Guidelines for the nomenclature of the human heat shock proteins

The expanding number of members in the various human heat shock protein (HSP) families and the inconsistencies in their nomenclature have often led to confusion. Here, we propose new guidelines for the nomenclature of the human HSP families, HSPH (HSP110), HSPC (HSP90), HSPA (HSP70), DNAJ (HSP40), and HSPB (small HSP) as well as for the human chaperonin families HSPD/E (HSP60/HSP10) and CCT (TRiC). The nomenclature is based largely on the more consistent nomenclature assigned by the HUGO Gene Nomenclature Committee and used in the National Center of Biotechnology Information Entrez Gene database for the heat shock genes. In addition to this nomenclature, we provide a list of the human Entrez Gene IDs and the corresponding Entrez Gene IDs for the mouse orthologs.     

Isoprostane nomenclature: Inherent problems may cause setbacks for the development of the isoprostanoid field

Do we have to bother about the isoprostane nomenclature? The widely accepted IUPAC isoprostane nomenclature provides an unambiguous and systematic terminology to name all theoretical possible isoprostanes. However, the currently accepted nomenclature system provides an unnatural framework which is not well suited to address certain biologically relevant questions. Artificial categorization of isoprostanoids into prostanoid families disrupts prostaglandin-ring core structures needed to describe biogenetic precursor–product relationships. In addition, the IUPAC system defines isoprostanoid families which comprise chemically heterogeneous isoprostanoids which largely differ in their physicochemical properties from those of the corresponding prostaglandins. As a result of this, alternative nomenclature systems such as the phytoprostane nomenclature system overcoming some inherent problems of the IUPAC nomenclature are still in use. However, different naming of isoprostanoids especially the classification of prostanoid family names has created considerable confusion. Therefore, a cautionary note on the current use of different nomenclature systems is necessary.     

A revised nomenclature for the human and rodent alpha-tubulin gene family

An essential component of microtubules, alpha-tubulin is also a multigene family in many species. An orthology-based nomenclature for this gene family has previously been difficult to assign due to incomplete genome builds and the high degree of sequence similarity between members of this family. Using the current genome builds, sequence analysis of human, mouse, and rat alpha-tubulin genes has enabled an updated nomenclature to be generated. This revised nomenclature provides a unified language for the discussion of these genes in mammalian species; it has been approved by the gene nomenclature committees of the three species and is supported by researchers in the field.     

Genetic evidence for historical continuity between populations of the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae) east and west of the Great Dividing Range

The freshwater Craterocephalus stercusmuscarum (Atherinidae) has a broad northern and south-eastern Australian distribution, and has been divided into two sub-species. Craterocephalus stercusmuscarum fulvus occurs in eastern and western flowing drainages of the southeast, while C. s. stercusmuscarum occurs in north eastern and northern flowing drainages. Four populations of each sub-species were sampled from different river systems to examine if genetic diversity was consistent with this nomenclature or a previously proposed vicariance hypothesis. Allozyme data did not support the notion that the subspecies were genetically distinct, but the mtDNA data showed that haplotypes from one sub-species, regardless of geography, were reciprocally monophyletic to haplotypes of the other subspecies. Thus, mtDNA genetic diversity was partitioned by prevailing taxonomy and the data suggest that C. s. fulvus populations in eastern and western flowing drainages may have had a relatively recent connection subsequently interrupted by geological events.     

Radioecological situation at the villages of the Techa river

The Techa river was contaminated in 1949-1956 from the nuclear enterprise "Mayak". The investigations were carried out in flood plain of the Techa river in 1992-2001. 90Sr and 137Cs stores were calculated in the soil-vegetation cover. There is uneven character of the spatial radionuclides contamination of the investigated area. The store with 90Sr changes from 25 to 930 kBq/m2 (0.7-25.0 Ci/km2) and that with 137Cs--from 30 to 1700 kBq/m2 (0.8-46.0 Ci/km2). In the preriver-bed soils the ratio 90Sr/137Cs increases with further from discharge point. Individual effective dose was calculated for the Brodocalmak population. 90Sr was revealed in the flood plain soils of the Iset river. The contribution of the contaminated Techa river and its flood plains soils accounted for as by incorporated radionuclides as background gamma-radiation does not exceed 0.13-0.17 mSv/yr if the contaminated Techa river utilization is limited. In other case the contribution of the contaminated Techa river increases to 1.6-3.0 mSv/yr. These values exceed international safety norms.     

Revision of the Nomenclature for the Bacillus thuringiensis Pesticidal Crystal Proteins

The crystal proteins of Bacillus thuringiensis have been extensively studied because of their pesticidal properties and their high natural levels of production. The increasingly rapid characterization of new crystal protein genes, triggered by an effort to discover proteins with new pesticidal properties, has resulted in a variety of sequences and activities that no longer fit the original nomenclature system proposed in 1989. Bacillus thuringiensis pesticidal crystal protein (Cry and Cyt) nomenclature was initially based on insecticidal activity for the primary ranking criterion. Many exceptions to this systematic arrangement have become apparent, however, making the nomenclature system inconsistent. Additionally, the original nomenclature, with four activity-based primary ranks for 13 genes, did not anticipate the current 73 holotype sequences that form many more than the original four subgroups. A new nomenclature, based on hierarchical clustering using amino acid sequence identity, is proposed. Roman numerals have been exchanged for Arabic numerals in the primary rank (e.g., Cry1Aa) to better accommodate the large number of expected new sequences. In this proposal, 133 crystal proteins comprising 24 primary ranks are systematically arranged.     

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.     

On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature

In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon name always refers to the same ancestor or ancestry is questionable.     

Decontamination of drinking water by direct heating in solar panels

A device was developed for direct heating of water by solar radiation in a flow-through system of copper pipes. An adjustable thermostat valve prevents water below the chosen temperature from being withdrawn. The results show that it is possible to eliminate coliform and thermotolerant coliform bacteria from naturally contaminated river water by heating to temperatures of 65 °C or above. Artificial additions of Salmonella typhimurium , Streptococcus faecalis and Escherichia coli to contaminated river water were also inactivated after heating to 65 °C and above. The total viable count could be reduced by a factor of 1000. The heat-resistant bacteria isolated from the Mlalakuva River (Tanzania) were spore-forming bacteria which exhibited greater heat resistance than commonly used test bacteria originating from countries with colder climates. To provide a good safety margin it is recommended that an outlet water temperature of 75 °C be used. At that temperature the daily production was about 50 l of decontaminated water per m² of solar panel, an amount that could be doubled by using a heat exchanger to recycle the heat.     

Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily

We present the BPIFAn/BPIFBn systematic nomenclature for the PLUNC (palate lung and nasal epithelium clone)/PSP (parotid secretory protein)/BSP30 (bovine salivary protein 30)/SMGB (submandibular gland protein B) family of proteins, based on an adaptation of the SPLUNCn (short PLUNCn)/LPLUNCn (large PLUNCn) nomenclature. The nomenclature is applied to a set of 102 sequences which we believe represent the current reliable data for BPIFA/BPIFB proteins across all species, including marsupials and birds. The nomenclature will be implemented by the HGNC (HUGO Gene Nomenclature Committee).     

Third meeting of the International Society for Phylogenetic Nomenclature: a report

The Third Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Dalhousie University in Halifax, Canada, from 20 to 22 July 2008. In addition to contributed talks, the conference included a progress report on the PhyloCode 'Companion Volume', a discussion of how to complete this book in a timely fashion, a demonstration of the online registration data base (RegNum), plenary talks, and Council and business meetings. Topics discussed at the meeting include problems created by rank-based nomenclature in various eukaryotic taxa, dealing with hybrids in rank-based and phylogenetic nomenclature, phyloinformatics, the choice of names to use when the taxonomic content associated with available names varies, teaching phylogenetic nomenclature, and the application of phylogenetic nomenclature to specific taxa.     

Survival of Yersinia enterocolitica in the environment

When Yersinia enterocolitica was introduced into soils (or physiological saline), very little decrease in the population was observed throughout the test period. If the soil was allowed to air dry slowly, only 0.1% (2.8 x 10(3) colony forming units/g of soil) of the original population added still remained viable by day 10. On the other hand, the introduced organisms disappeared rapidly in river water but their longevities could be extended significantly if a eucaryote inhibitor was added to the river water or the river water was passed through a 0.8-micron membrane filter to remove eucaryotic predators. Furthermore, the rapid decrease of the Yersinia population coincided with an increase in numbers of protozoans. However, when Yersinia was added to filter-sterilized river water or when small numbers of the organism, below the threshold level believed necessary for active predation to occur, were added to the river water, no response in predators was observed; nevertheless, the population of Yersinia still showed a continued decline. When the organism was introduced into sephadex-treated river water or groundwater, its survival improved significantly compared with its survival in nontreated water samples. Low ambient temperature dramatically increased its ability to survive in the aquatic environment. It is concluded that, in addition to the temperature factor, the longevity of Y. enterocolitica in river water is chiefly regulated by predators and toxin producers.     

A proposed unified nomenclature for the enamelled components of the molar teeth of the Cricetidae (Rodentia)

The primitive topography of the enamelled surface of molar teeth of the Cricetidae is described as expressed in the fossil Cricetodontinae. Morphological variations in the molar structure of different subgroups among the Cricetidae are interpreted as derivations from this cricetodontine pattern. Eleven available naming systems for such components are surveyed, and a new unifying nomenclature is proposed, based on the Cope-Osborn cusp homologies for mammals. Names for enamel cusps, cuspules, styles, lophs, folds and islands are given, in an attempt to include in an overall general nomenclature the advantages of the most valuable, already available, nomenclatorial systems. The system purports to apply to all modifications of the cricetid crown molar pattern, and it claims to fulfil the need for a uniform nomenclature.     

An update of the S100 nomenclature

The plethora of names given to S100 proteins resulted in considerable confusion. Here we present the official and updated nomenclature of this protein family, approved by the HGNC (HUGO gene nomenclature committee) and ECS (European Calcium Society).     

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.