Minimising inter-laboratory variation when constructing a unified molecular database of plant varieties in an allogamous crop

The construction of large-scale databases of molecular profiles of plant varieties for variety identification and diversity analyses is of considerable interest. When varieties of an allogamous species such as oilseed rape are analysed and described using molecular markers such as microsatellites, care is needed to represent the variety in a meaningful yet useful way. It is possible to characterise such heterogeneous genotypes by analysing bulked samples comprising more than one individual seed or plant, but this approach may result in complex microsatellite profiles. Intuitively it would be reasonable to represent a variety by the common ‘major alleles’ in a profile, but how to define these ‘major alleles’ remains problematic. This paper describes methods of analysing DNA microsatellite data that will allow independent and objective data production at a number of laboratories. Methods for establishing allele scoring rules (thresholding) are described and the effect of these rules on the utility of the data is discussed.     

Massive Trentepohlia-bloom in a glacier valley of Mt. Gongga, China, and a new variety of Trentepohlia (Chlorophyta)

Trentepohlia is a genus of subaerial green algae which is widespread in tropical, subtropical, and also temperate regions with humid climates. For many years, small-scale Trentepohlia coverage had been found on the rocks of some glacier valleys on the northern slopes of Mt. Gongga, China. However, since 2005, in the Yajiageng river valley, most of the rocks are covered with deep red coloured algal carpets, which now form a spectacular sight and a tourist attraction known as ‘Red-Stone-Valley’. Based on morphology and molecular data, we have named this alga as a new variety: Trentepohlia jolithus var. yajiagengensis var. nov., it differs from the type variety in that its end cells of the main filament are often rhizoid, unilateral branches. This new variety only grows on the native rock, both global warming and human activity have provided massive areas of suitable substrata: the rocks surfaces of the Yajiageng river valley floodplain were re-exposed because of heavy debris flows in the summer of 2005; plus human activities such as tourism and road-building have also created a lot of exposed rock! In summer, the glaciers of the northern slopes of Mt. Gongga have brought to the valleys wet and foggy air, ideal for Trentepohlia growth. The cells of the new variety are rich in secondary carotenoids (astaxanthin?), which helps the algal cells resistance to strong ultraviolet radiation at high altitudes (they are only found on rock surfaces at alt. 1900–3900 m); the cells are also rich in oils, which gives them high resistance to cold dry winters.     

Poxviruses and apoptosis: a time to die

All known apoptosis modulators in poxviruses have been shown to function as inhibitors. The mechanistic classes of these poxvirus-encoded inhibitors are quite diverse, and indicate that a wide variety of distinct host proteins in cellular apoptotic pathways have been targeted for inhibition by individual poxviruses.     

DyP-type peroxidases: a promising and versatile class of enzymes

DyP peroxidases comprise a novel superfamily of heme-containing peroxidases, which is unrelated to the superfamilies of plant and animal peroxidases. These enzymes have so far been identified in the genomes of fungi, bacteria, as well as archaea, although their physiological function is still unclear. DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity. Moreover, these enzymes are able to oxidize a variety of organic compounds of which some are poorly converted by established peroxidases, including dyes, β-carotene, and aromatic sulfides. Interestingly, accumulating evidence shows that microbial DyP peroxidases play a key role in the degradation of lignin. Owing to their unique properties, these enzymes are potentially interesting for a variety of biocatalytic applications. In this review, we deal with the biochemical and structural features of DyP-type peroxidases as well as their promising biotechnological potential.     

Optimal complete block designs to adjust for interplot competition with a covariance analysis

Optimal complete block designs are given for variety trials with interplot competition. In the paper, competition is modeled using height differences between neighboring varieties. When variety heights are known at the design stage, a simulated annealing algorithm is proposed. The optimal designs tend to reduce height differences between neighboring varieties. When variety heights are not known in advance, neighbor-balanced designs at distances 1 and 2 are shown to have optimality properties.     

Iron uptake in fungi: a system for every source

Fungi have a remarkable capacity to take up iron when present in any of a wide variety of forms, which include free iron ions, low-affinity iron chelates, siderophore-iron chelates, transferrin, heme, and hemoglobin. Appropriately, these unicellular eukaryotes express a variety of iron uptake systems, some of which are unique to fungi and some of which are present in plants and animals, as well. The reductive system of uptake relies upon the external reduction of ferric salts, chelates, and proteins prior to uptake by a high-affinity, ferrous-specific, oxidase/permease complex. This system recognizes a broad range of substrates. The non-reductive system exhibits specificity for siderophore-iron chelates, and transporters of this system exhibit multiple substrate-dependent intracellular trafficking events.     

Comparative structural anatomy of the complement anaphylatoxin proteins C3a, C4a and C5a

The anaphylatoxins are a family of proteins produced during the course of complement activation as the result of cleavage by specific serine proteases. These proteins are involved in a variety of biological functions, including inflammation. Comparative modeling techniques have been used to produce structures for C4a and C5a from the crystal structure of C3a. All three structures have conserved interior residues but very different external side chains and surface shapes and properties. Comparison of the anaphylatoxin structures and of the sequence conservation among different species suggests possible locations for their receptor binding sites and for their specificity residues which permit regulated proteolytic cleavage from precursor.     

Tyrosine phosphatases as a superfamily of tumor suppressors in colorectal cancer

Phosphorylation and dephosphorylation processes catalyzed by numerous kinases and phosphorylases are essential for cell homeostasis and may lead to disturbances in a variety of vital cellular pathways, such as cell proliferation and differentiation, and thus to complex diseases including cancer. As over 80 % of all oncogenes encode protein tyrosine kinases (PTKs), protein tyrosine phosphatases (PTPs), which can reverse the effects of tyrosine kinases, are very important tumor suppressors. Alterations in tyrosine kinase and phosphatase genes including point mutations, changes in epigenetic regulation, as well as chromosomal aberrations involving regions critical to these genes, are frequently observed in a variety of cancers. Colorectal cancer (CRC) is one of the most common cancers in humans. CRCs occur in a familial (about 15 % of all cases), hereditary (about 5%) and sporadic (almost 75-80 %) form. As genetic-environmental interrelations play an important role in the susceptibility to sporadic forms of CRCs, many studies are focused on genetic alterations in such tumors. Mutational analysis of the tyrosine phosphatome in CRCs has identified somatic mutations in PTPRG, PTPRT, PTPN3, PTPN13 and PTPN14. The majority of these mutations result in a loss of protein function. Also, alterations in the expression of these genes, such as decreased expression of PTPRR, PTPRO, PTPRG and PTPRD, mediated by epigenetic mechanisms have been observed in a variety of tumors. Since cancer is a social and global problem, there will be a growing number of studies on alterations in the candidate cancer genes, including protein kinases and phosphatases, to determine the origin, biology and potential pathways for targeted anticancer therapy.     

Initial morphological diversity as a criterion in deciphering turbellarian phylogeny

The most profound structural variety in morphofunctional systems and morphogenetic mechanisms, i.e. the highest morphological diversity, is observed in those groups where these systems and mechanisms are evolutionarily most primitive. Here, such variety can involve the basic body plan of a given phylum and the types of morphogenesis characteristic of it. This correlation provides a new criterion of evolutionary primitiveness, namely, the criterion of initial morphological diversity.The highest morphological diversity among turbellarian groups is observed in the order Acoela. Acoel turbellarians are archaic in most of their features, apparently being a group near the base of the turbellarian phylogenetic tree. Among other turbellarians there are a few groups that also are archaic in some few features (above all, the Catenulida), although on the whole they are more advanced than the Acoela. The Turbellaria as a whole is notable for its morphological diversity in comparison with other classes of the Scolecida.     

Allele frequencies after a bottleneck

The effect that a recent change in population size (a “bottleneck”) has on the genetic composition of a random sample of genes is studied. The population is assumed to evolve as in the Wright-Fisher model with infinitely many neutral alleles. Simple analytic formulas are found for such quantities as the probability distribution and moments of the total number of alleles, the allelic “frequency spectrum,” and the homozygosity, in the sample. Numerical examples are given which compare these results with those obtained previously by a variety of other methods.     

The role of NAD(P)H oxidoreductase (DT-Diaphorase) in the bioactivation of quinone-containing antitumor agents: a review

Bioactivation of quinone-containing anticancer agents has been studied extensively within the context of the chemistry and structure of the individual quinones which may result in various mechanisms of bioactivation and activity. In this review we focus on the two electron enzymatic reduction/activation of quinone-containing anticancer agents by DT Diaphorase (DTD). This enzyme has become important in oncopharmacology because its activity varies with tissues and it has been found to be elevated in tumors. Thus, a selective tumor cell kill can exist for agents that are good substrates for this enzyme. In addition, the enzyme can be induced by a variety of agents, a fact that can be used in chemotherapy. That is induction by a nontoxic agent followed by treatment with a good DT-Diaphorase substrate. A wide variety of anticancer drugs are discussed some of which are not good substrates such as Adriamycin, and some of which are excellent substrates. The latter category includes a variety of quinone containing alkylating agents.     

Development of a nutrient medium to culture microorganisms of the genus Campylobacter

The nutrient media developed in the USSR and CSR for the isolation of campylobacteria are multi-purpose as they enable the isolation of campylobacteria not only from material derived from patients with acute intestinal infection, but also from the internal organs of healthy and diseased animals and poultry as well as from a variety of objects in the environment.     

Scottish Birchwoods and their conservation — a Review

Summary

The communities of vascular plants found in Scottish birch woods are briefly described. Birchwoods originate in a variety of ways which affects their likely value for nature conservation. This is discussed using specific examples. The conservation of birchwoods to meet a variety of objectives is considered.     

A network involving Rho-type GTPases, a paxillin and a formin homologue regulates spore length and spore wall integrity in the filamentous fungus Ashbya gossypii

Fungi produce spores that allow for their dispersal and survival under harsh environmental conditions. These spores can have an astonishing variety of shapes and sizes. Using the highly polar, needle-shaped spores of the ascomycete Ashbya gossypii as a model, we demonstrated that spores produced by this organism are not simple continuous structures but rather consist of three different segments that correlate with the accumulation of different materials: a rigid tip segment, a more fragile main spore-compartment and a solid tail segment. Little is currently known about the regulatory mechanisms that control the formation of the characteristic spore morphologies. We tested a variety of mutant strains for their spore phenotypes, including spore size, shape and wall defects. The mutants that we identified as displaying such phenotypes are all known for their roles in the regulation of hyphal tip growth, including the formin protein AgBni1, the homologous Rho-type GTPases AgRho1a and AgRho1b and the scaffold protein AgPxl1. Our observations suggest that these proteins form a signalling network controlling spore length by regulating the formation of actin structures.     

Proliferating cell nuclear antigen: More than a clamp for DNA polymerases

DNA metabolic events such as replication, repair and recombination require the concerted action of several enzymes and cofactors. Nature has provided a set of proteins that support DNA polymerases in performing processive, accurate and rapid DNA synthesis. Two of them, the proliferating cell nuclear antigen and its adapter protein replication factor C, cooperate to form a moving platform that was initially thought of only as an anchor point for DNA polymerases δ and ε. It now appears that proliferating cell nuclear antigen is also a communication point between a variety of important cellular processes including cell cycle control, DNA replication, nucleotide excision repair, post-replication mismatch repair, base excision repair and at least one apoptotic pathway. The dynamic movement of proliferating cell nuclear antigen on and off the DNA renders this protein an ideal communicator for a variety of proteins that are essential for DNA metabolic events in eukaryotic cells.     

Intermediate filaments: a historical perspective

Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years.     

Proton-sensing and lysolipid-sensitive G-protein-coupled receptors: a novel type of multi-functional receptors

OGR1, GPR4, G2A, and TDAG8 share 40% to 50% homology with each other and seem to form a family of GPCRs. They have been described as receptors for lipid molecules such as sphingosylphosphorylcholine, lysophosphatidylcholine, and psychosine. Recent studies, however, have revealed that these receptors also sense extracellular protons or pH through histidine residues of receptors and stimulate a variety of intracellular signaling pathways through several species of hetero-trimeric G-proteins, including G_s, G_i, G_q, and G_12/13. Thus, this family of GPCR seems to recognize both lipid molecules and protons as ligands. Although our knowledge of proton-sensing and lysolipid-sensitive GPCRs is preliminary, the receptor levels and ligand levels especially protons are both sensitively modulated in response to a variety of microenvironmental changes. These results suggest a multiple role of proton-sensing GPCRs in a variety of physiological and pathophysiological states.     

Acid-base buffering in organ preservation solutions as a function of temperature: new parameters for comparing buffer capacity and efficiency

Control of acidity and preventing intracellular acidosis are recognized as critical properties of an effective organ preservation solution. Buffer capacity and efficiency are therefore important for comparing the relative merits of preservation fluids for optimum hypothermic storage, but these parameters are not available for the variety of organ preservation solutions of interest in transplantation today. Moreover, buffer capacity is dependent upon both concentration and pH such that buffer capacity is not easily predicted for a complex solution containing multiple buffer species. Using standard electrometric methods to measure acid dissociation constants, this study was undertaken to determine the maximum and relative buffer capacities of a variety of new and commonly used hypothermic preservation solutions as a function of temperature. The reference data provided by these measurements show that comparative buffer capacity and efficiency vary widely between the commonly used solutions. Moreover, the fluids containing zwitterionic sulfonic acid buffers such as Hepes possess superior buffering for alpha-stat pH regulation in the region of physiological importance.