Planning and Analysis of Axon Degeneration Screening Experiments

Background: Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. Methods: We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. Results: We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. Conclusion: The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.

Download Full-text

CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

PLoS ONE ◽

10.1371/journal.pone.0184281 ◽

2017 ◽

Vol 12 (9) ◽

pp. e0184281 ◽

Cited By ~ 9

Author(s):

Qingyi Cao ◽

Jian Ma ◽

Chen-Hao Chen ◽

Han Xu ◽

Zhi Chen ◽

...

Keyword(s):

Web Server ◽

Screening Experiments

Download Full-text

Discussion of “21st century screening experiments: What, why, and how”

Quality Engineering ◽

10.1080/08982112.2015.1100464 ◽

2016 ◽

Vol 28 (1) ◽

pp. 111-114 ◽

Cited By ~ 2

Author(s):

Peter Goos

Keyword(s):

21St Century ◽

Screening Experiments

Download Full-text

Axon degeneration: Mechanisms and implications of a distinct program from cell death

Neurochemistry International ◽

10.1016/j.neuint.2010.01.013 ◽

2010 ◽

Vol 56 (4) ◽

pp. 529-534 ◽

Cited By ~ 14

Author(s):

Tingting Yan ◽

Yan Feng ◽

Qiwei Zhai

Keyword(s):

Cell Death ◽

Axon Degeneration

Download Full-text

Production of Structured Phosphatidylcholine with High Content of Myristic Acid by Lipase-Catalyzed Acidolysis and Interesterification

Catalysts ◽

10.3390/catal8070281 ◽

2018 ◽

Vol 8 (7) ◽

pp. 281 ◽

Cited By ~ 9

Author(s):

Anna Chojnacka ◽

Witold Gładkowski

Keyword(s):

Myristic Acid ◽

Rhizomucor Miehei ◽

Egg Yolk ◽

Thermomyces Lanuginosus ◽

Molar Ratio ◽

Acyl Donor ◽

Thermomyces Lanuginosus Lipase ◽

Screening Experiments ◽

Miehei Lipase ◽

Acyl Donors

Synthesis of structured phosphatidylcholine (PC) enriched with myristic acid (MA) was conducted by acidolysis and interesterification reactions using immobilized lipases as catalysts and two acyl donors: trimyristin (TMA) isolated from ground nutmeg, and myristic acid obtained by saponification of TMA. Screening experiments indicated that the most effective biocatalyst for interesterification was Rhizomucor miehei lipase (RML), whereas for acidolysis, the most active were Thermomyces lanuginosus lipase (TLL) and RML. The effect of the molar ratio of substrates (egg-yolk PC/acyl donor), enzyme loading, and different solvent on the incorporation of MA into PC and on PC recovery was studied. The maximal incorporation of MA (44 wt%) was achieved after 48 h of RML-catalyzed interesterification in hexane using substrates molar ratio (PC/trimyristin) 1/5 and 30% enzyme load. Comparable results were obtained in toluene with 1/3 substrates molar ratio. Interesterification of PC with trimyristin resulted in significantly higher MA incorporation than acidolysis with myristic acid, particularly in the reactions catalyzed by RML.

Download Full-text