Predictive models for population performance on real biological fitness landscapes.

Bioinformatics
William RoweJoshua Knowles

Abstract

Directed evolution, in addition to its principal application of obtaining novel biomolecules, offers significant potential as a vehicle for obtaining useful information about the topologies of biomolecular fitness landscapes. In this article, we make use of a special type of model of fitness landscapes-based on finite state machines-which can be inferred from directed evolution experiments. Importantly, the model is constructed only from the fitness data and phylogeny, not sequence or structural information, which is often absent. The model, called a landscape state machine (LSM), has already been used successfully in the evolutionary computation literature to model the landscapes of artificial optimization problems. Here, we use the method for the first time to simulate a biological fitness landscape based on experimental evaluation. We demonstrate in this study that LSMs are capable not only of representing the structure of model fitness landscapes such as NK-landscapes, but also the fitness landscape of real DNA oligomers binding to a protein (allophycocyanin), data we derived from experimental evaluations on microarrays. The LSMs prove adept at modelling the progress of evolution as a function of various controlling paramet...Continue Reading

References

Aug 30, 1990·Nature·A D Ellington, J W Szostak
Sep 7, 1987·Journal of Theoretical Biology·S Kauffman, S Levin
Oct 25, 1994·Proceedings of the National Academy of Sciences of the United States of America·W P Stemmer
Oct 28, 1998·Proceedings of the National Academy of Sciences of the United States of America·L GiverF H Arnold
Oct 29, 2000·Advances in Protein Chemistry·C A VoigtZ G Wang
Sep 16, 2003·Journal of Molecular Biology·Lori A RoweIchiro Matsumura
Dec 20, 2003·Organic & Biomolecular Chemistry·Marina AlexeevaNicholas J Turner
Jun 9, 2005·Journal of Molecular Biology·D Allan DrummondFrances H Arnold
Dec 17, 2008·Journal of Theoretical Biology·David C WedgeJoshua Knowles
Jul 25, 2009·Journal of the Royal Society, Interface·William RoweJoshua Knowles
Nov 26, 2009·Nature Reviews. Molecular Cell Biology·Philip A Romero, Frances H Arnold

❮ Previous
Next ❯

Citations

Mar 6, 2013·Molecular BioSystems·Alexander E LobkovskyEugene V Koonin
Dec 24, 2011·PLoS Computational Biology·Alexander E LobkovskyEugene V Koonin
Jan 2, 2014·Analytical Chemistry·Emily R BillingeMark Platt
Jan 19, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Douglas B Kell
Mar 2, 2019·BMC Systems Biology·Nishant GeraldSupreet Saini
Jun 30, 2017··Martin ZaeffererAndreas Fischbach

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of the Royal Society, Interface
William RoweJoshua Knowles
Proceedings of the National Academy of Sciences of the United States of America
Alexander E LobkovskyE V Koonin
© 2021 Meta ULC. All rights reserved