scholarly journals Historian: accurate reconstruction of ancestral sequences and evolutionary rates

2016 ◽  
Author(s):  
Ian Holmes
Keyword(s):  
Ancestral Sequence ◽  
Evolutionary Rates ◽  
Evolutionary Models ◽  
Ancestral Reconstruction ◽  
Estimation Of Parameters ◽  
Rate Estimation ◽  
Creative Commons ◽  
Link Type ◽  
Ancestral Sequences ◽  
Simulation Results

AbstractReconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally-informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/ihh/indelhistorian under the Creative Commons Attribution 3.0 US license. Contact: Ian Holmes [email protected].

scholarly journals Ancestral Sequence Reconstructions of MotB Are Proton-Motile and Require MotA for Motility

2020 ◽  
Vol 11 ◽  
Author(s):  
Md Imtiazul Islam ◽  
Angela Lin ◽  
Yu-Wen Lai ◽  
Nicholas J. Matzke ◽  
Matthew A. B. Baker
Keyword(s):  
Ion Selectivity ◽  
Power Source ◽  
Ancestral Sequence ◽  
Ancestral Reconstruction ◽  
Aquifex Aeolicus ◽  
Independent Manner ◽  
B Subunit ◽  
Ancestral Sequences ◽  
Sequence Reconstruction ◽  
A Subunit

The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H+) or sodium (Na+) ions. The transmembrane (TM) domain of the B-subunit of the stator complex is crucial for ion selectivity, as it forms the ion channel in complex with TM3 and TM4 of the A-subunit. In this study, we reconstructed and engineered thirteen ancestral sequences of the stator B-subunit to evaluate the functional properties and ionic power source of the stator proteins at reconstruction nodes to evaluate the potential of ancestral sequence reconstruction (ASR) methods for stator engineering and to test specific motifs previously hypothesized to be involved in ion-selectivity. We found that all thirteen of our reconstructed ancient B-subunit proteins could assemble into functional stator complexes in combination with the contemporary Escherichia coli MotA-subunit to restore motility in stator deleted E. coli strains. The flagellar rotation of the thirteen ancestral MotBs was found to be Na+ independent which suggested that the F30/Y30 residue was not significantly correlated with sodium/proton phenotype, in contrast to what we had reported previously. Additionally, four among the thirteen reconstructed B-subunits were compatible with the A-subunit of Aquifex aeolicus and able to function in a sodium-independent manner. Overall, this work demonstrates the use of ancestral reconstruction to generate novel stators and quantify which residues are correlated with which ionic power source.

scholarly journals FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

2020 ◽  
Author(s):  
Milos Musil ◽  
Rayyan Tariq Khan ◽  
Andy Beier ◽  
Jan Stourac ◽  
Hannes Konegger ◽  
...  
Keyword(s):  
Ancestral Sequence ◽  
Reconstruction Algorithms ◽  
Ancestral Reconstruction ◽  
Web Interface ◽  
Computational Tools ◽  
Ancestral Sequence Reconstruction ◽  
Ancestral Sequences ◽  
Native Proteins ◽  
Sequence Reconstruction ◽  
History Of

Abstract There is a great interest in increasing proteins’ stability to widen their usability in numerous biomedical and biotechnological applications. However, native proteins cannot usually withstand the harsh industrial environment, since they are evolved to function under mild conditions. Ancestral sequence reconstruction is a well-established method for deducing the evolutionary history of genes. Besides its applicability to discover the most probable evolutionary ancestors of the modern proteins, ancestral sequence reconstruction has proven to be a useful approach for the design of highly stable proteins. Recently, several computational tools were developed, which make the ancestral reconstruction algorithms accessible to the community, while leaving the most crucial steps of the preparation of the input data on users’ side. FireProtASR aims to overcome this obstacle by constructing a fully automated workflow, allowing even the unexperienced users to obtain ancestral sequences based on a sequence query as the only input. FireProtASR is complemented with an interactive, easy-to-use web interface and is freely available at https://loschmidt.chemi.muni.cz/fireprotasr/.

scholarly journals Erratum to: Voltage-gated Sodium Channels and Blockers: An Overview and Where Will They Go?

2020 ◽  
Author(s):  
Zhi-mei Li ◽  
Li-xia Chen ◽  
Hua Li
Keyword(s):  
Open Access ◽  
Sodium Channels ◽  
Voltage Gated ◽  
Internet Portal ◽  
Creative Commons ◽  
Link Type ◽  
Voltage Gated Sodium Channels

The article “Voltage-gated Sodium Channels and Blockers: An Overview and Where Will They Go?”, written by Zhi-mei LI, Li-xia CHEN, Hua LI, was originally published electronically on the publisher’s internet portal on December 2019 without open access. With the author(s)’ decision to opt for Open Choice, the copyright of the article is changed to © The Author(s) 2020 and the article is forthwith distributed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.The original article has been corrected.Corresponding authors: Li-xia CHEN, Hua LI

A Novel Symbol Rate Estimation Algorithm for Phase Modulating Signals in Wireless Communications

2013 ◽  
Vol 443 ◽  
pp. 392-396
Author(s):  
Peng Zhou ◽  
Chi Sheng Li
Keyword(s):  
Signal To Noise Ratio ◽  
Estimation Algorithm ◽  
Frequency Resolution ◽  
Phase Shift Keying ◽  
Phase Jump ◽  
Rate Estimation ◽  
Awgn Channel ◽  
Symbol Rate ◽  
Shift Keying ◽  
Simulation Results

In this paper, we proposed a new symbol rate estimation algorithm for phase shift keying (PSK) and qua drawtube amplitude modulation (QAM) signals in AWGN channel First we constructe a delay-multiplied signal, from which we obtaine the modulated information. Then we calculated the instantaneous autocorrelation of the delay-multiplied signal to pick out the phase jump. To eliminate the restriction of frequency resolution in fast Fourier transform, we performed a Chirp-Z transform to find out the exact spectral line which represente the symbol rate of the signal to be analyzed. Compared with the existing algorithms, it is a simple solution that has a better performance and accuracy in low signal-to-noise-ratio channel conditions. Simulation results show that the probability of relative estimating deviation below 0.1% reaches 100% and the average and standard variance of absolute estimation deviation are at the magnitude of 10-2 when SNR is over 2dB.

scholarly journals Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ryutaro Furukawa ◽  
Wakako Toma ◽  
Koji Yamazaki ◽  
Satoshi Akanuma
Keyword(s):  
Low Temperature ◽  
Catalytic Properties ◽  
Amino Acid Sequences ◽  
Ancestral Sequence ◽  
Kinetic Properties ◽  
Reconstruction Technique ◽  
Thermally Stable ◽  
Ancestral Sequence Reconstruction ◽  
Ancestral Sequences ◽  
Sequence Reconstruction

Abstract Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.

scholarly journals Correction to: A review on the flow instability of nanofluids

2019 ◽  
Author(s):  
Jianzhong Lin ◽  
Hailin Yang
Keyword(s):  
Open Access ◽  
Flow Instability ◽  
Open Access Publication ◽  
Creative Commons ◽  
Link Type

The article [A review on the flow instability of nanofluids], written by [Jianzhong LIN, Hailin YANG], was originally published Online First without Open Access. After publication in volume [40], issue [9], page [1227-1238] the author decided to opt for Open Choice and to make the article an Open Access publication. Therefore, the copyright of the article has been changed to © The Author(s) [2019] and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

scholarly journals Correction to: Cavitation of water in hardened cement paste under short-term desorption measurements

2019 ◽  
Vol 52 (6) ◽  
Author(s):  
Ippei Maruyama ◽  
Jiří Rymeš ◽  
Matthieu Vandamme ◽  
Benoit Coasne
Keyword(s):  
Cement Paste ◽  
Hardened Cement ◽  
Hardened Cement Paste ◽  
Short Term ◽  
Creative Commons ◽  
Link Type

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, duplication.

scholarly journals Active Site-Induced Evolutionary Constraints Follow Fold Polarity Principles in Soluble Globular Enzymes

2019 ◽  
Vol 36 (8) ◽  
pp. 1728-1733 ◽  
Author(s):  
Alexander Mayorov ◽  
Matteo Dal Peraro ◽  
Luciano A Abriata
Keyword(s):  
Amino Acid ◽  
Active Sites ◽  
Metabolic Cost ◽  
Evolutionary Rates ◽  
Recent Analysis ◽  
Evolutionary Constraints ◽  
Evolutionary Models ◽  
Data Set ◽  
Soluble Enzymes ◽  
Amino Acid Preference

Abstract A recent analysis of evolutionary rates in >500 globular soluble enzymes revealed pervasive conservation gradients toward catalytic residues. By looking at amino acid preference profiles rather than evolutionary rates in the same data set, we quantified the effects of active sites on site-specific constraints for physicochemical traits. We found that conservation gradients respond to constraints for polarity, hydrophobicity, flexibility, rigidity and structure in ways consistent with fold polarity principles; while sites far from active sites seem to experience no physicochemical constraint, rather being highly variable and favoring amino acids of low metabolic cost. Globally, our results highlight that amino acid variation contains finer information about protein structure than usually regarded in evolutionary models, and that this information is retrievable automatically with simple fits. We propose that analyses of the kind presented here incorporated into models of protein evolution should allow for better description of the physical chemistry that underlies molecular evolution.

scholarly journals Erratum to: Anthropomorphism Indexes of the Kinematic Chain for Artificial Hands

2020 ◽  
Author(s):  
Immaculada Llop-Harillo ◽  
Antonio Pérez-González ◽  
Javier Andrés-Esperanza
Keyword(s):  
Open Access ◽  
Kinematic Chain ◽  
Internet Portal ◽  
Creative Commons ◽  
Link Type

The article “Anthropomorphism Indexes of the Kinematic Chain for Artificial Hands, written by Immaculada Llop-Harillo, Antonio Pérez-González, Javier Andrés-Esperanza, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on May 23rd 2020 without open access. With the author(s)’ decision to opt for Open Choice the copyright of the article changed in October 2020 to © The Author(s) 2020 and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.The original article has been corrected.

Yaw Rate Estimation for Vehicle Control Applications

1998 ◽  
Vol 120 (2) ◽  
pp. 267-274 ◽  
Author(s):  
N. Sivashankar ◽  
A. G. Ulsoy
Keyword(s):  
Experimental Validation ◽  
Vehicle Control ◽  
Operating Conditions ◽  
Angle Sensor ◽  
Control Applications ◽  
Rate Estimation ◽  
Yaw Rate ◽  
Wide Range ◽  
Simulation Results ◽  
Instrumented Vehicle

This paper describes a method for vehicle yaw rate estimation using two accelerometers and a steer angle sensor. This yaw rate estimate can be used as an inexpensive alternative to commercial yaw rate sensors in vehicle control applications. The proposed method combines two complementary approaches to yaw rate estimation using accelerometers. This new method is superior to either method used by itself. This paper presents the new approach, supporting analyses, simulation results and experimental validation. The simulation results are based upon both linear and nonlinear vehicle dynamics models and include important effects such as sensor drift and noise, disturbances acting on the vehicle, and model uncertainties. The experimental validation is based on test data from a specially instrumented vehicle driven on a test track. These results indicate that the proposed yaw rate estimation scheme performs well for a wide range of operating conditions and is not difficult to implement.

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