Molecular phylogeny of siboglinid annelids (a.k.a. pogonophorans): a review

Siboglinid, or pogonophoran, annelids are tubicolous worms that rely on chemoautotrophic endosymbionts for nutrition. Three clades within the siboglinids are recognized: Frenulata, Vestimentifera, and Monilifera. As a group, these worms have received considerable attention from molecular phylogenetists. Most studies have focused either on the evolutionary origins of the group or on the relationships within vestimentiferans, which live at hydrocarbon seeps and hydrothermal vents. Here I review the literature to date on siboglinid molecular phylogeny and summarize the clade’s evolution. The vestimentiferans have been well studied, especially in the eastern Pacific. The seep taxon Lamellibrachia is basal in the clade with vent species being more derived. Recent studies of seeps are finding new species and suggest that habitat depth can be correlated with species boundaries. In contrast to the vestimentiferans, frenulate evolution has been poorly studied. Despite their greater apparent diversity, frenulate specimens have not been sampled so extensively, and thus little is known about their evolution. Sclerolinum, also referred to as Monilifera, is a recognized genus of siboglinids that forms the sister group to Vestimentifera. Like the frenulates, little is known about the history of this group. Our present understanding of siboglinid phylogeny has, in large part, been dictated by insufficient sampling effort.     

On a generalization of a result of W. G. Cochran

A relationship due to W.G. Cochran showing the effect on leastsquares regression coefficients of marginalizing over or conditioningon an explanatory variable is generalized to quantile regressioncoefficients. The condition under which conditioning does notinduce interaction or effect reversal is shown. Examples aregiven. The discussion is simplest when all variables are continuous;the extension to discrete variables is outlined.     

Design a questionnaire.

The design of questionnaires is a craft which has been badly neglected by the medical profession. A questionnaire should be appropriate, intelligible, unambiguous, unbiased, capable of coping with all possible responses, satisfactorily coded, piloted, and ethical. The key steps in designing a questionnaire are to: decide what data you need, select items for inclusion, design the individual questions, compose the wording, design the layout and presentation, think about coding, prepare the first draft and pretest, pilot, and evaluate the form, and perform the survey. Despite the apparently complicated nature of the task, theoretical knowledge is no substitute for practical experience.     

Biogenesis of a photosystem I light-harvesting complex. Evidence for a membrane intermediate.

CAB-7p is a chlorophyll a/b binding protein of photosystem I (PSI). It is found in light-harvesting complex I 680 (LHCI-680), one of the chlorophyll complexes produced by detergent solubilization of PSI. Two types of evidence are presented to indicate that assembly of CAB-7p into PSI proceeds through a membrane intermediate. First, when CAB-7p is briefly imported into chloroplasts or isolated thylakoids, we initially observe a fast-migrating membrane form of CAB-7p that is subsequently converted into PSI. The conversion of the fast-migrating form into PSI does not require stroma or ATP. Second, trypsin treatment of thylakoids containing radiolabeled CAB-7p indicates that there are at least two membrane forms of the mature 23-kD protein. The predominant form is completely resistant to proteolysis; a second form of the protein is cleaved by trypsin into 12- and 7-kD polypeptides. We interpret this to mean that the intermediate is a cleavable form that becomes protease resistant during assembly. This notion is supported by the observation that CAB-7p in LHCI-680 is largely cleaved by trypsin into 12- and 7-kD polypeptides, whereas CAB-7p in isolated PSI particles is trypsin resistant. In vitro, we generated a mutant form of CAB-7p, CAB-7/BgI2p, that was able to integrate into thylakoid membranes but was unable to assemble into PSI. The membrane form of CAB-7/BgI2p, like LHCI-680, was predominantly cleaved by trypsin into 12- and 7-kD fragments. We suggest that the mutant protein is arrested at an intermediate stage in the assembly pathway of PSI. Based on its mobility in nondenaturing gels and its susceptibility to protease cleavage, we suggest that the intermediate form is LHCI-680. We propose the following distinct stages in the biogenesis of LHCI: (a) apoprotein is integrated into the thylakoid, (b) chlorophyll is rapidly bound to apoprotein forming LHCI-680, and (c) LHCI-680 assembles into the native PSI complex.     

Topographic anatomical data on the a.testicularis, a.ductus deferentis and a.cremasterica in ram

130 Ram testes have been used in the study, and the following methods were applied to fill and study the testical arteries: r?ntgenography, stereor?ntgenography, corosive method, Indian ink and gel injections. Variabilities occur as to the site where the a.testicularis arises in rams. Individual differences can also be observed in the arrangement of the epididymal arteries, in most cases, however, they arise from the first loops of the convolution. Both epididymal arteries are considerably thinner than the testicular artery, forming 2 independent vessel convolutions, located at both sides of the convolution of the a.testicularis, and not interfering with the loops of the latter. A.accessoria testis has been found in one ram only. 2 to 3 large waved loops can be observed in the pars marginalis and the a.testicularis of the ram. Bifurcation mostly occurs in the second third of the margo epididymidis. Individual variations have been found at further ramification of the rr.testiculares. The shape of the lobulus testis is indicated by the centripetal branch with its centrifugal twigs. In rams the a.ductus deferentis forms anastomoses both with the branches running from the a.epididymidis caudalis and the a.cremasterica.     

FlyBase: a Drosophila database. Flybase Consortium.

FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references.     

Becoming a face expert.

Young children do not form representations of newly encountered faces as efficiently as do adults. A first step in explaining this difference, like any age-related change, is locating its source. A major source of the improvement is acquisition of knowledge of faces per se, as opposed to age-related changes in general pattern encoding or memorial skills. Two consequences of expertise at individualizing members of classes that share a basic configuration are known: a large inversion effect and a caricature advantage. It is possible that both of these effects reflect increased reliance, with expertise, on configuration distinguishing features. Several phenomena that indicate that inversion interferes with the encoding of configural aspects of faces are reviewed. Finally, developmental data are presented that confirm the suspicion that there are at least two distinct sources of the vulnerability of face encoding to inversion, perhaps reflecting two distinct senses of 'configural encoding' of faces, only one of which is implicated in adult expertise at face encoding.     

Theodoropoulos, D.I. Invasion biology. Critique of a pseudoscience.

The back cover of this book states that ‘contrary to theclaims of the nativists, research shows that man-dispersed speciesincrease biological diversity, benefit ecosystems, and act asan important force for healing the planet’. This is anuncompromising statement, and David Theodoropoulos divides hisdevelopment of the arguments supporting this statement intothree parts. Part I (Chapters 1–6) is ‘Nature, Dispersaland Reaction’. Part II (Chapters 7 and 8) is ‘Why?Psychology, Politics and Pseudoscience’. Part III (Chapters9–11) is ‘Humanity and Diversity’. There isalso an ‘Introduction’ including a summary of findingsand ‘An outline for a new theory of anthropogenic dispersal’,     

Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium

A new chemolithotrophic nitrite-oxidizing bacterium, for which the name Nitrospira marina is proposed, was isolated from the Gulf of Maine. N. marina is a Gramnegative curved rod which may form spirals with 1 to 12 turns. Cells have a unique periplasmic space and lack intracytoplasmic membranes and carboxysomes. N. marina is an obligate chemolithotroph, but best growth is obtained in a mixotrophic medium. N. marina may be one of the most prevalent nitrite-oxidizing bacteria in some oceanic environments. Type strain is field with American Type Culture Collection (ATCC 43039).     

Interruption-deficient mutants of bacteriophage T5. II. Properties of a mutant lacking a specific interruption.

An examination was made of the properties of T5HA4, a mutant of bacteriophage T5 that lacks the single-chain interruption that occurs at 7.9% from the left end of the genome. The DNAs of T5HA4 and the wild type were compared by electrophoresis in agarose gels of both single-stranded fragments produced by denaturation and duplex fragments generated by sequential treatment with exonuclease III and SI nuclease. These studies demonstrated that T5HA4 also lacks an interruption that occurs at 99.6% in wild-type DNA. The interruptions at 7.9 and 99.6% therefore occur within the 8.3% of T5 DNA that is terminally repetitious. Evidence on the location of other interruptions within the terminal repetition was also obtained. Analysis of T5HA4 with a restriction endonuclease indicated that the interruption deficiency is not due to a deletion or addition mutation. The injection of T5HA4 DNA into a host bacterium was found to occur, as with the wild type, in a two-step manner. The interruption at 7.9% is therefore not required for stopping DNA transfer after the initial 8% segment has been injected.     

Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes

While a large number of aerobic free-living protists have been described within the last decade, the number of new anaerobic or microaerophilic microbial eukaryotic taxa has lagged behind. Here we describe a microaerophilic genus and species of amoeboflagellate isolated from a near-shore marine site off the coast at Plymouth, Massachusetts: Subulatomonas tetraspora nov. gen. nov. sp. This taxon is closely related to Breviata anathema based on both microscopical features and phylogenetic analyses of sequences of three genes: SSU-rDNA, actin, and alpha-tubulin. However, Subulatomonas tetraspora nov. gen. nov. sp. and B. anathema are morphologically distinctive, differ by 14.9% at their SSU-rDNA locus, and were isolated from marine and 'slightly brackish' environments, respectively. Phylogenetic analyses of these two taxa plus closely related sequences from environmental surveys provide support for a novel clade of eukaryotes that is distinct from the major clades including the Opisthokonta, Excavata, Amoebozoa and 'SAR' (Stramenopile, Alveolate, Rhizaria).     

Gulose as a constituent of a glycoprotein.

The aldohexose gulose was identified as a constituent of a hydroxyproline-rich glycopeptide derived from the glycoprotein SSG 185. This glycoprotein is part of the extracellular matrix of the green alga Volvox carteri. The gulose residue occupies a terminal position in the corresponding saccharide.     

From a phylogenetic tree to a reticulated network.

In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.     

Metarhizium frigidum sp. nov.: a cryptic species of M. anisopliae and a member of the M. flavoviride complex

The anamorph genus Metarhizium is composed of arthropod pathogens, several with broad geographic and host ranges. Members of the genus, including "M. anisopliae var. frigidum" nomen nudum and Metarhizium flavoviride, have been used as biological insecticides. In a recent revision of the genus the variety "M. anisopliae var. frigidum" was suggested to be a synonym of M. flavoviride based largely on ITS sequence phylogenetic analysis. In this study we conducted morphological evaluations and multigene phylogenetic analyses with EF-1alpha, RPB1 and RPB2 for strains of M. flavoviride and "M. anisopliae var. frigidum." Included in these evaluations were the ex-type of M. flavoviride var. flavoviride and what likely would be considered the "ex-type' of the invalidly published taxon "M. anisopliae var. frigidum". Based on morphological and molecular evidence we conclude that "M. anisopliae var. frigidum" is distinct from M. flavoviride and the taxon M. frigidum sp. nov. is described.     

Thermal enzymes. III. Apyrase from a thermophilic Bacterium

An enzyme, apyrase, obtained from thermophile No. 2184 possesses heat stability at 65 °C., the temperature preferred by the organism for growth.Apyrase from the thermophile has an activation energy of 9600 cal./ mole. Its Michaelis constant is 0.00065 at 60 °C. The enzyme is inhibited by fluoride, citrate, and copper, but is activated by magnesium.Apyrase from a mesophilic bacterium, although possessing a fair amount of stability in the presence of substrate, does not have the resistance to heat possessed by the thermophile enzyme.The apyrase from potato is inactivated readily on heating in the absence of adenosine triphosphate.     

Towards a biomolecular computer.

A new version of computing and information processing devices may result from major principles of information processing at molecular level. Non-discrete biomolecular computers based on these principles seems to be capable of solving problems of high computational complexity. One of the possible ways to implement these devices is based on biochemical non-linear dynamical systems. Means and ways to materialize biomolecular computers are discussed.