Musaespora,a genus of pyrenocarpous lichens with campylidia,and other additions to the foliicolous lichen flora of New Guinea

Abstract: The new lichen genus Musaespora is described from Java and Papua New Guinea. It is the first known pyrenocarpous lichen genus with campylidia, and appears to belong to the Aspidotheliaceae. Three species are described, two foliicolous species from Papua New Guinea and one corticolous species from Java. In addition, a list is given of the foliicolous lichen flora of the site in Papua New Guinea, where the foliicolous Musaespora species have been found, two more new foliicolous species are described, Echinoplaca hispida and Sporopodium lucidum, and 19 species are recorded for the first time form Papua New Guinea.     

ADDITIONS AND CORRECTIONS TO THE FOLIICOLOUS LICHEN FLORA OF COSTA RICA. THE FAMILY ARTHONIACEAE,WITH NOTES ON THE GENUSSTIRTONIA

The taxonomy of the foliicolous members of Arthoniaceae (Arthonia, Arthothelium, Cryptothecia, Ermothecella) in Costa Rica is revised.Cryptothecia farkasiaesp. nov. is described, being closely related toStirtonia sprucei, and bearing pycnidia reminiscent ofEremothecella. Arthonia lividofuscais placed in synonymy withA. aciniformis. Pycnidia and pycnospores are further described forArthonia leptosperma, A. cyanea, A. palmulacea, A. trilocularis, Arthothelium cingulatum, Stirtonia spruceiandS. macrocephala, and campylidia were found on thalli ofArthonia aciniformis. Arthonia nigratulaandCryptothecia candidaare reported for the first time from Costa Rica, and new localities are given for previously reported species. Ecological data are provided, and the relationships between foliicolous members of the Arthoniaceae are discussed.     

Neue Gattungen der FamilieLecideaceae s. lat. (Lichenes)

Six new genera are designated for the predominantly foliicolous specíes with hyaline, septate ascospores originally included in the artificial generaBacidia, Catillaria andLopadium. These areFellhanera gen. n. which, on the basis of ascus structure, belongs to the familyPilocarpaceae and includes 19 species, as well asBadimia gen. n. (6 species),Barubria gen. n. (1 species),Loflammia gen. n. (3 species),Calopadia gen. n. (6 species) andLogilvia gen. n. (1 species) which with the previously described generaLasioloma R. Sant. andTapellaria Müll. Arg. em.R. Sant. are classified in the familyEctolechiaceae as they are related toSporopodium Mont. The campylidia, special reproductive organs of the lichens concerned, are present in all members of the family. They are considered to be phylogenetically derived from apothecia. The conidia they produce vary in shape and structure and can be divided into different types, each of which is characteristic of a particular genus. The necessary new combinations are introduced in an appendix.     

ECOLOGY OF FOLIICOLOUS LICHENS AT THE ‘ BOTARRAMA ’ TRAIL (COSTA RICA), A NEOTROPICAL RAINFOREST. IV. SPECIES ASSOCIATIONS,THEIR SALIENT FEATURES AND THEIR DEPENDENCE ON ENVIRONMENTAL VARIABLES

A community ecology approach using an association of species test and a principal component analysis resulted in the recognition of two major and two minor foliicolous lichen communities in a neotropical rainforest. The major communities are governed by microclimatic factors, one characteristic of the shady understorey and the other confined to light gaps. The minor communities are due to subtle phorophyte preferences towards palm and dicot leaves. The shady understorey community is dominated by the families Arthoniaceae , Opegraphaceae , Trichotheliaceae and Pilocarpaceae , which predominantly have Phycopeltis as their phycobiont, thin thalli, abundant sexual reproduction, small ascospores produced in high numbers, and pycnidial conidiomata. The light-gap community is mainly composed of the families Gomphillaceae and Ectolechiaceae , with Trebouxia as their phycobiont, thickly crystalline or whitish, dispersed thalli, frequent asexual reproduction, large ascospores produced in low numbers, and specialized campylidia and hyphophores as conidiomata. Phycobiont, thallus structure, and the mode of reproduction are considered as adaptations to different microsites, whereas the shape and size of ascospores and conidia seem to be of less importance. The foliicolous lichen communities reflect the spatial and temporal structure of the forest, in particular the continuity of the shady understorey in comparison to the discontinuity of the light gaps. While the formation of the shady understorey community follows more deterministic patterns, the light-gap community exhibits high stochasticity.     

Chemistry,Anatomy and Morphology of Foliicolous Species of Fellhanera and Badimia (Lichenized Ascomycotina: Lecanorales)

A comparison of secondary chemistry and a variety of anatomical and morphological characters of Fellhanera and Badimia (Pilocarpaceae) has been conducted in an effort to clarify the systematic position of both genera. Based on our results we conclude that Fellhanera and Badimia are closely related and separated mainly by the slightly different paraphyses, amyloid reactions of their asci, apothecial size, and the presence or absence of campylidia. Fellhanera badimioides sp.n. is described, and the following systematic changes are proposed: Badimia cateilea (Vain.) comb.n. B. lecanorina (Zahlbr.) comb.n., B. tuckermanii (R.Sant.) comb.n. and Fellhanera stanhopeae (Müll. Arg.) comb.n.     

Establishing a Framework for a Natural Area Taxonomy

The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.     

On a stochastic version of a modified Nicholson-Baily model

‘Deterministic’ models in population dynamics often are really approximations to stochastic models, justified by an appeal to ‘the law of large numbers’. It is proposed to call such models ‘pseudodeterministic’. Four questions are discussed in this article: (1) What errors may be made by equating deterministically predicted values to expectations? (2) When, and in what sense, may numbers be assumed to be large? (3) How large are the variances, coefficients of variations, etc., as assigned to the variables in the stochastic versions of the models? (4) What role may pseudodeterministic models play in empirical research, where problems of statistical reliability arise? As an example, a modified Nicholson-Bailey model of the interaction between insect parasitoids and their hosts is discussed; the modification consists of assigning a random (density-independent) mortality to the parasitoid population. A stochastic version of this model is discussed. The expectation of the final host density is compared with the value computed from the deterministic model. The latter value is systematically lower than the former. The magnitude of the difference depends on parameter values. The variability to be expected with the stochastic model is characterized by the coefficient of variation of the final host density; its dependence on parameter values and initial conditions is discussed. It is concluded that it is worthwhile in practical applications to estimate parasitoid mortality, and that the coefficient of variation in real situations may be far from negligible.     

Biological function in a non-native partially folded state of a protein

As structural flexibility is known to be required for enzyme catalysis and pattern recognition and a significant fraction of eukaryotic proteins appear to be unfolded or contain unstructured regions, biological activity of conformational states distinct from fully folded structures could be more common than previously thought. By applying a procedure that allows the recovery of enzymatic activity to be monitored in real time, we show that a non-native state populated transiently during folding of the acylphosphatase from Sulfolobus solfataricus is enzymatically active. The structural characterization of this partially folded state reveals that enzymatic activity is possible even if the catalytic site is structurally heterogeneous, whereas the remainder of the structure acts as a scaffold. These results extend the spectrum of biological functions carried out in the absence of a folded state to include enzyme catalysis.     

Analysis of lateral diffusion from a spherical cell surface to a tubular projection.

Cell surfaces are often heterogeneous with respect to the lateral distribution and mobility of membrane components. Because lateral mobility is related to membrane structure, measurement of a particular component's local diffusion coefficient within a distinct surface region provides useful information about the formation and maintenance of that region. Many structurally interesting cell surface features can be described as narrow tubular projections from the body of the cell. In a companion paper, we consider the thin "tethers" that can be mechanically drawn from the red blood cell membrane, and we measure the transport of fluorescent integral proteins from the surface of the cell body onto the tether. In this paper we present an analysis to describe the surface diffusion of membrane particles from a spherical shell onto a thin cylindrical process. Provision is made for different rates of diffusion within the two morphologically distinct regions. The relative role of each region in controlling the diffusive flux between regions is determined primarily by a single dimensionless parameter. This parameter incorporates the ratio of the two diffusion coefficients as well as the dimensions of each region. The analysis can be applied to a fluorescence photobleaching experiment in which the extended process is bleached. If the dimensions of the spherical cell body and the cylindrical extension are known, then the diffusion coefficients of both regions can be determined from the experimental fluorescence recovery curve.     

Slow folding of a three-helix protein via a compact intermediate

The KIX domain of CREB binding protein (CBP) forms a small three-helix bundle which folds autonomously. Previous equilibrium unfolding experiments led to the suggestion that folding may not be strictly two-state. To investigate the folding mechanism in more detail, the folding kinetics of KIX have been studied by urea jump fluorescence-detected stopped-flow experiments. Clear evidence for an intermediate is obtained from the plot of the natural log of the observed rate constant versus denaturant concentration, the chevron plot, and from analysis of the initial fluorescence amplitudes of the stopped-flow experiments. The chevron plot exhibits a change in shape, rollover, at low denaturant concentrations, characteristic of the formation of an intermediate. The kinetic data can be fit to a three-state model involving a compact intermediate. An on-pathway model predicts that the position of the intermediate lies close to the native state. The folding rate in the absence of denaturant is 260 s(-)(1) at pH 7.5 and 25 degrees C. This is significantly slower than the rates of other helical proteins similar in size. The slow folding may be due to the necessity of forming a buried polar interaction in the native state. The potential functional significance of the folding intermediate is discussed.     

Rapid classification of a protein fold family using a statistical analysis of dipolar couplings

MOTIVATION: One of the primary aims of the structural genomics initiative is the determination of representative structures from each protein fold family. Given this objective, it is important to rapidly identify proteins that belong to a family that is already well populated (so they can be eliminated from further studies), or more importantly identify proteins that represent new families of fold. RESULTS: A method for rapid classification to a fold family by the statistical analyses of unassigned the (15)N-(1)H residual dipolar couplings is presented. The required NMR data can be quickly acquired and analyzed. Using this method, structure determination efforts can be focused on more unique and interesting structures, and the overall efficiency in the construction of an information-rich library can be increased.     

Refolding of a membrane protein in a microfluidics reactor

Membrane protein production for structural studies is often hindered by the formation of non-specific aggregates from which the protein has to be denatured and then refolded to a functional state. We developed a new approach, which uses microfluidics channels, to refold protein correctly in quantities sufficient for structural studies. Green fluorescent protein (GFP), a soluble protein, and bacteriorhodopsin (BR), a transmembrane protein, were used to demonstrate the efficiency of the process. Urea-denatured GFP refolded as the urea diffused away from the protein, forming in the channel a uniform fluorescent band when observed by confocal microscopy. Sodium dodecyl sulphate-denatured BR refolded within the channel on mixing with detergent–lipid mixed micelles. The refolding, monitored by absorbance spectroscopy, was found to be flow rate dependent. This potential of microfluidic reactors for screening protein-folding conditions and producing protein would be particularly amenable for high-throughput applications required in structural genomics. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Scraping a living: a review of littorinid grazing

Littorinid snails are predominantly herbivorous and the versatility of their radulae enables them to feed on a variety of macroscopic and microscopic plants in a diversity of habitats. Some are selective feeders preferring some species of algae to others, and rejecting some even after a prolonged period of starvation. Different species of snail exhibit different preferences. The factors affecting the attractiveness and edibility of food plants are discussed and food value considered.Foraging behaviour of littorinids is briefly reviewed in relation to the influence of chemical cues from the algae. Littorinids appear to be able to select or reject algae without having ingested them, having perceived the plants from a distance, moving towards favoured foods (or habitat-providing plants) and away from those that it rejects. The nature of the chemical cues emitted by the algae is discussed. Temporal patterns of foraging activity show some evidence of an endogenous component which can be overridden by responses to environmental conditions. These patterns place restraints on energy intake.The structural and chemical defences used by algae against littorinid grazing are considered. The importance of polyphenolic compounds is evaluated. The effects of grazing as a selective agency and a factor influencing algal populations are discussed. There is some evidence that life history patterns are a response to grazing. The influence of external physical factors, such as salinity on grazing pressure is demonstrated.Finally, the impact of littorinid snails on intertidal communities is assessed in relation to their abundance and biogeographical distribution. The relative importance of littorinids is contrasted on shores possessing or lacking limpets.     

Life as a planetary phenomenon

The success of recent spacecraft from the U.S.A. and the U.S.S.R. has given us a wealth of new data about the planets in our solar system. We can now develop a much better rationale for the reasons that abundant life is only found on our planet. Mars, smaller and more distant from the Sun, may nevertheless hold clues to the early development of Earth's atmosphere. The origin of life on Mars early in that planet's history cannot be ruled out. Titan offers a contemporary example of extremely primitive conditions, where chemical reactions resembling those that preceded the development of life on Earth may be occurring today. Venus and Jupiter illustrate the need for a planet to be the right size and the right distance from the sun if chemical evolution leading to the origin of life is to occur.     

A Coalescent Model for a Sweep of a Unique Standing Variant

The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical “hard sweep” hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite-alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep and multiple-mutation soft sweeps. We find that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps. Samples from multiple populations and/or time points have the potential to ease this difficulty.     

CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities.     

Coherent interaction of a relativistic electron beam with a plasma

Results are presented from experimental studies of the interaction of a modulated relativistic electron beam with a plasma. The electron energy spectra at the exit from the interaction chamber are measured for electron beams with energies of about 50 and 20 MeV. The coherent interaction of an electron beam with a microwave-driven plasma is studied. It is shown that, in strong electric fields that can be generated in the coherent interaction, the beam current is very sensitive to the phase of the microwave field.