A single structural type in the regular surface layer of Aeromonas salmonicida

The surface protein array of Aeromonas salmonicida (or A-layer) appears, in negatively stained preparations, as two distinct patterns, type I and type II. Type I patterns were restricted to, and predominated in, darkly stained areas, whereas lighter staining regions exclusively displayed type II patterns. The type I morphology was faithfully reproduced in computer-simulated superimpositions of type II patterns, as was the intermediate transition zone frequently seen between the two patterns. Variations in the lattice constant of both patterns, presumably due to artifactual flattening, demonstrated that these patterns could not be distinguished on this basis. The conceptual model presented points to the type II pattern as the only single A-layer structural type. We propose the use of the terms type 1/type II to exclusively describe the morphological patterns that appear upon negative staining and the open/closed nomenclature to describe the conformations that a single structural type can adopt.     

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.     

An Update on Connexin Genes and their Nomenclature in Mouse and Man

Gap junctions, composed of connexin protein subunits, allow direct communication through conduits between neighboring cells. Twenty and twenty-one members of the connexin gene family are likely to be expressed in the mouse and human genome, respectively, 19 of which can be grouped into sequence-orthologous pairs. Their gene structure appears to be relatively simple. In most cases, an untranslated exon1 is separated by an intron of different lengh from exon2 that includes the uninterrupted coding region and the 3′-untranslated region. However, there are several exceptions to this scheme, since some mouse connexin genes contain different 5′-untranslated regions spliced either in an alternative and/or consecutive manner. Additionally, in at least 3 mouse and human connexin genes (mCx36, mCx39, mCx57 and hCx31.3, hCx36, as well as hCx40.1) the reading frame is spliced together from 2 different exons. So far, there are two nomenclatures to classify the known connexin genes: The “Gja/Gjb” nomenclature, as it is currently adopted by the NCBI data base, contains some inconsistencies compared to the “Cx” nomenclature. Here we suggest some minor corrections to co-ordinate the “Gja/Gjb” nomenclature with the “Cx” nomenclature. Furthermore, this short review contains an update on phenotypic correlations between connexin deficient mice and patients bearing mutations in their orthologous connexin genes.     

Classification of qh regions in human chromosomes 1, 9, and 16 by C-banding

Summary We present a classification for secondary constriction (qh) regions with C-banding technique in chromosomes 1,9, and 16 by means of comparing them to the short arm of chromosome 16. It is simple and convenient and can be used routinely. It can be incorporated into the modified Paris nomenclature system.     

An update on connexin genes and their nomenclature in mouse and man

Gap junctions, composed of connexin protein subunits, allow direct communication through conduits between neighboring cells. Twenty and twenty-one members of the connexin gene family are likely to be expressed in the mouse and human genome, respectively, 19 of which can be grouped into sequence-orthologous pairs. Their gene structure appears to be relatively simple. In most cases, an untranslated exon1 is separated by an intron of different lengh from exon2 that includes the uninterrupted coding region and the 3'-untranslated region. However, there are several exceptions to this scheme, since some mouse connexin genes contain different 5'-untranslated regions spliced either in an alternative and/or consecutive manner. Additionally, in at least 3 mouse and human connexin genes (mCx36, mCx39, mCx57 and hCx31.3, hCx36, as well as hCx40.1) the reading frame is spliced together from 2 different exons. So far, there are two nomenclatures to classify the known connexin genes: The "Gja/Gjb" nomenclature, as it is currently adopted by the NCBI data base, contains some inconsistencies compared to the "Cx" nomenclature. Here we suggest some minor corrections to co-ordinate the "Gja/Gjb" nomenclature with the "Cx" nomenclature. Furthermore, this short review contains an update on phenotypic correlations between connexin deficient mice and patients bearing mutations in their orthologous connexin genes.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

An atlas of the brain of the horseshoe crab Limulus polyphemus

An atlas of the brain of the horseshoe crab Limulus polyphemus is developed. All of the neuronal groups are identified and named, and regions of neuropil are segregated and named where possible. The nomenclature incorporates functionally neutral earlier names and assigns geographical names to newly distinguished structures. The atlas provides a basis for correlating the results of neuroanatomical, neurophysiological, and neurochemical studies, which yield information about individual neurons or groups of neurons in this species.     

An Update on Connexin Genes and their Nomenclature in Mouse and Man

Gap junctions, composed of connexin protein subunits, allow direct communication through conduits between neighboring cells. Twenty and twenty-one members of the connexin gene family are likely to be expressed in the mouse and human genome, respectively, 19 of which can be grouped into sequence-orthologous pairs. Their gene structure appears to be relatively simple. In most cases, an untranslated exon1 is separated by an intron of different lengh from exon2 that includes the uninterrupted coding region and the 3'-untranslated region. However, there are several exceptions to this scheme, since some mouse connexin genes contain different 5'-untranslated regions spliced either in an alternative and/or consecutive manner. Additionally, in at least 3 mouse and human connexin genes (mCx36, mCx39, mCx57 and hCx31.3, hCx36, as well as hCx40.1) the reading frame is spliced together from 2 different exons. So far, there are two nomenclatures to classify the known connexin genes: The “Gja/Gjb” nomenclature, as it is currently adopted by the NCBI data base, contains some inconsistencies compared to the “Cx” nomenclature. Here we suggest some minor corrections to co-ordinate the “Gja/Gjb” nomenclature with the “Cx” nomenclature. Furthermore, this short review contains an update on phenotypic correlations between connexin deficient mice and patients bearing mutations in their orthologous connexin genes.     

The olfactory receptor gene superfamily: data mining, classification, and nomenclature

The vertebrate olfactory receptor (OR) subgenome harbors the largest known gene family, which has been expanded by the need to provide recognition capacity for millions of potential odorants. We implemented an automated procedure to identify all OR coding regions from published sequences. This led us to the identification of 831 OR coding regions (including pseudogenes) from 24 vertebrate species. The resulting dataset was subjected to neighbor-joining phylogenetic analysis and classified into 32 distinct families, 14 of which include only genes from tetrapodan species (Class II ORs). We also report here the first identification of OR sequences from a marsupial (koala) and a monotreme (platypus). Analysis of these OR sequences suggests that the ancestral mammal had a small OR repertoire, which expanded independently in all three mammalian subclasses. Classification of ``fish-like' (Class I) ORs indicates that some of these ancient ORs were maintained and even expanded in mammals. A nomenclature system for the OR gene superfamily is proposed, based on a divergence evolutionary model. The nomenclature consists of the root symbol `OR', followed by a family numeral, subfamily letter(s), and a numeral representing the individual gene within the subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A, and OR7E12P is an OR pseudogene of family 7, subfamily E. The symbol is to be preceded by a species indicator. We have assigned the proposed nomenclature symbols for all 330 human OR genes in the database. A WWW tool for automated name assignment is provided. Received: / Accepted:     

VIRUS DISEASES OF CACAO IN WEST AFRICA: I. CACAO VIRUSES 1A, 1B, 1C AND 1D

As an introduction to this series of papers, a brief history is given of swollen-shoot disease of cacao in the Gold Coast, and the nomenclature for cacao viruses is discussed.
The symptoms of four virus diseases of cacao are described in detail, together with experimental data under the headings: cross-immunity reactions, latent period, seed transmission, staining reaction, heat inactivation and rate of spread.     

An investigation of the mechanism of the reciprocal differential staining of BUdR-substituted and unsubstituted chromosome regions.

After treatment with hot NaH₂PO₄ at pH 9, BUdR-substituted and unsubstituted chromosome regions are palely and intensely stained with Giemsa, respectively; however, after treatment with the same solution at pH 4, the reciprocal staining patterns are produced, i.e. these chromosome regions are intensely and palely stained, respectively. The nature of the mechanisms responsible for this reciprocal differential Giemsa staining of BUdR-substituted and unsubstituted chromosome regions has been investigated by Feulgen staining, electron microscopy, and radioisotope analyses involving scintillation counting and autoradiography. The results indicate that different mechanisms are responsible for the two types of staining effect. The high pH NaH₂PO₄ treatment preferentially extracts BUdR-substituted DNA into the treatment solution, relative to unsubstituted DNA. The collective evidence from this and other work suggests that BUdR-substituted DNA in the chromosomes is partially photolysed by exposure to daylight during the harvesting procedure, and the degraded DNA is subsequently solubilized and extracted during the high pH treatment. This quantitative reduction of DNA in the BUdR-substituted chromosome regions results in pale Giemsa staining of these regions. The low pH NaH₂PO₄ treatment does not produce a significant extraction of either BUdR-substituted or unsubstituted DNA into the treatment solution; rather, there may be a redistribution of the unsubstituted DNA relative to the BUdR-substituted DNA such that the unsubstituted DNA is preferentially dispersed outside the boundaries of the chromosomes onto the surrounding area of the slide. It is suggested that the BUdR-substituted chromosome regions stain relatively intensely with Giemsa after the low pH treatment because the DNA in these regions is less dispersed than that in the unsubstituted regions.     

Distribution of spontaneous chromosome breaks in human chromosomes

Summary Localization of chromosome breaks in human chromosomes was analyzed in 264 peripheral lymphocyte cultures. Three hundred and sixty-nine chromosome breaks could be exactly localized to a chromosome band or region of the Paris Conference nomenclature. The distribution of breaks in the chromosome regions was found to be nonrandom. Chromosome 3 alone had 23% of the breaks and region 3p2 had 13% of the total breaks. Some other chromosome regions, such as 5p1, 9q1, 14q2, and 16q2 also displayed clustering of breaks. Sex chromosomes had less breaks than expected. Spontaneous chromosome breaks were almost exclusively located in the lightly stained G bands.Supported by grants from the Foundation for Pediatric Research and Research Foundation of Orion Corporation Ltd.     

Reciprocal Giemsa staining of late DNA replicating regions produced by low and high pH sodium phosphate

A procedure is described whereby late replicating, BUdR-substituted chromosome regions stain intensely with Giemsa, thus producing the reciprocal staining patterns compared to those obtained by all other BUdR-Giemsa procedures where BUdR-substituted regions appear pale staining. This method may be more convenient than pre-existing techniques for demonstrating late replicating chromosome regions, and may provide a higher degree of resolution of the late replicating regions. The finding that BUdR-substituted regions can be made to stain either intensely or palely with Giemsa, depending on the pH of the pretreatment NaH₂PO₄ solution, may have important implications concerning the mechanism of BUdR-induced chromosome differentiation.     

Designation of Streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes

The 16S and 23S rRNA of various Streptomyces species were partially sequenced and screened for the presence of stretches that could define all members of the genus, groups of species, or individual species. Nucleotide 929 (Streptomyces ambofaciens nomenclature [J.L. Pernodet, M.T. Alegre, F. Boccard, and M. Guerineau, Gene 79:33-46, 1989]) is a nucleotide highly unique to Streptomyces species which, in combination with flanking regions, allowed the designation of a genus-specific probe. Regions 158 through 203 of the 16S rRNA and 1518 through 1645 of the 23S rRNA (helix 54 [Pernodet et al., Gene 79:33-46, 1989]) have a high potential to define species, whereas the degree of variation in regions 982 through 998 and 1102 through 1122 of the 16S rRNA is less pronounced but characteristic for at least certain species. Alone or in combination with each other, these regions may serve as target sites for synthetic oligonucleotide probes and primers to be used in the determination of pure cultures and in the characterization of community structures. The specificity of several probes is demonstrated by dot blot hybridization.     

Designation of Streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes.

The 16S and 23S rRNA of various Streptomyces species were partially sequenced and screened for the presence of stretches that could define all members of the genus, groups of species, or individual species. Nucleotide 929 (Streptomyces ambofaciens nomenclature [J.L. Pernodet, M.T. Alegre, F. Boccard, and M. Guerineau, Gene 79:33-46, 1989]) is a nucleotide highly unique to Streptomyces species which, in combination with flanking regions, allowed the designation of a genus-specific probe. Regions 158 through 203 of the 16S rRNA and 1518 through 1645 of the 23S rRNA (helix 54 [Pernodet et al., Gene 79:33-46, 1989]) have a high potential to define species, whereas the degree of variation in regions 982 through 998 and 1102 through 1122 of the 16S rRNA is less pronounced but characteristic for at least certain species. Alone or in combination with each other, these regions may serve as target sites for synthetic oligonucleotide probes and primers to be used in the determination of pure cultures and in the characterization of community structures. The specificity of several probes is demonstrated by dot blot hybridization.     

History of the enzyme nomenclature system

Naming things is essential for people to understand one another, no matter what language or field of interest is involved. This is as true for enzymes, genes and chemicals as it is for birds, food, flowers, etc. Effective communication requires a lack of ambiguity, but, in practice, ambiguities abound even between people who use the same language in different parts of the world, or even within the same country. Whereas ambiguities in the words used for common objects or actions have been the basis for many, more-or-less memorable jokes, they can also cause a great deal of confusion. Such linguistic chaos is welcomed by many as being a part of a diverse heritage that should be preserved at all costs to prevent us from descending into Orwellian 'newspeak'. However, in the sciences, there are distinct advantages in others being able to understand what one is doing. Many groups have stressed the need for standardized, universally accepted systems of nomenclature in chemistry, genetics, enzymology, etc. However, it is the universal acceptance that usually causes the problem. It is rare to find people who will admit that they find nomenclature to be an interesting subject, but many who profess contempt for it will get very excited if it is suggested that their pet nomenclature should be changed in the interest of clarity or uniformity. This account will consider the development of the enzyme nomenclature system, its benefits, shortcomings and future prospects.     

The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily

The Rab/Ypt/Sec4 family forms the largest branch of the Ras superfamily of GTPases, acting as essential regulators of vesicular transport pathways. We used the large amount of information in the databases to analyse the mammalian Rab family. We defined Rab-conserved sequences that we designate Rab family (RabF) motifs using the conserved PM and G motifs as "landmarks". The Rab-specific regions were used to identify new Rab proteins in the databases and suggest rules for nomenclature. Surprisingly, we find that RabF regions cluster in and around switch I and switch II regions, i.e. the regions that change conformation upon GDP or GTP binding. This finding suggests that specificity of Rab-effector interaction cannot be conferred solely through the switch regions as is usually inferred. Instead, we propose a model whereby an effector binds to RabF (switch) regions to discriminate between nucleotide-bound states and simultaneously to other regions that confer specificity to the interaction, possibly Rab subfamily (RabSF) specific regions that we also define here. We discuss structural and functional data that support this model and its general applicability to the Ras superfamily of proteins.     

A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci

In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci ( BM1824 , BM2113 , ETH10 , ETH225 , INRA023 , SPS115 , TGLA122 , TGLA126 , TGLA227 , ETH3 , TGLA53 , BM1818 , CSRM60 , CSSM66 , HAUT27 and ILSTS006 ) for bovine genotyping ( Bos taurus ). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis.     

Connexin43: a protein from rat heart homologous to a gap junction protein from liver

Northern blot analysis of rat heart mRNA probed with a cDNA coding for the principal polypeptide of rat liver gap junctions demonstrated a 3.0- kb band. This band was observed only after hybridization and washing using low stringency conditions; high stringency conditions abolished the hybridization. A rat heart cDNA library was screened with the same cDNA probe under the permissive hybridization conditions, and a single positive clone identified and purified. The clone contained a 220-bp insert, which showed 55% homology to the original cDNA probe near the 5' end. The 220-bp cDNA was used to rescreen a heart cDNA library under high stringency conditions, and three additional cDNAs that together spanned 2,768 bp were isolated. This composite cDNA contained a single 1,146-bp open reading frame coding for a predicted polypeptide of 382 amino acids with a molecular mass of 43,036 D. Northern analysis of various rat tissues using this heart cDNA as probe showed hybridization to 3.0-kb bands in RNA isolated from heart, ovary, uterus, kidney, and lens epithelium. Comparisons of the predicted amino acid sequences for the two gap junction proteins isolated from heart and liver showed two regions of high homology (58 and 42%), and other regions of little or no homology. A model is presented which indicates that the conserved sequences correspond to transmembrane and extracellular regions of the junctional molecules, while the nonconserved sequences correspond to cytoplasmic regions. Since it has been shown previously that the original cDNA isolated from liver recognizes mRNAs in stomach, kidney, and brain, and it is shown here that the cDNA isolated from heart recognizes mRNAs in ovary, uterus, lens epithelium, and kidney, a nomenclature is proposed which avoids categorization by organ of origin. In this nomenclature, the homologous proteins in gap junctions would be called connexins, each distinguished by its predicted molecular mass in kilodaltons. The gap junction protein isolated from liver would then be called connexin32; from heart, connexin43.