Classifications of the clinical forms of arterial hypertension (AH) are aimed at differentiating it on etiological grounds; we propose a classification that is based on the common pathogenesis of hydrodynamic pressure elevation in the intravascular pool of the intercellular medium, i.e. arterial blood pressure (BP). We believe that there are only three options for hydrodynamic pressure elevation in a mechanical model of the cardiovascular system: 1) a decrease in the volume of the arterial bed at a constant volume of intravascular fluid; 2) an increase in the volume of intravascular fluid at a constant volume of the vascular bed; and 3) increased blood flow resistance at constant volumes of the vascular bed and intravascular fluid. These options cover all clinical forms of AH in which AP increase is governed by common mechanisms. The first option can be related to AH occurring in pheochromoblastoma, glucocorticoid hyperproduction and psychoemotional stress. The second is associated with AH developing in excessive NaCl consumption with food, increased aldosterone production in Conn's syndrome (primary aldosteronism) and reduced production of atrial natriuretic peptide by phylogenetically modified myocytes of the right atrium. The third option can be linked to all forms of increased peripheral blood flow resistance in the arterial bed occurring in coarctation of the aorta, renovascular hypertension, impaired flow (endothelium)-dependent vasodilation and moderate spasm of muscular arterioles, arterial wall lesion in atherosclerosis, atheromatosis and atherothrombosis, Takayasu syndrome, and obliterating endarteritis. Elevation of BP in erythemia, under the effect of leukocyte colony-stimulating factor and after injection of a recombinant erythropoietin can also be regarded within the frames of the third option. From the viewpoint of general biology, all forms of AH developing against the background of impaired biological function of transcytosis (macropinocytosis) and crossing by food substrates and humoral mediators of bilayer structures between the common and local pools of the intercellular medium, i.e. blood-brain barrier can be referred to as a hematoencephalitic form. Arterial hypertension developing in impaired transcytosis across the blood-brain barrier (endothelium+ astrocytes bilayer), an encephalopathic form; endothelium+ podocytes bilayer, a renal form; endothelium+trophoblasts, placental AH; endothelium +/- pheumocytes, pulmonary AH; and endothelium+intimal macrophages, atherosclerosis-related AH. Normal AP points to: 1) the physiological level of transcytosis between all pools of the intercellular medium; 2) the absence of peripheral blood flow resistance in the arterial bed; 3) normal function of muscle arterioles; and 4) the physiological levels of metabolic processes in all paracrine cell communities in vivo.

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al.(1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.

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.

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.

The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.

A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program described can handle up to 100 sequences of 1200 residues each. The approach is based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. The results obtained using the package appear to be as sensitive as those from any other available method.