Assessment of vegetation cover by lichen-indication methods (by the example of the north of Central Siberia)

The vegetation cover in the north of Central Siberia has been assessed from lichenological data. The approaches and methods of lichen-based indication of the state of vegetation cover have been developed with the application of the data on diversity of lichens and lichen synusias, their projective cover and morphological deviations. The species of lichens and synusias that can be used for indication purposes have been defined. The changes in the characteristics of the lichen component in vegetation cover under the increasing chemical air pollution caused by industrial plants have been examined. The early deviations are indicated by morphological changes of lichen thalli, species depletion, and diversity of lichen synusias. Practical recommendations on lichen indication of the vegetation cover in the north of Siberia have been given.     

Recommendations for the presentation of NMR structures of proteins and nucleic acids – IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.     

2004 Nomenclature for the chicken major histocompatibility (<Emphasis Type="Italic">B</Emphasis> and <Emphasis Type="Italic">Y</Emphasis> ) complex

The first standard nomenclature for the chicken (Gallus gallus) major histocompatibility (B) complex published in 1982 describing chicken major histocompatibility complex (MHC) variability is being revised to include subsequent findings. Considerable progress has been made in identifying the genes that define this polymorphic region. Allelic sequences for MHC genes are accumulating at an increasing rate without a standard system of nomenclature in place. The recommendations presented here were derived in workshops held during International Society of Animal Genetics and Avian Immunology Research Group meetings. A nomenclature for B and Y (Rfp-Y) loci and alleles has been developed that can be applied to existing and newly defined haplotypes including recombinants. A list of the current standard B haplotypes is provided with reference stock, allele designations, and GenBank numbers for corresponding MHC class I and class II sequences. An updated list of proposed names for B recombinant haplotypes is included, as well as a list of over 17 Y haplotypes designated to date.     

Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains

The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals. Within the European Network for Human Congenital Imprinting Disorders we have discussed these issues and designed a nomenclature for naming imprinted DMRs as well as for reporting methylation values. We apply these recommendations for imprinted DMRs that are commonly assayed in clinical laboratories and show how they support standardized database submission. The recommendations are in line with existing recommendations, most importantly the Human Genome Variation Society nomenclature, and should facilitate accurate reporting and data exchange among laboratories and thereby help to avoid future confusion.     

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.

     

FELASA guidelines for the production and nomenclature of transgenic rodents

The standardized nomenclature of rodent strains, genes and mutations has long been the focus of careful attention. Its aim is to provide proper designation of laboratory animals used in research projects and to convey as much information on each strain as possible. Since the development of different techniques to mutate the genome of laboratory rodents on a large scale, the correct application of current nomenclature systems is of increased significance. It facilitates not only the accurate communication of scientific results but is indispensable in controlling the dramatically increased number of transgenic animal models in experimental units, archives and databases. It is regrettable that many publications, especially on transgenic rodents, use vague and inappropriate strain designation. This situation should definitely be improved, particularly considering the increasingly emphasized importance of genetic background on the phenotype of mutations. The aim of these guidelines is to raise awareness about specific features of production and of the current nomenclature system used for transgenic rodents.     

Seeking parsimony in landscape metrics

Numerous metrics describing landscape patterns have been used to explain landscape-scale habitat selection by birds. The myriad metrics, their complexity, and inconsistent responses to them by birds have led to a lack of clear recommendations for managing land for desired species. The amount of a target land cover type in the landscape (percentage cover) often has been a useful indicator of the likelihood of species occurrence or of habitat selection; is it also a more adequate and parsimonious measure for explaining species distributions than patch size or more complex measures of landscape configuration? We examined responses of 6 woodland-interior bird species to the percentage tree cover within prescribed areas and to patch size, edge density, and other metrics. We examined responses in 2 landscapes: a mixed woodland-savanna and an eastern deciduous forest. For these 6 species, percentage tree cover explained bird occurrence as well as or better than other measures in both study areas. We then repeated the analysis on a larger group of woodland species, including those associated with woodland edges. The bird species we studied had varied responses to landscape metrics, but percentage tree cover was the strongest explanatory variable overall. Although percentage cover estimated from remotely sensed data is an inexact representation of habitat in the landscape, it does appear to be reliable and easy to conceptualize, relative to other measures. We suggest that, at least for woodland habitat, percentage cover is a broadly useful measure that can be helpful in pragmatic questions of explaining responses to landscapes or in anticipating responses to landscape change. © 2011 The Wildlife Society.     

The species of Geissorhiza (Iridaceae) of Thunberg's herbarium (Uppsala, Sweden)

The complex typification and nomenclature of the eight species of Geissorhiza based on Thunberg's Cape collections, is reviewed critically in preparation for a complete revision of the genus. These species, initially assigned to Ixia , were described by Thunberg and von Linné fil., founded on collections of twelve different species. Some well known species require changes to their nomenclature; G. rochensis sensu Ker becomes G. radians (Thunb.) Goldbl.; while Ixia scillaris Thunb. nom. illeg., based on three different species is lectotypified and shown to be G. scillaris Spreng., a species quite distinct from G. juncea , with which it has often been confused. Arguments for considering the name G. secunda illegitimate are reviewed. The species long known by this epithet must be called G. aspera Goldbl. Lectotypes have been designated for G. monanthos, G. radians, G. scillaris and G. setacea , none of which have been satisfactorily typified before.     

Electrostatic interactions in the association of proteins: an analysis of the thrombin-hirudin complex.

The role of electrostatic interactions in stabilization of the thrombin-hirudin complex has been investigated by means of two macroscopic approaches: the modified Tanford-Kirkwood model and the finite-difference method for numerical solution of the Poisson-Boltzmann equations. The electrostatic potentials around the thrombin and hirudin molecules were asymmetric and complementary, and it is suggested that these fields influence the initial orientation in the process of the complex formation. The change of the electrostatic binding energy due to mutation of acidic residues in hirudin has been calculated and compared with experimentally determined changes in binding energy. In general, the change in electrostatic binding energy for a particular mutation calculated by the modified Tanford-Kirkwood approach agreed well with the experimentally observed change. The finite-difference approach tended to overestimate changes in binding energy when the mutated residues were involved in short-range electrostatic interactions. Decreases in binding energy caused by mutations of amino acids that do not make any direct ionic interactions (e.g., Glu 61 and Glu 62 of hirudin) can be explained in terms of the interaction of these charges with the positive electrostatic potential of thrombin. Differences between the calculated and observed changes in binding energy are discussed in terms of the crystal structure of the thrombin-hirudin complex.     

Abbreviated nomenclature for cyclic and branched homo- and hetero-detic peptides.

Amino acid sequences and linear or head-to-tail cyclopeptides can be represented conveniently in one-line text formulae using the three-letter symbols. However, other - but nonetheless important - topologies of peptides are 'side chain-to-head (or tail)', 'backbone-to-backbone', 'side chain-to-side chain' cyclopeptides, 'side chain-to-side chain' connected peptide strands, and branched peptides (like peptide dendrimers). In general, such structures cannot be described using the three-letter symbols in one-line text: a chemical structure editor is required for symbolic representations according to the IUPAC-IUBMB recommendations. The aim of this contribution is to offer an unambiguous and general nomenclature system that enables researchers to represent all cyclic and branched homo- and hetero-detic peptides in a coherent manner in one-line text - as long as their as constituents can be represented in (three)-letter codes. The application of this new nomenclature would overcome the existing difficulties and provide a way to express complex situations in the shortest way in order to highlight more clearly the salient points in a given scientific communication.