Helix-coiled transition in heteropolymers. I. Ground-state energy

A new technique is presented for treating the ground state of an heteropolymer with a random sequence of components. An exact system of equations is found for determining the ground state energy E which is equal to the polymer free energy f in the lowest-order approximation in T/V (V/2 is the large “surface” energy arising at the boundaries between coiled and “helical” sections: V ? T, U_k; U₁ and –U₂ are the free energies of the components counted from the corresponding coiled state energies). These equations are essentially simplified at certain fixed values of the ratio U₁/U₂. For integer values of U₂/U₁ and U₁/U₂ a solution is obtained with an accuracy exp(–V/U_k). The ground-state energy as a function of U₁ and U₂ is shown to be highly irregular: its derivatives have jumps at an infinite number of points. These jumps provide a fine structure of the melting curves. A smoothed over the jumps function E′ is found by way of analytic continuation from the integer values of U₁/U₂ and U₂/U₁. The accuracy of the approximation f ≈ E is estimated and the correctional term of order T/V is determined.     

Seed morphology of Erica L. sect. Loxomeria Salisb. ex Benth., sect. Eremocallis Salisb. ex Benth. and sect. Brachycallis I. Hansen,and its systematic implications

Abstract

Several quantitative and qualitative seed characters of the seven European species of Erica sect. Loxomeria, Eremocallis and Brachycallis were studied. Two main seed types are found based on size and shape: regular ellipsoid or oblong seeds of ca. 0.4 mm for E. ciliaris and the E. tetralix group, and curved to kidney‐shaped seeds of 0.6–0.9 mm for E. cinerea, E. maderensis and E. terminalis. The testa surface in E. ciliaris is reticulate, with indented outer periclinal walls. Erica cinerea has inflated outer anticlinal walls. This character is exclusive for this species within the European (and nearby areas) species of the genus. The seeds of E. maderensis are similar to those of E. terminalis. According to seed morphology, the classical infrageneric classification, by which E. terminalis would be grouped with the E. tetralix group in sect. Eremocallis and E. maderensis in sect. Brachycallis with E. cinerea, is artificial.     

Haplodontium zangii X.R.Wang & J.C.Zhao,sp. nov. (Bryaceae,Bryopsida) from Xizang,China

Haplodontium zangii X.R.Wang &; J.C.Zhao, a new moss species from Xizang, China, is described and illustrated. Previously, specimens of H. zangii have been identified as Mielichhoferia himalayana Mitt. However, H. zangii is distinctly different from M. himalayana in having excurrent costae with short awns (vs long denticulate awns), short-pyriform capsules, 0.8–1?mm (vs long-pyriform capsules, 2.5–3?mm), and densely papillose exostome teeth (vs smooth or vertically striped exostome teeth). Haplodontium zangii is similar to H. macrocarpum (Hook.) J.R.Spence, which was traditionally placed in Mielichhoferia Nees &; Hornsch. as M. macrocarpa (Hook.) Bruch &; Schimp. The main differences between H. zangii and H. macrocarpum are in the morphology of the leaves, capsules, guide cells, and stomata. Mielichhoferia himalayana and another Chinese species of Mielichhoferia, M. sinensis Dix., are also transferred to Haplodontium Hampe, a new genus in the bryoflora of China, as H. himalayanum (Mitt.) X.R.Wang &; J.C.Zhao and H. sinensis (Dix.) X.R.Wang &; J.C.Zhao. A morphological comparison and a key to the three species of Haplodontium in China as well as to H. macrocarpum, a species that is likely to be found in China, are provided.     

Opalinidae in African Anura. II. Genera Protozelleriella n. g. and Zelleriella

During 1988 and 1989, 409 specimens of southern African Anura, comprising 50 species in 9 families, were checked for opalinids in the cloaca. Protozelleriella devilliersi n. g., n. sp. was found in three of four Capensibufo rosei (Bufonidae); Zelleriella africana Sandon, 1938 in two of three Bufo angusticeps and one of 20 B. garmani (Bufonidae) plus three of 12 Phrynobatrachus natalensis, 12 of 19 Tomopterna cryptotis, seven of 14 T. delalandii, three of seven T. krugerensis and one of six T. natalensis (all Ranidae); Z. gambieri n. sp. in one of six T. natalensis; Z. garlandi n. sp. in two of six Kassina maculata (Hyperoliidae); Z. sandoni n. sp. in two of 20 B. garmani, two of six K. maculata, one of seven K. senegalensis and one of four Leptopelis mossambicus (Hyperoliidae) plus one of five Phrynomerus bifasciatus (Microhylidae) and two of 19 T. cryptotis. It is suggested that the Ranidae (in particular the genus Tomopterna) and the Hyperoliidae are among the major carriers of Zelleriella in the Afrotropical Region.     

Plagiochila atlantica F. Rose,sp. nov.—P. amhagiosa auct.

Abstract

The Irish plant which, following Mitten, has commonly been referred to as Plagiochila ambagiosa Mitt. is specifically different from the type of P. ambagiosa, and is therefore described as Plagiochila atlantica F. Rose, sp. nov. It is now known from very restricted areas in Western Ireland, Western Scotland and North-western France.     

The erection of Pelecanema n. g. (Nematoda: Spirurida: Acuariidae), with redescriptions of P. sirry (Khalil, 1931) n. comb. and P. pelecani (Johnston & Mawson, 1942) n. comb.

Pelecanema n. g. is erected for P. sirry (Khalil, 1931) n. comb., syn. Synhimantus sirry Khalil, 1931 (type-species) and P. pelecani (Johnston & Mawson, 1942) n. comb., syn. Dispharynx pelecani Johnston & Mawson, 1942. In the structure of its cordons, consisting of two rows of delicate cuticular plates, the new genus is similar to Synhimantus Railliet, Henry & Sisoff, 1912, Dispharynx Railliet, Henry & Sisoff, 1912, Chordatortilis Machado de Mendon?a & Olivera de Rodrigues, 1965 and Parachordatortilis Mutafchiev, Santoro & Georgiev, 2010. Pelecanema sirry, a parasite of Pelecanus onocrotalus L. and P. crispus Bruch (Pelecaniformes, Pelecanidae) in Africa (Egypt and Senegal) and Europe (Ukraine and Bulgaria), is redescribed using light and scanning electron microscopy on the basis of specimens from P. crispus from Bulgaria. Pelecanema pelecani, a parasite of Pelecanus conspicillatus Temminck in Australia, is also redescribed using light microscopy on the basis of specimens from its type-host and type-locality. In contrast to a previous opinion recognising Pelecanema sirry and P. pelecani as synonyms, the two species are considered distinct and P. pelecani is validated.     

Kinetics of formation of fibrin oligomers. I. Theory

The course of formation of fibrin oligomers is treated theoretically for the condition that self-assembly of fibrin monomers is rapid compared with the loss of A peptides by the enzymatic action of thrombin. The rate constant for removal of the second A peptide is taken to be larger than that for the first by an arbitrary factor q; the association of activated A sites with their complementary a sites is assumed to be random and independent of oligomer size. Two types of oligomers are considered: noncovalently bonded protofibrils formed by the staggered overlap of thrombin-activated monomers and covalently bonded linear oligomers formed by factor XIIIa-mediated end-to-end ligation of adjacent monomers within protofibrils. Oligomers of the first type, if ligated, are dissociated to oligomers of the second type by solubilization in SDS–urea. Theoretical curves are presented for x _w and x ′_w (weight-average degree of polymerization of staggered overlap and linear ligated oligomers, respectively) and for the weight fractions of monomer, dimer, and decamer of both ligated and unligated species as functions of y, the fraction of A peptide removed; and also for w_x and w′_x, the weight fractions of x-mer of the respective oligomer types, as a function of x at y = 0.5. With increasing q, the maximum w_x or w′_x that a low oligomer will reach during the reaction decreases and the size distribution is broadened toward larger oligomers. Comparison with experiment is made in a companion paper.     

Revision of Corallinaceae (Corallinales,Rhodophyta): recognizing Dawsoniolithon gen. nov., Parvicellularium gen. nov. and Chamberlainoideae subfam. nov. containing Chamberlainium gen. nov. and Pneophyllum

A multi‐gene (SSU, LSU, psbA, and COI) molecular phylogeny of the family Corallinaceae (excluding the subfamilies Lithophylloideae and Corallinoideae) showed a paraphyletic grouping of six monophyletic clades. Pneophyllum and Spongites were reassessed and recircumscribed using DNA sequence data integrated with morpho‐anatomical comparisons of type material and recently collected specimens. We propose Chamberlainoideae subfam. nov., including the type genus Chamberlainium gen. nov., with C. tumidum comb. nov. as the generitype, and Pneophyllum. Chamberlainium is established to include several taxa previously ascribed to Spongites, the generitype of which currently resides in Neogoniolithoideae. Additionally we propose two new genera, Dawsoniolithon gen. nov. (Metagoniolithoideae), with D. conicum comb. nov. as the generitype and Parvicellularium gen. nov. (subfamily incertae sedis), with P. leonardi sp. nov. as the generitype. Chamberlainoideae has no diagnostic morpho‐anatomical features that enable one to assign specimens to it without DNA sequence data, and it is the first subfamily to possess both Type 1 (Chamberlainium) and Type 2 (Pneophyllum) tetra/bisporangial conceptacle roof development. Two characters distinguish Chamberlainium from Spongites: tetra/biasporangial conceptacle chamber diameter (<300 μm in Chamberlainium vs. >300 μm in Spongites) and tetra/bisporangial conceptacle roof thickness (<8 cells in Chamberlainium vs. >8 cells in Spongites). Two characters also distinguish Pneophyllum from Dawsoniolithon: tetra/bisporangial conceptacle roof thickness (<8 cells in Pneophyllum vs. >8 cells in Dawsoniolithon) and thallus construction (dimerous in Pneophyllum vs. monomerous in Dawsoniolithon).     

PHYCOLOGICAL NOTES. H. EUGLENA MYXOCYLINDRACEA SP. NOV.12

A previously undescribed species of Euglena, E. myxocylindracea, sp. nov., is described from soil in a garden and in a while pine woods in Pike County, Pa. In addition to the, type, an organism (No. 457) in the Culture Collection of Algae. Indiana University, hitherto designated E. viridis var. terricola. is transferred to E. myxocylindracea as var. terricola. Differences such as the usual absence of an emergent flagellum, or the presence of an extremely short one (ca. 3.5–4 μ), and the dominance of a palmelloid state in a variety of liquid and solid culture media in which the cells secrete dichotomously branching slimy cylinders distinguish the new species from E. viridis.     

Bryophytes of St Helena,South Atlantic Ocean. 1. Three new species of Cololejeunea (Jungermanniales,Lejeuneaceae), C. dianae sp. nov., C. sanctae-helenae sp. nov. and C. grossestyla sp. nov.

Abstract

Three new species of Cololejeunea, C. dianae M. Wigginton, C. sanctae-helenae M. Wigginton and C. grossestyla M. Wigginton are described and illustrated from St Helena, South Atlantic Ocean. Details of their distributions are provided, and differences between the new taxa and other species of Cololejeunea are discussed. This is also the first report of the genus Cololejeunea from St Helena.     

Miliusa cambodgensis sp. nov. (Annonaceae) from Cambodia and M. astiana,M. ninhbinhensis spp. nov. from Vietnam

The genus Miliusa in Cambodia and Vietnam is reviewed. Cambodia and Vietnam each harbors six species of Miliusa, including three which are described as new to science: one from Cambodia (Miliusa cambodgensis sp. nov.), the other two from Vietnam (M. astiana and M. ninhbinhensis spp. nov.). In addition, a complete nomenclature and relevant information about the Miliusa species previously known from Cambodia and Vietnam are provided, including keys to the Cambodian and Vietnamese species, the designation of a lectotype for M. baillonii and the synonymization of M. balansae var. elongatoides, M. chunii and M. sinensis with M. balansae.     

Pleospora drummondii spec. nov. und ihr Anamorph Stemphylium drummondii spec. nov.

Pleospora drammondii spec. nov. and its anamorph Stemphylium drammondii spec. nov. The causal organism of a leaf spot disease on Phlox drummondii is described as Pleospora drummondii spec. nov. and its anamorph Stempbylium drummondii spec, nov. — in contrast to earlier reports from the USA, in which the fungus was identified as S. botryosum.     

Studies in Heterobasidiomycetes,Part 38*)Sphacelotheca polygoni-persicariae G. Demi & Oberw. spec. nov.

A new species, Sphacelotheca polygoni-persicariae, parasitizing the ovaries of Polygonum persicaria L. is described. This smut, collected several times in Madeira, Portugal, differs from other species of that genus, by its host plant and the reticulated teliospore ornamentation. On the basis of the morphological and ultrastructural characters of S. polygoni-persicariae, in connection with some recently published data on siderophore formation and 5S ribosomal RNA sequences it can be assumed that 1) members of the genus Sphacelotheca are separated from typical Ustilago species of Poaceae, 2) Sphacelotheca is restricted to species parasitizing Polygonaceae, and 3) species of Sphacelotheca and Microhotryum as well as those Ustilago species which parasitize in the flowers of Polygonaceae are closely related.     

Elevation of Francisella philomiragia subsp. noatunensisMikalsen et al. (2007) to Francisella noatunensis comb. nov. [syn. Francisella piscicida Ottem et al. (2008) syn. nov.] and characterization of Francisella noatunensis subsp. orientalis subsp. nov., two important fish pathogens

Aims: This study was conducted to clarify the taxonomic status of Francisella sp. strain Ehime‐1, a fish pathogen, in relation to the fish pathogens F. piscicida and F. philomiragia subsp. noatunensis and to F. philomiragia subsp. philomiragia. Methods and Results: Francisella sp. Ehime‐1 was compared to F. piscicida, F. philomiragia subsp. noatunensis and several F. philomiragia subsp. philomiragia isolates through sequencing of the 16S rRNA‐gene and several house‐keeping genes and determination of biochemical and phenotypic properties. Results show that F. piscicida is indistinguishable from F. philomiragia subsp. noatunensis by sequence and phenotypic traits. Francisella sp. Ehime‐1 and F. philomiragia subsp. noatunensis are clearly separated from F. philomiragia. Francisella sp. Ehime‐1 is biochemically, phenotypically and genetically different from F. philomiragia subsp. noatunensis (=F. piscicida), but DNA–DNA hybridization does not clearly support establishment as a separate species (level of relatedness 64% and 73·4%, mean 68·7%). Conclusions: We propose to elevate F. philomiragia subsp. noatunensis to species rank as F. noatunensis comb. nov., while F. piscicida is considered a heterotypic synonym of F. noatunensis comb. nov. Evidence suggests that Francisella sp. Ehime‐1 represents a novel subspecies of F. noatunensis, for which the name F. noatunensis subsp. orientalis subsp. nov. is proposed (=DSM21254^T, = LMG24544^T). Significance and Impact of the Study: This study contributes to the taxonomy and characteristics of fish‐pathogenic Francisella spp.     

On the morphology of Leiomitra mastigophoroides R.M.Schust. (Trichocoleaceae)

A better circumscribed morphological concept of Leiomitra mastigophoroides with its monospecific subgenus Leiomitra subg. Brachygyna from Dominica Island is given. Leiomitra mastigophoroides is characterized by the gynoecia restricted to short lateral branches, rare presence of ventral Acromastigum-type branching, presence of stem paraphyllia, and superficial cilia on marginal parts of the leaf disc. The species is newly confirmed from Peru in addition to Dominica Island. The monospecific subgenus Brachygyna is retained as an isolated element of the genus Leiomitra, because although L. mastigophoroides is unique in terms of the gynoecial position within the family Trichocoleaceae, other vegetative characters, except for the Acromastigum-type branches, are similar to other species of Leiomitra subg. Leiomitra.     

Dicrocoeliidae (Trematoda: Digenea) of Australian mammals with description of Dicrocoelium antechini n. sp., Athesmioides aiolos n. g., n. sp. and Platynosomum burrman n. sp.

Dicrocoelium antechini n. sp. is described from the bile ducts of Antechinus swainsonii and A. stuartii (Marsupialia: Dasyuridae) from New South Wales. The species differs from all others in the genus in that the caecal bifurcation is well posterior to the ventral sucker and testes. Athesmioides aiolos n. g., n. sp. is described from Rattus fuscipes and R. lutreolus from New South Wales and from R. norvegicus, R. lutreolus and Pseudomys higginsi from Tasmania (all Rodentia: Muridae). The genus Athesmioides is characterised by the presence of unilateral vitelline follicles and an undivided caecum. Platynosomum burrman n. sp. is described from Isoodon macrourus (Marsupialia: Peramelidae) from the Northern Territory. It differs from other species in a combination of characters regarding the shape of the forebody, the arrangement of the gonads, the disposition of the uterus and the size of the eggs. The taxonomic status of Platynosomum australiense (Sandars, 1958), Brachylecithum insulare Angel & Pearson, 1977 and Brachylecithum hydromyos Angel & Pearson, 1977 are summarised. Records are presented of undescribed dicrocoeliids from the marsupials Petaurus breviceps, Planigale maculata and Dasyurus hallucatus and the murids Rattus fuscipes and Melomys sp.     

Phylogeny and taxonomy of Halimeda incrassata,including descriptions of H. kanaloana and H. heteromorpha spp. nov. (Bryopsidales,Chlorophyta)

The tropical green algal genus Halimeda is one of the best studied examples of pseudo-cryptic diversity within the algae. Previous molecular and morphometric studies revealed that within Halimeda section Rhipsalis, Halimeda incrassata included three pseudo-cryptic entities and that the morphological boundaries between H. incrassata and Halimeda melanesica were ill-defined. In this paper, the taxonomy of H. incrassata is revised: two pseudo-cryptic entities are described as new species, Halimeda kanaloana and Halimed heteromorpha, while H. incrassata is redefined to encompass a single, monophyletic entity. Similarities and differences between the three species and H. melanesica are discussed. Monophyly of H. heteromorpha, which was questioned in a former study, is reinvestigated using sets of 32 ITS1–ITS2 and 21 plastid rps3 sequences and various alignment and inference methods. The phylogenetic relationships within Halimeda section Rhipsalis are inferred from nuclear 18S–ITS1–5.8S–ITS2 and concatenated plastid sequences (tufA & rpl5–rps8–infA) and interpreted in a biogeographic context.     

Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum,Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov.

Two new methanogenic bacteria, Methanocorpusculum sinense spec. nov. strain DSM 4274 from a pilot plant for treatment of distillery wastewater in Chengdu (Province Sichuan, China), and Methanocorpusculum bavaricum spec. nov. strain DSM 4179, from a wastewater pond of the sugar factory in Regensburg (Bavaria, FRG) are described. Methanocorpusculum strains are weakly motile and form irregularly coccoid cells, about 1 μm in diameter. The cell envelope consists of a cytoplasmic membrane and a S-layer, composed of hexagonally arranged glycoprotein subunits with molecular weights of 90000 (Methanocorpusculum parvum), 92000 (M. sinense), and 94000 (M. bavaricum). The center-to-center spacings are 14.3 nm, 15.8 nm and 16.0 nm, respectively. Optimal growth of strains is obtained in the mesophilic temperature range and at a pH around 7. Methane is produced from H₂/CO₂, formate, 2-propanol/CO₂ and 2-butanol/CO₂ by M. parvum and M. bavaricum, whereas M. sinense can only utilize H₂/CO₂ and formate. Growth of M. sinense and M. bavaricum is dependent on the presence of clarified rumen fluid. The G+C content of the DNA of the three strains is ranging from 47.7–53.6 mol% as determined by different methods. A similar, but distinct polar lipid pattern indicates a close relationship between the three Methanocorpusculum species. The polyamine patterns of M. parvum, M. sinense and M. bavaricum are similar, but distinct from those of other methanogens and are characterized by a high concentration of the otherwise rare 1,3-diaminopropane. Quantitative comparison of the antigenic fingerprint of members of Methanocorpusculum revealed no antigenic relationship with any one of the reference methanogens tested. On the basis of the distant phylogenetic position of M. parvum and the data presented in this paper a new family, the Methanocorpusculaceae fam. nov., is defined.     

Isothecium myosuroides var. brachythecioides (Dixon) Braithw. reinstated as a species,I. interludens Stirt.

The taxon currently known as Isothecium myosuroides var. brachythecioides (Dixon) Braithw. is reinstated as a species, I. interludens Stirt., the name originally assigned by Stirton when it was first described. The morphological characters separating I. myosuroides s.s. and I. interludens are summarised. The sporophytes of I. interludens, described here for the first time, differ in shape, and pattern of exothecial cells from those of I. myosuroides. A molecular analysis based on variation of the ITS region shows that I. holtii Kindb. and I. alopecuroides (Lam. ex Dubois) Isov. are not monophyletic, calling for a re-assessment of these species, whereas the monophyly of the other species, including I. interludens, cannot be rejected. The analysis failed, however, to yield molecular synapomorphies for I. interludens and other species within I. myosuroides s.l., which we interpret as the incomplete sorting of alleles among recently evolved species. Isothecium interludens is a European endemic with a hyperoceanic temperate distribution. Its nested position within a clade including the two Macaronesian endemics I. prolixum (Mitt.) M.Stech and I. montanum Draper, Hedenäs, M.Stech, T.Lopes & Sim-Sim is suggestive of a Macaronesian origin, in line with the idea that the European Atlantic fringe flora assembled during the course of the last interglacial from Macaronesian ancestors. Isothecium therefore offers a model of prime importance for the study of ongoing speciation in mosses.