A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
An Event-Driven Approach for Studying Gene Block Evolution in Bacteria
[article]
2015
arXiv
pre-print
Preserved Fulltext
Other Versions
To address this problem we introduce an event-based method for tracking gene block evolution in bacteria. ...
An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. ...
For these 38 operons and related orthologous gene blocks, we show an implementation of the event-driven approach to operon evolution. ...
arXiv:1501.00302v2
fatcat:77ya53djzfcvbl3qclqeggwp2y
An event-driven approach for studying gene block evolution in bacteria
2015
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
To address this problem, we introduce an eventbased method for tracking gene block evolution in bacteria. ...
An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. ...
For these 38 operons and related orthologous gene blocks, we show an implementation of the event-driven approach to operon evolution. ...
doi:10.1093/bioinformatics/btv128
pmid:25717195
pmcid:PMC4481853
fatcat:ygphaizjvvepdkhpj2xuarq3ym
Targeting evolution of antibiotic resistance by SOS response inhibition
2021
Computational and Structural Biotechnology Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The regulators of homologous recombination involved in the processes of DNA repair should be considered as potential targets for blocking. ...
Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-depended mutagenesis and horizontal gene transfer pathways. ...
Julia Gorelik, and Michael Gorelik for critically reading the manuscript and valuable comments. ...
doi:10.1016/j.csbj.2021.01.003
pmid:33552448
pmcid:PMC7843400
fatcat:ceiij7o4cza6hcvqnn6o3c6f5e
Comparative Genomics Suggests That an Ancestral Polyploidy Event Leads to Enhanced Root Nodule Symbiosis in the Papilionoideae
2013
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In this study, we explored this role using an integrated comparative genomic approach and conducted gene expression comparisons and gene ontology enrichment analyses. ...
Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae. Molecular Biology and Evolution, 30 (12). pp. 26022611. ...
Acknowledgments and funding information We are grateful to the International Peach Genome Initiative for the assembled and annotated draft ...
doi:10.1093/molbev/mst152
pmid:24008584
fatcat:svgkasvdffezretdc335x5w3ci
Unraveling a tangled skein: Evolutionary analysis of the bacterial gibberellin biosynthetic operon
[article]
2019
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
for microbes to gain an advantage in these interactions. ...
Additionally, a maximum-parsimony ancestral gene block reconstruction algorithm was employed to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacteria ...
An event is a change in the gene block between any two species with homologous gene blocks. ...
doi:10.1101/868042
fatcat:st7lqmiy65dkhopxvey3qajfcm
Evolution ofbopAGene inBurkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion
2016
BioMed Research International
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The results of this study clearly demonstrated the role of convergent evolution in the evolution of how bacteria evade autophagy. ...
Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available. ...
These results indicted the bopA gene was not acquired from the eukaryotes through a recent HGT event.
BopA Gene in Bacteria. ...
doi:10.1155/2016/6745028
pmid:28018913
pmcid:PMC5149610
fatcat:hrexjqhnezak3j6bqrwgusnxhi
Replacing and Additive Horizontal Gene Transfer in Streptococcus
2012
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes ...
Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. ...
Acknowledgments The authors thank Xavier Didelot for assistance with ClonalOrigin. ...
doi:10.1093/molbev/mss138
pmid:22617954
pmcid:PMC3472495
fatcat:bmdlt4uzcrf3jao7p5x2bngoty
Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon
2020
mSphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
for microbes to gain an advantage in these interactions. ...
gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions. ...
An event is a change in the gene block between any two species with homologous gene blocks. ...
doi:10.1128/msphere.00292-20
pmid:32493722
pmcid:PMC7273348
fatcat:xxqypfz7pncwhaavbhlgwd26ay
Ecology drives a global network of gene exchange connecting the human microbiome
2011
Nature
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Correspondence and requests for materials should be addressed to E.J.A. (ejalm@mit.edu).
Author Contributions ...
However, an alternative explanation for these observations is that closely related bacteria colonize similar environments, creating an apparent ecological effect that is actually driven by shared evolutionary ...
An average pairwise distance of 7,000 km separates bacteria engaging in HGT. ...
doi:10.1038/nature10571
pmid:22037308
fatcat:ib3dy5vtgzatff7wq7ds3wlnwi
Tempo and mode of early gene loss in endosymbiotic bacteria from insects
2006
BMC Evolutionary Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
loss could be driven by the selective importance of genes. ...
rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. ...
We are grateful to Jacqui Shykoff for her critical review of the manuscript and her help in revising the english. ...
doi:10.1186/1471-2148-6-56
pmid:16848891
pmcid:PMC1544356
fatcat:es2vknegbjbihcx5bwnqtpsskq
The Microbial Engines That Drive Earth's Biogeochemical Cycles
2008
Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. ...
These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. ...
The study of biogeography includes the study of patterns in space, in time, and along environmental gradients. ...
doi:10.1126/science.1153213
pmid:18497287
fatcat:xg62vppglrhujohl76rhsz52ce
Synthetic Biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production
2012
FEBS Letters
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The genes encoding the enzymes for their biosynthesis are normally organized in gene clusters, which include also the information for resistance (in the case of antibacterial compounds), regulation, and ...
Here we report examples for the synthesis of building blocks and possibilities to modify and optimize antibiotic biosynthesis, exemplary for the synthesis of the manipulation of the synthesis of the glycopeptide ...
These examples let us assume that primordial gene duplication events were the beginning of such enzyme evolutions. ...
doi:10.1016/j.febslet.2012.04.025
pmid:22710162
fatcat:vx7vqrpuuvhyndmfhp6plnh7cy
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
2005
Nature Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
We used an analogous procedure for loss events, analyzing all branches starting from nodes in which both A and B were present. ...
Although gene duplication may have been an important source for network changes during the early evolution of pathways 1 , the above analyses suggest that horizontal gene transfer was the dominant genetic ...
doi:10.1038/ng1686
pmid:16311593
fatcat:c5r2h57hcvawzjg557yosst7re
Soybean (Glycine max) NF-Y (Nuclear Factor of Y Box) gene family and its potential role under stress conditions and nodulation
2018
Journal of Plant Biology and Crop Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In this study, GmNF-Y genes were investigated through an extensive data mining using several bioinformatics approaches. ...
Results showed that during evolution, GmNF-Y genes arose by block duplication and subfuctionalization processes could be occurring in this family. ...
An unequal crossover mechanism should have driven the evolution in this subunit. Soybean experienced whole genome duplication during their evolution. ...
doi:10.33582/2637-7721/1009
fatcat:5jnoqobkxndntpx3a6fpq7g6me
Positive Selection in Bifidobacterium Genes Drives Species-Specific Host–Bacteria Communication
2019
Frontiers in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We used the maximum likelihood approach to detect positive selection in the PFNA genes. ...
Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial ...
The sites with PP > 0.95 are marked with an asterisk. The most reliable candidates for positive selection verified with an additional approach are highlighted in black. ...
doi:10.3389/fmicb.2019.02374
pmid:31681231
pmcid:PMC6803598
fatcat:pyk2j4easzgb3gqewnvhfolfyy
« Previous
Showing results 1 — 15 out of 15,653 results