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

The relationship of carbohydrate metabolism to protein metabolism. IV. The effect of substituting fat for dietary carbohydrate.

Publisher Summary This chapter discusses structure and biosynthesis of human placental peptide hormones. Most studies have centered on chorionic gonadotropin (hCG) and placental lactogen (WL), but there is also evidence of a chorionic thyrotropin (hCT) and a chorionic follicle-stimulating hormone (hCFSH), though these have been much less extensively explored. Reports have also been published suggesting the synthesis by the placenta of an ACTH, a melanocyte-stimulating hormone, relaxin, oxytocin, vasopressin, and renin, all analogous to the corresponding peptide hormones formed elsewhere by nonpregnant subjects. In addition to these hormonally active peptides, the placenta secretes into the plasma a placenta-specific heat-stable alkaline phosphatase and a series of other proteins (globulins) found only in the blood of pregnant women. Several of these plasma globulins have been shown by immunofluorescence to be present in high concentration in the syncytiotrophoblast of the human placenta. The chapter deals mainly with human chorionic gonadotropin and human placental lactogen, and briefly discusses the evidence regarding other proteins secreted by the placenta.

Structure and biosynthesis of human placental peptide hormones.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/4AAC6DDAA5619893A18E2746CB9ED5D8/S0029665160000177a.pdf/div-class-title-the-nutritional-regulation-of-ribonucleic-acid-metabolism-in-the-liver-cell-div.pdf

The nutritional regulation of ribonucleic-acid metabolism in the liver cell.

— It has previously been shown that the disaggregation of brain polysomes and suppression of brain protein synthesis observed in rats given the amino acids l-dopa or l-5-HTP is mediated by the decarboxylation products dopamine and serotonin. Present studies demonstrate that the poly-some disaggregation is caused by the interactions of the monoamines with specific receptor sites. Thus, dopa-induced disaggregation is blocked if rats are pretreated with haloperidol or pimozide (but not methysergide or cyproheptadine), while 5-HTP-induced disaggregation is blocked by methysergide or cyproheptadine (but not by haloperidol or pimozide).



Pretreatment of rats with MK-486, a drug that inhibits dopa decarboxylase in blood vessels and peripheral tissues but not brain, does not block dopa-induced brain polysome disaggregation; hence this disaggregation depends on the interaction of dopamine with receptors in the brain parenchyma. Brain polysomes are not disaggregated in rats given intraperitoneal apomorphine (or intracisternal dopamine). The disaggregation caused by dopa is not reduced in animals pretreated with sufficient intracisternal 6-hydroxydopamine to cause major damage to catecholaminergic nerve terminals.

Participation of dopamine- and serotonin- receptors in the disaggregation of brain polysomes by L-dopa and L-5-HTP.

Munro and Mukerji1 observed that the feeding of single large doses of certain individual amino-acids, notably glycine, methionine and leucine, caused a marked stimulation of uptake of phosphorus-32 by rat-liver ribonucleic acid (RNA) during the next 18 h. In the case of methionine and leucine, but not of glycine, this action was abolished by adrenalectomy2. It was therefore proposed that the increased incorporation of phosphorus-32 into liver RNA after feeding methionine or leucine was due to release of adrenocortical hormones, which are known to induce changes in liver RNA metabolism3. The experiments reported here show that, within a 24-h period of administering methionine or leucine to rats, there is an elevation of blood corticosterone-level. Administration of other amino-acids or of casein does not have this effect. These observations would thus appear to confirm the proposed mechanism of action of methionine and leucine on liver RNA metabolism.

Hamish N. Munro

Papers

The relationship of carbohydrate metabolism to protein metabolism. IV. The effect of substituting fat for dietary carbohydrate.

Structure and biosynthesis of human placental peptide hormones.

The nutritional regulation of ribonucleic-acid metabolism in the liver cell.

Participation of dopamine- and serotonin- receptors in the disaggregation of brain polysomes by L-dopa and L-5-HTP.

Blood corticosterone levels in the rat after administration of amino acids.