Molecular phylogeny and proposed classification of the simian picornaviruses.

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the Enterovirus genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in Picornaviridae. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.     

Molecular phylogeny of methanogens associated with flagellated protists in the gut and with the gut epithelium of termites

The molecular phylogeny of methanogenic archaea associated with the flagellated protist species Dinenympha and Microjoenia in the gut of termites, Reticulitermes speratus and Hodotermopsis sjoestedti, and those attached to the gut epithelium was examined based on PCR-amplified small-subunit ribosomal RNA genes. The sequences identified were classified into six groups within the genus Methanobrevibacter, including groups of yet uncharacterized novel species. Closely related methanogens were shared between Microjoenia and some Dinenympha cells in each termite. The methanogens harbored by the flagellates were phylogenetically different from the methanogens associated with the gut epithelium, suggesting that distinct methanogen species showed distinct spatial distributions in the termite gut.     

Hydrodynamic theory of swimming of flagellated microorganisms.

A theory of the type commonly used in polymer hydrodynamics is developed to calculate swimming properties of flagellated microorganisms. The overall shape of the particle is modeled as an array of spherical beads which act, at the same time, as frictional elements. The fluid velocity field is obtained as a function of the forces acting at each bead through Oseen-type, hydrodynamic interaction tensors. From the force and torque equilibrium conditions, such quantities as swimming velocity, angular velocity, and efficiency can be calculated. Application is made to a spherical body propelled by a helical flagellum. A recent theory by Lighthill, and earlier formulations based on tangential and normal frictional coefficients of a curved cylinder, CT and CN, are analyzed along with our theory. Although all the theories predict similar qualitative characteristics, such as optimal efficiency and the effect of fluid viscosity, they lead to rather different numerical values. In agreement with Lighthill, we found the formalisms based on CN and CT coefficients to be somewhat inaccurate, and head-flagellum interactions are shown to play an important role.     

Motility of flagellated bacteria in viscous environments.

The lowest viscosity that immobilized flagellated bacteria such as Psedomonas aeruginosa, Spirillum serpens, and Escherichia coli was 60 centipoise (cp). Much higher viscosities (1,000 cp and higher) were required to immobilize two flagellated bacteria selectively isolated from nature by methods based on their ability to migrate through agar gels. The latter finding indicates that certain flagellated bacteria have the ability to swim through environments of relatively high viscosity. It is suggested that these flagellated bacteria possess a specialized type of motility apparatus suited to viscous conditions present in their habitats.     

Obligate amoebae of the protostelids: significance for the concept of Eumycetozoa

Most flagellate Eumycetozoa have a non-flagellate, or obligately amoeboid, trophic state which differentiates from the amoebo-flagellate state and gives rise to the fruiting body. This study examines the morphology, general ultrastructure, and microtubular systems of the obligate amoebae of three flagellate protostelids with typical amoebo-flagellate states. The obligate amoebae of all three species are morphologically distinct indicating that the obligately amoeboid state has evolved independently in the history of each species. Therefore, obligate amoebae may be useful for defining separate evolutionary groups within the Eumycetozoa.     

Adsorption kinetics of laterally and polarly flagellated Vibrio.

The adsorption of laterally and polarly flagellated bacteria to chitin was measured, and from the data obtained, a modified Langmuir adsorption isotherm was derived. Results indicated that the adsorption of laterally flagellated Vibrio parahaemolyticus follows the Langmuir adsorption isotherm, a type of adsorption referred to as surface saturation kinetics, when conditions are favorable for the production of lateral flagella. When conditions were not favorable for the production of lateral flagella, bacterial adsorption did not follow the Langmuir adsorption isotherm; instead, proportional adsorption kinetics were observed. The adsorption of some polarly flagellated bacteria exhibited surface saturation kinetics. However, the binding index (the product of the number of binding sites and bacterial affinity to the surface) of polarly flagellated bacteria differed significantly from that of laterally flagellated bacteria, suggesting that polarly flagellated bacteria adsorb to chitin by a different mechanism from that used by the laterally flagellated bacteria. From the results of dual-label adsorption competition experiments, in which polarly flagellated V. cholerae competed with increasing concentrations of laterally flagellated V. parahaemolyticus, it was observed that laterally flagellated bacteria inhibited the adsorption of polarly flagellated bacteria. In contrast, polarly flagellated bacteria enhanced the adsorption of V. cholerae. In competition experiments, where V. parahaemolyticus competed against increasing concentrations of other bacteria, polarly flagellated bacteria enhanced V. parahaemolyticus adsorption significantly, whereas laterally flagellated bacteria only slightly enhanced the process. The direct correlation observed between surface saturation kinetics, the production of lateral flagella, and the ability of laterally flagellated bacteria to inhibit the adsorption of polarly flagellated bacteria suggests that lateral flagella represent a component of bacterial structure that is important in the adsorption of laterally flagellated bacteria to surfaces. A model for adsorption events of laterally flagellated bacteria is proposed, based on the evidence presented.     

On the TPPP-like proteins of flagellated fungi

TPPP-like proteins, exhibiting microtubule stabilizing function, constitute a eukaryotic superfamily, characterized by the presence of the p25alpha domain. TPPPs in the strict sense are present in animals except Trichoplax adhaerens, which instead contains apicortin where a part of the p25alpha domain is combined with a DCX domain. Apicortin is absent in other animals and occurs mostly in the protozoan phylum, Apicomplexa. A strong correlation between the occurrence of p25alpha domain and that of the eukaryotic cilium/flagellum was suggested. Species of the deeper branching clades of Fungi possess flagellum but others lost it thus investigation of fungal genomes can help testing of this suggestion. Indeed, these proteins are present in early branching Fungi. Both TPPP and apicortin are present in Rozellomycota (Cryptomycota) and Chytridiomycota, TPPP in Blastocladiomycota, apicortin in Neocallimastigomycota, Monoblepharomycota and the non-flagellated Mucoromycota. Beside the “normal” TPPP occurring in animals, a special, fungal-type TPPP is also present in Fungi, in which a part of the p25alpha domain is duplicated. Dikarya, the most developed subkingdom of Fungi, lacks both flagellum and TPPPs. Thus it is strengthened that each ciliated/flagellated organism contains p25alpha domain-containing proteins while there are very few non-flagellated ones where p25alpha domain can be found.     

A nuclear DNA phylogeny and proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae)

The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus , Phyllastrephus and Chlorocichla . We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus , Thescelocichla, Baeopogon and Chlorocichla , although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A . importunus and A . gracilirostris , which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love ( Pyrrhurus scandens ) is placed within Phyllastrephus . We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.     

Photosensory transduction in the flagellated alga,Euglena gracilis

Euglena were cultured under 3 W m^-2 constant white light. In culture medium, cells show immediate and long lasting step-down photophobic responses and photoaccumulation behavior to blue light if dim red light-adapted for 30 min. However, if cells are suspended in buffered, saltcontaining solutions (adaptation buffers), strong step-down photobehavior and photoaccumulation responses are not observed for several hours. These behaviors gradually increase in strength to reach a maximum after 6–12 h; after which a stable response is maintained. The relative rates of appearance and the relative strengths of the responses are influenced by the concentrations of Ca²⁺ and K⁺, but not H⁺ or Na⁺ ions, in the adaptation buffers. Expression of the stepdown photobehavior thus requires that the cells adapt to the chemical environment in which they are suspended.Abbreviations Hepes N-2-hydroxypiperazine-N-2-ethanesulfonic acid - Mes 2(N-morpholino)-ethanesulfonic acid - Pipes piperazine-N,N-bis (2-ethanesulfonic acid) - Taps tris(hydroxymethyl) methylaminopropanesulfonic acid This work was supported, in part, by grant No. PCM-79-05320 from the U.S. National Science Foundation to B.D.     

Ultrastructural studies of protostelids: The cyst stage ofCavostelium bisporum

Summary The ultrastructure of encystment stages in the flagellate protostelidCavostelium bisporum was studied with sectioned material fixed in sequential glutaraldehyde-OsO₄.Major features of encystment were (1) intensive release of vesicles via the plasmalemma, (2) deposition just exterior to the plasmalemma of membranous structures similar to the latter, (3) disappearance of food vacuoles with their concentrically lamellate, membranous residues, and (4) alterations in the complex of kinetosomes, microtubules, and Golgi apparatus that characterizes the flagellate stage. In view of the possible phylogenetic origin of myxomycetes from the protostelids, the ultrastructure of encystment in the two groups is compared.Supported by U.S. National Science Foundation, Grant GB-7392.Partially supported by FundaÇÃo de Amparo à Pesquisa, SÃo Paulo, Brasil.     

A strategy for sequence phylogeny research.

Minimal mutation trees, and almost minimal trees, are constructed from two data sets, one of phenylalanine tRNA sequences, and the other of 5S RNA sequences, from a diverse range of organisms. The two sets of results are mutually consistent. Trees representing previous evolutionary hypotheses are compared using a total weighted mutational distance criterion. The importance of sequence data from relatively little-studed phylogenetic lines is stressed. A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods.     

A proposed nomenclature for bile acids.

A proposal is made for a system of nomenclature of the more common unconjugated and conjugated bile acids. Acceptable trivial names for bile acids are tabulated, and guidelines are proposed for using these existing trivial names as roots to create acceptable semi-systematic names for other bile acids, as well as for new natural bile acids that will be discovered in the future. The term alpha-hyocholic is recommended to replace hyocholic, and beta-hyocholic to replace omega-muricholic. The term murideoxycholic acid is recommended for 3 alpha,6 beta-dihydroxy-5 beta-cholan-24-oic acid. Proposals are also made for bile acids with epimeric hydroxy groups, for unsaturated bile acids, and for bile acids with oxo- and/or hydroxy-oxo- substituents on the nucleus and/or on the side chain. For conjugated bile acids, the term "aminoacyl amidates" is recommended to replace "amidates" for bile acids conjugated in N-acyl linkage with amino acids. Nomenclature for other types of conjugates (sulfates, glucuronides, glucosides) is included as well as abbreviations. It is recommended that the historic tradition of naming a newly discovered bile acid after the species from which it was isolated be abandoned, and that in the future such a bile acid should be named using the principles contained in this paper.     

Adsorption of polarly flagellated bacteria to surfaces

Studies have been made of the initial stages in adsorption of several polarly flagellated marine bacteria to glass surfaces. Bacteria attach at the pole of flagellar insertion, and after a brief period (from a few seconds to a few minutes) of rotation around the attachment axis, become immobile. Soma do not spin or gyrate while the organisms rotate slowly. Flagellar activity continues for several minutes after soma immobilization. Tween 80 inhibits bacterial attachment, and deflagellated organisms do not adsorb to glass. Bacteria rendered nonmotile with sodium azide (NaN₃) rapidly adsorb to glass and cannot be removed by washing with artificial seawater or a solution of 2.4% NaCl. It is proposed that both flagella-surface and somasurface interactions are involved in bacterial attachment. Bacterial flagella may play an important ecological role as attachment organelles.     

A detailed phylogeny for the Methanomicrobiales

The small subunit rRNA sequence of twenty archaea, members of the Methanomicrobiales, permits a detailed phylogenetic tree to be inferred for the group. The tree confirms earlier studies, based on far fewer sequences, in showing the group to be divided into two major clusters, temporarily designated the "methanosarcina" group and the "methanogenium" group. The tree also defines phylogenetic relationships within these two groups, which in some cases do not agree with the phylogenetic relationships implied by current taxonomic names--a problem most acute for the genus Methanogenium and its relatives. The present phylogenetic characterization provides the basis for a consistent taxonomic restructuring of this major methanogenic taxon.