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.     

On the identity of Pohlia flexuosa Harv. with P. muyldermansii Wilcz. & Dem.

Abstract

The identity of Pohlia flexuosa Harv. with P. muyldermansii Wilcz. & Dem. is established. Recent gatherings from several Asiatic countries demonstrate that material of P. flexuosa occurs with propagula identical with those of P. muyldermansii var. muyldermansii, of var. pseudomuyldermansii Arts, Nordhorn-Richter and Smith and with a mixture of both and intermediate types of propagulum; var. pseudomuyldermansii cannot therefore be upheld as distinct. It is postulated that P. flexuosa has been introduced into Europe in two distinctive clones.     

A J E Smith,M.A., D.Phil., D.Sc. (1935–2012)

Abstract

Based on morphology and phylogenetical analyses of nrITS sequences, the Andean endemic Plagiochila (Jamesoniella) dependula is placed in Plagiochila sect. Fuscoluteae. Perianths, oil bodies and sporophytes are described for the first time. Morphologically, P. dependula is characterized by entire, dorsally mostly shortly decurrent, laterally appressed, reniform leaves which are covered by irregular papillae and membranous wax platelets, papillose oil bodies, intercalary androecia with opposite bracts that overlap dorsally, a plagiochilid perianth with an entire mouth, a 250 μm thick capsule wall with thickenings in all layers, large 1–4 celled spores, and bispiral elaters. Morphotypes of Plagiochila fuscolutea with laterally appressed leaves differ from P. dependula by an at least moderately decurrent, broad dorsal leaf base, a ±smooth upper leaf surface, and by its often toothed leaf apices. Plagiochila wolframii is placed in the synonymy of P. fuscolutea. Maximum likelihood and parsimony analyses of 29 Plagiochila ITS sequences resolve P. dependula in a well-supported clade with several other representatives of P. sect. Fuscoluteae. Branch lengths within sect. Fuscoluteae point to a sudden diversification. Accessions of P. heterophylla s.str. from Great Britain (formerly known as P. atlantica) and Costa Rica form an unsupported monophyletic lineage.     

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.     

PALEOZOIC LYCOPSID FRUCTIFICATIONS. I. LEPIDOCARPON PETRIFACTIONS

A reinvestigation of the 4 American species of Lepidocarpon described from petrifactions and of Illiniocarpon cadyi, also described from petrifactions, shows that they are all conspecific. When they, in turn, are compared with specimens of the British petrifaction L. lomaxi, no significant differences can be demonstrated. The criteria cited as diagnostic for the American petrifaction species of Lepidocarpon were found to fail as bases of discrimination when 400 specimens of Lepidocarpon found in coal balls of Pennsylvanian age were studied. Measurements and observations made of a sample size of 136 of these 400 specimens reveal a degree of variation compatible with that of a single species. All previously described American and British petrifaction taxa fall within (or not significantly beyond) this range of variability of a single species as determined from this sample. Additional evidence concerning the 3-dimensional sporophyll structure of this one species of Lepidocarpon and the configurations obtained by certain planes of section through it have served to demonstrate that Illiniocarpon cadyi is in reality a taxon based on sectioned structures of the sporophyll of this Lepidocarpon species. Under the rules of priority, this species of Lepidocarpon and the following are assigned to Lepidocarpon lomaxi: Illiniocarpon cadyi, Lepidocarpon ioense, L. magnificum (megasporangiate form), L. crenatum and L. palmerensis. On the basis of the morphological evidence, the British petrifaction described as Lepidocarpon wildianum is also equated with L. lomaxi.     

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.     

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.     

Systematic revision of the genus Phycodrys (Delesseriaceae,Rhodophyta) from New Zealand,with the descriptions of three new species,P. novae-zelandiae sp. nov., P. franiae sp. nov. and P. adamsiae sp. nov.

Two species of Phycodrys, Phycodrys quercifolia (Bory) Skottsberg and Phycodrys profunda E.Y.Dawson were previously recorded from New Zealand. However, an examination of Phycodrys collections from the New Zealand region showed that all were morphologically different from P. quercifolia (Type locality: the Falkland Islands) and P. profunda (Type locality: CA, USA). RbcL sequence analyses established that the New Zealand Phycodrys species formed a natural assemblage within the genus, consisting of three new species: P. novae-zelandiae sp. nov., P. franiae sp. nov. and P. adamsiae sp. nov. Phycodrys novae-zelandiae is the largest of the three, up to 20 cm in height, with a distinct midrib and multicellular, opposite to subopposite lateral macroscopic veins. It has entirely monostromatic blades except near the midrib and veins, and its procarp contains a three-celled sterile group one (st1) and a one-celled sterile group two (st2). Phycodrys franiae was previously treated as a cryptic species among herbarium collections of P. ‘quercifolia’. It is smaller (4–11 cm high) with weakly developed midribs and veins, the blade is tristromatic throughout, except at the growing margins, and the procarp consists of a four-celled st1 and a two–three-celled st2. Phycodrys adamsiae, previously reported as P. profunda, is a small decumbent or prostrate plant, 1–8 cm long, with a midrib and inconspicuous lateral veins. The blades are tristromatic with serrated margins, two–four-celled surface spines and multicellular marginal holdfasts that differ from those of Californian specimens. The tetrasporangia are borne on marginal bladelets. Phylogenetic analyses place the New Zealand species in a separate group that is distantly removed from most other Phycodrys species.     

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.     

Michelia sonlaensis Q.N. Vu,sp. nov. (Magnoliaceae) from northern Vietnam

Michelia sonlaensis Q.N. Vu, a new species of Michelia from Son La province, northern Vietnam is described. The new species is assigned to the genus Michelia (separated from Magnolia), subfamily Magnolioideae based on general morphology. It is closely similar to M. xianianhei and M. mannii, but differs mainly in having a leaf‐lamina that is elliptic, thinly leathery, larger, with lower surface yellowish white villous (easily visible by eyes and feeling by hand), brachyblasts and outside bracts yellowish‐white sericeous, flowers light green to cream white in colour, and nine tepals with the outside of all tepals silky hairy at base.     

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).     

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).     

Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov.

Ascomycete yeasts that both ferment and assimilate xylose were reported previously as associates of insects living in woody substrates. Most notable have been reports of Pichia stipitis-like yeasts that are widely associated with the wood-boring beetle, Odontotaenius disjunctus (Coleoptera: Passalidae), in the eastern United States. Our continuing investigation of insect gut yeasts has lead to the discovery of two new xylose-fermenting yeasts that phylogenetic analysis places as sister taxa. The beetle hosts, O. disjunctus and Phrenapates bennetti (Coleoptera: Tenebrionidae), are similar in habitat and appearance, and the presence of similar gut yeasts is an additional common feature between them. Here we describe the new yeast genus Spathaspora, the type species S. passalidarum, and its sister taxon Candida jeffriesii and discuss their natural history, including a comparison with Pichia stipitis, another member of a guild of xylose-fermenting yeasts with similar metabolic traits. In addition a morphologically distinct yeast ascospore type is described for Spathaspora.     

Trois Especes Nouvelles d'Ophryoglenes: O. gelifera n. sp., O. mucosa n. sp., O. multimicronucleata n. sp. (Cilies Holotriches Peniculiens)

SYNOPSIS. A previous study with P. de Puytorac on O. bacterocaryon(3) has shown the methods of studying this Ciliate and has specified the general and buccal morphology, the morphogenesis, and the biology of vegetative individuals (theront, trophont, tomont, tomites) of this species. Three species we are describing now offer numerous common features with O. bacterocaryon. We consider them as the proper characters of genus Ophryoglena and we only insist on the specific particularities of O. gelifera, O. mucosa and O. multimicronucleata. O. gelifera is a large Ophryoglene differing from the others by a slightly asymetric, curved, spindle-shaped theront; the ellipsoidal tomont secretes abundant and clear jelly. The theront possesses one thick spindle-shaped macronucleus, one voluminous spherical micronucleus, fitting with the macronucleus. Its somatic infraciliature is dense, its buccal infraciliature is characteristic, especially in the shape of peniculus P1. This species cannot be mistaken for O. pectans Mugard(2) although it is rather near it. O. mucosa is a very small Ophryoglene. The theront has one thick elliptical macronucleus, one small micronucleus; the buccal orifice is not kidney-shaped, but quite pointed in front; there is no tragus; the somatic infraciliature is not close; the peniculus P1 is characteristic. The tomont is ellipsoidal and surrounded by a thick mucous gangue. The tomites are not close together. O. mucosa is very different from O. gelifera and O. pectans Mugard(2). O. multimicronucleata. Near to O. polymicrocaryon Mugard(2), this Ophryoglene differs from it by the small size of all its vegetative elements and especially by its nuclear-apparatus. The latter includes numerous (5 to 6) bulky spherical micronuclei and one macronucleus looking like blackpudding which can be compared to that of O. singularis Canella and Trinchas(1). The theront is spindle-shaped and of a dark-grey colour. The spherical tomont secretes a mucous gangue which is not very thick. Besides, the somatic infraciliature and buccal in fraciliature of the theront (peniculus P1 especially) make O. multi micronucleata quite distinct from O. polymicrocaryon Mugard(2).     

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.     

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.