intelligence towards previously intractable scientific problems. However, current implementations have not allowed communities to propose experiments to test all emerging hypotheses at scale or to modify hypotheses in response to experiments. We report high-throughput methods for molecular characterization of nucleic acids that enable the large-scale videogame-based crowdsourcing of functional RNA sensor design, followed by high-throughput functional characterization. Iterative design testing of thousands of crowdsourced RNA sensor designs produced near-thermodynamically optimal and reversible RNA switches that act as self-contained molecular sensors and couple five distinct small molecule inputs to three distinct protein binding and fluorogenic outputs—results that surpass computational and expert-based design. This work represents a new paradigm for widely distributed experimental bioscience.One Sentence SummaryOnline community discovers standalone RNA sensors.

High-throughput functional characterization of miRNAs in cytogenetically defined AML subgroups

2013 ◽  
Vol 225 (03) ◽  
Author(s):  
R Jammal ◽  
S Emmrich ◽  
K Henke ◽  
J Kuipers ◽  
M Heuvel vd ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization

scholarly journals High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Zachary Armstrong ◽  
Feng Liu ◽  
Sam Kheirandish ◽  
Hong-Ming Chen ◽  
Keith Mewis ◽  
...  
Keyword(s):  
High Throughput ◽  
Glycoside Hydrolase ◽  
Plant Biomass ◽  
Functional Characterization ◽  
Environmental Dna ◽  
Functional Screening ◽  
Biomass Degradation ◽  
Genomic Context ◽  
Or Gene

ABSTRACT Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by β-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-β-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides. IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.

Design and Characterization of a Fluorescent Reporter Enabling Live-cell Monitoring of MCT8 Expression

2021 ◽  
Author(s):  
Adina Sophie Graffunder ◽  
Sarah Paisdzior ◽  
Robert Opitz ◽  
Kostja Renko ◽  
Peter Kühnen ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Live Cell ◽  
Monocarboxylate Transporter ◽  
Start Codon ◽  
Future Application ◽  
Gene Assay ◽  
Cell Monitoring

AbstractThe monocarboxylate transporter 8 (MCT8) is a specific thyroid hormone transporter and plays an essential role in fetal development. Inactivating mutations in the MCT8 encoding gene SLC16A2 (solute carrier family 16, member 2) lead to the Allan-Herndon-Dudley syndrome, a condition presenting with severe endocrinological and neurological phenotypes. However, the cellular distribution pattern and dynamic expression profile are still not well known for early human neural development. Objective Development and characterization of fluorescent MCT8 reporters that would permit live-cell monitoring of MCT8 protein expression in vitro in human induced pluripotent stem cell (hiPSC)-derived cell culture models. Methods A tetracysteine (TC) motif was introduced into the human MCT8 sequence at four different positions as binding sites for fluorescent biarsenical dyes. Human Embryonic Kidney 293 cells were transfected and stained with fluorescein-arsenical hairpin-binder (FlAsH). Counterstaining with specific MCT8 antibody was performed. Triiodothyronine (T3) uptake was indirectly measured with a T3 responsive luciferase-based reporter gene assay in Madin-Darby Canine Kidney 1 cells for functional characterization. Results FlAsH staining and antibody counterstaining of all four constructs showed cell membrane expression of all MCT8 constructs. The construct with the tag after the first start codon demonstrated comparable T3 uptake to the MCT8 wildtype. Conclusion Our data indicate that introduction of a TC-tag directly after the first start codon generates a MCT8 reporter with suitable characteristics for live-cell monitoring of MCT8 expression. One promising future application will be generation of stable hiPSC MCT8 reporter lines to characterize MCT8 expression patterns during in vitro neuronal development.

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