New light on tautomerism of purines and pyrimidines and its biological and genetic implications

The tautomerism of the natural 1-substituted pyrimidines and 9-substituted purines found in nucleic acids has been re-examined in the light of new experimental data on various nitrogen heterocycles in solution, in the gas phase and, in part, in low-temperature inert matrices. The results are compared with those obtained by quantum chemical calculations, including improved versions of the latter. Examples are presented of natural nucleosides which exhibit appreciable tautomerism in solution,e.g. formycins A and B, isoguanosine, but are not found in DNA. Illustrations are given of synthetic promutagenic nucleosides with pronounced tautomerism in solution relevant to their role in mutagenesis, such as the N⁴-hydroxy-and N⁴-methoxy cytidines. The amino-imino tautomeric equilibria of the promutagenic N⁶-hydroxy-and N⁶ -methoxy-adenosines are highly dependent on the solvent medium, the proportion of the imino species varying from 10% in CCl₄ to 90% in aqueous medium. The type of base pairing of these is dependent on the conformation of the exocyclic hydroxy or methoxy groups. At the monomer level, addition of a potentially complementary base leads to a shift in the tautomeric equilibrium in favour of the species which pairs with this base. Biological and genetical implications of the foregoing are described.     

Caradoc strophomenoid and plectambonitoid brachiopods from Wales and the Welsh Borderland

Abstract: Ordovician strophomenoidean and plectambonitoidean brachiopods are reviewed and partially redescribed from the Caradoc (Sandbian to Early Katian) age rocks of Wales and the Welsh Borderland of England, then forming part of the Avalonia Terrane. There are 51 nominal species available, of which 12 are synonymised here and many transferred to different genera. Strophomenoids occurred sporadically, often rarely but occasionally abundantly, particularly in mid‐shelf benthic assemblages, and 21 named species and subspecies are noted, including the new Kiaeromena (Kiaeromena) harperi, as well as six in open nomenclature. The common genus Kjaerina, with six species known from the area, is revised in detail. In contrast to the strophomenoids, plectambonitoids were more common in shallow and mid‐shelf assemblages, including Eoplectodonta (Eoplectodonta) abigailae sp. nov., with Sowerbyella in particular dominating many bedding planes, and 17 named species are reviewed, as well as three in open nomenclature. The distinctive Gunningblandella, hitherto known only from Australia and Kazakhstan, is recorded for the first time from Europe. The Avalonian strophomenides are compared with those from neighbouring terranes, particularly Laurentia and Baltica, during a time when the seas between those terranes were narrowing, and the faunas from the three terranes are found to be largely similar at the generic level, although there are few species in common. In contrast, there are few genera in common between those three terranes and the Mediterranean Province of Northwestern Gondwana.     

Distribution, mechanisms and evolutionary significance of clonality and polyploidy in weevils

Abstract 1 Genetical mtDNA relationships of 41 taxa of weevils were examined using cladistics. Ingroup taxa belong to Otiorhynchus scaber and O. nodosus and outgroup comparison was made with O. singularis. All three species are minor forest pests. 2 Otiorhynchus scaber specimens are either diploid sexuals or diploid, triploid and tetraploid clones, from two different populations (Slovenia and Austria) that belong to two different evolutionary lineages. Otiorhynchus nodosus specimens are tetraploid clones. Both species show geographical parthenogenesis, as do many other Otiorhynchus species. 3 Mitochondrial data indicate that O. nodosus clones are more closely related to Slovenian sexuals of O. scaber than these are to sexuals from Austria. It also shows that almost all clones of O. scaber collected in one of the two regions where sexuals are found are more closely related to sexuals from the other region. 4 Three different hypotheses that may explain the distribution of O. scaber, mechanisms important for the evolution of the clones and implications of the presence of Wolbachia are discussed. 5 We conclude that parthenogenesis is likely to be linked to hybridization in O. scaber and that hybridization events between ancestors of O. nodosus and O. scaber are the probable cause of the presence of O. nodosus in the ingroup. We also find that polyploid clones are superior colonizers compared to sexuals and diploid clones, in O. scaber. 6 The results suggest that systems where both sexuals and clones exist are more complex than previously suggested. The mapping of genetic variation in clonal complexes and the tracing of clonal origins may be useful in pest management.     

Plant calcium signaling and monitoring: pros and cons and recent experimental approaches

Summary This review focusses on Ca²⁺-mediated plant cell signaling and optical methods for in vivo [Ca²⁺] monitoring and imaging in plants. The cytosolic free calcium concentration has long been considered the central cellular key in plants. However, more and more data are turning up that critically question this view. Conflicting arguments show that there are still many open questions. One conclusion is that the cytosolic free Ca²⁺ concentration is just one of many cellular network parameters orchestrating complex cellular signaling. Novel experimental strategies which unveil interference of cellular parameters and communication of transduction pathways are required to understand this network. To date only optical methods are able to provide both kinetic and spatial information about cellular key parameters simultaneously. Focussing on calcium there are currently three classes of calcium indicators employed (i.e., chemical fluorescent dyes, luminescent indicators, and green-fluorescent-protein-based indicators). Properties and capabilities as well as advantages and disadvantages of these indicators when used in plant systems are discussed. Finally, general experimental strategies are mentioned which are able to answer open questions raised here.Abbreviations CTZ coelenterazine - GFP green-fluorescent protein - FRET fluorescence resonance energy transfer - [Ca²⁺] calcium ion concentration - CaM calmodulin - CDPKs calmodulindomain protein kinases - IP₃ inositol 1,4,5-trisphosphate     

Biology and Evolution of Beneficial and Detrimental Viruses of Animals, Plants, and Fungi

Virtually every type of organism may serve as a host for viruses. In some hosts, virus presence may be considered beneficial to humans; in other hosts, viruses are considered detrimental. Examples of viruses that are considered beneficial to humans include those that are used for biological control of organisms that themselves are considered detrimental to humans, such as plant pathogenic fungi. Viruses are extremely variable in terms of morphology, structure, and genome organization. However, viruses that attack hosts from different kingdoms may be related, deriving from the same phylogeny. This paper summarizes some of the properties of three related families of viruses that attack hosts in different kingdoms: the animal-infecting Picornaviridae, the plant-infecting Potyviridae, and the fungus-infecting Hypoviridae. Properties of these viruses that set them apart from each other and factors that may affect their evolution are discussed.     

CADEIA and REJECT

CADEIA and REJECT are computer codes for generating γ-γ and γ-X true-coincidence lines for calculation of correction factors for absolute counting of gamma rays in a low energy photon detector. They are written in FORTRAN 77. True-coincidence lines are generated by CADEIA; they are submitted to selection by REJECT according to the rejection criteria defined by L. Moens et al. and F. De Corte. Final relevant lines for true-coincidence correction factors are given as output of REJECT.     

Cryptosporidiosis and giardiasis in dogs and cats: Veterinary and public health importance

Dogs and cats are the only domestic animals that still routinely reside in the same domicile as their owners around the world, and hence the interest in their role as reservoirs of potentially zoonotic agents. In the case of cryptosporidiosis and giardiasis, current data suggests that dogs and cats do not routinely share their infections with healthy people. Dogs are hosts of Cryptosporidiumcanis and Giardiaduodenalis Assemblages C and D. Cats are hosts to Cryptosporidiumfelis and G. duodenalis Assemblage F. Dogs and cats (and other animals) are sometimes infected with sub-Assemblage AI, an Assemblage also found in people, but people usually have sub-Assemblage AII. Unfortunately, severely immunocompromised individuals and malnourished children can be made ill by infections with C. canis and C. felis. People should practice good sanitation and hygiene to minimize environmental contamination and contact with the infectious (oo)cysts that may be shed by their pets.     

Freshwater Copepods and Rotifers: Predators and their Prey

Three main groups of planktonic animals inhabit the limnetic zone of inland waters and compete for common food resources: rotifers, cladocerans and copepods. In addition to competition, their mutual relationships are strongly influenced by the variable, herbivorous and carnivorous feeding modes of the copepods. Most copepod species, at least in their later developmental stages, are efficient predators. They exhibit various hunting and feeding techniques, which enable them to prey on a wide range of planktonic animals from protozoans to small cladocerans. The rotifers are often the most preferred prey. The scope of this paper is limited to predation of freshwater copepods on rotifer prey. Both cyclopoid and calanoid copepods (genera Cyclops, Acanthocyclops, Mesocyclops, Diacyclops, Tropocyclops, Diaptomus, Eudiaptomus, Boeckella, Epischura and others) as predators and several rotifer species (genera Synchaeta, Polyarthra, Filinia, Conochilus, Conochiloides, Brachionus, Keratella, Asplanchna and others) as prey are reported in various studies on the feeding relationships in limnetic communities. Generally, soft-bodied species are more vulnerable to predation than species possessing spines or external structures or loricate species. However, not only morphological but also behavioural characteristics, e.g., movements and escape reactions, and temporal and spatial distribution of rotifer species are important in regulating the impact of copepod predation. The reported predation rates are high enough to produce top-down control and often achieve or even exceed the reproductive rates of the rotifer populations. These findings are discussed and related to the differences between the life history strategies of limnetic rotifer species, with their ability to quickly utilize seasonally changing food resources, and adjust to the more complicated life strategies of copepods.     

Pennsylvanian fusulinids and calcareous algae from Sonora (northwestern Mexico), and their biostratigraphic and palaeobiogeographic implications

Pennsylvanian carbonates are widespread in Sonora (Mexico) and contain a diverse biota of foraminifers and calcareous algae. Detailed studies here are devoted to the outcrops of the Sierra Agua Verde and Cerro El Tule. The Late Atokan (early Late Moscovian part), Desmoinesian (= late Late Moscovian) and Missourian (= Kasimovian) stages are especially rich in fusulinids and algae. The principal zones of fusulinids of Wilde encountered are A3, DS1 and MC1–2. New data are given about the genera Fusulinella, Parawedekindellina, Zellerella, Komia and Paraepimastopora, in order to establish migrations or vicariances between Mexico and Palaeotethys.     

Classification and naming of dyes,stains and fluorochromes

A classification of dyes and other colorants is proposed, based on the chemical features responsible for their visibility and generally consonant with the writings of modern color chemists. The scheme differs in several respects from that of the Colour Index (CI), but it retains some traditional small groups of dyes that include biological stains. Natural dyes, recognized as a group in the CI, are placed with or near synthetic dyes with identical or similar chromophores. The new scheme also provides categories for dyes and fluorochromes that do not have places in the CI classification. Some CI categories, including lactones, aminoketones and hydroxyketones, are not recognized in this new scheme, which is adopted in the forthcoming 10th edition of Conn's Biological Stains: a Handbook of Dyes and Fluorochromes for Use in Biology and Medicine. Some rules are also set out for the spelling of trivial names, which has long been inconsistent in scientific literature. The ending '-ine' is used for compounds derived from organic bases (e.g., fuchsine and thionine, not fuchsin or thionin), and names ending in '-in' are for compounds that are not bases or their derivatives (e.g., eosin and phloxin, not eosine or phloxine). Initial capital letters are used only for words that are names of people or places (e.g., Nile blue or Congo red) and for the 'generic' components of CI application names (as in Acid yellow 36). Other words, including trade names that have fallen into common usage are not capitalized (e.g., alcian blue, biebrich scarlet, coomassie blue). The recommended spellings of some dyes differ from those commonly seen in vendors' catalogs and in biological publications, but they are generally consistent with English and American dictionaries, with recent writings in English by color chemists, and with the trivial names of other organic compounds.     

中国大陆北热带及亚热带地区樟科、壳斗科物种多样性及其生物地理格局分析

以中国大陆北热带及亚热带地区优势科樟科、壳斗科植物为研究对象,利用专著发表大量的样方数据和物种分布数据,分析樟科、壳斗科与群落构建的关系、它们各大属的地理分布格局,探讨影响其分布的可能历史原因。结果表明:中国大陆北热带及亚热带地区森林乔木层优势科为樟科、壳斗科、山茶科、杜鹃花科。樟科、壳斗科物种丰富度均与其所在群落的物种丰富度呈现一定的正相关,樟科对群落构建的贡献较大。樟科、壳斗科植物种的空间多样性分布中心均出现在我国亚热带中部偏南地区。樟科的厚壳桂属、琼楠属以及壳斗科的锥属物种多样性分布中心主要在南亚热带及北热带区域,以广西、云南省份的南部为主。樟科的樟属、新木姜子属、润楠属、木姜子属及壳斗科的柯属、青冈属主要分布在我国大陆北热带及亚热带中部偏南的地区,其多样性分布中心与樟科、壳斗科科水平的物种多样性分布中心极为相似。樟科的山胡椒属、楠属、黄肉楠属,壳斗科的栎属主要分布在研究区域中部以西的地区。研究结果佐证物种的生态学特性以及生物地理学历史综合作用导致目前樟科和壳斗科植物的生物多样性分布格局。     

Rhizoctonia solani and orchid seed

Summary

One hundred and sixty-two agarics are recorded for Hirta and two from Dùn, two islands situated off the West coast of Scotland in the St. Kilda complex. The agarics are described in relation to the ecological noda proposed by McVean for the higher plant communities of the islands. Omphalina ericetorum and Nolanea staurospora were by far the commonest species: eighttaxa which are not in the New British Check List are recorded from Hirta. An appendix dealing with the taxonomy and nomenclature of the more critical species in the list is given.     

Structure and Histochemistry of Stomata and Epidermal Cells in Five Species of Polypodiaceae

The epidermal structure of the five species of ferns, Arthromeriswallichiana (Spr.) Ching., Drymoglossum piloselloides (Prest.),Drynaria quercifolia (L.) J. Smith, Lepisorus nudus (Hook.)Ching. and Pyrrosia nuda (Gies.) Ching., has been investigated.Fifteen types of stomatal structures have been identified ofwhich copolo-desmocytic and coperi-desmocytic are new types.Four more possible stomatal structures: ccpolo-peri-, codesmo-polo-,codesmo-peri- and duplodesmocytic, are suggested. Localizationof starch, insoluble polysaccharides, protein and lipids hasbeen examined histochemically in the guard cells, subsidiarycells and epidermal cells. In Drynaria starch plastids and plastidscontaining both starch and protein are present in guard cells.Starch plastids are present in the subsidiary cells of all speciesexcept in Arthromeris, whereas, they are present in epidermalcells of only Drymoglossum and Lepisorus. Granular or amorphousinsoluble polysaccharides (other than starch) are present inguard cells of all the species, in the subsidiary cells of Arthromeris,Drynaria and Pyrrosia, and in the epidermal cells of Pyrrosia.Except in Pyrrosia lipids are present in the guard cells. Subsidiarycells of Drynaria and the epidermal cells of Arthromeris andDrynaria show lipid bodies. The presence of plasmodesmata andectodesmata is demonstrated in the epidermal cells of Drymoglossum.     

Kinetic and biochemical properties of high and low redox potential laccases from fungal and plant origin

The electrochemical studies of laccase–mediator systems are aimed at understanding the mechanism of their redox transformation and their efficiency in both homogeneous and heterogeneous reactions; this topic has paramount application spanning from bleaching of paper pulp and the enzymatic degradation of lignin to the biosensors and biofuel cell development. In this paper four different laccases from Trametes hirsuta (ThL), Trametes versicolor (TvL), Melanocarpus albomyces (r-MaL) and Rhus vernicifera (RvL) were characterized from both biochemical and electrochemical points of view. Two of them (TvL and ThL) are high redox potential and two (RvL and r-MaL) are low redox potential laccases. The outline of this work is focused on the determination of catalytic and bioelectrochemical properties of these four enzymes in homogenous solution as well as immobilized onto electrode surface in the presence of a set of different redox mediators. The results measured in the homogenous reaction system correlated well with those measured with the immobilized enzymes. In addition, they are in good agreement with those reported with reference techniques, suggesting that the electrochemical methods employed in this work can be applied well in place of the traditional techniques commonly used for the kinetic characterization of laccases. These results are also discussed in terms of the known amino acid sequences and three-dimensional (3D) structures of the laccases.     

Sequence and characterization of 6 Lea proteins and their genes from cotton

Lea genes code for mRNAs and proteins that are late embryogenesis abundant in higher plant seed embryos. They appear to be ubiquitous in higher plants and may be induced to high levels of expression in other tissues and at other times of ontogeny by ABA and/or desiccation. Presented here are the genomic and cDNA sequences for 6 of these genes from cotton seed embryos and the derived amino acid sequences of the corresponding proteins.The Lea genes contain the standard sequence features of eucaryotic genes (TATA box and poly (A) addition sequences) and have 1 or more introns. Sequences differences between cDNA and genomic DNA confirm the existence of small multigene families for several Lea genes. The amino acid composition and sequence for the Lea proteins are unusual. Five are extremely hydrophilic, four contain no cys or trp and 4 have sequence domains that suggest amphiphilic helical structures. Hypothetical functions in desiccation survival, based on amino acid sequence, are discussed.     

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

Background  

The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.     

Synthesis and degradation of termination and premature-termination fragments of beta-galactosidase in vitro and in vivo.

A number of abnormal polypeptides which are products of the lacZ gene in Escherichia coli have been characterized. A variety of experiments indicates that one class of at least nine different fragments arises from premature termination of protein synthesis. They have been detected as products of protein synthesis both in vitro and in vivo, although the percentage of fragments made in vitro is greater than that in vivo. The percentage of total Z gene-encoded protein which is found as fragments is estimated to be roughly 23% in vivo. This means that about 31% of the total number of β-galactosidase monomers synthesized are prematurely terminated molecules. The average molecular weight of the polypeptides produced is 91,000. This corresponds to a termination event occurring on the average once every 3200 codons. The sites at which termination occurs appear to be specific and are located primarily near the 3′-end of the gene.Polypeptides synthesized in vitro and in vivo from templates containing mutations in the Z gene have also been compared. Most of the mutationally generated fragments synthesized in vitro are stable, unlike their in vivo counterparts, which are often rapidly degraded. One fragment, however, generated by an early amber mutation in the Z gene, is degraded in the in vitro system. The mechanism of degradation appears to be specific for small abnormal polypeptides. Internal reinitiation polypeptides generated by nonsense mutations, which have been found in vivo, are not detected in the in vitro protein synthesis system under the conditions used here.     

Prions and lymphoid organs: Solved and remaining mysteries

Prion colonization of secondary lymphoid organs (SLOs) is a critical step preceding neuroinvasion in prion pathogenesis. Follicular dendritic cells (FDCs), which depend on both tumor necrosis factor receptor 1 (TNFR1) and lymphotoxin β receptor (LTβR) signaling for maintenance, are thought to be the primary sites of prion accumulation in SLOs. However, prion titers in RML-infected TNFR1^−/− lymph nodes and rates of neuroinvasion in TNFR1^−/− mice remain high despite the absence of mature FDCs. Recently, we discovered that TNFR1-independent prion accumulation in lymph nodes relies on LTβR signaling. Loss of LTβR signaling in TNFR1^−/− lymph nodes coincided with the de-differentiation of high endothelial venules (HEVs)—the primary sites of lymphocyte entry into lymph nodes. These findings suggest that HEVs are the sites through which prions initially invade lymph nodes from the bloodstream. Identification of HEVs as entry portals for prions clarifies a number of previous observations concerning peripheral prion pathogenesis. However, a number of questions still remain: What is the mechanism by which prions are taken up by HEVs? Which cells are responsible for delivering prions to lymph nodes? Are HEVs the main entry site for prions into lymph nodes or do alternative routes also exist? These questions and others are considered in this article.