Robustness of Recovery in Locating Array-Based Screening Experiments

Author(s):  
Stephen A. Seidel ◽  
Charles J. Colbourn ◽  
Violet R. Syrotiuk
2020 ◽  
Vol 26 (42) ◽  
pp. 7672-7693 ◽  
Author(s):  
Bifang He ◽  
Anthony Mackitz Dzisoo ◽  
Ratmir Derda ◽  
Jian Huang

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.


PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184281 ◽  
Author(s):  
Qingyi Cao ◽  
Jian Ma ◽  
Chen-Hao Chen ◽  
Han Xu ◽  
Zhi Chen ◽  
...  

Catalysts ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 281 ◽  
Author(s):  
Anna Chojnacka ◽  
Witold Gładkowski

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.


2007 ◽  
Vol 84 (5-8) ◽  
pp. 1694-1697 ◽  
Author(s):  
C. Crozatier ◽  
I. Tapsoba ◽  
L.P. Xu ◽  
D. Han ◽  
L. Sensebé ◽  
...  

2011 ◽  
Vol 10 (8) ◽  
pp. 1100-1109 ◽  
Author(s):  
Ci Fu ◽  
Priyadarshini Iyer ◽  
Amrita Herkal ◽  
Julia Abdullah ◽  
Angela Stout ◽  
...  

ABSTRACT A screening procedure was used to identify cell fusion (hyphal anastomosis) mutants in the Neurospora crassa single gene deletion library. Mutants with alterations in 24 cell fusion genes required for cell fusion between conidial anastomosis tubes (CATs) were identified and characterized. The cell fusion genes identified included 14 genes that are likely to function in signal transduction pathways needed for cell fusion to occur ( mik-1 , mek-1 , mak-1 , nrc-1 , mek-2 , mak-2 , rac-1 , pp2A , so/ham-1 , ham-2 , ham-3 , ham-5 , ham-9 , and mob3 ). The screening experiments also identified four transcription factors that are required for cell fusion ( adv-1 , ada-3 , rco-1 , and snf5 ). Three genes encoding proteins likely to be involved in the process of vesicular trafficking were also identified as needed for cell fusion during the screening ( amph-1 , ham-10 , pkr1 ). Three of the genes identified by the screening procedure, ham-6 , ham-7 , and ham-8 , encode proteins that might function in mediating the plasma membrane fusion event. Three of the putative signal transduction proteins, three of the transcription factors, the three putative vesicular trafficking proteins, and the three proteins that might function in mediating cell fusion had not been identified previously as required for cell fusion.


2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Tahira Naz ◽  
Yusuf Nazir ◽  
Shaista Nosheen ◽  
Samee Ullah ◽  
Hafiy Halim ◽  
...  

Carotenoids produced by microbial sources are of industrial and medicinal importance due to their antioxidant and anticancer properties. In the current study, optimization of β-carotene production in M. circinelloides strain 277.49 was achieved using response surface methodology (RSM). Cerulenin and ketoconazole were used to inhibit fatty acids and the sterol biosynthesis pathway, respectively, in order to enhance β-carotene production by diverting metabolic pool towards the mevalonate pathway. All three variables used in screening experiments were found to be significant for the production of β-carotene. The synergistic effect of the C/N ratio, cerulenin, and ketoconazole was further evaluated and optimized for superior β-carotene production using central composite design of RSM. Our results found that the synergistic combination of C/N ratios, cerulenin, and ketoconazole at different concentrations affected the β-carotene productions significantly. The optimal production medium (std. order 11) composed of C/N 25, 10 μg/mL cerulenin, and 150 mg/L ketoconazole, producing maximum β-carotene of 4.26 mg/L (0.43 mg/g) which was 157% greater in comparison to unoptimized medium (1.68 mg/L, 0.17 mg/g). So, it was concluded that metabolic flux had been successfully redirected towards the mevalonate pathway for enhanced β-carotene production in CBS 277.49.


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