Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.

/pdf/modeltest-testing-the-model-of-dna-substitution-2dmippvvyz.pdf

MODELTEST: testing the model of DNA substitution.

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

https://www.zora.uzh.ch/id/eprint/155669/1/ZORA_NL_155669.pdf

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.

16S ribosomal DNA amplification for phylogenetic study.

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

/pdf/jmodeltest-phylogenetic-model-averaging-4hpp3p5d0f.pdf

jModelTest: Phylogenetic Model Averaging

Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282--283, Bioinformatics, 18, 77--82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.

Availability: http://cd-hit.org

Contact: [email protected]

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

https://www.kidney-international.org/article/S0085-2538(15)31966-9/pdf

Energy and protein intakes as determinants of nitrogen balance.

THE inhibition of protein synthesis by cycloheximide seems to occur at some stage later than the formation of aminoacyl-tRNA and its subsequent transfer to the ribosome1. Studies of the action of cycloheximide on intact cells2,3 have led to the proposal that the inhibitor has two sites of action at the ribosome level, one involving chain initiation and the other chain elongation. Using a cell-free protein-synthesizing system, we4 have observed that cycloheximide can inhibit polysome aggregation in much smaller doses than are needed to prevent chain elongation. With this system, we also observed that the action of the inhibitor on chain elongation could be partially reversed by adding high concentrations of glutathione to the incubation medium. This communication presents evidence that the site of this action of cycloheximide and its reversal by glutathione is the sulphydryl-dependent enzyme transferase II. Skogerson and Moldave5 have suggested that transferase II is identical with translocase, an enzyme responsible for transferring the peptidyl-tRNA from the acceptor to the peptidyl site on the ribosome, with concomitant hydrolysis of GTP. We have now demonstrated that this specific hydrolysis of GTP is inhibited by cycloheximide, and that this effect can also be partially reversed by raising the concentration of glutathione in the medium.

In vitro Inhibition of Peptide Synthesis and GTP Hydrolysis by Cycloheximide and Reversal of Inhibition by Glutathione

Eighteen placentas from a middle-class North American urban population (Boston) and 20 placentas from a Central American urban population of low socioeconomic status (Guatemala) were examined by morphometric techniques including an image quantizer. Placental mass was 14% less in the Guatemalan group. Total mass of peripheral villi was decreased 24% with a proportional reduction in trophoblast mass; on the other hand the mass of the stem villi was only 5% less than in Boston. Villous and capillary surfaces of the peripheral villi were reduced 22% and 38% respectively in the Guatemalan group while stem villous surfaces and capillary surfaces were actually increased 20% and 40% respectively. No significant differences were found in the cross-sectional areas of villi in the two populations. Because of this similarity of dimensions of average villi in the two groups the reduction in villous mass and surface areas could only be attributed to a decreased number of villi in the Guatemalan group. Perivillous fibrin was unexpectedly prominent in the Guatemalan placentas and was often associated with mononuclear infiltration suggesting parenchymal placental disease. (excerpt)

Comparison of placentas from two socioeconomic groups. I. Morphometry.

Isolation and quantitation of Nτ-methylhistidine in actin and myosin of rat skeletal muscle: Use of pyridine elution of protein hydrolysates on ion-exchange resins

Ferritin has a protein shell of 5 X 10(6) Da consisting of 24 subunits of two types, a heavier (H) chain of 21,000 Da and a lighter (L) chain of 19,000 Da. A cDNA clone of the messenger for the L subunit has been isolated from a human monocyte-like leukemia cell line. The clone contains an open reading frame of 522 nucleotides coding for an amino acid sequence matching 97% of the published sequence of human liver ferritin L subunit determined by sequenator, but it corresponds to only 55% of the reported amino acid sequence of a human liver H-subunit clone. Nevertheless, computer analysis of the subunit conformations predicted from the open reading frames of the L and H clones shows that most of the amino acid differences are conservative and would allow both subunits to form the five alpha-helices and beta-turns established by x-ray crystallography for horse spleen ferritin subunits. This suggests that L and H subunits are structurally interchangeable in forming an apoferritin shell. The 5' untranslated region of our human ferritin L clone has considerable homology with that of the rat liver ferritin L clone in the region immediately upstream from the initiator codon, notably showing an identical sequence of 10 nucleotides at the same position in both subunit clones that may participate in regulating the known activation of ferritin mRNA after iron administration. Extensive homology, including several blocks of nucleotides, was identified between the 3' untranslated regions of the human and rat L clones. The common structural features of the H and L subunits lead us to conclude that they have diverged from a single ancestral gene.

http://www.pnas.org/content/82/10/3139.full.pdf

Hamish N. Munro

Papers

Energy and protein intakes as determinants of nitrogen balance.

In vitro Inhibition of Peptide Synthesis and GTP Hydrolysis by Cycloheximide and Reversal of Inhibition by Glutathione

Comparison of placentas from two socioeconomic groups. I. Morphometry.

Isolation and quantitation of Nτ-methylhistidine in actin and myosin of rat skeletal muscle: Use of pyridine elution of protein hydrolysates on ion-exchange resins

Structure of human ferritin light subunit messenger RNA: comparison with heavy subunit message and functional implications.