A maximum likelihood approach to the detection of selection from a phylogeny

Golding, Brian; Felsenstein, Joseph

doi:10.1007/bf02102078

Cited by 51 publications

(38 citation statements)

References 33 publications

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“…An unrooted phylogenetic tree was generated using FITCH (22) with the default parameters plus the additional options of randomizing the input order of sequences and global rearrangement optimization. The representative tree was produced using the MEGA 3.1 software package (33).…”

Section: Reverse Transcription-pcr (Rt-pcr)mentioning

confidence: 99%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, PH15 (PH15) and CNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.Staphylococcus epidermidis, a member of the novobiocin-susceptible coagulase-negative staphylococci, is an important opportunistic pathogen and a major cause of nosocomial infections (42, 55). S. epidermidis predominantly colonizes the mucous membranes, groin, and axillar areas, as well as the cutaneous system of human body, with bacterial counts of up to 10 to 10 3 CFU/cm 2 (26). S. epidermidis is usually considered a harmless commensal microorganism; however, infections can occur in immunocompromised individuals and in patients with indwelling or implanted medical devices such as prosthetic heart valves and joint prostheses, where the staphylococci penetrate cutaneous and mucosal barriers (79). With the increasing use of such devices in medical practice, several million people are affected by complications arising from S. epidermidis infections (49). The widespread use of various antimicrobial agents, including penicillins, macrolides, aminoglycosides, and semisynthetic penicillins such as methicillin, has now led to the emergence of multiple-drug-resistant S. epidermidis strains (21, 72).Two S. epidermidis genomes have been sequenced: those of the non-biofilm-forming, non-infection-associated strain ATCC 12228 and the infecti...

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Section: Reverse Transcription-pcr (Rt-pcr)mentioning

confidence: 99%

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Daniel¹,

Bonnen

Fischetti³

2007

J Bacteriol

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“…Second, for each position i in a regulatory site we assume there is a (generally unknown) set of four selection coefficients for the possible nucleotides at this position, which are constant through time and, in the limit of large time, lead to the set of equilibrium frequencies w ␣ i . Following Golding and Felsenstein (1990), Halpern and Bruno (1998) have shown that, in the weak mutation limit of the standard Kimura-Ohta theory, one can uniquely determine substitution rates in terms of the mutation rates and the equilibrium frequencies w ␣ i . In particular, if r ␣␤ i is the rate of substitution from ␤ to ␣ at position i, µ ␣␤ the rate of mutation from ␤ to ␣, and w ␣ i the equilibrium frequency of ␣ at this position, we have (Halpern and Bruno 1998) …”

Section: Evolutionary Modelmentioning

confidence: 99%

Universal patterns of purifying selection at noncoding positions in bacteria

Molina¹,

Nimwegen²

2007

Genome Res.

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To investigate the dependence of the number of regulatory sites per intergenic region on genome size, we developed a new method for detecting purifying selection at noncoding positions in clades of related bacterial genomes. We comprehensively quantified evidence of purifying selection at noncoding positions across bacteria and found several striking universal patterns. Consistent with selection acting at transcriptional regulatory elements near the transcription start, we find a universal positional profile of selection with respect to gene starts and ends, showing most evidence of selection immediately upstream and least immediately downstream from genes. A further set of universal features indicates that selection for translation initiation efficiency is the major determinant of the sequence composition around translation start in all clades. In addition to a peak in selection at ribosomal binding sites, the region immediately around translation start shows a universal pattern of high adenine frequency, significant selection at silent positions, and avoidance of RNA secondary structure. Surprisingly, although the number of transcription factors (TF) increases quadratically with genome size, we present several lines of evidence that small and large genomes have the same average number of regulatory sites per intergenic region. By comparing the sequence diversity of the most and least conserved DNA words in intergenic regions across clades we provide evidence that the structure of transcription regulatory networks changes dramatically with genome size: Small genomes have a small number of TFs with a large number of target sites, whereas large genomes have a large number of TFs with a small number of target sites each.

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“…The sequence used for comparison is rat Kv3, except for human Kv3.4b. Analysis by the parsimony method was performed using the PROTPARS program in the Phylogeny Inference Package (Golding and Felsenstein, 1990). The Drosophila Shaw K ϩ channel was used as the outgroup.…”

Section: Resultsmentioning

confidence: 99%

A C-Terminal Domain Directs Kv3.3 Channels to Dendrites

Deng¹,

Rashid²,

Fernandez³

et al. 2005

J. Neurosci.

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Pyramidal neurons of the electrosensory lateral line lobe (ELL) of Apteronotus leptorhynchus express Kv3-type voltage-gated potassium channels that give rise to high-threshold currents at the somatic and dendritic levels. Two members of the Kv3 channel family, AptKv3.1 and AptKv3.3, are coexpressed in these neurons. AptKv3.3 channels are expressed at uniformly high levels in each of four ELL segments, whereas AptKv3.1 channels appear to be expressed in a graded manner with higher levels of expression in segments that process high-frequency electrosensory signals. Immunohistochemical and recombinant channel expression studies show a differential distribution of these two channels in the dendrites of ELL pyramidal neurons. AptKv3.1 is concentrated in somas and proximal dendrites, whereas AptKv3.3 is distributed throughout the full extent of the large dendritic tree. Recombinant channel expression of AptKv3 channels through in vivo viral injections allowed directed retargeting of AptKv3 subtypes over the somadendritic axis, revealing that the sequence responsible for targeting channels to distal dendrites lies within the C-terminal domain of the AptKv3.3 protein. The targeting domain includes a consensus sequence predicted to bind to a PDZ (postsynaptic density-95/Discs large/zona occludens-1)-type protein-protein interaction motif. These findings reveal that different functional roles for Kv3 potassium channels at the somatic and dendritic level of a sensory neuron are attained through specific targeting that selectively distributes Kv3.3 channels to the dendritic compartment.

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A maximum likelihood approach to the detection of selection from a phylogeny

Cited by 51 publications

References 33 publications

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

First Complete Genome Sequence of TwoStaphylococcus epidermidisBacteriophages

Universal patterns of purifying selection at noncoding positions in bacteria

A C-Terminal Domain Directs Kv3.3 Channels to Dendrites

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