scholarly journals Output Domain Downscaler

Author(s):  
Mert Büyükmıhçı ◽  
Vecdi Emre Levent ◽  
Aydin Emre Guzel ◽  
Ozgur Ates ◽  
Mustafa Tosun ◽  
...  
Keyword(s):  
2016 ◽  
Vol 109 (4) ◽  
pp. 509-522 ◽  
Author(s):  
Hsien-Ming Lee ◽  
Chao-Tsai Liao ◽  
Ying-Chuan Chiang ◽  
Yu-Yin Chang ◽  
Yu-Tzu Yeh ◽  
...  

2021 ◽  
Author(s):  
Anna Miriam John ◽  
Harsimranjit Sekhon ◽  
Jeung-Hoi Ha ◽  
Stewart N Loh

Protein conformational switches are widely used in biosensing. They are typically composed of an input domain (which binds a target ligand) fused to an output domain (which generates an optical readout). A central challenge in designing such switches is to develop mechanisms for coupling the input and output signals via conformational change. Here, we create a biosensor in which binding-induced folding of the input domain drives a conformational shift in the output domain that results in a 6-fold green-to-yellow ratiometric fluorescence change in vitro, and a 35-fold intensiometric fluorescence increase in cultured cells. The input domain consists of circularly permuted FK506 binding protein (cpFKBP) that folds upon binding its target ligand (FK506 or rapamycin). cpFKBP folding induces the output domain, an engineered GFP variant, to replace one of its β-strands (containing T203 and specifying green fluorescence) with a duplicate β-strand (containing Y203 and specifying yellow fluorescence) in an intramolecular exchange reaction. This mechanism employs the loop-closure entropy principle, embodied by folding of the partially disordered cpFKBP domain, to couple ligand binding to the GFP color shift. This proof-of-concept design has the advantages of full genetic encodability, ratiometric or intensiometric response, and potential for modularity. The latter attribute is enabled by circular permutation of the input domain.


2008 ◽  
pp. 2316-2337 ◽  
Author(s):  
Ana Isabel Canhoto

The use of automated systems to collect, process and analyse vast amounts of data is now integral to the operations of many corporations and government agencies, in particular it has gained recognition as a strategic tool in the war on crime. Data mining, the technology behind such analysis, has its origins in quantitative sciences. Yet, analysts face important issues of a cognitive nature both in terms of the input for the data mining effort, and in terms of the analysis of the output. Domain knowledge and bias information influence which patterns in the data are deemed as useful and, ultimately, valid. This chapter addresses the role of cognition and context in the interpretation and validation of mined knowledge. We propose the use of ontology charts and norm specifications to map how varying levels of access to information and exposure to specific social norms lead to divergent views of mined knowledge.


2011 ◽  
pp. 84-105 ◽  
Author(s):  
Ana Isabel Canhoto

The use of automated systems to collect, process and analyse vast amounts of data is now integral to the operations of many corporations and government agencies, in particular it has gained recognition as a strategic tool in the war on crime. Data mining, the technology behind such analysis, has its origins in quantitative sciences. Yet, analysts face important issues of a cognitive nature both in terms of the input for the data mining effort, and in terms of the analysis of the output. Domain knowledge and bias information influence which patterns in the data are deemed as useful and, ultimately, valid. This chapter addresses the role of cognition and context in the interpretation and validation of mined knowledge. We propose the use of ontology charts and norm specifications to map how varying levels of access to information and exposure to specific social norms lead to divergent views of mined knowledge.


2010 ◽  
Vol 192 (24) ◽  
pp. 6336-6345 ◽  
Author(s):  
María A. Mussi ◽  
Jennifer A. Gaddy ◽  
Matías Cabruja ◽  
Brock A. Arivett ◽  
Alejandro M. Viale ◽  
...  

ABSTRACT Light is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogen Acinetobacter baumannii senses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing of Candida albicans filaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of the A. baumannii ATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminal blue-light-sensing-using flavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of the Acinetobacter genus, was named blue-light-sensing A (blsA). Interestingly, temperature plays a role in the ability of A. baumannii to sense and respond to light via the BlsA photoreceptor protein.


2007 ◽  
Vol 189 (20) ◽  
pp. 7206-7212 ◽  
Author(s):  
Divya N. Amin ◽  
Barry L. Taylor ◽  
Mark S. Johnson

ABSTRACT The Aer receptor guides Escherichia coli to specific oxygen and energy-generating niches. The input sensor in Aer is a flavin adenine dinucleotide-binding PAS domain, which is separated from a HAMP/signaling output domain by two membrane-spanning segments that flank a short (four-amino-acid) periplasmic loop. In this study, we determined the overall membrane organization of Aer by introducing combinations of residues that allowed us to differentiate intradimeric collisions from interdimeric collisions. Collisions between proximal residues in the membrane anchor were exclusively intra- or interdimeric but, with one exception, not both. Cross-linking profiles were consistent, with a rigid rather than flexible periplasmic loop and a tilted TM2 helix that crossed TM2′ at residue V197C, near the center of the lipid bilayer. The periplasmic loop formed a stable neighborhood that (i) included a maximum of three Aer dimers, (ii) did not swap neighbors over time, and (iii) appeared to be constrained by interactions in the cytosolic signaling domain.


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